In Silico Drug Discovery and Design: Theory, Methods, Challenges, and Applications, 1st Edition (Paperback) book cover

In Silico Drug Discovery and Design

Theory, Methods, Challenges, and Applications, 1st Edition

Edited by Claudio N. Cavasotto

CRC Press

558 pages | 26 Color Illus. | 71 B/W Illus.

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pub: 2017-07-26
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Description

In Silico Drug Discovery and Design: Theory, Methods, Challenges, and Applications provides a comprehensive, unified, and in-depth overview of the current methodological strategies in computer-aided drug discovery and design. Its main aims are to introduce the theoretical framework and algorithms, discuss the range of validity, strengths and limitations of each methodology, and present applications to real world problems in the drug discovery arena. Special emphasis has been given to the emerging and most pressing methodological challenges in in silico drug discovery and design.

The book assumes a basic knowledge of physical principles and molecular modeling. Particular attention has been paid to outline the underlying physico-chemical foundation of the methods described, thus providing the necessary background to avoid a "black-box" approach. In each self-contained chapter, this is presented together with the latest developments and applications, and the challenges that lie ahead.

Assembling a unique team of experts to weigh in on the most important issues influencing modern computational drug discovery and design, this book constitutes both a desktop reference to academic and industrial researchers in the field, and a textbook for students in the area of molecular modeling and drug discovery.

Comprised of 18 chapters and divided into three parts, this book:

  • Provides a comprehensive, unified, and in-depth overview of the current methodological strategies in computer-aided drug discovery and design
  • Outlines the underlying physico-chemical foundation of the methods described
  • Presents several applications of computational methods to real world problems in the drug design field
  • Helps to avoid a "black-box" approach to in silico drug discovery
  • Constitutes an actual textbook for students in the area of molecular modeling and drug discovery
  • Gives the reader the adequate background to face the current challenges of the field

In Silico Drug Discovery and Design: Theory, Methods, Challenges, and Applications describes the theoretical framework, methods, practical applications and case examples relevant to computer-aided drug lead discovery and design. This text will surely aid in understanding the underlying physical foundation of computational tools and their range of application, thus facilitating the interpretation of simulation results.

Reviews

"… an ambitious book which delivers a great deal of material in one volume. … a useful addition to the small number of accessible and authoritative books on the subject."

ChemMedChem, 2016, 11, 638

"… With this book the lids on the algorithm black boxes are lifted and all within the field can clearly see their inner workings. … This book also has the capacity to enthusiastically galvanize those at the cutting-edge of algorithm development. The Thorny problems remaining are illuminated and attacked with vigor, such as how target flexibility and solvation at molecular interfaces can be more accurately modeled and how this may ultimately feed into a better determination of BINDING free energies and the calculation of accurate kinetic parameters."

—Dr. Paul A Bates, The Francis Crick Institute

"… a solid, current, well-written and well-organized set of reviews of important topics in in silico drug discovery. It should be useful for readers, ranging from students to senior scientists, who are looking for accessible overviews of this material."

—Mike Gilson, University of California, San Diego, USA

Table of Contents

The Physical Basis of Ligand Binding

Thomas Simonson

Force-Field Representation of Biomolecular Systems

Meagan C. Small and Alexander D. MacKerell, Jr.

Library Design, Chemical Space, and Drug Likeness

Hugo O. Villar

Ligand-Based Drug Discovery and Design

Álvaro Cortés-Cabrera, Pedro A. Sánchez Murcia, Antonio Morreale, and Federico Gago

Pharmacophore Modeling and Pharmacophore-Based Virtual Screening

Muhammad Akram, Teresa Kaserer, and Daniela Schuster

Protein-Ligand Docking: From Basic Principles to Advanced Applications

Christoph A. Sotriffer

Protein-Ligand Docking: Virtual Screening and Applications to Drug Discovery

Antonella Ciancetta and Stefano Moro

Protein Structure Modeling in Drug Design

Damián Palomba and Claudio N. Cavasotto

Implicit Solvation Methods in the Study of Ligand-Protein Interactions

William Zamora, Josep M. Campanera, and F. Javier Luque

Toward Complete Cellular Pocketomes and Predictive Polypharmacology

Ruben A. Abagyan and Bryn Taylor

MM-GB/SA Rescoring of Docking Poses: Tricks of the Trade

Cristiano R. W. Guimarães

Free Energy Calculations of Ligand-Protein Binding

Rainer Bomblies, Manuel Luitz, and Martin Zacharias

Molecular Mechanics/Coarse-Grained Simulations as a Structural Prediction Tool for GPCRs/Ligand Complexes

Francesco Musiani, Alejandro Giorgetti, and Paolo Carloni

Fragment-Based Methods in Drug Design

Márton Vass, Gergely Makara, and György Miklós Keseru

Role of Water Molecules and Hydration Properties in Modeling Ligand-Protein Interaction and Drug Design

Alfonso T. García-Sosa

How Protein Flexibility Can Influence Docking/Scoring Simulations

Pietro Cozzini, Luca Dellafiora, Tiziana Ginex, and Francesca Spyrakis

In Silico Approaches Assisting the Rational Design of Low Molecular Weight Protein-Protein Interaction Modulators

Bruno O. Villoutreix, Melaine A. Kuenemann, David Lagorce, Olivier Sperandio, and Maria A. Miteva

Incorporating Binding Kinetics in Drug Design

Chung F. Wong

About the Editor

Claudio N. Cavasotto earned his MSc and PhD in physics from the University of Buenos Aires. He conducted his postdoctoral training at The Scripps Research Institute after which in 2002 he moved to MolSoft LLC, La Jolla, California, as senior research scientist, where he remained until 2007. He then became assistant and associate professor at the School of Biomedical Informatics at the University of Texas Health Science Center at Houston. In 2012 he moved to the Biomedicine Research Institute of Buenos Aires-Partner Institute of the Max Planck Society, where he is head of Computational Chemistry and Drug Design. His research interests are primarily biomolecular simulation, computer-aided drug discovery and cheminformatics. His group develops and applies computational methods to study molecular interactions in biological systems, and to design molecules which modulate targets of pharmaceutical relevance.

Subject Categories

BISAC Subject Codes/Headings:
MED071000
MEDICAL / Pharmacology
MED072000
MEDICAL / Pharmacy