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AN: 961615 ; Roy, Kunal.; Quantitative Structure-Activity Relationships in Drug Design, Predictive Toxicology, and
Risk Assessment
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Quantitative StructureActivity Relationships in
Drug Design, Predictive
Toxicology, and Risk
Assessment
Kunal Roy
Jadavpur University, India
A volume in the Advances in Chemical and
Materials Engineering (ACME) Book Series
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Quantitative structure-activity relationships in drug design, predictive toxicology, and risk assessment /
Kunal Roy, editor.
p. ; cm.
Includes bibliographical references and index.
Summary: “This book discusses recent advancements in the field of QSARs with special reference to their application in
drug development, predictive toxicology, and chemical risk analysis”--Provided by publisher.
ISBN 978-1-4666-8136-1 (hardcover) -- ISBN 978-1-4666-8137-8 (ebook)
I. Roy, Kunal, 1971- , editor.
[DNLM: 1. Drug Design. 2. Quantitative Structure-Activity Relationship. 3. Drug Antagonism. 4. Drug-Related Side
Effects and Adverse Reactions. 5. Risk Assessment. QV 745]
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2015000076
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Titles in this Series
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Processing Techniques and Tribological Behavior of Composite Materials
Rajnesh Tyagi (Indian Institute of Technology (BHU), Varanasi, India) and J. Paulo Davim (University of Aveiro,
Portugal)
Engineering Science Reference • copyright 2015 • 410pp • H/C (ISBN: 9781466675308) • US $225.00 (our price)
Handbook of Research on Diverse Applications of Nanotechnology in Biomedicine, Chemistry, and Engineering
Shivani Soni (Alabama State University, USA) Amandeep Salhotra (City of Hope National Medical Center, USA)
and Mrutyunjay Suar (KIIT University, India)
Engineering Science Reference • copyright 2015 • 820pp • H/C (ISBN: 9781466663633) • US $395.00 (our price)
Innovative Applications and Developments of Micro-Pattern Gaseous Detectors
Tom Francke (Myon, Sweden) and Vladimir Peskov (CERN, Switzerland)
Engineering Science Reference • copyright 2014 • 303pp • H/C (ISBN: 9781466660144) • US $215.00 (our price)
Handbook of Research on Nanoscience, Nanotechnology, and Advanced Materials
Mohamed Bououdina (University of Bahrain, Bahrain) and J. Paulo Davim (University of Aveiro, Portugal)
Engineering Science Reference • copyright 2014 • 617pp • H/C (ISBN: 9781466658240) • US $365.00 (our price)
Quantum and Optical Dynamics of Matter for Nanotechnology
Mihai V. Putz (West University of Timisoara, Romania)
Engineering Science Reference • copyright 2014 • 527pp • H/C (ISBN: 9781466646872) • US $180.00 (our price)
Advanced Solar Cell Materials, Technology, Modeling, and Simulation
Laurentiu Fara (Polytechnic University of Bucharest, Romania) and Masafumi Yamaguchi (Toyota Technological
Institute, Japan)
Engineering Science Reference • copyright 2013 • 354pp • H/C (ISBN: 9781466619272) • US $195.00 (our price)
Computational Gas-Solids Flows and Reacting Systems Theory, Methods and Practice
Sreekanth Pannala (Oak Ridge National Laboratory, USA) Madhava Syamlal (National Energy Technology Laboratory, USA) and Thomas J. O’Brien (National Energy Technology Laboratory, USA)
Engineering Science Reference • copyright 2011 • 500pp • H/C (ISBN: 9781615206513) • US $180.00 (our price)
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Editorial Advisory Board
Emilio Benfenati, Istituto di Ricerche Farmacologiche Mario Negri, Italy
Eduardo A. Castro, La Plata University, Argentina
Asim K. Debnath, New York Blood Center, USA
S. P. Gupta, National Institute of Technical Teachers’ Training and Research (NITTTR), India
Lemont B. Kier, Virginia Commonwealth University, USA
Jerzy Leszczynski, Jackson State University, USA
Bono Lučić, Ruđer Bošković Institute, Croatia
Paul L. A. Popelier, Manchester Institute of Biotechnology, UK
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Table of Contents
Foreword .............................................................................................................................................xvi
Preface ...............................................................................................................................................xviii
Acknowledgment .............................................................................................................................. xxiv
Chapter 1
An Introduction to the Basic Concepts in QSAR-Aided Drug Design ................................................... 1
Maryam Hamzeh-Mivehroud, Biotechnology Research Center & School of Pharmacy, Tabriz
University of Medical Sciences, Tabriz, Iran
Babak Sokouti, Biotechnology Research Center, Tabriz University of Medical Sciences,
Tabriz, Iran
Siavoush Dastmalchi, Biotechnology Research Center & School of Pharmacy, Tabriz
University of Medical Sciences, Tabriz, Iran
Chapter 2
The “ETA” Indices in QSAR/QSPR/QSTR Research .......................................................................... 48
Kunal Roy, Jadavpur University, India
Rudra Narayan Das, Jadavpur University, India
Chapter 3
Evolution of Multivariate Image Analysis in QSAR: The Case for a Neglected Disease ....................84
Matheus P. Freitas, Federal University of Lavras, Brazil
Mariene H. Duarte, Federal University of Lavras, Brazil
Chapter 4
Quantitative Structure-Activity/Property/Toxicity Relationships through Conceptual Density
Functional Theory-Based Reactivity Descriptors ...............................................................................123
Sudip Pan, Indian Institute of Technology Kharagpur, India
Ashutosh Gupta, Udai Pratap Autonomous College, India
Venkatesan Subramanian, Central Leather Research Institute, India
Pratim K. Chattaraj, Indian Institute of Technology Kharagpur, India
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Chapter 5
Importance of Applicability Domain of QSAR Models ..................................................................... 180
Kunal Roy, Jadavpur University, India
Supratik Kar, Jadavpur University, India
Chapter 6
QSAR of Antioxidants ........................................................................................................................ 212
Omar Deeb, Al-Quds University, Palestine
Mohammad Goodarzi, Katholieke Universiteit Leuven, Belgium
Chapter 7
QSAR Studies on Bacterial Efflux Pump Inhibitors ........................................................................... 238
Khac-Minh Thai, University of Medicine and Pharmacy at HCMC, Vietnam
Trong-Nhat Do, University of Medicine and Pharmacy at HCMC, Vietnam
Thuy-Viet-Phuong Nguyen, University of Medicine and Pharmacy at HCMC, Vietnam
Duc-Khanh-Tho. Nguyen, University of Medicine and Pharmacy at HCMC, Vietnam
Thanh-Dao Tran, University of Medicine and Pharmacy at HCMC, Vietnam
Chapter 8
Integrated in Silico Methods for the Design and Optimization of Novel Drug Candidates: A Case
Study on Fluoroquinolones – Mycobacterium tuberculosis DNA Gyrase Inhibitors ......................... 269
Nikola Minovski, National Institute of Chemistry, Slovenia
Marjana Novič, National Institute of Chemistry, Slovenia
Chapter 9
Computational Approaches for the Discovery of Novel Hepatitis C Virus NS3/4A and NS5B
Inhibitors ............................................................................................................................................. 318
Khac-Minh Thai, University of Medicine and Pharmacy at HCMC, Vietnam
Quoc-Hiep Dong, University of Medicine and Pharmacy at HCMC, Vietnam
Thi-Thanh-Lan Nguyen, University of Medicine and Pharmacy at HCMC, Vietnam
Duy-Phong Le, University of Medicine and Pharmacy at HCMC, Vietnam
Minh-Tri Le, University of Medicine and Pharmacy at HCMC, Vietnam
Thanh-Dao Tran, University of Medicine and Pharmacy at HCMC, Vietnam
Chapter 10
QSAR Models towards Cholinesterase Inhibitors for the Treatment of Alzheimer’s Disease ........... 354
C. Gopi Mohan, Amrita Institute of Medical Sciences and Research Centre, India
Shikhar Gupta, National Institute of Pharmaceutical Education and Research, India
Chapter 11
Ligand- and Structure-Based Drug Design of Non-Steroidal Aromatase Inhibitors (NSAIs) in
Breast Cancer ...................................................................................................................................... 400
Tarun Jha, Jadavpur University, India
Nilanajn Adhikari, Jadavpur University, India
Amit Kumar Halder, Jadavpur University, India
Achintya Saha, University of Calcutta, India
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Chapter 12
Computational Techniques Application in Environmental Exposure Assessment .............................471
Karolina Jagiello, University of Gdansk, Poland
Tomasz Puzyn, University of Gdansk, Poland
Chapter 13
QSAR-Based Studies of Nanomaterials in the Environment .............................................................. 506
Valeria V. Kleandrova, University of Porto, Portugal
Feng Luan, Yantai University, China & University of Porto, Portugal
Alejandro Speck-Planche, University of Porto, Portugal
M. Natália D. S. Cordeiro, University of Porto, Portugal
Chapter 14
Quantitative Nanostructure-Activity Relationship Models for the Risk Assessment of
NanoMaterials ..................................................................................................................................... 535
Eleni Vrontaki, NovaMechanics Ltd., Cyprus & University of Athens, Greece
Thomas Mavromoustakos, University of Athens, Greece
Georgia Melagraki, NovaMechanics Ltd., Cyprus
Antreas Afantitis, NovaMechanics Ltd., Cyprus
Chapter 15
QSPR/QSAR Analyses by Means of the CORAL Software: Results, Challenges, Perspectives ....... 560
Andrey A. Toropov, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Italy
Alla P. Toropova, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Italy
Emilio Benfenati, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Italy
Orazio Nicolotti, Università degli Studi di Bari “Aldo Moro”, Italy
Angelo Carotti, Università degli Studi di Bari “Aldo Moro”, Italy
Karel Nesmerak, Charles University in Prague, Czech Republic
Aleksandar M. Veselinović, University of Niš, Serbia
Jovana B. Veselinović, University of Niš, Serbia
Pablo R. Duchowicz, Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas
INIFTA (UNLP, CCT La Plata-CONICET), Argentina
Daniel Bacelo, Universidad de Belgrano, Argentina
Eduardo A. Castro, Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas INIFTA
(UNLP, CCT La Plata-CONICET), Argentina
Bakhtiyor F. Rasulev, Jackson State University, USA
Danuta Leszczynska, Jackson State University, USA
Jerzy Leszczynski, Jackson State University, USA
Compilation of References ............................................................................................................... 586
About the Contributors .................................................................................................................... 688
Index ................................................................................................................................................... 701
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Detailed Table of Contents
Foreword .............................................................................................................................................xvi
Preface ...............................................................................................................................................xviii
Acknowledgment .............................................................................................................................. xxiv
Chapter 1
An Introduction to the Basic Concepts in QSAR-Aided Drug Design ................................................... 1
Maryam Hamzeh-Mivehroud, Biotechnology Research Center & School of Pharmacy, Tabriz
University of Medical Sciences, Tabriz, Iran
Babak Sokouti, Biotechnology Research Center, Tabriz University of Medical Sciences,
Tabriz, Iran
Siavoush Dastmalchi, Biotechnology Research Center & School of Pharmacy, Tabriz
University of Medical Sciences, Tabriz, Iran
The need for the development of new drugs to combat existing and newly identified conditions is
unavoidable. One of the important tools used in the advanced drug development pipeline is computeraided drug design. Traditionally, to find a drug many ligands were synthesized and evaluated for their
effectiveness using suitable bioassays and if all other drug-likeness features were met, the candidate(s)
would possibly reach the market. Although this approach is still in use in advanced format, computational
methods are an indispensable component of modern drug development projects. One of the methods
used from very early days of rationalizing the drug design approaches is Quantitative Structure-Activity
Relationship (QSAR). This chapter overviews QSAR modeling steps by introducing molecular descriptors,
mathematical model development for relating biological activities to molecular structures, and model
validation. At the end, several successful cases where QSAR studies were used extensively are presented.
Chapter 2
The “ETA” Indices in QSAR/QSPR/QSTR Research .......................................................................... 48
Kunal Roy, Jadavpur University, India
Rudra Narayan Das, Jadavpur University, India
Descriptors are one of the most essential components of predictive Quantitative Structure-Activity/
Property/Toxicity Relationship (QSAR/QSPR/QSTR) modeling analysis, as they encode chemical
information of molecules in the form of quantitative numbers, which are used to develop mathematical
correlation models. The quality of a predictive model not only depends on good modeling statistics, but
also on the extraction of chemical features. A significant amount of research since the beginning of QSAR
analysis paradigm has led to the introduction of a large number of predictor variables or descriptors. The
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