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Nyi Mekar Saptarini

Q S A R and D rug
D e s ig n
C omp ounds + biological
activ ity

Q S
A R

N ew comp ounds w ith

imp rov ed biological activ ity

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Compounds with similar structures are often

biologically active.

This activity may be either similar but
different in potency and unwanted side
effects or different to the original compound

structure - activity relationships (SAR).

A study of the SAR of a lead compound and
its analogues used to determine the
pharmacophore and unwanted side effects.

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This information used to develop a new drug

↑ activity, a different activity from an
existing drug and ↓ unwanted side effects.

SAR are determined by making minor
changes to the structure of a lead to produce
analogues and assessing the effect these
structural changes have on biological activity.

These changes classified as changing :

1. the size and shape of the carbon skeleton,
2. the nature and degree of substitution, and
3. the stereochemistry of the lead.

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The structural changes
↑ lipid character
↑ activity

[better membrane penetration (n = 3–6)] or ↓ activity
[reduction in their water solubility]

Changing the structure could result in an

analogue that is too big to fit its intended
target site.

Computer assisted molecular modelling
(CAMM) can alleviate this problem, provided
that the structure of the target is known or
can be simulated with some degree of
accuracy.

It is emphasized : CAMM is possible to
predict the effect of structural changes there
will be numerous exceptions to the
predictions
all analogues must be
synthesized and tested.

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1. Changing size and shape

The ways to modified are :
1. changing the number of methylene
groups in chains and rings,
2. ↑ or ↓ the degree of unsaturation, and
3. introducing or removing a ring system.

The structural change result in
analogues that exhibit either a different
potency or a different type of activity..

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2. Introduction of new substituents

Occupy a previously unsubstituted position or
replace an existing substituent.

New substituent will impart its own
characteristic chemical, pharmacokinetic and
pharmacodynamic properties to the analogue.

The choice of substituent depend on the
properties that the development team decide to
enhance in an attempt to meet their objectives.

It should be realized that the practical results
will often be different from the theoretical
predictions.

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a. The introduction of a group in an

unsubstituted position

Result in analogues with a different size and

shape.

It may introduce a chiral centre
formation
of stereoisomers.

It may impose conformation restrictions on
some of the bonds in the analogue .

It may increase the rate of metabolism, a
reduction in the rate of metabolism or an
alternative route for metabolism .

It may change the duration of action and the
nature of any side effects.

Harmes et al. : the lack of antihistamine activity

in the ortho-methyl analogue because of
restricting rotation about the C–O bond.
This prevents the molecule from adopting the
conformation necessary for antihistamine
activity.

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• The position of substitution is critical

↑ or ↓ activity.
• Ex. the antihypertensive clonidine with its
o,o’-dichloro substitution is more potent
than its m,p-dichloro analogue
the
bulky chloro groups impose a
conformation restriction on clonidine

b. The introduction of a group by replacing an

existing group

Exhibit the general stereochemical and

metabolic changes.

Using the concept of isosteres.

Isosteres are groups that exhibit some
similarities in their chemical and/or
physical properties
similar
pharmacokinetic and pharmacodynamic
properties
same type of activity.

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QSAR is an attempt to remove the

element of luck from drug design by
establishing a mathematical relationship
in the form of an equation between
biological activity and measurable
physicochemical parameters.

The parameters : lipophilicity, shape
and electron distribution
major
influence on the drug’s activity.

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QSAR defined in the form of numbers from practical data that is

thought to be related to the property the parameter.

It possible to measure or to calculate the parameters for a group of
compounds to the biological activity by mathematical equations
using statistical methods such as regression analysis.

These equations used to make a more informed choice as to which
analogues to prepare.

Ex. statistical data from other compounds used to calculate the
theoretical value of a specific parameter for an as yet
unsynthesized compound.

Substituting this value in the appropriate equation relating activity to
that parameter
calculate the theoretical activity of this unknown
compound.

The main properties that influence drug’s

activity

Lipophilicity is a measure of a drug’s solubility in
lipid membranes
determine how easily a
drug passes through lipid membranes : partition
coefficients.

The electronic effects of the groups within the
molecule will affect its electron distribution

bearing on how easily and permanently the
molecule binds to its target molecule : Hammett
s constants

Drug size and shape
determine how close
enought to its target site in order to bind to that
site : Taft Ms steric constants

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biological activity = function{parameter(s)}

The activity expressed as log[1/C] : the

minimum concentration required to cause a
defined biological response.

If there is a poor correlation between the
values of a specific parameter and the drug’s
activity, other parameters must be playing a
more important part in the drug’s action, and
so they must also be incorporated into the
QSAR equation.

1. Lipophilicity
a. Partition coefficients (P)

Drug has to pass through biological membranes to reach
its site of action
organic medium/aqueous system
partition coefficients .

The n-octanol–water system is chosen because it appears
to be a good mimic of lipid polarity and has an extensive
database.

More accurate results obtained if the organic phase is
matched to the area of biological activity being studied.

Ex. n-octanol gives the most consistent results for drugs
absorbed in the GI tract, olive oil gives more consistent
correlations for drugs crossing the blood–brain barrier,
chloroform gives more consistent values for buccal
absorption.

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log (1/C) = k1 logP + k2

Small range : linear relationship.

log (1/C) = − k1(logP)2 + k2logP+k3

Larger ranges : parabolic relationship.

Max value (log P0) : an optimum balance
between aqueous and lipid solubility for
maximum biological activity.

Below P0 the drug will be reluctant to enter
the membrane.

Above P0 the drug will be reluctant to leave
the membrane.

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b. Lipophilic substituent constants (π)

π represent the group contribution to the
partition coefficient.

π = log PRH - log PRX

When several substituents are present, the
value of π for the compound is the sum of
the π values of each substituents.

The value of π depend on :

1. the structural environment of the substituent

the values relevant to the type of
structure being investigated may be used in
determining activity relationships.
2. the solvent system used to determine the
partition coefficients
the most is n-
octanol/water system.

+ π : higher lipophilicity than hydrogen

− π : lower lipophilicity than hydrogen

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2. Electronic effects

Nonpolar drugs in unionized form are
more readily transported through
membranes than polar drugs and drugs
in their ionized forms.

When the drug reaches its target site,
the distribution of electrons in its
structure will control the type of bond it
forms with that target, which in turn
affects its biological activity.

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σ)
a. The Hammett constant (σ

The distribution of electrons within a
molecule depends on the nature of the
electron withdrawing and donating groups
found in that structure
Hammett
constants (σX)

Hammett used σ to calculate equilibrium and
rate constants for chemical reactions.

σX = logKBX - logKB

σX = pKB - pKBX

The σ value depend on substituent is an overall

electron donor or acceptor.

− σ : the substituent is electron donor group :
KB > KBX

+σ : the substituent is electron withdrawing
group : KB < KBX.

The value of σX contains inductive and
mesomeric (resonance) contributions, and so
varies with the position (m and p) of that
substituent in the molecule.

Inductive and Swain–Lupton constants are
attempts to quantify the inductive and
mesomeric effects of a substituent.

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Definition of Hammett ρ
O O
C C
OH O
+ H
X X

substituent σ p Eq. constant log K Hammett Plot

-NH2 -0.66 0.00000554 -5.25649 -3.7
-OCH3 -0.27 0.000015 -4.82391 -3.9
-4.1
-CH3 -0.17 0.000023 -4.63827 -4.3
Log K

-4.5
-H 0.00 0.000034 -4.46852
-4.7
y = 0.9992x - 4.5305
-Cl 0.23 0.000055 -4.25964 -4.9
R2 = 0.9907
-5.1
-COCH3 0.5 0.000088 -4.05552 -5.3
-CN 0.66 0.000128 -3.89279 -1 -0.5 0 0.5 1
sigma p
-NO2 0.78 0.000166 -3.77989
σ p v alues are obtained from the best fit line hav ing a slop e = 1

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Hammett postulated : the σ values calculated

for benzoic acids could be valid for those ring
substituents in a different series of similar
aromatic compounds
good for meta and
para substituents, but not for ortho substituents.

The latter is believed to be due to steric
hindrance and other effects, such as
intramolecular hydrogen bonding.

Hammett constants only apply to substituents
directly attached to a benzene ring
other
electronic constants, ex. Taft constant.

Attempts to relate biological activity exclusively
to the values of Hammett substitution and
similar constants have been largely
unsuccessful, since electron distribution is not
the only factor involved.

3. Steric effects
The parameter used to show the
relationship between the shape and size
(bulk) of a drug, the dimensions of its
target site and the drug’s activity was :

the Taft steric parameter (Es),

the Charton’s steric parameter (n),

the Verloop’s steric parameters, and

the molar refractivity (MR).

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a. The Taft steric parameter (Es )

Taft (1956) used the relative rate constants of the acid
catalysed hydrolysis of α-substituted methyl ethanoates to
define his steric parameter because it had been shown
that the rates of these hydrolyses were almost entirely
dependent on steric factors.

the value of Es =0 when X =CH3.

The values for Es obtained for a group using the
hydrolysis data are applicable to other structures
containing that group.

The methyl based Es values can be converted to H based
values by adding 1.24 to the corresponding methyl based
values.

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b. Molar refractivity (MR)

The molar refractivity is a measure of both the
volume of a compound and how easily it is
polarized.

n is the refractive index, M is the relative mass and

ρ is the density of the compound.

Although MR is calculated for the whole molecule, it
is an additive parameter
the MR values for a
molecule can be calculated by adding together the
MR values for its component parts.

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c. Other parameters

van der Waals’ radii,

Charton’s steric constants, and

the Verloop steric parameters.
They have all been used to correlate
biological activity to structure with varying
degrees of success.

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Hansch analysis attempts to mathematically

relate drug activity to measurable chemical
properties.

It is based on Hansch’s proposal that drug
action could be divided into two stages:
1. the transport of the drug to its site of
action;
2. the binding of the drug to the target site.

Each stages is dependent on the chemical
and physical properties of the drug and its
target site.

Hansch postulated that the biological activity

of a drug could be related to these
parameters by simple mathematical
relationships based on the general format:
log 1/C = k1(partition parameter) +
k2(electronic parameter) + k3(steric
parameter) + k4

C is the min concentration required to cause
a specific biological response and k1, k2, k3
and k4 are numerical constants obtained by
feeding the values of the parameters into a
suitable computer statistical package.

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The parameter values are obtained either

from the literature (e.g. π, σ, Es) or
determined by experiment (e.g. C, P etc.).

In investigations where more than one
substituent is changed, the value of a
specific parameter may be expressed in the
Hansch equation as either the sum of the
values of that parameter for the individual
substituents or independent individual
parameters.

The general form Hansch equations is

The accuracy of a Hansch equation depend on:

1. the number of analogues (n) used: the
greater the number, the higher the probability
of obtaining an accurate Hansch equation;
2. the accuracy of the biological data used in
the derivation of the equation. The degree of
variation normally found in biological
measurements means that a statistically
viable number of measurements should be
taken for each analogue and an average
value used in the derivation of the Hansch
equation;
3. the choice of parameter (see ‘Craig plots’)

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The accuracy of a Hansch equation assessed

from the values of the standard deviation (s)
and the regression constant (r).

s << : the better the data fits the equation.

r < 0.9 : unsuitable parameter(s) were used to
derive the equation or there is no relationship
between the compounds used and their activity.

Hansch equations may be used to predict the
activity of an as yet unsynthesized analogue.

When the predicted activity is different from the
observed value
the activity is affected by
another factors, such as the ease of
metabolism.

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Hansch analysis used to give an indication

of the importance of the influence of a
parameter on the mechanism by which a
drug acts.

log 1/C = 1.78π − 0.12σ + 1.674

The small value of the coefficient for σ
relative to that of π
the electronic effects
do not play an important part in the action of
the drug.

CRAIG PLOTS

Craig plots are two dimensional plots of
one parameter against another .

The plot is divided into four sections
corresponding to the positive and negative
values of the parameters.

They are used, in conjunction with an
already established Hansch equation for a
series of related aromatic compounds, to
select the aromatic substituents that are
likely to produce highly active analogues.

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Ex. Hansch analysis of aromatic compounds

yields the Hansch equation:

log 1/C = 2.67π − 2.56σ + 3.92

Higher 1/C need +π value and − σ value.

The use of a Craig plot does not guarantee
that the resultant analogues will be more
active than the lead because the parameters
used may not be relevant to the mechanism
by which the analogue acts.

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The Topliss decision tree is a flow diagram that

in a series of steps directs to produce a series
of analogues.

The method is most useful when it is not
possible to make the large number of
compounds necessary to produce an accurate
Hansch equation.

Its use is limited because it requires the lead
compound to have an unfused aromatic ring
system and it only produces analogues that are
substituents of that aromatic system.

The Topliss method also depends on the user
being able to rapidly measure the biological
activity of the lead compound and its analogues.

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The investigation starts with the conversion of the

lead into the first analogue at the top of the tree,
either the 4-chloro analogue or the isopropyl
analogue.

The activity of this analogue is measured and
classified as either less (L), approximately the
same (E) or significantly greater (M) than that of
the original lead.

If the activity is greater than the lead the

next analogue to be prepared is the next
one on the M route.

If the activity of the analogue is less
than the lead the next step is to produce
the analogue indicated by the L route.

If the activity is the same as the lead the
E route is followed and the appropriate
analogue synthesized.

This procedure is repeated, the activity
of each new analogue being compared
with that of its precursor in order to
determine which branch of the tree gives
the next analogue.

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U nfused aromatic ring

An aliphatic side chain

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example

A compound A (Figure 4.8) is active against S. aureus

and activity of this compound and its analogues can
be readily assessed by a biological method.

The first step in the Topliss approach is to synthesize
the 4-chloro derivative (B) of A
the activity of B >
A.

Then following the M branch the Topliss tree indicates
that the next analogue to produce is the 3,4-dichloro
derivative (C) of A
the activity C < B.

The Topliss tree shows that the next most promising
analogue is the 4-trifluromethyl derivative of (D) of A.

One would also synthesize and biologically test the
2,4-dichloro (E) and the 4-nitro analogues (F) of A

emphasized that the decision tree is not a
synthetic pathway for the production of each of the
analogues.

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The synthetic route for producing each

of the suggested analogues would vary
for each analogue and would use the
most appropriate starting materials.

The Topliss decision tree does not give
all the possible analogues but it is likely
that a number of the most active
analogues will be found by this method.

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