Chromatography and Its Applications PDF

CHROMATOGRAPHY
ANDITSAPPLICATIONS

EditedbySasikumarDhanarasu
Chromatography and Its Applications

Edited by Sasikumar Dhanarasu
Published by InTech
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Copyright 2012 InTech

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Contents
Preface IX
Chapter 1 Column Liquid Chromatography 1

Changming Zhang, Zhanggen Huang and Xiaohang Zhang
Chapter 2 Column Chromatography

for Terpenoids and Flavonoids 13
Glin Saltan itolu and zlem Bahadr Ackara
Chapter 3 Chromatographic Separation and

Identification of Sildenafil and Yohimbine
Analogues Illegally Added in Herbal Supplements 51
Hakan Gker, Maksut Cokun and Glgn Ayhan-Klcgil
Chapter 4 Purification of Marine Bacterial

Sialyltransferases and Sialyloligosaccharides 69
Toshiki Mine and Takeshi Yamamoto
Chapter 5 Simple Preparation of New

Potential Bioactive Nitrogen-Containing
Molecules and Their Spectroscopy Analysis 87
Vladimir V. Kouznetsov, Carlos E. Puerto Galvis,
Leonor Y. Vargas Mndez and Carlos M. Melndez Gmez
Chapter 6 Wound Healing and

Antibacterial Properties of Leaf Essential
Oil of Vitex simplicifolia Oliv. from Burkina Faso 109
Magid Abdel Ouoba, Jean Koudou, Noya Some,
Sylvin Ouedraogo and Innocent Pierre Guissou
Chapter 7 Use of Associated Chromatographic

Techniques in Bio-Monitored Isolation
of Bioactive Monoterpenoid Indole
Alkaloids from Aspidosperma ramiflorum 119
Talita Perez Cantuaria Chierrito, Ananda de Castro Cunha,
Luzia Koike, Regina Aparecida Correia Gonalves
and Arildo Jos Braz de Oliveira
VI Contents
Chapter 8 Secondary Metabolites 131

Tnia da S. Agostini-Costa, Roberto F. Vieira,
Humberto R. Bizzo, Dmaris Silveira and Marcos A. Gimenes
Chapter 9 Biomarkers 165

Yasser M. Moustafa and Rania E. Morsi
Chapter 10 Quantification of Antimalarial

Quassinoids Neosergeolide and
Isobrucein B in Stem and Root Infusions
of Picrolemma sprucei Hook F. by HPLC-UV Analysis 187
Rita C. S. Nunomura, Ellen C. C. Silva,
Sergio M. Nunomura, Ana C. F. Amaral,
Alade S. Barreto, Antonio C. Siani and Adrian M. Pohlit
Chapter 11 Purification of Peptides from

Bacillus Strains with Biological Activity 201
Mara Antonieta Gordillo and Mara Cristina Maldonado

Preface
Chromatographyisapowerfulseparationtoolthatisusedinallbranchesofscience,
and is often the only means of separating components from complex mixtures. The
Russian botanist Mikhail Tswett coined the term chromatography in 1906. The first
analyticaluseofchromatographywasdescribedbyJamesandMartinin1952,forthe
useofgaschromatographyfortheanalysisoffattyacidmixtures.
Awiderangeofchromatographicproceduresmakesuseofdifferencesinsize,binding
affinities, charge, and other properties. Many types of chromatography have been
developed. These include Column chromatography, High performance liquid
chromatography (HPLC), Gas chromatography, Size exclusion chromatography, Ion
exchangechromatographyetc.
In this book contains more details about the applications of chromatography by

various research findings. Each and every topics of this book have included lists of
references at the end to provide students and researchers with starting points for
independent chromatography explorations. I welcome comments, criticisms, and
suggestionsfromstudents,facultyandresearchers.
Dr.D.Sasikumar
DepartmentofBiochemistry,CollegeofMedicine,
UniversityofHail,Hail,
KingdomofSaudiArabia
Column Liquid Chromatography

Changming Zhang, Zhanggen Huang and Xiaohang Zhang
State Key Laboratory of Coal Conversion,
Institute of Coal Chemistry,
Chinese Academy of Sciences, Taiyuan,
China
1. Introduction
In the processing of coal and petroleum, there are many products produced such as gas and
lighter liquid which is easy to use. At the same time, there is heavy material produced
which is difficult to use. Such as, in crude oil refine processing, oil thermal cracking and
catalytic cracking of petroleum, many residua oils, asphalts, and heaviest waste residual
will be produced. The quantity of heavy oils is often large. So, it is important to study the
property of heavy oils.
The column liquid chromatography (CLC) is an important and indispensable analysis
method to study heavy oils. It is not only a separation means, but is also analysis means,
especially for analysis of hydrocarbon group type.
Hydrocarbon group type analysis means the determination of the following classes of
compounds:
1. Saturated compounds, including paraffinic and naphthenic hydrocarbons.
2. Aromatic compounds, (containing at least one benzene ring). Their molecules
containing one benzene ring are classified as mono-aromatics, those with two aromatic
rings as di-aromatics, etc.
3. Resins, including polar substances containing elements other than C and H in the
molecule (nitrogen, sulphur and oxygen in particular)
4. Asphaltenes, including polar substances and asphaltenes only soluble in one or two
polar solvents such as quinoline , which have large molecular weight and high aromatic
ring number.
Now analysis methods existed have some deficiencies. Such as GC method can not be used
to analyze compounds having high boiling point. The application of high performance
liquid chromatography (HPLC) to hydrocarbon group-type analysis is characteristic with its
high efficiency, high speed, and high sensitivity. But HPLC is only suitable for analysis of
substances soluble in n-pentane [1].
TLC-FID [2-3] method can be also used to analysis the THF-soluble party in asphalt-samples
and show great advantages. But, the components were combusted during TLC-FID analysis
2 Chromatography and Its Applications
process and this lack made it not suitable for other analysis with preparation fraction. It
should be pointed that the conventional method such as ASTM method use amount of
solvent is large and some solvents has high toxicity [4, 5]. Moreover, there are too
troublesome for some operation in traditional method. Hence, the separation of products
containing heavy components remains a difficult task up to now.
Refereeing the literatures [4-10], the authors of this paper establish an optimum CLC
method to analyze group-type of heavy oils through a series of studies. This paper detail
introduces this method and its many applications which include preparation of high-level
road asphalt, the characterization of molecular weight distributions (MWDs) and analysis of
heterocyclic aromatic components of heavy oils.
2. The establish of CLC method

2.1 Column, support and heating apparatus
The dimension of glass chromatographic column is 90 mm length and 6 mm I. D. Silica gel
with particle size range from 100 to 200 meshes was provided by marine chemical plant of
Qingdao China. Silica gel was active under temperature of 180oC for 4 hours before use.
Oxide of alumna 0.047-0.147 mm used was purchased from chemical and medical reagent
company in Shanghai China. Muffle furnace (50C-1000C) and oven was used for sample
preparation and heating.
2.2 Reagents
N-heptane, dichloromethane, trichloromethane as eluent solvents all were analytical grade
reagents produced by Tianjin Chemical Reagent Factory (China). Pure reagents as model
compounds were supplied by Aldrich Chemical Company (USA), including tetracosane
(99.5% pure), dibenz[ah]anthracen ( 98%, pure), and acetanilide ( 99% pure), etc.
2.3 Analytical instruments

Fourier transforms FT-IR spectra were measured by a Bio-Rad Excalibur Series FTS 3000
spectrometer in the range of 4000-400 cm1 using KBr pellets. 1H NMR measurements were
made with a Bruker Avance 500 spectrometer operating at 500.1 MHz.
3. The establish of group-type analysis method by CLC

3.1 Optimum chromatographic condition
As a base line, some pure reagents were chosen as model components prepared for CLC.
These model compounds were tetracosane for saturates, dibenz[ah]anthracen for aromatics
and acetanilide for resins. There is no appropriate pure reagent used for asphaltene fraction,
so the insoluble fraction of tetrahydrofuran in one asphalt sample was used for asphaltene
fraction.
Through a series of investigations,the optimum chromatographic operation was performed.
The final optimum conditions were obtained as follows: Chromatographic column was glass
column being 90 mm length, 6 mm i.d. The amount of silica gel used was from 1 to 1.5 gram.
Column Liquid Chromatography 3
The amount of alumina was from 1.5 to 1.8 gram. Total sample used was about 0.1 gram.
The solvent of heptanes, mixture of heptanes/ dichloromethane (1/2.5, V/V) and mixture of
dichloromethane/ trichloromethane (1/3, V/V) were as elutes corresponding to saturated
hydrocarbon, aromatic hydrocarbon and resin respectively. The amount of heptanes,
heptanes/ dichloromethane, and dichloromethane/ trichloromethane was 20ml, 35ml and
30ml respectively. Each fraction collected was dried in vacuum under 60oC until the weight
keep constant.
Through above group analysis, the experimental deviation and recovery of CLC method are
summarized in Table 1. From Table, it can be seen that the average of deviation and recover
are -1.546% and 100.681% respectively; the results are good.
Pure Weight of Content Determination Deviation Recover

No.
Reagents preparation W% W% W% %
Tetracosane 0.0547(g) 100 98.095 -1.905 98.095 1017
Tetracosane 0.0508 100 97.964 -2.036 97.964 1020
Tetracosane 0.0311 27.154 26.658 -0.496 98.173 1201
Tetracosane 0.0285 26.571 25.638 -0.933 96.489 1202
Average -1.343 97.680
Dibenz(ah)anthracen 0.042 100 98.095 -1.805 98.095 1030
Dibenz(ah)anthracen 0.0442 100 97.964 -2.036 97.964 1103
Dibenz(ah)anthracen 0.0259 22.629 20.909 -1.720 92.399 1201
Dibenz(ah)anthracen 0.0294 27.402 26.843 -0.559 97.960 1202
Average -1.530 96.605
Acetanilide 0.0875 100 97.600 -2.400 97.600 1024
Acetanilide 0.0247 23.024 22.642 -0.382 98.341 1202
Acetanilide 0.0365 100 96.438 -3.562 96.438 1222
Acetanilide 27.402 26.843 -0.559 97.853 1201
Average -1.726 97.558
Asphltene 0.0261 22.815 24.790 1.975 108.657 1201
Asphltene 0.0395 100 94.937 -5.063 94.937 1211
Asphltene 0.0387 100 98.450 -1.550 98.450 1301
Average -1.546 100.681
Table 1. Experimental deviation and recovery of model compound.
3.2 Check of chromatographic resolution rate by FT-IR

The result of CLC method was checked by Fourier transform infrared (FT-IR) method .The
spectra IR were acquired in the transmission mode as 64 scan in the IR range from 4000 to
500cm-1 at a resolution of 4cm-1. KBr standard pellets were used, and the samples were dried
and then mixed with KBr, ground, and palletized.
IR spectrums of pure reagents including tetracosane, dibenz(ah)anthracen and acetanilide
were obtained and used for standards. The IR spectrums of different fractions collected from
flow out separated of the mixture reagents, and spectrums were compared with above
standard spectrums. The results were shown in Figure 1.
Tetracosane
Fraction 1
Absorbance
Dibenz[ah]anthracen
Fraction 2
Acetanilide
Fraction 3
4000 3500 3000 2500 2000 1500 1000 500

-1
Wavenumber (cm )
Fig. 1. Infrared spectrum for pure reagents and different fraction.
It is important to indicate that the IR spectra of fraction 1 collected (from 1202# sample)
show similarity with pure tetracosane reagent. IR spectra for fraction 2 and fraction 3 show
accordant results with dibenz(ah)anthracen and acetanilide respectively.
1
3.3 Check of chromatographic resolution rate by H NMR
The CLC method was checked also by 1H NMR. It measured different fractions collected
from flow out separated of the mixture reagents and spectrums were compared with above
standard spectrums. The high resolution 1H NMR spectra of pure model compounds and
fraction 1-3 are shown in Figure 2.
It is difficult to separate complex and heavy sample, however the IR and 1H NMR analysis
of the prepared fractions from CLC were all good agreement with pure reagents. This
observation indicate the optimum CLC parameter in this work guarantee a good qualitative
results.
Tetracosane
Fraction 1
Dibenz(ah)anthracen
Fraction 2
Acetanilide
Fraction 3
0 2 4 6 8 10
ppm
Fig. 2. 1H NMR results of pure reagents and different fraction.
3.4 Evaluation of analysis of group composition by CLC

The recover rate and experiment deviations for model compounds were summarized in
Table 1. It can be seen that the experiment result are fine.
Compared with routine ASTM method, these optimum chromatographic conditions show
many advantages. First, the reagent and sample consumed was fewer than total solvent of
300 ml of classic ASTM method. Second, the dichloromethane and trichloromethane used in
present study, compared with toluene and benzotrichloride used, has lower toxicity.
4. Applications of group type analysis by CLC

4.1 The application in making high grade road asphalt
Coal is used as the main source of energy in China. The crude oil produced in China is
paraffinic; therefore, it is not suitable for road asphalt. China is trying to produce high grade
road asphalt from the mixture of coal and petroleum [11, 12].
Three asphalt samples from petroleum and coal processing for high grade paving asphalt
were characterized by established method. Sample NE-6, NE-9, NE-11 were the heavy
products by co-processing of Shijiazhuang oil (a petroleum factory in China) and Yanzhou
coal (a typical coal in China). The coal and oil ratio was 1:1. Among asphalt samples, the
preparation of NE-6 sample was under the role of Fe catalyst during co-processing. NE-9
sample was related to Mo catalyst. The sample TLA is from Trindid Lake Asphalt. The
results of group type analysis for four asphalt samples were shown in Table 2.
Name Test Saturates Aromatics Resins Asphaltenes

NE-6 (1) 5.496 60.154 17.327 17.023
(2) 4.986 58.230 20.128 15.855
Average 5.241 59.191 18.727 16.439
Deviation 0.255 0.961 1.401 0.584
NE-9 (1) 9.950 21.379 52.906 15.765
(2) 8.001 22.087 52.348 17.554
Average 8.975 21.733 52.627 16.659
Deviation 0.974 0.354 0.279 0.895
NE-11 (1) 7.375 66.379 23.659 2.586
(2) 8.497 67.984 20.850 2.668
Average 7.936 67.182 22.254 2.627
Deviation 0.561 0.802 1.404 0.041
TLA (1) 5.496 60.154 17.327 17.023
(2) 4.986 58.230 20.928 15.855
Average 5.241 59.191 19.128 16.439
Deviation 0.255 0.961 1.800 0.584
Table 2. Results of groups composition of asphalts (W%).
From Table 2 it can be seen that the application of established method to real asphalt
samples show good results. Different samples have different group composition
characterize. The experiment deviations of contents(W%) are in the ranges from 0.255% to
1.800%.
FTIR experiments were performed to check the qualitative ability of established method. IR
spectra of saturated fraction, aromatic fraction and resin fraction for sample NE-9 were
shown in Figure from 3 to 5. It is important to note intense absorption peaks for saturated
fraction (Fig.3). Based the standard IR handbook, the absorption peaks around 719.45cm-1,
1377.17 cm-1, 2850.78 cm-1, 2918.29 cm-1 and 2959.79 cm-1 was attributed to characteristics
peak for (CH2)N N>6,(CH3),sCH3,as (CH2) and as CH3 respectively. These data
show that the prepared saturated fraction has a high purity.
As Figure 4 show, the absorption peaks around 748.38 cm-1, 812.03 cm-1, 877.61 cm-1 and
3049.45 cm-1 belong to character peak of aromatic C-H absorption. The peaks at 1602.84 cm-
1,1580 cm-1 and 1410 cm-1 were characteristics absorption peak of aromatic carbon.
Obviously, the obtained aromatic hydrocarbon fraction has a good purity.

2.5
2918.29
2.0
1.5 2959.79 2850.78

Absorbance
1.0
2972.23
0.5 1463.97
1377.17
719.45
0.0
4000 3500 3000 2500 2000 1500 1000 500

-1
Wavenumber(cm )
Fig. 3. Infrared spectrum of the saturated hydrocarbon fraction of sample NE-9.
0.5 2920.22
0.4
1377.17
Absorbance
0.3 748.38
2852.71 1456.25
812.03
0.2 877.61
1602.84
0.1 3049.45 1689.29 1118.71

3331.41 1033
0.0
4000 3500 3000 2500 2000 1500 1000 500

-1
Wavenumber(cm )
Fig. 4. Infrared spectrum of the aromatic fraction of sample NE-9.
The results from Figure 5 show that the resin fractions concentrate some oxygen-containing
compounds. This conclusion can be approved by the appearing peak around 1215.15 cm-1,
which is characteristics absorption peak for phenol compounds, and peak around 3649.31
cm-1, which is characteristics absorption peak for dissociate OH. The peaks at 1033.84 cm-1
and 1608.63 cm-1 attribute to the absorption from OH and C-O-C group. This is
comprehensible because OH group in the structure the phenol connects to the aryl group,
which may induce some aromatic absorption peaks.
The FTIR results show high resolution of CLC method established. It is difficult to separate
complex and heavy sample, however the IR analysis of the prepared fractions from the CLC
chow all good results This observation indicate that chromatographic parameter guarantee a
good qualitative results.
0.20
2924.08
0.15
2953.57 1456.25
1608.63
Absorbance
0.10 2824.30
806.36
3049.45
880.72 774.98
0.05 3649.31
1215.15
1033.84
0.00
4000 3500 3000 2500 2000 1500 1000 500

-1
Wavenumber(cm )
Fig. 5. Infrared spectrum of the resin fraction of sample NE-9.
4.2 The determination of MWDs by CLC coupled with SEC

Among characteristics of heavy oil, the size exchange chromatography (SEC) can be used to
determine molecular weight distributions (MWDs), weight average molecular weight (Mw)
and number average molecular weight (Mn), etc. With heavy oil of a group as example, the
conditions of SEC are summarized as follows.
The analysis conditions are: a Shimadzu LC-10A high performance liquid chromatograph
with an SPD-10AUP UV detector, the chromatographic column of SHIMPACK -801 (30 cm
length, 0.8 cm i.d., polystyrene 6 m), mobile phase of THF; flow rat with 1.2 ml/min;
column temperature at 25oC.
The SEC chromatograms are shown in Figure 6, MWDs results are listed in Table 3.
In Figure 6, the sources of coal asphalt , KP petroleum asphalt, ethylene residue oil and
vacuum residue oil are from Shanxi coking plant in China, Korea refining, Xinjiang oil
refinery in China and Saudi Arabia's oil refining, respectively.
Vacuum residue
Ethylene residue
KP Petroleum asphalt
Coal asphalt
0 2 4 6 8 10
Tr / Min
Fig. 6. The SEC chromatograms of typical heavy oils.
W%
Samples Mw M5000 M3000 M1000 M500
M>5000 M<300
-3000 -1000 -500 -300
Coal asphalt 1032.200 1.658 2.802 21.199 29.730 22.745 21.863
KP Petroleum
1905.674 0.804 17.169 59.899 12.274 3.979 5.873
asphalt
Ethylene residue
764.788 0.191 7.481 15.201 9.648 9.666 57.810
oil
Vacuum residue oil 1886.698 3.683 1.490 61.166 20.566 6.399 6.693
Table 3. The MWDs of typical heavy oils
How much is the representative characteristics of this SEC method? This is an important
problem to need know to treating these spectra and data of SEC. The so-called
"representative refers that extent which could be determined out of sample. Because most
present SEC method is only suitable to compounds having UV adsorbent and soluble of
THF, so, it is needed to know representative of whole sample. This problem will be
completed only by CLC. Because the four groups: saturates, aromatics, resins and
asphaltenes quantitatively could be obtained by CLC determination, then the

"representative "(R index) will be calculated as the following.
R =100 %- Wasp % -Wa1k % (1)

Which R represents the representation index; Wasph % and Wa1k % represent the weight
percent of asphaltene in sample and the weight percent of saturated hydrocarbons in
sample, respectively.
With samples of Figure 6 as example, their R indexes from this CLC analysis are listed in
Table 4.
Name of samples (1) (2) (3) Average Max of deviation %

Coal asphalt 73.64 72.89 73.86 73.46 -0.78
KP petroleum asphalt, 99.33 99.28 98.76 99.12 -0.36
Ethylene residue oil 90.36 89.87 90.56 90.26 -0.43
Vacuum residue oil 96.17 96.21 95.76 96.05 0.33
Table 4. The R indicators.
These results show that the CLC coupled with SEC is an effective mean to analyze MWDs.
4.3 Analysis of resin component by CLC coupled with HPLC

As components of resin of heavy oil are very complicated, so to analyze them is very
difficult by only one method. However, CLC coupled with high performance liquid
chromatography (HPLC) can separate successfully, quality and quantity these compositions.
Because the resin fraction got concentrate oxygen-containing compounds and other hetero-
atom-containing compounds by CLC separation, then the analysis of these hetero-atom-
containing compounds became easy to by HPLC. With slurry oil (Tianjing Refinery of
China) as an example, the analysis of components in resin was summarized as follows.
The preparation of resin fraction was same as that of above description of CLC; the HPLC
was performed on a Shimadzu LC-3A chromatogram with a SPD-1 UV detector, operated at
254 nm. Two ODS (4.620 cm) columns in series were operated at 40 oC with methanol
/water=78:22(V/V) as the mobile phase, flowing at a rate of 0.8 ml/min. Typical separation
chromatogram is shown in Figure 7.
From Figure 7 it can be seen the high resolution separation rate of complex compositions,
these confirmed that the CLC preparation is successful and HPLC analysis is better.
The three qualitative methods of HPLC were selected to determine compositions of resin
fraction. The three methods [13] are follows.
1. The qualitative method of relative retention time (RRT).
2. The qualitative method of stop- flow UV scanning.
3. The qualitative method of UV characteristic index V.
The quantitative determination of compositions was by the method of external standard (E-
X) and the calculation formula uses the following.
Wx % = ( Rex /Cx) * (Sx / Sex) * (Vex /Vx ) *Res% (2)

where Wx % is the weight content percent of x composition in heavy oil sample, Rx % and
Cex % are the concentration of preparation solution of resin fraction and external standard
solution, respectively, Sx and Sex are the peak areas of component x and external standard,
respectively, Vex and Vx are the injection volumes of external standard solution and resin
solution, respectively, Res% is the weight percent of resin fraction in heavy oil sample. The
qualitative and quantitative results are in Table 5.
200
15
6
150
13 16
21
9 20
12
100 19 24
30
11
14 27
8 18 22
4 7 28 31
10 33
50 39
5 17 26
23 29 35 36 38
32
34 37 40
0
0 20 40 60 80
T r/M in .
Fig. 7. HPLC chromatogram of resin fraction.
Number Quantitative Number Quantitative

Component Component
of peak results of peak results (ppm)
9 3-Methyl indole 610 15 N-phenyl pyrrole 800
10 Quinoline 240 16 7,8-Benzoquinoline 1000
Phenanthrene-
11 240 18 p-phenyl phenol 500
quinone
12 Carbazole 500 20 N-phenyl indole 600
13 4-Methylquinoline 640 24 Dibenzofuran 630
14 2-Amino-phenol 570 33 N-Ethyl carbozole 370
Note ppm 35 2,2,-Biquinoline 290
Table 5. Results of components of resin (ppm).
5. Conclusion
A modified method for group type analysis of asphalt using CLC was established. The
small-type CLC technique shows many advantages, such as high resolution rate, rapid
operation, and requires minimal quantities of sample and solvent. The both of IR and 1H
NMR results check the high resolution of this method.
The CLC method compared with routine ASTM method, the reagents used in this method
are small amount and lower toxicity. These are beneficial to environmental protection and
human health. This is very important for modern analysis.
The CLC method of this paper is an important and indispensable analysis method to study
heavy oils. It is not only a separation means, but is also analysis means.This method was
successfully applied to many analysis aspects, such as making high grade road asphalt,
characterizing MWDs and analysis heterocyclic of aromatic compositions of heavy oils.
The analysis of heavy oil is a long and difficult task. We systematically summarized these
studies and hope that these will help our colleagues.
6. References
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of some residual oils and asphalts by HPLC. Preprints, Division of petroleum
chemistry[C].INC. American Chemical Society, 1989, 34(2):240-246.
[2] Zhe Wang, Changming Zhang. A study on the relationship between the composition
and the usage of asphaltic heavy oil. Preprints, Division of petroleum
chemistry[C].INC. American Chemical Society, 1992, 37(3):933-936.
[3] Zhang Changming, Li Aiying, Li Ying, Zhang linmei. Instrumental analysis and
systematic investigation on heavy oils from coal. Chinese journal of Chromatography ,
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[4] Copyright by the ASTM international. Standard test method for separation of asphalt into
four fractions. 2002, Thu Dec 05 15; 56; 14.
[5] Shu-an Qian, Peng-zhou Zhang, Bai-ling Li, Structural characterization of pitch
feedstocks for coke making. Fuel, 1995, 64(8): 1085-1091.
[6] Standard of geologic office of the Peoples Republic of China, Analytical method of class
composition for crude oil and extract organic,1987,05-23.
[7] Justin D, Fair, Chad M.Kormos, Flash column chromatograms estimated from thin-layer
chromatography data. Journal of Chromatography A, 2008, 1211:49-54.
[8] Davies, Don R., Johnson, Todd M. Isolation of three components from spearmint oil: An
exercise in column and thin-layer chromatography. J. Chem. Educ. 2007,84(2):318-320.
[9] B. Concho-Grande, M. Rodriguez-Comesafia, J.Simal-Gandara, Sample HPLC
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[10] B Liawruangrath, S. Liawruangrath, High performance thin layer chromatographic
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[11] Yongbing Xue, Jianli Yang, Zhenyu Liu, Zhiyu Wang, Zengnou Liu,Yunmei Li,Yuzhen
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Catalysis Today 2004,98:333-338.
[12] Aroon Shenoy, Prediction of high temperature rheological properties of aged asphalts
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2
Column Chromatography
for Terpenoids and Flavonoids
Glin Saltan itolu and zlem Bahadr Ackara
Ankara University,
Turkey
1. Introduction
Natural products have coming from various source materials including terrestrial plants,
terrestrial microorganisms, marine organisms, terrestrial vertebrates and invertebrates have
importance as they provide an amazing source of new drugs as well as new drug leads and
new chemical entities for further drug development (McCurdy & Scully, 2005; Chin et al.,
2006). Morphine, vincristine, codeine, digitoxin, quinine, galantamine and taxol are just
some of the typical examples of drugs that have been introduced from natural sources
(Heinrich et al., 2004; Balunas & Kinghorn, 2005).
Natural products can be mainly divided into three groups such as primary metabolites,
secondary metabolites and high molecular weight polymeric materials (Hanson, 2003).
Primary metabolites including nucleic acids, amino acids, sugars; occur in all cells and play
a central role in the metabolism and reproduction of the cells. High molecular weight
polymeric materials such as cellulose, lignins and proteins take a part in the cellular
structure. Secondary metabolites, small molecules which are not essential for the growth
and development of the producing organism have importance because of their biological
activities on other organisms. Natural product term refers to any naturally occurring
compounds but in most cases mean secondary metabolite (Hanson 2003; Sarker et al., 2005).
Secondary metabolites mainly consist of these following groups:
- Terpenoids and steroids
- Fatty acid derivatives and polyketides
- Alkaloids
- Phenylpropanoids
- Nonribozomal polypeptides
- Enzyme cofactors (McMurry, 2010).
2. Isolation of terpenoids and flavonoids by column chromatography

2.1 Terpenoids
Terpenoids are the most widespread, chemically interesting groups of secondary
metabolites with over 30,000 known compounds including steroids (Wang et al., 2005;
Umlauf, 2004). Many terpenes have biological activities and are used for the treatment of
human diseases. Among the pharmaceuticals, the anticancer drug Taxol and the
antimalarial drug Artimesinin are two of the most renowned terpene-based drugs.
Terpenoids and steroids are originated from isoprenoit (C5) units derived from isopentenyl
(3-methyl-3-en-1-yl) pyrophosphate. These C5 units are linked together in a head-to-tail
manner. Based on the number of the isoprene units, terpenoids are classified as
monoterpenes (C10), sesquiterpenes (C15), diterpenes (C20), sesterpenes (C25), triterpenes
(C30), tetraterpenes (C40) and polyterpenes (Wang et al., 2005). Mono and sesquiterpenes are
the main constituents of the essential oils. However di- and triterpenoids which are not
volatile compounds, generally found in gums and resins. Tetraterpenoids constitute a group
of terpenoids called as carotenoids. This group includes carotenes, xanthophylls and
carotenoic acids and the most important polyterpenoid is the rubber (Sameeno, 2007;
Raaman, 2006).
Terpenoids are chemically lipid-soluble compounds and they can be extracted with
petroleum ether generally. Sesquiterpene lactones, diterpenes, sterols and less polar
triterpenoids extraction can be also performed by using benzene, ether and chloroform.
Ethyl acetate and acetone extracts contain oxygenated diterpenoids, sterols and
triterpenoids. Ethanol, methanol and water led to the extraction of highly oxygenated
namely polar triterpenes as well as triterpenoid and sterol glycosides. Total extraction of the
material carried out by any polar solvents such as acetone, aqueous methanol (%80) and
aqueous ethanol and then re-extraction with hexane, chloroform and ethyl acetate is also
leads to successive extraction of terpenoids and sterols (Harborne, 1998; Bhat, 2005).
Gas-Liquid Chromatography (GLC) is known as the best method for analyses of terpenoids
especially mono- and sesquiterpenoids. Isolation of the mono- and sesquiterpenoids is also
achieved by preparative GLC currently. Thin layer chromatography (TLC) can be used as
another rapid, useful method for terpenoids and sterols detection with concentrated H2SO4
and heating due to all terpenoids and steroids (except carotenoids) are colourless
compounds. TLC is also allowing to the isolation of various classes of terpenoids on silica
gel and silver nitrate impregnated silica gel coated plates (Harborne, 1998; Bhat, 2005).
For isolation of various terpenoids especially sesqui-, di-, tri- and tetraterpenoids as well as
sterols column chromatography is convenient method. As stationary phase silica gel,
alumina, cellulose, sephadex, polyamid are used for the separation of different types of
secondary metabolites but of this silica gel is the most extensively used adsorbent for
particularly nonpolar and medium polar compounds including terpenoids and sterols.
Silver nitrate impregnated silica gel is also provide separation of terpenoids containing
unsaturation (Bhat, 2005; Sarker et al., 2006). Terpenoids are generally alicyclic compounds
and isomerism is common. Due to the twisted cyclohexane ring, in chair form, different
geometric conformations are possible depending on the substitution around the ring.
Therefore, stereochemistry is commonly found in terpenoids. These structural features may
cause artifact formation during isolation procedure (Harborne, 1998).
2.1.1 Monoterpenoids
The monoterpenoids which are composed of the condensation of two isoprene units are
important components of essential oils (Gould, 1997). They are widely distributed in nature,
most of which have been found in higher plants. However a number of halogenated
Column Chromatography for Terpenoids and Flavonoids 15
derivatives have been isolated from marine organisms and have been found in defense and
pheromonal secretions of insects. Monoterpenes have intensely purgent odors and they are the
most common volatile compounds in plants responsible for fragrance and flavor. Therefore
monoterpenes have a great commercial interest for food industry as well as perfume and
fragrance industry (Robbers et al., 1996). Geraniol, a major component of geranium oil
(Pelargunium graveolens) and its isomer, linalool; citral a major constituent of lemon oil, is
obtained commercially from lemon grass oil (Cymbopogon flexuosus), menthol is found in the
essential oil of the field mint, Mentha arvensis, and possesses useful physiological properties
including local anaesthetic and refreshing effects, terpineol and -pinene are found in pine oil
(turpentine), camphor, which was isolated from the camphor tree, Cinnamomum camphora are
some of the typical examples of monoterpenoids (Hanson, 2003).
Isolation for mono- as well as sesquiterpenoids the classic procedure is obtaining essential
oils by steam distillation. However extraction with non-polar solvents such as petroleum
ether, ether and hexane can be preferred due to artifact formation at the raised temperatures
(Harborne, 1998). Adsorbtion chromatography on silica gel is the simplest and most
effective method for separation of terpenoids and GLC is used commonly for identification
as well as isolation of the monoterpenoids. Column chromatography is also a valid method
for fractionation of monoterpenoids. Isocratic elutions with solvents such as pentane,
petroleum ether, hexane or gradient elution with mixtures of solvents in increasing polarity
leads to successive isolation (Sur, 1991). Additionally, faster techniques of column
chromatography such as flash chromatography may be preferred due to conventional
column chromatography for separating procedure is time-consuming and frequently gives
poor recovery owing to band tailing (Ikan, 1991).
The genus Tagetes belongs to the Asteraceae family. Tagetes minuta has essential oil and
ocimenone which was reported to have mosquito larvicidal activity is the major constituent
of this oil. Separation of the essential oil of T. minuta on silica gel column eluting with Et2O
resulted in 10 fractions which the first four of these led to the isolation of (Z)--ocimene,
dihydrotagetone, (Z)-tagetone (Z)-ocimenone and (E)-ocimenone. Additionally, 3,7-
dimethyloct-1-en-6-one, 3,7-dimethyl-5-hydroxyoct-1-en-6-one and 3,7-dimethyloct-1,7-
dien-6-one were obtained by rechromatography of fraction V respectively (Garg & Mehta,
1998). Tagetes patula L. another species from this genus allows to the isolation of acyclic
monoterpene glycosides. Methanolic extract of the flowers was separated on silica gel
column chromatography using CHCl3-MeOH mixtures to yield 2-methyl-6-methylen-2,7-
octadiene 1-O--D-glucopyranoside (Garg et al., 1999).
HO
O
OH
R O
O OH
HO
R=H 3,7-dimethyloct-1-en-6-one
2-methyl-6-methylen-2,7-octadiene 1-O--D-
R=OH 3,7-dimethyl-5-hydroxyoct-1-en-6-one
glucopyranoside
R=H, 7 3,7-dimethyloct-1,7-dien-6-one
Artemisia tridentata ssp. vaseyana, Artemisia cana ssp. viscidula and Artemisia tridentata ssp.
spiciform led to the isolation of monoterpenoids. For each plant sample, air-dried ground
leaves and flower heads were extracted with pentane in soxlet extractor. The extracts were
concentrated in vacuo, and vacuum short path distilled to yield yellowish oils. The each oil
isolated from A. tridentata ssp. vaseyana, A. cana ssp. viscidula and A. tridentata ssp. spiciformis
was separated by flash chromatography on silica gel using 19:1 hexane-EtOAc followed by
4:1 hexane-EtOAc except for the oil isolated from A. tridentata ssp. spiciformis which was
flash chromatographed with 9:1 hexane-EtOAc as the second solvent system. A. tridentata
ssp. vaseyana essential oil was separated into three major fractions by column
chromatography. GC analysis of the first chromatographic fraction indicated the presence of
four constituents. Two major compounds were isolated and identified by comparison of
spectral data to literature values. The first was 1,8 cineole (eucalyptol) and the second was
trans-3-(1-oxo-2-methyl-2-propenyl)-2,2-dimethylcyclopropylmethanol which is thermally
unstable and isolated as its GC artifact 2,4-diisopropenyl-5H-furan. The third compound
was 2,2-dimethyl-6-isopropenyl-2H-pyran and the fourth was 2,3-dimethyl-6-isopropyl-4H-
pyran. Thujone was determined as the major components of the second fraction. In the third
fraction sabinol, chrysanthemol, chrysanthemyl acetate, fraganyl acetate, fraganol and 2-
isopropenyl-5-methylhexa-trans-3,5-diene-1-ol were identified as the major components.
Four major constituents obtained from Artemisia cana ssp. viscidula chromatographic
separation and the compounds were identified as santolina triene, -pinene, rothrockene
and artemisia trien was found to be in first fraction. The second of four chromatographic
fractions gave five components; artemiseole, 1-8 cineole, trans-3-(1-pylmethanol) which is
thermally unstable and isolated as its GC artifact 2,4-diisopropenyl-5H-furan, 2,2-dimethyl-6-
isopropenyl-2H-pyran, 2-isopropenyl-5-methylhexa-trans-3,5-diene-1-ol. Crysanthemal as well
as eight compounds identified as camphor, isolyratol, lyratol, chrysanthemol, chrysanthemyl
acetate, fraganyl acetate, fraganol and 2-isopropenyl-5-methylhexa-trans-3,5-dien-1-ol eight
compounds were isolated by preparative GC from the third and fourth chromatographic
fraction of A. cana ssp. viscidula respectively. Volatile oils obtained from the neutral pentane
extract of A. tridentata ssp. spiciformis were flash chromatographed into five separate fractions
to give mainly known compounds. The first fraction containing hydrocarbons was analyzed
by preparative GC and contained santolina triene, -pinene, camphene and rothrockene.
Fraction two contained artemiseole, 1,8-cineole and oxidosantolina triene, fraction three
contained lyratal, thujone and camphor and fraction four contained sabinyl acetate and
chrysanthemyl acetate. The final alcohol fraction contained -santolina alcohol, sabinol,
chrysanthemol, isolyratol, lyratol and lavandulol (Gunawardena et al., 2002).
OH
O O
2,2-dimethyl-6-isopropenyl-2H- 2,3-dimethyl-6-isopropyl-4H- 2-isopropenyl-5-methylhexa-trans-

pyran pyran 3,5-diene-1-ol
OH
OH
CHO
artemisia triene chrysanthemal chrysanthemol lavandulol

O HO
1,8-cineole thujone sabinol santoline triene
O
-pinene artemiseole camphor camphene
Artemisia annua L. (sweet wormwood; Compositae), the source of the potent anti-malarial drug
artemisinin, has been the subject of extensive phytochemical investigations over the past two
decades. Sesquiterpenoids are the most abundant compounds in this species. Additionally,
monoterpenoids, diterpenoids and flavonoids have been isolated. The seeds of A. annua were
frozen in liquid N2 and converted into a powder by grinding with a pestle and mortar. The
powder was repetitively extracted with CH2Cl2, dried (MgSO4) and solvent removed under
reduced pressure to yield an aromatic green gum which was subjected to gradient (hexane-
EtOAc 5 to 100%) column chromatography yielding 32 crude fractions. The crude fractions
from column chromatography were further purified by repeated prep HPLC, using n-hexane-
EtOAc-HOAc in varying proportions, according to the polarity of the crude fraction which
was under investigation. Three monoterpenoids which was identified as 4-hydroxy-2-
isopropenyl-5-methylene-hexan-1-ol, 1,10-oxy--myrcene hydroxide and 1,10-oxy--myrcene
hydroxide, was isolated together with sesquiterpenoids and diterpenoid (Brown et al., 2003).
O
O
HO
OH OH OH
4-hydroxy-2-isopropenyl
1,10-oxy--myrcene hydroxide 1,10-oxy--myrcene hydroxide
5-methylene-hexan-1-ol
Artemisia judaica (L.) is a perennial fragrant shrub which grows widely in the deserts and
Sinai Peninsula of Egypt. Mixture of the dry leaves of A. judaica, A. monosperma and A. hera
alba is very common anthelmintic drug in the most of North African and Middle East
countries under Arabic name of Shih. It has been reported that A. judaica essential oil has
two major constituents as piperitone and trans-ethyl cinnamate. Piperitone showed
insecticidal activity against Callosobruchus maculatus. Piperitone was isolated from aerial
parts of the plant. Dried and powdered aerial parts of A. judaica were hydrodistilled in a
Clevenger-type apparatus. The essential oil, pale yellow, was obtained and was dried over
anhydrous sodium sulphate. The essential oil was chromatographed on silica gel column
using hexane, 2.5% acetone-hexane, 10% acetone-hexane and acetone solvent system to give
45 fractions of 200 ml of each. The resulting fractions were concentrated under reduced
pressure and examined by TLC to offer two main fractions. Fractions 1017 was subjected to
silica gel column eluted with chloroform to offer of piperitone (Abdelgaleil et al., 2008).
piperitone
-Pinene type monoterpenoids have been isolated from the aerial parts of Artemisia
suksdorfii. Extraction was performed by using CH2Cl2 at room temperature and after
concentrated, subjected to column chromatography on silica gel. Gradient mixtures of
hexane and CH2Cl2 and then CH2Cl2 and methanol were used for elution to obtain five
fractions. Fraction 3 and 4 were separated on silica gel column and eluted with n-hexane-
CH2Cl2 to yield Fraction 1-A and 1-B. Further purification with elution by using hexane:
CH2Cl2-MeOH (5:7:0.5) of fraction 1-A on sephadex LH-20 column resulted in isolation of
two -pinene-type monoterpenoids; 7-hydroxymyrtenol and 7-hydroxymyrtenal
(Mahmoud & Ahmed, 2006).
HO H HO H
CH2OH CHO
7-hydroxymyrtenol 7-hydroxymyrtenal
The Mentha genus (Labiatae) has importance as sources of essential oil production in the
world. Additionally some members of this genus are used as herbal teas and spices.
Menthone, mentol, menthyl acetate, neo-isomenthyl acetate, 1-menthyl--D-glucopyranosyl,
1-menthyl-6-O-acetyl--D-glucopyranosyl have been identified mainly in various species.
Mentha longifolia is widely distributed in Eurasia and tropical Asia. Longifone, a new chloro
derivative of menthone was isolated from the aerial parts of the M. longifolia. After
concentrated to dryness methanolic extract was re-diluted in water and then extracted with
EtOAc. EtOAc soluble part subjected to silica gel column chromatography using hexane,
hexane-CHCl3, CHCl3 and CHCl3-MeOH as mobile phase. Fraction that eluted with 20%
CHCl3 in hexane yielded with longifone (M.S.Ali et al., 2002).
HO
Cl
longifone
Passiflora quadrangularis L. (badea) is widely distributed in some regions of tropical America.

Fruits of the plant are used locally to prepare different kinds of drinks with a pleasant and
refreshing aroma. Two oxygenated monoterpenoids were isolated from the fruits extract
whose odour strongly resembled the aroma of fresh fruit. After fruits were blended,
pentane-CH2Cl2 (1:1) was used for extraction. Obtained organic extract was dried over
Na2SO4 and concentrated. The concentrated extract was subjected to silica gel column
chromatography with the following eluant solutions; pentaneEt2O (9:1), pentaneEt2O
(2:1), pentaneEt2O (1:1), pentaneEt2O (1:2) and Et2O to obtain five fractions, fraction I to V,
respectively. Fraction III and fraction V were further fractionated by column chromatography
over silica gel using hexaneAcOEt (7:1 - 4:1) as eluents to yield (2E)-2,6-dimethyl-2,5-
heptadienoic acid and (3S)-(5E)-2,6-dimethyl-5,7-octadiene-2,3-diol respectively. To obtain
glycoside of (2E)-2,6-dimethyl-2,5-heptadienoic acid and (3E)-3,7-dimethyl-3-octene-1,2,6,7-
tetrol fruits pulp was blended in a mixer with the pH adjusted to 7.0 with 5 N NaOH. After
centrifugation supernatant was subjected to XAD-2 column chromatography and eluted with
water then MeOH. The MeOH eluate was fractioned by multilayer coil counter current
chromatography using CHCl3-MeOH-H2O (7:13:18) to yield fifty fractions. Fractions 20-30
were rechromatographed on silica gel column chromatography using CHCl3-MeOH (7:1, 5:1,
4:1, 3:1) mixtures. Fractions eluted with CHCl3-MeOH (7:1) gave (2E)-2,6-dimethyl-2,5-
heptadienoic acid--D-glucopyranosyl ester. (3E)-3,7-dimethyl-3-octene-1,2,6,7-tetrol was
obtained from fractions eluted with CHCl3-MeOH (5:1) after column chromatography on
silica gel using EtOAc-BuOH-H2O (8:2:5) (Osorio et al., 2000).
HO
O
C
OH
COOH HO OH
O
(2E)-2,6-dimethyl-2,5-heptadienoic acid -D-
(2E)-2,6-dimethyl-2,5-heptadienoic acid
glucopyranosyl ester
OH
HO HO
H OH
OH
(3S)-(5E)-2,6-dimethyl-5,7-octadiene-2,3-diol (3E)-3,7-dimethyl-3-octene-1,2,6,7-tetrol
Alpinia kadsumadai Hayata is native to Hainan Island in Southern to China and has traditional
usage in Chinese medicine as an antiemetic and for treatment of stomach disorders. Aerial
parts of the A. kadsumadai contain monoterpenoids, sesquiterpenoids, diarylheptanoids,
chalcones and flavonoids. CH2Cl2 extract of the aerial parts were subjected to column
chromatography on silica gel and eluted with hexane-EtOAc mixture in increasing polarity.
Fractions eluted with 15% EtOAc-hexane gives 1-terpinen-4-ol (Ngo &Brown, 1998).
OH
1-terpinen-4-ol
Carum carvi L., Caraway (Umbelliferae) has been used as a popular aromatic herb and spice
since antiquity and has been cultivated in Europe since the Middle Ages. Its fruit has been
used for medicine and in cooking, and is listed in British, German and European
pharmacopoeia. For medicinal purpose, it is used to relieve flatulent indigestion, colic and
bronchitis. Studies on the fruits have revealed that the essential oil, and many
monoterpenoids (d-carvone (main; 5060%), l-limonene, carvacrol, trans-carveol, d-
dihydrocarveol, l-dihydrocarveol, etc.) have been identified as the constituents. It was
reported that monoterpeneoids have also been identified in the water soluble extracts of
caraway. Commercial caraway was extracted with 70% methanol at room temperature.
After evaporation of the solvent, the residue was partitioned into etherwater, EtOAc
water. Removal of the solvent from each phase gave the ether, EtOAc and aqueous extracts,
The aqueous extract was chromatographed over Amberlite XAD-II (H2OMeOH). The
methanol eluate was subjected to Sephadex LH-20 (MeOH) to give eight fractions (AH).
Fraction B was chromatographed over silica gel (CHCl3MeOHH2O (17:3:0.2-4:1:0.1-
7:3:0.5)-MeOH) to give 14 fractions (B1B14). Fraction B3 was passed through a Lobar RP-8
column (MeCNH2O (3:17)) to give nine fractions (B3-1B3-9), and fraction B3-5 was subjected
to HPLC (ODS, MeCNH2O (3:37)). The main fraction was acetylated with Ac2O and
pyridine, and the acetylated fraction was subjected to HPLC (ODS, MeCNH2O (2:3)) to
give two fractions. These two fractions were deacetylated by heating in a water bath with
5% NH4OHMeOH for 2 h, and passed through Sephadex LH-20 (MeOH) to give (1R, 2R,
4S)-p-menthane-1,2,8-triol and Rel-(1S, 2S, 4R, 8R)-p-menthane-1,2,8-triol. Fraction B3-7 was
subjected to HPLC (ODS, MeCNH2O (1:9)) to give (1S, 2S, 4S, 8R)-p-menthane-2,8,9-triol;
(1S, 2S, 4S, 8S)-p-menthane-2,8,9-triol; (1S, 2R, 4R, 8R)-p-menthane-2,8,9-triol and (1S, 2R, 4R,
8R)-p-menthane-2,8,9-triol. Fraction B3-7 was subjected to HPLC (ODS, MeCNH2O (1:9) to
give Rel-(1R, 2S, 4R, 8S)-p-menthane-2,8,9-triol; Rel-(1R, 2S, 4R, 8R)-p-menthane-2,8,9-triol;
Rel-(1S, 2S, 4R, 8S)-p-menthane-2,8,9-triol and Rel-(1R, 2S, 4R, 8R)-p-menthane-2,8,9-triol.
From this mixture, Rel-(1R, 2S, 4R, 8R)-p-menthane-2,8,9-triol was isolated by silica gel
column chromatography (CHCl3MeOHH2O (9:1:0.1)). Fraction B9 was subjected to a Lobar
RP-8 column (MeCNH2O (3:17)) and HPLC (CHA, MeCNH2O (9:1)) to give (1S, 2R, 4R,
8S)-p-menthane-2,8,9-triol-9-O--D-glucopyranoside respectively. Fraction B11 was also
subjected to a Lobar RP-8 column (MeCNH2O (3:17)) and HPLC (CHA, MeCNH2O (9:1))
to give (1S, 2R, 4S)-p-menthane-1,2,8-triol-8-O--D-glucopyranoside respectively. Fraction
B10 was passed through a Lobar RP-8 column (MeCNH2O (3:17)) to give eight fractions (B10-
1B10-8). Fraction B10-4, fraction B10-5 and B10-7 were subjected to HPLC (CHA, MeCNH2O
(9:1)) to give (1S, 2S, 4R)-p-menthane-1,2,10-triol-2-O--D-glucopyranoside, (1S, 2S, 4R, 8R)-
p-menthane-1,2,9-triol-2-O--D-glucopyranoside, and (1S, 2R, 4R, 8S)-p-menthane-2,8,9-triol-
4-O--D-glucopyranoside respectively (Matsumura et al., 2001).
OH OH
OH
OH
HO HO
(1S, 2S, 4S, 8R)-p-menthane 2,8,9-triol (1R, 2R, 4S)-p-menthane-1,2,8-triol
OH OH
HOH2C HO
OH HO
O
HO O O OH
O
HO CH2OH
OH
OH
(1S, 2R, 4R, 8S)-p-menthane-2,8,9-triol-4-O--D- (1S, 2R, 4S)-p-menthane-1,2,8-triol-8-O--D-
glucopyranoside glucopyranoside
Carvacrol, one of the essential oil components of Monarda punctata was obtained as a lipase
inhibitor. Lipase is an enzyme that hydrolyzes triacylglycerols (TGs). The digestion and
absorption of natural lipids begins with hydrolysis by pancreatic lipase. The activity of this
enzyme greatly affects the metabolism of fat and the concentration of TG in blood. Recently,
inhibitors of lipase and lipid absorption have been isolated from natural sources with the
aim of preventing and treating metabolic syndrome. Monarda punctata L. (Lamiaceae) is a
traditional herbal medicine of North American Indians used as a remedy for colds and a
treatment for nausea, vomiting, and rheumatic pains. Carvacrol was obtained from M.
punctata essential oil. Powdered whole plants of M. punctata were extracted with acetone
H2O (80:20). The extract was suspended in H2O, and extracted with Et2O. The ether extract
was suspended in EtOHH2O (8:2), and extracted with hexane. The hexane soluble extract
was passed through a silica gel column yielding 14 fractions, one of which, eluted with
CHCl3-MeOH (99:1) was an essential oil fraction whose major component was carvacrol.
The H2O layer extract was a red-brown syrup. It was dissolved again in H2O, and the
aqueous solution was passed through a porous polymer gel column and eluted with H2O,
MeOHH2O (80:20) and MeOH. The MeOHH2O (80:20) eluate was subjected to on a
reversed-phase column chromatography using ODS (Cosmosil 140C18-OPN) and eluted
with 20%, 30%, 40%, 50%, 60%, 80% MeOH in H2O, and MeOH (fractions 1A1G). Fraction
1C was subjected to YCCC and HPLC, yielding monoterpenoid glycosides monardins (A-F)
together with flavonoids and some other phenolic compounds (Yamada et al., 2010).
OH
HO HO HO
O O O O O O
HO HO HO
OH
HO HO HO
OH OH OH OH
2-methyl-5-(1-methylethyl)
carvacrol monardin C monardin E
phenyl -D-glucopyranoside
2.1.2 Sesquiterpenoids
Sesquiterpenoids are generally synthesized by the mevalonate pathway and they are formed
from three C5 units (Dewick, 2009). The sesquiterpenoids which widely distributed in nature
have similar properties to monoterpenoids and generally be less volatile than
monoterpenoids (Robbers et al., 1996; Heinrich et al., 2004; Dewick, 2009). -Bisabolol, a
major component of matricaria (Matricaria chamomilla); -bisabolene which contributes to the
aroma of ginger (Zingiber officinale); costunolide a bitter principle found in the roots of
chicory (Cichorium intybus); parthenolide, an antimigraine agent in feverfew are some of the
naturally occurring sesquiterpenoids (Dewick, 2009).
Artemisinin, antimalarial drug, is one of the most important sesquiterpene obtained from
sweet wormwood, Artemisia annua L. (Asteraceae). This plant is known as Qinghao and has
been used for the treatment of fevers and malaria in China for many centuries. The methyl
ether of dihydroartemisinin that was developed for enhancing the solubility of the
compound whilst retaining the biological activity is used clinically (Heinrich et al., 2004;
Klayman et al., 1984). Artemisinin isolated from the leaves of A. annua. Petroleum ether
extract of the plant was chromatographed on silica gel (70-230 mesh) using 7.5% EtOAc in
CHCl3 solvent system. Artemisinin was isolated as fine white crystals in second fraction
(Klayman et al., 1984).
H
O
O
H
H
O
O
artemisinin
Curcuma zedoaria Roscoe (Zingiberaceae), also known as white turmeric, zedoaria or gajutsu,
has been used for menstrual disorders, dyspepsia, vomiting and for cancer traditionally.
This plant has also been used for the treatment of cervical cancer in Chinese traditional
medicine. C. zedoaria rich source of essential oils and many sesquiterpenoids as well as
curcuminoids have been isolated (Syu et al., 1998; Lobo et al., 2009). Zedoarol, germacrone,
curdione, -elemene and curzeone are sesquiterpenoids which were isolated from C. zedoaria
Shiobara et al (1986). CH2Cl2 extracts of the plant was chromatographed on silica gel using
hexane-EtOAc gradient. Fraction 11 was rechromatographed after evaporation on Sephadex
LH-20 using CHCl3-MeOH (1:1) to afford curzeone. Zedoarol obtained from separation of
fraction 21 on silica gel using hexane-EtOAc (97:3) and sephadex LH-20 (CHCl3-MeOH, 1:1)
respectively. Further separation of fraction 63 on silica gel (CH2Cl2) followed by on
Sephadex LH-20 (CHCl3-MeOH, 1:1) led to the isolation of germacrone (Shiobara et al.,
1986). Ar-Turmerone and -turmerone were obtained also from C. zedoaria rhizomes.
Methanolic extract of the rhizomes were prepared and then was suspended in distilled
water and partitioned with CHCl3. After evaporation CHCl3 extract was subjected to
column chromatography on silica gel and eluted with gradient mixtures of CHCl3 and
MeOH (20:1 to 1:1) to afford eight fractions. Further separation was performed on fraction 2
on silica gel by column chromatography eluting with CHCl3 and MeOH in increasing
polarity (100:1 to 1:1) to obtain five subfractions. Subfraction 2 led to the isolation of ar-
turmerone and -turmerone after preparative TLC (hexane-EtOAc, 97:3) (Hong et al., 2001).
O
O
OH
O O
zedoarol germacrone curzeone
O
O O
curdione -elemene ar-turmerone - turmerone

Daucus carota L. (Umbelliferae) is widely distributed in the world. Fruits of the plant have
been used commonly as a medicine for the treatment of ancylostomiasis, dropsy, chronic
kidney diseases and bladder afflictions in Chinese medicine. Flavonoids, anthocyanins,
chromones, coumarins as well as sesqiterpenoids have been isolated from the D. carota.
Sesquiterpenoids were isolated from the fruits of the plant. Fruits of the plant were extracted
with 95% aqueous EtOH. Partition of the EtOH extract was performed with petroleum ether,
CHCl3, EtOAc and BuOH respectively, after suspended in H2O. The CHCl3 layer was
fractionated on silica gel by column chromatography with gradient elution of petroleum
ether-EtOAc (7:1-1:7) to yield 10 fractions. Fraction 6 was chromatographed on silica gel
column chromatography petroleum ether-EtOAc (3:1-1:1) to give 5 subfractions. Subfraction
3 was separated by Sephadex LH-20 with MeOH followed by silica gel CHCl3-Et2O (8:1) to
obtain daucusol. Daucuside, a sesquiterpenoid glycoside was also isolated from the BuOH
layer. Column chromatography on silica gel with eluting gradient of CHCl3-Et2O (15:1-8:1)
allows obtaining eight fractions. Repeated column chromatography on silica gel with
CHCl3-MeOH (9:1) provides five subfractions. Daucuside was obtained by purification of
subfraction 2 using preparative HPLC (20% aqueous MeOH) (Fu et al., 2010).
HO
HO
H
O
HO O H
O
HO HO
OH O OH
HO
daucusol daucuside
Tanacetum parthenium (L.) Schultz. Bip. (Asteraceae) known as feverfew, leaves have been
used as antipyretic or febrifuge. Recent studies have revealed that feverfew effective in
migraine by substantially reducing the frequency and severity of the headache. Responsible
compound appears to be parthenolide, a germacranolide type sesquiterpenoid lactone.
Parthenolide was reported to act as serotonin antagonist resulting in an inhibition of the
release of serotonin from blood platelets. Parthenolide was isolated from the leaves of T.
parthenium. Extraction of the plant material was done after exhaustive maceration in
ethanol-water (90:10) at room temperature in the dark. The extract was filtered, evaporated
under vacuum, and lyophilized. Subsequently, the hydroalcoholic extract was
chromatographed on a silica gel column with hexane, CH2Cl2, EtOAc, MeOH, and MeOH-
H2O (90:10). Next, the CH2Cl2 fraction was chromatographed on a silica gel column with
different mixtures of solvents. The hexane- CH2Cl2 fraction resulted in isolation of
parthenolide (Robbers et al., 1998; Tiuman et al., 2005).
O
O
O
parthenolide
Valeriana officinalis L. (Valerianaceae) known as valerian, is used in the treatment of

conditions involving nervous excitability, such as hysterical states and hypochondriasis as
well as insomnia. The main components of the valerian roots are the iridoids and volatile oil.
Volatile oil contains numerous compounds including monoterpenoids, sesquiterpenoids
(Heinrich et al., 2004). Valerenane sesquiterpeneoids were isolated from a CH2Cl2 extract of
the Valeriana roots. Extract was concentrated and combined with 2% NaOH. Then aqueous
layer were acidified and extracted with petroleum ether-Et2O (2:1) to obtain extract A . The
remaining CH2Cl2 extract was washed with H2O and concentrated under vacuum. The
residue was dissolved in petroleum ether and concentrated after filtration to yield extract B.
Isolation procedure of extract B was performed on silica gel column using petroleum ether-
Et2O mixture in increasing polarity. Fractions 26-34 contains Z-valerenyl acetate and E-/Z-
valerenyl isovalerate which were isolated by means of preparative TLC (hexane-Et2O, 4:1)
followed by preparative GC. Extract A was dissolved in pentane and stored at -20 oC after
evaporation. Separation of the extract A was done using column chromatography on silica
gel and eluted with petroleum ether-Et2O mixture from 10 upto 100%. Valerenic acid and
hydroxyvalerenic acid were obtained from the 20 % Et2O and 100% Et2O fractions
respectively by preparative TLC (hexane-Et2O, 1:4). Acetoxy valerenic acid was also
obtained from remaining pentane extracts by preparative TLC using hexane-Et2O (3:2) (Bos
et al., 1986).
R1 H
R2
R1 R2
CHO H valerenal
COOH H valerenic acid
COOH OH hydroxyvalerenic acid
COOH OAc acetoxyvalerenic acid
CH2OR
R
H valerenol
Ac E-valerenyl acetate
CO-CH2-CH(Me)2 E-valerenyl isovalerate
CH2OR
R
Ac Z-valerenyl acetate
CO-CH2-CH(Me)2 Z-valerenyl isovalerate
2.1.3 Diterpenoids
The diterpenoids are a large group of non-volatile terpenoids based on four isoprene units
(Robbers et al., 1996).
Many of the diterpenoids are wood resin products. Abietic acid is the major component of
colophony. Gibberellins are the best known plant hormones, taxol is used in the treatment of
breast and ovarian cancer obtained from Pacific yew (Taxus bravifolia), are the known
diterpenoids from nature (Hanson, 2003).
Taxol (Paclitaxel), a diterpenoid isolated from Taxus brevifolia Nutt. (Taxaceae), also known as
the Pacific yew, used clinically in ovarian, breast, lung and prostate cancer effectively (Robbers
et al., 1996; Wall & Wani, 1996; Heinrich et al., 2004). Taxol has been isolated from T. brevifolia
using many different chromatographic techniquies and one of the way was described by
Senihl et al. (1984) which employs normal phase chromatography columns for the separation
procedures and includes multiple (seven) steps respectively as follows; 1. Extraction with
alcohol and concentration, 2. Partition between water and dichloromethane, 3. Filtration
chromatography, 4. Silica column chromatography, 5. Alumina chromatography. 6. Medium
pressure silica column chromatography, 7. Preparative HPLC. For the other analogues, two or
three other chromatographic columns, followed by preperative HPLC, were used.
O
AcO OH
CH3
H3C
O O
CH3
O CH3
N
H
O
OH OH AcO
O
O
taxol
Ginkgo biloba, (Ginkgoaceae) one of the oldest living plant species dating back more than 200
million years, is often reffered to as living fossil. Medicinal uses of G. biloba was described
in the Chinese Materia Medica more than 2.000 years ago and is used to treat memory and
cognitive impairment, for which it has moderate efficacy with minimal side effects. The
ginkgo leaves contain many active ingredients, including flavonoids, terpene trilactones
(Jacobs & Browner, 2000). Triterpene lactones namely ginkgolides and flavonoids are
believed to be associated with pharmacological activities of G. biloba extracts. While
flavonoids can be obtained from many other plants, ginkgolides are unique compounents of
the G. biloba extracts (Jaracz et al., 2004). It has been reported that flavone glycosides of the
rutin type probably reduced the capillar fragility and reduce blood vessel which may
prevent ischemic brain damage. Ginkgolides have been shown to inhibit platelet activating
factor (PAF) as well as increasing blood fluidity and ciculation. In Europe ginkgo extract is
sold as an approved drug (Robbers et al., 1996). It has been reported that many extraction
methods have been developed for the extraction triterpene lactones efficiently such as using
organic solvents, water, pressurized water or supercritical fluids. From these enriched
extracts terpenic compounds can be separated by fractional recrystalization, repeated
column chromatography, reversed phase HPLC, chromatography with Sephadex LH-20 or
more efficiently by chromatography on NaOAc impregnated silica gel. In the following
method was described by Jaracz et al. (2004) for the isolation of bilobalide and ginkgolides
using column chromatography. The enriched triterpene trilactone extract was
chromatographed on silica gel column. The column eluted with EtOAc-hexane solvent
mixtures. The initial solvent system was EtOAc-hexane (3.5:6.5). Content of EtOAc in eluent
was increased gradually in six steps to EtOAc-hexane (6.5:3.5). The fractions collected at
EtOAc-hexane (4.5:5.5) contained bilobalide. Pure bilobalide was obtained as white powder
after washing with Et2O. The fractions collected at EtOAc/hexane (5:5) and (5.5:4.5)
contained mixture of ginkgolide A/B and ginkgolide C/J, respectively. Ginkgolide mixtures
were separated using further chromatographic methods to yield pure compounds (Jaracz et
al., 2004). A simple preparative method for the isolation and purification of ginkgolides and
bilobalide (ginkgo terpene trilactones) was also developed by Beek & Lelyveld (1997).
Ginkgo biloba leaf extracts were used for extraction. After a partition step with EtOAc, the
enriched intermediate extract was separated into the individual terpenes by medium-
pressure liquid chromatography on silica impregnated with 6.5% NaOAc with a gradient
from petroleum etherEtOAc to EtOAcMeOH. After recrystallization from H2OMeOH,
all ginkgolides could be isolated in high purity. After a selective extraction with H2O, leaves
could also be used as a starting material (Beek & Lelyveld, 1997).
R2 O H
O
O
O
O
O
OH
R1
HO
O
R3
R1 R2 R3
ginkgolide A OH H H
ginkgolide B OH OH H
ginkgolide C OH OH OH
ginkgolide J OH H OH
ginkgolide M H OH OH
O
OH
O O O
C(CH)3
O
O
HO
O
bilobalide
Salvia divinorum Epling & Jativa is known as hallucinogenic mint and traditionally used by
Mazatec Indians of Oaxaca, Mexico in traditional medicine primarily for its psychoactive
effects (Giroud et al., 2000; D.Y.W.Lee et al., 2005). Salvinorin A, a neoclerodane diterpenoid
has been isolated and identified as the responsible compound for psychoactive effects.
Additionally, salvinorin A have found to have high affinity and selectivity for the kappa
opioid receptor is one of the three main types of opioid receptors (D.Y.W.Lee et al., 2005).
The discovery of kappa opioid receptor as the molecular target of salvinorin A has opened
up many opportunities for drug discovery and drug development for a number of
psychiatric and non-psychiatric disorders (Vortherms & Roth, 2006; Li et al 2007). Salvinorin
A isolated from the leaves of the S. divinorum. Dried leaves of the plant were sequentially
extracted with hexane, acetone and MeOH. The acetone extract was fractioned by flash
column chromatography with an equal mixture of activated carbon Celite 545. The column
was eluted with acetone and hexane. The supernatant of the acetone extract was
chromatographed on a silica gel column and eluted with CHCl3-acetone to give five
fractions. The fraction eluted with CHCl3-acetone (20:1) was subjected to repeated silica gel
column chromatography with a gradient of hexane and EtOAc (15:1-1:1) to afford
subfractions. Combined subfractions were purified on silica gel column by CHCl3-EtOAc
(20:1-10:1) or hexane-EtOAc (5:1-2:1) solvent systems to yield salvinorin A together with
other diterpenoids such as salvinorin B, -C, -D, -E, -F, -G, divinatorin C, -D, -E, hardwickiic
acid (D.Y.W.Lee et al., 2005).
O
O
O
H H
O O
O
O
O
salvinorin A
2.1.4 Triterpenoids
The triterpenoids are formed from six isoprene units biosynthetically and widely distributed
in nature including plants, microorganisms, animals and humans. Typical examples of the
triterpenoids are steroids which have many important functions in mammals such as sex
hormones (Robbers et al., 1996; Heinrich et al., 2004).
Oleanolic acid and its isomer ursolic acid are triterpenoids that exist widely in plants as well
as in foods as their free forms or as their glycosides. Oleanolic acid and ursolic acid are well
known for their hepatoprotective effects. They are used alone or in combination with other
hepatoprotective ingredients as oral medications (Liu, 1995; 2005). It has also been reported
that oleanolic acid and ursolic acid act at various stages of tumor development to inhibit
tumor initiation and promotion, as well as to induce tumor cell differentiation and apoptosis
(Liu, 2005). Oleanolic acid and ursolic acid have been isolated many natural sources.
Oleanolic acid was obtained from grape as antimicrobial compound. Raisins were extracted
with MeOH by maceration. The extract was concentrated and suspended in % 90 MeOH
and then partitioned with hexane, CHCl3 and EtOAc respectively. The hexane soluble
extract was subjected to silica gel column chromatography and eluted with mixture of
CHCl3-MeOH (1:0-0:1) to give nine fractions. Fraction 3 was separated on silica gel VLC
column and eluted with hexane:isopropyl alcohol gradient mixtures (98:2 50:50) to yield
oleanolic acid (Rivero-Cruz et al., 2008). Another example can be given for oleanolic acid
isolation from Salvia officinalis. Leaves of the Salvia officinalis were extracted with MeOH and
then extract was partitioned with EtOAc and n-BuOH respectively. EtOAc fraction was
chromatographed on silica gel column chromatography using following solvent systems
hexane-EtOAc (10:1-3:1-1:1)-CHCl3-MeOH (10:1)-MeOH to give 4 fractions. Fractions 2 and
3 give diterpenes as well as oleanolic acid after column chromatography on ODS (MeOH-
H2O 60:40-90:10) followed by preparative HPLC (MeOH-H2O, 85:15) (Ninomiya et al., 2004).
Ursolic acid was isolated from Sambucus ebulus L. (Elder) as anti-inflammatory agent. Isolation
was carried out from ethanolic extract of the dwarf elder. Initial seperation was performed by
means of liquid-liquid extraction of the crude extract with petroleum ether, diethyl ether,
EtOAc and BuOH respectively. Diethyl ether fraction was subjected to silica gel column
chromatography and petroleum ether and increasing amounts of ethyl acetate was used as
mobile phase to afford eight fractions. Fraction 4 was divided in CH2Cl2 as soluble and
insoluble part. CH2Cl2 insoluble part was subjected to liquid-liquid using petroleum ether,
EtOAc, ACN and butyl-methyl ether (10:1:5:2). The lower layer was separated by high-speed
counter current chromatography (HSCCC) using petroleum ether, EtOAc, ACN and butyl-
methyl ether (10:1:5:2) to obtain three fractions and remained insoluble part. Insoluble part
subjected to crystallization with mixture of ACN and tetrahydrofuran to afford ursolic acid as
white platelets (Schwaiger et al., 2011). Ursolic acid was also obtained from many of the plants.
One of them is Orthosiphon stamineus Benth., (Lamiaceae), a native plant to tropical Eastern
Asia. Dried leaves of the plant were extracted with MeOH. After filtration and concentration,
the crude extract was suspended in H2O and partitioned with hexane, CHCl3, EtOAc and
BuOH. The CHCl3 soluble fraction was applied to silica gel column chromatography and
eluted with EtOAc-hexane (7:3) to yield 5 fraction. Further purification by preparative TLC
using EtOAc-hexane (3:2) led to the isolation of ursolic acid (Hossain & Ismail, 2010).
COOH COOH
HO HO
oleanolic acid ursolic acid

Curcurbita pepo (pumpkin) belongs to Cucurbitaceae family is used as a vegetable for human
consumption and also use in traditional medicine. Cucurbita pepo is used in the therapy of
minor disorders of the prostate gland and the urinary bladder. Cucurbita pepo has received
considerable attention in recent years because of the nutritional and health values of the
seeds. The seeds are excellent source of protein and also pharmacological activity such as
antidiabetic, anti fungal and antioxidant. Diets riched in pumpkin seeds have also been
associated with lower levels of gastric, breast, lung and colorectal cancer. Seeds and fruit
parts of cucurbits are reported to possess purgative, emetic and antihelmintic properties due
to the secondary metabolite cucurbitacin content. Cucurbitacins are important functional
component found in Cucurbitaceae and constitute a group of diverse triterpenoid
substances which are well known for their bitterness and toxicity. They are highly
oxygenated, tetracyclic triterpenes containing a cucurbitane skeleton and they are divided
into twelve categories which range from cucurbitacins A to T. Specific forms of
cucurbitacins are known to have varying potencies with regard to particular activities and
effects. It is known that, for example, cucurbitacins B and D are the most potent feeding
stimulants for diabroticite beetles, while cucurbitacin D exhibits anti-ovulatory activity in
mice, and cucurbitacin B, D, and E all exhibit cytotoxic and anti-tumor effects. Several
cucurbitane and hexanorcucurbitane glycosides and other types of triterpenoids have been
isolated from the fruits of Cucurbita pepo (Gill & Bali, 2011). To obtain cucurbitacins, a liquid
is obtained from cucurbitacin-containing plant material by compressing is extracted with a
non-polar solvent to remove waxes, pigments, fatty acids, lipids and terpenes from the
cucurbitacin-containing solution. For isolation and separation of cucurbitacins, retaining
aqueous cucurbitacins-containing liquid is applied to a silica gel column chromatography,
preferably the flash column chromatography. Elution is performed with a moderately polar
solvent (e.g., CH3Cl) firstly and then the column is eluted with a suitable mixture of solvents
(e.g., CH3Cl and acetone, toluene and acetone, EtOAc and acetone, or CH3Cl and acetone),
preferably in a ratio of about 95:5 by volume. This elution is collected essentially consists of
the cucurbitacin B, which may then be additionally purified and dried. Then column is
eluted with a second suitable mixture of solvents (e.g., CH3Cl, acetone and MeOH; EtOAc,
acetone and MeOH; or CH3Cl, acetone and MeOH), preferably in a ratio of about 90:5:5 by
volume. This elution is collected essentially contains cucurbitacin D. Finally, the silica gel
column is eluted with a third suitable solvent mixture (e.g., CH3Cl, acetone and MeOH;
EtOAc, acetone and MeOH; or CH3Cl, acetone and MeOH), preferably in a ratio of 80:5:15
by volume. This elution is collected mainly consists of the cucurbitacin E (Subbiah, 1999).
O
HO
OH
O
OH
H H
HO
cucurbitacin D
Centella asiatica (L.) Urban (Umbelliferae) (Gotu kola), is widely cultivated as a spice or
vegetable and is used in treatment of skin diseases, rheumatism, inflammation mental illness,
epilepsy, diarrhea and wounds. Polyacetylenes, flavonoids and triterpenoids have been
isolated from this plant and among them triterpenoids are major and the most important
components of C. asiatica, regarded as a marker constituent in terms of quality control. The
triterpenes obtained from C. asiatica are mainly pentacyclic triterpenic acids and their
respective glycosides, belonging to ursane- or oleanane-type, including asiatic acid,
asiaticoside, madecassic acid, madecassoside, brahmoside, brahmic acid, brahminoside,
thankuniside, isothankuniside, centelloside, madasiatic acid, centic acid, cenellic acid, betulinic
acid, indocentic acid, etc (Zeng & Qin, 2007; Nhiem et al., 2011). Chromatographic separation
of the triterpenoids and their glycosides were performed from methanolic extract of the plant
leaves. MeOH extract was suspended in H2O and partitioned with EtOAc. EtOAc soluble
fraction was then subjected to column chromatography on silica gel and eluted with gradient
of CHCl3-MeOH (50:1-1:50) to yield five fraction. Fraction 1 was rechromatographed on silica
gel using CHCl3-MeOH (10:1) as an eluent to give four subfractions. Subfraction 3-4 give
asiatic acid and quadranoside IV after purification on RP-18 column with MeOH-H2O (5:1)
and MeOH-H2O (4:1) respectively. The H2O soluble fraction was chromatographed on Diaion
HP-20P column eluted with step gradient of MeOH in H2O yielding the five fractions. Fraction
2 was rechromatographed on RP-18 column and eluted with acetone /H2O (2:1) to yield four
subfractions. Subfraction 1 was separated on a silica gel column using CHCl3/MeOH/H2O
(30:10:1) as solvent system to afford asiaticoside G. Asiaticoside and asiaticoside F were
obtained from subfraction 2 by means of further purification on silica gel column using CHCl3-
MeOH-H2O (35:10:1) (Nhiem et al., 2011).
R2
O
R1
OR3
HO
OH
R1 R2 R3
OH H H asiatic acid
OH OH Sugar asiaticoside G
OH H Sugar asiaticoside
H H Sugar asiaticoside F
OH H Glc quadranoside IV
Calendula officinalis L., (Asteraceae), (Marigold) is popular medicinal herb and cosmetic in
Europe and in America. This plant has been recorded various national pharmacopoeias as
well as European Pharmacopoeia. Marigold has been used for wound healing and topical
anti-inflammation. The anti-inflammatory properties of the plant flowers have been
attributed to triterpenoids some of which are lauryl, myristoyl and palmitoyl esters of
faradiol. Calendula flowers were extracted using supercritical fluid extraction method under
500 bar pressure, 50 C and 35kg h-1 carbon dioxide flow. Prepared extract was separated on
silica gel column chromatography and eluted with petroleum ether-CHCl3-MeOH (50:49:1)
to yield four fractions. Fraction 4, containing triterpenoid esters, was rechromatographed
using low-pressure liquid chromatography on Lobar LiChroprep RP-18. Elution was carried
out using MeOH to obtain nine subfractions. Fraction 3 gives faradiol-3-O-laurate. Faradiol-
3-O-myristate and faradiol-3-O-palmitate was obtained from fraction 4 and maniladiol-3-O-
myristate as well as maniladiol-3-O-palmitate were purified from fraction 5 by further
separations in HPLC (Hamburger et al., 2003).
OH OH
RO RO
R= laurate faradiol-3-O-laurate
R= myristate maniladiol-3-O-myristate
R= myristate faradiol-3-O-myristate
R= palmitate maniladiol-3-O-palmitate
R= palmitate faradiol-3-O-palmitate
Panax ginseng C.A. Meyer has been used as a traditional medicine in China for thousand of
years. Ginseng root is one of the most important oriental medicines and is used worldwide to
combat stress and disturbances of the central nervous system, for hypothermia, for its
antioxidant and organ-protective actions, and for radio-protection. The name ginseng often
leads to some confusion due to its use for different plants with different phytochemical
constituents. True ginsengs are plants in the genus Panax from which Asian ginseng (Panax
ginseng) and American ginseng (Panax quinquefolium) have received the most interest for
phytomedicinal use. However, Eleutherococcus senticosis, a completely different plant not even
in the genus Panax, is sometimes referred to as Russian or Siberian ginseng (Briksin 2000;
Fukuda et al., 2000; Park et al., 2002; Ruan et al., 2010). There are two types of preparations
from ginseng: white ginseng prepared by drying after peelling off and red ginseng prepared
by steaming and drying (Shibata, 2001). Ginseng root contains dammarane and oleanane type
saponins as well as polyacetylene derivatives and polysaccharides. Triterpene saponins called
as ginsenosides are the well known chemical constituents of ginseng. More than 30
ginsenosides have been identified in ginseng. Ginsenosides Rb1, Rb2, Rc, Rd, Rg1, Rg2 and Re
are the major constituents of white and red ginsengs. However Rg3, Rg5, Rg6, Rs1, Rs2 and Rs3
are known to be only compounds that have been isolated from red ginseng (Park et al., 2002).
Some partly deglycosylated saponins such as Rh1, Rh2 and Rg3 are obtained from red ginseng
as artifacts produced during steaming (Shibata, 2001). Ginsenosides, Rb1, Rb2, Rc, Rd, Re, Rf,
Rg1, and Rg2 are considered to be the most relevant for pharmacological activity (Briskin,
2000). Ruan et al. (2010) isolated a new ginsenosides from fresh roots of Panax ginseng together
with known ginsenosides Rb1, Rb2, Rc and Rd. Ginseng roots was extracted with MeOH-H2O
(4:1) five times and then extract was concentrated to dryness under reduced pressure at 40 oC.
The crude extract was suspended in H2O and subjected to D-101 resin column
chromatography using MeOH-H2O (0:1, 3:2) as eluents to afford total ginsenosides. Total
ginsenosides was applied to silica gel column and eluted with CHCl3-MeOH-H2O (6:4:1) to
yield three fractions. Fraction 1 was further chromatographed on preparative HPLC eluted
with gradient CH3CN-H2O 20% to 50%) to give the ginsenoside Rb1, Rb2, Rc and Rd and Ra3
(Ruan et al. 2010). In another study ginsenosides were isolated from dried rootlet of ginseng
which was steamed at 120 for 3 hours in an autoclave. Steamed ginseng was extracted with
MeOH under reflux for 2 hr. The solvent was removed in vacuo to yield MeOH extract, which
was suspended in water and extracted with CH2CI2. The remaining aqueous layer was
extracted with water-saturated n-BuOH The n-BuOH fraction was concentrated in vacuo to
yield BuOH fraction, which was subjected to silica gel column chromatography. Five fractions
were obtained using stepwise gradient elution (EtOAc-MeOH-H20, 40:1: 1 - 10:1: 1). Fraction 3
was chromatographed over silica gel using EtOAc-MeOH- H20 = 25:1:1 solvent. Ginsenosides
Rs4 and Rs5 were obtained from fraction 3, which were further purified on Ag-impregnated
preparative TLC using EtOAc-MeOH-H20, 15:1:1 solvent. They were further purified over
semi-preparative HPLC using a reverse-phase column (LiChrospher 100 RP-18, 250 mm x 10
mm i.d.) with 60% CH3CN eluent to isolate ginsenoside Rs4 and Rs5. Fraction 2 was
chromatographed over silica gel using hexane-isopropyl alcohol = 6:1 solvent to give Rs6 and
Rs7 rich fractions. The fractions were further purified by semi-preparative HPLC using a
reverse-phase column (LiChrospher 100 RP-18, 250 mm xl0 mm i.d.) with 50% ACN eluent to
yield ginsenosides Rs6 and Rs7 (Park et al., 2002).
RO
O
HO
HO
HO O
OH
HO
O O
HO
HO
O
HOOCH2COCO
O
HO
HO
OH
R = -glc ginsenoside Rb1
R = -ara(p) ginsenoside Rb2
R = -ara(f) ginsenoside Rc
R = -H ginsenoside Rd
Ganoderma lucidum (Fr.) P. Karst. belongs to the family of Ganodermataceae (Basidiomyetes),

has been used since ancient times. G. lucidum was believed to cure many kinds of diseases,
and it was considered as an elixir that could revive the dead by the ancient people. G.
lucidum possess important biological activities including anti-tumor, antimicrobial, antiviral
(especially anti-HIV activities) and antiaging activities. It has been reported since the first
triterpenoid ganoderic acid A was reported more than 150 compounds have been identified
from Ganoderma spp. Triterpenoids are main components of this genus and have importance
for their pharmacologic properties (Cheng et al., 2010). The air-dried and powdered fruit
bodies of G. lucidum were extracted with EtOH-H2O. The crude extract was washed with
petroleum ether to remove fatty acids, then extracted with CH2Cl2 to give the total
triterpenoids fraction. An aliquot of the CH2Cl2 extract was applied to a silica gel column
eluted successively with CHCl3MeOH (200:11:1 gradient system) to obtain 5 fractions.
Fraction 2 was subjected to a silica gel column eluted with petroleum etherEtOAc (10:11:1
gradient system) to afford six fractions, F21F26. F21 was subjected to Sephadex LH-20
column chromatography (petroleum etherCHCl3MeOH, 2:1:1), then recrystallized to
afford ganoderic acid DM. F22 was applied to a Sephadex LH-20 (petroleum etherCHCl3
MeOH, 2:1:1), and then further purified by semipreparative HPLC (MeOHH2O, 90:10) to
afford ganodermanondiol and ganoderic acid T-Q. F23 was recrystallized to obtain
lucidadiol, F24 was extensively subjected to silica gel column chromatography (petroleum
etherCHCl3Me2CO, 8:1:1), Sephadex LH-20, and then further purified by semipreparative
HPLC to give ganoderol B, lucidumol A and 15-hydroxy-3-oxo-5-lanosta-7,9,24(E)-trien-
26-oic acid. F25 was purified by semipreparative HPLC (MeOH-H2O, 70:30, detection
wavelength, 252 nm) to give 3-hydroxy-5-lanosta-7,9,24(E)-triene-26-oic acid and 15,26-
dihydroxy-5-lanosta-7,9,24(E)-trien-3-one. F26 was applied to a succession silica gel
column (400600 mesh, CHCl3-MeOH, 100:1-10:1 gradient system) and Sephadex LH-20 (PE-
CHCl3-MeOH, 2:1:1) chromatography to afford 3-hydroxy-7-oxo-5-lanosta-8,24(E)-dien-
26-oic acid, ganodermanontriol, 3,7-dihyroxy-12-acetoxy-11,15,23-trioxo-5 -lanosta-8-
en-26-oic acid methyl ester, ganoderiol F and lucideric acid A. In the same manner, F3 was
applied to a silica gel column (400600 mesh) eluted with PE (6090 C)Me2CO (7:13:1) to
afford 6 fractions, F31F36. Each fraction was subjected to silica gel column chromatography
and repeated semipreparative HPLC to afford ganoderic acid D, 11-hydroxy-3,7-dioxo-5 -
lanosta-8,24(E)-dien-26-oic acid, 11-hydroxy-3,7-dioxo-5 -lanosta-8,24(E)-dien-26-oic acid,
lucidone A, ganolucidic acid E, 4,4,14, -trimethyl- 3,7-dioxo-5 -chol-8-en-24-oic acid,
ganoderic acid F ganoderenic acid D, ganoderic acid E, ganoderic acid J, ganoderenic acid F.
F4 was separated by repeated column chromatography (CHCl3-MeOH, 100:1-5:1 gradient
system) and semipreparative HPLC (MeOH-H2O, 40:60, detection wavelength, 252 nm) to
afford ganoderic acid B, ganoderic acid A, 7,12-dihydroxy-3,11,15,23-tetraoxo-5-
lanosta-8-en-26-oic acid, 12-hydroxy-3,7,11,15,23-pentaoxo-5-lanosta-8-en-26-oic acid,
OH
O H
OH
O OH
H
ganoderic acid A
ganoderenic acid B, methyl ganoderate H, 12-acetoxy-7-hydroxy-3,11,15,23-tetraoxo-5 -

lanosta-8,20-dien-26-oic acid, methyl ganoderic acid B, 12-acetoxy-3,7-dihydroxy-
11,15,23-trioxo-5-lanosta-8,20-dien-26-oic acid, ganolucidic acid A, methyl lucidenate C,
12-acetoxy-3,7,11,15,23-pentaoxo-5 -lanosta-8-en-26-oic acid ethyl ester, ganoderic acid H
and ganoderic acid AM1. Whereas fraction F5 was separated by repeated column
chromatography (CHCl3-MeOH, 100:1-1:1 gradient system) and semipreparative HPLC
(MeOH-H2O, 30:70, detection wavelength, 252 nm) to give compounds 3,7,15-
trihydroxy-11,23-dioxo-5-lanosta-8-en-26-oic acid, ganoderic acid K, ganoderic acid G,
ganoderenic acid A (Cheng et al., 2010).
Cimicifuga racemosa or Actaea racemosa L. (Black cohosh), Ranunculaceae, is known as well-
known herbal medicine with health benefits in treating painful menstrual periods and
menopausal disorders. This plant is used primarily as a hormon-free phytomedicine in the
treatment of climacteric symptoms related to menopause. It has been clarified that main
components of the rhizoma are cycloartane type triterpenoids and their glycosides such as
actein, 27-deoxyactein and several cimicifugosides as well as isoflavones, alkaloids and
phenylpropanoids have been identified in Black cohosh (Chen et al., 2002; Watanabe et al.,
2002; Heinrich et al., 2004; Z.Ali et al., 2007; Li et al., 2007; Borelli & Ermst, 2008; Nian et al.,
2011). Chen et al. (2002) isolated actein, 26-deoxyactein and 23-epi-26-deoxyactein from the
rhizomes of A. racemosa. Rhizomes of the plant were extracted with MeOH and then
concentrated under vacuum to yield a syrup residue. A sample of the residue was
suspended in H2O-MeOH (9:1) and fractionated by successive partitions with EtOAc and
BuOH respectively. The EtOAc-soluble fraction was subjected to column chromatography
on silica gel and eluted with CHCl3, CHCl3-MeOH (10, 20, 30, 40, 50, 75 %) and MeOH
respectively to afford 8 fractions. Fraction 5 was subjected to a normal phase silica gel
column chromatography by elution of petroleum ether-EtOAc mixture in increasing polarity
to give 10 subfractions. 26-deoxyactein was obtained by direct crystallization from
subfraction 5. The main liquor was sequentially subjected to RP-18 chromatographic column
separation eluted by ACN-H2O followed by normal phase silica gel separation eluted by
petroleum ether-EtOAc-MeOH (10:7:0.5) to obtain actein. Subfraction 3 was subjected to a
RP-18 column separation eluted by ACN-H2O and MeOH-H2O followed by silica gel
column separation eluted with petroleum ether-EtOAc-MeOH (10:5:0.5) to yield 23-epi-26-
deoxyactein (Chen et al., 2002). Another isolation procedure was described by Watanabe et
al. (2002). Methanolic extract of the rhizomes of C. racemosa was concentrated under vacuum
and the viscous concentrate was passed through a Diaion HP-20 column and eluted with
30% MeOH, 50% MeOH, MeOH, EtOH and EtOAc successively. Fractions eluted with 50%
MeOH were subjected to column chromatography on silica gel eluting with stepwise
gradient mixtures of CHCl3-MeOH- H2O (19:1:0, 9:1:0, 40:10:1, 20:10:1) and finally with
MeOH to afford 7 fractions. Fraction 4 rechromatographed on silica gel column
chromatography eluting with CHCl3-MeOH (30:1, 10:1, 5:1) and ODS silica gel with MeOH-
H2O (8:5) to give 25-O-acetyl-12-hydroxycimigenol 3-O--L-arabinopyranoside. Fraction 5
gave 12-hydroxycimigenol 3-O--L-arabinopyranoside after separation on ODS silica gel
column chromatography eluted with MeOH- H2O (8:5). Fraction 7 was chromatographed on
silica gel eluting with CHCl3-MeOH (9:1) and ODS silica gel with MeOH- H2O (4:3)
respectively to obtain 12,21-dihydroxycimigenol 3-O--L-arabinopyranoside. The MeOH
eluate portion was separated on silica gel and eluted with CHCl3-MeOH (19:1, 9:1, 4:1, 2:1)
mixture and MeOH finally to yield four fractions. Fraction 2 was subjected to column
chromatography on silica gel and eluted with CHCl3-MeOH to obtain two subfractions (2a-
2b). Subfraction 2a suspended in MeOH and after filtration rechromatographed on silica gel
column chromatography eluting with CHCl3-MeOH (30:1, 19:1) and ODS silica gel with
ACN-H2O (1:1) and MeOH- H2O (8:3) as well as on Sephadex LH-20 with MeOH
respectively to obtain cimicigenol 3-O--L-arabinopyranoside, 25-O-methoxycimicigenol 3-
O--L-arabinopyranoside, 23-O-acetylshengmanol 3-O--L-arabinopyranoside, 27-
deoxyactein and actein. The remain subfraction 2b led to the isolation of cimiracemoside F,
cimiracemoside G, cimiracemoside H and 822R, 23R, 24R)-12-acetyloxy-16, 23:22,25-
diepoxy-23,24-dihydroxy-9,19-cyclolanostan-3-yl -L-arabinopyranoside (Watanabe et al.,
2002). Actaea podocarpa which is also known as Cimicifuga americana (Summer cohosh) led to
the isolation of cyclolanostane type glycosides named podocarpasides (A-G) that was
reported by Z.Ali et al. (2007).
O
OAc
O R
O
H
H
O
O
HO
HO H
OH
R= H 26-deoxyactein
R=OH actein
O
OAc
O
O
O
O
HO
HO H
OH
23-epi-26-deoxyactein
2.1.5 Tetraterpenoids
Members of this class also called as carotenes or carotenoids because of their occurrence in the
carrot (Daucus carota). Carotenoids are naturally occurring pigments and they are responsible
for the yellow, orange, red and purple colors of plants as well as bacteria and algae (Robbers et
al., 1996; Heinrich et al., 2004). Fruits and vegetables are rich sources of carotenoids and it has
been revealed that carotenoids are strong antioxidant compounds for the prevention of cancer
and other human diseases (Burns et al., 2003). Numerous epidemiological studies have
demonstrated that carotenoids may be responsible for the beneficial effects associated with the
intake of green and yellow vegetables and fruits for cancer prevention in humans. It has been
become clear that not only -carotene but also -carotene and lycopene, some xanthophylls
such as lutein, canthaxanthin, fucoxanthin, halocynthiaxanthin, etc. possess significant cancer
chemopreventive effects (Maoka et al., 2001).
The carotenoids can be divided into two groups. Hydrocarbons, soluble in petroleum ether
is the first group, orange-red carotenoids , , -carotene, red-carotenoid lycopene are
typical samples of hydrocarbon carotenoids. The second group called as xanthophylls which
mainly contains oxygenated derivatives (alcohols, aldehydes, ketones, epoxides and acids)
such as lutein, crytoxanthin, rhodoxanthin, violaxanthin, crocetin and ext. are soluble in
ethanol (Ikan, 1991).
General isolation procedure of carotenoids was described by Kimura & Rodriguez-Amaya
(2002) using column chromatography. Carotenoids are widely distributed in leafy vegetables;
therefore they are providing good sources for isolation. Cold acetone exctract was prepared
from lettuce, partitioned to petroleum ether, and then concentrated under vacuum to obtain
crude extract. The crude extract was separated on MgO-Hyflosupercel (1:1 activated for 2 h at
110 C) column chromatography using ether-petroleum ether (8%) and acetone-petroleum
ether (10-15%, 15-18%, 25-40, 60-70%) as mobile phase to yield -carotene, lactucaxanthin,
violaxanthin, lutein, neoxanthin, chlorophylls respectively. All fractions eluted with petroleum
ether containing acetone were washed four or three times with water in a separatory funnel to
remove the acetone and then dried with Na2SO4. This method allows to efficiently and quickly
separation of carotenoids (Kimure & Rodriguez-Amaya, 2002).
Lycopene, known as tomato pigment, is widely distributed in nature. It was isolated from
Tamus communis firstly. Lycopene can be extracted from tomato paste with MeOH-CH2Cl2
mixture after dehydration of tomato paste by MeOH. The extract was concentrated, and
then crystallized twice from benzene by the addition of MeOH to obtain lycopene of 98 to
99% purity. Further purification can be achieved by column chromatography on calcium
hydroxide (Ikan, 1997).
H3C
CH3 CH3
H3C CH3
H3 C
CH3
CH3 CH3
CH3
lycopene
Palm oil contains carotenoids. Palm oil mill effluent that is remaining part of the palm oil
industry was extracted with hexane. Hexane extract was evaporated and then subjected to
column chromatography on silica gel. Elution was performed by hexane to obtain -
carotene successively. The best separation procedure was performed with the 1:6 ratio of
extracted oil: silica gel and the 40 C temperature (Ahmad et al., 2009).
H3C
CH3 CH3
H 3C CH3
H3 C
CH3
CH3 CH3
CH3
-carotene
Ripe fruits of paprika (red pepper), which are used widely as vegetables and food colorants,
are good source of carotenoid pigments. The red carotenoids in paprika (Capsicum annuum
L.) are mainly capsanthin, capsorubin and capsanthin 3,6-epoxide (Maoka et al., 2001). The
methanol (MeOH) extract of the fruits of C. annuum L. was partitioned between n-hexane-
Et2O (1:1) and 10% aqueous NaCl. The organic layer was concentrated to dryness. The
residue was subjected to silica gel column chromatography using hexane, hexane-ether (8:2),
hexane-ether (7:3), hexane-ether (5:5), ether, ether-acetone (2:8), ether-acetone (5:5) and
acetone, successively. Each fraction was further purified by HPLC on a C18 reversed phase
column with CH2Cl2-CH3CN (2:8) as the eluent. Capsanthin obtained from fractions eluted
with ether-acetone (5:5) from silica gel column, Capsanthin 3-ester from eluted with hexane-
ether (1:1) from silica gel column, Capsanthin 3,3-diester eluted with hexane-ether (8:2)
from silica gel column; Capsorubin eluted with ether-acetone (2:8) from silica gel column,
Capsorubin 3,3-diester eluted with hexane-ether (7:3) from silica gel column. Capsanthin
3,6-epoxide eluted with ether-acetone (2:8) from silica gel column. Cucurbitaxanthin A 3-
ester eluted with ether-hexane (3:7) from silica gel column (Maoka et al., 2001). Latoxanthin,
a minor carotenoid was isolated from the fruits of Capsicum annuum var. lycopersiciforme
flavum, yellow paprika. Exract of the yellow paprika was subjected to column
chromatography and eluted with hexane-acetone mixture (3:7). Repeated chromatography
on CaCO3 column and then crystallization in benzene-hexane led to the isolation of
latoxanthin as red crystals (Nagy et al., 2007).
OH
CH3
H3C
CH3 H3C
CH3 CH3 H3C
O
CH3
CH3 CH3
HO
CH3
Capsanthin
2.2 Flavonoids
Flavonoids are one of the largest groups of secondary metabolites and widely distributed in
leaves, seeds, bark and flowers of plants with more than 4000 different structures which are
classified according to their chemical structures as follows; flavones, flavonols, flavanones,
dihydroflavonols, isoflavones, anthocyanins, catechins and calchones. Flavonoids which are
part of human diet are thought to have positive effects on human health such as reducing
risk of cardiovascular diseases and cancer. Most of the beneficial effects of flavonoids are
attributed to their antioxidant and chelating abilities (Cook & Samman, 1996; Peterson &
Dwyer, 1998; Heim et al., 2002; Rijke et al., 2006). Flavonoids are structurally related
compounds with a chromane-type skeleton with a phenyl substituent in the C2 or C3
position (Rijke et al., 2006). They are consisting of phenylpropane (C6-C3) unit derived from
shikimic acid pathway and C6 unit derived from polyketide pathway biosynthetically
(Heinrich et al., 2004).
Flavonoids are present generally as mixtures and it is very rare to find only one single
flavonoid components in plants (Harborne, 1998). They are phenolic compounds and
hydroxyl groups often located at positions 3, 5, 7, 3, 4 and/or 5. One or more of these

hydroxyl groups are frequently methylated, acetylated, prenylated or sulphated. Flavonoids
are present in plants as aglycone or as their glycosides generally (Rijke et al., 2006).
Extraction of the flavonoids can be performed with solvents that are chosen according to
their polarity. Less polar aglycones such as isoflavones, flavanones, dihydroflavonols, higly
methylated flavones and flavonols can be extracted with CH2Cl2, CHCl3, ether, EtOAC.
However the more polar aglycones including hydroxylated flavones, flavonols, chalcones
and flavonoid glycosides are generally extracted by polar solvents such as acetone, alcohol,
water and their combinations (Harborne, 1975; 1998). Many different chromatographic
techniques are employed for flavonoids isolation among them column chromatography
remains the most useful technique for large scale isolation procedure. Conventional open-
column chromatography is still widely used because of its simplicity and its value as an
initial separation step. Preparative work on large quantities of flavonoids from crude plant
extracts is also possible. Silica gel, polyamide, sephadex, cellulose are commonly used
adsorbents. Silica gel is recommended mainly for separation of less polar flavonoids
(isoflavones, flavanones, dihydroflavonols and highly methylated/acetylated flavones and
flavonols). However, some flavonoid glycosides also can be purified on silica gel using more
polar solvents as eluants. Cellulose can be considered as a saceld-up form of paper
chromatography. Cellulose is suitable for separation of all class of flavonoids and their
glycosides. However, cellulose has low capacity and limited resolving power. Sephadex led
to the isolation of compounds on the basis of their molecular size. The hydroxypropylated
dextran gel, Sephadex LH-20 is designed for use of with organic solvents or water/solvent
mixtures. For Sephadex gels, as well as size exclusion, adsorption and partition mechanisms
operate in the presence of organic solvents. Although methanol and ethanol can be used as
eluents for proanthocyanidins, acetone is better for displacing the high molecular weight
polyphenols. Slow flow rates are also recommended. Open-column chromatography with
certain supports (silica gel, polyamide) suffers from a certain degree of irreversible
adsorption of the solute on the column. Modifications of the method such as dry-column
chromatography, vacuum liquid chromatography are also provide practical usage for the
rapid fractionation of plant extracts. VLC with a polyamide support has been reported for
succesive separation of flavonol glycosides. Medium-pressure liquid chromatography
O O O O
H H
H H
OH H OH
O O O O
flavone flavonol flavonone dihydroflavonol
O
+
O O
H
H
OH OH
O
H H H O
isoflavone catechin anthocyanin chalcone
(MPLC) which is a closed column (generally glass) connected to a compressed air source or
a reciprocating pump covers is also a simple alternative method to open-column
chromatography or flash chromatography, with both higher resolution and shorter
separation times. MPLC columns have a high loading capacity, up to a 1:25 sample-to-
packing-material ratio, and are ideal for the separation of flavonoids. In MPLC, the columns
are generally filled by the user. Particle sizes of 25 to 200 m are usually advocated (15 to 25,
25 to 40, or 43 to 60 m are the most common ranges) and both slurry packing and dry
packing is possible. When compared a shorter column of larger internal diameter with a
long column of small internal diameter (with the same amount of stationary phase)
resolution is increased. Choice of solvent systems can be efficiently performed by TLC or by
analytical HPLC (Harborne, 1975; 1998; Andersen & Markham, 2006).
Vitex agnus-castus (Verbenaceae), (Chasteberry or chaste-tree), is used for the treatment of
management of female reproductive disorders including premenstrual problems (PMS),
menopausal symptoms, and insufficient milk production. The German Commission E
recommends it for menstrual problems, mastalgia, and premenstrual syndrome. The specific
chemical components responsible for its clinical effects have not been determined but some
iridoids, terpenoids as well as flavonoids have been isolated from the leaves or fruits (Hirobe
et al., 1997; Hadju et al., 2007). Hirobe et al. (1997) was described the isolation of luteolin,
artemetin, isorhamnetin, 4, 5-dihyroxy-3, 3, 6, 7-tetramethoxyflavone as well as four luteolin
caffeoylglucoides. Fruits of the chasteberry were powdered and extracted with MeOH. The
concentrated extract was partitioned between H2O and hexane, CHCl3, BuOH respectively.
BuOH fraction was subjected to HP-20 column chromatography and eluted with H2O, 40%,
60% and 80% MeOH respectively to yield five fractions (Fr. A-E). Fr. D was subjected to
further separation on Sephadex LH-20 and then silica gel column chromatography and elution
was performed by CHCl3-MeOH (1:1) and CHCl3-MeOH-H2O (8:9:1-6.7:3:0.3) succesively.
Further purification was performed by means of ODS MPLC and HPLC with MeOH-H2O and
ACN-H2O to obtain luteolin 6-C-(4-methyl-6-O-trans-caffeoylglucoide), luteolin 6-C-(6-O-
trans-caffeoylglucoide), luteolin 6-C-(2-O-trans-caffeoylglucoide) and luteolin 7-O-(6-p-
benzoylglucoide), luteolin and isorhamnetin. To obtain 4, 5-dihyroxy-3, 3, 6, 7-
tetramethoxyflavone and artemetin hexane extract was subjected to column chromatography
and eluted with hexane-EtOAc (10:0-0:10) followed with EtOAc-MeOH (1:1). The EtOAc-
MeOH (1:1) eluate was subsequently separated using ODS MPLC and finally purified by
means of ODS HPLC elution with 80% MeOH (Hirobe et al., 1997).
Dried and powdered flowering stems of V. agnus castus were extracted with MeOH and
extracts were evaporated under reduced pressure to yield syrupy residue. The MeOH
extract was dissolved in H2O and partitioned with CHCl3 followed by BuOH. A part of the
BuOH phase was fractionated on a silica gel column eluting with a gradient solvent system
(CHCl3-MeOH) to give nine main fractions (Frs. A-I). Fraction G was further
chromatographed over silica gel column eluting with EtOAc-MeOH-H2O (100:5:2 to
100:17:13) to yield eight fractions (Frs. G1-8). Fr G6 was applied to repeated column
chromatographies (CC) over Sephadex LH-20 eluted with MeOH to afford isoorientin
(Luteolin 6-C-glucoside) and luteolin 7-O-glucoside. Fr. G2 was subjected to column
chromatography on Sephadex LH-20 using MeOH to give compound (2-O-trans-
caffeoylisoorientin. Fractionation of Fr. F by open CC on silica gel using EtOAc-MeOH-H2O
(100:17:13) yielded subfractions F1-6 . Fr. F2 was submitted to Sephadex LH-20 CC (MeOH)
to afford pure 6-O-transcaffeoylisoorientin (Kuruzm-Uz et al., 2008).
OH
HO O
OH
OR3
O
R2O OR1
HO
OH O
R1 =H, R2=CH3, R3=trans caffeoyl luteolin 6-C-(4-methyl-6-O-trans-caffeoylglucoide)

R1 =R2=H, R3=trans caffeoyl luteolin 6-C-(6-O-trans-caffeoylglucoide)
R1 = trans caffeoyl, R2=R3=H luteolin 6-C-(2-O-trans-caffeoylglucoide)
R6
R1 O
R5
R2 R4
R3 O
R1 =O-Glc(6-p-hydroxybenzoyl) R2=R4=H, R3=R5=R6=OH luteolin 7-O-(6-p-benzoylglucoide)

R1 =R2=R4=R5=OCH3, R3=R6=OH 4, 5-dihyroxy-3, 3, 6, 7-
tetramethoxyflavone
R1 =R3=R5=R6=OH, R2=R4=H luteolin
R1 =R2=R4=R5=R6=OCH3, R3=OH artemetin
R1 =R3=R4=R6=OH, R5=OCH3, R2=H isorhamnetin
OH
OH
HO O OH
O O
OH O
OH
OH
O OH
OH HO
OH O HO
HO OH O
HO
isoorientin lutelin-7-glycoside
Isoflavonoids such as puerarin, daidzin and daidzein was isolated from Pueraria lobata
(Willd) Ohwi roots. Pueraria roots are used in Chinese traditional medicine with gegen
names for common cold. Daidzein, also known as soya isoflavon has spazmolytic activity.
Pueraria roots were extracted with acetone to separate non-glycosidic flavonoids. Acetone
extract was separated on silica gel column chromatography using hexane-EtOAc mixture to
obtain daidzein, formononetin and puerarol. The residue was extracted against MeOH and
then concentrated to dryness under vacuum. To obtain crude extract were dissolved in H2O
and extracted with BuOH to separate glycosidic compounds which were further fractitioned
chromatographically on Sephadex LH-20 eluting with MeOH. The glycosidic mixture was
chromatographed over silica gel column using CHCl3-MeOH-H2O (40:16:3) to separate
puerarin, daidzin and other glycosides mixtures. Further purification of glycosides mixture
was performed by HPLC (Ohshima et al., 1987).
HO O HO O O
O
OH
HO
HO
O O
OH OH
daidzein daidzin
Crataegus species (Hawthorn), (Rosaceae) is a traditional medicinal plant that possess

beneficial effects on the heart and blood circulation. Crataegus monogyna and C. laevigata are
the most often used species. Dried flowers, leaves and fruits are mainly used for mild to
moderately severe heart failure and coronary heart diseases. Oligomeric procyanidins and (-
)-epicatechin as well as flavonoids are known as the main active constituents (Svedstrm et
al., 2002; Szer et al., 2006). C. laevigata flowers and leaves methanolic water extract led to
the isolation of procyanidins. Methanolic-water extract was prepared in an ultrasonic bath
and then extract was concentrated to a smaller volume under vacuum. Concentrated extract
was partitioned with petroleum ether and EtOAc respectively. The EtOAc soluble part
evapoarated to the dryness and subjected to column chromatography on polyamide CC 6
column eluting with MeOH, MeOH-H2O (7:3) and Et2O-H2O (7:3). Fractions 18-33 allow the
isolation of (-)-epicatechin after purification by preparative HPTLC. Epicatechin dimmers;
epicatechin-(48)-epicatechin (procyanidin B-2); catechin-(48)-epicatechin
(procyanidin B-4); epicatechin-(46)-epicatechin (procyanidin B-5) were obtained from the
43-75 and 117-121 fractions by column chromatography on Sephadex LH-20 uaing EtOH as
eluents. Fractions 123-140 was separated with EtOH on Sephadex LH-20 to yield
procyanidin trimers, epicatechin-(48)-epicatechin-(48)-epicatechin (procyanidin C-1);
epicatechin-(46)-epicatechin-(48)-epicatechin and tetramer epicatechin-(48)-
epicatechin-(48)-epicatechin-(48)-epicatechin (procyanidin D-1) (Svedstrm et al.,
2002). Many flavonoids such as hyperoside, rutin, and quercetin have also been isolated
from Crataegus species. The dried and powdered leaves of Crategus davisii were extracted
with petroleum ether and then with EtOH. The petroleum ether extract was concentrated
and extracted with 60% EtOH. The aqueous extract was concentrated and extracted with
CHCl3 (Extract A). The EtOH extract was concentrated and extracted with toluene, CHCl3
(Extract B) and EtOAc (Extract C) successively. Extract A was chromatographed first by
vacuum liquid chromatography (VLC) on silica gel with Petroleum ether-CHCl3-MeOH
mixtures. Fractions 11-12 (CHCl3-MeOH 80:20) were then chromatographed on a
chromatotron (silica gel) again with PE-CHCl3-MeOH mixtures and from fraction 42
(petroleum ether-CHCl3, 20:80 ) crataequinone B were obtained. Extract B was
chromatographed first by VLC on silica gel with toluene-Et2O-MeOH mixtures. Fractions 6-
8 (toluene-Et2O, 75:25 to 60:40) were then chromatographed on a chromatotron (silica gel)
again with toluene-Et2O-MeOH mixtures and from fractions 40-48 ( toluene-Et2O 30 : 70 to
10:90 ) quercetin were obtained. Extract C was chromatographed first on a silica gel column
with toluene-EtOH mixtures. Main fractions 153-304 (toluene-EtOH, 50:50) were then
chromatographed on a chromatotron (silica gel) with toluene-CHCl3-EtOH mixtures and
from fractions 24-32 (CHCl3-EtOH, 50:50 to 30:70) hyperoside, vitexin 4-rhamnoside and
rutin were obtained using preparative PC (acetic acid-H2O, 15:85 ). Main fractions 305-380
(EtOH) were chromatographed on a polyamide column with H2O-EtOH mixtures and from
fractions 77-133 (H2O-EtOH, 80:20) vitexin 2-rhamnoside was obtained (Szer et al., 2006).
Apigenin, hesperetin, eriodictyol, luteolin, quercetin, luteolin-7-O-glucoside, hyperoside,
vitexin, vitexin-4-O-rhamnoside were isolated from Crataegus microphylla C. Koch. by

similar procedure (Melikolu et al., 2004).
OH OH
OH OH
HO O HO O
OH
OH
O
OH O
OH
OH O OH O HO
quercetin hyperoside
OH
OH
HO O
OH
HO
O OH
O
OH O OH
O
H3C O
HO
HO
OH
rutin
Cranberry (Vaccinium macrocarpon) fruits are excellent raw materials for juice production, as
they contain numerous antioxidants including phenolic compounds, vitamin C, minerals
and many others. Compounds present in the fruits of the Vaccinium species are reported to
play several roles in human health maintenance. Consumption of cranberries is found to
have protective effects against urinary tract infections. Health benefits such as reduced risks
of cancer and cardiovascular disease, are believed to be due to the presence of various
polyphenolic compounds, including anthocyanins, flavonols, and procyanidins. The potent
antioxidant properties of Vaccinium fruits have been well documented. Biological properties
of the fruit extract, rich in anthocyanins, include antioxidant capacity, astringent and
antiseptic properties, ability to decrease the permeability and fragility of capillaries,
inhibition of platelet aggregation, inhibition of urinary tract infection and strengthening of
collagen matrices via cross linkages. Cranberry extracts also exhibited a selective tumor cell
growth inhibition in prostate, lung, cervical, colon, and leukemia cell lines (Caillet et al.,
2011). To isolate cranberry phenolics, cranberry fruits were crushed, macerated with
aqueous acetone (80:20 acetone-H2O) and extracted at room temperature for with agitation.
The resulting extract was filtered, extraction was repeated on the remaining solids, and the
two aqueous acetone extracts were combined. The acetone was removed by rotary
evaporation at 35 C under high vacuum and frozen at 20 C. The extracts were pre-
purified using a method described below After removal of acetone, the aqueous layer was
partitioned into hexane to remove carotenoids, fats, and waxes, followed by additional
partitioning into ethyl acetate to selectively extract proanthocyanidins with anthocyanin

glycosides and flavonols. The ethyl acetate extract was concentrated by vacuum
evaporation. The ethyl acetate extract was dissolved in a small amount of methanol for
transfer to column chromatography system pre-packed with sephadex LH-20 (column size 100
45 mm). The column was subsequently eluted with water, 20% methanol in water, 60%
methanol in water, 100% methanol and 80% acetone in water. The water (first liter) eluate
yielded organic acids, with subsequent 20% methanol in water elution of anthocyanins, which
were pooled together on the basis of color and TLC. The fraction eluted with 60% methanol in
water, methanol, and 80% acetone in water yielded the flavonol glycoside fraction,
proanthocyanidin fraction. Further purification was performed using preparative HPLC to
obtain myricetin-3--galactoside, myricetin-3--arabinofuranoside, quercetin-3--galactoside,
quercetin-3--glucoside, quercetin-3-rhamnopyranoside, quercetin-3-O-(6-p-benzoyl)--
galactoside and epicatechins (monomer, dimer and trimer) (Singh et al., 2009) .
OH
OH
OH
OH
HO O
HO O
OH
HO
OH
O
OH O
OH O
OH OH
HO
epicatechin (monomer) myricetin-3-galactoside
OH
OH
OH
HO O OH
O HO O
OH OH
OH
OH
O
O OH OH
OH O
O
HO
CH2OH
OH
HO
epicatechin (dimer) myricetin-3-arabinofuranoside
OH
OH
HO O
OH
OH
OH
HO OH O
O
OH
OH
O OH
HO
OH
HO
epicatechin (trimer)
Resveratrol is known as 3, 5, 4-trihydroxystilbene, is widely used in medicine and health

products due to their important biological activities such as anti-inflammatory, anticancer,
and cardioprotective. Resveratrol is not widely distributed in plants and has been reported
that few fruits and vegatables contain. Polygonum cuspidatum (Polygonaceae) is one of the
richest sources of resveratrol (Soleas et al., 1997; Mantegna et al., 2012). Resveratrol was
isolated from Pleuropterus ciliinervis belonging to Polygonaceae (J.P.Lee et al., 2003). Dried
roots of the plant were extracted with MeOH. MeOH extract was evaporated to dryness and
suspended in H2O and then partitioned with hexane, EtOAc, BuOH, respectively. The
EtOAc soluble fraction was subsequently fractionated on silica gel column chromatography
and eluted with gradient of hexane-EtOAc (2-50%) and EtOAc-MeOH (5:1) to yield six
fractions. Fraction 4 rechromatographed on silica gel column using hexane-EtOAc gradient
mixture to afford resveratrol (J.P.Lee et al., 2003). Gnetum gnemon Linn. (Gnetaceae) from
Gnetum genus is known to contain abundant stilbene derivatives also led to the isolation of
resveratrol. Successive extraction of acetone, MeOH and 70%MeOH respectively was
performed. The acetone extract was subjected to silica gel column chromatography using
CHCl3-MeOH in increasing polarity as eluents to give eleven fractions. Fraction 1 gives
resveratrol together with other stilbenes after column chromatography of Fraction 1 on
Sephadex LH-20 (MeOH) (Iliya et al., 2003).
HO
OH
HO
Resveratrol
3. Conclusion
Remarkable advances have been accomplished in natural products isolation since the
discovery of chromatography. Natural products are present generally as mixtures which
makes hard to separation of them. Different chromatographic techniques such as paper

chromatography (PC), thin layer chromatography (TLC), gas liquid chromatography (GLC),
high performance liquid chromatography and column chromatography employ for
separation and purification of natural products. Amon them column chromatography which
is the oldest chromatographic technique, is still widely used especially for large scale
isolation procedure. Conventional open column chromatography is preferable because of its
simlicity. Different stationary phases can be available according to the polarity of the test
samples such as silica gel, bonded-phase silica gel, polyamide, sephadex, cellulose, ion-
exchange resins. However separation procedure in conventional column chromatography is
time consuming and this method suffers from a certain degree of irreversible adsorption of
the solute on the column. Vacuum liquid chromatography (VLC) a modified method of
conventional column chromatograhy provides practical usage for the rapid fractionation of
extracts. Medium-pressure liquid chromatography (MPLC) a closed column which
connected to a compressed air source or a reciprocating pump covers is also a simple
alternative method to open-column chromatography or flash chromatography.
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Products Drug Discovery and Therapeutic Medicine Terpenoids As Therapeutic Drugs As
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Monoterpene and Monoterpene Glycosides from Monarda punctata.
3
Chromatographic Separation and Identification

of Sildenafil and Yohimbine Analogues
Illegally Added in Herbal Supplements
Hakan Gker*, Maksut Cokun and Glgn Ayhan-Klcgil
Central Instrumental Analysis II Laboratory, Faculty of Pharmacy, Ankara University,
Tandogan, Ankara,
Turkey
1. Introduction
Herbal medicines are major source of aphrodisiacs and have been used worldwide for
thousands of years by different cultures and civilizations. Recently, consumption of dietary
supplements has been becoming more popular around the world. Unfortunately, the
adulteration of dietary supplements with undeclared synthetic chemical compounds is
steadily increasing according to the literature. Some herbal products advertised as all
natural have in contrast been found to contain synthetic PDE-5 inhibitors. There are
currently three PDE5 inhibitors Sildenafil (Langtry & Markham, 1999) (Viagra; Pfizer, New
York, US), Tadalafil (Meuleman, 2003) (Cialis; Eli Lilly, Indianapolis, US), and Vardenafil
(Keating & Scott, 2003) (Levitra; Bayer Pharmaceuticals Co, Wuppertal, Germany),
approved worldwide for the treatment of male erectile dysfunction, further two agents
Udenafil (Salem et al., 2006) (Zydena; Dong-A PharmTech Co, Korean), Mirodenafil (Jung,
2008) (Mvix, Life Science R&D Center of SK chemical, Beijing, Tianjin, Shanghai) were
licensed only in Korea. They produce vascular smooth muscle relaxation, promote penile
blood flow, and hence, induce erection. These kinds of commercially available herbal
aphrodisiac products have been spiked with the above-mentioned legal drugs, but also with
their analogues, which have not been subjected to formal pharmacokinetic or other
pharmacological testing in either humans or animals.
The practice of self-medication by an increasing number of patients, the incessant aggressive
advertising of these herbal aphrodisiacs, the invasion of the medicinal market with
uncontrolled dietary supplements and the absence of real directives amplifies the potential
health hazards to the community. Since the sildenafil is an chemical, it must not been found
in any foodstuffs, but an increasing number of sildenafil analogues have been discovered in
dietary and herbal supplements even in soft drinks, this number is steadily increasing and
some time their types are unknown and necrosis not observed instead of paracetamol.
Hence, it is prudent to test the safety and efficacy thus might have unknown and harmful
side-effects. Structural analogues are also synthetic chemicals with slightly altered chemical
structures and have similar erectile effects on the body. Nevertheless, it is not uncommon
* Corresponding Author
for chemicals with similar structures to possess slightly or entirely different before any new
chemical is licensed as drug for human use. This testing process is lengthy and costly; on
average, it takes 9.5 years and costs US$800 million to license a new drug. Many drug
analogues, without the aforementioned drug testing process, are available for human
consumption properties. Phenacetin, structurally similar to paracetamol, has been associated
with renal papillary necrosis not observed with paracetamol (Poon, 2007). Many drug
analogues, without the aforementioned drug testing process, are avaliable for human
comsuption via different channels. Examples include analogues of psychoactive drugs,
anabolic steroids, and Sibutramine which was one of the most abused compound as anti-
obesity drugs.
The most commonly reported side effects of sildenafil are headaches, flushing of the face,
upset stomach and nasal congestion. We met a dieatery supplement having combination of
sildenafil and paracetamol, probably in order to prevent headeache caused by sildenafil.
Other side effects include sensitivity to light, blurred vision, urinary tract infection, diarrhea
and dizziness. The main problem with sildenafil and analogues are that they interact with
many other medications. They can rapidly decrease blood pressure up to dangerously low.
They can interact with nitrates such as nitrogliserin, which are often prescribed to heart
patients. Sildenafil has not to be administrated to patients with heart problems taking nitrate
medications because of the severe potentiation of vasodilatory effects.
It is well known, the first developed and consequently the most famous phosphodiesterase
inhibitor is Sildenafil (Langtry & Markham, 1999) approved by the FDA in early April 1998.
Novel PDE5 inhibitor, Lodenafil carbonate, breaks down in the body to form two molecules
of the active drug lodenafil. This formulation has higher oral bioavailability than the parent
drug (Toque et al., 2008) Fig 1.
O O
N N
NH O HN
N O O O N
S S
N N O N N
N N
O O O O
Lodenafil carbonate
O
N
O O HN
N
S
N N
N
HO O
Lodenafil
Fig. 1. Prodrug lodenafil carbonate.
Chromatographic Separation and Identification of Sildenafil
and Yohimbine Analogues Illegally Added in Herbal Supplements 53
Avanafil was discovered by pharmaceutical developer Vivus as PDE5 inhibitors, the

safety and efficacy for erectile dysfunction, a possible lunch in 2012. It has a particular
advantage over its potential competitors, the effects are demonstrable very quickly (in 15
minutes or less) (Bell & Palmer, 2011) Fig 2.
N
OH
N N
Cl
N
H
N
O O N
H
N
Fig. 2. Avanafil.
The one of the last discovered illegal PDE-5 inhibitor is called as Acetylvardenafil which
was found in dieatery supplement known as MEGATON in USA (Lee et al., 2011).
Sulfonyl group of Vardenafil was substituted by an acetyl group Fig 3(a) .
O O O
N
O HN HN O HN
N N N
N N
N N N N
N
O O O
(a) (b) (c)
Fig. 3. (a) Acetylvardenafil; (b) Desulfovardenafil; (c) Gendenafil.
Another new analogue of vardenafil, Desulfovardenafil, in which the N-ethylpiperazine

ring and the sulphonyl group were removed from the vardenafil structure, was identified
for enhancing erectile function in herbal health product marketed, namely Power58
Platinum (Lai et al., 2007, Lam, 2007) Fig 3(b). New sildenafil analogues Gendenafil had an
acetyl group instead of sulfonyl-N-methylpiperazine moiety was determined as 5-[2-ethoxy-
5-acetyl-phenyl]-1-methyl-3-n-propyl-1,6-dihydro-7H-pyrazolo[4,3-d]pyrimidin-7-one (Lin
et al., 2008) Fig3(c). Other vardenafil analogue was found to be added illegally into a
dietary supplement marketed for male erectile dysfunction (MED). Its structure was
determined as 2-(2-ethoxyphenyl)-5-methyl-7-propyl-imidazo[5,1-f][1,2,4]triazin-4(3H)-one
and called Piperidenafil or Piperidino vardenafil or trivial name Pseudovardenafil (Park
et al., 2007; Lai et al., 2007b) Fig 4(a).
Very recently, two new analogues of sildenafil in which the piperazine ring and the sulfonyl
group were replaced by a piperazinone and a hydroxyethyl structure, respectively were
isolated from a herbal product in Germany. Based on the piperazinone structure, the
compounds were named Piperazinonafil in Fig 4(b) and Isopiperazinonafil (Wollein et al.,
2011) in Fig 4(c).
O O
N N
O HN O HN
O N N
N N
O HN
N
N
N N
HO
OH
O
N N
(a)
N N
(c)
(b)
Fig. 4. (a) Piperidenafil; (b) Piperazinonafil; (c) Isopiperazinonafil.
Another sildenafil analogue was detected from a health supplement claimed for human
MED, the structure of this new analogue was characterized as dithio-
desmethylcarbodenafil containing 2 thiocarbonyl groups instead of 2 carbonyl groups, and
4-methyl substitution on the piperazine ring, rather than 4-ethyl substitution when
compared to sildenafil (Ge et al., 2011) Fig. 5(a).
N O
N N
S S
O
N
O HN
N N
O HN
N N
N
S N HN N S O
O
N
(a) (b)
Fig. 5. (a) Dithio-desmethylcarbodenafil; (b) Nitroso-prodenafil.
Other new unapproved analogue of sildenafil was detected in capsules of a herbal dietary
supplement promoted as a libido enhancing product. This is the first time a PDE-5 inhibitor
and a potential NO donor were identified in one molecule. A hydrolysis experiment showed
that the new analogue was a prodrug of aildenafil and was therefore named nitroso-
prodenafil (Venhuis et al., 2011) Fig 5(b). Both PDE-5 inhibitors and nitrosamines cause
vasodilatation by increasing levels of NO. To their coincidental use is warned against
because it may cause a fatal drop in blood pressure. In addition, nitrosamines are known
carcinogens. The findings indicate the dangerous level of advancement in medicinal
chemistry by producers of unapproved drugs.
Tadalafil (Cialis) was approved in 2003 by the FDA as the third phosphodiesterase type 5
enzyme (PDE-5) inhibitor to treat MED (Meuleman, 2003). Then, different tadalafil
analogues have been found as adulterants in illegal products. Hasegawa et al. detected N-
octyl-nortadalafil Fig 6(a) together with cyclopentynafil Fig 6(b) in dietary supplement
(Hasegawa et al., 2008). Both of them are the first compounds reported to be new tadalafil
and sildenafil analogues.
O
O
N N
HN
N O O N
N S
H N N
O
N
O
O
O
(b)
(a)
Fig. 6. (a) N-octylnor-tadalafil; (b) Cyclopentynafil.
In Taiwan, one of the dietary supplement which was claimed on the treatment of male
erectile dysfunction was firstly screened in 2009 and Tadalafil and its doctored version was
newly identified. Since it is having amino group instead of methyl in tadalafil it was named
as aminotadalafil (Zou et al., 2006; Lin et al., 2009) Table-1. This compound has two
asymmetric carbons, theoritically two pairs of enantiomers exist. The chromatographic
separation of its stereoisomers was reported by using chiral LC-MS (Kurita et al., 2008).
Using this method, RR-Aminotadalafil and SR-Aminotadalafil were detected in some health
food. In addition, an interaction product of aminotadalafil was isolated from an illegal
health food product. The structure of the interaction product was elucidated and unknown
compound was characterized as condensation product of aminotadalafil and hydroxy-
methylfuraldehyde and is probably the result of a drug-excipient incompatibility (Hberli et
al., 2010) Fig 7.
O OH
N
N O
N
N
H
O
O
O
Fig. 7. Condensation product of aminotadalafil and hydroxymethylfuraldehyde.
Last flash development for the treatment of MED is discovering of Zoraxel (RX-10100) by
Rexahn Pharmaceutical company (Albersen et al., 2010). Zoraxel is containing clavulanic
acid that is centrally acting in the CNS and may be a more effective MED treatment for
patients who are responsive or unresponsive to PDE-5 inhibitors. It is being developed as an
orally administered, on-demand tablet to treat sexual dysfunction, and has extensive and
well-established safety in humans. For the future, it is being expected, Zoraxel will be on to
worldwide best-selling drug.
In our central instrumental analysis laboratory, we also try to detect these commercially
available supplements (which are sent by the Ministry of Food Agriculture and Livestock
of Turkey before it grants a license for import to Turkey) whether they possess new or
old sildenafil analogues by using high-performance liquid chromatography with diode
array detection and mass spectrometry (HPLC-DADMS) and nuclear magnetic resonance
(NMR) analyses, NMR is the only analytical technique which provides full structural
information from novel compounds, acquisition of MS data or comparison of retention
times may not be sufficient, in this case, LC-MS/NMR allowed to identify the adulterants
without any need for references (Kesting et al., 2010) this means that these kind of
analogues are not easy to detect by ordinary laboratory methods, we have identified the
listed analogues are given in Table 1-2 up to date. With the aim of evaluating the
potential risks of commercialized aphrodisiac products on consumer health, the aim of
present work is to investigate simple HPLC-MS method and NMR data of synthetic and
natural analogues of aphrodisiacs.
Table-1 shows the determination of some sildenafil and tadalafil analogues and Dapoxetin
HCl, in commercially available health supplements in Turkey. Their formulas, 1H-13C-NMR
spectra, ESI(+) m/e values and their LC chromatograms are given in Table 1 and Fig 8, 9,
respectively. Fig 9 shows the good separation of caffeine, some sildenafil analogues and
Default file
Sildenafil-T 2: Diode Array
4.75 TIC
100
2.71e4
0
Vardenafil-T 2: Diode Array
4.80 TIC
100
2.86e4
0
Tadalafil-T 2: Diode Array
3.84 TIC
100
2.59e4
0
Aminotadalafil-T 2: Diode Array
3.62 TIC
100
4.93e4
0
Nor-Carbodenafil-T 2: Diode Array
4.39 TIC
100
2.89e4
0 Time
1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00
Fig. 8. HPLC chromatogram of 4.75 (Sildenafil), 4.80 (Vardenafil), 3.84 (Tadalafil), 3.62
(Aminotadalafil), 4.39 (Nor-carbodenafil) (RT : Retention times as min).
*Detected in our lab. for the first time by us.

Table 1. Some synthetic PDE-5 inhibitors as analogues sildenafil and tadalafil were isolated by us.
Default file
1-9+Dap-Caff- 2: Diode Array
3.67 TIC
100
4.60e3
4.43
4.02
3.13
3.37
6.43
8.69
5.02
%
8.14
10.14
9.24
0 Time
1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00 12.00
Fig. 9. HPLC chromotogram of 3.13 (Caffeine), 3.37 (Dimethylacetildenafil), 3.67 (Udenafil),

4.02 (Noracetildenafil), 4.43 (Dimethylsildenafil), 5.02 (Dimethylhomosildenafil), 6.43
(Hydroxythiohomosildenafil), 8.14 (Thiomethisosildenafil), 8.69 (Thiosildenafil), 9.24
(Dapoxetine HCl), 10.14 (Thiohomomethisosildenafil) (RT : Retention times as min).
Dapoxetin HCl. Dapoxetine HCl, is reported to be a selective serotonin reuptake inhibitor

under investigation for the treatment of premature ejaculation (PE) (Li et al., 2009a). Since
we have met this compound in one of the herbal drinks for adults, we have added it to our
list. As it is well known, caffeine is very common for this kind of health supplements, it was
added to chromatogram as well.
1.1 Natural aphrodisiacs

Formulas, 1H-13C-NMR spectra, ESI(+) m/e values and LC-MS ion chromatograms of
natural aphrodisiacs are given in Table 2 and Fig. 10.
L- Arginine is not herb, but a nonessential amino acid, it is found naturally in foods such as
meat, dairy, poultry and fish, it also may be synthesized in the laboratory, in spite of there is
insufficient evidence to rate effectiveness for male fertility and female sexual problem, but it
is possible to see the ingredients of many aphrodisiacs, recently. It is also available as oral L-
arginine supplements, which some product manufacturers market as a "natural Viagra"
(Stanislavov & Nikolova, 2003).
Default file
L-ArgininHCl-T 1: Scan ES+
2.69 TIC
100
2.81 7.65e8
2.96
3.04
3.18
% 0.74 3.65 5.04 11.92 12.92
1.40 6.58 9.15 11.37
0 Time
2.00 4.00 6.00 8.00 10.00 12.00 14.00 16.00 18.00 20.00 22.00 24.00
Default file
L-ArgininHCl-T 285 (2.855) Cn (Cen,2, 80.00, Ht) 1: Scan ES+
175.5 2.57e7
100
118.2 176.4
129.7 158.6 168.5 171.3 197.4 207.8 257.2
140.8 142.5 144.6 177.7 187.8 189.5 212.8 222.5 236.9 238.5 251.5 252.9
0 m/z
120 130 140 150 160 170 180 190 200 210 220 230 240 250 260
Default file
Natural 2: Diode Array
3.19 TIC
100
4.48e4
2.72
7.18 8.64
%
4.30
0
Natural 1: Scan ES+
7.18 TIC
100 4.28 8.62 9.58e8
4.24 4.36
%
2.73 8.97
1.55 2.86 3.33 4.58 8.40 9.239.63
0.90 1.01 1.14 2.10 3.87 4.80 5.13 5.51 5.92 6.49 7.59 7.91 10.15 10.57 10.81 11.18
0 Time
1.00 2.00 3.00 4.00 5.00 6.00 7.00 8.00 9.00 10.00 11.00
Fig. 10. HPLC-MS ion chromatogram of 2.69 (L-Arginin HCl), 2.72 (Inosine), 3.19 (Icariin),
4.3 (Yohimbin), 7.18 (Imperatonin), 8.64 (Osthole). (RT : Retention times as min).
Compound M.w. Formulas 1H-NMR ppm

name ESI(+)m/z
NH2
L-Arginin HCl NH
N
(Stanislavov & 174 H (CD3OD): 1.27 (m, J=7.2Hz, 2H), 1.85
Nikolova, 2003) 175(M+H) H2N (q, J=7.2Hz, 2H), 3.21 (m, J=2.8Hz, 1H),
C6H14N4O2 OH 3.57 (t, J=6.4Hz, 1H), 4.6(s, 1H).
O
(CD3OD): 1.16 (q, 12Hz, 1H), 1.35-1.42
(m, 1H), 1.46-1.56 (m, 2H), 1.65-1.69 (m,
1H), 1.90 (qd, 1H), 1.99 (dq, J=10Hz,
1H), 2.23 (t, J=11.2Hz, 1H), 2.34 (dd,
J=12.0, 2.8Hz, 1H), 2.46 (dt, 1H), 2.62
N
Yohimbine N (td, J=11.2, 4.4, 1H), 2.72 (dd, J=15.6,
H H H 4.8Hz, 1H), 2.90 (dd, J=11.2, 3Hz, 1H),
(Saini et al., 2010;
2.93-3.02 (m, 1H), 3.1 (dd, J=11.2, 4.8Hz,
Melnyk et al., H
355 O 1H), 3.4 (br.d, J=11.8, 1H), 3.76 (s, 3H),
2011)
356(M+H) 4.23 (m, 1H), 6.95 (t, J=7.6Hz, 1H), 7.02
C21H26N2O3 O OH (t, 7.6Hz, 1H), 7.27 (d, J=7.6Hz, 1H),
7.36 (d, J=7.4Hz, 1H).
13C-NMR(CDCl3): 21.7, 23.3, 31.4, 34.3,
36.7, 40.7, 51.9, 52.3, 52.9, 59.8, 61.3, 66.9,

108.3, 110.7, 118.1, 119.4, 121.4, 127.4,
134.4, 135.9, 175.6.
O
Inosine N (DMSO-d6): 3.51 & 3.62 (m, 2H), 3.91 (q,
NH
(Deuster & 268 J=4Hz, 1H), 4.09 (t, J=4Hz, 1H), 4.46 (t,
N
Simmons, 2004) 269(M+H) O N J=5Hz, 1H), 5.1 (br.s, 1H), 5.15 (br.s, 1H),
HO 5.4 (br.s, 1H), 5.83 (d, J=4.4Hz, 1H), 8.04
C10H12N4O5
(s, 1H), 8.30 (s, 1H), 12.35 (br.s, 1H).
HO OH
(CD3OD): 0.9 (d, J=6Hz), 1.63 (s, 3H),
O
OH 1.72 (s, 3H), 3.15-3.75 (benzylic,
Icariin O O O
ethylenic and sugar protons), 3.89 (s,
(Liu et al., 2005; HO OH O 3H), 3.9-4.22 (sugar protons), 5.06 (d,
676
DellAgli, 2008) OH OH O OH J=7.2 Hz, 1H), 5.24 (t, 1H), 5.41 (d,
677(M+H) O
C33H40O15 OH
J=1.6Hz, H), 6.65 (s, 1H), 7.01 (d,
OH J=8.8Hz, 2H), 7.88 (d, J=8.8Hz, 2H)
(CDCl3): 1.67 (s, 3H), 1.84 (s, 3H), 3.53
Osthole
(d, J=7.2Hz, 2H), 3.92 (s, 3H), 5.22 (t,
(Liao et al., 2010) 244 O O O
J=7.2Hz, 1H), 6.23 (d, J=9.2Hz, 1H), 6.83
C15H16O3 245(M+H)
(d, J=8.6Hz, 1H), 7.29 (d, J=8.7Hz, 1H),
7.61 (d, J=9.2 Hz, 1H)
(CDCl3): 1.72 (s, 3H), 1.74 (s, 3H), 5.01
Imperatorin (d, 2H), 5.61 (t, J=7Hz, 1H), 6.37 (d,
270
(Liao et al., 2010) O J=9.2Hz, 1H), 6.81 (d, J=2.4Hz, 1H), 7.36
271(M+H)
C16H14O4 O O O (s, 1H), 7.69 (d, J=2.4Hz, 1H), 7.76
(d,J=9.2Hz, 1H)
Table 2. Natural aphrodisiacs were isolated by us from some herbal supplements.

Yohimbine is an alkaloid which are found naturally in Pausinystalia yohimbe, a classical

aphrodisiac which has been recently revalued for its pro-sexual properties and extensively
commercialized without control in some countries (Saini et al., 2010, Melnyk et al., 2011) .
However, there is little evidence on its efficacy in the treatment of ED and it is, therefore, not
currently recommended (Albersen et al., 2010).
Inosine is a nucleoside consisting of ribose and hypoxanthine, most commonly found in
supplements that claim to be energy promoters, naturally it is found in brewers yeast and
organ meats, however it can be synthesized in laboratory (Deuster & Simmons, 2004). Their
nerve-stimulating action probably enhances sexual functions or help to remedy sexual
functions when these are reduced due to degeneration of nerve tissue.
Icariin is one of the primary active component of Epimedium extracts, which has been used
to treat impotence and improve sexual function by acting as PDE5 inhibitor as nafil
derivatives (Liu et al., 2005; DellAgli, 2008). Since the illegally using of synthetic nafil
derivatives have been prohibited, recently icariin has become very attractive by the drug
manufacturers and suppliers, because of its natural character. Nowadays, the percentage
ratio of Icariin in the commercial Epimedium extracts has been increased over 80-90.
However there is no sufficient information about its pharmacological profiles and safety.
Further investigation needs to be done to examine any benefits that could occur from
supplements.
Osthole and imperatorin, coumarin compounds have been reported to exhibit various
biological activities (Liao et al., 2010). It was reported that, both of them were found to help
relax the corpus cavernosa of the penis, which would potentially help with blood flow, in
phenylephrine-precontracted endothelium-intact rabbit corpus cavernosum (Chen et al.,
2000; Chiou et al., 2001), however there is no information for human uses.
Herbal medications are being progressively utilized all over the world and it is believed that
herbal remedies are not hazards, however some adverse reactions have been increased.
Tribulus terrestris is frequently used because of its aphrodisiac effect. But there is an article
(Talasaz, 2010), which reports a case of T-terrestris-induced hepatotoxicity, nephrotoxicity
and neurotoxicity in an Iranian male patient.
In this text, we also present a new sildenafil analogue was found to have been added
illegally to a herbal drinks marketed for the enhancement of sexual function. This analogue
has never been found. Therefore, it prompted us to elucidate its structure. The structure was
determined as 5-[5-[[(3,5-dimethyl-1-piperazinyl]sulfonyl]-2-propoxyphenyl]-1,6-dihydro-1-
methyl-3-propyl-7H-pyrazolo [4,3-d]pyrimidin-7-one. Owing to the inclusion of a methylene
group in dimethylsildenafil, the detected compound was called Dimethyhomosildenafil.
The sample was purified with column chromatography. The IR, HPLC-/MS (ESI+), and
completely assigned NMR data of dimethylhomosildenafil have been observed.
2. Material and methods

2.1 Equipments
Uncorrected melting points were measured on an Bchi B-540 capillary melting point
apparatus. 1H (400 MHz) and 13C(100 MHz) NMR spectra were recorded employing a
VARIAN MERCURY 400 MHz FT spectrometer, with CDCl3 as solvent. Chemical shifts ()
are in ppm relative to TMS. The LC/MS were taken on a Waters Micromass ZQ connected
with Waters Alliance HPLC, using ESI(+) method, with C-18 column. Elemental analyses
were performed by Leco CHNS-932. The infrared spectrum was recorded in the 600-3600
cm-1 range using a Jasco FT-IR-420 spectrometer and KBr pellets.
2.2 Extraction and isolation

The water contents of the alminyum can (250 ml) were extracted with the mixture of
dichloromethane-methanol (95:5) and evaporated, residue was directly carried out to a open
column with silica gel 60 (0.04-0.063 mm) and eluted with dichloromethane-isopropanol
(97:3). Fractions were collected and analyzed by TLC. All of the fractions having the target
compound were collected and the solvent was evaporated and crystallization of the residue
from ethanol gave 0.021g of white powder compound was obtained, m.p: 189-190oC, Anal.
Calcd. for C24H34N6O4S. 0.5 HOH: C 56.34, H 6.90, N 16.42, S 6.27. Found: C 56.47, H 6.95, N
16.21, S 6.28.
2.3 Structure identification

2.3.1 NMR correlation data of dimethylhomosildenafil
Dimethylhomosildenafil was dissolved in CDCl3 and subjected to 1D and 2D NMR
spectroscopic analysis (1H, 13C, DEPT, homo-COSY, HSQC and HMBC). The data are shown
in Table 2.
2.3.2 Analysis condition of HPLC/MS

LC-MS coupled with positive and negative (ESI+) Electro Spray method was used to
determine its molecular weight. The HPLC of LC/MS was carried out on a column
XTerra MS C-18 (4.6 X250 mm,5 m) with Acetonitrile: Methanol:0.05 M Ammonium
acetate in water (55:20:25) as mobile phase. The flow rate was 0.9 mL/min, the injection
volume was 5 L and the appropriate running time (at least 15 min). The eluate was
monitored by a photo-diode array detector at 254 nm. The analytical condition of mass
was as follows: capillary voltage :3.41 kV, cone voltage : 26 V, source temperature : 100 oC
: desolvation temperature : 350oC. The HPLC chromatogram of dimethylhomosildenafil is
given in Fig 2 with 5.02 min. rt values. This method was carried out all the given HPLC-
MS analysis in this text.
Table 3 shows the 1H-NMR, 13C-NMR, DEPT, COSY, HSQC and HMBC spectral data of
isolated compound 1, which were similar to that of dimethylsildenafil. The spectroscopic
numbering used is given in Table 3. The difference of this compound, than
dimethylsildenafil is related with ether protons connected to the C-19. Here is one more
metyhlene group as propoxy. The 3,5-dimethyl protons of piperazine were observed at H
1.05 (d, 6H) as expected, in the HMBC spectrum the correlation of H-28,29/H-24,26, DEPT
and HSQC results indicated that dimethyl group attached to C24-26. Since the 2,6-
diequatorial methyl groups would be lower energetic form, so the configuration is
established as a cis diequatorial methyl configuration as shown in Table 1 as it is in the
methisosildenafil (Reepmeyer & Avignon, 2009). The IR spectrum of

dimethylhomosildenafil is given in Fig 11. This compound also must be put on the
inspection list for illegal health-related substances because of the unknown safety and
toxicity profile.
Fig. 11. IR spectrum of Dimethylhomosildenafil.

29 O 10
25
CH3 27 8
HN 6 N1
O HN 7
H 3C 23 N 15 N2
28 H
S
H 5 N 9 3
O 14 12
4
11
17
19 O 20 13
18
22
21
No 13C 1H DEPTa COSY HMBC

3 146.7 --- C-3/H-12 C-3/H-11
5 147.2 --- C-5/H-15
6 -- 10.84(br.s,1H) ---
7 153.8 --- ---
8 124.7 --- C-8/H-10
9 138.6 --- C-9/H-11
10 38.4 4.27(s,3H) 3 ---
11 27.99 2.93(t,2H,J=7.2 Hz) 2 H-11/H-12 C-11/H-13, C-11/H-12
H-12/H-11,
12 22.5 1.84(m,2H,J=7.6 Hz) 2 C-12/H-13, C-12/H-11
H-12/H-13
13 14.3 1.01(t,3H,J=7.6 Hz) 3 H-13/H-12 C-13/H-12, C-13/H-11
14 129.4 --- -- C-14/H-18
15 131.1 8.81(d,1H, Jm=2 Hz) 1 H-15/H-17 C-15/H-17
16 121.2 --- C-16/H-18
7.84(dd,1H,Jo=8.8 Hz, H-17/H-18,
17 131.8 1 C-17/H-15
Jm=2 Hz) H-17/H-15
18 113.2 7.16(d,1H,Jo=8.8 Hz) 1 H-18/H-17 ----
C-19/H-15, C-19/H-17
19 159.7 ---
C-19/H-18, C-19/H-20
20 72.1 4.26(t,2H,J=7.2 Hz) 2 H-20/H-21 C-20/H-21, C20/H-22
H-21/H-20,
21 22.54 2.05(m,2H,J=6.8 Hz) 2 C-21/H-20, C-21/H-22
H-21/H-22
22 10.85 1.19(t,3H,J= 7.6 Hz) 3 H-22/H-21 C-22/H-21, C-22/H-20
1.93(t,2H, J=10.4 Hz,
H-23,H-27
axial) & 3.68(dd,2H,
23,27 52.3 2 axial/ C-23,27/H-28,29
J=10.4 Hz, J=1.6 Hz
H-24,H-26
equatorial)
H-24,H-26/
H-23,H-27
3.03(m, 2H, J=3.6 Hz, C-24,26/H-28,29
24,26 50.5 1 axial
axial) C-24,26/H-23,27
H-24,H-26/
H-28,H-29
H-28,H-29/
28,29 19.5 1.05(d,6H,J=6.8 Hz) 3 ---
H-24,H-26
ppm in CDCl3, J in Hz a) Number in DEPT is the number of attached protons.
Table 3. NMR data of Dimethylhomosildenafil.
3. Conclusion
Oral PDE5 inhibitors are the treatment of choice for MED. The physiological mechanism of
erection involves release of nitric oxide (NO) in the corpus cavernosum as a result of sexual
stimulation. NO then activates the enzyme guanylate cyclase, which results in increased
levels of cyclic guanosine monophosphate (cGMP), leading to smooth muscle relaxation in
blood vessels supplying the corpus cavernosum and allowing inflow of blood. Nafil
derivatives have no direct relaxant effect on isolated human corpus cavernosum, but
enhance the effect of NO by inhibiting PDE5, which is responsible for degredation of cGMP
in the corpus cavernosum. When sexual stimulation causes local release of NO, inhibition of
PDE5 by nafil analogues causes increased levels of cGMP in the corpus cavernosum,
resulting in smooth muscle relaxation and inflow of blood to the corpus cavernosum. This
mode of action means that PDE5 inhibitors are ineffective without sexual stimulation. The
PDE-5 inhibitors have helped many men with MED, and the FDA indicate that Sildenafil
citrate, Vardenafil HCl and Tadalafil are safe and well-tolerated when taken as directed by
men who have gotten approval from their doctors. These drugs must not been used without
medical examination or prescription. PDE-5 inhibitors also increase the risk of a variety of
cardiovascular diseases, including heart attack, myocardial infarction, and sudden death.
The medication may interact with other drugs which should be mortal, e.g. synergic effect
with alpha-blockers. Other side effects associated with PDE-5 drugs, such as priapism,
severe hypotension, increased intraocular pressure and sudden hearing loss and blidness.
The PDE-5 inhibitors must not buy over the internet or other non-standart source,
otherwise, the men run several risk, such as it should be counterfeit product that does not
have the legal structural compound which has been untested for safety or no same purity as
the real drug.
4. Acknowledgment
We thank Prof. Dr. Erden Banolu (Gazi University, Faculty of Pharmacy, Ankara) for
providing sample of Homothiomethisosildenafil which was also isolated from the herbal
dietary supplement by him. Central Instrumental Analysis Lab. of Pharmacy, Faculty of
Ankara University provided support for acquisition of the IR, NMR, HPLC-MS
spectrometers and elemental analyzer used in this work.
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4
Purification of Marine Bacterial

Sialyltransferases and Sialyloligosaccharides
Toshiki Mine and Takeshi Yamamoto
Glycotechnology Business Unit, Japan Tobacco Inc.,
Japan
1. Introduction
Sialic acids are important components of carbohydrate chains and are usually found at the
terminal position of the carbohydrate moiety of glycoconjugates (Angata & Varki, 2002;
Schauer, 2004). Sialyloligosaccharides of glycoconjugates play important roles in many
biological processes (Gagneux & Varki, 1999; Varki, 1993). The transfer of sialic acids to
carbohydrate chains is performed by specific sialyltransferases in the cell (Angata & Varki,
2002; Vimr et al., 2004). Thus, sialyltransferases are considered to be key enzymes in the
biosynthesis of sialylated glycoconjugates. Detailed investigations of the biological functions
of sialylated glycoconjugates require an abundant supply of the target compounds. To date,
many sialyltransferases, and the genes encoding them, have been isolated from various
sources including mammalian, bacterial, and viral sources (Schauer, 2004; Sujino et al., 2000;
Yamamoto et al., 2006). During our research, we have isolated over 20 bacteria that produce
sialyltransferase and have revealed the characteristics of these enzymes (Kajiwara et al.,
2009; Yamamoto, 2010). In this chapter, we will introduce our research activities focusing on
methods for (1) screening bacteria for glycosyltransferase activity; (2) purifying native
sialyltransferases from marine bacteria; and (3) synthesizing and purifying
sialyloligosaccharides produced by marine bacterial sialyltransferases.
Sialic acid is a family of acidic monosaccharides comprising over 50 naturally occurring
derivatives of neuraminic acid (5-amino-3,5-dideoxy-D-glycero-D-galacto-2-nonulosonic acid
or Neu) (Angata & Varki, 2002; Vimr et al., 2004). Structurally, sialic acid is one of the more
complicated naturally occurring monosaccharides and is based on a skeleton of nine carbons
(Schauer, 2004). N-acetylneuraminic acid (Neu5Ac), N-glycolylneuraminic acid (Neu5Gc),
and 2-keto-3-deoxy-D-glycero-D-galacto-nonulosonic acid (deaminoneuraminic acid, KDN),
are the three most common members of this family (Angata & Varki, 2002; Schauer, 2004).
The structure of Neu, Neu5Ac, Neu5Gc and KDN are shown in Figure 1. Although sialic
acid is widely distributed in higher animals and some classes of microorganisms, only
Neu5Ac is ubiquitous (Angata & Varki, 2004). Usually, sialic acid exists in the carbohydrate
moiety of glycoconjugates, including glycoproteins and glycolipids, and is linked to the
terminal positions of the carbohydrate chains of the glycoconjugates. Many studies have
been carried out to clarify the structure-function relationship of carbohydrate chains
containing sialic acid. These studies have revealed that Neu5Ac is the most common sialic
acid component of carbohydrate chains and sialylated carbohydrate chains of
glycoconjugates play significant roles in many biological processes including inflammation,

glycoprotein clearance from circulation, cell-cell recognition, cancer metastasis, and virus
infection (Kannagi, 2002; Paulson, 1989). Sialyltransferases commonly transfer Neu5Ac from
cytidine 5-monophospho-N-acetylneuraminic acid (CMP-Neu5Ac) to various acceptor
substrates (Angata & Varki, 2002). Thus, sialyltransferases are thought to be one of the
important enzymes in the biosynthesis of sialylated glycoconjugates.
HO OH OH
HO
HO HO
HOOC HOOC
H 2N O H 3COCHN O
HO OH HO OH
(A) (B)
HO OH HO OH
HO HO
HOOC HOOC
HOH2 COCHN O HO O
HO OH HO OH
(C) (D)
(A) Neuraminic acid (Neu), (B) N-acetylneuraminic acid (Neu5Ac), (C) N-glycolylneuraminic acid
(Neu5Gc), (D) deaminoneuraminic acid (KDN).
Fig. 1. Structures of sialic acids.
Among the biological phenomena described above, the relationship between the
carbohydrate chain structure of the host cell and host cell recognition by influenza virus is
one of the best investigated (Suzuki, 2005; Weis et al., 1988). Many reports have shown that
influenza A and B viruses bind via viral hemagglutinin to host cell surface receptors that are
Neu5Ac- or Neu5Gc-linked glycoproteins or glycolipids (Suzuki, 2005). Furthermore, these
influenza viruses also recognize the carbohydrate chain structure of the host cell (Connor et
al., 1994). Confirming evidence has shown that avian influenza viruses recognize
Neu5Ac2-3Gal1-3/4GlcNAc structures, and that human influenza viruses recognize
Neu5Ac2-6Gal1-3/4GlcNAc structures (Connor et al., 1994; Suzuki, 2005). The host cell
specificities of the influenza A and B viruses are determined mainly by the linkage of
Neu5Ac or Neu5Gc to the penultimate galactose residues and core structure of the host
glycoproteins or glycolipids. For this reason, the distribution of Neu5Ac and Neu5Gc and
their linkage patterns on the host cell surface are important determinants of host tropism.
A large variety of oligosaccharides exist in nature. For example, many kinds of
sialyloligosaccharides, such as 3-sialyllactose, 6-sialyllactose, and sialyllacto-N-neotetraose,
are contained in milk of various animals (Kunz et al., 2000); however, the purification and
isolation of sialyloligosaccharides from natural sources is very difficult due to their
structural complexity. Therefore, the research use and development of drugs that depend on
Purification of Marine Bacterial Sialyltransferases and Sialyloligosaccharides 71
sialyloligosaccharides relies on sialyloligosaccharide synthesis by chemical or enzymatic

methods. Although many methods for the synthesis of sialyloligosaccharides including
chemical- and enzyme-based methods using glycosyltransferases have been developed, it is
still difficult to synthesize large amounts of sialyloligosaccharides. Therefore, only a limited
amount and only a few kinds of sialyloligosaccharides are currently available as research
reagents. In this chapter, we introduce our results with regard to methods for screening for
bacterial glycosyltransferases, purification of native sialyltransferases from bacteria, and the
synthesis and purification of sialyloligosaccharides produced by marine bacterial
sialyltransferases. The methodologies introduced in this chapter might to be useful for
screening of bacteria that produce other types of glycosyltransferases, purification of
membrane-binding proteins, and purification of oligosaccharides.
2. Screening bacteria for sialyltransferase activity

2.1 Basic screening method
Samples of seawater, sea-sand, mud, seaweed, and small animals including various kinds of
fishes and shells, were collected from various coastal locations in Japan. Bacteria that grew
on marine agar 2216 or nutrient agar (Becton-Dickinson, Franklin Lakes, NJ, USA) that was
supplemented with 2% NaCl at 15C, 25C, or 30C were isolated from the samples.
Aliquots of the bacteria were suspended in 10% glycerol and stored at 80C. For each
bacterial isolate, 6 mL of marine broth 2216 (Becton-Dickinson) in a 15-mL test tube was
inoculated with bacteria and cultivated at 15C, 25C, or 30C for 18 h on a rotary shaker
(180 rpm). After the cultivation, bacteria were harvested from 2 to 4 mL of the culture broth
by centrifugation and then suspended in 200 L of 20 mM sodium cacodylate buffer (pH
6.0) that contained 0.2% Triton X-100, lysed by sonication on ice, and measured immediately
for sialyltransferase activity. Sialyltransferase activity was confirmed as follows: the reaction
mixture (30 L) consisted of the bacterial lysate as the sample of enzyme, 120 mM lactose,
2.3 mM CMP-Neu5Ac (Nakarai Tesque, Kyoto, Japan), 4620 Bq CMP-[4,5,6,7,8,9-14C]-
Neu5Ac (Amersham Biosciences, Little Chalfont, UK), 100 mM BisTris buffer (pH 6.0), 0.5
M NaCl, and 0.03% Triton X-100. The reaction was carried out at 25C for 2 h. The reaction
mixture was then diluted with 5 mM sodium phosphate buffer (pH 6.8) to a final volume of
2 mL, and applied to a column (0.5 2 cm) of Dowex-1 8 (phosphate form, Bio-Rad
Laboratories, Hercules, CA, USA). The eluate (2 mL) was collected directly into a
scintillation vial for counting. The radioactivity of [4, 5, 6, 7, 8, 9-14C]-Neu5Ac that had
transferred to the acceptor substrate in the eluate was measured by using a liquid
scintillation counter, and the amount of Neu5Ac transferred was calculated. Unreacted
CMP-Neu5Ac was not eluted in this buffer concentration. Using this procedure, we have
isolated many bacteria that possess sialyltransferase activity. Many of the marine bacteria
that produced sialyltransferases were classified in genus Photobacterium or the closely
related genus Vibrio. For instance, Photobacterium phosphoreum JT-ISH-467 that showed 2,3-
sialyltransferase activity was isolated from the outer skin of Japanese common squid,
Todarodes pacificus (Tsukamoto et al. 2007); Photobacterium damselae JT0160 that expressed
2,6-sialyltransferase activity was isolated from seawater (Yamamoto et al., 1998);
Photobacterium sp. JT-ISH-224 that contained both 2,3- and 2,6-sialyltransferase activities
was isolated from the gut of Japanese barracuda, Sphyraena pinguis (Tsukamoto et al., 2008);
and Photobacterium leiognathi JT-SHIZ-145 that expressed 2,6-sialyltransferase activity was
isolated from the outer skin of Japanese squid, Loliolus japonica (Yamamoto et al., 2007).
2.2 Simultaneous measurement of several glycosyltransferases activities

To assess the activities of various glycosyltransferases, not only sialyltransferases, we
performed the enzyme assay using a mixture of the donor substrates of glycosyltransferases
(GDP-fucose, the common donor substrate of fucosyltransferase; UDP-galactose, the common
donor substrate of galactosyltransferase; and UDP-GlcNAc, the common donor substrate of N-
acetyl-glucosaminyltransferase), and a mixture of the acceptor substrates of
glycosyltransferases (4-Nitrophenyl -D-galactopyranoside {Gal--pNp}; 4-Nitrophenyl -D-
galactopyranoside {Gal--pNp}; 4-Nitrophenyl N-acetyl--D-galactosaminide {GalNAc--
pNp}; 4-Nitrophenyl N-acetyl--D-galactosaminide {GalNAc--pNp}; 4-Nitrophenyl N-acetyl-
-D-glucosaminide {GlcNAc--pNp}; 4-Nitrophenyl N-acetyl--D-glucosaminide {GlcNAc--
pNp}; 4-Nitrophenyl -D-glucopyranoside {Glc--pNp}; 4-Nitrophenyl -D-glucopyranoside
{Glc--pNp}; 4-Nitrophenyl -L-fucopyranoside {Fuc--pNp}; 4-Nitrophenyl -L-
fucopyranoside {Fuc--pNp}; 4-Nitrophenyl -D-mannopyranoside {Man--pNp}; and 4-
Nitrophenyl -D-mannopyranoside {Man--pNp}), and bacterial lysate described in 2.1 as the
enzyme sample. An example of results obtained by using this method is shown in Figure 2.
Fig. 2. Screening assay for glycosyltransferase activities.
High levels of radioactivity were observed in the eluates from the reaction mixture of
samples #1 and #8, respectively, when the reaction was performed in the presence of
acceptor substrate. From this result, it was strongly expected that lysates prepared from
bacteria number #1 and #8 contained fucosyltransferase, galactosyltransferase and/or N-
acetylglucosaminyltransferase. NC; negative control, +AC; containing acceptor substrate
mixture in the reaction mixture, -AC; no acceptor substrate mixture in the reaction mixture.
The reaction mixture (50 L) consisted of the following: a sample of enzyme, a mixture of 0.5
mM acceptor substrates consisting of 4-nitrophenyl compounds, as described above, a
mixture of 0.5 mM donor substrates consisting of sugar-nucleotides as described above, 4620
Bq UDP-[U-14C]-galactose, 4620 Bq UDP-N-acetyl-D-[U-14C]-glucosamine, 4620 Bq GDP-[U-
14C]-fucose (Amersham Biosciences, Little Chalfont, UK), 100 mM bis-Tris buffer (pH 6.0), 10
mM MnCl2, and 3 mM ATP. The reaction was carried at 25C for 16 to 18 h. After the
reaction, 100 L of water was added to the reaction mixture, and the mixture was applied to
a Sep-Pac Vac 50cc column (Waters, Milford, MA, USA) that was conditioned with ethanol
and equilibrated with water. The column was washed twice with 1 mL of water and the
reaction product was eluted with 1 mL of 70% ethanol. One millilitre of scintillation cocktail
was added to the eluate, and the radioactivity of the mixture was measured by using a liquid
scintillation counter. In this way, we could detect glycosyltransferase activities, comprising
fucosyltransferase, galactosyltransferase and/or N-acetylglucosaminyltransferase activity,
simultaneously in marine bacteria. To clarify which of the glycosyltransferase activities the
bacteria displayed, the enzymatic reaction was performed independently with each of the
donor substrates in turn. The two bacteria that showed glycosyltransferase activity in Figure 2
were shown to specifically produce fucosyltransferase.
2.3 Screening by lectin staining

Lectins are sugar-binding proteins that are highly specific for their sugar moieties. The lectin
Sambucus sieboldiana agglutinin (SSA) recognizes the Neu5Ac2-6Gal or Neu5Ac2-6GalNAc
structure of sialyloligosaccharides in glycoconjugates (Shibuya et al., 1989). Kajiwara et al.
carried out lectin staining of the cells of P. damselae JT0160, P. leiognathi JT-SHIZ-145, P.
phosphoreum JT-ISH-467, and Photobacterium sp. JT-ISH-224, by using biotin-labeled SSA, and
then examined the cells by using differential interference contrast (DIC) and fluorescence
microscopy (Kajiwara et al., 2010). Lectin staining was carried out as follows: the 4 bacterial
species described above were cultivated in nutrient broth supplemented with 2% (w/v) NaCl
at 25C for 18 h on a rotary shaker. The bacterial cells were collected by centrifugation (8,000g,
15 min, 4C) and suspended in 25 mM Tris-HCl buffer 8 (pH 7.5). The suspensions were
spotted onto glass slides, fixed with a 4% (w/v) paraformaldehyde solution at room
temperature for 15 min, and blocked with a 5% (w/v) bovine serum albumin (BSA)
phosphate-buffered saline (PBS) solution. After the glass slides were washed, biotin-labeled
SSA (5 mg mL1) was added and the cells were incubated at room temperature for 2 h. After
the cells were washed 4 times with PBS, Alexa 594-labeled streptavidin (Invitrogen, Carlsbad,
CA, USA) solution (5 mg mL1) was added and the incubation was continued at room
temperature for 1 h. After 5 washes with PBS, the cells were mounted using Prolong Gold
antifade reagent (Invitrogen) and observed by using DIC and fluorescence microscopy. The
SSA bound to Photobacterium sp. JT-ISH-224, P. damselae JT0160, and P. leiognathi JT-SHIZ-145.
These Photobacterium strains produce 2,6-sialyltransferases, so the lectin staining indirectly
detected 2,6-sialyltransferase-producing bacteria (Fig. 3). SSA did not bind to P. phosphoreum
JT-ISH-467, which produces only 2,3-sialyltransferase. Therefore, the SSA lectin might be
useful to screen for not only Neu5Ac2-6Gal and/or Neu5Ac2-6GalNAc structures on the
bacterial cell surface but also to screen for the production of 2,6-sialyltransferase. We consider
that this method would be applicable to the screening of other glycosyltransferases by
changing the type of lectin used. We have confirmed that one of the two bacteria that showed
fucosyltransferase activity, described in section 2.2, was detected by biotin-labeled Aleuria
aurantia lectin (AAL, from Seikagaku Kogyo), which recognizes the fucose residue in
carbohydrate chains (Kochibe & Furukawa, 1980).
3. Purification of sialyltransferase from the native bacterium

For the purification of a protein, it is necessary and important to find the appropriate
conditions for enzyme solubilization, including solubilization efficiency, and the most
efficient combination of chromatography processes. Each process has a different separation
mode, and it is crucial to conduct a detailed study of the conditions required for each
process. Crude extracts are commonly used in such studies, but care must be taken to
ISH224, Photobacterium sp. JT-ISH-224; Pd0160, P. damselae JT0160; SHIZ145, P. phosphoreum JT-SHIZ-
145; SSA, fluorescence microscopy of cells stained with Sambucus sieboldiana agglutinin (SSA); DIC,
differential interference contrast microscopy of the cells shown in the SSA panels.
Fig. 3. Lectin staining of Photobacterium strains by Sambucus sieboldiana agglutinin.
minimize protease activity, which may decompose the target enzyme. Furthermore, it is
necessary to consider the pH of the buffers used in the purification steps as well as the
temperature employed during the preparation of the extracts and the purification process.
For details of general procedures and methods for protein purification, we recommend that
you refer to other textbooks (e.g., Deutscher, 1990; Scopes,.1982). Here, we describe
examples of the purification of sialyltransferase from marine bacteria.
3.1 Purification of 2,6-sialyltransferase from P. damselae JT0160

3.1.1 Preparation of the crude extract from P. damselae cells
The first step in the purification of a protein is the preparation of an extract containing the
protein in a soluble form. During the purification of sialyltransferase from P. damselae, we
examined in detail the conditions for preparing a crude extract containing the target enzyme
in a soluble form (Yamamoto et al., 1998). The method that we established was deemed
appropriate for the preparation of a crude extract containing sialyltransferase because no
decrease in sialyltransferase activity was detected during the procedure. We determined
that the most important factor in the preparation of the crude extract was the timing of the
cell lysis after cultivation. For instance, almost no sialyltransferase activity was detected in
crude extract prepared from cryopreserved cells of P. damselae. The procedure for crude
extract preparation was as described below.
1. After cultivation, P. damselae JT0160 cells were harvested from the culture by
centrifugation (6,000 g, 20 min).
2. The harvested cells were suspended in 20 mM sodium cacodylate buffer (pH 6.0)
containing 0.2% Triton X-100 and 1 M NaCl, and were sonicated immediately (<4C)
until the absorbance at 660 nm reached 30% or less of that of the original cell
suspension.
3. The sonicated solution was centrifuged (100,500g, 60 min) and the supernatant was
dialyzed, using cellulose tubing, against 20 mM sodium cacodylate buffer (pH 6.0)
containing 0.2% Triton X-100.
4. After dialysis, the precipitate was removed by centrifugation (100,500g, 60 min) to
obtain the clarified extract.
3.1.2 Purification of sialyltransferase by using column chromatography

Sialyltransferase produced by P. damselae was then purified from the crude extract by a
combination of 4 steps of column chromatography. The conditions and method used for
each chromatography step are described below.
1. Q-Sepharose column chromatography. A column of Hi-Load 26/10 Q Sepharose HP (
2.6 10 cm; GE Healthcare Science, Buckinghamshire, UK) was equilibrated with 20 mM
sodium cacodylate buffer (pH 6.0) containing 0.2% Triton X-100. Clarified extract was
applied to the column, and the column was washed with 150 mL of the same buffer.
Enzyme fractions were eluted with a linear gradient of 0 to 1 M NaCl in the buffer. The
fractions exhibiting sialyltransferase activity (active fractions) were collected and
pooled. Desalting of the active fractions was performed by dialysis, using cellulose
tubing, against 20 mM sodium cacodylate buffer (pH 6.0) containing 0.2% Triton X-100.
2. Hydroxyapatite column chromatography. A column of hydroxyapatite ( 2 10 cm;
Bio-Rad Laboratories) was equilibrated with 20 mM sodium cacodylate buffer (pH 6.0)
containing 0.2% Triton X-100. After the application of the enzyme solution obtained in
step 1, the column was washed with the same buffer. The enzyme fraction was eluted
with a gradient of 0 to 0.35 M potassium phosphate. The active fractions were
collected and pooled, and then concentrated by ultrafiltration using Molecut L
(exclusion molecular mass, 10 kDa ; Millipore, Billerica, MA, USA).
3. Gelfiltration column chromatography. A column of Hi-Load 26/60 Sephacryl S-200 HE
( 2.6 60 cm; GE Healthcare Science, Buckinghamshire, UK) was equilibrated with 20
mM sodium cacodylate buffer (pH 6.0) containing 0.2% Triton X-100 and 0.1 M NaCl.
The enzyme solution obtained in step 2 was applied to the column and eluted with the
same buffer. The active fractions were collected and pooled. Desalting of these
fractions was performed by dialysis, using cellulose tubing, against 20 mM sodium
cacodylate buffer (pH 6.0) containing 0.2% Triton X-100.
4. CDPhexanolamine-agarose column chromatography. A column of CDP
hexanolamine-agarose ( 1 3 cm) was equilibrated with 20 mM sodium cacodylate
buffer (pH 6.0) containing 0.2% Triton X-100. The enzyme solution (4 mL) obtained in
step 3 was applied to the column. The column was washed with 8 mL of the same
buffer. The enzyme was eluted with 6 mL of 2 M NaCl, and active fractions were
collected and pooled.
The purity and yield of the enzyme at each step is summarized in Table 1.
Volume Total protein Total activity Specific activity Yield Purification

Purification step
(mL) (mg) (U) (U/mg) (%) (fold)
Crude extract 760 2584 21.1 0.008 100 1
Q Sepharose 240 552 12.4 0.022 59 2.8
Hydroxyapatite 120 85 8 0.094 38 11.8
Sephacryl S-200 30 20.1 6.7 0.3 32 37.5
CDP-hexanolamine-agarose 15 0.75 4.1 5.5 19 687.5
Table 1. Purification of sialyltransferase from cell lysate of Photobacterium damselae.
The enzyme was purified 688-fold, with a yield of 19%. The purified enzyme migrated as a
single polypeptide with a molecular mass of 61 kDa by SDS-polyacrylamide gel
electrophoresis under denaturing conditions.
3.2 Purification of 2,3-sialyltransferase from P. phosphoreum JT-ISH-467

3.2.1 Preparation of the crude extract from P. phosphoreum cells
The crude extract containing sialyltransferase from P. phosphoreum cells was prepared by the
method described in section 3.1.1, with slight modifications (Tsukamoto et al., 2007), and
then crude extract containing the soluble form of the enzyme was prepared.
3.2.2 Purification of sialyltransferase from P. phosphoreum by using column

chromatography
Sialyltransferase produced by P. phosphoreum was purified from the crude extract by a
combination of 5 steps of column chromatography. The conditions and method used for
each of the column chromatography steps are described below.
1. DEAE column chromatography. The clarified crude extract was applied to a Hi-Prep
16/10 DEAE FF column ( 1.6 10 cm; GE Healthcare Science) equilibrated with 20 mM
bis-Tris buffer (pH 6.0) containing 0.3% Triton X-100. After the column was washed
with the same buffer, the enzyme was eluted with a linear gradient of 0 to 1 M NaCl in
the same buffer. The fractions with sialyltransferase activity were pooled and then
diluted to three times the original volume with 20 mM potassium phosphate buffer (pH
6.0) containing 0.3% Triton X-100.
2. Hydroxyapatite column chromatography. The enzyme solution obtained in step 1 was
applied to a hydroxyapatite column ( 1.5 11.3 cm; Bio-scale CHT20-I; Bio-Rad
Laboratories) that was equilibrated with 20 mM potassium phosphate buffer (pH 6.0)
containing 0.3% Triton X-100. After the column was washed with the same buffer, the
enzyme was eluted with a linear gradient of 20 to 500 mM potassium phosphate. The
active fractions were pooled, and then diluted to two times the original volume with
20 mM potassium phosphate buffer (pH 6.0) that contained 0.3% Triton X-100.
3. Mono Q column chromatography (pH 6.0). The enzyme solution obtained in step 2 was
loaded onto a column of Mono Q 10/100 GL ( 1 10 cm; GE Healthcare Science) that
was equilibrated with 20 mM potassium phosphate buffer (pH 6.0) containing 0.3%
Triton X-100. After the column was washed with the same buffer, the enzyme was
eluted with a linear gradient of 0 to 1 M NaCl in the same buffer. The "active" fractions
were pooled, and then diluted to three times the original volume with 20 mM bis-Tris
buffer (pH 7.0) containing 0.3% Triton X-100.
4. Mono Q column chromatography (pH 7.0). The enzyme solution obtained in step 3 was
applied to a column of Mono Q 10/100 GL equilibrated with 20 mM bis-Tris buffer (pH
7.0) containing 0.3% Triton X-100. After the column was washed with 20 mM bis-Tris
buffer (pH 7.0) containing 0.3% Triton X-100, the enzyme was eluted with a linear
gradient of 0 to 1 M NaCl in the same buffer. The "active" fractions were pooled.
5. Superdex 200 column chromatography. The enzyme solution obtained in step 4 was
loaded onto Hi-Load 16/60 Superdex 200 pg ( 1.6 60 cm; GE Healthcare Science) that
was equilibrated with 20 mM bis-Tris buffer (pH 7.0) containing 0.3% Triton X-100 and
0.2 M NaCl and eluted with the same buffer. The active fractions were collected and
pooled.
The results for the purification of the enzyme are summarized in Table 2.
Volume Total protein Total activity Specific activity Yield Purification

Purification step
(mL) (mg) (U) (mU/mg) (%) (fold)
Crude extract 3155 6159 8.40 1.4 100 1
DEAE 410 932 3.10 3.4 37 3
Hydroxyapatite 264 153 1.30 8.2 15 6
Mono Q (pH 6.0) 12 24 0.96 39 11 29
Mono Q (pH 7.0) 1.5 1.7 0.52 315 6.2 29
Superdex 200 1.5 0.2 0.10 457 1.2 333
Table 2. Purification of sialyltransferase from cell lysate of P. phosphoreum.
The enzyme was purified 333-fold, with a yield of 1.2%. Because no affinity chromatography
step was used, the yield of the protein purification in this case was very low. Therefore,
preparing affinity gels with the appropriate ligand for the target enzyme is very important
in the purification process.
4. Enzymatic synthesis and purification of sialyloligosaccharides

4.1 Synthesis of sialyloligosaccharides by recombinant sialyltransferases from
marine bacteria
Chemoenzymatic synthesis of various sialyloligosaccharides by mammalian
sialyltransferases, and the purification of the product, has been reported (Sabesan &
Paulson, 1986). However, mass-production of sialyloligosaccharides by using mammalian-
derived sialyltransferases remains problematic because the enzymes are unstable and
difficult to produce as recombinant proteins in Escherichia coli. In comparison to mammalian
sialyltransferases, bacterial sialyltransferases are generally more stable and productive in E.
coli protein-expression systems (Tsukamoto et al., 2007, 2008; Yamamoto et al., 2006), and
they show a broader acceptor substrate specificity (Izumi & Wong, 2001; Yu et al., 2005).
Here, we report the methods that we developed to use recombinant sialyltransferases from
marine bacteria to successfully produce large quantities of 6-sialyllactose and synthesize
various sialyloligosaccharides.
4.1.1 Synthesis of 6-sialyllactose from lactose and CMP-Neu5Ac by using purified

recombinant 2,6-sialyltransferase from P. damselae JT0160
Purified recombinant 2,6-sialyltransferase from P. damselae JT0160 shows broader acceptor
substrate specificity than that of the mammalian enzymes. For example, it could transfer
Neu5Ac to not only disaccharides but also mono- and tri-saccharides efficiently, and
provided the corresponding sialosides (Fig. 4; Kajihara et al., 1996; Yamamoto et al., 1998).
Below, we describe an example of the enzymatic synthesis of 6-sialyllactose (sialoside 1).
1. The reaction mixture was composed of 20 mg (55 mol) of lactose (Gal1-4Glc), 79 mg
(110 mol) of CMP-Neu5Ac, and 0.6 U of the purified enzyme in 0.5 mL of 100 mM bis-
Tris buffer (pH 6.0).
2. The reaction mixture was incubated at 30C for 2 h.
3. The product formed by the enzymatic reaction was analyzed by using thin layer
chromatography (TLC) as follows: a small amount of the enzymatic reaction mixture
was applied to a pre-coated silica gel plate (60 F254, Merck, Darmstadt, Germany),
which was then developed with 2-propanol/acetic acid/water (3:2:1 v/v); for
visualization of the organic compounds, the plate was dipped into a solution of 5% v/v
sulfuric acid in ethanol and then heated.
HOOC OH
HO
HOOC OH
HO O OHOH
O OHOH HO O
O OHO
HO O O HO O
HO OHO HO
O O OH
OH OH AcHN OH
AcHN OH OH
O OH
HO
OH
(A) (B)
HO OH
HO HOOC
HOOC HO OH
OH O
O
AcHN
O O OHOH O OH
OH O HO
HO O OHO AcHN OH OH
HOOC O NHAc
HO
HO OH OH
O
AcHN OH OH
(C) (D)
HO OH
HOOC
AcHN O OH
HO O
HO O
OMe
HO
OH
(E)
(A) 6-sialyllactose (sialoside 1), (B) 2-fucosyl-6-sialyllactose (sialoside 2), (C) 3, 6-disialyllactose (sialoside
3), (D) 6-sialyl-N-acetylgalactosamine (sialoside 4), (E) 6-sialyl-methyl--D-galactopyranoside (sialoside 5).
Fig. 4. Structures of sialosides 15.
4.1.2 In vivo synthesis of 6-sialyllactose by using genetically engineered E. coli

Recently, we succeeded in mass-producing 6-sialyllactose by using a genetically engineered
E. coli strain expressing the Photobacterium sp. JT-ISH-224 gene for 2,6-sialyltransferase
(Drouillard et al., 2010). Our method was developed from a microbiological system for the
large-scale production of 3-sialyllactose that used high cell-density cultures of a genetically
engineered E. coli strain expressing the Neisseria meningitidis gene for 2,3-sialyltransferase
(Fierfort & Samain, 2008). To date, we have achieved the production of 6-sialyllactose with a
final concentration greater than 30 g L1 of culture medium, by continuously feeding the
culture with an excess of lactose. A detailed report of the production conditions is provided
in Drouillard et al. (2010).
4.1.3 Synthesis of various sialyloligosaccharides by using purified recombinant 2,3-

sialyltransferase from Photobacterium sp. JT-ISH-224
Using the procedure described in section 4.1.1, we could enzymatically produce 3-
sialyllactose (sialoside 6) by using 2,3-sialyltransferase instead of 2,6-sialyltransferase.
While using a recombinant 2,3-sialyltransferase derived from Photobacterium sp. JT-ISH-224
to produce 3-sialyllactose, we detected a by-product in the enzymatic reaction mixture and
determined its structure to be 2,3-disialyllactose (sialoside 7; Mine et al., 2010a). This
recombinant 2,3-sialyltransferase can also transfer Neu5Ac from CMP-Neu5Ac to the -
anomeric hydroxyl groups of mannose and 6-mannobiose to produce sialosides 8 & 9,
respectively (Mine et al., 2010b), and transfer Neu5Ac to inositols to produce sialosides 10 &
11 (Mine et al., 2010c). The structures of sialosides 611 are shown in Figure 5.
OH HO
OH HO
HO OH O O
O OH HOOC O
OHO HO O
HOOC HO
HO O O HO OH HOOC
O OOH
HO OH OH
O
HO AcHN OH OH HO O
AcHN OH
HO OH
AcHN OH
(A) (B)
HO
HO
OH O
HO OH OH OH OH
HOOC HOOC
O OH OH HO OH OH
OH O O O NHAc OH O O NHAc
O
OH OH
OH OH
(C) (D)
HO OH
HO OH
OH COOH HO
OH COOH OH
O HO OH
AcHN OH
O OH AcHN O OH
O OH
OH
HO OH OH
(E) (F)
(A) 3-sialyllactose (sialoside 6), (B) 2, 3-disialyllactose (sialoside 7), (C) sialyl-6-mannobiose (sialoside
8), (D) sialyl-mannose (sialoside 9), (E) sialyl-1D-chiro-inositol (sialoside 10), (F) sialyl-epi-inositol
(sialoside 11).
Fig. 5. Structures of sialosides 611.
4.2 Purification of sialyloligosaccharides by use of column chromatography

In general, for the separation of oligosaccharides, it is convenient to utilize high-
performance liquid chromatography (HPLC), and various types of columns, such as reverse-
phase columns, ion-exchange columns, and gel-filtration columns, that are commercially
available. Because Neu5Ac is negatively charged, it is comparatively easy to separate
sialyloligosachharide(s) from other neutral oligosaccharides by using anionexchange
column chromatography (Sabesan & Paulson, 1986). For further purification of the
compound, gelfiltration column chromatography is effective.
The conditions and method used for each column chromatography step are described below.
4.2.1 Separation of the sialyloligosaccharide and unreacted substrates from the

enzymatic reaction mixture
The basic procedure for anionexchange column chromatography is as follows:
1. The reaction mixture was diluted with 10 mL of deionized water and introduced onto
an Econo column (1.0 cm 10 cm; Bio-Rad Laboratories) containing AG1-X2 ion
exchange resin (phosphate form; 200400 mesh).
2. The column was washed with 3 column volumes (~ 30 mL) of deionized water.
3. Elution of the sialyloligosaccharide was performed twice with 10 mL each of 5, 10, 50,
100, 500, or 1000 mM potassium phosphate buffer (pH 6.8).
4. An aliquot of each eluted fraction was analyzed by using TLC, as described in section
4.1.1.
The column volume required for separation is dictated by the scale of the synthetic reaction.
For 10 mg or less of acceptor substrate, all of the reaction product will bind to the resin
described above. For more than 100 mg of acceptor substrate, it is desirable to either
perform the chromatography process at least twice, or to increase the amount of resin by
using a larger column (e.g., 2.5 cm 10 cm).
An example of results obtained for the separation of sialyloligosaccharide by using the
above procedure is shown in Figure 6.
A N D R FT Wash 5mM 10mM 50mM 100mM 500mM 1M

Fig. 6. TLC analysis of fractions separated by using anionexchange column
chromatography.
The reaction solution after enzymatic reaction of substrates with recombinant 2,6-
sialyltransferase from P. damselae JT0160 strain contained unreacted lactose and CMP-
Neu5Ac, free Neu5Ac as result of hydrolysis of CMP-Neu5Ac, and the product. The
contents of the fractions eluted with 5, 10, 50, 100, 500, and 1000 mM potassium phosphate
buffer (pH 6.8) are shown. A, lactose; N, Neu5Ac; D, CMP-Neu5Ac; R, reaction solution
after enzymatic reaction; FT, flow-through.
Many mono-sialyloligosaccharides composed of di-, tri- or tetra-saccharide eluted with 5 to
10 mM potassium phosphate buffer. We also demonstrated that disialyloligosaccharides,
such as sialosides 3 (Fig. 4) and 7 (Fig. 5), eluted with 100 mM potassium phosphate buffer.
In contrast, many of the unreacted acceptor substrates passed through the column because
of their electrically neutral property. Unreacted CMP-Neu5Ac and free Neu5Ac, resulting
from the hydrolysis of CMP-Neu5Ac during the reaction, were eluted with 500 and 50 mM
potassium phosphate buffer, respectively (Fig. 7). Therefore, it is easy to separate these
compounds in the enzymatic reaction mixture with this column chromatography process.
A N D R FT Wash 5mM 10mM 50mM 100mM 500mM 1M

Fig. 7. Separation of mono-sialyloligosaccharide and di-sialyloligosaccharide from the
reaction solution by using anionexchange column chromatography.
The reaction solution after enzymatic reaction with recombinant 2,3-sialyltransferase from
Photobacterium.sp. JT-ISH-224 strain contained unreacted lactose, CMP-Neu5Ac, free
Neu5Ac, and both the mono-sialyloligosaccharide (sialoside 6) as main product (black
arrow) and the di-sialyloligosaccharide (sialoside 7) as by-product (red arrow). The contents
of the fractions eluted with 5, 10, 50, 100, 500, and 1000 mM potassium phosphate buffer (pH
6.8) are shown. A, lactose; N, Neu5Ac; D, CMP-Neu5Ac; R; reaction solution after enzymatic
reaction, FT, flow-through.
During the stepwise elution described above, we sometimes observed that both the reaction
product and free Neu5Ac were present in the same fraction. In this case, the separation of
these compounds can be improved by increasing the volume of 10 mM potassium
phosphate buffer (e.g., using 35 column volumes of the buffer).
This basic procedure for the separation of sialyloligosaccharide in the enzymatic reaction
mixture is more effective when the enzyme reaction produces a single mono-
sialyloligosaccharide. If the reaction mixture contains a variety of mono-sialyloligosaccharides,
it is preferable to perform the preparative chromatography using a different column, such as
TSKgel Amide-80 (Tosoh Bioscience, Tokyo, Japan) (Endo et al., 2009).
For further purification of the sialyloligosaccharide, we performed gelfiltration column

chromatography. The procedure is as follows:
1. The fractions containing glycosidic Neu5Ac were evaporated to dryness.
2. The dried residue was dissolved in 2.5 mL of deionized water and then loaded onto a
Sephadex G-15 column ( 1.6 70 cm) and eluted with deionized water under a 2.5
mL/min flow rate and collected in increments of 1 mL.
3. The fractions containing glycosidic Neu5Ac were pooled and evaporated to dryness.
The purpose of this process is to remove salt carried from the former chromatography process.
The product was eluted in the 30th to 50th fractions (Fig. 8). When Neu5Ac was mixed with the
product, it could be separated from the product under a lower flow rate (e.g., 1.0 mL/min).
The purity of sialyloligosaccharides obtained by using a combination of the two
chromatography processes described above is usually more than 95% (data not shown).
A D N C 30 31 32 35 40 44 45 46 48
Fraction No.
Fig. 8. TLC analysis of the fractions separated by use of gelfiltration column chromatography.
The product is usually contained in the 30th to 50th fraction eluted during the gelfiltration
column chromatography; a typical example is shown. A; lactose, D; CMP-Neu5Ac, N;
Neu5Ac, C; 6-sialyllactose standard.
4.2.2 Alternative anion-exchange column chromatography method for large-scale

purification of 6-sialyllactose
As mentioned in section 4.1.2, a large volume of solution containing 6-sialyllactose could be
prepared by using high cell-density cultures of a genetically engineered E. coli strain. In such
cases, we performed an alternative anionexchange column chromatography process. At the
end of the fermentation, the whole culture was permeabilized by autoclaving at 100C for 50
min. The mixture was centrifuged at 7,000g for 30 min and the supernatant containing the
oligosaccharides was removed. The pH of the extracellular fraction was lowered to 3.0 by
the addition of a strong cation-exchange resin (Amberlite IR120 H+ form, Sigma-Aldrich
Japan, Tokyo), and the proteins that were precipitated by this process were removed by
centrifugation. The pH of the clear supernatant was then adjusted to 6.0 by the addition of a
weak anion exchanger (Dowex 66 free base form; Sigma-Aldrich Japan) and, after decanting,
the supernatant was loaded onto a Dowex 1 (HCO3 form, Sigma-Aldrich Japan) column (5
x 20 cm). After the column was washed with distilled water, the acidic oligosaccharides
retained on the Dowex 1 resin were eluted with 100 mM NaHCO3. The eluted fractions
containing acidic oligosaccharides were pooled and the NaHCO3 was removed by treatment
with Amberlite IR120 (H+ form) until the pH reached 3. The pH was then adjusted to 6.0
with NaOH and the acidic oligosaccharide fraction was freeze-dried.
4.2.3 Separation of various sialyl-compounds by using HPLC

Anionexchange column chromatography is a powerful method for separating a single
mono-sialyloligosaccharide from the other components in the sample solution; however, it is
impossible to separate one mono-sialyloligosaccharide from another mono-
sialyloligosaccharide, such as 6-sialyllactose or 3-sialyllactose, by using this method. In
such cases, HPLC can be used successfully for the separation, as described by Endo et al.
(Endo et al., 2009). In this protocol, the HPLC system is equipped with a TSKgel Amide-80
column (particle size 5 mm, 4.6 250 mm; Tosoh Bioscience), and is run at 40C with a
flow rate of 1mLl/min, and the eluates are monitored with a UV (195 nm) detector. The
elution conditions are as follows: 0 to 15 min isocratic elution with 75% acetonitrile in 15
mM potassium phosphate buffer (pH 5.2); and 15 to 45 min linear gradient elution with a
gradient of 75% to 50% acetonitrile in 15 mM potassium phosphate buffer (pH 5.2).
Some examples of HPLC chromatograms produced for sialyl-compounds synthesized as
described in section 4.1 are shown in Figure 9.
Fig. 9. Chromatograms of some sialyl-compounds.

The sample solution (150 mL) containing sialyl-compound(s) was separated as described in
section 4.2.3. A; an example of the separation of two mono-sialyloligosaccharides,
B; examples of the chromatogram of various mono-sialyloligosaccharides.
5. Conclusion
It is now possible to produce large amounts of sialyloligosaccharides by using newly
developed methods, including chemoenzymatic methods and fermentation methods. It is
also possible to produce huge quantities of sialyltransferase enzymes. However, large-scale
production of other glycosyltransferases, such as N-acetylglucosaminyltransferase or
fucosyltransferase, is still difficult. For this reason, it is of great importance to identify
enzymes that could be used in the production of other glycosyltransferases and to establish
mass-production methods for these enzymes.
6. Acknowledgment
The authors would like to thank Ms. Hitomi Kajiwara for her valuable comments and all of
their collaborators.
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5
Simple Preparation of New

Potential Bioactive Nitrogen-Containing
Molecules and Their Spectroscopy Analysis
Vladimir V. Kouznetsov, Carlos E. Puerto Galvis,
Leonor Y. Vargas Mndez and Carlos M. Melndez Gmez
School of Chemistry, Industrial University of Santander, Bucaramanga,
Colombia
1. Introduction
The impact of research on the small molecules chemistry is difficult to quantify and
currently, it is still one of the most active areas of organic chemistry, medicinal chemistry
and lately chemical biology. In recent years, a lot of interest has been shown in the
preparation of nitrogen-containing compounds due to their numerous biologically
significant activities. But it is the separation and purification process of the new synthetized
organic molecules, the ones that take a key role in drug design and development.
Many texts about the simple and optimal preparation of bioactive compounds have been
published, and in this chapter the multicomponent reactions and efficient linear process,
which allow the synthesis of this kind of structures, will be discussed. However, the
purpose of this chapter is to reveal those important aspects that finally determined why a
molecule can be used and distributed as a drug: their preparation, purification, and
characterization.
In almost all organic synthetic methodologies the purification process use simple column
chromatography techniques (gravity or external pressure) using different support materials
(solid adsorbents) as the stationary phase. Column chromatography is advantageous over
most of the other chromatographic techniques because it can be used in both analytical and
preparative applications. After the preparation and purification of a new compound has
been realized, it becomes the characterization step. New purified molecules must be
strongly characterized to determine its structural configuration. Among different analysis
techniques, NMR experiments and X-Ray crystallography are the most efficient ways to
determine the relative stereochemistry and, in suitable cases, also the absolute configuration
of the obtained products.
In the development of our medicinal program directed to small molecules for drug delivery,
the strategies for the preparation of nitrogen-containing molecules such as substituted
indoles, tetrahydroquinolines, and N-substituted amides of carboxylic acids are illustrated
in this chapter as well as their synthetic applications and analytic characterization. The
discussion is complemented with a deep explanation of the analytical techniques employed
for their isolation and purification including the spectroscopic and spectrometric techniques
using for the elucidation structure for every new compound.
2. Simple preparation of new N-aryl-N-(3-indolmethyl) acetamides and their

spectroscopic analysis
The vital importance of derivatives like indole-3-acetic acid, as a hormone responsible for
the plant growth, and tryptophan, as a constituent of proteins and indispensible precursor
of indole alkaloids, enhances the current interest for the design of simple and efficient
synthetic routes for the preparation of molecules with the indole skeleton.
The research of the indol chemistry has been and it is still one of the most active areas of
heterocyclic chemistry. In the past decades, a lot of interest has been shown in the
preparation of substituted indoles due to their numerous biologically significant activities
(Gribble, 2003). The derivatives of 3-indolylmethanamine 1 are the important intermediates
of natural and natural-like products, such as hydro--carboline and pyrido[4,3-b]indole
derivatives (Wynne & Stalick, 2002; Molina et al., 1996). This 3-indolyl methanamine motif is
also embedded in numerous indole alkaloids from the simple alkaloid gramine 2 to complex
aspidospermine alkaloid 3 (Baxter et al., 1999; Saxton, 1998) (Fig. 1).
Fig. 1. Relevant natural alkaloids derived from the 3-indolylmethanamine system.
As a result of their biological and synthetic importance, a variety of methods have been
reported for the preparation of 3-substituted indoles, using indol or 3-indolcarboxyaldehyde
as starting materials. Generally, the Mannich reaction (Dai et al., 2006) and the catalyzed
Friedel-Crafts alkylation reactions of indoles (Ke et al., 2005; Zhao et al., 2006; Jiang et al.,
2005; Shirakawa & Kobayashi, 2006) are considered as a powerful carbon-carbon bond
process to afford the 3-indolylmethanamine derivatives 1. However, another synthetic route
to access to these compounds by using 3-indolcarboxyaldehyde, via its imino derivatives, is
valid. This route has been used by our laboratory, which recently started an own medicinal
program directed to small molecules for drug delivery. The particular interest in 3-
indolylmethanamine derivatives molecules, that could serve as useful precursors to many
drug-like indolic or quinolinic compounds, is based on the evaluated antiparasitic
properties of some analogues (Kouznetsov et al., 2004a, Kouznetsov et al., 2004b; Vargas et
al., 2003). In this novel direction, the simple preparation of new (3-indolmethyl)acetamide
and (1-acetylindolmethyl-3)acetamide, regulating only the solvent nature, is the relevant fact
that has not been described and it gives the opportunity to prepare more of this kind of
compounds.
Simple Preparation of New Potential Bioactive
Nitrogen-Containing Molecules and Their Spectroscopy Analysis 89
2.1 Synthesis and purification of the new the (3-indolmethyl)acetamide and

(1-acetylindolmethyl-3)acetamide
Aldimines are valuable starting materials not only for different N-containing heterocycles
but also to diverse secondary heteroaromatic amines (Hutchins & Hutchins, 1991), which
represent good candidates for bio-screening with diverse types of activities (Kleemann &
Engel, 2005; Evers et al., 2005). Thus, the N-aryl imine 6, the main and value starting, can be
prepared from commercially available 3-indolaldehyde 4 and 2-cyanoaniline 5, according to
published methods (Colyer et al., 2006). This aldimine is obtained as a white and stable solid
after purification by recrystallization in 95 % yield (Fig. 2). The method employed to obtain
the precursor 7, is one of the most known procedures to reduce an aldimines with an excess
of NaBH4 in methanol, protocol that is still the reaction of choice to produce secondary
amines in reasonably good yield. Thus, N-(2-cyanophenyl)-N-(3-indolylmethyl)amine 7 is
prepared as was described and was obtained as white solid in 70 % yield after purification
through recrystallization (Bello et al., 2010). This example, in which the main precursor is
prepared in a linear process and purified by recrystallization, represents an excellent
technique that avoids the loss of value material and it will be increase the global yields of
the final product.
Fig. 2. Synthesis and reduction of the aldimine 6 to give the desired secondary amine 7 in
excellent overall yields.
Besides the efficient preparation and easily purification of compound 7, this amine has
interesting structural elements to use in the synthesis of different indolic heterocycles. In
this case, the study of its acetylation by acetic anhydride is showed.
First, to a stirred solution of amine 7, using in toluene as solvent due to the insolubility of
compound 7 in polar common solvents (CH3CN, CH2Cl2, AcOEt and DMF), it is added Et3N
and acetic anhydride, the mixture is refluxed for appropriate time to obtain the N-(2-
cyanophenyl)-N-(3-indolmethyl)acetamide 8 in acceptable yield (50 %) after purification
using silica gel 60 Mesh and using a mixture of hexane: ethyl acetate (2:1) as an eluent.
Then, the acetylating reaction described above was performed between the amine and an
excess acetic anhydride in the presence of Et3N at 100 C, without the organic solvent
(toluene). After the usual workup, the diacetylated indole 9 is obtained in good yield (85 %)
using the same parameters employed to the purification of compound 8. This simple change
in the reaction conditions could afford different acetamides based on the 3-indolyl
methanamine motif (Fig. 3). This finding reveals a selective process to protect different
amino groups and represents a good protocol to the synthetic organic chemistry, especially
within those processes that require a particular position protection.
Fig. 3. Synthesis and purification of the N-aryl-N-(3-indolmethyl)acetamides 8 and 9.
2.2 Characterization of the N-aryl-N-(3-indolmethyl)acetamides 8 and 9 by

spectroscopy and spectrometric techniques
The structures of the C-3 substituted indoles 7-9 were confirmed on the basis of recorded
analytical and spectral data and are supported by inverse-detected 2D NMR experiments.
The IR spectrum of compound 7 illustrates the characteristic absorption bands at 3402 and
3352 cm-1 assignable to tension vibrations of CH2-N-H and N-Hindol, respectively. Its 1H
NMR spectrum displays a duplet at 4.56 ppm (J = 4.9 Hz) ppm corresponding to two
protons coupling with the neighbor N-H proton (br. s, 4.84 ppm), which suggest the
presence of the methylenic unit linked to the N-H function. The peaks find at 7.17-7.3, 7.36-
7.40 and 7.63 ppm reveals the presence of aromatic protons of the indole moiety. The 13C
NMR spectra, also showed all expected characteristic peaks at 39.4 (CH2), 117 (CN), and
95.6-150.2 (aromatic carbons).
The mass spectrometric analysis of compound 8 gives a molecular ion peak M+, at m/z 289,
suggesting the molecular formula C18H15N3O, and indicating that the acetyl group is
coupling with 7. The acetamide 8 displayed characteristic infrared absorption bands with a
single amine absorption band at 3342 cm-1 and with a carbonyl sign at 1701 cm-1 suggesting
the acetylation reaction involvement of the CH2-N; this is the band appearing at high wave
number of the corresponding N-Hindol vibration tension in the IR spectrum. Its 1H NMR
spectra analysis showed a singlet at 2.58 ppm corresponding to three protons which belong
to the acetyl group and another singlet at 4.55 ppm due to the presence of the methylenic 3-
CH2-N indolic protons. This signals multiplicity is explained by assuming the proton N-H
next to it, substituted now for the acetyl group, which leaves no possibility to H,H coupling,
while it does happen with the amine 7.
The 13C NMR spectrum of the acetamide 8 displayed characteristic carbonyl signal at 168
ppm, this is strong evidence to the new acetyl group bonded to the molecule; in addition to
a signal at 39.3 and 23.9 ppm, showing the presence of CH2 and CH3 in the molecule.
Introduction of an acetyl group into the molecule affects the chemical shift of the hydrogen
bonded to the aromatic carbon close to the acetylatin nitrogen; this appears at 116 ppm for
the compound 7 and at 123 ppm for the acetamide 8. The signal at 39.3 ppm for CH2-N has
been distinguished on the basis of the DEPT-135 experiment. On the basis of these spectral
studies, compound 8 was characterized as the N-(2-cyanophenyl)-N-(1H-indol-3-
ylmethyl)acetamide.
The new compound 9 gave a molecular ion peak at m/z 331 in the mass spectrometric
analysis, corresponding to the molecular formula C20H17N3O2 as indicated by its EI-MS. The
loss of 43 units (one acetyl group) generates the same mass spectrum as the acetamide 8. The
IR spectrum of this molecule shows bands at 1704 and 1654 cm-1, assignable to two carbonyl
groups while the N-H absorption bands are not observed in the region of 3300-3400 cm-1.
The 1H NMR spectrum showed, as expected, two singlets at 22.4 and 23.9 ppm, which
integrated for three protons each. In the case of the methylenic protons, they appeared to be
diasterotopic resonating at the high field frequencies 4.75 and 5.46 ppm with a coupling
constant J = 15 Hz, usual constant value to a germinal coupling. Of course, the aromatic
protons were also assigned.
The 13C NMR spectrum showed all expected characteristic peaks at 169.4 (ArN-CO-), 168.5
(ArindolN-CO-) ppm, in addition to a signal at 117.3 ppm showing the presence of CN in
the molecule. Besides, methyl carbons at 23.9 (ArindolNCO-CH3) and 22.4 (ArNCO-CH3) ppm
and the methylene carbon at 42.8 ppm were also displayed in the 13C NMR.
With respect to the characterization of the diacetamide 9, through X-ray diffraction, the
monoclinic system was determined with the compound crystallized at 25C from heptane-
ethyl acetate (2:1) (Fig. 4).
Fig. 4. X-Ray structure of the diacetamide 9.
The crystallized material has the following cell constants: a = 11.1184(19) , b = 8.0048(13) ,
c = 20.534(4) and space group P 21/n (Table 1), possessing the different bond lengths of
the molecule constituent atoms was also extracted with this technique (Table 1).
From this data, the different bond lengths of the two amide bonds present within the
structure were as expected. Even knowing the double bond character of the amide bonds, in
this case, the amide bond distance between the aliphatic nitrogen N2 and C12 is 1.364 ,
while the distance between the aromatic nitrogen N1 and C9 is 1.388 .
Crystal morphology White parallelepipede

Chemical formula C20H17N3O2
Molecular weight 331.13
Crystal system Monoclinic
Space group P21/n
Cells constants a = 11.1184(19) , b = 8.0048(13) and c = 20.534(4) ,
= 90, = 94.281(4), = 90
Volume 1822.4(5) 3
Absorption coefficient 0.82 mm-1
Temperature 293(2) K
Range for data collection 1.99-28.09
Index range h = -13 28, k = -9 7, l = -23 23
R 0.0567
Rw 0.0582
Threshold expression >2sigma(l)
Diffraction radiation M0K
0.71070
Table 1. Crystal data and structure refinement parameters of diacetamide 9.
From this data, the different bond lengths of the two amide bonds present within the
structure were as expected. Even knowing the double bond character of the amide bonds, in
this case, the amide bond distance between the aliphatic nitrogen N2 and C12 is 1.364 ,
while the distance between the aromatic nitrogen N1 and C9 is 1.388 .
These data correspond with the thought that the amide bond N2-C12 is shorter because of
the electron withdrawing inductive effect from the -cyanophenyl substituent and the
possibility of the nitrogen non-shared electrons to be delocalized on the amide bond
through a mesomeric effect giving this bond a stronger double bond character.
On the other hand, the amide bond N1-C9 is longer because the nitrogen non-shared
electrons are compromised with the aromatic system and they are not as available to be
delocalized on the amide bond giving it less double bond character (Table 2).
2.3 Conclusions
An efficient, economic, and fast synthetic route was designed and its illustrated in this
section showing the possible construction of the N-aryl-N-(3-indolmethyl)acetamides with
the incorporation of the indolic core as a structural analogues of some alkaloids.
The acylation method is worth as a regioselective process because the conditions variations
lead to the mono- or di-acetamide. The characterization of the obtained compounds through
different techniques gives evidence enough and strong support with regard to the success of
the proposed scheme.
Number Atom 1 Atom 2 Length ()

1 O1 C9 1.220
2 O2 C12 1.221
3 N1 C7 1.415
4 N1 C8 1.405
5 N1 C9 1.388
6 N2 C11 1.473
7 N2 C12 1.364
8 N2 C14 1.430
9 N3 C20 1.143
10 C1 C2 1.449
11 C1 C8 1.338
12 C1 C11 1.489
13 C2 C3 1.385
14 C2 C7 1.404
15 C3 H3A 0.931
16 C3 C4 1.371
17 C4 H4A 0.929
18 C4 C5 1.378
19 C5 H5A 0.931
20 C5 C6 1.377
21 C6 H6A 0.930
22 C6 C7 1.384
23 C8 H8A 0.930
24 C9 C10 1.481
25 C10 H10A 0.960
26 C10 H10B 0.961
27 C10 H10C 0.961
28 C11 H11A 0.971
29 C11 H11B 0.971
30 C12 C13 1.497
31 C13 H13A 0.961
32 C13 H13B 0.960
33 C13 H13C 0.960
34 C14 C15 1.387
35 C14 C19 1.364
36 C15 C16 1.388
37 C15 C20 1.427
38 C16 H16A 0.930
39 C16 C17 1.363
40 C17 H17A 0.929
41 C17 C18 1.360
42 C18 C18A 0.929
43 C18 C19 1.397
44 C19 H19A 0.931
Table 2. Bond lengths between the molecule atoms of diamide 9.
3. A convenient procedure for the synthesis of new quinoline derivatives and

their spectroscopic analysis
Quinoline and tetrahydroquinoline structures are essential feature of many natural
products. These heterocycles play a key role in heterocyclic and medicinal chemistry. Their
syntheses by various methodologies have been published extensively (Kouznetsov et al,
2005; Kouznetsov et al., 1998; Katrizky et al., 1996; Jones, 1984).
Polyfunctionalized tetrahydroquinolines (THQs) are molecules of great interest in
organic synthesis due to the fact that many natural products present this system in
their structure, and these compounds exhibit diverse biological activities (Glushenko
et al., 2008; Broch et al., 2008; Ichikawa et al., 2004; Morsali, et al., 2004; Chen et al.,
2000).
Apart from their marked bioactivities, THQs are also important and reliable precursors
in quinoline preparation, another group of heterocyclic molecules that has a great number
of pharmacological properties (Trpkovska et al., 2003). An efficient route for the preparation
of THQs is the acid-catalyzed Povarov reaction that is classified as imino Diels-
Alder cycloaddition (Kouznetsov, 2009; Paazderski et al., 2007; Kouznetsov & Mora, 2006;
Youssed et al., 2003) that permits the condensation of anilines, aldehydes, and electron-rich
alkenes using acidic catalysts under mild conditions to afford new substituted
tetrahydroquinolines.
For any Direct Oriented Synthesis (DOS) methodology towards the synthesis of bioactive
substituted tetrahydroquinolines and quinolones, this route represents an easily and
scalable approach for the investigations on the synthesis of small drug-like
(tetrahydro)quinoline molecules containing C-2 aryl fragment, those synthesis could be
accomplished via cycloaddition reactions. In this order, this section explain the simple
preparation of new N-(2-nitrophenyl-1,2,3,4-tetrahydroquinolin-4-yl) pyrrolidin-2-ones using
BiCl3-catalyzed three component Povarov reaction between nitrobenzaldehydes, toluidine
and N-vinylpyrrolidin-2-one, and their transformations into potentially bioactive 2-aryl-
tetrahydroquinoline derivatives, N-amidyl substituted at the C-4 position.
3.1 Synthesis of new N-(2-nitrophenyl-1,2,3,4-tetrahydroquinolin-4-yl) pyrrolidin-2-

ones
Having an experience in the construction of diverse heterocycles containing nitrogen via
multi-component Povarov reaction, (Kouznetsov et al., 2010; Kouznetsov et al., 2007;
Kouznetsov et al., 2006). The preparation of the selected tetrahydroquinoline compounds 14
and 15 was achieved using BiCl3 as a catalyst for the three-component imino Diels-Alder
cycloaddition between toluidine 10, nitrobenzaldehydes 12 and 13 and N-vinylpyrrolidin-2-
one 11 (NVP) (Bermudez et al., 2011) (Fig. 5).
These reactions proceeded smoothly in MeCN and at room temperature giving
final products, substances easy to purify by column chromatography using silica gel
as a support and a mixture of petroleum ether and ethyl acetate (2:1) as an isocratic
eluent. The N-(2-nitrophenyl-1,2,3,4-tetrahydroquinolin-4-yl) pyrrolidin-2-ones 14 and 15 can
be obtained with good respective yields 95% and 70% (Table 3) as a easily handle
solids.
Fig. 5. Synthesis of nitrophenyl-tetrahydroquinolines using the multi-component imino

Diels-Alder reaction.
Molecular Molecular
Comp. IR (KBr), , cm-1 mp, oC Yield (%)
Formula Weight
3394, 2947, 2916,
14 C20H21N3O3 351.40 222-223 95
1666, 1620
3271, 2972, 2916,
15 C20H21N3O3 351.40 242-243 70
2854, 1666
Table 3. Physical description, IR data and yields of the 2-nitrophenyl tetrahydroquinolines
14,15.
3.2 Characterization of the N-[6-methyl-2-(4-nitrophenyl)-1,2,3,4-tetrahydroquinolin-4-

yl] pyrrolidin-2-one 14 by spectroscopy and spectrometric techniques
The structures of the C-2 substituted tetrahydroquinolines 14 and 15 were confirmed on the
basis of analytical and spectral data and were supported by inverse-detected 2D NMR
experiments. The IR spectrum show the characteristic absorption bands of the compound 14
at 3394 and 1666 cm-1, assignable to the amine and amide group, respectively, and the nitro
group signals at 1512 and 1342 cm-1. Their mass spectrum showed a molecular ion m/z: 351,
it coincided with the molecular weight (351 g/mol). The 1H NMR spectrum of this
compound presented the 4-H proton signal at 5.69 ppm, observed as a double doublet with
the coupling constants 6.4 Hz and 11.1 Hz.
This fact suggested axial-axial and axial-equatorial interactions between 4-H and 3-H
protons. On the other hand, the 2-H proton signal was observed at 4.65 ppm with the
coupling constants 3.1 Hz and 10.7 Hz that indicated at vicinal axial-axial and axial-
equatorial interactions (Fig. 6).
The high value of the coupling constant (10.7-11.1Hz) of the 4-H and 2-H protons confirmed
the axial proton configurations; therefore, substituents of the C-2 and C-4 positions of
tetrahydroquinoline ring have the equatorial disposition, respectively.
On the other hand, it was found by the COSY experiment that the signal at 2.13-1.99 ppm
belongs to the 3-H proton, observing the 3-H (4-H) (2.131.99 ppm) and 4.65 ppm (2-H) and
5.69 ppm (4-H) cross peaks interactions (Fig. 7).
Fig. 6. 1H NMR spectra of N-[6-methyl-2-(4'-nitrophenyl)-1,2,3,4-tetrahydroquinolin-4-yl]

pyrrolidin-2-one 14.
Fig. 7. COSY spectrum of N-[6-methyl-2-(4'-nitrophenyl)-1,2,3,4-tetrahydroquinolin-4-yl]

pyrrolidin-2-one 14.
The nitro-isomer 15 has similar chemical behavior in the spectra data. The chemical
structures of the obtained N-(1,2,3,4-tetrahydroquinolin-4-yl) pyrrolodin-2-one molecules
were strongly confirmed through IR, 1H and 13C NMR analyses.
However, having a possible mechanism of realized multi-component condensation, we
could anticipate the various diastereomers the cis or trans configuration. For these reasons,
further structural studies were realized.
3.3 X-Ray diffraction single crystal study

Samples crystals of both compounds of interest were growth by slow evaporation in
ethanol. However, the difficulty to obtain suitable crystals from compound 15 only allows
performing the study for the compound 14. The diffraction data of the compound 14 were
collected at 273K using a CCD area detector with graphite-monochromatic Mo K radiation
( = 0.71073 ).
This data were computed using Bruker-AXS software. For solution and refinement of the
structure Shelxs-97 and Shelxl-97 (Sherldrick, 1997a; Sheldrick, 1997b) were used respectively.
Molecular and crystal structures were obtained using Mercury software (Allen, 2002).
The molecular structure for the compound is presented in the Figure 8, where a cis
conformation of the C-2 and C-4 substituents is evident, as well as a chair configuration that
adopts tetrahydroquinoline system.
Fig. 8. Representation of the unit cell of N-[6-methyl-2-(4-nitrophenyl)-1,2,3,4-

tetrahydroquinolin-4-yl] pyrrolidin-2-one 14.
The details of cell data and refinement for the compound 14 are summarized in Table 4.
a = 9.109 (2)
b = 9.2812 (5)
Unit cell parameters c = 11.011 (3)
= 90.939 (6)
= 100.023 (6)
= 93.309 (6)
Volumen 913.998 3
System Triclinic
Space Group P-1 (No. 2)
Z 2
Table 4. Crystallographic data obtained by four-circle diffractometry.
The structure packing is showed in the Figure 9 and finally, the powder profile simulated by
the single crystal data is shown in Figure 10.
Fig. 9. Molecular packing of the unit cell of N-[6-methyl-2-(4-nitrophenyl)-1,2,3,4-

tetrahydroquinolin-4-yl] pyrrolidin-2-one 14.
By means of single crystal study of the compound N-[6-methyl-2-(4-nitrophenyl)-1,2,3,4-

tetrahydroquinolin-4-yl] pyrrolidin-2-one 15 was determined that crystals obtained from
ethanol crystallizes in the triclinic system with space group P-1 (No 2).
Fig. 10. Diffraction profile of N-[6-methyl-2-(4-nitrophenyl)-1,2,3,4-tetrahydroquinolin-4-yl]

pyrrolidin-2-one 14 simulated in Mercury software.
Table 5 shows the atomic positions. Carbon-bound H-atoms positions were idealized
(C-H=0.93 ), with H atoms riding on the atoms to which they were attached.
Number Label Xfrac Yfrac Zfrac

1 O1 0.3653 0.1204 0.8134
2 O2 -0.2751 0.1442 -0.069
3 O3 -0.2013 0.3615 -0.0633
4 N1 0.4385 0.1546 0.3218
5 N2 0.3999 0.2993 0.6826
6 N3 -0.1902 0.242 -0.0246
7 C1 0.2924 0.1252 0.3587
8 C2 0.281 0.2232 0.4685
9 C3 0.4102 0.2053 0.576
10 C4 0.5578 0.2277 0.5329
11 C5 0.5642 0.1906 0.4089
12 C6 0.7043 0.1999 0.3716
13 C7 0.8288 0.2495 0.4491
14 C8 0.8236 0.2933 0.5723
15 C9 0.6885 0.2777 0.6119
16 C10 0.3777 0.2485 0.7914
17 C11 0.3736 0.3751 0.8765
18 C12 0.3898 0.5036 0.8068
19 C13 0.4078 0.4576 0.6777
20 C14 0.1688 0.1496 0.2534
21 C15 0.1696 0.2758 0.1861
22 C16 0.0548 0.3036 0.0958
23 C17 -0.0664 0.2057 0.0701
24 C18 -0.0721 0.0818 0.135
25 C19 0.0456 0.0548 0.2264
26 C20 0.9644 0.3544 0.6587
Table 5. Atomic positions in the unit cell of N-[6-methyl-2-(4-nitrophenyl)-1,2,3,4-
tetrahydroquinolin-4-yl] pyrrolidin-2-one (14).
3.4 Conclusions
The synthesis of two new nitro-isomers of N-(tetrahydroquinolinyl) pyrrolidin-2-ones using a
versatile and simple methodology called the three component imino Diels-Alder
cycloaddition is illustrated as an excellent route for the preparation of novel kind of
structures, the spectral analysis showed the 2-Haxial, 4-Haxial configuration; therefore the di-
equatorial disposition of the C-2 and C-4 substituent that confirmed the formation of the
endo-adduct during a Diels-Alder cycloaddition process.
The full characterization of N-[6-methyl-2-(4-nitrophenyl)-1,2,3,4-tetrahydroquinoline-4-yl]
pyrrolidin-2-one 14 was possible due to the single crystal X-ray diffraction studies, given the
following data: the compound 14 crystallizes in the triclinic system with a = 9.109(2) , b =
9.281(5) , c = 11.011(3) , = 90.939 (6), = 100.023 (6), = 93.309 (6), Z = 2, space group
P-1 [No. 2], and V = 1054.0 A3.
4. Convenient and scaleable three-step synthesis of new N-benzyl (pyridyl)

cinnamamides from substituted (hetero)aromatic aldehydes
The relatively stable amide bond is not only common in natural-occurring materials like
peptides and vitamins, it is also found in many synthetic substances. Among these
important and interesting class of organic molecules: N-benzylcinnamides and N-
phenylcinnamides have been always the focus of attention of organic, bioorganic and
medicinal chemists due to their many useful synthetic applications (Takasu et al., 2003;
Bernini et al., 2006; Nair et al., 2007) as well as their diverse (bio)chemical properties (Curtis
et al., 2003; Tamiz et al., 1999; Lewis et al., 1991). Moreover, N-amide cinnamic acid
derivatives are frequently presented in the nature (Mbaze et al., 2009; Vasques et al., 2002).
Both types of amides could be prepared generally via acylation reactions of the
corresponding benzylamines or anilines and cinnamic acid derivatives (anhydrides or acyl
halides) that are frequently used in the preparation of drug candidate molecules (Carey et
al., 2006). However, the known acylation reactions for N-benzylcinnamides preparation
employ hazardous and corrosive reagents (e.g., SOCl2, PCl3, (COCl)2, NEt3) besides the
starting functionalized benzylamines are not commercially available products, and almost
any of their functional groups needs to be protected to ensure chemoselective amide
formation (Nesterenko et al., 2003).
Considering the reported biological properties of certain N-arylcinnamides and N-
benzylcinnamides that have showed in vitro antimycotic activity (Leslie et al., 2010) and the
inhibition of the transcription of carcinogenic genes in infected cells (Sienkiewicz et al.,
2007). The need of an easy, rapid and green protocol for the synthesis of these kind of
compounds is necessary to explore new pharmacological targets, and in this order the
challenge of the organic chemistry is currently focused on the design of novel
methodologies that suppress the use of acyl chloride (including any dangerous reagent
required for their synthesis) and promoting the direct condensation between carboxylic
acids and amines, coupling that currently is performed using efficient promoters such as
N,N'-dicyclohexylcarbodiimide (DCC) (Amma & Mallouk, 2004), (benzotriazol-1-
yloxy)tripyrrolidinophosphonium hexafluorophosphate (ByPOB) (McCalmont, 2004; Baures
et al; 2002), triethylamine (Walpole, et al., 1993) and boron-based catalysts like BH3.THF
(Huang et al., 2007).
The search of bioactive not only requires a good synthetic route, all the reagents must be
stable and inexpensive to improve the structural complexity as in the biological properties.
In this case, the integrity of most of the benzylamines is compromised when they are
exposed to air moisture or even stored at low temperatures for a long period of time (Nazih
& Heissler, 2002). A way to prevent this effects is based on choosing an appropriate strategy
that enables the preparation of the desired amount benzylamines at lower cost than those
acquired commercially, which could be possible by reduction of nitriles (Haddenham et al.,
2009) and oximes (Gannett et al., 1988).
The green protocol described in this section is directed to enhance the disadvantages
already described for the existing methodologies. Considering first the excellent chemical
reactivity of aldehyde group against hydroxylamines nucleophilicity to give oximes, this
part was based on the existing methodologies which were improved according to the green
chemistry principles with the use of less hazardous Na2CO3 as a base to release the
nucleophile (Dallinger & Kappe, 2007; Roberts & Strauss, 2005; Yadav & Meshram, 2001;
Varma, 1999). The posterior reduction of the prepared oximes give the functionalized
benzylamines (pyridylmethylamines) in quantitative yield, this allows the coupuling of the
corresponding amines, without further purification, with cinnamic acid in the presence of
boric acid to afford the final products in agreement to our previous experience synthesizing
this type of compounds (Hernandez et al., 2008).
4.1 Synthesis of new N-benzyl (pyridyl) cinnamamides from substituted

(hetero)aromatic aldehydes
The choice of diverse (hetero)aromatic aldehydes 16a-k was motived by the interest in quest
for N-hetarylmethyl cinnamamides with antioxidant and anticancer properties. The direct
condensation of 16a-k and hydroxylamine in the presence of Na2CO3 is realize in an
ethanol/water medium. Thus, a mixture of aldehydes 16a-k, Na2CO3 and hydroxylamine
hydrochloride was mixed in deionized water for 5 min. at room temperature, and then a
small amount of the respective aldehyde was added for a period of another 5 minutes. The
reaction mixture was stirring for 15 min. and after traditional work-up, the pure products,
the substituted aldoximes 17a-k were obtained in quantitative yield (Fig. 11).
Fig. 11. Preparation of the respective (hetero)benzylamines from the aldehydes 16a-k in a
scalable methodology.
Taking into consideration that one of the most atom-economical procedures for the
preparation of an amine is hydrogenation of an oxime in which the only by-product is
water, we addressed also to this approach (Trost, 1995; Trost, 1991). Having in our hands the
eleven solid and stable aldoximes 17a-k obtained in first step, each of them was
hydrogenated at room temperature overnight under H2 atmosphere using 10 % palladium
on charcoal in ethanol (Fig. 11).
The hydrogenation mixture obtained in the second step is filtered through celite and the
filtrate was concentrated to dryness allowing the crude amine 18a-k, which was quickly
added, without any further purification, to an anhydrous toluene solution of trans-cinnamic
acid 19 in the presence of B(OH)3 (10 % mol) at 110 C for 6-10 h (Fig. 12).
The required workup at the end of the reaction can be perform in two ways: one consist in
the precipitation of the product of interest with a solution of NaHCO3 and their subsequent
washing with water or that can be purified with column chromatography depending on the
complexity of the final crude. For the second choice, the recommended support is neutral or
basic alumina (Al2O3) due to the acidity of the trans-cinnamic acid that will remain from the
Fig. 12. Rational design of the three-step synthesis of the corresponding N-benzyl cinnamides
from substituted (hetero) aromatic aldehydes.
reaction. An acid support like common silica gel (SiO2) will retain both substances (the
amide of interest and the residual cinnamic acid). After the method of preference for the
purification of the amides has applied, the final products the N-benzylcinamides 20a-k were
obtained in excellent yields and with a high purity level (Table 6).
Comp. 20 R1 R2 R3 R4 Yield (%)

a H Cl H H 80
b H OCH3 H H 87
c H OCH3 OCH3 H 91
d H OH OCH3 H 67
e H OCH3 OH H 72
f OCH3 OCH3 OCH3 H 95
g -OCH2O- H H 94
h H H -C4H4- 92
i H H H =N 84
j H H =N H 89
k H =N H H 90
Table 6. Synthesized N-benzyl cinnamides 20a-k.
The 1H NMR spectra of the compounds 20 display a general group of characteristic signals
for this series. For example, in the cinnamide 20g spectrum the methylene protons at 4.47
ppm (2H, d, J = 5.7 Hz, -CH2) is the signal that is observed in high fields, signal that is
coupling with the N-H signal, observed as a triplet at 5.99 ppm (1H, J = 5.7 Hz, NH). The
analysis of olefinic protons indicate the trans configuration of the final products when the
high value of the coupling constant observed is compared with the typical value for the cis
configuration: in the case of compound 20g, and for the entire 11 synthetized molecules, the
assignment of the proton at 6.41 ppm (1H, d, J = 15.7 Hz, =CHCO) and the coupling in trans
form with the other olefinic proton, the one that appears at lower fields, at 7.66 ppm (1H, J =
15.7 Hz, =CHPh) confirmed the configuration of all the products (Fig. 13).
Fig. 13. 1H-NMR spectrum of the N-(3,4-methylenedioxybenzyl) cinnamamide 5g.
4.2 Conclusions
The improvement of the existing methodologies for the preparation of benzylamines, is
described as protocol that enhances the efficiently, easily, rapidly and safety way in which
the oximes can be obtained, leading to explore their synthetic use in the preparation of more
complex systems or evaluate their pharmacological properties as a potential reactivators of
the acetylcholinesterase enzyme (Sinko et al., 2010) or their allergenic activity (Bergstrm et
al., 2008).
Taking into account that boronic compounds have showed catalytic activity in peptide
synthesis, it is demonstrated also that boric acid is a practical and useful catalyst for
amidation between cinnamic acid and the prepared benzylamines due to its remarkable
catalytic potential. The notable features of this procedure are mild and green reaction
conditions, good reaction rates, cleaner reaction profiles and excellent global yields for a
linear synthesis of three steps. The recollected spectral data described for N-benzyl
cinnamides should be reliable in the structural analysis of natural cinnamides and these
substances could serve as a model for small-molecule screening towards new bioactive
compounds.
5. Acknowledgment
The authors acknowledgment to COLCIENCIAS: contract No. 432-2004, RC-3662011 and
CENIVAM: CPS 015-2011, and the Universidad Industrial de Santander: throught to the VIE
division, for the financial support given during the development of these researches.
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6
Wound Healing and Antibacterial

Properties of Leaf Essential Oil
of Vitex simplicifolia Oliv.
from Burkina Faso
Magid Abdel Ouoba1, Jean Koudou2* , Noya Some3,
Sylvin Ouedraogo2,3 and Innocent Pierre Guissou1,2
1Unit of Teaching and Research (UFR) of Health Sciences, University of Ouagadougou,
2Laboratory of Chemistry of Natural Products, Faculty of Sciences,
University of Bangui, Bangui,

3Institute of Research in Health Sciences, CNRST, Ouagadougou,
1,3Burkina Faso
2Central African Republic
1. Introduction
Vitex simplicifolia Oliv. (Verbenaceae) is a perennial shrub or small tree which grows to a
height of aproximatively 8 m and is widely distributed from Egypt to Guinea. In Burkina
Faso, the plant is used for internal or external use to treat various diseases like skin diseases,
dermatitis, bilharzia, migraines, fever, aches, amoebiasis, sore teeth, colic, infant
tetanus(Nacoulma,1996). Our ethnobotanical investigations have revealed that this plant is
also used in the treatment of skin infections and wounds healing. In Burkina Faso, infectious
diseases are the leading cause of infant mortality (2.37%) and maternal (14.6%), therefore
they constitute public health problems. The treatment of skin diseases dates back to ancient
times, and many treatments were using medicinal plants. About 30% of traditional remedies
are used to treat wounds and skin lesions, compared to only 1-3% of modern drugs (Mantle
et al., 2001). The healing process is an immune response that begins after injury and takes
place in three stages: vascular and inflammatory stage, phase of tissue repair and phase of
maturation. A drug having simultaneously the potential antioxidant and antimicrobial
activities may be a good therapeutic agent to accelerate cicatrization and wound healing
[Houghton et al., 2005; Phillips et al., 1991; Heike et al., 1999]. Aromatherapy is now
considered to be another alternative way in healing people, and therapeutic values of
aromatic plants lie in their volatile constituents such as monoterpenoids, sesquiterpenoids
and phenolic compounds that produce a definite physiological action on the human body
[Bruneton, 1993].To the best of our knowledge, there is no report on pharmacological
studies of this plant. The present work reported results of a detailed investigation of
* Corresponding Author
cicatrization and antibacterial activities of the leaf essential oil with the aim to contributing
to the search for beneficial uses of this plant.
2. Materials and methods

2.1 Animals
The experiments were conducted using six male and female rabbits aged 7 months and
weighing between 10.05 and 20.06 kg, housed alone under 12h light-dark cycle, controlled
humidity (75%), and temperature (20-25C) conditions with free access to food and water
[Draize et al., 1944]. In addition, three other rabbits were taken as controls. The experiments
were carried out according to the method as described previously [Draize et al., 1944] in
accordance with the guidelines for the care of laboratory animals and ethical guidelines for
the investigation of experimental pain in conscious animals and revised by Official Journal
of France (1971/04/21).
2.2 Plant material and extraction

The leaves of V. simplicifolia Oliv were collected in January 2007 from the Kadiogo region,
village of Balgui, 10 km near Ouagadougou, Burkina Faso. A voucher specimen was
identified by Pr. Jeanne Millogo, botanist (University of Ouagadougou) and deposited at the
herbarium of IRSS of Ouagadougou.
Dried and powdered leaves (500g) were subjected to hydrodistillation for 4h with a clavenger-
type apparatus. The essential oil was collected and dried, after decantation, over anhydrous
sodium sulfate and stored in refrigerator at 4C for further use [Ouoba et al., 2009].
2.3 Reference bacteria strains

Microorganisms used in this study were:
Bacillus cereus LMG13569BHI, Listeria innocua LMG13568BHI, Staphylococcus aureus ATCC
25293BHI, Staphylococcus camorum LMG 13567BHI, Staphylococcus aureus ATCC9144BHI,
Enterococcus faecalis CIP103907BHI, Proteus mirabilis CIP104588, Shigella dysenteria CIP5451,
Salmonella enterica CIP105150, Escherichia coli CIP105182. These strains were identified by the
conventional methods and tested. Bacteria were obtained from stock cultures of the
laboratory of pharmacology and clinic biochemistry of CRSBAN, University of
Ouagadougou. The bacteria stock cultures were maintained on Mller-Hinton agar and
which were stored at 4C.
2.4 Wound healing activity

Assessment of the healing power of the oil was performed using the method [Draize et al.,
1944], on 6 male and female rabbits housed in individual cages. Both flanks of each rabbit
were shaved, deeply incised prior to application of the essential oil. Rabbits were fixed
horizontally from their ears and legs. One flank was covered with a compress soaked with
0.44 mg (0.50 ml) of the pure oil and held by a sticking-plaster, the other untreated flank
serving as control. The same operation was repeated with Cicatryl as a reference standard,
with a dose of 1 g per flank. The rabbits were returned to their cages after treatment.
Wound Healing and Antibacterial Properties
of Leaf Essential Oil of Vitex simplicifolia Oliv. from Burkina Faso 111
Observation of the evolution of wound healing versus time was carried out at 48h and 96h
after treatment. All of the tests were made in duplicate.
2.5 Antibacterial activity

Determination of the strain sensitivity
The test was performed using Mller-Hinton medium for bacteria using disk diffusion
method following the National Committee for Clinical Laboratory Standards methods
[Kiehlbauch et al., 2000]. Overnight broth cultures of each strain were prepared in nutriment
Broth (Diagnostic Pasteur, France). The final concentration of each inoculums was got
making dilution of each strain in 9 % NaCl solution. The turbidity of each inoculum was
compared with McFarland 0.5 solution. The final concentration of each inoculum
(approximatively 5.105 CFU / ml) was confirmed by viable count on Plate Count Agar
(Merck, Germany). 3l of essential oil was put on every disk (8 mm diameter).
Positive and negative growth controls were performed for every test. The plates were
incubated aerobically at 30C or 37 C for 24 hours. The bacterial sensitivity to the essential
oil was assessed by measuring the diameter of inhibition zone and recorded if the zone of
inhibition is greater than 9 mm. The inhibition zones were compared with that of
ampicilline (BIO-RAD Marne- la- coquette, France) and tetracycline (BIO-RAD Marne- la-
coquette, France). All of the tests were made in triplicate.
Determination of MIC and MBC values
A broth microdilution method was used to determine the minimum inhibitory
concentration (MIC) and the minimum bactericidal concentration (MBC) [Bassol et al.,
2003] All tests were performed in Mueller-Hinton Broth (Becton Dickinson, USA). A serial of
double of each essential oil was prepared in 96 well-plates over the range 0.03-8% (v/v). The
broth was supplemented with tween 80 at a concentration of 0.1% in order to enhance
essential oil solubility. The tween 80 was at the final concentration of 0.001% (v/v).
Overnight broth cultures of each strain were prepared in Nutrient Broth (Diagnostic
Pasteur, France) and the final concentration in each well was adjusted to 5 x 105 CFU/ml
following inoculation. The concentration of each inoculum was confirmed by viable count
on Plate Count Agar (Merck, Germany).
Positive and negative growth controls were included in every test. The tray was incubated
aerobically at 30 C (Reference Gram-negative strain) or 37 C (Reference and isolated
Gram-positive) and MICs were determined. The MIC defined as the lowest concentration of
the essential oil at which the microorganism tested does not demonstrate visible growth. To
determine MBCs, 10l suspension were taken from each well and inoculated in Mueller
Hinton Agar (Becton Dickinson, USA) for 24 h at 30 or 37 C. The MBC is defined as the
lowest concentration of the essential oil killing 99.9% of bacteria inocula [Michel Briand,
1986]. All tests were performed in triplicate.
Statistical analysis
Data were expressed as meanSEM. A one way variance was use to analyse data. p<0.01
represented significant difference between means (Duncans multiple range test).
3. Results
3.1 Analyses
GC and GC/MS analyses of the essential oil composition of Vitex simplicifolia were as
previously described [Ouoba et al., 2009] The oil contained monoterpenoids as predominant
(71.02%). Among monoterpene hydrocarbon, myrcene (53.50%) had been found as the major
component and four components were detected as predominant: -pinene (5.13%), -pinene
(2.48%) and -phellandrene (1.38%). In the oxygenated fraction, 10 monoterpenes (6.32%)
and 12 sesquiterpenes (5.58%) were present with linalool (4.70%) and humulen-1,2- epoxyde
(1.15%) as the major constituents. Among mono and sesquiterpenes three ketones are
detected as minor compounds piperitone (0.05%) cis-jasmone (0.11%) and salvia-4(14)en-1-
one (0.07%). No phenolic compound has been detected in the oil.
3.2 Wound healing activity

Experiments on rabbits showed that the oil has a healing effect. As shown in Table1, the
different stages of evolution of healing capacity of essential oil in comparison with those of
cicatryl and natural immunity of rabbit. The different stages of evolution of healing were
characterized by changes in the color of the wound over time, the closure of lacerations and
the absence of erythema and edema of the wounds.
wounds from 6 to 10
rabbits treated wounds at 48h wounds at 96h
days
vascular and inflammatory
maturation stage
stage
Essential oil (end of cicatrization)
tissue rpair stage
complete healing
maturation stage (start)
maturation stage
stage tissue repair stage (end)
Cicatryl (end of cicatrization)
tissue rpair stage maturation stage (start)
complete healing
tissue repair stage (end) maturation stage
Rabbits stage
maturation stage (end of cicatrization)
untreated tissue rpair stage
(start) complete healing
Table 1. Different stages of evolution of wounds healing.
3.3 Determination of the strain sensitivity

The results showed that almost of the bacterial strains were sensitive to Vitex simplicifolia
essential oil (Table2). Staphylococcus aureus ATCC9144 BHI (zone of inhibition 34.5mm) was
the most sensitive bacteria tested. Only Bacillus cereus LMG 13569 BHI was not sensible to
Vitex simplicifolia (zone of inhibition 8.5mm) (Fig1).
(1a) Salmonella enterica
(1b) Shigella dysenteria
(1c) Staphylococcus aureus

Fig. 1. Inhibition zones for some bacterial strains.
Reference strains Origin V. s Amp Te
Enterococcus faecalis CIP 103907 BHI CIP 21 35 20

Bacillus cereus LMG 13569 BHI LMG 8.5 31 22
Listeria innocua LMG 13568 BHI LMG 16.5 45 12
Staphylococcus aureus ATCC 25293 BHI ATCC 24.5 56 27
Staphylococcus camorum LMG 13567 BHI LMG 19.5 54 21
Staphylococcus aureus ATCC 9144 BHI ATCC 34.5 40 32
Escherichia coli CIP 105182 CIP 10.5 43 21
Proteus mirabilis CIP 104588 CIP 11.5 21 18
Shigella dysenteria CIP 5451 CIP 24.5 11 22
Salmonella enterica CIP 105150 CIP 28 36 24
V.s.: Vitex simplicifolia Amp: ampicilline Te: tetracycline
Table 2. Diameter of inhibition zone (mm) of bacteria growth.
3.4 Determination of antibacterial activity

The MICs and MBCs of Vitex simplicifolia essential oil were consigned in Table3. Five
bacterial strains were selected and tested because of their highest sensitivity to essential oil.
The oil inhibited the growth of these bacteria with MIC of 0.50% except for Staphylococcus
aureus ATCC 9144BHI that was more sensitive with MIC of 0.25%. The results of MBC
demonstrated a bacteriostatic effect.
Reference strains Origin MIC MBC MBC/MIC

Enterococcus faecalis
CIP 103907 CIP 0,5 8 16
Escherichia coli CIP
105182 CIP 0,5 4 8
Listeria innocua
LMG 135668 LMG 0,5 4 8
Staphylococcus
aureus ATCC 25293 ATCC 0,5 8 16
Staphylococcus
camorum LMG LMG 0,5 8 16
13567
Staphylococcus
aureus ATCC 9144 ATCC 0.25 1 4
BHI
Table 3. Minimum inhibitory concentration, minimum bactericidal concentration data
(%v/v) obtained by microdilution method.
4. Discussion
Wound healing is very complex, it involves a sequence of multifactorial events including
several cellular and biochemical processes. These processes aim to ensure the regeneration
and reconstruction of anatomical and functional disturbances of the skin[Chattopadhyay et

al., 2002]. The repair of damaged tissues occurs as a sequence of events that included
inflammation, proliferation and migration of different cell types [Sidhu et al., 1999]. At the
dose of 0.44 mg used only once the essential oil healed wounds for 96h. Essential oil of Vitex
simplicifolia accelerated the three stages of cicatrization process: vascular and inflammatory,
tissue repair and maturation. While at the dose of 1000 mg used only once, cicatryl exhibited
a complete healing with for 7 days against 10 days for the effect of natural immunity of
rabbit. In the phase of maturation a renewal of the skin was seen, the old skin started to fall
and made way for the new. The essential oil of Vitex simplicifolia exhibited a stronger healing
effect than cicatryl and natural immunity. This effect could be due to the presence of ketones
in the oil that activated the healing process with stimulating of new cell growth, reducing
old scare tissue in wound and were highly immunostimulatory [Willem, 2004]. The presence
of minor compounds as aldehydes and sesquiterpenes activated anti inflammatory, calming
and sedative effects. Thus, their low proportion allowed to consider possible synergistic
effects of these compounds in the oil. The significant presence of monoterpenoids in the oil
might cause analgesic, antioxidative, antiseptic effects and stimulating the immune system
[Mertz et al., 1993].
In other hand, the skin infections are in most cases due to staphylococci with the
pathogenic species is Staphylococcus aureus. It is responsible for suppurative infections,
widespread and food poisoning. Thus, wound infections are most common in developing
countries because of poor sanitation. Staphylococcus aureus, Shigella dysenteria, Salmonella
enterica, Escherichia coli are important microorganisms causing an infection of the wound
[Mansouri et al., 2011]. The best sensitivity to Vitex simplicifolia essential oil was,
respectively, obtained on Staphylococcus aureus ATCC 9144 BHI (34.5mm), Salmonella
enterica CIP 105150 (28mm), Shigella dysenteria CIP 5451(24.5mm), Staphylococcus aureus
ATCC 25293 BHI (24.5mm), Enterococcus faecalis CIP 103907 BHI(21mm). Following the
results in Table 2 the different strains were less sensitive to V.s than ampicilline, while
shigella dysenteria CIP 5451 was sensitive to V.s. The most important information was that
essential oil exhibited more activity on Staphylococcus aureus ATCC 9144 BHI (34.5mm),
Salmonella enterica CIP 105150 (28mm) Shigella dysenteria CIP5451(24.5mm) than
tetracycline and ampicilline (Shigella dysenteria CIP 5451, 11mm). The essential oil failed to
inhibit Staphylococcus aureus ATCC 9144 BHI at the lowest MIC 0.25%. The essential oil
was bacteriostatic for Staphylococcus aureus ATCC 9144 BHI, Escherichia coli CIP 105182
and Listeria innocua LMG 135668. The most resistant strains with highest MBC (8%) were
Enterococcus faecalis CIP 103907, Staphylococcus aureus ATCC 25293 and Staphylococcus
camorum LMG 13567. Considering MICs and MBCs no significant difference could be seen
between Gram-positive and Gram-negative bacteria. The chemical composition of the oil
consisted of various constituents. Therefore, the determination of the component
responsible for activity was very difficult. Furthermore the essential oil consists of
complex mixture of numerous constituents. Major or minor compounds might cause the
bacteriostatic and cicatrization activities exhibited, terpinene-4-ol and other monoterpenes
in essential oil may act as antiseptic, anti-inflammatory and antimicrobial: myrcene,
sabinene, terpinene, cadinene and limonene [Sinan Dayisoylu et al. 2009]. In addition, the
presence of -pinene, -pinene [Houghton Peter, 2004] terpinen-4-ol [Lee et al., 2001] and
-terpinene[Sonboli et al., 2005] were responsible of antioxidative and antiseptic activities

of essential oils studied. However, caryophyllene oxide, E-nerolidol humulene epoxide-
1,2 possessed antiinflammatory activity [Chavan et al., 2010; Yu-Tang et al., 2008; Wanjohi
Mwangi et al., 2009] Possible synergistic and antagonistic effects compounds in V.
simplicifolia essential oil should also be taken into consideration. These reports are
compatible with our results in the present study.
5. Conclusion
This study shows in vivo wound healing activity and in vitro bacteriostatic effect of Vitex
simplicifolia essential oil. The oil demonstrates the strongest wound cicatrization activity
than cicatryl and natural immunity. In addition the oil may help to prevent wound
infections and others such diarrhoea, dysentery and skin diseases. These results indicate
that the plant could be use as a natural potential remedy for healing wounds and
antiseptic agent. Further investigations will be performed by determination of analgesic,
antioxidant and anti inflammatory activities of the essential oil and to expand to other
Vitex species.
6. Remarks
1. Choice of rabbits: we have chosen rabbits because of they were available in the
laboratory and cheaper. They were also very easy to be used in the cicatrization effect
than mice and rats
2. The resolution of photographs depend of the quality of the apparatus, we deleted them
because we have not a best quality. We are sorry for the bad quality of photos. Thank
you for your understanding.
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Cinnamon (Cinnamomum osmophloeum) twig. Bioresource Technology 99, 3908-
3913
7
Use of Associated Chromatographic

Techniques in Bio-Monitored Isolation
of Bioactive Monoterpenoid Indole
Alkaloids from Aspidosperma ramiflorum
Talita Perez Cantuaria Chierrito1, Ananda de Castro Cunha1, Luzia Koike2,
Regina Aparecida Correia Gonalves1 and Arildo Jos Braz de Oliveira1
1Department of Pharmacy, State University of Maring, Maring, Paran State,
2StateUniversity of Campinas, Chemistry Institute, Campinas-SP,
Brasil
1. Introduction
The genus Aspidosperma (Apocynaceae) have been commonly used in folk medicine as
potential antimalarial agents; in the treatment of leishmaniasis; uterus and ovary
inflammations; as a contraceptive; in diabetes; stomach disorders; against cancer; fever and
rheumatism (Oliveira et al, 2009). It commonly grows in tropical America, extracted from
trees ranging 2 to 60 m in height. It is found in a variety of habitats from the dry fields of
south-central Brazil, Paraguay, and Argentina to the inundated river margins of the
Amazon basin (Tanaka, 2006). The main constituents of the Aspidosperma genus are indole
alkaloids, a class of substances with a wide range of pharmacological activities such as
cholinesterase inhibitors, analgesic, anti-inflammatory, bactericidal, oestrogenic, stimulant
and depressant of the central nervous system (CNS) (Zocoler et al, 2005).
1.1 Chromatographic systems in Aspidosperma genus

Several methods are available for the analysis and identification of known indole alkaloids.
Analysis of complex mixtures is frequently done by means of Thyn Layer Chromatography
(TLC), through comparison of Rf values obtained in different solvent systems, and also by
comparison between specific color reactions of components of the mixture and reference
compounds. TLC remains one of the preferred methods for qualitative analysis of known
compounds since it requires neither sophisticated equipment nor extensive sample
preparation. For quantitative analysis, High Performance Liquid Chromatography (HPLC)
systems linked to a UV detector are commonly used. By coupling HPLC to a photodiode
array UV detector makes it possible to combine the information over retention times and the
UV spectrum of each compound, and in some cases, it also enables the quantification of
overlapping peaks. Capillary Gas Chromatography (GC) analysis has been described for
several classes of alkaloids. A major advantage of GC over the above-mentioned methods is
its enhanced sensitivity and high resolution. Another advantage is its easy coupling to a
mass spectrometer that allows the identification of new and minor compounds of a mixture
without laborious isolation procedures, which makes it a particularly attractive method
when no decomposition due to the high temperatures applied in GC occurs (Dagnino, 1991).
This chapter shows different chromatographic techniques (TLC, Preparative Thyn Layer
Chromatography (PTLC), Classical Liquid Column Chromatography (CLCC), GC and
HPLC) to isolate and characterize indole alkaloids of Aspidosperma ramiflorum species.
1.1.2 Aspidosperma ramiflorum species

Aspidosperma ramiflorum Muell. Arg. species commonly known as guatambu, had been
studied in 1996 by Reis et al., who were able to isolate the monoterpenoid indole alkaloids,
ramiflorine A (1), ramiflorine B (2), 10-methoxy-geissoschizol (3) and -yohimbine (4). After
that, Oliveira 1999 isolated beyond these compounds the 16-(E)-isositrikine (5), all them
from stem barks (Figure 1).
Fig. 1. Major monoterpenoid indole alkaloids from Aspidosperma ramiflorum. Marvin was
used for drawing, displaying and characterizing chemical structures, substructures and
reactions, Marvin 5.4.1.1, 2011, ChemAxon available on ( http://www.chemaxon.com ).
The basic crude extract from stem barks of A. ramiflorum showed a good antileishmanial
activity (Ferreira et al., 2004), which we attributed to the presence of indole alkaloids, and
soon after, we described the fractionation, purification and isolation of alkaloids responsible
Use of Associated Chromatographic Techniques in Bio-Monitored Isolation
of Bioactive Monoterpenoid Indole Alkaloids from Aspidosperma ramiflorum 121
for the activity against Leishmania (L.) amazonensis (Tanaka et al., 2007). Our results revealed
that dimeric corynanthe alkaloids Ramiflorines A (1) and B (2) were responsible for the
activity against promastigote forms of L. amazonensis with significant activity (LD50 values of
16.3 1.6 g/ml and 4.9 0.9 g/ml, respectively). Tanaka et.al. (2006) evaluated the
antibacterial activities of the crude methanol extract, fractions obtained after acid-base
extraction and pure compounds from the stem barks of Aspidosperma ramiflorum and both
Ramiflorines showed significant activity against S. aureus (MIC = 25 g/mL) and E. faecalis
(MIC = 50 g/mL), with EC50 of 8 and 2.5 g/mL for Ramiflorines A and B, respectively,
against S. aureus.
2. General methods of alkaloids extraction

From crude alcoholics or hidroalcoholics extracts obtained from parts of the plant material,
two methods already described in the literature may be used for preliminary extraction of
alkaloids; both methods take into account the basic nature of these compounds in order to
concentrate them in pKas nearby and produce more purified fractions, preceding the phases
of isolation and identification of substances. The first method consists of a complete acid-
base partition (Figure 2), employing solvents such as chloroform or dichloromethane,
Fig. 2. Complete acid-base extraction from crude extract of A. ramiflorum.

extracting alkaloids in three levels of pH (acid, neutral and basic) (Marques et al., 1996). In
this extraction is possible to obtain four alkaloidal rich fractions: acidic fraction (1A), neutral
precipitate fraction (NP), neutral fraction (1B) and basic fraction (1C). The second consists of
a simplified acid-base partition (Figure 3), employing the same solvents, but with the
absence of extraction at neutral pH in order to eliminate sample neutral substances, getting
only two alkaloidal rich fractions: acidic fraction (1A) and basic fraction (1C) (Oliveira et al.,
1999; Tanaka et al., 2007).
Fig. 3. Simplified acid-base extraction from crude extract of A. ramiflorum.
3. Chromatographic analysis
Chromatography is a physical-chemical method of separation and several are available for
the analysis and identification of known indole alkaloids, the applicable to species A.
ramiflorum are described below.
3.1 Thin Layer Chromatographic TLC

3.1.1 Analytical TLC
As said before, analysis of complex mixtures is frequently done by TLC. It remains one of
the preferred methods for qualitative analysis of known compounds since it requires neither
sophisticated equipment nor extensive sample preparation (Dagnino et al., 1991). The
analytical TLC contributes greatly to a preliminary characterization of the alkaloidal extract
and fractions obtained from A. ramiflorum. Although the substances present in various parts
of this species, ramiflorine A (1), ramiflorine B (2), 10-metoxy-geissoschizol (3), -yohimbine
(4), ()-16-(E)-Isositsirikine (5), they are already known and described (Marques, 1998;
Marques et al, 1996; Oliveira, 1999; Ferreira et al., 2004), TLC plates at Rf values of substances
determined and revealed by UV light and specific reagents such as p-anisaldehyde and
Dragendorff allow a prior identification of substances quickly and conclusively. Under UV
light, substances with chromophore, i.e. conjugated systems absorb radiation and become
fluorescent, since the stationary phase contains fluorescence indicator, the reactive p-
anisaldehyde blush indole nucleus of purple and the reactive Dragendorff blush nitrogen
compounds of orange. Figure 4 shows two TLC plates with samples of A. ramiflorum
obtained by the team of Laboratory of Biotechnology of Synthetic and Natural Products of
the State University of Maring PR, Brazil (LABIPROS), under the following conditions:
stationary phase commercial chromatoplate of aluminum in normal phase silica gel 60 F254
fluorescence indicator; mobile phase (S1) chloroform, dichloromethane, ethyl acetate,
methanol in the proportions of (4:1:4.5:0.5 v/v) in environment saturated with ammonia
hydroxide; samples applied in strips by mini glass capillaries revealed with p-anisaldehyde
and Dragendorff, respectively, confirming the presence of monoterpene indole alkaloids
indlicos (MIA) in samples of the species A. ramiflorum through stains well demarcated and
staining characteristics.
A B
CE 1A PN 1B 1C PN FA CE 1A PN 1B 1C PN FA
Fig. 4. A- Alkaloidal factions of A. ramiflorum revealed with p-anisaldehyde; B- Alkaloidal

fractions of A. ramiflorum revealed with Dragendorff.
Variations on the combination of solvents and eluents generated changes in Rf values for the
same substance, as exemplified in Table 1, in which the same substances subject to the
eluent system 1 (S1) used by the team LABIPROS have Rf values distinct from the subject to
the eluent system 2 (S2) used by Oliveira (1999).
Substances
Stationary
Composition of Eluent Systems (v/v) applied on TLC Rf values
Phase
plates
Chloroform,dichloromethane, (1) 0.45
ethyl acetate, methanol in the (2) 0.32
Slica Gel 60
(S1) proportions of 4.5:4:1.5:0.5 +
F254
saturation with ammonia (3) 0.22
hydroxide
Chloroform, ethyl acetate, (1) 0.76
Slica Gel 60
(S2) methanol + saturation with (2) 0.30
F254
ammonia hydroxide (3) 0.36
Table 1. Variations of Rf values of the same substances spotted on TLC plates subject
different systems of eluents.
3.1.2 Preparative TLC PTLC

The difference between the PTLC and the TLC is that, while the last employed to separation,
identification and determination, not allows the retrieval of the sample, the preparative
chromatography is a purification process and allows the isolation of pure substances
contained in a mixture. Although there are many techniques developed for the isolation of
natural products, PTLC is pretty used, being considered a relatively simple and inexpensive
technique for separation and purification of small quantities of substances intended for
chemical and physical-chemical studies. Although the migration time and the removal of
the bands of substances are not easy and efficient, the LABIPROS team isolated by means of
PTLC, stem barks and leaves of A. ramiflorum the same substances already isolated by other
teams using different techniques (Marques et al, 1996; Ferreira et al, 2004). Figure 5 shows a
preparative board applied, eluted and reveled in UV light 254 nm, one of alkaloidal
fractions obtained from acid-base extraction of A. ramiflorum, composed of three main
substances, of class MIA. The conditions employed in this technique were the same as
described in the previous section for TLC, with the exception of the plates which were in
size 20 x 20 cm with 1.0 mm thickness of silica gel 60 F254 , and the sample was apllied in
continuous line, with the help of a cotton brush. Figure 6, presents the TLC made to monitor
and confirms the isolation by PTLC, demonstrated by natural spots in each application.
1
2
3
Fig. 5. PTLC alkaloidal fraction of A. ramiflorum composed of three majority substances of

class MIA, viewed by UV irradiation at 254 nm.
Fig. 6. TLC of the three major substances isolated by PTLC A. ramiflorum.
3.2 Classical liquid column chromatography

The majority of classical liquid column chromatography (CLCC) procedures for separating
indole alkaloids from Aspidosperma use an adsorbent stationary phase as silicagel and the
eluents employed reflect the polarity of alkaloids under investigation (Henrique et al., 2010;
Barbosa et al., 2010). The majority of indole alkaloids are tertiary bases with fairly low
polarity, so that mixtures containing a major part of a less polar solvent (e.g., chloroform,
toluene) with a small proportion of more polar solvent (e.g., acetone, ethanol, methanol) are
frequently cited (Henrique et al., 2010; Barbosa et al., 2010; Kobayashi et al., 2002). The use of
technical variations of CLCC as flash, vacuum, low and medium pressure liquid
chromatography has become common in the indole alkaloids isolation. Aspidosperma
ramiflorum alkaloidal extract was also fractionated on a silica gel column, elutting with
CHC13 with increasing amounts of MeOH (Marques et al., 1996).
3.3 Gas chromatography

Capillary gas chromatography (GC) analysis has been described for several classes of
alkaloids. The major advantage of GC over the above-mentioned methods is its enhanced
sensitivity and high resolution. Another advantage, it is easy coupling to a mass
spectrometer (Biemann, 2002) that allows the identification of new and minor compounds of
a mixture without laborious isolation procedures, which makes it a particularly attractive
method when no decomposition due to the high temperatures applied in GC occurs but the
widespread application of this technique is limited by volatility of more polar alkaloids.
The number of articles describing capillary GC analysis of underivatized alkaloids is
continuously increasing, including indole alkaloids (Dagnino et al., 1991; Gallagher et al.,
1995; Cardoso et al., 1997; Cardoso et al., 1998, Zocoler et al., 2005). Based on some of these
works we developed a simple, rapid, sensitive, and reproducible technique for the
qualitative and quantitative analyses of Aspidosperma alkaloids by capillary GC. The analysis
can be done because of a slightly polar and relatively short capillary column which we have
used here, with 10 m long, which enabled a rapid analysis but with a good resolution of
different components (Figure 7). Thus, we separated alkaloids representing different
chemical skeleton types from A. pyricollum, A. olivaceum, A. pyrifolium, A. polyneuron and A.
ramiflorum. Using capillary GC, we were able to achieve complete separations of the
Fig. 7. GC-MS chromatogram of basic fraction (1C). Peaks - 1: internal standard

(Tryptophol); 2: uleine; 3:Aspidofractine; 4: Apparicine; 5: 12-Demethoxy-aspidospermine; 6:
Aspidospermine; 7: Olivacine; 8: 15-Demethoxy-pyrifoline; 9: Pyrifolidine; 10: 15-Methoxy-
pyrifolidine; 11: Aspidofiline; 12: Pyrifolidine; 13: 15-Methoxy-pyrifolidine; 14:
Aspidoscarpine (Oliveira , 1999).
Fig. 8. GC-MS chromatogram of basic fraction (1C). Peaks 1: internal standard

(Tryptophol); 2: 1,2-Dihydro-olivacine; 3: Methoxy-1,2-dihydro-olivacine; 4: 10-Methoxy-
geissoschizol (Oliveira et al., 1999).
compounds as example in the A. olivaceum analysis, Figure 7. The mass spectrum of each
individual peaks was determined by GC-MS under identical conditions, and the expected
molecular weight and fragmentation patterns were observed for all the compounds. For A.
ramiflorum analysis by GC five indole alkaloids were isolated and characterized as follows:
10-methoxy-geissoschizol (3), (E)-isositsirikine (5), ramiflorine A(1) e ramiflorine B (2) from
stem barks and -yohimbine (4) from seeds, but only 10-methoxy-geissoschizol, (E)-
isositsirikine and -yohimbine could be used as standards in GC analysis as shown in
Figure 8. The compounds ramiflorine A and ramiflorine B are dimeric basic alkaloids, with
high molecular weight and less volatile and they are therefore not analyzable under the
used conditions. For this reason, we developed a HPLC analysis for A. ramiflorum alkaloids
which is shown below.
3.3.1 Gas chromatography analysis

The stem barks of A. olivaceum and A. ramiflorum were extracted on EtOH:H2O (70:30) and
submitted an acid-basic extraction procedure in agreement with described in Figure 3. The
basic and acid chloroform extracts were weighted (30 mg), which were diluted in 9 mL of a
solution of CH2Cl2:MeOH (80:20, v/v). This mixture were homogenized and submitted to a
filtration in a small column of silica-gel 60 Merck (1g) and were eluted with a solution of
CH2Cl2:MeOH (80:20, v/v). The filtrate was evaporated and the residue was dissolved in 2.5
mL of this solution and subsequently analyzed by GC or GC-MS. Standard compounds
were obtained from Aspidosperma (Oliveira, 1999) using classic phytochemical extraction and
separation methods and were identified by comparison of physical (mp, []D) and
spectroscopy data (UV, 1H and 13C NMR) with literature values. The purity of the
compounds was determined by gas chromatography using FID and MS detector. The GC
analyses were done using a Hewlett-Packard 3396A gas chromatograph equipped with a
FID. A DB-5 capillary column (12 m, 0.25 mm i.d. x 0.2 mm film thickness, J & W Scientific,
CA) was used for this analysis. Hydrogen was utilized as the carrier gas, and the optimized
oven temperature program was 100-225 C, linear increase 15 C/min, after 225-260 C in
linear increase 2.5 C/min, and 260 C held for 10 min. Temperatures of the injector port and
detectors were held at 270 C. The injectors were operated in split mode (1:50). One
microliter of all solutions was injected in all analysis. GC-MS analysis was carried out on HP
5970B gas chromatograph equipped with a MS detector. The temperature program was the
same used for GC-FID analysis.
3.4 High Performance Liquid Chromatography

Despite the large number of Aspidosperma alkaloids isolated and their biological importance,
there are very few reports on the HPLC analysis of extracts of species from this genus
(Jacome et al., 2003; Jacome et. al., 2004). This can be explained due to HPLC that has been
used in great extent to the analysis of different types of alkaloids, problems still exist,
because analysis of this compound still occur with a low efficiency, large and asymmetric
peaks, attributed to the dual retention mechanism (Philipson et al., 1982; Verpoorte &
Baherheim, 1984; Stockigt et al., 2002). For A. ramiflorum analysis by HPLC, the three majors
indole alkaloids were isolated and characterized as follows: 10-methoxy-geissoschizol (3),
ramiflorine A(1) and ramiflorine B (2) from stem bark and -yohimbine (4) from seeds,
which were used as standards in HPLC analysis, as shown in Figures 9A and B. To
minimize the negative effects attributed to the dual retention mechanism, a methodology
described by Giroud el al. (1991) to Chinchona legderiana was adapted to A. ramiflorum
alkaloidal extract analysis, with some minor modifications, which allowed a good
separation of it majority compounds (Figure 9B). The main modification made was the
addition of octane sulfonic acid to mobile phase. The presence of this component allowed
that the separation to be mediated by more types of interaction, because it acts by an ion
pair formation mechanism, increasing the resolution and efficiency of analysis.
Fig. 9. A: high performance liquid chromatography (HPLC) chromatogram of standards

mixture isolated from Aspidosperma ramiflorum; B: HPLC chromatogram of alkaloidal extract.
Peaks 1: internal standard (tryptophol); 2: 10-methoxy-geissoschizol; 3: ramiflorine A; 4:
ramiflorine B.
3.4.1 High Performance Liquid Chromatography analysis

For HPLC analysis, the crude extract of A. ramiflorum (Ferreira et al., 2007) was dissolved in
CH2Cl2:MeOH (80:20 v/v) and 10 L were injected into a Waters -Bondapak RP-18 (reverse
phase, 4.6 mm x 250 mm) column at 40C. Solvent A was 100 mmol/L ammonium formate
in 0.12% octane sulfonic acid (v/v), formic acid and acetonitrile (88:4:8, v/v), while solvent B
consisted of 100 mmol\L aqueous ammonium formate containing 0.12% octanesulfonic acid
(v/v)/formic acid/acetonitrile (64:4:32, v/v). The separation was carried out using a
mixture of solvent A and, a progressively increasing amount of B (0, 10, 40, 90, 100%) during
60 min. The flow rate was 1.3 ml min-1. The effluent was monitored with a photodiode-
array detector with windows at 222 nm and 254 nm and also by mass spectral analysis of
isolated eluates.
4. Conclusions
The development of the TLC solvent system for Aspidosperma ramiflorum alkaloids at the
beginning of this article clearly shows that TLC and PTLC as a routine and classical method
appreciated in alkaloid separation techniques, can still be optimized with introduction of
new methodologies as desorption electrospray ionization (DESI) which can permit coupled
TLC with mass spectrometry (Jackson et al., 2009). This is not necessarily true for alkaloid
determination by GC, because decomposition can occur due to the high temperatures
applied and however widespread application of this technique is limited by volatility of
more polar alkaloids. HPLC is a classical method for alkaloids separations and allowed a
good separation of majority compounds in A. ramiflorum alkaloids but can still be optimized.
However, the pre-purification of crude alkaloid extract will be a crucial step for all analytical
procedure described. The applicability of different chromatographic techniques for the
separation and identification of crude mixtures of bioactive A. ramiflorum indole alkaloids
has thus been demonstrated.
5. References
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Aspidosperma illustre (Apocynaceae). J. Braz. Chem. Soc., 21, 1434-1438.
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Alkaloids to Heparin. J Am Soc Mass Spectrom, 13, 1254-1272.
Cardoso, C. A. L.; Vilegas, W. & Honda, N. H. (1998).Qualitative determination of indole
alkaloids, triterpenoids and steroids of Tabernaemontana hilariana J. Chromatogr., A.
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Cardoso, C. A. L.; Vilegas, W. & Pozetti, G. L. (1997).Gas chromatographic analysis of indole
alkaloids from Tabernaemontana hilariana. J. Chromatogr.,A, 788, 204.
Dagnino, D., J. Schripsema, A. Peltenburg, R. Verpoorte & K. Teunis. (1991). Capillary gas
chromatographic analysis of indole alkaloids: investigation of the indole alkaloids
present in Tabernaemontana divaricata cell suspension culture. J. Nat. Prod. 54:1558
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Ferreira, I., Leon, L., Gobbi Filho, L., Lonardoni, M., Silveira, T., Machado, G. & Oliveira, A.,
(2004). Antileishmanial activity of alkaloidal extract from Aspidosperma
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Gallagher C. A.; Hough L. B.; Keefner S. M.,; Seyed-Mozaffari A.; Archer S.; & Glick S. D.,
(1995). Biochemical Pharmacology, Vol. 49, No. 1, pp. 73-79.
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W. M. A. & vandergreef, J. (1991). Thermospray liquid-chromatography mass-
spectrometry (TSP LC MS) analysis of the alkaloids from Cinchona in vitro
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Aspidosperma vargasii e A. desmanthum. Qumica Nova, 33, 284-287.
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Jcome, R. L. R. P.; Oliveira, A. B.; Raslan, D. S. & Wagner, H. (2004).Estudo qumico e perfil
cromatogrfico das cascas de Aspidosperma parvifolium A. DC. (Pereira). Quim.
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Jcome, R. L. R. P.; Souza, R. & Oliveira, A.B. (2003).Comparao cromatogrfica entre o
extrato de Aspidosperma parvifolium e o fitoterpico "Pau-Pereira". Rev. Bras.
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(2002). Subincanadines A-C, Novel Quaternary Indole Alkaloids from Aspidosperma
subincanum. J. Org. Chem., 67, 6449-6455.
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ramiflorum. Phytochemistry, v. 41, n. 3, pp.963-967.
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CG/MS e HPLC: Anlise Qualitativa e Quantitativa. Teste Bioautogrfico; Cultura
de Tecidos e Clulas Vegetais e rota de Preparao dos Compostos Dimricos
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8
Secondary Metabolites
Tnia da S. Agostini-Costa1, Roberto F. Vieira1,
Humberto R. Bizzo2, Dmaris Silveira3 and Marcos A. Gimenes1
1Embrapa Genetic Resources and Biotechnology, Braslia
2Embrapa Food Technology, Rio de Janeiro,
3Health Sciences Quality, University of Brasilia, Braslia,
Brazil
1. Introduction
Secondary metabolites are organic molecules that are not involved in the normal growth
and development of an organism. While primary metabolites have a key role in survive of
the species, playing an active function in the photosynthesis and respiration, absence of
secondary metabolites does not result in immediate death, but rather in long-term
impairment of the organisms survivability, often playing an important role in plant
defense. These compounds are an extremely diverse group of natural products synthesized
by plants, fungi, bacteria, algae, and animals. Most of secondary metabolites, such as
terpenes, phenolic compounds and alkaloids are classified based on their biosynthetic
origin. Different classes of these compounds are often associated to a narrow set of species
within a phylogenetic group and constitute the bioactive compound in several medicinal,
aromatic, colorant, and spice plants and/or functional foods.
Secondary metabolites are frequently produced at highest levels during a transition from
active growth to stationary phase. The producer organism can grow in the absence of their
synthesis, suggesting that secondary metabolism is not essential, at least for short term
survival. A second view proposes that the genes involved in secondary metabolism provide
a genetic playing field that allows mutation and natural selection to fix new beneficial
traits via evolution. A third view characterizes secondary metabolism as an integral part of
cellular metabolism and biology; it relies on primary metabolism to supply the required
enzymes, energy, substrates and cellular machinery and contributes to the long term
survival of the producer (Roze et al, 2011).
A simple classification of secondary metabolites includes tree main groups: terpenes (such
as plant volatiles, cardiac glycosides, carotenoids and sterols), phenolics (such as phenolic
acids, coumarins, lignans, stilbenes, flavonoids, tannins and lignin) and nitrogen containing
compounds (such as alkaloids and glucosinolates). A number of traditional separation
techniques with various solvent systems and spray reagents, have been described as having
the ability to separate and identify secondary metabolites. This chapter proposes to discuss
major secondary metabolites classes (terpenoids, phenolic compounds and alkaloids) with
different chemical structures and functions being screened, separated, fractionated, purified
or analyzed using various adsorbents and eluents through column chromatography (CC)
and thin layer chromatography (TLC).
2. Terpenoids
Terpenoids are the largest and most diverse family of natural products, ranging in structure
from linear to polycyclic molecules and in size from the five-carbon hemiterpenes to natural
rubber, comprising thousands of isoprene units. All terpenoids are synthesized through the
condensation of isoprene units (C5) and are classified by the number of five-carbon units
present in the core structure (Mahmoud et al. 2002). Many flavor and aromatic molecules,
such as menthol, linalool, geraniol and caryophyllene are formed by monoterpenes (C10),
with two isoprene units, and sesquiterpenes (C15), with three isoprene units. Other bioactive
compounds, such as diterpenes (C20), triterpenes (C30) and tetraterpenes (C40) show very
special properties and will be also discussed in this chapter.
2.1 Monoterpenes and sesquiterpenes (Plant volatiles)

Plant volatiles are typically lipophilic liquids with high vapor pressures. Non-conjugated
plant volatiles can cross membranes freely and evaporate into the atmosphere when there
are no barriers to diffusion. The number of identified volatile chemicals synthesized by
various plants exceeds 1000 and is likely to grow as more plants are examined with new
methods for detecting and analyzing quantities of volatiles that are often minute (Pichersky
et al. 2006; Dudareva et al., 2004). Studying the volatile fraction requires analytical methods
and technologies that not only evaluate its composition exhaustively but also monitor
variations in its profile and detect trace components characterizing the plant being
investigated (Bicchi et al., 2011).
The gas chromatography (GC and GC-MS) is a very powerful analytical tool for the
identification of essential oil components. However, GC-MS has its limitations. Isomers
usually give very similar mass spectra. This is particularly true for terpenes and even more
for sesquiterpenes. Therefore, a favorable match factor between mass spectra is not
sufficient for identification (Zellner et al., 2010). Retention indices have been used, together
with mass spectrometry, for the proper identification of essential oils composition.
Misidentification is not rare, however, either if a non-authentic mass spectra library is used,
which means a database built with data from the literature, not from the analysis of real
standards, or by misuse of retention indices (Joulain & Knig, 1998). CC has been applied to
solve this problem. After isolation, a NMR analysis can be performed for the unknown or
suspect compound, so that the correct mass spectrum and retention index can be recorded.
Despite the advances in analytical methods to evaluate the composition of essential oil, CC
remains a powerful technology for separation and characterization of specific compounds of
interest. Column chromatography has been largely used and reported for searching and
identification of new molecules, sometimes associated with their antimicrobial, antibacterial
and antifungal activities. Also, this technique has been successfully used to obtain sufficient
amounts of a substance for the investigation of its biological properties and allowing the
detection of its olfactory properties. Isolation is also applied to and, very important for
volatiles, to evaluate its odor.
Secondary Metabolites 133
2.1.1 Compound identification

The major constituents present in the volatile oils of different aromatic species may also be
isolated or fractionated by silica gel on preparative TLC or CC. For example, the essential oil
of Tanacetum chiliophyllum was subjected to silica gel CC, using a solvent mixture of n-
hexane and ethyl acetate, to isolate one of its major components, dihydro--cyclogeranyl
hexanoate (Salamci et al, 2007).
Djabou et al. (2010) have characterized the essential oils of Teucrium massiliense L. from
Corsican and Sardinian islands, using a combination of capillary GC/retention indices,
GC/MS and 13CNMR spectroscopy after fractionation on CC. A mixture of all Corsican oil
samples was submitted to flash chromatography [FC; silica gel, elution with n-pentane, then
with diethyl ether]. The polar fraction was separated on silica gel and 14 fractions were
eluted with a mixture of n-pentane and diethyl ether of increasing polarity to give the major
components: 6-methyl-3-heptyl acetate, 3-octyl acetate, isobutyl isovalerate, germacrene D
and linalool. Successive CC revealed the unknown compound 6-methyl-3-heptyl acetate.
Chemical investigations on the essential oil of Lippia integrifolia performed by CC (silica gel
using n-hexane with increasing amounts of diethyl ether), followed by HPLC, GCMS, 1H
and 13C-NMR spectroscopy led to the identification of 78 components. A new sesquiterpenic
alcohol, trans-africanan-1-ol, was identified (Coronel et al. 2006).
Sutour et al. (2008) studied the essential oil of Mentha suaveolens ssp. insularis (Req.) Greuter,
finding pulegone to be the major constituent. However, the second most abundant
component of the essential oil remained unknown, being isolated by repeated
chromatography on silica gel and submitted to a full set of NMR experiments, and identified
as cis-cis-p-menthenolide. Fractions were eluted with a gradient of solvents of increasing
polarity (pentane:diethyl ether 100:00:100).
The essential oil from the leaves of Piper hispidinervum, a native species from the Amazon, is
very rich in safrole (Maia et al., 1987). During an extensive agronomical study with this
species, a population produced an essential oil rich in a different phenylpropanoid (up to
78%). The mass spectrum was identical to that of myristicin (Figure 1). However, a
difference of near 30 units in retention index between myristicin and the phenylpropanoid
was strong evidence that it was another compound, probably a myristicin isomer. No
retention indices were available for the two possible isomers, croweacin and sarisan. For
identification, the unknown compound was isolated by CC on silica gel and eluted with
hexane-ethyl acetate mixtures. After 1H and 13CNMR studies, it was identified as sarisan
(Bizzo et al., 2001).
Fig. 1. Possible isomers of myristicin from the oil of a population of Piper hispidinervum;
sarisan was the actual compound present.
Evaluating the essential oils from the leaves of 40 individuals of Croton cajucara Benth. from
a germplasm bank in Manaus (State of Amazonas, Brazil), Quadros et al. (2011) observed
some plants, instead of linalool, produced an oil rich in a hydroxylated sesquiterpene. The
mass spectrum was very similar to that of 5-hydroxycalamenene. After the last edition of
Adams' reference book (Adams, 2007), it was verified that the retention index of the
sesquiterpenic alcohol did not correspond to that of 5-hydroxycalamenene. The oil was
chromatographed over silica gel with hexane and hexane-ethyl acetate mixtures. The
fraction containing the compound of interest was re-chromatographed on a silica gel
preparative TLC plate with hexane-ethyl acetate (90:10). The purified compound was
extracted from the silica with chloroform. Two clear singlets in the aromatic hydrogens at
6.56 and 6.94 ppm instead of a doublet pointed to a 7-hydroxy-substituted structure (Figure
2). Chemical shifts were in good agreement with published data for cis-7-hydroxycalamene.
Fig. 2. Hydroxylated sesquiterpenes from Croton cajucara.
Sometimes, despite all careful efforts and extensive study, wrong structure assignment is
published. For example, a new triquinane sesquiterpenic alcohol was isolated from the
essential oil of Anemia tomentosa var. anthriscifolia by CC on silicagel with a hexane-ethyl
acetate gradient. A new structural formula, namely ()-epi-presilphiperfolan-1-ol, was
initially proposed, after extensive 1D- and 2D-NMR analyses, as well as by GCMS, chiral
bidimensional GC, dehydration reactions, and a comparative (GIAO/DFT) theoretical study
of the 13C NMR chemical shifts (Pinto et al., 2009a). Further examination by X-ray diffraction
and vibrational circular dichroism studies, however, led to its reassignment to ()-9-epi-
presilphiperfolan-1-ol (Figure 3), also a new compound. Its absolute configuration was
established as 1S,4S,7R,8R,9S (Joseph-Nathan et al., 2010).
Fig. 3. Isomers of ()-presilphiperfolan-1-ol: the 9-epi-isomer was isolated from Anemia

tomentosa var. anthriscifolia essential oil.
2.1.2 Olfactory analysis

Aroma concentrate separated from an aqueous solution of Haze honey by adsorptive CC
had stronger aroma intensity than that separated by other methods. Fractions separated by
preparative GC were sniffed to evaluate the sensory importance of the volatile compounds
of Haze honey. Benzeneacetaldehyde, linalool, phenethyl alcohol, p-cresol, p-anisaldehyde,
methyl-p-anisaldehydes, trimethoxybenzene, 5-hydroxy-2-methyl-4H-pyran-4-one, and lilac

aldehydes seemed to contribute to Haze honeys aroma (Shimoda et al., 1996).
Shimoda et al. (1995) reported that a column extraction method was applied to the
separation of volatile compounds from infusions of green tea and black tea, wherein their
aromas degrade during distillation even under reduced pressure, and from sake, wherein
ethyl alcohol disturbs a quantitative separation of volatile compounds.
Linalool is a very frequent terpenoid in essential oils, usually responsible for the scent of a
specific plant, such as mint, basil, and other plant species. In order to evaluate the effect on
humans of inhalation of linalool enantiomers (Figure 4), repeated flash chromatography was
used to isolate R-(-)-linalool from lavender essential oil, while (S)-(+)-linalool was obtained
from coriander oil and commercial linalool (Sugawara et al. 2000).
Fig. 4. Linalool enantiomers.
The Australian finger lime (Citrus australasica), an endemic Australian species, is an unique
citrus fruits in terms of their size, shape and aroma. The fractionation of finger lime peel oil
by chromatography on silica gel (with a gradient of pentane:ether) was able to identify a
high number of terpenyl esters enriched in a medium polar fraction. This included
citronellyl and geranyl esters, commonly found in lime peel oils, but also several less
common (Z)-3-hexenyl esters and bornyl esters. In finger limes these compounds, together
with isomenthone, menthol, carvone, cis-3-hexenol and methyl salicylate, may also
contribute to the characteristic fresh green aroma of the fruits (Delort et al., 2009).
L-menthyl-L-lactate [(2S, 1R, 2S, 5R)-2-isopropoyl-5-methylcyclohexyl 2-hydroxy-
propanoate, LM-LL] is widely used as a cooling compound in mint flavors, fruit flavors, oral
care products, confections and beverages. L-menthyl-L-lactate was identified in
dementholized cornmint oil from India by comparing mass spectrum and retention time
with a reference sample on two columns. Separation was achieved by increasing polarity of
the hexanemethyl-tert-butyl-ether (MTBE) gradient on a flash chromatography column
packed with silica gel. It is worth noting that L-menthyl-L-lactate was identified in M.
arvensis oils from India but not in M. piperita oils from the USA. Model experiments proved
that LM-LL is formed during water vapor distillation of mint leaves in the presence of lactic
acid. Lactic acid is spontaneously formed when mint herb is stored for some days in a
humid environment. A prolonged storage of damp mint herb may increase formation of
lactic acid and thus give rise to the formation of LM-LL during distillation. The presence of
lactic acid will be influenced by the agricultural practice employed (Gassenmeier, 2006).
Gas chromatography-olfactometry (GCO), gas chromatographymass spectrometry (GC

MS) and preparative CC were used to identify the key odorants present in laboratory-
extracted clementine oil from Spain. Almost 50 odorants were identified using GCO, many
of which were unsaturated aldehydes with high odor spectrum values. - and -sinensal,
trans-4,5-epoxy-(E)-2-decanal, (E,Z)-2,6-dodecadienal and linalool were found to dominate
clementine oil aroma. Enrichment of the oxygenates using preparative CC provided further
identification of a total of 50 aldehydes, which were originally present in the oil at
concentrations not high enough to produce a response using GCO (Chisholm et al., 2003).
2.1.3 Biological activities

Human enteropathogens (Campylobacter jejuni, Campylobacter coli, and Campylobacter lari
strains) were inhibited by the essential oil of wild Daucus carota L. DCEO. Major components
of the essential oil responsible for the antibacterial activity were isolated on CC and
identified as (E)-methyl-isoeugenol and elemicin (Rossi et al., 2007).
Confertifolin (6,6,9a-trimethyl-4,5,5a,6,7,8,9,9a-octahydronaphtho[1,2-c] furan-3 (1H)-one),
isolated from the essential oil of Polygonum hydropiper L. (Polygonaceae) leaves using CC,
showed activity both against bacteria and fungi. The oil was chromatographed on a column
packed with silica gel and eluted with hexane-ethyl acetate gradient solvent system with
increasing polarity, yielding 117 fractions (Duraipandiyan et al., 2010).
The essential oil of Daucus crinitus Desf. was submitted to flash chromatography (silica gel,
using petroleum ether with increasing amounts of diethyl ether as eluent), and fractions were
analyzed by GC-MS. Those containing the isochavicol esters were gathered for the preparation
of isochavicol. The antibacterial and antifungal activities of the whole essential oil, of these two
esters, and of isochavicol itself, were investigated against a wide range of bacteria and fungi.
Additionally, their antimalarial and antiradical properties were also evaluated, showing an
interesting antiplasmodial activity of isochavicol (Lanfranchi et al., 2010).
Patchouli oil obtained from Pogostemon cablin (Blanco) Benth and its main constituent,
patchouli alcohol, were tested for their repellency and toxicity against Formosan
subterranean termites (Coptotermes formosanus Shiraki). Both were found to be toxic and
repellent. The fraction containing patchouli alcohol was purified by silica CC, and its purity
was determined by GC-MS. Unusual tissue destruction was noted inside the exoskeleton of
the termite after patchouli alcohol was topically applied to the dorsum (Zhu et al., 2003).
A successful breeding program of Cannabis sativa cultivars with a low content of the
hallucinogenous D-9-tetrahydrocannabinol (THC) is a prerequisite to avoid drug abuse of
hemp. Four TLC systems for analyzing cannabinoids were compared, being able to identify
the absence of THC in the hemp essential oils from five commercial fiber varieties. The
system using HPTLC, RP-18 and acetonitrile-water (9:1) achieved the best separation of
hallucinogenous and non-hallucinogenous cannabinoids (Novak et al., 2001).
Nine fractions of essential oil extracted from Thymus praecox were separated by silica gel CC
and the fractions were demonstrated to have antioxidant activity (Ozen et al, 2011). The
essential oil of Coriandrum sativum was submitted to silica gel on dry-CC, resulting in six
fractions. Essential oil and its fractions presented antimicrobial potential against Candida
yeast infections (Begnami et al, 2010). Essential oils, distilled from seeds of Coriander sativum
and Carum carvii and from leaves of Ocimum basilicum, were fractionated by silica gel over
CC and tested in the laboratory for volatile toxicity against three stored rice pests. Fractions,
where combinations of products occurred with or without other minor compounds, were
often more toxic than any one compound alone (Lopez et al, 2008).
The main component of the essential oil of Anemia tomentosa var. anthriscifolia, ()-9-epi-
presilphiperfolan-1-ol (Figure 3) was isolated by CC over silica gel, eluted with hexane and
hexane-ethyl acetate (95:5), then tested against Mycobacterium tuberculosis (H37Rv) and M.
smegmatis. A minimum inhibitory concentration of 120 g/ml was recorded for M.
tuberculosis (Pinto et al., 2009b).
2.2 Diterpenes and sesterterpenes

The diterpene compounds arise from geranylgeranyl diphosphate, and present 20 carbon
units in their basic skeletal type. One of the simplest and most important of the diterpenes is
phytol (Figure 5), a reduced form of geranylgeraniol, which forms the lipophilic side-chain
of the chlorophylls (Vetter and Schrder, 2011).
Cyclization reactions of geranylgeranyl diphosphate led to many structural types of
diterpenoids, presenting a large range of polarity nature, from apolar hydrocarbons such as
cembrene (Villanueva and Setzer, 2010), a 14-membered ring, to fully oxidized skeleton of
virescenoside (Figure 5), isolated from marine fungus Acremonium striatisporum (Ebel, 2010).
OH
phytol
HO
H
HO
H OH
O O OH
OH
cembrene OH
virescenoside W OH
Fig. 5. Diterpenes phytol, cembrene and virescenoside W.
Sesterterpenes (C25) may be the least common group of terpenoids. This class of compounds
arises from geranylfarnesyl diphosphate (Figure 6), which by cyclization can give rise to
various skeletal types, presenting different oxidation levels and several biological activities.
Although many examples of these natural terpenoids are known, they are primarily isolated
from fungi and marine organisms.
Considering the large range of polarity nature presented by both diterpene and
sesterterpene, the isolation and purification techniques vary and can be classic TLC,
preparative thin-layer chromatography (PTLC), CC, flash chromatography (FC), or modern
high performance liquid chromatography (HPLC), multiflash chromatography, vacuum
liquid chromatography (VLC), solid-phase extraction and others (Lanas, 2008). However,
the most important factor that has to be considered before designing an isolation protocol is
the nature of the target compound, such as solubility (hydrophobicity or hydrophilicity),
acidbase properties, charge, stability, molecular size. Taking these factors into account, the
choice of chromatographic methods and the stationary phases to be used are important for
the design of a purification system.
Silica gel-based material is the most usual stationary phase. However, polyamide,
Sephadex LH-20, alumina (Al2O3), florisil and others are also used, mainly for isolation of
more polar compounds (Ajit-Simh et al., 2003). The air-dried and ground roots of Peltodon
longipes were extracted with hexane. The methanol soluble fraction of the hexane crude
extract was subjected to open CC on silica gel 60 eluted with hexane/ethyl acetate step
gradient. After subsequent purification, several abietane diterpenes were isolated, including
royleanone, inuroylleanol, deoxyneocryptotanshinone and 7-ethoxyroyleanone (Figure 6)
(Fronza et al., 2011).
OPP
OH
O O
HO
O
OH
O O
geranylfarnesyl diphosphate royleanone inuroylleanol
OH
OH
O O
O O
deoxyneocryptotanshinone 7-a-ethoxy royleanone
Fig. 6. Geranylfarnesyl diphosphate and abietane diterpenes from Peltodon longipes.

The sesterterpenes 24-O-methylmanaolide and 24-O-ethylmanaolide (Figure 7), besides

others, were isolated from the sponge Luffariella cf. variabilis. Briefly, the frozen sponge
tissue was extracted by methanol:chloroform (1:2). The crude extract was successively
partitioned between equal volumes of aqueous methanol and a solvent series of hexane,
carbon tetrachloride and chloroform. The hexane fraction was subjected to silica gel
columns, using eluents of increasing polarity from hexane: ethyl acetate (Gauvin-Bialecki et
al., 2008).
Olefins can form co-ordination products with silver ions, and this ability has been used for
chromatographic separation of several terpenes, mainly those with a carbon skeleton higher
than C20. The procedure to prepare the modified silica was described as follows: Silver
nitrate (AgNO3) in water (1:2 w:v) is added to silica. After water evaporation, the residue is
dried in oven at 130 oC for 15 h, resulting in an almost white powder that should be stored
in a dark bottle. Column packing is carried out in the same way as ordinary silica gel
column; however, should be wrapped in dark paper or built with amber glass (Norin and
Westfelt, 1963).
Methyl ester from kaurenoic acid, iso-kaurenoic acid and grandiflorenic acid (Figure 7) were
purified by using argentum silica (Batista et al., 2010). The diterpene acids were isolated
from aerial parts of Wedelia paludosa. The plant material was extracted by percolation first
using hexane, followed by ethanol. The crude ethanol extract was chromatographed over
silica gel column. A mixture of these three compounds was obtained and further submitted
to isocratic CC on silica gel impregnated with 20% of AgNO3, eluting with hexane:diethyl
ether 97:3 (Batista et al., 2010).
O
O O O
R
OH
COOH
R= CH3 24-O-methylmanaolide
R = CH3CH2 24-O-ethylmanaolide kaurenoic acid
COOH COOH
iso-kaurenoic acid grandiflorenic acid
Fig. 7. Sesterterpenes 24-O-methylmanaolide and 24-O-ethylmanaolide from Luffariella cf.

variabilis and diterpene acids isolated from Wedelia paludosa.
Polyamide 6 (-aminopolycaprolactam) has been used in our laboratory to isolate polar

natural products due to its low cost and re-usability. The pre-treatment of polyamide is
carried out as follows: before column package, polyamide should be washed with methanol,
rinsed with distilled water, and poured into the glass column, using an approximate
proportion of 1 kg of polyamide to 10 L of each solvent, in order to eliminate oligomers and
other impurities (Ye et al., 2011). After elution with H2O until column stabilization, elution is
performed with H2O and a miscible polar solvent (usually methanol) gradient. In our
experience, the same polyamide column can be re-used to obtain an additional amount of
the obtained substance after the followed procedure: the column should be washed starting
with 100% methanol to 100% H2O. We did not observe any substantial reduction in quality
of column performance for five consecutive recovery procedures, using the same sample.
A polyamide column was used in the first step to obtain diterpenes from aerial parts of
Euphorbia pannonica. The plant material was extracted by methanol at room temperature.
The obtained crude extract was partitioned by H2O and dichloromethane and the organic
fraction was chromatographed on a polyamide column with mixtures of methanol and H2O
(2:3, 3:2 and 4:1) as eluent. The fraction obtained with methanolH2O (3:2) was subjected to
silica gel VLC using a gradient system of cyclohexane, chloroform and acetone (3:2:0, 1:1:0,
2:3:0, 3:7:0, 1:4:0, 10:40:1, 4:16:1 and 1:4:1). After purification, two tigliane-type diterpenes,
4,12-dideoxy(4)phorbol-20-benzoate-13-isovalerianate and 4,12-dideoxy(4)phorbol-20-
benzoate-13-isobutyrate (Figure 8), were isolated (Sulyok et al., 2009). Sephadex LH-20
column was used to isolate halisulfate 1 (16) from dark brown sponge. The freeze-dried
sponge was extracted by methanol. After the solvent had been filtered and removed, the
residue was partitioned between dichloromethane and water. The organic extracts were
dried over sodium sulfate and evaporated to obtain a dark brown oil that was
chromatographed on Sephadex LH-20 with 1:1 methanol-dichloromethane as eluant to
obtain two antimicrobial fractions. Fraction B gave crystals of halisulfate 1 (Figure 8) from
dichloromethane (Kernan and Faulkner, 1988).
2.3 Triterpenes
Triterpenes (C30) are a large class of compounds presenting a number of important
biological activities; they arise from squalene, a coupling of two farnesil diphosphate units
(Abe, 2007).
Cyclization of squalene, or squalene oxide leads to a large number of diverse structural
triterpene skeletal types (with 30 carbons), such as lupane, oleane, ursane types (Tantillo,
2011).
Steroids are modified triterpenoids, lacking the three methyl groups at C-4 and C-14. Sterols
are characteristic of eukaryotes. In bacteria they are sparsely distributed with limited array of
products (Summons et al., 2006). Skeletal modifications, especially to the side-chain, originate
a wide range of biologically important natural products, e.g. sterols, steroidal saponins,
cardioactive glycosides, bile acids, corticosteroids, and mammalian sex hormones (Abe, 2007).
Saponins are a group of natural compounds presenting triterpenoidal or steroidal aglycone,
designated genin or sapogenin, covalently linked to one or more sugar moieties (Augustin
et al., 2011).
O O
O O
HO HO
H H H
H H
H
H O H
O O O
O
O
4,12-dideoxy(4)phorbol-20-benzoate-13- 4,12-dideoxy(4)phorbol-20-benzoate-13-
isovalerianate isobutyrate
HO
OH
OSO3Na
halisulphate 1
Fig. 8. Tigliane diterpenes from Euphorbia pannonica and halisulphate isolated from dark
brown sponge.
The most usual technique to isolate triterpenes and steroids is by silica open column. As an
example, six triterpenes were isolated from petroleum ether extract of Azorella trifurcata
whole plant (Areche et al., 2009). The crude extract was chromatographed over silica gel
using a petroleum etherethyl acetate gradient. The fraction eluted with 20% ethyl acetate
was purified by CC on silica gel impregnated with 10% AgNO3, furnishing four triterpenes:
lanost-7-en-3-ol, lanost-9(11)-en-3-ol , lanosta-7,24-dien-3-ol and cycloartenol (Figure 9).
The acetylation product from the fraction eluted with 40% ethyl acetate, after purification by
argentum silica gel CC, yielded the triterpenes lanosta-7,24-dien-3-yl acetate and 28-
acetoxycycloartenyl acetate (Areche et al., 2009).
Several cycloartane-type saponins were isolated from Astragalus wiedemannianus methanol
crude extract (Polat et al., 2010). Plant material was extracted under reflux. After filtration
and solvent removal, the methanol crude extract was solved in water and successively
partitioned with hexane, dichloromethane and butanol saturated with water. The butanol
fraction was submitted to VLC on reversed-phase material (Lichropep RP-18), employing a
H2O:methanol gradient. Fractions developed with H2O:methanol 2:8 were rich in saponins.
The first fraction was chromatographed over Lichropep RP-18 (H2O:methanol gradient). The
obtained sub-fractions were submitted to new chromatographic procedures, depending on

the nature of target compounds furnishing the saponins.
HO HO
lanost-7-en-3-ol lanost-9(11)-en-3-ol
R
R
R1
R= OH lanosta-7,24-dien-3-ol R= OH , R1= H cycloartenol
R= OAc lanosta-7,24-dien-3-yl acetate R=R1=OAc 28-acetoxycycloartenyl acetate
Fig. 9. Triterpenes from Azorella trifurcata.
2.4 Tetraterpenes (Carotenoids)

More than 650 carotenoids (C40) are found in nature, constituting the largest group of
natural dyes. The carotenoids are substances with very special properties possessed by no
other group of substances; these form the basis of their many varied functions and actions in
all kinds of living organisms (Britton, 1995). Carotenoids are biosynthesized by plants, algae,
fungi, yeasts and bacteria.
The carotenoids are isoprenoid compounds, biosynthesized by tail-to-tail linkage of two
geranylgeranyl diphosphate molecules. This produces the parent C40 carbon skeleton from
which all the individual variations are derived. This skeleton can be modified: a) by
cyclization at one end or both ends of the molecule to give the seven different end groups; b)
by changes in hydrogenation level, and c) by addition of oxygen-containing functional
groups. Carotenoids that contain one or more oxygen functions are known as xanthophylls,
the parent hydrocarbons as carotenes (Britton, 1995). After being absorbed through human
diet, some carotenes, among them -carotene (Figure 10), are pro-vitamin A; other, such as
lycopene (Figure 10) , are important due to their antioxidant properties.
Carotenoid extracts have been screened by TLC and separated by CC, involving liquid-solid
chromatography (adsorption). Various adsorbents have been applied in carotenoid analysis,
including Al2O3, silica, magnesium oxide (MgO), calcium hydroxide [Ca(OH)2], calcium
carbonate [CaCO3], siliceous earth as hyflosupercell and others. In normal phase CC, the
adsorption affinity depends on the number of conjugated double bonds, cyclization and the
presence of oxygen substituents (Rodriguez-Amaya, 1999). CC has been used for separations
of mixtures of carotenes and xanthophylls, aiming for mainly analytical determinations,
standard purifications, biological evaluations of carotenoids and the purification of
synthesized carotenoids, especially by flash chromatography.
Separations on basic adsorbents such as MgO and Ca(OH)2 are mainly determined by the
number and type of double bonds in the carotenoid molecules (Bernhard, 1995). The
procedure for isolating and purifying carotenoid standards was established because of the
difficulty in obtaining standards commercially. The procedure consists of carotenoid
extraction with cold acetone, partition to petroleum ether in a separatory funnel with
addition of water, concentration in a rotatory evaporator and chromatographic separation of
carotenoids on CC developed with petroleum ether containing increasing percentages of
ethyl ether and acetone (Rodriguez-Amaya, 1999). A variety of carotenoid standards (some
of them are represented on Figure 10) have been isolated and purified using
MgO:Hyflosupercel (1:1) CC developed with 2-8% ethyl ether in petroleum ether and 2-95%
acetone in petroleum ether: 98% -carotene (isolated from carrot), 94% lycopene, 99% -
cryptoxanthin, 91% -carotene and 91% rubixanthin (from pitanga) (Porcu e Rodriguez-
Amaya, 2008), 9197% neoxanthin, 9598% violaxanthin, 97100% lactucaxanthin, 9296%
lutein, 93% -cryptoxanthin, 96% zeaxanthin and 9099% -carotene (from lettuce, papaya
or green corn) (Kimura & Rodriguez-Amaya, 2002; Oliveira & Rodriguez-Amaya, 2007) and
97% trans--carotene, 99% cis-violaxanthin, 97% trans-violaxanthin, 92% prolycopene and
94% lutein (from passion fruit extracts) (Wondracek et al, 2011). The -cryptoxanthin elutes
before lycopene (Figure 10) in MgO: Hyflosupercel and after lycopene in Al2O3 column,
indicating that the influence of cyclization is greater than that of the presence of hydroxyl
substituents in the MgO:Hyflosupercel column (Rodriguez-Amaya, 1999).
MgO:Hyflosupercel on CC has been also widely used to analysis the main carotenoids of
tropical fruits such as Pouteria campechiana (Agostini-Costa et al, 2010) and to evaluate the
variation in the carotenoid composition of Malpighia glabra pulp (Agostini-Costa et al, 2003)
and Eugenia uniflora fruit (Porcu & Rodriguez-Amaya, 2008). Hydrocarbon carotenes, such
as -carotene, lycopene, -carotene, -carotene and xanthophylls such as -cryptoxanthin,
violaxanthin and neoxanthin (Figure 10), were extracted from these tropical fruits, separated
by MgO: Hyflosupercel on CC developed with ethyl ether and acetone gradient in
petroleum ether, identified by chemical tests and quantified by visible spectroscopy. The
chromatographic behavior of carotenoids bears a definite relationship with theirs structure.
Although these data cannot be used as the sole criteria for identifying carotenoids, they
serve as useful complementary information (Rodriguez-Amaya, 1999). Carotenoids of
Lycium barbarum L. fruits, a traditional Chinese herb that possesses vital biological
properties, were isolated by a column containing MgO: diatomaceous earth. The -carotene
was eluted with n-hexane, -cryptoxanthin and neoxanthin with ethyl acetate and
zeaxanthin with ethyl acetate-ethanol (80:20 v/v). The zeaxanthin fraction was the most
effective in scavenging hydroxyl-free radicals (Wang, 2010).
Other basic materials, especially Ca(OH2), ZnCO3 and CaCO3, are particularly useful for
separating geometrical isomers (Bernhard, 1995). Five lutein derivatives (four isomers and
two epoxides) were isolated and separated from inflorescences of Solidago canadensis L. and
from flowers of Chelidonium majus L., using CaCO3 CC developed with different
compositions of toluene-hexane and acetone-hexane. They were identified as lutein-5,6-
epoxide, (9Z)-lutein-5,6-epoxide, (9Z,9Z)-lutein (neolutein C), (9Z)- and/or (9Z)-lutein

(neolutein B) and (13Z)- and/or (13Z)-lutein (neolutein A), in addition to (all-E)-lutein,
violaxanthin, (9Z)-violaxanthin, flavoxanthin and/or chrysanthemaxanthin (Horvath et al.,
2010). Xanthophylls, such as 5,6-diepikarpoxanthin, mutatoxanthin, anteraxanthin,
zeaxanthin, -cryptoxanthin and apo-carotenoids, such as capsorubin, capsochrome,
capsanthin 5,6-epoxide and capsanthone, were also isolated from Asparagus falcatus using
CaCO3 as adsorbent on CC (Deli et al, 2000). The isomers of -carotene present in acetone
extracts from Malpighia glabra pulp (Agostini-Costa et al, 2003) and from Annona coriaceae
fruit (Agostini et al., 1996) were separated on Ca(OH)2 CC eluted with 2% ethyl ether in
petroleum ether.
Separations on silica and Al2O3 are mainly determined by carotenoid polarity. The
hydrocarbon carotenes are weakly adsorbed, whereas xanthophylls, containing polar
substituents, especially hydroxyl groups, are adsorbed more strongly (Bernhard, 1995). A
novel carotenoid (xanthophyll) derivative, lutein-3-acetate, extracted from senescing leaves
of rice, was isolated and purified using silica gel TLC (Kusaba, 2009). Phytofluene, -
carotene, -carotene, lycopene, zeinoxanthin, cryptoxanthin and lutein (Figure 10) were
separated from ripe and partly ripe Mormodica charantia seeds and tomatoes through Al2O3
and MgO CC (Rodriguez et al., 1975). The main carotenoid (xanthophyll) in the orange
muscle of Yesso scallop was isolated and purified by acetone extraction and silica gel CC. Its
structure was identified as that of pectenolone (3,3-dihydroxy-,-caroten-4one) (Figure
10) (Li et al, 2010).
Fig. 10. Main carotenoids discussed in this chapter.

Carotenoid extracts of eight species of lichens were separated by Al2O3 column and divided
into fractions on silica gel TLC and analyzed by ion-pairing in reverse-phase HPLC.
Fourteen carotenoids, such as -carotene, -carotene, -cryptoxanthin, lutein, zeaxanthin,
canthaxanthin, astaxanthin, violaxanthin and neoxanthin (Figure 10) were separated and
identified (Czeczuga et al, 2010). Stereoisomers and epoxy/carbonyl derivatives of -
carotene were separated through Al2O3 CC developed with 10-60% diethyl ether in n-hexane
(Marty and Berset, 1990).
CC on silica gel 60 was also used for partial separation of carotenoids and DEAE-Toyopearl
650 M to remove B Chlorophyll and polar lipids during carotenoid isolation from a
thermophilic filamentous photosynthetic bacterium Roseiflexus castenholzii. Purified fractions
provided keto-myxocoxanthin and methoxy-keto-mycoxanthin (Figure 10), besides keto-
myxocoxanthin glucoside, keto-myxocoxanthin glucoside ester, myxocoxanthin,
myxocoxanthin glucoside ester and others (Takaichi et al., 2001). The major polar
carotenoids, myxoxanthophyll and ketomyxoxanthophyll, produced by two cyanobacterias
(Anabaena sp. and Nostoc punctiforme), were also isolated and purified first on a column of
silica gel 60. The -carotene was eluted with hexane, non-polar carotenoids were eluted with
acetone/hexane (2:8) and polar carotenoids were eluted with acetone methanol (9:1, v/v).
The polar carotenoids (last fraction) were then loaded on a column of DEAE-Toyopearl 650
M and the carotenoids were eluted with acetone/hexane (1:1 v/v) and finally purified on
silica gel TLC developed with dichloromethane/ethyl acetate/acetone/methanol (2 : 4 : 2 :
1, v/v) to give myxoxanthophyll and ketomyxoxanthophyll (Takaichi et al., 2005).
3. Phenolic compounds
Phenolic compounds are widely distributed in nature. Their chemical structures may vary
greatly, including simple phenols (C6), such as hydrobenzoic acid derivatives and catechols,
as well as long chain polymers with high molecular weight, such as catechol melanins (C6)6,
lignins (C6-C3)n and condensed tannins (C6-C3-C6)n. Stilbenes (C6-C2-C6) and flavonoids (C6-
C3-C6) are phenolic compounds with intermediate molecular weight that present many
pharmacological and biological activities. Flavonoids, including anthocyanins, flavonols
(such as quercetin and myricetin), isoflavones (such as daidzein and genistein) and others
are formed by multiple biosynthetic branches that originate from chalcone.
Phenolic compounds have been widely fractionated in medicinal, aromatic and food plants
using CC. Repeated silica gel, sephadex-LH20, RP-18, RP-8, MCI-gel, diaion and toyopearl
chromatography columns have been used to fractionate simple phenolics, flavonoids and
tannins from kernels and nuts (Zhang et al, 2009; Karamac, 2009), fruits such as apples, Morus
nigra, Punica granatum (Lee et al, 2010; Pawlowska et al, 2008); olive oil (Khanal et al, 2011), tea
(Gao et al, 2010; Liu et al, 2009), seeds such as lentils (Amarowicz & Karamac 2003), medicinal
species, including Ulmus davidiana and Tridax procumbens (Jung et al, 2008; Agrawal, 2011); and
aromatic plants, including mint and sage (She et al, 2010; Wang et al, 1998).
Separations on silica are mainly determined by polarity, where phenolic compounds
containing more hydroxyl groups are adsorbed more strongly. Separations on Sephadex
LH-20, a crosslinked dextran-based resin for gel permeation, are mainly determined by
molecular sizing of the phenolic compound, outside of adsorption and partition mode.
Phenolic acids (such as ferulic acid and gallic acid), flavonoids (such as flavonol, catechins
and anthocyanidins derivatives) and procyanidins (Figure 11) from fruits of wild black
berry Aristotelia chilensis were obtained using flash and open CC on silica gel and Sephadex
LH-20 eluted with hexane, hexane-ethyl acetate (1:1); ethyl acetate-methanol (1:1) and
methanol (Cespedes et al., 2010).
Pyrogallol and phenolic acids were purified from defatted extract of Juglans regia kernels by
repeated CC on Sephadex LH-20 eluted with methanol, followed by silica gel CC developed
with chloroformacetone 40:1, v/v. Ethyl gallate was obtained by recrystallization from
methanol. Protocatechuic acid was obtained after CC on Sephadex LH-20 eluted with
CH2Cl2EtOH, 1:1, v/v and further purification with silica gel CC developed with
Chloroformmethanol, 20:1. Gallic acid and 3,4,8,9,10-pentahydroxydibenzo[b,d]pyran-6-
one (Figure 11) were separated by silica gel CC and eluted with a mixture of chloroform
methanol (Zhang, 2009). High-molecular-weight tannins (Figure 11) of defatted walnut,
hazelnut and almond kernels were also isolated by CC on Sephadex LH-20 gel eluted with
50% (v/v) acetone (Karamac, 2009). The ethanol fraction of Dipteryx lacunifera kernels was
found to exhibit high radical scavenging activity and was subjected to further fractionation.
CC over silica gel with gradient from chloroform to methanol and Sephadex LH-20 eluted
with methanol afforded (-)-eriodictyol, (-)-butin, luteolin, 3,4,7-trihydroxyflavone, butein
and sulfuretin (Junior et al., 2008).
The total polyphenols from red wine isolated during vinification and storage were isolated
by CC and their contribution to wine sensory properties and antioxidant activity was
evaluated. Wine samples were evaporated and loaded onto an open CC packed with
LiChroprep RP-18; the column was washed with distilled water followed by methanol to
recover total polyphenols extract, further separated by HPLC (Sun et al., 2011).
The alkyl esters of protocatechuic acid (Figure 11) were synthesized and the crude product
was then purified by CC using petroleum ether/ethyl ether (7:3 to 5:5) as eluent. The
increase in the length of ester alkyl chain attached to the catecholic ring had influenced the
stabilization of the radicals formed in the oxidation process. Alkyl protocatechuate
compounds demonstrated a higher radical-scavenging activity than the natural antioxidant
protocatechuic acid. Moreover, the introduction of alkyl groups in the carboxylic acid led to
a significant increase in lipophilicity influenced by the antioxidant activity of protocatechuic
acid derivatives (Reis et al., 2010).
The virgin olive oil phenol was partitioned successively with hexane and ethyl acetate and
fractionated by CC on silica gel and Sephadex LH-20 to give a dialdehydic form of decarboxy-
methyl ligstroside aglycone (p-HPEA-EDA) (Figure 11), a phenolic compound that activates
AMP-activated protein kinase to inhibit carcinogenesis (Khanal et al., 2011). Phenols and
tocopherols were also removed from olive oil by CC over Al2O3 during to evaluate changes in
the phenolic composition of virgin oil during frying. The concentration of hydroxytyrosol (3,4-
DHPEA) and its secoiridoid derivatives (3,4-DHPEA-EDA and 3,4-DHPEA-EA) in virgin olive
oil decreased rapidly when the oil was repeatedly used for preparing fried food. However,
tyrosol (p-HPEA) and its derivatives (p-HPEA-EDA and p-HPEA-EA) in the oil were much
more stable during frying operations (Gomez-Alonso et al., 2003).
Phytoalexins are secondary metabolites that plants synthesize for self-defense, and they
have shown great promise in chronic disease prevention. The best known example is
resveratrol (Figure 11), an induced phytoalexin found in yeast-infected grape skin (Wu et al.,
2011). Peanuts also contain several active components including flavonoids, phenolic acids,
phytosterols, alkaloids and stilbenes. The latter are characterized by a 1,2-diphenylethylene
backbone usually derived from the basic unit of trans-resveratrol (3,5,4-trihydroxy-stilbene)

(Lopes et al, 2011). Peanut seeds, when affected by injuries, pathogenic infections, fungal
contamination, insect damage and UV light, could produce phytoalexins such as stilbenoid
derivatives (resveratrol, arachidins, 3-isopentadienyl-3,5,4-trihydroxystilbene, SB-1,
chiricanine A, and arahypins), and pterocarpanoid derivatives (e.g., aracarpene-1 and
aracarpene-2). Silica gel column eluted with hexane and hexane ethyl acetate (7:3) was used
for fractionation the phytoalexin extract from peanut before analysis by HPLC (Wu et al.,
2011). Neutral Al2O3 - silica gel 60 C18 (1:1 w/w) eluted with 80% ethanol was used as a
clean-up column to separate interfering co-eluting with resveratrol from peanut extracts
(Potrebko & Resurreccion, 2009).
Fig. 11. Main phenolic compounds discussed in this chapter.

A highly efficient column chromatographic extraction of curcumin from Curcuma longa was
proposed by Zhan et al., 2011. Curcumin (Figure 11) was extracted with minimum use of
solvent, minimum volume and high concentration of extraction solution by CC. Turmeric
material was loaded into a column with 2-fold of 80% ethanol. After dissolving target
compounds, the column was eluted with 80% ethanol. For non-cyclic CCE procedure, 8-fold
of eluent was collected, while for cyclic CCE procedure, only the first 2-fold of eluent was
collected as extraction solution. A more than 99% extraction rate for curcumin was obtained
in both procedures, compared to a 59% extraction rate through the ultrasonic-assisted
extraction with 10-fold of 80% ethanol.
A lipid- and essential oil- free infusion of Cymbopogon citratus leaves was fractionated on
Lichroprep RP-18 column eluted with water and with aqueous methanol solutions. Dry
residue was recovered in 50% aqueous ethanol and was fractionated by gel chromatography
on a Sephadex LH-20 using ethanol as mobile phase. All the fractionation process provided
three major fractions: a tannin rich fraction; a flavonoid rich fraction and two phenolic acid
rich fractions. Tannin and phenolic acid were the fractions responsible for the anti-
inflammatory effect through inhibition of transcription factor NF-kB, inducible nitric oxide
synthase expression and nitric oxide production. These fractions probably had a synergistic
effect (Francisco et al., 2011).
Oligomeric procyanidins (Figure 11) in apples were extracted with boiled water and
purified on an ADS-17 macroporous resin column to obtain a procyanidin extract. The
extract was fractionated according to its degree of polymerization on a Toyopearl TSK HW-
40 column eluted with methanol to give procyanidins B2 (epicatechin-(4-8)-epicatechin)
and C1 (epicatechin-(4-8)-epicatechin-(4-8)-epicatechin). This method was suitable for the
preparation of procyanidin oligomers (from dimers through tetramers in one run) for
laboratory research, and is potentially applicable to large-scale production in industry (Xiao
et al., 2008).
Thea (Theaceae) is traditionally used for producing tea, one of the most popular beverages
consumed in the world due to its polyphenol-rich content, which are reported to have
various bioactivities, such as antioxidative, antimicrobial, antitumor and antimutagenesis
(Liu et al, 2009). Camellia sinensis and some other species from the genus Camellia have also
been used for making tea and are consumed widely (Gao et al, 2010). More than 96 phenolic
compounds were identified in C. sinensis tea. The hydrolyzable tannin epigallocatechin
gallate was the major phenolic component of green tea and partially fermented teas, while
fully fermented black teas had traces of epigallocatechin gallate but contained theaflavins.
Glycosylated flavonoids, catechins, proanthocyanidins (condensed tannins) and phenolic
acid derivatives were found too (Lin et al., 2008). Aqueous acetonic extract of green tea (C.
crassicolumna) further partitioned with ethyl acetate and purified by CC led to the
identification of various fractions obtained by CC over Sephadex LH-20 eluted with ethanol.
Further repeated CC on MCI-gel CHP20P, Sephadex LH-20, and Toyopearl HW-40F, eluted
with methanol/H2O (0:1-1:0) gave five flavan-3-ols, five flavonol glycosides, three
hydrolyzable tannins, two chlorogenic acid derivatives and three simple phenolic
compounds (Liu et al, 2009). Phenolic compounds were also isolated from the leaves of C.
pachysandra. The ethyl acetate and aqueous fractions were separately subjected to repeated
CC over Diaion HP-20SS, Sephadex LH-20, MCI-gel CHP20P, and Toyopearl HW-40F to
give 22 phenolic compounds, including nine hydrolyzable tannins, 11 flavonol glycosides
and two simple phenols, without caffein or catechin (Gao et al., 2010).
A new phenolic compound was isolated and purified from butanol fraction of Chinese
olive (Canarium album L.) fruit through AB-8 adsorption resin CC washed with water to
remove impurities and eluted with 90% (v/v) aqueous ethanol to get the phenolic eluents.
The phenolic were further separated on a polyamide CC eluted with aqueous ethanol to
give several fractions, the ethanol concentration being increased from 0 to 100% in
increments of 20%. Fraction obtained from 20% aqueous ethanol was further purified on
TSK Toyopearl HW-40 (S) CC developed with aqueous ethanol 0 to 20% to get the
purified new compound established as 3-o-galloyl quinic acid butyl ester (Figure 11) (He
et al., 2009). Polyamide CC eluted with water and 50%, 70% and 100% aqueous methanol
further facilitated GC-MS and HPLC separation of phenolic compounds in Euphrasia
rostkoviana (Blazics et al., 2008).
Lycium barbarum L., a traditional Chinese herb, possesses vital biological properties, such as
prevention of cancer and age related macular degeneration. Flavonoids and phenolic acids
extracted from fruits of this plant were separated using a Cosmosil 140 C18 OPN column,
with phenolic acids being eluted with deionized water and neutral flavonoids with
methanol. The flavonoid fraction showed the most pronounced effect in scavenging free
radicals, chelating metal ions and reducing power (Wang et al., 2010).
Eight polyphenolic acids were isolated from the aereal part of Mentha haplocalix extracted
with aqueous acetone 70% at room temperature. Repeated CC on silica gel (developed with
chloroformmethanolH2O, 9:1:0.1 to 7:3:0.5), Sephadex LH-20 and MCI-gel CHP20P and
ODS-A, eluted with H2OMethanol (1:0 to 0:1) afforded rosmarinic acid, cis-salvianolic acid,
lithospermic acid (Figure 11), propanoic acid, sodium lithospermate B, magnesium
lithospermate B, and lithospermic acid B. Lithospermic acid B, sodium lithospermate B and
magnesium lithospermate B displayed stronger activities than the other compounds (She et
al., 2010). Ten phenolic compounds were also isolated from a butanol fraction of sage
extracts, using repeated CC on silica gel, Lichroprep RP-18 and Sephadex LH20. Among
them, the most active antioxidants were found to be rosmarinic acid and luteolin-7-O--
glucopyranoside (Wang et al, 1998).
4. Alkaloids
Alkaloids are defined as basic compounds synthesized by living organisms containing one
or more heterocyclic nitrogen atoms, derived from amino acids (with some exceptions) and
pharmacologically active. The class name is directly related to the fact that nearly all
alkaloids are basic (alkaline) compounds. Alkaloids constitute a very large group of
secondary metabolites, with more than 12,000 substances isolated. A huge variety of
structural formulas, coming from different biosynthetic pathways and presenting very
diverse pharmacological activities are characteristic of the group (Brielmann et al., 2006).
Archeological evidence has demonstrated the use of alkaloids (plant parts or extracts) since
4000 B.C., and they continue to be very important today (Roberts & Wink, 1998). Poppy
(Papaver somniferum) and opium have been known and used since antiquity by Sumerians,
Arabs, Persians, Egyptians and Greeks. Morphine, obtained from the poppy latex, was the
first crude drug isolated. It was named after Morpheus, the god of dreams, one of the sons
of Hypnos, the god of sleep, in Greek mythology (Wink, 1998). Morphine is legally used
nowadays as an analgesic for severe pain.
Alkaloids are associated with a wide range of pharmacological activities. Many are toxic and
can cause death, even in small quantities. Some have antibiotic activities and others interfere
with behavior patterns, such as antidepressants (reserpine) and hallucinogens (mescaline). It
seems alkaloid function in plants and animals is linked to defense mechanisms. Toxicity is a
good weapon to inhibit the action of predators, like herbivores.
4.1 Alkaloids from plants

CC is a very important and much used technique in alkaloid isolation and analysis. Usually,
after CC, the sample is re-chromatographed either by preparative TLC or HPLC, in order to
obtain a pure sample for spectroscopic studies.
Phytochemical investigation in plants from the genus Kopsia (Apocynaceae) led to the
discovery of different classes of alkaloids, presenting antileishmanial, antimitotic and
antitumor activities. From Kopsia hainanensis, a native medicinal plant from Hainan, China,
two new pentacyclic indole alkaloids have been isolated (Chen et al., 2011). The acidic
partition of the methanol extract was neutralized and extracted with chloroform. Alkaloids,
as basic substances, can be protonated in acidic media and therefore remain in the aqueous
phase. This strategy has been very useful for the isolation of this class of compounds. The
pH of the aqueous phase is further adjusted and alkaloids are extracted with a solvent. The
concentrated extract was repeatedly submitted to CC over silica gel and eluted with a
gradient of chloroform-methanol, alkalinized with a small quantity of triethylamine to give
kopsahainanine B. One fraction was re-chromatographed over reversed-phase silica gel and
Sephadex LH-20, using methanol-water and pure methanol as eluents, respectively, to give
kopsahainanine A (Figure 12).
Fig. 12. Pentacyclic indole alkaloids from Kopsia hainanensis.
The butanolic fraction of Lobelia chinensis Lour. was chromatographed on reversed phase
Diaion HP 20 gel, eluted with water-methanol in to six fractions. Fraction 6 was re-
chromatographed on Sephadex LH-20 followed by preparative silica gel TLC and 7.3 mg of
lobachine (Figure 13), a new alkaloid, were isolated (Kuo et al., 2011).
From Campylospermum flavum, a medicinal plant from Cameroon, flavonoids, flavones,
chalcones and alkaloids have been isolated. Among them, a new indole alkaloid,
flavumindole (Figure 13), was obtained from the methanol extract after partition with ethyl
acetate-water and purification on silica gel, Sephadex LH-20 and RP18 silica gel, eluted with
dichloromethane-methanol mixtures, pure methanol and methanol-water mixtures,
respectively (Ndongo et al., 2011). The isolated alkaloid presented a cytotoxicity of 90%
according to by brine shrimp (Artemia salina) test.
Fig. 13. Lobachine, a new alkaloid from Lobelia chinensis and flavumindole, from
Campylospermum flavum.
Nine indole alkaloids were isolated from the roots, bark and leaves of Tabernaemontana
salzmannii (Apocynaceae). The alkaloids were fully identified by spectroscopic methods and
mass spectra by comparison with literature data (Figueiredo et al., 2010). The
dichloromethane extract was repeatedly chromatographed over silica gel eluted with
dichloromethane-methanol mixtures. Coronaridine, 3-oxo-coronaridine, (19S)-heyneanine,
voacangine, isovoacangine, hydroxyisovoacangine, isovoachristine and olivacine (Figure 14)
were isolated. For voachalotine, a further chromatographic step was necessary on
preparative TLC (silica gel) eluted with dichloromethane-methanol (99:1). After an in vitro
screening, it was observed that isovoacangine and voacangine alkaloids were able to induce
apoptosis cell death in human leukemic cells, line THP-1.
Fig. 14. Alkaloids from Tabernaemontana salzmannii.
Already having an extremely diverse variety in structural formulas, new and (therefore)
unusual carbon skeletons have continued to be found in alkaloids research. That was the
case reported by Hitotsuyanagi et al. (2010), in a study with Stemona sessilifolia. Plants of the
genus Stemona are rich sources of alkaloids, and two new ones were isolated by CC of the
acidic partition from the methanolic extract of the roots. Sessilifoliamide K and
sessilifoliamide L were structurally related, presenting an unusual pyrido[1,2-a]azonine
skeleton (Figure 15), which can be derived from tuberosteminol-type alkaloids, previously
described occurring in Stemona genus.
Fig. 15. New unusual pyrido[1,2-a]azinone alkaloids from Stemona sessilifolia.
4.2 Alkaloids from fungi

Probably the most famous (and infamous) alkaloid producing fungi are the ergots (family
Hypocreaceae). Ergotism (holy fire) has killed thousands due to contaminated rye, and even
in the last century many cases were reported (Wink, 1998). However, there is a plethora of
alkaloid producing-fungi, with different structures and biological activities. Three new
alkaloids, lyconadin D, lyconadin E and complanadine E (Figure 16) were isolated from
Lycopodium complanatum (Lycopodiaceae) by Ishiuchi et al. (2011). The acidified methanolic
extract was partitioned with ethyl acetate. The pH of the aqueous phase was adjusted and
extracted with chloroform. After solvent evaporation, the chloroform-soluble materials were
chromatographed on an amino silica gel column and eluted with hexane-ethyl acetate
mixtures, then with a chloroform-methanol-water system. The fractions eluting with pure
chloroform were re-chromatographed over silica gel, and lyconadin D and lyconadin E were
isolated. Part of the chloroform soluble fraction was eluted with chloroform-methanol over a
Sephadex LH-20 column. The fractions were further purified by HPLC (C18 column) to yield
complanadine E, a dimeric unsymmetrical alkaloid.
Fig. 16. New alkaloids from moss Lycopodium complanatum.
The mosses of the genus Lycopodium in particular are very prone to produce complex
polycyclic alkaloids, with important biological activities, such as inhibition of acetylcholine
esterase. From three different species of Lycopodium, ten new alkaloids were isolated and
characterized (Katakawa et al., 2011). Dihydrolycopoclavamine (Figure 17) was isolated
from the extract of L. serratum after chromatography on amino silica gel and elution with
hexane-chloroform. For L. clavatum, after neutralization of the acidic fraction from the
methanolic extract, it was submitted to flash chromatography over silica gel and eluted with
a chloroform-methanol gradient, then chloroform-methanol-aqueous ammonium hydroxide
and pure methanol. One fraction was re-chromatographed on amino silica gel with hexane-
chloroform mixtures leading to licopoclavamine A. Another fraction was re-
chromatographed on silica gel to give lycopoclavamine B (Figure 17). A similar procedure
was applied to L. squarrosum, from which lycoposquarrosamine A, acetyllycoposerramine-
U, 8--hydroxyfawcettimine, 8--hydroxyfawcettimine, 8--acetoxyfawcettimine, 8--
acetoxyfawcettimine and lycoflexine N-oxide were isolated. It is quite remarkable that all
these compounds were separated solely by means of CC using silica gel, amino silica gel or
Al2O3, and solvent mixtures of hexane, chloroform, methanol and ethyl acetate.
Fig. 17. Alkaloids from Lycopodium clavatum, L. serratum and L. squarrosum.
4.3 Marine alkaloids

The marine environment has emerged as a promising source of new substances with
medicinal application. Considering only sponges, for example, more than 15,000
compounds have been isolated and characterized, including terpenoids, nucleosides,
alkaloids and steroids.
Guanidine alkaloids were isolated from Monanchora arbuscula after CC over Sephadex LH-20
with methanol then repeatedly over silica gel and eluted with chloroform-ethyl acetate-
methanol mixtures. The compounds (Figure 18) were identified by 1H and 13C NMR, IR and
MS (Ferreira et al., 2011).
Fig. 18. Guanidin alkaloids from sponge Monanchora arbuscula.
Two new brominated arginine-derived alkaloids were isolated from the Red Sea sponge
Suberea mollis (Aplysinellidae), namely subereamine A and subereamine B (Figure 19).
Halogenated compounds are common in marine natural products. The subereamines were
isolated after CC on Sephadex LH-20 of the ethyl acetate extract, followed by
chromatography on silica gel with dichloromethane-methanol mixtures and preparative
HPLC on C18 column (Shaala et al., 2011).
Fig. 19. Brominated alkaloids from sponge Suberea molis.
The first natural products containing a 1H-oxazolo [40,50:4,5] benzo[1,2,3-de] [1,6]

naphthyridine ring system were isolated from a Suberites sp. sponge collected in Okinawa,
Japan. Named respectively, nakijinamines C and E (Figure 20), they constitute a group of
heteroaromatic alkaloids, hybrids of aaptamine-type and bromoindole alkaloids (Takahashi
et al., 2011). Other 23 aaptamine-type alkaloids have been isolated so far, but none contain
the hybrid ring system. Another new alkaloid was isolated, namely nakijinamine D, which
does not contain the oxazolo ring. The sponges were extracted with methanol and the
residue partitioned with ethyl ether and water. The aqueous phase was extracted with
butanol and subjected to reversed phase CC (C18) followed by repeated HPLC also on a C18
column. The alkaloids were isolated initially as racemates. Antifungal activity was recorded
for nakijinamines C and E against Aspergillus niger.
Fig. 20. New heteroaromatic alkaloids from Suberites sp.
Marine sponges of the genus Asteropus have been reported to contain a variety of
compounds, such as saponines, sterols and pteridine derivatives. The concentrated
methanolic extract was partitioned between water and dichloromethane. The water phase
showed toxicity to brine shrimp larvae and was partitioned with butanol. The butanolic
extract was submitted to medium pressure liquid chromatography over ODS-A with a
methanol gradient. A fraction selected according to the toxicity test result was
chromatographed over Sephadex LH-20. The sub-fractions were purified by reversed phase
HPLC. The pyroglutamyl alkaloids were new compounds (Figure 21), and therefore fully
characterized by spectroscopic methods (Li et al., 2011).
Fig. 21. Pyroglutamyl dipeptides and tetrahydro--carboline alkaloids from Asteropus sp.
Carboline alkaloids were also found in tunicates of the genus Eudistoma. After purification
on Sephadex LH-20, the methanolic extract of Eudistoma glaucus was chromatographed on a
silica gel column with hexane-ethyl acetate mixtures, and then on another column with
amino silica gel, also eluted with the same solvents. Normal phase HPLC led to the isolation
of eudistomidin H (Figure 22) and eudistomidin I. Eudistomidins H and I were new
compounds containing a unique fused-tetracyclic ring system consisting of a tetrahydro -
carboline ring and a hexahydropyrimidine ring. Using the same stationary phases, but
changing the solvent system to chloroform-methanol, eudistomidin K was obtained. For
eudistomidin J, the last solvent system was also applied, but without the need for a HPLC
separation step (Suzuki et al., 2011).
Fig. 22. Carboline alkaloids from tunicate Eudistoma glaucus.
Pyridoacridine alkaloids are responsible for the bright colors observed in sponges and
ascidians. Two new pyridoacridine alkaloids, namely 13-didemethylamino-
cycloshermilamine D and dimethyl-deoxyamphimedine (Figure 23), were isolated from the
purple chromotype of the Western Mediterranean morph Cystodytes dellechiajei together with
other six known alkaloids of the same kind (Bry et al., 2011). The ascidians were extracted
with methanol-dichloromethane-trifluoroacetic acid mixture followed by reverse phase CC.
The purple fraction obtained was chromatographed three successive times on reverse phase
columns eluted with a methanol-water gradient. After reverse phase semi-preparative
HPLC, the two new alkaloids were isolated.
Fig. 23. New pyridoacridine alkaloids from morph Cystodytes dellechiajei.
In this way, the phytochemical investigation of alkaloids has been deeply dependent on CC
techniques. Careful and patient repeated CC has led to the isolation of some structurally
varied and fascinating compounds, even without the use of modern HPLC methods. To be
more efficient and to enhance productivy, of course, combined approaches are the common
practice.
It is worth emphasizing the great opportunity that marine organisms offer to researchers
looking for biologically active compounds and synthetic models. The real treasures at the
bottom of the sea may not come from shipwrecks, but are those which have been lying (or,
better, living) there since long before human beings set foot on earth.
5. Conclusion
Even in laboratories with good HPLC and GC-MS facilities, the traditional and classical
methods of TLC and CC are still widely used, for rapid preliminary screening of extracts, for
isolating and purifying bioactive compounds of secondary metabolism for further study, for
comparison of samples with standards and for monitoring chemical synthesis or the course
of reactions.
6. Acknowledgment
Authors thank Embrapa for financial support to the chapter production.
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9
Biomarkers
Yasser M. Moustafa and Rania E. Morsi
Egyptian Petroleum Research Institute,
Egypt
1. Introduction
Generally, biomarkers are naturally occurring, ubiquitous and stable complexes that are
objectively measured and evaluated as an indicator of a certain state. It is used in many
scientific fields; medicine, cell biology, exposure assessment, astrobiology, geology and
petroleum.
Biomarkers "biological markers" in medicine are complex compounds that can be used as an
indicator of a particular disease state or some other physiological state of an organism.
Biomarkers have been defined also as cellular, biochemical or molecular alterations that are
measurable in biological media such as human tissues, cells or fluids (Hulka et al., 1990).
Broader definitions include biological characteristics that can be objectively measured and
evaluated as an indicator of normal or abnormal biological processes, pathogenic processes
or pharmacological responses to a therapeutic intervention (Naylor, 2003).
Biomarkers can also reflect the entire spectrum of disease from the earliest manifestations to
the terminal stages. Characterization of the healthy and diseased cells, when identifying a
specific biomarker as an indicator of cancer, is a needed research strategy for validating
biomarkers. For the nervous system, as an example, there is a wide range of techniques used
to gain information about the brain in both the healthy and diseased state. These may
involve measurements directly on biological media (e.g. blood or cerebrospinal fluid) or
measurements such as brain imaging which do not involve direct sampling of biological
media but measure changes in the composition or function of the nervous system (Mayeux ,
2004). Moreover, the pharmaceutical industry is beginning to rely on biomarkers
information and their importance to the future of drug discovery and development.
In practice, biomarkers science includes tools and technologies that can aid in
understanding the prediction, cause, diagnosis, progression, regression, and/or the outcome
of disease treatment which provide a dynamic and powerful approach to understand the
spectrum markers and offer the means for homogeneous classification of a disease and risk
factors which can extend the base information about the underlying pathogenesis of disease.
2. Petroleum biomarkers
Due to the variety of geological conditions and ages under which oil was formed, every
crude oil exhibits a unique biomarker fingerprint. Crude oils compositions vary widely
depending on the oil sources, the thermal regime during oil generation, the geological
migration and the reservoir conditions. Crude oils can have large differences in:
1- distribution patterns of the n- alkanes, iso-alkanes and cyclic- alkanes as well as the
unresolved complex mixture (UCM) profiles 2- relative ratios of isoprenoid to normal
alkanes 3- distribution patterns and concentrations of alkylated polynuclear aromatic
hydrocarbons (PAHs) homologues. Most of these constituents undergo changes in their
chemical structure by time as an effect of several factors among which are the biodegradation
and weathering. Relative to other hydrocarbon groups in oil, there are some compounds that
are more degradation-resistant in the environment as for example; Pristane, phytane, steranes,
triterpanes and porphyrins. These undegradable compounds are known as Biomarkers.
Trebs (1934) was the first one to develop the biomarkers concept, with his pioneering work on
the identification of porphyrins in crude oils suugesting that these porphyrins are generated
from chlorophyll of plants. Blumer et al. (1963) and Blumer & Thomas (1965) isolated pristane
from recent marine sediments and concluded that it was derived from the phytol side chain of
chlorophyll. Later, other workers reported the present of various classes of degradation-
resistant organic compounds and recognized their biomarker implementations.
Petroleum biomarkers can thus be defined as complex organic compounds derived from
formerly living organisms found in oil (Mobarakabad et al., 2011). They show little or no
changes in their structure from the parent organic molecules and this distinguishes
biomarkers from other compounds (Maioli et al., 2011). Various biomarkers formed under
different geological conditions and ages can occur in different carbon ranges exhibiting
different biomarker fingerprints.
From the identification point of view, biomarkers are the most important hydrocarbon
groups in petroleum because they can be used for chemical fingerprinting which provides
unique clues to the identity of source rocks from which petroleum samples are derived, the
biological source organisms which generated the organic matter, the environmental
conditions that prevailed in the water column and sediment at the time, the degree of
microbial biodegradation and the thermal history (maturity) of both the rock and the oil.
The information from biomarker analysis can be used also to determine the migration
pathways from a source rock to the reservoir for the correlation of oils in terms of oil-to-oil
and oil-to-source rock and the source potential. Also chemical analysis of biomarkers
generates information of great importance to environmental forensic investigations in terms
of determining the source of spilled oil, differentiating and correlating oils and monitoring
the degradation process and weathering state of oils under a wide variety of conditions.
Terpanes and steranes are highly resistant to biodegradation but few studies have shown
that they can be degraded to certain degree under severe weathering conditions i.e,
extensive microbial degradation (Chosson, 1991).
2.1 Biomarkers analysis

The commercial availability of Gas Chromatography- Mass Spectroscopy (GC-MS) and
associated data systems in the mid-1970s led to use the biomarkers for a wide variety
purposes. The complex structure of biomarkers and the possible presence in low
concentrations make a pressing need for more sensitive and precise analysis. The
development of analytical methodologies and the combination between these methods are
of great importance to separate, monitor and detect the absolute concentrations and
structure of petroleum biomarkers. The use of "hybrid" or "hyphenated" techniques, which
are a combination of different separate techniques, increases the analytical power of the
Biomarkers 167
used methods. GC-MS can be considered as the most popular method used in the
characterization of major biomarker groups. GC provides the significant advantage of the
separation of different structures of biomarkers while MS can accurately detect and identify
these structures. The concept and the development of these instrumentations will be briefly
mentioned.
2.1.1 Separation by chromatographic techniques

Chromatography is the separation of a mixture of compounds into their individual
components primarily according to their volatilities. There are numerous chromatographic
techniques but gas chromatography (GC) is the most important one. It has a number of
advantages over other separation techniques. It can identify (qualitate) and measure the
amount (quantitate) various sample components.
Fig. 1. Schematic diagram of gas chromatograph.
The GC column is the heart of the system; the structure of the stationary phase and the
packed material greatly influence the separation of the compounds and affect the time of
separation (retention time). Two types, packed and capillary columns, have been used. The
advantages in capillary columns over packed columns are in obtaining practically improved
resolution in order to give fine structured chromatographic fingerprints. The column is
placed in an oven where the temperature can be controlled very accurately over a wide
range of temperatures. As compounds come off the column, they enter a detector for
identification. Figure 2 represent the carbon number range distribution of common
hydrocarbons in crude oil and petroleum products.
2.1.2 Identification by spectroscopic techniques

There are different types of detectors that can be employed depending on the compounds to
be analyzed. Mass spectrometry (MS) has very common use in analytical laboratories that
study a great variety of compounds and provides a satisfactory tool for obtaining specific
fingerprints for classes and homologous series of compounds resolved by gas
chromatography. The technique has both qualitative and quantitative uses include
identifying and determining the structure of a compound by observing its fragments.
The mass spectrometer has long been recognized as the most powerful detector for gas
chromatography. Typical MS instruments consist of three modules; an ion source: which can
Fig. 2. Representative model of carbon number distribution in petroleum hydrocarbons.
Fig. 3. Schematic diagram of mass spectrometer.
convert the separated constituent into ions, a mass analyzer: which sorts and separates ions
by their masses by applying electromagnetic fields and a detector: which calculate the
abundances of each ion present by a quantitative method to generate signals. The size of the
signals corresponds to the amount the compound present in the sample.
Characterization of some major biomarker groups is largely achieved using the following
MS fragment ions:
alkyl-cyclohexanes: m/z 83
methyl-alkyl-cyclohexanes: m/z 97
Biomarkers 169
isoalkanes and isoprenoids: m/z 113, 127, 183

sesquiterpanes: m/z 123
adamantanes: m/z 135, 136, 149, 163, 177, and 191
diamantanes: m/z 187, 188, 201, 215 and229
tri-, tetra-, penta-cyclic terpanes: m/z 191
25-norhopanes: m/z 177
28,30-bisnorhopanes: m/z 163, 191
steranes: m/z 217, 218
5(H)-steranes: m/z 149, 217, 218
5(H)-steranes: m/z 151, 217, 218
X diasteranes: m/z 217, 218, 259
methyl-steranes: m/z 217, 218, 231, 232
monoaromatic steranes: m/z 253
triaromatic steranes: m/z 231
The m/z 191 fragment is often the base peak of mass spectra of biomarkers. In general,
GC/MS chromatograms of terpanes (m/z 191) are characterized by the terpane distribution
in a wide range from C19 to C35 with C29 - and C30 -pentacyclic hopanes and C23 and
C24 tricyclic terpanes being often the most abundant. As for steranes (at m/z 217 and 218),
the dominance of C27,C28 and C29 homologues. Figure 4, as a representative model, shows
API: American Petroleum Institute. The larger the API, the greater the amount of the light components the
oil contains and with decreasing the API, the amounts of medium and heavy weight components increase.
Fig. 4. GC-MS chromatograms at m/z 191 for light to heavy crude oils.
GC-MS chromatograms at m/z 191 for light (API > 35), medium (API: 2535), and heavy
(API < 25) crude oils (Wang et al., 2006).
3. Diagnostic ratios of biomarkers

Biomarker diagnostic parameters have been long established and are widely used by
geochemists for oil correlation; determination of organic input and precursors, depositional
environment, assessment of thermal maturity and evaluation of in-reservoir oil
biodegradation (Peters et al., 2005). Diagnostic ratios (DRs) can either be calculated from
quantitative (i.e., compound concentrations) or semi-quantitative data (i.e., peak areas or
heights). Also, many diagnostic ratios currently used in oil spill and environmental studies.
Oiloil correlations are based on the concept that the composition of biomarkers in spill
samples does not differ from those of the candidate source oils. Most biomarkers in spill
samples and source oils, in particular those homologous series of biomarkers with similar
structure, show little or no changes in their diagnostic ratios. An important benefit of
comparing diagnostic ratios of spilled oil and suspected source oils is that concentration
effects are minimized. In addition, the use of ratios (rather than absolute values) tends to
induce a self-normalizing effect on the data because the variations due to the fluctuation of
instrument operating conditions day-to-day, operator, and matrix effects are minimized.
Therefore, comparison of diagnostic ratios reflects more directly differences of the target
biomarker distribution between samples.
Biomarker classes Diagnostic ratios

Acyclic Isoprenoids
pristane/phytane
pristane/n-C17
phytane/n-C18
Terpanes
C21/C23 tricyclic terpane
C23/C24 tricyclic terpane
C23 tricyclic terpane/C30 hopane
C24 tricyclic terpane/C30 hopane
C24 tertracyclic/C26 tricyclic (S)/C26 tricyclic (R) terpane
C2718, 21-trisnorhopane/C27 17, 21-trisnorhopane
C28 bisnorhopane/C30 hopane
C29-25-norhopane/C30 hopane
C29-30-norhopane/C30 hopane
oleanane/C30 hopane
moretane(C30 hopane)/C30 hopane
gammacerane/C30 hopane
tricyclic terpanes (C19-C26)/C30 hopane
C31 homohopane (22S)/C31 homohopane (22R)
C32 bishomohopane (22S)/C32 bishomohopane (22R)
C33 trishomohopane (22S)/C33 trishomohopane (22R)
Relative homohopane distribution
(C31-C35)/C30 hopane
homohopane index
Biomarkers 171
Biomarker classes Diagnostic ratios

Steranes
Relative distribution of regular C27-C28-C29 steranes
C27 /C29 steranes (at m/z 218)
C27 /(C27 + C28 + C29) (at m/z 218)
C28 /C29 steranes (at m/z 218)
C28 /(C27 + C28 + C29 ) (at m/z 218)
C29 /(C27 + C28 + C29 ) (at m/z 218)
C30 sterane index: C30/(C27 to C30) steranes selected
diasteranes/regular steranes
Regular C27-C28-C29 steranes/C30-hopanes
Monoaromatic steranes
C27-C28-C29 monoaromatic steranes (MA) distribution.

Triaromatic steranes
C20 TA/(C20 TA + C21 TA)
C26 TA (20S)/sum of C26 TA (20S) through C28 TA (20R)
C27 TA (20R)/C28 TA (20R)
C28 TA (20R)/C28 TA (20S)
C26 TA (20S)/[C26 TA (20S) +C28 TA (20S)]
C28 TA (20S)/[C26 TA (20S) +C28 TA (20S)]
Table 1. Examples of some diagnostic ratios of biomarkers frequently used for the
environmental forensic studies.
4. Examples of parameters used in fingerprinting

4.1 Normal -alkanes characteristics
The distribution of n-alkanes in crude oils can be used to indicate the organic matter source
(Duan and Ma, 2001). For example, the increase in the n-C15 to n-C20 suggests marine
organic matters with contribution to the biomass from algae and plankton (Peters and
Moldowan, 1993). Oil samples characterized by uniformity in n-alkanes distribution
patterns suggest that they are related and have undergone similar histories with no signs of
biodegradation (Ficken et al. 2000 and Duan and Ma, 2001).
4.2 Carbon preference index (CPI)

Carbon preference index, obtained from the distribution of n-alkanes, is the ratio obtained by
dividing the sum of the odd carbon-numbered alkanes to the sum of the even carbon-
numbered alkanes. CPI is affected by both source and maturity of crude oils (Tissot and Welte,
1984). CPI of petroleum oils ranging about 1.00 generally shows no even or odd carbon
preference indicates mature samples. Also, it can be used in source identification; petroleum
origin contaminants characteristically have CPI values close to one (Maioli et al., 2011).
4.3 Degree of waxiness

The degree of waxiness can be expressed by the C21-C31/C15-C20 ratios. The oils
characterized by high abundance of n-C15to n-C20 n-alkanes in the saturate fractions
reflecting low waxy (Moldowan et al., 1994). Generally, the degree of waxness < 1 reveals
low waxy nature and suggests marine organic sources (Peters and Moldowan, 1993) mainly
of higher plants deposited under reducing condition.
5. Examples of parameters used in biomarker fingerprinting

5.1 Pristane/phytane ratio
Both pristine (2,6,10,14- tetramethyl pentadecane) and phytane (2,6,10,14- tetramethyl
hexadecane) are derived from the phytol side chain of chlorophyll, either under reducing
conditions (phytane) or oxidizing conditions (pristane). Also both pristine and phytane
became dominant saturated hydrocarbon components of highly weathered crude oils until
they are degraded (Moustafa et al., 2004).
The pristane/phytane (Pr/Ph) ratio is one of the most commonly used correlation
parameters which have been used as an indicator of depositional environment (Peters et al.,
2005). It is believed to be sensitive to diagenetic conditions; Pr/Ph ratios substantially below
unity could be taken as an indicator of petroleum origin and/or highly reducing
depositional environments. Very high Pr/Ph ratios (more than 3) are associated with
terrestrial sediments. Pr/Ph ratios ranging between 1 and 3 reflect oxidizing depositional
environments (Hunt, 1996).
According to Lijmbach (1975) low Pr/Ph values (<2) indicate aquatic depositional
environments including marine, fresh and brackish water (reducing conditions),
intermediate values (24) indicate fluviomarine and coastal swamp environments, whereas
high values (up to 10) are related to peat swamp depositional environments (oxidizing
conditions).
5.2 Isopreniods/n-alkanes
Waples (1985) stated that by increasing maturity, n-alkanes are generated faster than
iosprenoids in contrast to biodegradation. Accordingly, isopreniods/n-alkanes (Pr/n-C17
and Ph/n-C18) ratios provide valuable information on biodegradation, maturation and
diagenetic conditions. The early effect of microbial degradation can be monitored by the
ratios of biodegradable to the less degradable compounds. Isoprenoid hydrocarbons are
generally more resistant to biodegradation than normal alkanes. Thus, the ratio of the
pristane to its neighboring n-alkane C17 is provided as a rough indication to the relative
state of biodegradation. This ratio decreases as weathering proceeds.
5.3 Steranes (m/z 217) distribution

The distribution of steranes is best studied on GC/MS by monitoring the ion m/z=217
which is a characteristic fragment in the sterane series. It is agreed that the relative amounts
of C27-C29 steranes can be used to give indication of source differences (Lijmbach, 1975).
For example, predominance of C28, C29 and C30 steranes indicate an origin of the oils
derived mainly from mixed terrestrial and marine organic sources, while oils show slightly
low abundance of C28 and C29 and relatively higher concentrations of C27 steranes indicate
more input of marine organic source.
Biomarkers 173
5.4 Triterpanes (m/z 191) distribution

Together with steranes, triterpanes belong to the most important petroleum hydrocarbons
that retain the characteristic structure of the original biological compounds. Tricyclic,
tetracyclics hopanes and other compounds contribute to the terpane fingerprint mass
chromatogram (m/z=191) are commonly used to relate oils and source rocks (Hunt, 1996).
Mass fragmentogram at m/z=191 can be used to detect triterpanes in the saturate
hydrocarbon fraction.
5.4.1 Tricyclic terpanes

Aquino et al. (1983) indicated that tricyclic terpanes are normally associated with marine
source. In addition it has been used as a qualitative indicator of maturity (Van Grass, 1990).
In high mature oils, the tricyclic terpanes is dominated more than in low mature oils (Hunt,
1996).
5.4.2 Homohopanes
The homohopanes (C31 to C34) are believed to be derived from bacteriopolyhopanol of
prokaryotic cell membrane. C35 homohopane may be related to extensive bacterial activity
in the depositional environment (Ourisson et al., 1984). Homohopane index can be used as
an indicator of the associated organic matter type, as it can also be used to evaluate the
oxic/anoxic conditions of source during and immediately after deposition of the source
sediments (Peters and Moldowan, 1991). Low C35 homohopanes is an indicator of highly
reducing marine conditions during deposition whereas high C35 homohopane
concentrations are generally observed in oxidizing water conditions during deposition,
consistent with the oxic conditions (Peters and Moldowan, 1991).
5.4.3 Gammacerane
Gammacerane, originally thought to be as hypersalinity indicator (Sinninghe-Damste et al.,
1995), is associated with both marine and lacustrine environments of increasing salinity
(Waples and Machihara, 1991; and Peters and Moldowan, 1993).
Fig. 5. Gammacerane chemical structure.

5.4.4 Ts/Tm
The ratio of Ts (trisnorneohopane) to Tm (trisnorhopane) more than (0.5) was found to
increase as the portion of shale in calcareous facies increases (Hunt, 1996). Van Grass (1990)
stated that Ts/Tm ratios begin to decrease quite late during maturation but Waples and
Machihara (1991) reported that Ts/Tm ratio does not appear to be appropriate for
quantitative estimation of maturity.
5.4.5 C29/C30 hopanes ratios

C29/C30 hopanes ratios are generally high (>1) in oils generated from organic rich
carbonates and evaporates (Connan et al., 1986).
5.4.6 Steranes/17 (H)-hopanes ratio

The regular steranes /17(H)-hopanes ratio reflects input of eukaryotic (mainly algae and
higher plants) versus prokaryotic (bacteria) organisms to the source rock. The
sterane/hopane ratio is relatively high in marine organic matter with values generally
approaching unity or even higher. In contrast, low steranes and sterane/hopane ratios are
more indicative of terrigenous and/or microbially reworked organic matter (Suzuki et
al.,1996).
5.4.7 Bisnorhopanes
It is believed that sediments containing large amounts of bisnorhopane were deposited
under anoxic conditions (Mello et al., 1988). Bisnorhopanes are types of pentacyclic
triterpanes present in significant concentrations in oil. Bisnorhopanes are observed in
Guatemalan evaporites (Connan et al., 1986) and frequency reported in other biogenic
siliceous rocks of the circum-Pacific region (Katz and Elrood, 1983).
5.5 Metalloporphyrins
Porphyrins are the tetrapyrole compounds; the porphyrin nucleus consists of four pyrrole
rings joined by four methine bridges giving a cyclic tetrapyrrole structure. The majority of
these compounds are thought to originate from various chloropigments produced by
phototrophic organisms of the geological past (Yui et al., 2007). Metalloporphyrins has
become a valuable tool in the determination of the origin and maturity of the organic matter
(Doukkali et al., 2002; Chikaraishi et al., 2005 and Ohkouchi et al., 2006). The porphyrin
structure consists of a porphyrin nucleus with various groups of side chains occupying
some or all of its peripheral positions.
Metalloporphyrins were extracted from asphaltene and maltene fractions using adsorption
column chromatography (Faramawy et al., 2010). Porphyrins occur as etioporphyrin (Etio),
Benzo-etio, deoxophylloerythroetioporphyrin (DPEP), Benzo-DPEP and tetrahydrobenzo-
DPEP (THBD). The distribution of different types of metalloporphyrins is useful for
interpreting transformation of kerogen into bitumen, depositional environments and
maturation levels of deposited organic matters.
Biomarkers 175
Fig. 6. Structures of different types of metalloporphyrins.
6. Developments in GC-MS instrumentation

The low biomarker concentrations in oils (often in the range of several parts per million) in
the presence of a highly complex petroleum hydrocarbon matrix especially weathered oils,
the variety of chemical classes present in oils and the possible co-elutions in conventional
chromatographic separations make the identification of biomarkers a more difficult task.
The development of more reliable, highly selective, fast and sensitive separation and
identification tools for biomarker analysis purposes can be considered as one of the most
important research points in this field for a meaningful biomarker analysis.
The use of comprehensive two-dimensional gas chromatography (GC GC) coupled to

time-of-flight mass spectrometry (TOFMS) was found to be a powerful tool for overcoming
some problems and limitations since it (i) separates substances using two interconnected
capillary columns containing different stationary phases and (ii) uses the fast data
acquisition of time-of-flight analyzer as a robust registry for GC GC (Aguiar et al., 2001).
In their work, Aguiar et al. (2001) used this technique to overcome the co-elution between
tri- and pentacyclic terpanes separated by extracted ion chromatograms (EIC) for ions of
mass-to-charge ratio (m/z) 191. The biomarker analysis by GC GCTOFMS was much
better than in previous works using one-dimensional GC. Co-elutions between tri- and
pentacyclic terpanes were clearly resolved in the second column. Noteworthy separation
between the C30 hopane and C30 dimethylated homohopane was achieved and overlap of
hopanes with steranes in the m/z 217 was eliminated. Besides hopanes, dimethylated tri-
and tetracyclic terpanes were identified. These findings indicate the superiority of GC
GCTOFMS as a technique for separation and identification of biomarkers in oils due to its
high sensitivity, specificity and capability to elucidate compounds structure with high
spectral resolution.
Comprehensive two-dimensional gas chromatography (GCGC) has also been used to
separate and identify alkylated aromatics (naphthalenes, biphenyls, fluorenes,
phenanthrenes and chrysenes), sulfur-containing aromatics (dibenzothiophenes,
benzonaphthothiophenes), steranes, triterpanes, and triaromatic steranes. These biomarkers
were separated into easily recognizable bands in the GCGC chromatogram. Methods used
to identify the bands included peak matching with chemical standards and comparison with
GC/MS extracted ion chromatograms (Frysinger and Gaines, 2001). By designing mass
spectrometers that can determine m/z values accurately to four decimal places, it is possible
to distinguish different formulas having the same nominal mass. Since a given nominal
mass may correspond to several molecular formulas, lists of such possibilities are especially
useful when evaluating the spectrum of an unknown compound.
GC/MS/MS is an operation based on the covariant scan of electrostatic magnetic fields on
the trisector double focusing mass spectrometer providing more accurate data. The
quadraupole is a common mass separator gives a sufficient sensitivity and selectivity
however, high resolution mass spectrometry (HRMS) is also used due to its ability to
provide quantitative data for compounds present in complex mixtures for biomarkers
analysis. Triple quadrupole GC/MS offers a viable alternation for the rapid, routine analysis
providing excellent precision, sensitivity, selectivity, and dynamic range (Thermo-
application note 10261).
Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) benefits from
ultra-high mass resolving power (greater than one million), high mass accuracy (less than 1
ppm) and rapid analysis which make it an attractive alternative for the analysis of different
and wide range of petroleum products (Klein et al., 2003).
It should be noted, however, that there is no single fingerprinting technique that can fully
and readily meet the objectives of biomarkers investigation and quantitatively allocate
hydrocarbons to their respective sources, particularly for complex hydrocarbon mixtures or
extensively weathered and degraded oil residues. Combined and integrated multiple tools
are often necessary under such situations.
Biomarkers 177
7. Data analysis by computerized techniques

Data analysis is an important part of chemical fingerprinting and a broad collection of
statistical techniques has been used for evaluation of data.
After separation and identification of biomarkers, principal component analysis PCA, a
mathematical procedure, can be used for analyses of chromatograms using a fast and
objective procedure with more comprehensive data usage compared to other fingerprinting
methods. The discriminative power of PCA can be enhanced by deselecting the most
uncertain variables or scaling them according to their uncertainty.
For example, preprocessing of GC-MS chromatograms followed by principal component
analysis (PCA) of oil spill samples collected from the coastal environment in the weeks after
the Baltic Carrier oil spill and from the tank of the Baltic Carrier (source oil) was carried out
(Christensen et al., 2005). The preprocessing consists of baseline removal by derivatization,
normalization, and alignment using correlation optimized warping. The method was
applied to chromatograms of m/z 217 (tricyclic and tetracyclic steranes) of oil spill samples
and source oils. The four principal components were interpreted as follows: boiling point
range (PC1), clay content (PC2), carbon number distribution of sterols in the source rock
(PC3), and thermal maturity of the oil (PC4). The method allows for analyses of
chromatograms using a fast and objective procedure and with more comprehensive data
usage compared to other fingerprinting methods.
8. Previous studies in Egypt

8.1 Egyptian Western Desert
The Western Desert covers about 700,000 square kilometers (equivalent in size to Texas) and
accounts for about two-thirds of Egypt's land area. This immense desert to the west of the
Nile spans the area from the Mediterranean Sea south to the Sudanese border. The chemical
fingerprinting of oils in this area is a great interesting research area for many proposes as for
example identifying the sources of petroleum oil or complex environmental pollutants. The
original sources of complex mixtures can often be identified by the relative abundance of
some major individual compounds (e.g n-alkanes) forming a chemical pattern by ratios of
specific constituents or by identifying source-specific compounds or markers (e.g
triterpanes) in the environmental sample being investigated (Peters et al., 2005). These
parameters depend mostly on the preburial environments of the living organisms, the
depositional environments of the organic matter and the diagenetic processes in the source
rocks.
In their work, Roushdy et al. (2011) utilize biomarkers characteristics together with bulk
geochemical parameters to identify and characterize the crude oils and to assess the
respective depositional environments and maturation. Variation of crude oil-gravities in the
Western Desert reflects different stages of oil migration and accumulation as well as
different oil source rocks in the same and different ages (Zein El Din et al., 1990).The authors
attempt to assess the correlation between the crude oil samples and the potential source
rocks to confirm the indigenous sources for the petroleum generation of some oilfields of the
North Western Desert. This target was made throughout the study in detail of the analytical
results for three crude oil samples collected from three oilfields in the North Western Desert
oilfields (Meleiha, Misaada and Qarun) as well as three extract samples (Baharia, Kharita
and Khtataba) from formations ranging in age from Upper Cretaceous to Middle Jurassic.
Fig. 7. Map of Egypt showing the main oil and gas fields.
The specific geochemical parameters have been assessed by the aid of gas chromatography
and gas chromatographic-mass spectrometric analyses of the saturated fractions. The degree
of the correlation between crude oils and the extracted samples was determined by
studying the correlation scores for both oils and extracts. Eight correlation parameters
have been studied for this purpose includes: saturates%, saturates/aromatics ratio,
Cmax, C21+C22/C28+C29, CPI, pristane/phytane, pristane/n-C17 and pristane+n-
C17/phytane+n-C18. An overall correlation score was obtained for each oil and extract by
summing up the contribution from each parameter. The GC/FID chromatogram of the
Meleiha crude oil sample is characterized by a monotonically decreasing homologous series
of heavy normal alkanes (n-C25 to n-C30) and display odd carbon preference at n-C15 which
reflects mature oils originated mainly from non-marine origin mainly terrestrial organic
matters deposited under slightly oxidizing environment and slightly mixed with inputs
from marine source (Hunt, 1996). The mode of distribution of n-paraffins in the crude oils of
Misaada and Qarun oilfields show that the maximum abundance is at n- C15 to n-C25
reflecting marine origin.
The steranes distribution of crude oils was studied. Meleiha crude oil was found to be
characterized by low predominance of C27 steranes and slightly high abundance of C28 and
C29 indicating that the Meleiha oil is believed to be generated from both marine shales and
carbonates enriched in marine algae with more contribution from terrestrial organic sources
deposited under saline conditions. It reveals that the Meleiha oil is derived mainly from
terrestrial organic sources.
Biomarkers 179
The high concentrations of C27 - C29 diasteranes in case of Meleiha oil indicate input of
marine organic source with more contribution from terrestrial organics (Waples and
Machihara, 1992). The high diasteranes concentration compared to regular steranes suggest
a clay rich source rock because the clay is required to catalyze the steroids transformation to
diasteranes (Peters and Moldowan, 1991). Misaada and Qarun oils are characterized by
slightly lower predominance of C27 steranes and higher abundance of C28 and C29 steranes
indicating inputs from marine organic sources (Waples and Machihara, 1992). Moreover, the
distributions of regular steranes C29, C27 and C28 on the ternary diagram reveal also more
contribution from marine organic sources. The diasteranes concentrations compared to
regular steranes is low, suggesting a clay rich source rock.
The crude oil samples of Qarun and Misaada oilfields have Pr/n-C17 and ph/n-C18 ratios
0.28, 0.47 and 0.1, 0.1, respectively reflecting mostly mature and originated mainly from
marine organic sources deposited under reducing environment. The crude oil of Meleiha
oilfield has Pr/n-C17 and ph/n-C18 of 0.40 and 0.28 indicating mixed organic sources.
Terpanes biomarkers distributions derived from the m/z 191 mass chromatograms show
that the C21-C25 tricyclic terpanes of Meliha oil appear to be the largest components which
may support that the oil of Meleiha oilfield is more mature and sourced mainly from marine
carbonate source rocks. At the same time, the C23, C24 and C25 tricyclic terpanes are
generally of lower values compared with C22 indicating that the oil has some inputs from
terrestrial organic materials (Hunt, 1996). The unusual low amounts of C30 extended
hopanes seem to be associated with mixed organic sources (Moldowan et al., 1985). This
phenomenon can be displayed by the low ratio of C29/C30 extended hopanes.
On the other hand, The C30 hopanes are the largest components in the series C27-C34 in oil
samples from Misaada and Qarun oilfields. This indicates that the organic materials in these
oils were originated mainly from saline and hypersaline environments (Peters and
Moldowan, 1993). The extended hopanes are available as paleo environmental indicator
(Waples and Machihara, 1992). The unusual large amounts of C30 hopanes seem to be
associated with marine sources (Moldowan et al., 1985).
Bisnorhopanes are types of pentacyclic triterpanes present in significant concentrations in oil.
Bisnorhopanes are observed in Guatemalan evaporites and frequency reported in other
biogenic siliceous rocks of the circum-Pacific region (Connan et al., 1986). It is believed that
sediments containing large amounts of bisnorhopane were deposited under anoxic conditions
(Mello et al., 1988). The crude oils of Misaada oil field have relatively higher amounts of C28
bisnorhopane indicating more anoxic environment than Qarun and Meleiha oils.
Carbon preference index (CPI) values of the studied crude oils are close to unity, ranging
from (0.94 to1.04) indicating mature crude oils.
Pr/Ph ratio of the oil sample from Meleiha oilfield is 3.0 indicating oxidizing depositional
environment of the crude oil while the crude oils from Qarun and Misaada oil fields have
Pr/Ph ratios of 0.63 and 2.00 respectively reflecting that these crude oils were deposited
under transitional (reducing oxidizing) environments. These results indicate good
correlation between crude oils from Qarun and Misaada oilfields with slight correlation to
crude oil from Meleiha oilfield.
Oil: source correlation reflect a good correlation between the extract samples of Kharita and
Khatatba source rocks and crude oils from Meleiha and Qarun oilfields. The extract of
Bahariya source rock shows slight correlation with Meleiha oil and differ from the other oil
samples. These evidences indicate that Kharita and Khtataba source rocks seem to act as
sources and reservoirs for oil generation in the Qarun and Misaada oilfields while the oil
generation of Meleiha oilfield seems to be migrated from Bahariya source rocks.
8.2 Suez Gulf

The Gulf of Suez occupies the northwestern arm of the Red Sea between Africa proper (west)
and the Sinai Peninsula (east) of Egypt. The length of the gulf, from its mouth at the Strait of
Jubal to its head at the city of Suez, is 195 miles (314 km) and it varies in width from 12 to 20
miles (19 to 32 km). Because the importance occurrence of crude oil in the Gulf of Suez, the
biological markers was analyzed to evaluate the geochemical relationships between the oils
recovered from some oil fields within the Gulf of Suez to assess and investigate oil
characterization, maturation, source depositional environments and oil families.
Roushdy et al. (2010) evaluate the geochemical relationships between the oils recovered
from some oil fields within the Gulf of Suez. This target was achieved through analytical
results of GC and GC-MS analysis for seven crude oil samples collected from seven oilfields
namely: Ras Badran, Belayim marine, Belayim Land, Rahmi, West Bakr, Esh El Mellaha and
Geisum distributed within the Gulf of Suez. These samples are representative for the
producing horizon zones (Belayim, Rudies and Nuhkul formations.) of Upper- Lower
Miocene age characterized by limestone facies with depths ranging from 2250 to 8286 ft.
Geochemical parameters based upon acyclic isoprenoids, steranes and terpanes coupled
with bulk geochemical parameters indicated whether the crude oils are of marine, terrestrial
or mixed marine-terrestrial origin.
Biomarkers analyses of crude oils from the Gulf of Suez suggest that oils are more mature
and derived mainly from mixed organic sources from terrestrial and marine inputs
contribution to the biomass from algae and plankton in different saline environments.
A few discrepancies that appear between the results obtained by using the different
parameters can be related to the alteration caused by the number of processes (physical,
chemical and/or biological) affecting part of the source related biomarkers pattern of the oil
after generation and/or primary migration from the source rock.
In another study, two genetic families based on biomarker analyses of oils were isolated
from the Gulf of Suez, Egypt. Oils from Ras Fanar and East-Zeit wells have high
gammacerance, low diasterances and high C33/C34 hopanes, consistent with an origin from
the Brown Limestone. Oils from the Gama and Amal-9 wells have low gammacerance, high
diasterances and oleanane indices > 20 %, indicating an angiosperm-rich Tertiary siliciclastic
source rock, probably the Lower Miocene Rudeis Formation (Peters et al., 2005).
(Younes et al., 2004) evaluated the depositional environments and maturation assessments
of source rocks from the central Gulf of Suez, Egypt utilizing the biomarker distributions in
nine crude oils derived from a synrift tectonic sequence of the central Gulf of Suez province.
No obvious variations were observed amongst the studied crude oils, suggesting that these
oils are all of the same genetic type. These oils features, a predominance of oleanane,
reaching 24%, and a relatively low gammacerane concentration of 10%, suggested that these
oils were derived from a terrigenous organofacies source rock with a significant angiosperm
higher land plants input deposited within the marginally mature syn-rift shale of Lower
Miocene Nukhul, Rudeis and Kareem formations of mixed kerogen types II-III. Maturity
Biomarkers 181
parameters based on various sterane isomerisation distributions and polycyclic aromatic

compounds indicate a low thermal maturation level for the generated hydrocarbons within
the syn-rift lithostratigraphic succession. These similarities in geologic occurrences and
biomarker characteristics suggest the possibility that the hydrocarbon expulsion could have
been initiated from deeply buried Miocene source rocks and trapped within the syn-rift
structures throughout the extensional faults of the central Gulf of Suez province.
(Barakat et al., 2000) studied the aliphatic and aromatic fractions of a beach tar sample from
the Mediterranean coast of Sidi Kreir, 37 Km west of the city of Alexandria by GC and
GC/MS techniques. A complete analysis was carried out to investigate chemical
composition changes, fate of weathered oil residue and possible source identification. The
distribution of sterane, hopane, mono-and triaromatic steroids, C2 and C3 phenanthrenes
and dibenzothiophenes and chrysenes, however, had remained unaltered by weathering.
The beach tar possessed geochemical features consistent with a marine carbonate or
evaporite source depositional environment under normal saline reducing conditions.
9. Current work
Applications of biomarkers in oil spill source identification
Although oil is the dominant energy source, oil spill occurs worldwide causing a severe
global environmental problems (Abostate et al., 2011). Egypt is suffering from oil pollution
owing to the increasing petroleum activities in the last decades. Environmental protection is
currently an important subject of increasing public and research concern and as a result,
special efforts have already been done so as to develop oil spill detection and fingerprinting.
Therefore, to unambiguously characterize, identify, categorize, and quantify all sources of
hydrocarbons entering the environment is very important for environmental damage
assessment, evaluation of the relative risks to the ecosystem posed by each spill and
selecting appropriate spill response and taking effective cleanup measures. Biomarkers are
the most important hydrocarbon groups for chemical fingerprinting which play a very
important role in source identification in environmental forensic investigations of oil spills.
It was a useful analogy to explain this type of forensic analyses for spilled oil. However, it
was recognized then, and remains true today, that the analyses of spilled oils do not have
the statistical discriminating power of the human fingerprint in the sense that each human
has an individual fingerprint. Analyses of spilled oils and potential sources are usually
undertaken by increasingly sophisticated chemical analyses until either all but one potential
source oil remains that cannot be distinguished from the spilled oil, or all potential sources
have been eliminated and the spill is then a "mystery". The presumption for success using
fingerprinting is that a complete collection of possible sources has been secured for the
matching analyses. The term "passive tagging" has been used in place of fingerprinting in
the past to describe the chemical analyses of oils. The term derives from the process of using
the chemicals naturally present in the oil as "tags". The "passive" part of the term was used
because there were proposals and some experiments conducted in the late 1960s and early
1970s to introduce "active tags" into various oil cargos to allow for identifying the oils if they
were spilled (Adlard, 1972). Various chemicals were proposed as active tags, but the
obvious international administrative and logistical effort needed to keep track of such
"active tags" prevented operational use of active tagging systems.
Nothing sparks concerns about contaminates in the environment quite like a petroleum
release. Unfortunately, the events of 2010 served to heighten the awareness and need to
have the capability to monitor and characterize the extent and breadth of the impact of these
events. Using petroleum biomarker analysis make it possible to accurately identify the
source of contaminates back to the specific origin as well as determining the absolute
concentrations of priority pollutant PAHs.
Generally, gas chromatograms of two oil samples are compared by comparing the envelop
shapes of the n-alkanes, the unresolved backgrounds and individual peak intensities. By
means of GC/MS, a big number of compound classes of oils may be separately detected and
compared. Computerized oil spill identification (COSI) may highly support analysts in GC
and GC/MS results evaluation and adds a new dimension to forensic oil spill
identification. It is greatly increases the possibilities for finding the sources of oil pollution.
The patterns of the biomarkers and a set of parameters based on the literature findings
was chosen to be investigated for most Egyptian crude oil and stored in the database in
order to construct an Egyptian computerized oil spill identification database of local
crude oils. Gas-chromatograms and mass-fragmentograms are rapidly produced from
raw GC- and GC/MS-data for comparing an unknown pollutant sample with any oil
sample stored in the database then simultaneously a much stronger connection between a
distinct oil spill and its actual source accurately established than before, as shown clearly
in Figure 8. These parameters allow a more objective, provable and defensible result
Fig. 8. Representative model of computerized oil spill identification matching.

Biomarkers 183
evaluation than the mere visual comparison of the chromatograms. In addition, these
parameters may also be used for finding oils in the database, which are similar to the spill
sample. The system is fast and greatly saves laboratory resources and reliable and
comfortable.
10. Conclusion
Biomarkers are naturally occurring, ubiquitous and stable complexes that are objectively
measured and evaluated as an indicator of a certain state. It is used in many scientific fields;
medicine, cell biology, exposure assessment, geology and astrobiology.
Due to the variety of geological conditions and ages under which oil was formed, every
crude oil exhibits a unique biomarker fingerprint. From the identification point of view,
biomarkers are the most important hydrocarbon groups in petroleum because they can be
used for chemical fingerprinting which provides unique clues to the identity of source rocks
from which petroleum samples are derived and the biological source organisms which
generated the organic matter, the environmental conditions that prevailed in the water
column and sediment at the time, the thermal history (maturity) of both the rock and the oil,
and the degree of microbial biodegradation.
GC-MS is considered the most widely used method for biomarkers detection and
identification which is a true combination of its separate parts (gas chromatography, GC and
mass spectrometry, MS). The mass spectrometer has long been recognized as the most
powerful detector for gas chromatography due to its high sensitivity, specificity and
capability to elucidate compound structure. Mass fragmentography provides a satisfactory
tool for obtaining specific fingerprints for classes and homologous series of compounds
resolved by gas chromatography. The development of more sensitive and selective
identification tool for biomarker analysis purpose especially for crude oils containing low
concentration biomarkers as weathered and light oils can be considered as one of the most
important research points in this field. After separation and identification of biomarkers,
principal component analysis PCA, a mathematical procedure, can be used for analyses of
chromatograms using a fast and objective procedure with more comprehensive data usage
compared to other fingerprinting methods. The discriminative power of PCA was enhanced
by deselecting the most uncertain variables or scaling them according to their uncertainty.
Chemical analysis of biomarkers generates information of great importance to
environmental forensic investigations in terms of determining the source of spilled oil. The
patterns of the biomarkers and a set of parameters were used to construct an Egyptian
computerized oil spill identification database. This can greatly increase the possibilities for
finding the sources of oil pollution by comparing an unknown pollutant sample with any
similar oil sample stored in the database. A much stronger connection between a distinct oil
spill and its actual source may be established than before.
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10
Quantification of Antimalarial Quassinoids

Neosergeolide and Isobrucein B in Stem and
Root Infusions of Picrolemma sprucei
Hook F. by HPLC-UV Analysis
Rita C. S. Nunomura1, Ellen C. C. Silva1,
Sergio M. Nunomura2, Ana C. F. Amaral3,
Alade S. Barreto3, Antonio C. Siani3 and Adrian M. Pohlit2
1Department of Chemistry, Amazon Federal University (UFAM), Amazon,
2Coordenation of Research in Natural Products,
Amazon National Institute (INPA), Amazon,

3Laboratory of Natural Products, Farmanguinhos,
Oswaldo Cruz Institute Foundation (FIOCRUZ), Rio de Janeiro,

Brazil
1. Introduction
Natural products have been very important to ensure the survival of the man, since the
ancient times, especially as remedies to treat different diseases. Today, despite the
development of new therapies and new ways of drug development (combinatorial
chemistry, ie); natural products continue to play a highly significant role in the drug
discovery and development process. (Newman, Cragg, 2007).
Even though fewer drugs have been approved as therapeutical agents lately, nature still
inspires the drug development for neglected diseases (malaria, tuberculosis and leishmania)
and alternative therapies such as phytotherapy. In both cases, medicinal plants, plants that
have been used by the folk medicine for years, are mostly studied. The World Health
Organization (WHO) recognized the importance of phytotherapy and the conservation of
medicinal plants that stated the importance of conservation is recognized by WHO and its
Member States and is considered to be an essential feature of national programmes on
traditional medicines (Akerele, 1991).
The successful use of some medicinal plants by local population for years, in many cases for
centuries, in the treatment of diseases or symptoms associated to some diseases is the basis
of the development of drugs or other therapeutical products from them. For instance,
artemisinin, a very potent antimalarial, including for drug-resistant malaria strains, was
isolated from Artemisia annua L., a plant from the traditional Chinese medicine used as
remedy for chills and fever for more than 2000 years (Agtmael et al. , 1999).
On the other hand, there is an increasing interest for medicines from nature. This interest in
products of plant origin is due to several reasons as possible side-effects from synthetic
drugs and the awareness that natural products are harmless. The world market for
phytomedicinal products was estimated in U$ 10 billion in 1997, with an annual growth of
6.5%. In Germany, 50% of phytomedicinal products are sold on medical prescription and the
cost being refunded by health insurance. This includes pharmaceutical formulations as plant
extracts or purified fractions called phytomedicines or herbal remedies. In many countries,
phytomedicines or herbal remedies are controlled as synthetic drugs and they have to fulfill
the same criteria of efficacy, safety and quality control (Rates, 2001).
However the quality control of phytomedicines poses a significant challenge due to the
complexity of a vegetable extract and column chromatography has proved to be a very
helpful and powerful technique. The quality control of Gingko biloba L. formulations is good
example of this challenge. Gingko leaves contains as active compounds flavonoids and
terpene lactones (gingkgolides and bilobalide) along with long-chain hydrocarbons, alicyclic
acids, cyclic compounds, sterols, carotenoids, among others. Most of the quality control of
Gingko preparations are based on column chromatography and that was reviewed elsewhere
already ( Sticher, 1992; van Beek, 2002).
Column chromatography, especially high performance liquid chromatography (HPLC), has
been extensively used in the quality control of plant extracts and phytomedicines
formulations, because of its characteristics. The chosen technique must be able to identify
the interested compounds (active principles) that are normally not volatile and, in some
cases, occur at very small concentrations. Ideally this technique should also be capable to
quantify the interested compounds, so one can establishes dosages for the phytomedicine
formulation. The required efficiency and selectivity for qualitative and quantitative analysis
of the effective components can be achieved by HPLC. Li et al. (2011) have recently reviewed
the use of different chromatography techniques, such as HPLC, in the quality control of
Chinese medicine.
Although, HPLC is a very powerful technique applied in the quality control of medicinal
plants, it is necessary to properly identify the active principles of the medicinal plant. This is
achieved combining the use of HPLC or other separation technique with a biological test.
The search for antimalarials from medicinal plants is one of the most successful examples of
this combination as mentioned earlier. In the Amazon region, there are a large number of
plants popularly used against malaria or associated symptoms (fever for instance). Milliken
(1997) has identified over hundreds of antimalarial plants used by local population in the
Amazon region. Many of these plants remained up to now without a study that could
confirm their antimalarial activity.
From the fewer plants studied so far, Picrolemma sprucei Hook. f., has been studied by our
research group. Herein we described the use of HPLC in the quality control of the
antimalarial quassinoids, neosergeolide and isobrucein B, the active principles of this
species.
Picrolemma sprucei Hook. f. (P. pseudocoffea Ducke is a commonly cited pseudonym) is a
widely distributed and important Amazonian medicinal plant. It is known in the Amazon
region by common names which call attention to its resemblance to the coffee plant: sacha-
caf in Peru (Duke & Vasquz 1994), caferana in Brazil (Silva et al. 1977) and caf lane or
tuukamwi in French Guiana (Grenand et al. 1987). Infusions of roots, stems, and leaves of P.
sprucei are traditionally used in different dosages and preparations for the treatment of
Quantification of Antimalarial Quassinoids Neosergeolide and Isobrucein B
in Stem and Root Infusions of Picrolemma sprucei Hook F. by HPLC-Uvanalysis 189
malaria fevers (Bertani et al. 2005, Vigneron et al. 2005, Milliken 1997), gastrointestinal
problems and intestinal worms (Moretti et al. 1982, Duke & Vasquz 1994). Also, the sale of
this plant is sometimes restricted by local vendors due to its use in provoking spontaneous
abortions.
Studies on the biological activity of infusions and other derivatives of P. sprucei have shown
that extracts of this plant have important antimalarial and antihelminthic activities. Bertani
et al. (2005) reported that a P. sprucei leaf infusion inhibited 78 % of Plasmodium yoelli rodent
malaria growth in vivo at a dosage of 95 mg/kg. Furthermore, these same authors reported
that of a total of 36 preparations from 25 traditionally used antimalarial plants from French
Guiana, P. sprucei leaf infusion had the greatest in vitro activity against the human malaria
parasite Plasmodium falciparum (median inhibition concentration, IC50=1.43 g.mL-1). These
results indicate P. sprucei leaf extracts have potential as antimalarials.
In 2006, Nunomura et al. showed that water and ethanol extracts of P. sprucei at
concentrations of 1.3 g.L-1 were lethal (90-95 % mortality) in vitro towards larvae of the
nematoide species Haemonchus contortus (Barber Pole Worm), a gastrointestinal nematode
parasite found in domestic and wild ruminants. These studies lend support to popular
assertions that infusions and other derivatives of P. sprucei have important antimalarial and
antihelminthic activities.
OH OH
CO2 CH3 O
HO HO CO2 CH3
OH O O
OAc O OAc
O O O O
1
2
OH
HO CO 2CH 3
O
O R
O
O O
3: R = OAc
4: R = OH
Fig. 1. Quassinoids from Picrolemma sprucei Hook.
Two quassinoids have been isolated from P. sprucei roots, stems and leaves and identified as
isobrucein B (1) (Moretti et al. 1982) and neosergeolide (2) (Schpector et al.1994, Vieira et al.
2000). Quassinoid is the name given to any of a number of bitter substances found
exclusively in the Simaroubaceae family (Polonsky 1973). Early reports on P. sprucei
composition from French Guiana (Moretti et al. 1982) described the isolation of sergeolide
(3), a structural isomer of 2 and a derivative, 15-deacetylsergeolide (4) (Polonsky et al. 1984),
from the leaves. Since confirmation of the structure of 2 by x-ray crystallography (Schpector
et al. 1994) and the systematic application of two-dimensional NMR techniques to the
identification of components of P. sprucei (Vieira et al. 2000, Andrade-Neto et al. 2007),
neither sergeolide nor its derivative have ever again been described and may be erroneous
structures.
Chemically, quassinoids are degraded triterpene compounds which are frequently highly
oxygenated. Many quassinoids exhibit a wide range of biological activities in vitro and/or in
vivo, including antitumor, antimalarial, antiviral, anti-inflammatory, antifeedant,
insecticidal, amoebicidal, antiulcer and herbicidal activities. For instance, bruceantin (5),
brusatol (6), simalikalactone D (7), quassin (8) and glaucarubinone (9) are some of the most
well-studied quassinoids and exhibit a wide range of biological activities (Guo et al. 2005).
OH OH
HO CO2CH3 HO
O O
OH
O O OR
OR
HO O O O O
5: R= COCH=CCH(CH3)2 7: R= COCH(CH3)C2H5
CH3
6: R= COCH=C(CH3)2
OH
OMe HO
O OH
O O
MeO O OR
H
O O O
O
H
8 9: R= COC(CH3)OHCH2CH3
Fig. 2. Quassinoids bruceantin, simalikalactone D, quassin, brusatol and glaucarubinone.
Isobrucein B (Fandeur et al. 1985) and neosergeolide (Andrade-Neto et al. 2007) display
significant in vitro antimalarial activity to the human malaria parasite P. falciparum. Recently,
the in vitro antimalarial activities of isobrucein B and neosergeolide were shown to be
comparable to antimalarial drugs quinine and artemisinin (Silva et al. 2009). According to
this same in vitro study, isobrucein B and neosergelide are as cytotoxic or as much as an
order of magnitude more cytotoxic than the antitumor drug doxorubicine towards several
human tumor strains. Additionally, isobrucein B has been shown to have important
antileukemic, antifeedant and leishmanicidal (Moretti et al. 1982; Nunomura, 2006).
Bertani et al. (2005) conveyed concern about the toxicity of infusions and other preparations
based on different parts of P. sprucei which is recognized in Amazonian traditional medicine
in general. Additionally, these authors were critical of the absence of knowledge of the
toxicity of infusions prepared from this species and lack of information available on the
quassinoid composition of these infusions in the study on toxicity published by Fandeur et

al. (1985), which focused only on the acute toxicity and antimalarial activity of isolated
quassinoid components o P. sprucei and not on toxicity and antimalarial activity of infusions.
Additional studies are needed to prove the in vivo efficacy and pharmacological activity of
these infusions as antimalarials with focus on the dose-effect and dose-response to define
the levels of toxicity. The aim of the present study was to develop a method for the
quantification of isobrucein B and neosergeolide in P. sprucei root and stem infusions based
on reversed-phase high performance liquid chromatography (HPLC) and ultraviolet
detection (UV).
2. Materials and methods

2.1 Reagents and solvents
Acetonitrile, HPLC grade, was purchased from Mallinckrodt Baker, Inc. (Xalostoc, Mexico).
The water used in all experiments was purified on a Milli-Q Plus System (Millipore,
Bedford, MA, USA).
2.2 Isolation of isobrucein B (1) and neosergeolide (2)

Two collections were performed on the main campus of the University of Amazonas, in
Manaus, Amazonas State, Brazil, in January and July of 1999. Voucher specimens are
deposited at the UFAM Herbarium (Silva 5729 & 5730) and INPA Herbarium (223883).
Identification was performed by Dr. Wayt Thomas as Picrolemma sprucei Hook. f. (Wayt
Thomas, personal communication). Roots and stems were cut into small pieces while fresh
and allowed to dry in the shade and were then ground. Air-dried powdered stems (890 g)
were extracted 3 times by maceration in hexanes at room temperature (1 week per
extraction). After concentration, hexane extract (4.79 g) was obtained. Next, the stems were
repeatedly infused in boiling water (Polonsky 1982) which resulted in aqueous solution (20
L). The aqueous solution was concentrated (2.0 L) then continuously extracted with
chloroform (40 h), that after total evaporation yielded chloroform extract (10.8 g).
Chloroform extract was purified on a column of silica gel which was eluted first with
chloroform (100 %), then a gradient of chloroform/methanol 99:170:30 (600 mL), 70:30
50:50 (600 mL), 50:5025:75 (600 mL), and 25:75100 % methanol (600 mL) and resulted in
171 collected fractions that were combined based on thin-layer chromatography (TLC)
analysis to yield 11 fractions. Fraction 9 (1.87 g) was purified on a column of silica gel which
was eluted first with 100 % hexane, then 80:20 hexane/chloroform (180 mL), 15:80:5
hexane/chloroform/acetone (800 mL), 10:80:10 hexane/chloroform/acetone (400 mL),
10:70:20 hexane/chloroform/acetone (1440 mL), 10:60:30 hexane/chloroform/acetone (500
mL), 10:50:40 hexane/chloroform/acetone (720 mL), acetone (500 mL), and methanol (500
mL) which resulted in 69 fractions that were combined based on TLC analysis. Combined
fraction 42-50 (360 mg) was re-crystallized from methanol/water and yielded colorless
crystals which were identified as pure 2 (73.9 mg) based on their spectral properties. The
supernatant was re-dissolved in methanol and the insoluble material was washed and
filtered resulting in 1 (62.0 mg), a white solid, which was identified based on its spectral
properties. The isolation of 1 and 2 yielded 0.57% and 0.68 %, respectively. The compounds
1 and 2 were identified on the basis of their IV, MS and NMR (1H, 13C, HOMOCOSY,
HMQC, HMBC and NOESY experiments) spectra analysis.
2.3 Preparation of root and stem infusions

P. sprucei infusions were prepared based on a popular recipe which is used to provoke
spontaneous abortions and with which toxic effects are associated according to locals. Stems
are the part most commonly used in these remedies. Shade-dried, ground root or stem (9.0 g)
was placed in a beaker and boiling deionized water (1.0 mL) was added. The beaker was
covered and allowed to stand for 10 min. After this time, the contents of the beaker was
filtered hot in a funnel with filter paper which resulted in root and stem infusions. A single
infusion was prepared from powdered, dried roots and another from powdered stems
obtained from mature plants.
2.4 Calculation of extractives

Infusion as prepared above was totally evaporated using rotary evaporation under vacuum
and a heated bath (< 50 C), then freeze-drying. The resulting dry extract was weighed and
divided by the mass of plant material used (9.0 g) in the preparation of each infusion and
expressed as a percentage (w/w) of extractives.
2.5 Preparation of samples of infusions for HPLC analysis

Freeze-dried extracts were dissolved in water to yield final concentrations of stem and root
extracts of 445 and 911 mg.L-1, respectively.
2.6 Preparation of standard solutions of isobrucein B (1) and neosergeolide (2)

Stock solutions of 1 and 2 were prepared at 0.63 g.L-1 and 0.50 g.L-1, respectively, in
methanol. Calibration standards were obtained by appropriate dilution of the stock
solutions with methanol. For 1, the concentrations used in calibration were 100, 50, 25, 10
and 5.0 mg.L-1. For 2, the concentrations used in calibration were 20, 10, 5.0 and 2.5 g.L-1. All
standard solutions were stored at -20 C until analysis and protected from light, remaining
stable for at least three months.
2.7 Apparatus and chromatographic conditions

The liquid chromatography system consisted of an LC-10 Shimadzu, with a SPD-10A UV
detector, LC-10AVp quaternary pump, SIL- 10A autosampler and a CBM-10A system
controller (Kyoto, Japan). A Supelcosil LC-18 analytical column (250 mm 4.6 mm i.d., 5 m
particle size) from Supelco (Bellefonte, PA, USA) was used for separation of 1 and 2. The
mobile phase consisted of a gradient of acetonitrile:0.05 % aqueous trifluoroacetic acid
delivered at 1.0 mL.min-1 as follows: initial (ti=0 min) 10:90, then linear gradient over 20 min
to 25:75, and this composition was maintained (isocratic) until the end of each run (tf=30
min). Flow rate was 1 mL.min-1. Quantification was performed using the detector set at a
wavelength of 254 nm. Injection volume was 50 L.
2.8 Analysis of Infusions by HPLC-UV and calibration curve

Chromatograms of pure 1 and 2 presented retention times of approximately 14 and 25 min,
respectively. The peaks corresponding to 1 and 2 were identified in each chromatogram of
the infusions with the help of injection of the standard solutions of 1 and 2 or with co-
elution (figure 3).
Fig. 3. A: chromatograms of root infusions with (back trace) and without (front trace)
addition of neosergeolide and isobrucein B at 254 nm. B: chromatogram of pure isobrucein B
(tR= 14.0 min) at 254 nm. C=chromatogram of neosergeolide (tR= 25.3 min) at 254 nm.
Several injections of standard solution were performed and then average areas were calculated
for each individual concentration injected for isobrucein B (1) and neosergeolide (2). The
calibration curves in the determination of 1 and 2 in P. sprucei stem and root infusions (Figure
4A and 4B, respectively) used in the determination of these components in P. sprucei stem and
root infusions were obtained by linear regression performed on the average areas versus
standard sample concentrations Y and X, respectively (figure 3) at 254 nm.
After calibration with standard samples of isobrucein B and neosergeolide, P. sprucei root
and stem infusions were analyzed. Samples of infusions were analyzed in triplicate and the
average values of the areas corresponding to the quassinoids neosergeolide and isobrucein
B were calculated. From these average areas, the concentration of each quassinoid was
calculated in the root and stem infusions using the linear equation generated during
calibration of each quassinoid.
Area
y = 1.147E+07x
R = 9.993E-01
1400000
1200000
A
1000000
800000
600000
400000
200000
0
-4.72E-16 0.01 0.02 0.03 0.04 0.05 0.06 0.07 0.08 0.09 0.1
C (mg/mL)
Area
y = 3.193E+08x
R = 9.917E-01
4000000
B
3000000
2000000
1000000
0
0 0.002 0.004 0.006 0.008 0.01 0.012
C (mg/mL)
Fig. 4. A: Calibration curve of isobrucein B (1); B: Calibration curve of neosergeolide (2).

3. Results and discussion

The quassinoids isolated from P. sprucei were identified by NMR techniques and compared
to literature (Moretti, et al. 1982, Vieira, et al. 2000). The chemical shifts of NMR 1H and 13C of
1 and 2 are presented in tables 1 and 2 respectively.
Carbon (C) (H) Literature (CDCl3/Py-5%)1

C H
1 81.1 4.17 (s) 81.3 4.26
2 197.0 - 197.6 -
3 124.3 6.11 (q; 2.8; 1.0) 124.5 6.11
4 163.0 - 162.6 -
5 51.6 2.92 (d; 12.1) 43.4 2.91
1.86 (ddd; 14.7; 12.1; 2.6); 2.40 (ddd;
6 28.5 28.2 1.86; 2.41
14.7; 2.8; 2.8)
7 83.1 4.75 (d) 81.7 4.75
8 45.5 - 45.8 -
9 42.8 2.34 (d; 4.0) 42.4 2.38
10 47.5 - 47.7 -
11 72.4 4.75 (sl) 74.3 4.75
12 75.8 4.28 (s) 75.1 4.12
13 80.5 - 81.7 -
14 43.5 3.04 (d; 12.4) 52.3 3.03
15 66.6 6.31 (sl) 67.8 6.30
16 167.0 - 167.6 -
29 22.5 1.96 (d; 1.0) 22.4 1.95
19 11.6 1.18 (s) 11.3 1.18
30 73.3 3.75 (dd; 7.7; 2.0); 4.81 (d; 7.7) 73.0 3.75; 4.81
21 172.6 - 169.5 -
1 169.0 - 170.7 -
2 20.4 2.09 (s) 20.5 2.08
OMe (5) 20.4 3.84 (s) - 3.83
H-(OH-1) - 4.54 (s) - -
H-(OH-12) - 3.25 (s) - -
1 Moretti et al. (1982).
Table 1. Chemical shifts in NMR 1H (500 MHz, CDCl3) and NMR 13C (125 MHz, CDCl3) of
isobrucein B (1).
Carbon (C) (H) Literature (CDCl3/CD3OD-5%)1

C H
1 162.8 - 161.89 -
2 149.7 - 148.91 -
3 115.9 5.71 (dd, 2.0, 2.0) 116.76 5.76 (t, 2.0)
2.41 (ddq, 1.6,
4 31.60 2.40 (m) 31.07
2.0, 6.8)
1.86 (ddd, 1.6,
5 45.70 1.82 (d, 2.0) 45.26
12.4, 14.0)
6a 29.0 2.22 (dd, 2.0, 2.0) 28.80 2.27 (dt, 14.0, 2.0)
6b 1.76 (dd, 2.0, 2.0) 1.73 (dt, 14.0, 2.0)
7 83.6 4.85 (d, 2.0) 83.55 4.76 (d, 2.0)
8 47.5 - 46.74 -
9 39.6 2.52 (d, 2.0) 39.06 2.34 (brd, 4.0)
10 42.7 - 42.06 -
11 75.0 4.59 (d, 6.0) 73.60 4.56 (d, 4.0)
12 77.1 4.32 (d, 6.0) 76.00 4.23 (brs)
13 82.3 - 81.74 -
3.29 (ddd, 15.0, 2.0, 2.0,
14 51.1 49.63 3.24 (brd, 11.0)
12.0)
15 68.5 6.04 (d, 12.0) 67.00 6.09
16 167.5 - 168.24 -
18 170.5 - 171.25 -
19 18.6 1.64 (s) 18.12 1.60 (s)
29 19.9 1.18 (d, 6.0) 19.55 1.20 (d, 6.8)
30a 74.2 4.78 (d, 8.0) 73.6 4.78 (d, 8.0)
30b 3.81 (dd, 8.0, 2.0) 3.77 (d, 8.0)
1 169.0 - 170.40 -
2 20.6 1.98 (s) 20.49 2.09 (s)
3 171.7 - 171.56 -
4 113.4 6.26 (s) 113.17 6.26 (d, 2.0)
OMe (5) 52.9 3.78 (s) 53.02 3,84 (s)
1 Vieira, et al. (2000)
Table 2. Chemical shifts in NMR 1H (200 MHz, CDCl3) and NMR 13C (50 MHz, CDCl3) of
neosergeolide (2).
The authenticity of standards is a key-step in quantitative analysis, especially in plant

extract analysis. In most cases, authentic standards are not available commercially and this
strengths the importance of liquid chromatography. Liquid chromatography enables the
isolation of authentic standards at different scales (from microgram until gram scale) and at
very high purity that can be used later to perform quantitative analysis. In our study,
combining open-column and planar chromatography, we were able to isolate several
milligrams of each pure standard, as can be observed at figure 3, that were then used in the
quantitative analysis of the quassinoids 1 and 2 in root and stem infusions of P. sprucei by
HPLC.
The structural authenticity of each standard can be confirmed by the use of modern
spectroscopy techniques as MS and NMR. Although these techniques are considered
complementary, normally NMR is much more informative. For instance, in our study,
HMBC experiments furnished conclusive information that not sergeolide, but neosergeolide
was isolated.
As described in the experimental section, samples of stem and root infusions were prepared
using approximately 9 g of crushed, dried stems are infused with 1 L of boiling water.
HPLC analysis of P. sprucei stem and root infusions resulted in the concentrations presented
in table 3.
Quassinoid Root infusion Stem infusion

mg.L-1 M mg.L-1 M
isobrucein B (1) 32.0 67.0 14.0 29.0
neosergeolide (2) 0.79 1.6 0.38 0.75
Table 3. Concentrations of isobrucein B (1) and neosergeolide (2) in P. sprucei stem and root
infusions determined by HPLC-UV at 254 nm.
Consistent with the data presented in table 1 the concentrations of both 1 and 2 are at least
twice as large in root infusions as in stem infusions. Interestingly, the percentage of
extractives of roots during infusion (5.1 %) is twice that of stems (2.5 %) which would seem
to be related to the greater concentration of these constituents in the root infusion.
Comparison of root and stem infusions shows that 1 is about 40 times as concentrated as 2 in
both stem and root teas on a molar basis. These data suggest that the more relevant active
principle in stem and root infusions analyzed is 1.
4. Conclusion
The HPLC analysis of infusions (aqueous extracts) of stems and roots of P. sprucei revealed
higher quantities of isobrucein B than neosergeolide, 40 fold, for both infusions. Considering
this information and in vitro activity of both compounds, it is very likely that isobrucein B
plays more important role for the antimalarial activity than neosergeolide.
More research is needed to describe seasonal, regional and specimen specific variation in P.
sprucei quassinoid composition which should have a direct influence on the composition of
stem and root infusions prepared from samples of different origins. Knowledge of the extent
of these variations, especially as they influence quassinoid composition in infusions, is of
fundamental importance given the valuable medicinal and dangerous toxic properties of
these widely used Amazonian remedies.
The high performance liquid chromatography has proved to be a powerful tool in the plant
extract analysis. The possibility to perform qualitative and quantitative analysis, by HPLC,
enables the development of new phytoterapeutical products from the Amazon biodiversity.
5. Acknowledgment
The autors wish to thank Dr Wanderli Pedro Tadei and CNPq/ FAPEAM - PRONEX, Rede
Malria for financial support to the publication of this chapter, Massuo Kato for use of
analytical HPLC apparatus and Profs. Norberto P. Lopes and Valquiria P. Jabor for helpful
comments regarding this manuscript.
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11
Purification of Peptides from Bacillus

Strains with Biological Activity
Mara Antonieta Gordillo and Mara Cristina Maldonado
Institute of Biotechnology, Faculty of Biochemistry, Chemistry and Pharmacy,
National University of Tucuman, Tucuman,
Argentina
1. Introduction
One of the greatest causes of loss in the food industry is postharvest diseases of fruits and
vegetables (Vero Mendez & Mondino, 1999). According to U.S.A. estimations this loss
reaches 20 - 25% whereas in developing countries the losses are often more severe due to
inadequate storage and transportation facilities (Sharma et al., 2009), but loss has generally
been considered to be approximately 10% to 40% depending on packinghouse technology
(Vero et al, 2002).
The surface of the fruit or vegetables is covered with fungal spores, bacterial cells and
yeasts, which they have acquired from the air during their development on the parent plant,
or which they have come in contact during picking or any of the stages of handling the
harvested produced. However not every fungal spore or bacterial cell can develop and
cause decay in the harvested product, even when conditions suitable for penetration and
development are present.
Harvested fruit and vegetables are naturally attacked by own typical pathogens. Fungi are
the principal decaying agents in fruit kept in cold storage chambers for long periods
(Teixid et al., 2001).
Fruits of tropical and subtropical origin (mango, papaya, avocado, etc.) are attacked by
Colletotrichum gloesporoides, which cause actracnose. Gloesporium musae attacks banana fruits
at the orchard, which becomes active only during the storage.
Diplodia natalensis, Phomopsis citri or Dothiorella gregaria invade the cut stem of tropical and
subtropical fruit. D. natalensis, Alternaria citri and P. citri the causal agent of postharvest
stem-end rot of citrus fruits.
During and after harvest, the citrus fruits are typically attacked by Penicillium italicum
(blue mold), Penicillium digitatum (green mold), Geotrichum candidum (sour rot), Alternaria
citri (black mold) and Fusarium sp. (Wilson & Wisniewski, 1989). P. digitatum is an
example of a specific fungus that attacks only citrus fruits. P. italicum can attack other
fruits and vegetables, whereas P. expansum, apple and pear pathogen, naturally attack
citrus fruits.
P. expansum, Botrytis cinerea, Gleosporium spp. Alternaria alternata and Stemphylium botryosum
are typical apple and pear pathogens. The main pathogens of peaches, apricots, nectarines
and plums are Monilia fruticola and Rhizopus stolonifer.
Each harvested fruits and vegetables has its own group of characteristic pathogens to which
is susceptible and for which its serves as suitable host.
Strawberries are attacked during the storage by the gray mold fungus (B. cinerea) and the
soft watery rot fungus (R. stolonifer).
Alternaria alternata is the major storage decay agent of harvested tomatoes. The main causal
agents of soft watery rot in harvested tomatoes are R. stolonifer, G. candidum and Erwinia spp.
(Barkai Golan, 2001).
Postharvest fruit diseases are controlled with careful manipulation practices and synthetic
fungicides like 2- 4 thiazalil benzimidazole and imidazole. This method is more widely used
against fungal decay because of its low cost and easy application. However, it presents
manifold objections since prolonged use generates resistance to synthetic fungicides by
major postharvest pathogens (Wilson & Wisniewski, 1994; Fogliata et al., 2001) and increases
chemical remainders in fruits with the consequent potentiality engendering iatrogenic
diseases (Lingk, 1991). In addition, world trends are moving towards reduced pesticide use
in fresh fruit and vegetables. Along with this trend, several physical and biological means
have been evaluated as safer alternatives for the use of chemical fungicides. The use of
microbial antagonists for the control of postharvest diseases received special attention, and
has been extensively investigated (Droby, 2006).
Most of the reported yeast and bacteria antagonists were naturally occurring on fruit
surfaces. Microbial biocontrol agents of postharvest diseases have been criticized mainly for
not providing as consistent or broad-spectrum control as synthetic fungicides. The first
generation of biological controls agents for postharvest spoilage relied on the use of single
antagonists. Perhaps it is unrealistic for us to expect disease control comparable to synthetic
fungicides by the use of single antagonists. It can be expected that enhancing efficacy of
biocontrol agents of postharvest diseases to an acceptable level would utilize a combination
of different biological and physical means (Droby, 2006).
The mechanism(s) by which microbial antagonists exert their influence on the pathogens has
not yet been fully understood. It is important to understand the mode of action of the
microbial antagonists because; it will help in developing some additional means and
procedures for better results from the known antagonists. It will also help in selecting more
effective and desirable antagonists or strains of antagonists (Wilson & Wisniewski, 1989;
Wisniewski & Wilson, 1992).
Several modes of action have been suggested to explain the biocontrol activity of microbial
antagonist. Still, competition for nutrient and space between the pathogen and the
antagonist is considered as the major modes of action by which microbial agents control
pathogens causing postharvest decay (Filonow, 1998; Ippolito et al., 2000; Jijakli et al., 2001).
In addition, production of antibiotics (antibiosis), direct parasitism, and possibly induced
resistance are other modes of action of the microbial antagonists by which they suppress the
activity of postharvest pathogens on fruits and vegetables (Janisiewicz et al., 2000; Barkai-
Golan, 2001; El-Ghaouth et al., 2004).
Purification of Peptides from Bacillus Strains with Biological Activity 203
2. Lipopeptides produced by Bacillus strain

Members of the Bacillus genus are often considered microbial factories for the production of
a vast array of biologically active molecules potentially inhibitory for phytopathogens
growth, such as kanosamine or zwittermycin A from B. cereus. Their spore-forming ability
also makes these bacteria some of the best candidates for developing efficient biopesticide
products from a technological point of view. Bacillus spores have a high level of resistance to
the dryness necessary for formulation into stable products. Bacillus subtilis strains are a rich
source of antimicrobial peptides with a high potential for biological control applications.
Bacillus subtilis has been used for genetic and biochemical studies for several decades, and
is regarded as paradigm of Gram-positive endospore-forming bacteria (Moszer et al.,
2002). Several hundred wild-type B. subtilis strains have been collected, with the potential
to produce more than two dozen antibiotics with an amazing variety of structures. All of
the genes specifying antibiotic biosynthesis combined amount to 350 kb; however, as no
strain possesses them all, an average of about 45% of a B. subtilis genome is devoted to
antibiotic production. Peptide antibiotics, also named lipopeptides, represent the
predominant class. They exhibit highly rigid, hydrophobic and/or cyclic structures with
unusual constituents like D-amino acids and are generally resistant to hydrolysis by
peptidases and proteases (Katz & Demain, 1977). Furthermore, cysteine residues are either
oxidized to disulphides and/or are modified to characteristic intramolecular CS
(thioether) linkages, and consequently the peptide antibiotics are insensitive to oxidation
(Stein, 2005).
Bacillus lipopepdides are synthesized non-ribosomally via large multi-enzymes (non-
ribosomal peptide synthetases, NRPSs) (Kowall et al., 1998; Stein, 2005, Finking & Marahiel,
2004). These biosynthetic systems lead to a remarkable heterogeneity among the
lipopeptides products generated by Bacillus with regards to the type and sequence of amino
acid residues, the nature of the peptide cyclization and the nature, length and branching of
the fatty acid chain (Ongena & Jacques, 2007).
Lipopeptides are classified into three families depending on their amino acid sequence:
iturins, fengycins and surfactins (Fig. 1) (Perez Garca, et al., 2011). The surfactins are
powerful biosurfactants, which show antibacterial activity but no marked fungitoxicity
(with some exceptions) (Ongena & Jacques, 2007).
Surfactin, a cyclic lipopeptide is one of the most effective biosurfactants know so far, which
was first reported in B. subtilis ATCC-21332. Because of its exceptional surfactant activity it
is named as surfactin. Surfactin can lower the surface tension from 72 to 27.9 mN/m and
have a critical micelle concentration of 0.017 g/L. The surfactin groups of compounds are
shown to be a cyclic lipoheptapeptide which contain a - hidroxy fatty acid in its side chain.
Recent studies indicate that surfactin shows potent antiviral, antymicoplasma, antitumoral,
anticoagulant activities as well as inhibitors of enzymes. Although, such properties of
surfactins qualify them for potential applications in medicine or biotechnology, they have
not been exploited extensively till date.
Lichenysin, produced by Bacillus licheniformis exhibited similar structure and
physicochemical properties to that of surfactin. B. licheniformis also produced several other
surface active agents which act synergistically and exhibit temperature, pH and salt stability.
Lichenysin A produced by Bacillus licheniformis strain BAS50, is characterized to
Fig. 1. Structures of representative members and diversity within the three lipopeptides
families synthesized by Bacillus species. Boxed structural groups are those that were shown
to be particularly involved in interaction with membranes and/or are supposed to be

important for biological activity in addition to the cyclic nature of the molecule (Peypoux, et
al, 1999; Bonnatin et al., 2003; Dufour et al., 2005; Ongena & Jacques, 2007).
contain a long chain beta-hydroxy fatty acid molecule. Iturin A, the first compound
discovered of the iturin group and its best known member, was isolated from a Bacillus
subtilis strain taken from the soil in Ituri (Zaire) and its structure was elucidated. The
subsequent isolation from other strains of Bacillus subtilis of five other lipopeptides such as
iturin AL, mycosubtilin, bacillomycin L, D, F and LC (or bacillopeptin) was reported (Ongena
& Jacques, 2007). All have a common pattern of chemical constitution, led to the adoption of
the generic name of iturins for this group of lipopeptides. The iturin groups of
compounds are cyclic lipoheptapeptides which contain a -amino fatty acid in its side chain.
Lipopeptides belonging to the iturin family are potent antifungal agents which can also be
used as biopesticides for plant protection.
Fengycin is a lipodecapeptide containing -hydroxy fatty acid in its side chain and comprises
of C15 to C17 variants which have a characteristic Ala-Val dimorphy at position 6 in the peptide
ring. Wang et al. (2004) demonstrated the identification of fengycin homologues produced by
B. subtilis by using electrospray ionization mass spectrometry (ESI-MS) technique.
These antibiotics are either cyclopeptides (iturins) or macrolactones (fengycins and surfactins)
characterized by the presence of L and D amino acids and variable hydrophobic tails. Iturins
display strong antifungal action against a wide variety of yeasts and fungi but only limited
antibacterial activity. Fengycins also show a strong fungitoxic activity, specifically against
filamentous fungi (Ongena & Jacques, 2007). The ability of various Bacillus strains to control
fungal soil borne, foliar and postharvest diseases has been attributed mostly to iturins and
fengycins (Ongena & Jacques, 2007; Romero et al., 2007; Arrebola et al., 2010).
The surfactin family encompasses structural variants but all members are heptapeptides
interlinked with a -hydroxy fatty acid to form a cyclic lactone ring structure (Peypoux et
al., 1999). Because of their amphiphilic nature, surfactins can also readily associate and
tightly anchor into lipid layers and can thus interfere with biological membrane integrity.
Iturin A and C, bacillomycin D, F, L and LC and mycosubtilin were described as the seven
main variants within the iturin family. They are heptapeptides linked to a -amino fatty acid
chain with a length of 14 to 17 carbons. The biological activity of iturins is different to
surfactins: they display a strong in vitro antifungal action against a wide variety of yeast
and fungi but only limited antibacterial and no antiviral activities (Moyne et al., 2001; Phae
et al., 1990). This fungitoxicity of iturins almost certainly relies on their membrane
permeabilization properties (Deleu et al., 2003).
However, the underlying mechanisms based on osmotic perturbation owing to the
formation of ion-conducting pores and not membrane disruption or solubilization as caused
by surfactins (Aranda et al., 2005).
3. Purification and identification of lipopeptides

Chemical and structural analysis of lipopeptides is carried out using a broad range of
techniques varying from simple colorimetric assays to sophisticated mass spectrometry (MS)
and sequencing techniques.
After extraction, the purification procedures of lipopeptides included chromatography

methods (TLC, Ion Exchange Chromatography and RP-HPLC). Each step of purification will
be monitored by bioassays. The bioassays could be bioautographic methods, dual culture
plate, etc.
Generally, identification of the relative percentage of the lipid and protein portions is carried
out using simple colorimetric assays, such as Bradford assay for protein determination
and spectroscopic methods (FTIR). The molecular mass determination of the compounds of
interest may be facilitated by mass spectrometry using assisted laser desorption ionization
time of flight mass spectrometry (MALDI-TOF MS).
This should be followed by analysis of the fatty acid portion and determination of the
peptide sequence using automated Edman degradation sequencing. This combined
approach would provide the necessary information required for complete structural
identification.
3.1 Purification of lipopeptides

3.1.1 Extraction and Thin Layer Chromatography (TLC)
Different solvents are used for extraction of lipopeptides from cell free supernatant. The
solvents used are n-hexane, ethyl acetate, petroleum ether, chloroform and methanol, to
determine the best solvent for extraction of antifungal compound (Kumar et al., 2009).
Yazgan et al., 2001 and Romero et al., 2007 used n-butanol for lipopeptides extraction.
The lipopeptide produced by cultures of Bacillus mojavensis strain ROB-2 was used to
compare the efficiencies of two purification methods. Method 1 involved acid precipitation
using 1 N HCl to adjust the pH of the cell-free culture fluid to 2 (Yakimov et al, 1995; Mc
Keen et al., 1986) followed by TLC. Method 2 used ammonium sulfate precipitation (40%)
followed by acetone extraction and TLC (Youssef et al., 2005).
Seventy-five percent of the biosurfactant activity remained in the cell-free culture fluid after
cell removal. The surface-active fraction obtained from the TLC plate by method 1 had 23%
7% of the activity originally presents in the culture, while the surface-active fraction
obtained from the TLC plate by method 2 had 63% 11% of the activity originally presents
in the culture (Youssef et al., 2005).
In order to identify the compounds responsible for antimicrobial activity, extracts of cell-free
culture filtrates Bacillus strains generally are separated in TLC sheets, using purified iturin
A, fengycin, and surfactin as standards. Thin layer chromatography is a simple method,
which can be used to detect the presence of lipopeptides while preparative TLC can be used
to purify small quantities (Symmank et al., 2002).
Once the butanol layer completely evaporated in vacuum at 40 C or the acid precipitation is
neutralized, the residue is dissolved in methanol for further chemical analysis. The
methanolic fractions are analyzed using TLC (Razafindralambo et al., 1993) with direct view
developed using distilled water spraying. A white spot formed with the same Rf value
when the plate was sprayed with water, indicating that the compound is lipophilic.
Cell free supernatant of Bacillus subtilis UMAF6614, UMAF6619, UMAF6639 and UMAF8561
and Bacillus amyloliquefaciens PPCB004 were evaluated by TLC and the spots with Rf values
similar to the standards fengycin (0.09), iturin A (0.3), and surfactin (0.7) (Romero et al., 2007
and Arrebola et al., 2010). To determine which lipopeptides were directly involved in fungal
inhibition, the bioautographies were performed using the pathogens as revealing
microorganism. It was found that the principal inhibitor was iturin A, which affected all
fungi analyzed in this study. Fengycin was also identified as an inhibitor of Lasiodiplodia
theobromae, Botryosphaeria sp., C. gloeosporioides, Fusicoccumaromaticum and Phomopsis persea.
Surfactine was able to inhibit L. theobromae, although slight inhibition of F. aromaticum and P.
persea was also observed (Fig. 2) (Arrebola et al., 2010).
Fig. 2. Bioautographic analysis on thin-layer chromatography plates where lipopeptide

extracts from Bacillus amyloliquefaciens PPCB004 were separated and the Rf of every
lipopeptide are indicated. (a) Lasiodiplodia theobromae, (b) Alternaria citri, (c) and (d)
Botryosphaeria sp., (e) Colletotrichum gloeosporioides, (f) Fusicoccum aromaticum, (g) Penicillium
crustosum, (h) Phomopsis persea. Fungal inhibition zones produced by iturin A activity is
indicated with white arrows.
The concentrated extracts from Bacillus MZ-7 run on silica TLC plates showed six bands
under UV light, having Rf values of 0.1, 0.15, 0.26, 0.37, 0.51 and 0.57. However, a plate
bioassay showed two active fractions, those with Rf values of 0.37 and 0.51. The spot with an
Rf value of 0.51 was ninhydrin negative and positive to 4,4'-bis (dimehtylamino)
diphenylmethane (TDM) reagent. These results indicated the absence of free amino groups
and the presence of peptide. The migration and chemical properties of the compound were
comparable to surfactin produced by B. subtilis strain ATCC 21332. The environmental
isolate B. subtilis MZ-7 produced more surfactin (170.5 mg/L) than did B. subtilis ATCC
21332 (109.5 mg/L) under the same conditions (Mutaz et al., 2007).
Maldonado et al., 2009 run silica gel plates 60 F254 (Merck, 2 mm) and are carried out with a
chloroformmethanolacetic acid (40:4:1) mixture (Batrakov et al., 2003). Plates are
developed under UV light at 254 and 365 nm and only one spot of Rf 0.67 is detected
(Kumar et al., 2009). The inhibitory activity of the spot was confirmed after TLC by
bioautographic assay. Besides the TLC plates were developed with ninhydrin and no spot
was observed. Thus, a peptide without free amino groups (cyclic structure) may be
presumed (Fig. 3).
Fig. 3. Bioautographic analysis on thin-layer chromatography plates where lipopeptides

extracts from Bacillus IBA 33 against Geotrichum candidum. M1 and M2 correspond to peaks
obtained from DEAE Sephacel chromatography.
3.1.2 Ion exchange chromatography and RP-HPLC

The development of efficient HPLC methods generally needs relatively pure biosurfactant
samples, which cannot be obtained without tedious isolation and purification operations.
Other technique frequently employed for the characterization and quantification of
biosurfactants has been DEAE ion exchange chromatography. This analysis can provide
qualitative information about biosurfactants.
The crude extract was applied to a low-pressure chromatography column (Bio-Rad
Laboratories, Hercules, CA) filled with DEAE-Sephacel (Pharmacia,Uppsala, Sweden)
equilibrated in 50 mM Tris-HCl, pH 7.5. A gradient of 0-0.4 M NaCl in buffer (50 mM, pH
7.5) was run through the column at 0.5 mL/min over a period of 160 min followed by
straight 0.4 M NaCl in buffer (50 mM, pH 7.5) for 40 min. The eluent was monitored at 280
nm, and fractions were collected every 5 min (Bechard et al., 1998).
They demonstrated that the antibiotic was retained by DEAE-Sephacel quite strongly but
eluted from the matrix in 0.4 M NaCl. Ion exchange chromatography separated the crude
antibiotic sample into four peaks. Antibiotic activity corresponds with the fourth and largest
peak on the chromatogram. Only 23% of the initial activity was recovered by ion exchange
chromatography, and the specific activity actually decreased relative to that in previous
purification step. A complete loss of activity was observed when the antibiotic was left in
the ion exchange eluent overnight. For this reason the ion exchange protocol was carried out
as quickly as possible at 4 C (Bechard et al., 1998) (Fig.4).
Wang et al., 2004 loaded the crude extract on a DEAE-Sepharose Fast Flow column pre-
equilibrated with buffer A (20 mmol/L Na2HPO4-NaH2PO4 pH 6.5). After washing the
column with buffer A, buffer B (20 mmol/L Na2HPO4-NaH2PO4 1 mol/L (NH4)2SO4 pH 6.5)
was used to elute the fraction containing fengycin homologues and this fraction was directly
loaded on a SOURCE 15 PHE hydrophobic interaction column pre-equilibrated with buffer
B. Most impurities were washed by buffer A and fengycin homologues were finally eluted
by Milli Q water. After adjusted to 30% acetonitrile/water by adding acetonitrile, this
fengycin-containing fraction was ready for ESI mass spectrometry analysis.
Fig. 4. Elution pattern of the HCl precipitate from DEAE-Sephacel equilibrated in 50 mM

Tris buffer, pH 7.5 (buffer A). The peptide was eluted from the column with a gradient of
0.100% buffer B (50 mM tris buffer, pH 7.5, containing 0.4 M NaCl). Flow rate 0.5 mL/min.
Bin Hu et al., 2007 collected the extract, boiled for half an hour, centrifuged at 10.000 g for 10
min and then applied to a DEAE-52 column (16 mm 15 cm) previously equilibrated with 50
mM Tris-HCl buffer (pH 7.5) containing 0.05 M NaCl. Antifungal fractions were obtained
from the elution with 0.50.7 M NaCl in the same buffer, concentrated by ultrafiltration with
a PM10 membrane (Amicon) and placed onto a Sephadex G-100 gel column (15 mm 80 cm).
The column was equilibrated with 10 mM ammonium acetate buffer and eluted with the
same buffer at a flow rate of 0.5 mL/min. Fractions containing antifungal active compounds
were collected, concentrated and lyophilized. Through these purification steps of antifungal
active compounds, fractions were determined by the absorbance at 280 nm and the anti F.
moniliforme fractions underwent further processing.
Maldonado et al. (2009) precipitated the extracted from Bacillus IBA 33 with ammonium
sulfate 40%, then loaded onto a DEAE-Sephacel (1.5 cm 9.15 cm) column previously
equilibrated with 50 mM TrisHCl buffer pH 7.5 (Bechard et al., 1998). After purification, the
chromatogram showed two inhibition peaks in a DEAE-Sephacel column. The first one,
exhibited 77% and the second peak had 64% inhibition against G. candidum (Fig.5).
HPLC is an excellent method for the separation of lipopeptides (Aguilar, 2004). The most
commonly employed technique is reversed phase chromatography, which results in the
separation of each lipopeptide structure based on polarity. The separated products are
detected by UV absorbance detection and each individual peak can be collected using a
fraction collector for further analysis of their structure. Coupling of HPLC with a mass
spectrometer provides preliminary information on the molecular mass of each component.
Purification with either HPLC-UV or HPLC-MS using different types of column chemistry is
also possible.
Gueldner et al., 1988 assayed the crude material dissolved in 50:50 methanol-water, and the
solution was chromatographed on a column of C-18 reversed-phase absorbent (Waters Prep
Pak 500). Elution with a stepwise gradient of methanol and water (from water up to 80%
methanol-water) eluted most of the lipopeptides. Further purification was achieved by
droplet counter current chromatography (DCCC) (Buchi B-670) using chloroform-methanol-

water (7:13:8) in the descending mode with the chloroform layer as the mobile phase. The
main peaks eluted in 300-500 mL of the chloroform layer. The active peptides started to
elute from the reversed-phase adsorbent at 65-70% ethanol-water and were completely
eluted with 80% methanol - 20% water. Bioassay of the C-18 column fractions with M.
fructicola showed activity in fractions that contained several peaks as analyzed by HPLC
(210 nm). Five HPLC peaks having a profile very similar to those published by Isogai et al.
(1982) for B. subtilis metabolites and collected from an analytical C-18 column were also
active in the M. fructicola bioassay. Peak 1 (PKl), corresponding to Iturin A-2.
Fig. 5. Bacillus sp. IBA 33 antifungal active compounds (AAC) purification step by DEAE-
Sephacel chromatography. Dark line: protein (absorbance at 280 nm), light line: AAC (%
inhibition).
Mutaz et al., 2007 realized quantitative analysis of surfactin by HPLC active fractions from
TLC were further purified by reversed-phase HPLC, using a Thermo Hypersil-Keystone
ODS (particle size, 5 m; column dimensions, 250 by 4.6 mm; Thermo Hypersil, USA). A
sample was applied with eluent A (0.1% (vol/vol) trifluoroacetic acid and 20% (vol/vol)
acetonitrile) and eluted with segmented gradients of eluent B (0.1% (vol/vol) trifluoroacetic
acid and 80% (vol/vol) acetonitrile) as follows: 40% eluent B for 30 min and 40 to 100%
eluent B for 10 min. The concentration of surfactin was determined from a calibration curve
made by correlating the emulsification index (E 24) with known amounts of surfactin
produced by B. subtilis ATCC 21332.
Romero, et al., 2007 analyzed first by TLC (Razafindralambo et al. 1993) and afterward by
RP-HPLC, using an analytical Zorbax C18 column, 4.6 mm in diameter by 150 mm long
(Agilent, Palo Alto, CA, U.S.A.) and solutions of 0.05% trifluoroacetic acid in acetonitrile and
in water, with a flow rate of 1 ml/min. The different groups of peaks from butanolic
extracts were fractionated by Flash chromatography as described earlier (Deleu et al., 1999;
Razafindralambo et al., 1993), followed by (semi)-preparative RP-HPLC using a Vydak C18
column, 22 mm in diameter by 250 mm long (Separations Group, Hesperia, CA, U.S.A.) and
the solutions mentioned above with a flow rate of 23 ml/min.
RP-HPLC analysis showed three main groups of peaks were observed at elution times
comparable with those observed for standard lipopeptides that correspond to iturin A,
fengycin and surfactin (Romero et al., 2007).
Arrebola et al., 2010 performed the analysis by reverse-phase HPLC (RP-HPLC) (Romero et
al., 2007) using extracts from Bacillus subtilis UMAF6614 and UMAF6639 as standards of
lipopeptides production.
The lipopeptide concentration was calculated using the Folin Ciocalteus reaction (Swain &
Hillis, 1959; Harborne, 1984). The results from RP-HPLC analysis showed three main groups
of compounds that correspond to bacillomycin, produced by UMAF6614 and iturin A
fengycin and surfactin by UMAF6639 (Fig. 6).
Fig. 6. Reverse-phase high-performance liquid chromatography analysis of lipopeptides

produced by Bacillus subtilis strains UMAF6614 and UMAF6639. Peaks corresponding to iturin
(It), bacillomycin (Bac), fengycin (Fen) and surfactin (Sf) are indicated. Detection is at 214 nm.
3.2 Identification of lipopeptides

3.2.1 Ultraviolet spectrum
The ultraviolet absorbance spectrum of the antibiotic was measured from the HPLC
chromatogram using a Waters 990 photodiode array detector. This device allowed for
the simultaneous measurement at all wavelengths from 200 to 600 nm as the antibiotic
eluted from the column. The absorbance spectrum for the lipopeptide is measured in
acetonitrile/1% acetic acid (68:32) between 200 and 600 nm. The antibiotic shows absorbance
maxima at 235, 278, and 285 nm (Fig.7), and there is no appreciable absorbance above 300
nm (Bechard et al., 1998).
Fig. 7. Ultraviolet spectrum of the peptide antibiotic inacetonitrile/1% acetic acid (68:32).
Maldonado et al, 2009 resuspended the samples (M1 and M2) obtained from Bacillus IBA in
HEPES buffer 10 mM NaCl 100 mM pH 7.1 to carry out absorption spectra between 250 and
280 nm wavelengths (Beckman DU 7500). They observed the same absorption bands for
both samples. Hence, this strain might be a producer of cyclic lipopeptides with antifungal
activity belonging to the iturin family. When the wavelength scanning was performed
between 250 and 380 nm, they founded absorbance maximums at 280 nm for both samples
(Fig. 8 a, b). Furthermore they might infered that the antifungal compounds have tyrosine or
tryptophan or both in their composition (Nelson & Cox, 2006). Bechard et al., 1998 reported
an absorbance maximum between 210 and 230 nm which they thought was due to the
Fig. 8. UV absortion spectra between 250 and 280 nm wavelengths a: peak one, b: peak two.
presence of tyrosine. However, they later discovered that it was a residue of -aminoacid 4
hydroxyphenilacetic which is structurally similar to tyrosine.
Kumar et al., 2009 dissolved 1 mg extract in 10 ml of methanol and the spectra were
recorded at 190-600 nm range. UV spectral data of antibiotic exhibited strong absorption
maxima ( max) at 254, 255 and 277 nm and there was no appreciable absorbance above 300
nm, which was corresponding to characteristic absorption of peptide bond. It is reported
that most of peptide antibiotics exhibit absorbance maxima at 210-230 and 270-280 nm
(Motta & Brandelli, 2002; Kurusu & Ohba, 1987). A peptide antibiotic cerein, obtained from
Bacillus cereus, shows UV absorbance peak at 250 and 273 nm.
3.2.2 Infrared spectrum (FTIR)

The infrared spectrum of the antibiotic was measured as a potassium bromide pellet.
Approximately one-third of the KBr mixture was pressed into a pellet (8 mm diameter)
using a non-evacuable Mini Press (Perkin-Elmer Norwalk, CT) and four scans of the sample
were taken using a Perkin-Elmer 1600 FTIR spectrophotometer. The FTIR spectrum of the
purified antibiotic is shown in (Fig.9). Characteristic absorption valleys at 1,540; 1,650, and
3,300 cm-1 indicate that the antibiotic contains peptide bonds. A lactone ring is suggested by
the absorption at 1,740 cm-1 and valleys that result from C- H stretching (2,950; 2,850; 1,460
and 1,400 cm-1) indicate the presence of an aliphatic chain (Bechard et al., 1998).
Fig. 9. Fourier transform IR spectrum (KBr pellet) and amino acid composition of the
peptide antibiotic.
Romero et al, 2007 performed active extracts from Bacillus subtilis strains. The Fourier
transform-infrared spectrum (FT-IR) analysis showed bands in the range of 1,630 to 1,680
cm1, resulting from the stretching mode of the CO-N bond (amide I band), and at 1,570 to
1,515 cm1, resulting from the deformation mode of the N-H bond combined with C-N
stretching mode (amide II band), both indicating the presence of a peptide component and
also bands at 2,855 to 2,960 cm1, resulting from typical CH stretching vibration in the alkyl
chain. Also was observed at 1,730 cm1 due to the lactone carbonyl absorption typical for
surfactin and fengycin families of lipopeptides.
Maldonado et al., 2009 showed the FT-IR spectrum of the antifungal compound in D2O, at a
concentration of 1 mg/mL. Samples were placed in a liquid cell assembled with CaF2
windows and 0.056 mm lead spacers. The spectrum was taken with a resolution of 2 cm-1
and three regions were observed. The one at 1,650 cm-1 assigned to the vibrational amida I
mode which shows the peptide link; another at 1,7101,740 cm-1 characteristic of carbonyl
groups in ester or ketone groups and another at 2,8502,950 cm-1 bands corresponding to
saturated CH links assigned to long chain fatty acids (Fig.10).
Fig. 10. a: Amida I region of FT-IR spectrum (1650 cm-1) of the antifungal compound at a
concentration of 1 mg/mL in D2O. Carbonyl groups (ester or ketone groups) region (1,710
1,740 cm-1) b: Saturated CH links region of FT-IR spectrum (2,8502,950 cm-1).
Sivapathasekaran et al., 2009 in order to reveal the chemical nature of the biosurfactant, the
HPLC purified isoforms from marine Bacillus strain (A, B, C and D) were performed by
Fourier transform-infrared spectrophotometry (FTIR) analysis. The purified samples were
dispersed in spectral-grade KBr (Merck, Darmstadt, Germany) and made into pellets by
applying pressure. The spectrum was generated in the range of 400 to 4,000 cm1 with a
resolution of 4 cm1. The spectral measurement of the compound was carried out in
transmittance mode with average of 32 data scans over the entire range of wave numbers
(Das & Mukherjee, 2005; Pueyo, 2009).
The IR absorption pattern for fractions A, B, C, and D (Fig. 11) revealed the presence of
peptide and carboxyl groups that indicated their lipopeptide nature (Desai & Bannat, 1997;
Thaniyavaran et al. 2003; Das & Mukherjee, 2005; Pueyo, 2009). The antimicrobial isoform
(fraction A) showed a transmittance valley at 3,274 cm1 as a result of NH stretching
indicating the peptide groups. Aliphatic chain was indicated by CH weak stretching
vibration observed in the range 2,930 cm1. The transmittance occurred in 1,658 cm1 due to
the amide I band frequency (CO stretching in the peptide bond) and transmittance at 1,531
cm1 range showed CO bonds. The transmittance at 1,390 cm1 range may be due to the
aliphatic chain of CH group. Similarly in fraction B, the NH stretching was observed at
3,477 cm1 with a broad valley of transmittance. The transmittance at 1,670 cm1 range
resulted in the stretching mode of CO bond and at 1,143 cm1 resulted in CN stretch. The
transmittance at 1,203 cm1 corresponding to CN stretch and at 1,440 cm1 and 2,364 cm1
due to the presence of aliphatic chain (CH stretching mode) was observed. The absorption
at 1,024 cm1 indicated a CO stretch. In fraction C, IR spectrum showed absorption at 3,109
cm1, 1,623 cm1, and 1,132 cm1 corresponding to strong absorption band of peptides,
resulted from the stretching mode of NH and CO bonds, respectively. The presence of CH
stretching at 1,398 cm1 indicated the presence of aliphatic chain. The absorption at 1,198
cm1 indicated a CN stretching. The IR spectrum for fraction D revealed absorption
corresponding to the presence of peptides at 3,087 cm1, 1,667 cm1, and 1,198 cm1
respectively. The CH stretching at 1,439 cm1 and 1,398 cm1 indicated the aliphatic chain
presence. In all the fractions (AD), the peaks observed at the 800600 cm1 range revealed
the presence of CH bend aliphatic chain (Sivapathasekaran et al., 2009).
Fig. 11. IR spectrum of HPLC purified surface-active lipopeptide isoforms produced by the
marine Bacillus circulans DMS-2 (MTCC 8281).
FTIR spectra of antifungal compound had a broad band centering around 3,421.5 cm-1
indicated an amino and hydroxyl group of amino acids (Kumar et al., 2009). Analysis of the
spectrum also shows typical absorption bands (1,670.5 and 1,539.8 cm-1) corresponding to N-
H stretching of proteins and peptides bonds (Maquelin et al., 2002). Additional absorption
valleys 1,418.4 and 1,488.6 cm-1 indicating (C-H) aliphatic side chain may be related with
predominance of hydrophobic amino acids such as Val, Leu and Ile or its contains fatty
acids in their structure (Bizani et al., 2005).
3.2.3 MALDI-TOF mass spectrometry

The lipopeptide molecules are detected, in their protonated form or as Na+ or K+ adducts, by
MALDI-TOF mass spectrometry in the m/z range of 1,4001,550 Da (Deleu et al., 2008).
Several literature reports are available that highlight the analysis and purification of
lipopeptide biosurfactants (Desai & Banat, 1997; Maneerat & Phetrong, 2007; Mukherjee et
al., 2009; Sen & Swaminathan, 2005). Although methods like ion exchange chromatography
(Mukherjee et al., 2006), thin layer chromatography (Desai & Banat, 1997), gel permeation
chromatography (Mukherjee et al., 2009) and ultrafiltration (Sen & Swaminathan, 2005; Lin
et al., 1998) have been used for the purification of lipopeptide biosurfactants, these
techniques have a serious limitation as they do not separate individual isoforms present in
the crude lipopeptide mixture.
Mutaz et al., 2007 studied the fractions correlated with surfactin from TLC and reverse
phase HPLC using MALDI-TOF-MS. The samples were mixed on the target plate with the
matrix solution (-hydroxycinnaminic acid in acetonitrile-methanol-water, 1:1:1). MALDI-
TOF-MS spectra was recorded by using a 337-nm nitrogen laser for desorption and
ionization. The mass spectrometer was operated in the refraction mode at an accelerating
voltage of 18 kV with an ion flight path that of 0.7 m. The delay time was 375 ns. Matrix-
suppression was also used and the mass spectra were averaged over 50 to 100 individual
laser shots. The laser intensity was set just above the threshold for ion production. Surfactin
isomers were anticipated to have an m/z range of 5001500. The variance of the m/z of 0.8
Da was considered acceptable.
Running MALDI-TOF-MS in refractron mode, was observed a cluster of peaks with
mass/charge (m/z) ratios between 1,036 and 1,058, which could be attributed to protonated
surfactin isoforms (Fig.12). The peak with a m/z ratio 1,045.86 corresponds to the mass of
[M+Na]+ ion of surfactin with a fatty acid chain length of 14 carbon atoms (Huszcza &
Burczyk, 2006).
Fig. 12. Surfactin cluster + Na+obtained by MALDI-TOF-MS.
Romero et al., 2007 confirmed the identification of the antifungal compounds (Lp-a, Lp-b
and Lp-c) by scoring the mass spectra contained in the purified fractions using an Ultraflex
MALDI-TOF mass spectrometer (Bruker Daltonics, Billerica, MA, U.S.A.) operated in
positive ion mode. The samples were prepared according to Williams et al. (2002). Mass
spectra were recorded by matrix-assisted laser desorption-ionization time of flight mass
spectrometry (MALDI-TOF-MS). The mass spectra of LP-a showed a series of mass number
of m/z = 1,030 to 1,074; those of LP-b, m/z = 1,034 to 1,095; and those of LP-c, m/z = 1,435 o
1,499 for UMAF6639 strain (Fig. 13).
Sivapathasekaran et al., 2009 analyzed the HPLC purified isoforms by matrix-assisted laser
desorption/ionization time-of-flight analysis (MALDI-TOF) for molecular mass
determination. The matrix used for co-crystallization was 2,5-dihydroxybenzoic acid (Sigma,
USA). A matrix stock solution was prepared in acetonitrile, methanol, TFA (5:4:1). Equal
volume of the purified sample and the matrix were mixed vigorously. After proper mixing,
Fig. 13. Mass spectra scored for the purified fractions LP-a, LP-b, and LP-c from Bacillus
subtilis UMAF6639 strain.
the sample was spotted on the target plate, dried, and was placed inside the sample cabinet of
Voyager DE-Pro MALDI-TOF spectrometer (Applied Biosystems Inc, CA, USA). The nitrogen
UV laser (337 nm) was used for desorption and ionization and a voltage of 20 kV was
maintained to accelerate the molecules. The molecules were separated according to their mass
and were detected by the ion detector set in reflector mode (Maneerat & Phetrong, 2007;
Leenders et al., 1999). The mass spectral analysis showed that all purified isoforms (fractions
AD) were lipopeptides and belonged to fengycin family (Vater et al., 2002).
The mass spectra of fraction A revealed the presence of a major peak of C16 lipopeptides
(1,482 Da and 1,484 Da) in their Na+ adduct form. Similarly, in fraction B showed the
presence of a major peak corresponding to protonated C16 lipopeptides (1,464 Da and 1,466
Da). In the surface-active fraction C, C16 lipopeptides were revealed as a major peak in their
H+ (1,492 Da) and Na+ (1,514 Da) adduct form, respectively. In the similar manner mass
spectra of fraction D, C15 isoform was detected in its protonated form (1,448 Da) and
K+adduct (1,480 Da) (Sivapathasekaran et al., 2009).
3.2.4 Electrospray ionization/collision induced dissociation (ESI/CID) mass

spectrometry (MS)
Fengycin homologues produced by Bacillus subtilis JA were analyzed. When each
homologue was subjected to ESI/CID analysis, ions representing characteristic
fragmentations were detected. These ions can help to identify the homologues; even
homologues of the same nominal mass can be discriminated by their ESI/CID spectra.
Based on the CID results, fengycin homologues can be correctly assigned (Wang et al., 2004).
They showed the ESI mass spectrum of a group of fengycin homologues purified from the
culture of B. subtilis JA. Peaks of m/z 1,435.7; 1,449.9; 1463.9; 1477.9; 1,491.8 and 1,506.0
represent different fengycin homologues (Fig.14). Each of these ions was selected as
precursor ion for further CID analysis. The results showed the appearance of productions of
these precursor ions had regularities: product ions of m/z 966 and 1,080 were found in the
CID spectra of precursor ions of m/z 1,435.7; 1,449.9 and 1,463.9; product ions of m/z 994
and 1,108 were found in CID spectra of precursor ions of m/z 1,491.8 and 1,506.0. Product
ions at m/z 1,080 and 966 can be explained as neutral loses of (fatty acid Glu) and (fatty
acid GluOrn), respectively, from the N-terminus segment of fengycin A (Fig.15). Ions at
m/z 1,063 and 949 found in the spectrum corresponded to neutral loses of ammonia
(17 Da) from m/z 1,080 and 966. Similarly, product ions with neutral loses of (fatty acid
Glu) and (fatty acid GluOrn) were also found in the CID spectra of precursor ions of m/z
1,491.8 and 1,506.0. But they appeared at m/z 1,108 and 994, exactly 28 Da higher than the
corresponding ions of fengycin A (Fig.16). The observation of mass difference reflected the
substitution of Ala for Val in the lactone ring and so homologues of m/z 1,491.8 and 1,506.0
belonged to fengycin B. In fact, product ions of m/z 1,209 and 1,237 representing the neutral
loses of the fatty acid chain were also detected respectively from the CID spectra of
fengycins A and B. But the abundance of these two ions was very low, so sometimes we
could not easily find them in the spectra.
An interesting phenomenon was found in the CID result of precursor ion at m/z 1,477.9 (Fig.
17) shows part of the entire CID spectrum). Product ions of m/z 966; 994; 1,080 and 1,108 were
all detected. This indicated both fengycins A and B contributed the peak of m/z 1,477.9.
Fig. 14. ESI mass spectrum of the fengycins produced by B. subtilisJA.
Fig. 15. Structure of fengycin A.
Fig. 16. Structure of fengycin B.

Fig. 17. CID spectrum of precursor ion of m/z 1477.9.
Romero et al, 2007 determined by ESI-MS-MS the amino acid sequences for the peptide
moiety. Samples of ring-opened lipopeptides by cleavage of the lactone bond (Williams et
al. 2002) were analyzed on an Esquire 3000 Plus ion trap mass spectrometer (Bruker
Daltonics) and sequences deduced by comparing the fragmentation spectra with the
available databases. When the amino acid compositions were determined, it was found that
the fraction LP-a contained Asp, Glu, Val, and Leu in a ratio of 1:1:1:4; fraction LP-b
comprised Asp, Ser, Glu, Pro, and Tyr in a ratio of 3:1:1:1:1; and fraction LP-c was composed
of Thr, Glu, Pro, and Ala or Val, Ile, Tyr, and Orn in a ratio of 1:3:1:1:1:2:1, corresponding to
strain UMAF6639 (Fig. 18).
Fig. 18. Mass spectra scored for the purified fractions LP-a, LP-b, and LP-c.
Fragmentation spectra observed by electrospray ionization ion trap mass spectrometry (ESI-
MS-MS) and amino acid sequences and fatty acid compositions deduced from the parental
peaks 1,008.7 (LP-a, surfactin), 1,065.4 (LP-b, iturin A), and 1,464 (LP-c, fengycin).
3.2.5 Edman degradation

Edman degradation is the classic technique for sequencing peptides using chemical methods
(Zachara & Gooley, 2000). The method provides an assignment for each residue in the
peptide, unlike amino acid analysis which only provides an indication of the ratio of amino
acids in the peptide. Edman experiments take place in an oxygen-free environment and
involve the modification of the N-terminal residue with phenylisothiocyanate to provide a
cleaved phenylthiohydantoin (PTH) amino acid. All of the chemical processes take place on
automated sequencers and are followed by a chromatographic step where the retention time
of the cleaved PTH amino acid is compared with the retention times of a series of PTH
modified amino acid standards to ascertain its identity. The method is relatively slow taking
approximately 45 min for each residue, however the amino acid assignment is called with a
high degree of confidence and less subject to interpretation, as can be the case with MS/MS
methods. The quality of sequence information obtained by the Edman method is subject to
the amount of starting material and its purity. For successful sequencing to take place,
peptides and proteins must be purified to near homogeneity by chromatographic methods
to prevent mixed sequencing during Edman experiments. Lipopeptides needs to be in the
open ring form for this type of analysis, which is carried out using mild alkaline hydrolysis.
4. Perspectives and conclusions

A great deal of research has been carried out the properly methods for fully characterization
of cyclic lipopeptides and their structures.
This review highlights the competitive advantage of efficient purification of surfactin,
fengycin and iturin with structural elucidation. Within each family, some structural
homologues are seemingly more active than others. In this regard, reverse-phase high-
performance liquid chromatography (RP-HPLC) could be extensively used because it is
efficient in separation and purification of isoforms (Lin et al., 1998; Thaniyavaran et al.,
2003). However the HPLC method, if not optimized, may lead to improper resolution of
peaks and longer elution times. Thus, an efficient high-resolution HPLC method is a
prerequisite for the purification up to the individual isoform level, required for subsequent
commercialization of a particular lipopeptide isoform as a potential therapeutic agent. The
products obtained with these methods shows a greater level of purity and profound
biological activity (Sivapathasekaran et al., 2009).
Mass spectrometry methods developed to rapidly characterize the lipopeptides nature.
The lipopeptides and moreover the particular isoforms could be exploited as a powerful
tools for the selection of useful strains in the context of biocontrol.
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CHROMATOGRAPHY

Chromatography and Its Applications

Copyright 2012 InTech

Publishing Process Manager Vedran Greblo

First published March, 2012

A free online edition of this book is available at www.intechopen.com

Chromatography and Its Applications, Edited by Sasikumar Dhanarasu

Chapter 1 Column Liquid Chromatography 1

Chapter 2 Column Chromatography

Chapter 3 Chromatographic Separation and

Chapter 4 Purification of Marine Bacterial

Chapter 5 Simple Preparation of New

Chapter 6 Wound Healing and

Chapter 7 Use of Associated Chromatographic

Chapter 8 Secondary Metabolites 131

Chapter 9 Biomarkers 165

Chapter 10 Quantification of Antimalarial

Chapter 11 Purification of Peptides from

In this book contains more details about the applications of chromatography by

Column Liquid Chromatography

2. The establish of CLC method

2.3 Analytical instruments

3. The establish of group-type analysis method by CLC

Pure Weight of Content Determination Deviation Recover

3.2 Check of chromatographic resolution rate by FT-IR

4000 3500 3000 2500 2000 1500 1000 500

Fig. 1. Infrared spectrum for pure reagents and different fraction.

3.4 Evaluation of analysis of group composition by CLC

4. Applications of group type analysis by CLC

Name Test Saturates Aromatics Resins Asphaltenes

Table 2. Results of groups composition of asphalts (W%).

Obviously, the obtained aromatic hydrocarbon fraction has a good purity.

1.5 2959.79 2850.78

4000 3500 3000 2500 2000 1500 1000 500

Fig. 3. Infrared spectrum of the saturated hydrocarbon fraction of sample NE-9.

0.1 3049.45 1689.29 1118.71

4000 3500 3000 2500 2000 1500 1000 500

4000 3500 3000 2500 2000 1500 1000 500

Fig. 5. Infrared spectrum of the resin fraction of sample NE-9.

4.2 The determination of MWDs by CLC coupled with SEC

Fig. 6. The SEC chromatograms of typical heavy oils.

asphaltenes quantitatively could be obtained by CLC determination, then the

R =100 %- Wasp % -Wa1k % (1)

Name of samples (1) (2) (3) Average Max of deviation %

4.3 Analysis of resin component by CLC coupled with HPLC

Wx % = ( Rex /Cx) * (Sx / Sex) * (Vex /Vx ) *Res% (2)

Fig. 7. HPLC chromatogram of resin fraction.

Number Quantitative Number Quantitative

2. Isolation of terpenoids and flavonoids by column chromatography

2,2-dimethyl-6-isopropenyl-2H- 2,3-dimethyl-6-isopropyl-4H- 2-isopropenyl-5-methylhexa-trans-

artemisia triene chrysanthemal chrysanthemol lavandulol

1,8-cineole thujone sabinol santoline triene

Passiflora quadrangularis L. (badea) is widely distributed in some regions of tropical America.

zedoarol germacrone curzeone

curdione -elemene ar-turmerone - turmerone

Valeriana officinalis L. (Valerianaceae) known as valerian, is used in the treatment of

oleanolic acid ursolic acid

Ganoderma lucidum (Fr.) P. Karst. belongs to the family of Ganodermataceae (Basidiomyetes),

ganoderenic acid B, methyl ganoderate H, 12-acetoxy-7-hydroxy-3,11,15,23-tetraoxo-5 -