CADD and Molecular

Modeling : Importance in
Pharmaceutical Development

Dr. Sanjeev Kumar Singh

Department of Bioinformatics
Alagappa University
e-mail- skysanjeev@gmail.com

Working at the Intersection

Structural Biology
Biochemistry
Medicinal Chemistry
Toxicology
Pharmacology
Biophysical Chemistry
Information Technology

Structural Biology
Fastest growing
area of biology
Protein and nucleic
acid structure and
function
How proteins
control living
processes

Medicinal Chemistry
Organic Chemistry
Applied to disease
Example: design
new enzyme
inhibitor drugs
doxorubicin (anti-cancer)

Pharmacology
Biochemistry of Human Disease
Different from Pharmacy: distribution
of pharmaceuticals, drug delivery
systems

New Ideas From Nature

Natural Products
Chemistry
Chemical Ecology
During the next two
decades: the major
activity in organismal
biology

Examples: penicillin,
taxol (anti-cancer)

Bio/Chem-informatics

The collection, representation and organisation of

chemical data to create chemical information, to which
theories can be applied to create chemical knowledge.

Aim

To examine how computational techniques can be used

to assist in the design of novel bioactive compounds.

To give an idea of how computational techniques can

similarly be applied to other emerging areas such as Bioinformatics, Cheminformatics &

Pharmainformatics.

Overview
Drug discovery process
How do drugs work?
Overview of Computer-Aided Drug
Design

Pharmaceutical/Agrochemical
Industry
Identification of novel compounds with useful and
commercially valuable biological properties.
vastly complex,
multi-disciplinary task
many stages over extended periods of time

Risk
most novel compounds do not result in a drug.
those that do may cause unexpected, long-term
side-effects.

Why CADD?
Drug Discovery today are facing a serious
challenge because of the increased cost and
enormous amount of time taken to discover
a new drug, and also because of rigorous
competition
amongst
different
pharmaceutical companies.

Drug Discovery & Development

Identify disease

Human clinical trials

(2-10 years)

le

Formulation

ND

Fi
IN le
D

Preclinical testing
(1-3 years)

Fi

Isolate protein
involved in
disease (2-5 years)

Find a drug effective

against disease protein
(2-5 years)
Scale-up

FDA approval
(2-3 years)

Drug Development Process

10,000s
compounds

develop
assay
lead
identification
lead
optimisation

1 drug

clinical
trials
to market

On average it takes 12 -15

years and costs ~$500 -800
million to bring a drug to
market

Cont

Technology is impacting this process

GENOMICS, PROTEOMICS & BIOPHARM.
Potentially producing many more targets
and personalized targets

HIGH THROUGHPUT SCREENING

Identify disease

Screening up to 100,000 compounds a

day for activity against a target protein

VIRTUAL SCREENING
Using a computer to
predict activity

Isolate protein

COMBINATORIAL CHEMISTRY
Rapidly producing vast numbers
of compounds

Find drug

MOLECULAR MODELING

Computer graphics & models help improve activity

IN VITRO & IN SILICO ADME MODELS

Preclinical testing

Tissue and computer models begin to replace animal testing

Automating the CADD Process

X-ray or
Homology
Med Chem/Combichem
Gene sequence data

LibmakerTM
Designed libraries

Skelgen

Designed Templates

Ligand binding data

Pharmacophore
Model

Library synthesis

Screening

Phases of CADD
Target discovery
Target
Identification

Target
Validation

Database
filtering
Similarity
analysis
VHTS

Lead discovery
Lead
Identification

Alignment
Biophores

Lead
Optimization

QSAR
ADMET

diversity Combinatorial de novo

selection
libraries
design

Computer Aided
Drug Design
(CADD)

SAVING 12 15 years, Costs: 500 - 800 million

US $

How Drugs Work

+

Enzyme

Substrate
Lock-and-key model

Enzyme-substrate
complex

Methodologies and strategies of

CADD:
Structure based drug design (SBDD)
DIRECT
DESIGN
Followed when the spatial structure of the
target is known.
Ligand based drug design (LBDD)
INDIRECT
DESIGN
Followed when the structure of the target is
unknown.

Computer-Aided Drug Design

3-D target structure unknown (LBDD)

Random screening if no actives are known

Similarity searching
Pharmacophore mapping
QSAR (2D & 3D) etc.
Combinatorial library design etc.

Structure-based drug design (SBDD)

Molecular Docking
De novo design

In Pharmacophore
Pharmacoporic Studies on ACE
inhibitors
Pharmacological Studies on HIV-1RT
Nucleosidic Inhibitors
Non-Nucleosidic Inhibitors
Interaction Energy Potency Correlation

What is Pharmacophore?
Pharmacophore model
Set of points in space defining the binding of ligands
with target.
Key factors in developing such a model are the
determination of functional groups essential for
binding, their correspondence from one ligand to
another, and the common spatial arrangement of these
groups when bound to the receptor

The pharmacophore model of HIV protease.

Pharmacophore..?
a molecular framework that carries (phoros) the
essential features responsible for a drugs
(pharmacon) biological activity Paul Erlich, early
1990
a set of structural features in a molecule that is
recognized at a receptor site and is responsible for
that molecules activity Peter Gund, 1977

Basic Features
A set of features common to a series of active
molecules
What are the features?

HBD
HBA
+ve &-ve charged groups and
Hydrophobic regions

Functional groups or molecules with similar

physical and chemical properties
Bioisosteres - substituents or groups that
have chemical or physical similarities and
which produce broadly similar biological
properties

Pharmacophore model
Set of points in space defining the binding of ligands
with target.
Key factors in developing such a model are the
determination of functional groups essential for
binding, their correspondence from one ligand to
another, and the common spatial arrangement of these
groups when bound to the receptor.

ACE
Angiotension
converting enzyme
Converts
angiotensinI to
angiotension II
Inhibits bradykinin
(vasodilator)
Vasoconstriction

ACE-inhibitor

Orally available
& potent drug

ACE distance map

4 points defined
Five distances
defined

Acceptor
Chargednegative

Donor

Hydrophobiccore

Pharmacophoric Features of
Nucleosidic HIV-1RT Inhibitors

3'-azido thymidine (AZT)

deoxy nucleoside
triphosphate (dNTP)

3'-nitro nucleoside

2',3' dideoxy nucleoside

2',3'- didehydro dideoxy nucleoside

MESP contours for nucleosidic drugs. Red coloured contours indicate a value of -.01 for
electrostatic potential and yellow contours indicate a value of -0.05

Concluding remarks on Nucleosidic

inhibitors
Different substituents at the 3 position show similar sugar ring puckering
and only slight differences in nucleosidic base disposition and interactions
protein.
MESP plots have clearly indicated that the charge environment of the
drugs is complementary to the receptor charge environment. Positive
potential areas have been observed in the active site of HIV-1RT where
DNA binding occurs.

Pharmacophoric Features of Nucleosidic HIV-1RT Inhibitors.

Arpita Yadav* and Sanjeev Kumar Singh Bioorg. & Med. Chem. 11, 2003, 1801.

Threshold interaction energy of NRTIs

(nucleosidic inhibitors for Reverse
transcriptase) to undergo competitive
inhibition
3.58

-14.13 kcal/mol

2'3' dideoxy thymidine

-13.33 kcal/mol

AZT -16.71 kcal/mol

-12

Interaction Energy
(Kcal/mol)

-14

2'3'-didehydro 2'3'-dideoxy thymidine

-12.39 kcal/mol

3-Nitro nucleoside
-21.30 kcal/mol

-16
-18
-20
-22
0

10

12

IC50 ( M)

Correlation of interaction energy with potency

oncluding remarks on interaction energy studie

Correlation graph indicates the requirement of a threshold binding

energy ~12 kcal/mol for the drug to be able to undergo competitive
inhibition efficiently. Less than this binding energy/ interaction energy will
make the drug ineffective or very high concentrations will be required for
inhibition of enzyme. Which may lead to cytotoxicity.

Threshold interaction energy of NRTIs (nucleosidic inhibitors for Reverse

transcriptase) to undergo competitive inhibition
Arpita Yadav* and Sanjeev Kumar Singh Bioorg. & Med. Chem. letts. 14, 2004,
2677-2680

Common binding mode for structurally

and chemically diverse non- nucleosidic
HIV-1RT inhibitors
2.514

2.514

2.021

lys101

4.0

Pyrrolyl hetro aryl sulfone with trovirdine

2.785

Pyrrolyl hetro aryl sulfone with lysine

2.514

lys101

2.785

Pyrrolyl hetro aryl sulfone with HEPT

Concluding remarks of Non nucleosidic

Conformational study of non-nucleosidic drugs indicated that each
drug has a V- shaped conformation.
Each drug has a -NH group in a position that it can make H- bond
with the carbonyl group of lysine 101 in conformity with earlier studies
on pyrrolyl hetero aryl sulfone. This indicates the importance of lysine
101 in binding NNRTIs.

Common binding mode for structurally and chemically diverse non- nucleosidic
HIV-1RT inhibitors"
Arpita Yadav* and Sanjeev Kumar Singh, THEOCHEM, 723, 2005, 205-209.

DISCO: DIStance COmparisons

Generate some number of low-energy conformations
for each active compound
The resulting conformations are represented by the
positions of potential pharmacophore points.
Hydrogen-bond donors and acceptors; charged
atoms; ring centroids; and centres of hydrophobic
regions.

Quantitative Structure-Activity
Relationships (QSAR)

A QSAR relates a numerical description of molecular structure

or properties to known biological activity

Activity = f (molecular descriptors)

Success of QSAR: right descriptors + right method (form of

f)

A QSAR should be

explanatory (for structures with activity data)

predictive (for structures without activity data)

A QSAR can be used to explain or optimise:

localised properties of molecules such as binding

properties

whole molecule properties such as uptake and distribution

3D QSAR
CoMFA and CoMSIA
Molecules are described by the values of
molecular fields calculated at points in a 3D
grid
The molecular fields are usually steric and
electrostatic
Partial least squares (PLS) analysis used to
correlate the field values with biological
activity
A common pharmacophore is required.

Using the Model

The PLS results are
presented as contour
plots
Steric Bulk:
Green = Steric
Favourable
Yellow = Steric
Unfavourable
Electrostatics:
Red = Electronegative
Favourable
Blue = Electronegative
Unfavourable

3D-QSAR CoMFA Study on Aminothiazole

Derivatives as Cyclin Dependent Kinase 2
Inhibitors
In this work we performed CoMFA study carried out on 47
aminothiazole derivatives as inhibitors of this protein kinase.

The models could be usefully employed to design selective CDK2

inhibitors and to find novel scaffolds through screening of
chemical databases.

Allignment

CoMFA Steric Contours

CoMFA Electrostatic Contours

Green contours stand for points where sterically bulkier groups are
anticipated to increase the biological activity.
The yellow contours are used to underscore the points where bulkier
groups could lower the biological property.
The electrostatic red plots show where the presence of a negative
charge is expected to enhance the activity.
The blue contours indicate where introducing or keeping positive
charges are expected to better the observed activity.
3D-QSAR CoMFA Study on Aminothiazole Derivatives as Cyclin Dependent Kinase 2
Inhibitors. Nigus Dessalew, Sanjeev Kumar Singh* and P.V. Bharatam QSAR Comb. Sci.,
26(1), 2007, 85-91.

QSAR WORK

The developed model showed a strong correlative and

predictive capability having a cross validated correlation
co-efficient of 0.747 for CDK4 and 0.755 for CDK2
inhibitions.

3D-QSAR CoMFA studies on Indenopyrazole as CDK2 Inhibitors.

Sanjeev Kumar Singh*, Nigus Dessalew, and P. V. Bharatam Eur.
J. of Med. Chem., 41, 2006, 1310-1319.

The conventional and predictive correlation coefficients

were found to be respectively 0.943 and 0.508 for CDK1
and 0.957 and 0.585 for CDK2.

3D-QSAR CoMFA Study on Oxindole Derivatives as Cyclin

Dependent
Kinase 1 (CDK1) and Cyclin Dependent Kinase 2
(CDK2) Inhibitors. Sanjeev Kumar Singh*, Nigus Dessalew, and P.
V. Bharatam, Med. Chem. 3(1), 2007, 75-84.

Structure Based Drug Design

Determine Protein Structure
Identify Interaction Sites
Discovery or design of
molecules that interact
with biochemical targets
of known 3D structure

De Novo Design

3D Database

Evaluate Structure
Synthesize Candidate
Test Candidate
Lead Compound

Structure based drug design

Molecular database mining
Compounds with best complementarity to
binding site are selected.
DOCK, Autodock, Flex X etc.
De novo drug designing
Virtual
modeling
and
optimization
structure
LUDI, CLIX, CAVEAT, LeapFrog etc.

of

Structural Targets
3D structure of target receptors determined
by
X-ray crystallography
NMR
Homology modeling
Protein Data Bank
Archive of experimentally determined 3D
structures of biological macromolecules

X-ray crystallography

NMR

Molecular docking
Virtual screening approach to predict receptorligand binding modes
Scoring method used
to detect correct bound conformation during
docking process
to estimate binding affinities of candidate
molecule after completion of docking

Docking algorithms
Molecular flexibility
both ligand and protein rigid
flexible ligand and rigid protein
both ligand and protein flexible
search algorithm
use to explore optimal positions of the ligand
within the active site
scoring function
value should correspond to preferred binding
mode
efficiency very important for database searching

Scoring function
Ligand-receptor binding is driven by
Electrostatics (including h-bonding)
Dispersion of vdws forces
Hydrophobic interaction
Desolvation of ligand and receptor
Molecular mechanics
Attempt to calculate interaction energy
directly

Docking

X-ray structure of complex

Ligand database

Target Protein

Molecular docking

Ligand docked into proteins active site

How do my ligands dock into the

protein?
Various approaches, including:
Shape (DOCK program)
incremental search methods (Flex X)
Monte Carlo/Simulated annealing (AUTODOCK, FLO)
Genetic algorithms (GOLD)
Molecular dynamics
Systematic search (Glide, Open Eye)
Two key issues
sampling
scoring/evaluating possible configurations/poses

Collaboration with
Prof. Shandhar Ahamad, National Institute of
Biomedical Innovation, Japan
Dr. Nigus Desselaw Addis Ababa University,
Ethiopia
Prof. J. Kastner, University of Stuttgart, Germany
Prof. K. Dharmalingam, Madurai Kamaraj Uni.,
Madurai
Dr. Arpita Yadav, CSJM University Kanpur

THANK YOU