See discussions, stats, and author profiles for this publication at: [Link]

net/publication/380814212

A Textbook of Computer Aided Drug Design

Book · May 2020

CITATIONS READS

0 93

4 authors, including:

Hitesh V. Shahare Khemchand R Surana

SNJB’s Shriman Suresh Dada Jain College of Pharmacy Divine College of Pharmacy, Satana, Nashik
7 PUBLICATIONS 3 CITATIONS 95 PUBLICATIONS 351 CITATIONS

SEE PROFILE SEE PROFILE

All content following this page was uploaded by Khemchand R Surana on 23 May 2024.

The user has requested enhancement of the downloaded file.

 Shahare
Surana
A Textbook of Upasani
Gedam
A Textbook of
Computer Aided Computer Aided
Drug Design
Drug Design

A Textbook of
About the Book
It gives us an immense pleasure to bring out this simplied book
of the subject Computer Aided Drug Design, Semester–VII, Final
Year. B. Pharmacy for students and teachers. This is an attempt to
meet the needs of students and researchers to understand and
grasp the knowledge in eld of CADD.
The authors have compiled this book as per syllabi laid down

Computer Aided Drug Design

by the Pharmacy Council of India. This book provides detailed
knowledge of design and discovery of lead molecules, rational
drug design processes, concept of QSAR and docking, various
strategies to develop new drug like molecules and various
molecular modeling softwares. To understand the basic
fundamentals, all units were explained in simplied way with the
gure, process ow charts and examples which enhances the
process of understanding. This book will provide an effective
learning experience and a resource for all the learners.

Studium Press (India) Pvt. Ltd. ISBN 93-85046-69-1

4735/22, 2nd Floor Prakash Deep Building (Near PNB), H.V. Shahare
Ansari Road, Darya Ganj, New Delhi-110002
Phone: +91-11-43240200-15 (15 lines)
K.R. Surana
Pvt Ltd
Fax: +91-11-43240215 Pvt Ltd
Pvt Ltd
C.D. Upasani
E-mail: pubdir@[Link]
Website: [Link] 9 789385 046698 S.S. Gedam
 This is Members Copy, Not for Sale. Downloaded on Thursday, May 23, 2024
kh
em
ch
an
d su
ra
na
41
1@
gm
ai
l.c
om
 This is Members Copy, Not for Sale. Downloaded on Thursday, May 23, 2024
kh
em
ch
an
d su
ra
na
41
1@
gm
ai
l.c
om
 om
A Textbook of
Computer Aided Drug

l.c
Design

ai
This is Members Copy, Not for Sale. Downloaded on Thursday, May 23, 2024

gm
(As per PCI Syllabus)

1@
41
na

Hitesh V. Shahare
Khemchand R. Surana
ra

Chandrasekhar D. Upasani
Shweta S. Gedam
su
d
an
ch
em

2020
kh

Studium Press (India) Pvt. Ltd.

 om
A Textbook of

l.c
Computer Aided Drug

ai
Design
This is Members Copy, Not for Sale. Downloaded on Thursday, May 23, 2024

gm
© 2020

1@
This book contains information obtained from authentic and highly regarded
sources. Reprinted material is quoted with permission, and sources are indicated.
A wide variety of references are listed. Reasonable efforts have been made to
41
publish reliable data and information, but the authors and the publisher cannot
assume responsibility for the validity of all materials or for the consequences of
their use.
na

All rights are reserved under International and Pan-American Copyright

Conventions. Apart from any fair dealing for the purpose of private study,
ra

research, criticism or review, as permitted under the Copyright Act, 1956, no

part of this publication may be reproduced, stored in a retrieval system or
transmitted, in any form or by any means–electronic, electrical, chemical,
su

mechanical, optical, photocopying, recording or otherwise–without the prior

permission of the copyright owner.
d
an

ISBN: 978-93-85046-69-8
ch

Published by:

Studium Press (India) Pvt. Ltd.

em

4735/22, 2nd Floor, Prakash Deep Building

(Near Delhi Medical Association)
Ansari Road, Darya Ganj, New Delhi-110 002
kh

Tel.: + 91-11-43240200-15 (15 lines); Fax: 91-11-43240215

E-mail: pubdir@[Link]

Printed at India
 om
FOREWORD

l.c
ai
This is Members Copy, Not for Sale. Downloaded on Thursday, May 23, 2024

gm
1@
I have gone through the book of Computer Aided Drug Design written
by Mr. H. V. Shahare and et al. for empowering Pharmacy and other
41
students through Studium Press (India) Pvt. Ltd, New Delhi. The
authors have rich experience in teaching and having research in the
field of CADD.
na

The style of presentation of this book is simply unique, giving a

deeper understanding of the subject. Many concepts with strategies of
ra

drug design, examples, lead identification, molecular modeling

softwares, QSAR approaches and methods and process of drug discovery
su

were explained with simplicity and ease.

I feel the book shall be really welcomed by both the students as

d

well as the teachers as a complete package covering the data in field of

an

CADD. There are question banks, MCQs provided at the end of each
unit, solving which shall help the students.
ch

I congratulate the authors for bringing out this book and wish
them for the very best success in this noble effort.
em

Dr. G. S. Talele
Professor & Principal
Matoshri College of Pharmacy
kh

Eklahre, Nashik, Maharashtra

 om
ACKNOWLEDGEMENT

l.c
ai
This is Members Copy, Not for Sale. Downloaded on Thursday, May 23, 2024

It gives us an immense pleasure to express special thanks for the time

gm
to time suggestions, efforts and co-operation provided for the publication
task by Dr. J. N. Govil Sir, Vice President, Studium Press (India) Pvt.
Ltd, New Delhi, and all the staff of Publishing House.

1@
And finally we would like to thank God for showering choicest
blessings on us and inspiring us always to do the best at every stage
of life.
41
Authors
na
ra
d su
an
ch
em
kh
 om
ABOUT THE AUTHOR(S)

l.c
ai
Prof. Hitesh V. Shahare is a Assistant Professor,
This is Members Copy, Not for Sale. Downloaded on Thursday, May 23, 2024

gm
Dept. Ph.’ Chem., SNJBs Shriman Sureshdada Jain
College of Pharmacy, Chandwad, Nashik. He
completed his M. Pharmacy from University Institute
of Chemical Technology, Mumbai in 2004. He is

1@
pursuing Ph. D. at SNJBs SSDJ Coll. Ph. Chandwad
in SPPU. He has total 14 years of teaching experience.
He has 40 research, review presentations/publications
41
in various journal of National & International repute. His area of
research includes Synthesis and biological evaluation, CADD. He has
received research grants to the tune of 11 Lakhs from DST, New Delhi
na

and BCUD, SPPU. He is a life member of Association of Pharmacy

teachers of India (APTI).
ra

Mr. Khemchand R. Surana working as Assistant

su

Professor in the Dept. Pharm. Chem. at Shri Shakti

Shaikshanik Sanstha Divine College of Pharmacy,
Satana, Nashik (Savitribai Phule Pune University,
d

Pune). He has obtained his graduation (B. Pharm)

an

degree at Savitribai Phule Pune University in 2016.

He obtained his Masters degree (M. S. Pharm) in
Medicinal Chemistry in 2018 from National Institute
ch

of Pharmaceutical Education and Research-Ahmedabad (NIPER-A)

with 2 years research experience. His area of research includes
em

Synthesis, Docking, Pharmacological activity and method Development.

kh
 A Textbook of Computer Aided Drug Design

Dr. Chandrasekhar D. Upasani is Professor &

Principal, SNJBs Shriman Sureshdada Jain College

om
of Pharmacy, Neminagar, Chandwad, Nasik. He holds
rich experience of over 25 years of teaching and
administrative experience He is former Dean and BOS
Chairman of faculty of Pharmacy, Savitribai Phule

l.c
Pune University, Pune. He is also associated with
other Universities of repute as BOS member and other

ai
administrative bodies. He is a President of Maharashtra state
This is Members Copy, Not for Sale. Downloaded on Thursday, May 23, 2024

Association of Pharmacy Teachers of India (APTI). He is Ph. D. guide

gm
in SPPU Pune and under his guidance; more than 15 students
completed their Ph. D. He is a conveyor of many national and state
level conferences. He has delivered several invited talk in various
conferences. He has completed number of major projects and published

1@
more than five books. His deep involvement in research is reflected
through 50 Publications/ Presentations in National & International
reputed journals. He has guided more than 30 M. Pharm students for
41
their research.
na

Prof. Shweta S. Gedam is Assistant Professor, Dept.

Pharmaceutics, Sandip Institute of Pharmaceutical
Sciences, Mahiravani, Nashik, Maharashtra. She has
ra

completed her M. Pharmacy from Sant Gadge Baba

Amravati University in 2011. She is pursuing Ph. D.
su

at SNJBs SSDJ Coll. Ph. Chandwad, from Savitribai

Phule Pune University. She has total 08 years of
d

teaching experience. She has 20 research and review

presentations/publications in various Conferences/Journals of National
an

& International repute. Her area of research includes nanoparticulate

drug delivery system. She is a life member of the Association of
ch

Pharmacy Teachers of India (APTI).

em
kh

viii
 Molecular Modeling

om
PREFACE

l.c
ai
This is Members Copy, Not for Sale. Downloaded on Thursday, May 23, 2024

The contents of the book Computer Aided Drug Design are designed

gm
and conform to the syllabi laid down by Pharmacy Council of India,
which is mandatory and followed by all Pharmacy Institutes throughout
the India. This book intended for Bachelor of Pharmacy course. The
book comprises total 05 units, exactly in the same order and with same

1@
contents as prescribed in syllabi of Pharmacy Council of India.

This book provides detailed knowledge of stages involved in design

41
and discovery of lead molecules, approaches involved in rational drug
design processes and analog based drug design.
na

This book also focuses on concept of SAR and QSAR, Hansch

analysis, Free Wilson analysis, 3D-QSAR approaches like COMFA and
COMSIA and types of physicochemical parameters.
ra

The users of this book will find the various strategies to develop
su

new drug like molecules, concept of pharmacophore mapping, process

involved in molecular docking and study on various molecular modeling
softwares.
d
an

It is also inclusive of informatics and methods in drug design,

molecular mechanics and quantum mechanics, energy minimization
methods and conformational analysis.
ch

All the Units have been much simplified to the need and grasp of
the students with sufficient illustrations, process flow charts, figures
em

and examples, so that students find them interesting.

All these units have Multiple Choice Questions, Long Answers

Questions and Short Answer Questions banks at the end of each unit.
kh

Thus keeping with our tradition, this book is unique in its style,
presentation and simplicity.

ix
 A Textbook of Computer Aided Drug Design

Here, we expect good and positive response for this book by both
the students and subject teachers for its quality and style of

om
presentation, deep content and lucid explanatory language. The
coverage of syllabus is complete and sincere reading and solving of
questions provided in the question banks, can assure the students of a
good grasp of the basics and gaining confidence to appear for any viva

l.c
voce or examination.

We wish an enjoyable learning for the students and satisfactory

ai
teaching for the teachers of subject Computer Aide Drug Design.
This is Members Copy, Not for Sale. Downloaded on Thursday, May 23, 2024

gm
Authors

1@
41
na
ra
d su
an
ch
em
kh

x
 Molecular Modeling

om
TABLE OF CONTENTS

l.c
ai
This is Members Copy, Not for Sale. Downloaded on Thursday, May 23, 2024

Foreword v

gm
Acknowledgement vi
About the Author(s) vii
Preface ix

1@
1. Drug Discovery and Drug Development 1
1. History 1
41
2. Introduction 2
3. Stages of Drug Development 4
na

4. Approaches to Drug Discovery 18

5. Rational Approaches Based on Traditional Medicine 21
6. Lead Discovery Based on Drug Metabolism 24
ra

7. Lead Discovery Based on Clinical Observation 26

8. Drug Design 27
su

9. SBDD Verses ABDD Bioisosterism 31

10. Factors Affecting Drug Discovery and Drug 38
Development
d

11. Summary 39
an

2. Quantitative Structure Activity Relationship 41

(QSAR)
ch

1. Introduction 41
2. History and Development 44
em

3. SAR Verses QSAR 45

4. Types of Physicochemical Parameters 48
5. QSAR 60
6. 3D-QSAR 72
kh

7. Applications of QSAR 76
8. Summary 77

xi
 A Textbook of Computer Aided Drug Design

3. Molecular Modeling and Virtual Screening 79

Techniques

om
1. Introduction 79
2. Virtual Screening (VS) 82
2.1 Drug Likeness Screening 90

l.c
2.2 Concept of Pharmacophore Mapping 97
2.3 Pharmacophore Based Drug Design 102
3. Molecular Docking 105

ai
3.1 Types of Docking 107
This is Members Copy, Not for Sale. Downloaded on Thursday, May 23, 2024

3.2 Major Steps Involved in Mechanics of Molecular 114

gm
Docking
3.3 Mechanics of Molecular Docking 115
3.4 Docking Approaches 120

1@
3.5 Homology Modelling 121
3.6 De Novo Drug Design 123
4. Docking Softwares 133
5. Applications and Importance of Molecular Docking 141
41
4. Informatics and Methomds in Drug Design 145
na

1. Introduction to Bioinformatics 145

2. Chemo-informatics 163
3. Applications of Bioinformatics 175
ra

4. Bioinformatics Software and Databases 177

su

5. Molecular Modeling 180

1. Introduction 180
d

2. Quantum Mechanics and Molecular Mechanics 188

3. Energy Minimization Methods 194
an

4. Conformational Analysis 195

5. Global Conformational Minima Determination 207
ch

Further Readings 211

Subject Index 215
em
kh

xii

View publication stats