Quantitative Structure Activity

Relationships
(QSAR)
QSAR: Quantifying the relationship between
physicochemical properties and biological
activity.
Advantages of QSAR studies:
QSAR enables calculation, in advance, what the
biological activity of a novel analog might be,
thus cutting down the number of analogs which
have to be made. It allows the medicinal chemist
some level of prediction.
 Disadvantages of QSAR:

1) QSAR studies are only approximative.

2) QSAR may be unuseful when many
physicochemical properties are involved
since it is not always possible to vary one
property without affecting another.
The most commonly studied hysicochemical properties:
1) Hydrophobic parameters.
2) The electronic parameter.
3) The steric parameter
 I- The hydrophobic parameter

Hydrophobicity Penetration Biological

to cell membrane activity

Hydrophobicity Binding to Biological

hydrophobic regions activity
In the receptor
Hydrophobicity Binding to Biological
serum albumin activity

Hydrophobicity Trapping in Biological

Adipose tissues activity

Hydrophobicity Solubility in the body Biological

Aqueous medium activity

Hydrophobicity Susciptibility to Biological

Metabolism and activity
subsequent elimination
 A) Quantifying hydrophobicity of
the entire molecule
• The hydrophobicity character of a drug
can be expressed by measuring its
partition coefficient (P).
• The partition coefficient: the relative
distribution of a drug between octanol and
water. Concentration of the drug in octanol
partition coefficient (P) = --------------------------
Concentration of the drug in water

P Hydrophobicity
• In a series of drugs with similar structure,
P is measured experimentally for each
drug, log P is calculated and plotted
against biological activity (log 1/C) to get a
graph
• Two types of graphs are possible:
a) Straight-line graph.
b) Parabolic graph.
a) Straight-line graph:
This happens when the drugs tested have a
small range of (log P) values (log P=1-4)
Log (1/C)

Log P
Straight line equation
Log (1/C) = K1 log P + K2
Once K1 and K2 are determined, we can predict the biological activity
Example:
QSAR: Hydrophobicity & binding to serum
albumin
• 40 drugs were tested: (P) was measured,
(log P) was calculated and plotted
against (log 1/C).
• The following equation was obtained:
Log (1/C) = 0.75 log P + 2.3
The positive values means a direct relationship
Hydrophobicity Binding to
serum albumin
Binding to serum albumin of a new compound can
be predicted by measuring its (P) and applying
the equation.
Remarks:
• How much a drug binds to serum albumin allows
us to estimate the effective dose of that drug.
• A drug exists in blood in equilibrium:
Drug bound to serum albumin drug unbound to serum albumin

• When bound to serum albumin, a drug cannot

interact with its receptor, therefore, the dose of
the drug should be based on the amount of
unbound drug in the blood
b) Parabolic graph
• This happens when some of the tested
compounds have very high (log P) values.

Parabolic equation:
Log(1/C)= -k1 (log P) 2 + k2 log P + k3
K1, K2 and K3 are constants
• The positive sign in front of log P implies
direct relationship in the first part of the
graph which is dominated by log P (when
P is small).
• The negative sign in front (log P)2 implies
inverse relationship in the last part of the
graph which is dominated by (log P)2
(when P is large).
 B) Quantifying hydrophobicity of a
substituent:
The substituent hydrophobicity constant (π):
• The hydrophobicity of a substituent can be
expressed by calculating (π).
• (π): a measure of how hydrophobic a
substituent is relative to hydrogen.
How (π) is calculatuent for a substituent (X) ??
1) Partition coefficient are measured
experimentally for a standard compound
without a substituent (X).
 Cl

Benzene Chlorobenzene
(log P = 2.13 (log P = 2.84

2) The following equation is applied:

πX = log PXp – log PH
Where πX = hydrophobicity of the substituent
(X).
PH = Partition coefficient of the standard compound
Px = Partition coefficient of the substituent X
 • From several studies, we have now tables
hydrophobicity of differrent aromatic and
aliphatic substituents.

Group CH3 t-Bu OH OCH3 CF3 Cl Br F

π 0.50 1.68 -1.16 0.47 1.07 0.39 0.60 -0.17

Aliphatic

π 0.52 1.68 -0.67 -0.02 1.16 0.71 0.86 0.14

Aromatic
Remarks
• The values for aromatic substituents are
different from those of aliphatic ones.
• (π) values are only approximative.
• (P) is a measure of the overall hydrophobicity of
a drug and therefore it comprises a measure of
drug transport across as membranes
• (π) is a measure of the hydrophobicity of a
specific substituent in the drug’s skeleton,
therefore it is significant only when that
substituent is involved in hydrophobic bonding
with the receptor.
• In some cases hydrophobicity is
significant for example, there is a very
little relationship between
hydrophobicity of antimalarial drugs
and their antimalarial activity. This
finding supported the finding that
antimalarial act on red blood cells
where hydophobicity is not important.
 II. Electronic effect
Ionization Tarnsport across
cell membrane
Electronic
effect

Polarity Binding to receptor

A) Quantifying the electronic effect of an

aromatic substituent:
The Hammett substitution constant (σ):
(σ) : a measure of the electron withdrawing or
electron donating ability of an aromatic
substituent.
 How (σ) is calculated ??
1) Dissociation constant for benzoic acid is
measured experimentally.
-
COOH COO

-
COO

KH =
COOH
2) Dissociation constant for benzoic acid
substituted with substituent (X) is measured
experimentally

. electron withdrawing
group X X
-
COOH COO + H+

electron donating
group X X
-
COOH COO + H+
The following equation is applied:

σX = log KX – log KH
Remarks:
• Electron withdrawing substituents have positive
(σ) values since they stabilize the carboxylate
anion and shift the equilibrium to the right. E.g.
NO2, Cl, CF3, CN
• Electron donating substituents have negative (σ)
values since they destabilize the carboxylate
anion and shift the equilibrium to the left. E.g.
CH3, CH3CH2, ………
• The Hammett constant takes into account
both inductive and mesomeric effect,
therefore, the value of (σ) depends on
whether the substituent is meta or para.
• (σ) cannot be measured for ortho
substituents steric and electronic effects
are strongly overlapped. This is the
limitation of Hammett equation.
• The inductive effect operates in all
positions while mesomeric effect operates
only in the ortho and para not in the meta.
Look at the electronic effect of the hydroxy
substituent:
meta nitro group-electronic effect on R is
inductive.
para hydroxy group-electronic influence on
R is due to inductive and resonance
effect.
Explanation:

Look at the electronic effect of the nitro

substituent: OH
meta nitro group-electronic effect on R is
inductive.
para nitro group-electronic influence on R is
due to inductive and resonance effect.
R
+
OH + +
OH OH OH

- -
: :
..
-
R R R R
 B) Quantifying the electronic effect of
an aliphatic substituent:
(σI): a measure of the electron withdrawing or electron
donating ability of an aliphatic substituent.
How (σI) is calculated??
1) The rate of hydrolysis of methyl acetate is measured
experimentally under basic and acidic conditions.
O O
C Hydrolysis
C
H3C O CH3 H3C OH + H3C OH

2) The rate of hydrolysis of methyl acetate having a

substituent (X) is measured experimentally.
 O O
C Hydrolysis
C
X CH2 O CH3 X CH2 OH + H3C OH

(σI) is measured by applying the equation.

Remarks:
• Only inductive effect is operating in case
of aliphatic substituents.
• Electron withdrawing substituents have
positive (σI) values while electron
donating substituents have negative (σI)
values
 III- Steric factors
• The bulk, size and shape of drug may
influence its ability to approach the binding
site.

• A bulky substituent may hinder the ideal

interaction between drug and receptor.
Alternatively, a bulky substituent may help
to orientate a drug properly for maximum
receptor binding.
A) Taft’s steric factor (Es)
How (Es) is calculated ??
Exactly like the calculation of (σI) but the
rate of hydrolysis of the ester is
measured only under acidic conditions.
As mentioned before, under acidic
conditions only the steric factor (Es) is
ivolved.
B) Molar refractivity (MR)
(MR): a measure of the volume occupied by an atom or
group of atoms.
(MR) is obtained from the following equation:

(n2 - 1) MW
MR = X
(n2 + 2) d

MW = molecular weight, d = density, n = refractive index

Remarks:
MW/d defines the volume.
(n2 -1) / (n2 + 2) is a correction factor that defines how
easily substituent can be polarized.
 C) Verloop steric Parameter:
• The steric factor is calculated by a computer
program called (STERIMOL).
• The program calculate the steric factor using
bond lengths, bond angles, van der Waals radii
and possible conformation of substituent.
B4 B3
O B3
B2
C H O C O
B1
O
B4
H

L
 Considering more than one
physicochemical property at the same
time
Hansch Equation:
• Hansch equation relate biological activity
to the most commonly used
physicochemical properties.
• If P is limited to a small range, the
equation will be linear.
Log (1/C) = k1 log P + k2 σ + k3 Es + k4
Examples:
1) Hansch equation for the adrenergic blocking activity for
beta-haloarylamines:
Log (1/C) = 1.22 π – 1.59 σ + 7.89

Y X 1
R
CH CH2 N 2
R

Analysis of the equation:

Activity increases when the substituent has a positive (π)
value (hydrophobic) and a negative (σ) value (electron
donating)
2) Hansch equation for the antimalarial
activity of phenanthrene aminocarbinols
Log (1/C) = -0.015 (log P)2 + 0.14 log P + 0.27 Σπx
+ 0.40 ΣπY + 0.65 Σ σx + 0.88
1
Σ σY + 2.34
R
N
2
HO R

Analysis of the equation:

• Activity increases slightly with increased
hydrophobicity of the molecule (small positive
log P).
• There is an optimum P value for activity
(the equation is parabolic).
• Hydrophobicity of of substituent Y is more
important for activity than hydrophobicity
of substituent X (0.4 > 0.27).
• Both substituents X and Y should be
electron withdrawing (positive values for
σx and σY).
• Electron withdrawing ability of substituent
Y is more important for activity than
electron withdrawing ability of substituent
X (0.88 > 0.65)
The Craig Plot:
• The Craig plot is a plot of the (p) values
on the X axis and the (s) on the Y axis .
For example, the Craig plot for para
aromatic substituents is shown below;
Advantages of Craig plot:
The Craig plot tells us:
• Which substituent has positive (p) and (s)
values. Which substituents have negative (p)
and (s) values, which substituents have one
positive and one negative values.
• Which substituents have similar (p) values
(ET, Br, CF3). They are interchangeable if (p)
is the principle factor.
• Which substituents have similar (s)
values (COOH, Cl, Br, I).
• Which substituents should be used in
QSAR study. Here, analogs should be
synthesized with substituents from each
quadrant and biological activity tested.
Which quadrant is relevant to biological
activity is determined. Then we
concentrate on substituent from that
quadrant.
The Topliss Scheme (Topliss tree).
• There are two Topliss schemes: one for
aromatic substituents and another for
aliphatic substituents).
• These schemes. Were drawn up by
considering the hydrophobicity and the
electronic factors of various substituents
and are designed such that optimum
substituent can be found as efficiently as
possible.
 Free-Wilson Approach
Method

•The biological activity of the parent structure is measured and compared with the
activity of analogues bearing different substituents
•An equation is derived relating biological activity to the presence or absence of
particular substituents

Activity = k1X1 + k2X2 +.…knXn + Z

•Xn is an indicator variable which is given the value 0 or 1 depending on whether the
substituent (n) is present or not
•The contribution of each substituent (n) to activity is determined by the value of kn
•Z is a constant representing the overall activity of the structures studied
 Free-Wilson Approach
Advantages

•No need for physicochemical constants or tables

•Useful for structures with unusual substituents
•Useful for quantifying the biological effects of molecular features that cannot be
quantified or tabulated by the Hansch method

Disadvantages

•A large number of analogues need to be synthesised to represent each different

substituent and each different position of a substituent
•It is difficult to rationalise why specific substituents are good or bad for activity
•The effects of different substituents may not be additive
(e.g. intramolecular interactions)