International Journal of Application or Innovation in Engineering & Management (IJAIEM)

Web Site: www.ijaiem.org Email: editor@ijaiem.org

Volume 10, Issue 6, June 2021 ISSN 2319 - 4847

An Importance and advancement of QSAR

parameters in modern drug design: A Review
Brij Kishore Tiwari1, Ashish Kumar2, Dr Subhadra Rajpoot2
1,2,
Department of applied science and Humanities , G.L.BajajInstitute of Technology and management
Gr. Noida (U.P.) Pin-201306
2
Department of applied science and Humanities, Amity University
Gr. Noida (U.P.) Pin-201306

ABSTRACT
From the last 30 years QSAR study become important to help in designing of drugs. Many software and hardware are used in
discovery of drugs. QSAR techniques employ powerful computers to generate large data bases result. Quantities structure
activity relationship and quantative structure property relationship is essentially computerised statistical methods which help to
explain the observed variance in the biological effect of certain classes of compound. It assumes that a biological activity of
certain compound is a function of various physico chemical properties are favourable to the concern activity. QSAR involve
themathematical and statistical analysis of SAR data which help to minimize the molecular modification. The ultimate
objective of the present study is to understand the force governing the activity of a particular compound. QSAR is thus a
scientific achievement and an economic necessity to reduce empiricism in drug designing. The purpose of this study is to
describe the techniques like ANN, multiple linearanalysis, partial least square method. The study further extent the types of
QSAR like 1D , 2D, 3D,4D,5D etc used in designing of molecule with the help of different software. QSAR is thus a scientific
achievement and an economic necessity to reduce an empiricism in drug design to ensure that every drug synthesized and
pharmacologically tested should be as meaningful as possible. The uses of different parameter are important to calculate
biological activity of molecule.
Key words: QSAR, Drug design, QSAR PARAMETER, MLR, ANN, Free energy model, Quantum mechanical
method.

INTRODUCTION
The introduction of Hansch method in 1964 enables chemist to describe SAR study in quantative terms.1during past
decade, QSAR started to develop from a more advance stage. Various methods used in QSAR analysis can be explain
that how the molecule is biological active or not. The activity of the molecules depends upon the different parameters
like hydration energy , molecular volume of molecule, parachore, Log P values etc.2 Physical organic chemistry deals
with characterisation of the structure and prediction of the properties, the descriptor for which are usually found
experimentally. If some property depends on the set of selective descriptor,3 the ordering of the structure will parallel
the ordering of properties. In other term the structure information is coded in these properties. The good correlation of
physico chemical properties with a particular set of indices may help in understanding the contribution of these
invariants in determining the property.4

QSAR PARAMETERS
Mainly three types of physico chemical parameters are used in qsar study. Hydrophobic parameters, electronic
paramerter, steric paramerter.5Hydrophobic parameter like partition coefficients log P , Pi substituent’s constant , Rm
chromatographic parameters log Rm, solubility parameter δ, elution time in HPLC log K and parachore [P] are used
in study.6-7
Electronicparameters can be divided in two parts 1. Experimental parameters 2.Theoretical parameters. Experimental
parameters are generally Ionization constant Pka and sigma substituent’s constants σ and σ2 and spectrochemical
shifts are described in term of ppm. Resonance effect R and field effect F and Ionization potential calculated in term of
I.8-9
The theoretical quantum mechanical indices10 MO indices are generally studied as atomic charge densities ϵ, atomic
net charge q, QT, Q, σ etc. and superdelocalisibilitySrn and energy of molecular orbital’sby ELEMO andEHOMO and other
parameters like N, NH, F[A] are also used to describe and calculate the data for result . The third type of parameters are
steric parameters like Taft's steric substituent’s constants ES andvandersWaals radii ϒ and inter atomic distances B, L ,
molar refractivity MR and molar volume MV are used for calculation of value to obtained biological

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activity.11Biological activity reflects the fundamental physico chemical properties of the bioactive compound. The
lipophilicity,polarity,chargesdistributions are main parameter to calculate biological activity.
Major problems in QSAR study arises because hydrophobic, electronic and steric effect overlap and cannot be separated
easily. The parameters which are used to obtain such relation can be divided in to two parts. Those which describe
mainly the physical properties of Skelton such as water solubility partition coefficient, chromatographic Rf value,
molecular weight, surface tension etc. And another parameters which describe the chemical properties like charge
densities, dipole moments, electron donor acceptor properties, Hammetts constant, Taft's steric constant.12-13

QSAR METHODS
There are various methods to calculate the qsar parameters. The introduction the hansch methods.In 1964 enables
chemist to describe the SAR studied in quantative term. There are various methods like free energy model and other
statistical methods, Pattern recognition, topological methods14,quantum mechanical methods and molecular
modelling15 are used for qsar analysis. The free energy model is used to describe the Hansch method for linear free
energy relationship calculation and other method is free wilson mathematical model.
The statistical methods are discriminate analysis, principal component analysis, Factor analysis, cluster analysis and
combined multivariate analysis. There are two way to get a quantative information about SAR, one may use QSAR
methods based on linear free energy relationship which relate the biological activity of a molecule with contributions
from various free energy related physicochemical parameter of the substituent’s. In other approach mathematical model
are used other than linear free energy relationship.

SUBSTITUENT CONSTANT
When any dose of drug is given to patients than the molecules change its confirmation from Site of administration to
site of action. Each confirmation has its differentenergy. The pharmacokinetics and pharmacodynamics property are
based on Lipophilic (Log P)16, electronic sigma and steric featureEs of the drug molecule. The biological activity BA
can be calculated by the equation

Log (BA)= a logP + b Sigma +c Es+d

Where a, b, c and d are the numerical values.

LINEAR RELATIONSHIP BETWEEN LOG P AND BIOLOGICAL ACTIVITY

Meyer and Overtonproposed first linear relationship who find that the narcotics activity of various organic compounds
paralleled there oil water partition coefficients.17Exactly linear relationship between lipophilicity and biological activity
(log 1/c)18 is frequently observed , especially for the binding of drugs by proteins, for drugs eliciting unspecific toxic,
anaesthetic, bactericidal, fungicidal , narcotic or hemolytic properties. The straight line obtained (y= mx+c) when log P
and log1/c are plotted.
Log1/c= a logP+b
In such a linear relationship, the biological activity increases as the lipophilicity increases.

NON- LINEAR RELATIONSHIP BETWEEN LOG P AND BIOLOGICAL ACTIVITY

Linear relationship between lipophilicity and biological activity apply to certain range of lipophilocity. If lipophilicity
exceeds a definite limit, a more or less Sharpedecrees of biological activity result for each series of compounds and each
type of biological activity. In linear equations lipophilicity limits are still beyond the ranges of optimum lipophilicity. If

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there were no optimum lipophilicity in each series, compound with infinite biological activity would result if only their
lipophilicity were high enough. In series of compounds where biological activity is dependent mainly upon
lipophilicity, one can not go on increasing the biological activity indefinitely by increasing lipophilicity of the
compound. Activity rises to a maximum (log Po) and then decline.

CHROMATOGRAPHIC PARAMETERS
Other parameter Rm is used to describe the lipophilicity of drug molecule. In 1965 Boyce and milborrow suggested the
use of Rm value19 from reverse phase thin layer chromatography (TLC)
as alternate lipophilicity parameter in QSAR.
Rm = log (1/Rf -1)

However Rm values cannot be regarded as true equilibrium parameters. Usually silica gel plates are impregnated with
liquid paraffin’s , silicone oil, ethyl oleate or n -octanol as stationary phase. While mobile phase may consist of mixture
of polar solvents like methonol, ethynolaceton with water or aqueous buffer solution. There are many advantages of
using Rm value instead of partition coefficient.

OTHER PARAMETERS RELATED TO LIPOPHILICITY

For defining the lipophilicity other parameters like solubility parameter 20 and dissolution rate constant are used.
Yalkowasky and Valvani have correlated molecular surface area21 with the lipophilicity of polar compounds. Other
physico chemical parameter like molar volume MV, molecular refrectivityMR22, vanderwaals volume Vw and
parachore PA can also be correlated with lipophilicity.23-24
M=Mw/d where Mw is molecular weight and d is density.

MR= n2-1 MW where n is refractive index.

n2+2 d

PA= r1/4 MW/d where r is surface tension

Molarrefractivity is a volume term, but is also proportional to electron polarisibility25. Hence its calculation in qsar is
difficult. If the confirmation dependent steric effect are eliminated molar refractivity may be used as a measure of
dispersion and dipole induced dipole forces. Molar refractivity and parachore may be regarded as corrected molar
volumes. The lipophilicity however not be correlated with molar volume, molar refractivity and parachore if polar
compound are induced.
The capacity factor (log k) determined by HPLC is an indicator of lipophilicity.
K =tr - to
to
wheretr and to are retention time of solute and unretened compound for a series eluted by
methanol–water mobile phase. Centrifugal counter cartography is used to measure partition coefficient.

ELECTRONICS PARAMETER
The polar charecters of drug are calculated by electronic paramete26. σm is called hammett constant for meta
substituents derived from ionisation of benzoic acid.27σpis known is hammett constant for para substituents derived
from ionisation of benzoic acid. σp- Hammet constant used when there is direct conjugation between substituents and

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reaction centre derived from aniline and phenols. σ P+is calledH.C. brown constant derived from solvolysis of di
methyl phenyl carbonyl chlorides. σ1 constant describing solely polar effect. σR constant describing solely mesmeric
effect28.σ* is Taft's polar substituents constants29 derived from hydrolysis of aliphatic esters. Sigma parameter is
haemolytic constant for substituents interacting with a free radical reaction. F and R are field and resonance
components derived for linear combination of σm and σp values. The main commonly used electronic parameter is
Hammett substituents constantswhich can be obtained from the dissociation constant KX and KH of the benzoic acid.

σ =logKx – log KH= log(Kx/KH)=pKaH-pKax

The substituents constant σis depends on Delta G; free energy arises due to dissociation of benzoic acid. Hammetts told
that and electron withdrawing group attached to aromatic ring of benzoic acid would enhance the acid strength of
carboxylic group.

STERIC SUBSTITUTENTS CONSTANTS

Drug receptor interaction is depending on steric features of drug. Bulky group delayed the activity of drug receptor
interaction30. L.P. Hammett studentTaft’s proposed a numerical scale Es in 1956 to determine the drug receptor
interaction based of favourable confirmation of the molecule. Many parameters are used to describe the steric value of
the substituents. The taft's constant Es is derived from the acid hydrolysis of aliphatic esters.
Log (K/ko)=Es
Where K=Rate of acid hydrolysis of substituted esters and Ko=rate of hydrolysis of parents esters. For explaining the
steric feature the molecular refractivity, Vander Waals radii, molecular weight and molecular connectivity indices can
be used.31More value of Es greater is the steric effect affecting intramolecular or intermolecular hindrance to drug
receptor interaction.
Molar refractivity is the other steric parameter based on lorentz equation.

MR= (n2-1) MW
(n2+2) d
Where n= index of refration at the sodium D line
mw= molecular wt of compound.
d= density.
Larger the value of MR greeter the steric contribution.
If the substance is in liquid form the than molar refractivity value can be calculated by using the Lorentz-Lorentz
equation
MR= MW(n2-1)
d (n2+2) ( cm3/mol )

Where mw = molecular wt. N= index of refrection at 20 0C

d = density at 20 0c.

Molecular connectivity indexes are the third type of steric parameter. The degree of branching in given compound is
described by molerconncetivity indexes. Connectivity indexes can be calculated by writing Skelton formula without the
hydrogen atom.
Insert Formula x X=E (deltai) etc.

Substructure environment, degree of branching, unsaturation is represented bymolecular connectivity.

The steric parameter parachore [P] is defined as molar volume Vwhich has been corrected for force of intermolecular
attraction by multiplying with the fourth root of surface tension.
[P] = VY1/4=My1/4 Where M molecular weight D density.
D
Boiling point and density arenon-additive properties were also correlated with steric feature.

Effect of steric and electronic parameters on lipophilicity: - Due to inductive effect overall lipophilicity32is affected and
electron withdrawing groups increases Pie value when a hydrogen bonding group is involve. The nitro group and
hydroxyl group present at aromatic Skelton , the electron withdrawing inductive effect of the phenyl ring and the nitro
group make the non-bonded electrons on the hydroxyl group less available for hydrogen bonding. Theσ and Es is a

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function of QSAR activity. Hence compound having substituents with almost the same value of these parameters may
be considered as isomeric bioisosters.

EXPERIMENTAL DETERMINATION OF PARTITION COEFICIENT

The partition coefficient [P] is the drug distributionbetween organic phase octanol andaquoes phase water.
[P]= concentration of drug in n -octanol
Concentration of drug in water
The partition coefficient33 is not independent of concentration and ideally infinite dilution should be used in the study.
The lipophilic molecule the low concentration 10-5m below the critical micelle concentration in aquous phase should be
used. For prevent the ionisation of drug the 0.1 N Hcl or 0.1 N NaOH may be used.

[p] = [C] n – octanol

(1-α) [C] H2O where alpha is the degree of ionization.

METHODS USED IN QSAR STUDIES

Shake flask method and random walk model of drug transportation is used in qsar.34
Leinear free energy related method used in qsar study. In this approach interaction of drug molecule with biological
activity studied with relation to thermodynamic function. It is also called linear free energy (LFE) or extra
thermodynamic method. This methods is expressed as
BA = f ( ∆L /∆H, ∆E, ∆Es)depending upon the circumstances this equation can be modified as
log BA = b π + a
= c Pka+a
=dEs+a
= b π+cpka+a
= b π + dEs+a
= b π +cPka+dEs+a

Hansch model and free wilson model are included in liener free energy method.
According to hansch model there are two types of dependent liener and nonliner .
Hansch suggested two processfirstly the journey of drug from the point of entry in the body and secondly drug receptor
interaction in the body. Biological activity will be as follows

log BA = a log P + b σ + c Es+d ........ linear

log BA= a log P + b (logP)2 ................. non linear
in free wilson model
log BA= contribution of unsubstituted parent compound+ contribution of corresponding substitutents. Free wilson
approach is fast, simple, cheap method where no substitution constant like Pi, sigma, Es were considered. If structural
is complex than no. of possible substituents will be more at desired positions. Hence the efficiency of this method will
be high.

MOLECULAR MODELLING
It is a technique which describe the actual shape, confirmation, size of the molecules which intract with receptors. It is
the branch of science that help in designing of drugs with the help of computers and software’s. The three
dimensionalstructural confirmation analysis to correlate physiochemical paramerts with the biological activity. The
softwares used for molecular modeling35. aregenrally molecular modeling pro, amber, Hydra, SYBL, FRODO etc.
Thesesoftware’s are available for calculation of molecular properties for search of new lead compounds.
Toplissdecision tree method help to select a limited no. of substituents which will give good relation between π, σ,and
Es. If the biological activity will increases it can be attributed to positive value of π, σ.

REGRATION ANALYSIS
The multiple linearregreation method (MLR) 36 is used to determine the biological active molecule from the large data
pool. MLR is the method used to predict the relationship between two of more explanatory variables by creating a
linear equation. Inqsar correlation coefficient r is calculated with the help of graph. Ploting a graph is prefer method to
obtained biological activity. The term correlation coefficientr , number of compound utilised n, standard deviation S,
and statical validity F is calculated in this method. A regression equation is derived to obtain high value of
regressioncoefficient r which indicate the significant of regreation analysis while low value of regreation analysis r

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indicate the substituent constant is not important. For a better correlation large no of compound must be used. The
value of r must be related to n number of compound for example if r = 0.87 for n=10 is better correlation with r = 0.98
and n=3.
The value of statndard deviation S is large means larger is the accuracy with which the expected activity of new
compound can be judge.
The term regreation parameter r 2value help us to understand whether other parameters should be remain counted or
uncounted. Greater the value of r2 lesser the value of variance data that remains unaccounted by the equation.
The term F evaluate in qsar for the statical validity of a particular equation.

QSPR IN DRUG DESIGN

Quantative structure property relationship37 used in drug design.
The term absortion, distribution, metabolism and elimination is used in pharmacodynamics and pharmacokinetics. The
knowledge of rate constant is essential for calculation of dose and dose intervals, estimation of bioavailability and
prediction of toxic effect of drug. Pharmacokineticsbehaviour of drugs depends upon QSPR parameters these
parameters are absorption rate constants Ka, metabolism rate constant Km, elimination rate constant Kel, volume of
distributionVd and degree of plasma protein binding Ka .

ANN (ARTIFICIAL NEURAL NETWORK)

ANNhave been used widely for designing of qsar model between a set of molecular descriptor obtained from the MLR
and observed activity.38 ANN is a good method in qsar to solve the problums arising in pharmaceutical process and
product developments.

PURPOSE OF QSAR
QSAR techniques gives hints about the activity of molecules so it save the time and coast of synthesis of chemical
molecule. It saves time and effort in clinical trials. It provides the information about the biological activity of the
molecules from the large data of molecules so it save time and coast of synthetic chemist.

APPLICATION OF QSAR
QSAR help to know the biological active compounds in a series of molecules. It also gives idea about the toxic
substances. It also for cast the biological activity of molecules. It also provides idea about pharmacological response of
the molecule in better way. It can be also used to know the surface active agents, purfume, dye and fine chemicals.
QSAR provides idea about selection of proper substituents. It is also provide idea about drug receptor interaction. It also
provide idea about correlation between various type of parameters and pharmacokinetics feature of drug.

QSAR STEPS
Structural Entry and molecular modelling

Descriptor Generation

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Feature selection

Construct model
MLRA or CNN

Model validation

CONCLUSION
QSAR is basically used to determine the biological activity of drug but now a day’s 3D qsar is very important to
correlate the structure feature with the biological activity and its toxic effect if any.
Various newly parameters are used and values calculated with the help of different qsarsoftware’are important to
calculate biological activity. Now a day’s 4D qsar, 5D qsar, 6D qsar are used but 3D qsar is the base of all model for
researcher. Various parameters like electronic, steric etc are used to search the most potent drugs for disease. The role
of use of physicochemical parameters is not limited because hydrophobic parameters, electronic parameters, and steric
parameters are very important and base of to calculate newly parameters.

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