Drug Design: Structure- and Ligand-Based Approaches

doi:10.1017/CBO9780511730412

Structure-based (SBDD) and ligand-based (LBDD) drug design are extremely important and active areas of research in both the academic and commercial realms. This book provides a complete snapshot of the field of computer-aided drug design and associated experimental approaches. Topics covered include X-ray crystallography, NMR, fragment-based drug design, free energy methods, docking and scoring, linear-scaling quantum calculations, QSAR, pharmacophore methods, computational ADME-Tox, and drug discovery case studies. A variety of authors from academic and commercial institutions all over the world have contributed to this book, which is illustrated with more than 200 images. This is the only book to cover the subject of structure and ligand-based drug design, and it provides the most up-to-date information on a wide range of topics for the practising computational chemist, medicinal chemist, or structural biologist. Professor Kenneth Merz has been selected as the recipient of the 2010 ACS Award for Computers in Chemical & Pharmaceutical Research that recognizes the advances he has made in the use of quantum mechanics to solve biological and drug discovery problems.

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Contents

Frontmatter
pp i-iv
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Contents
pp v-vi
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Contributors
pp vii-viii
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Preface
pp ix-x
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DRUG DESIGN
pp xi-xii
STRUCTURE- AND LIGAND-BASED APPROACHES
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1 - Progress and issues for computationally guided lead discovery and optimization
pp 1-14
- By William L. Jorgensen
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PART I - STRUCTURAL BIOLOGY
pp 15-16
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2 - X-ray crystallography in the service of structure-based drug design
pp 17-29
- By Gregory A. Petsko, Dagmar Ringe
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3 - Fragment-based structure-guided drug discovery: strategy, process, and lessons from human protein kinases
pp 30-40
- By Stephen K. Burley, Gavin Hirst, Paul Sprengeler, Siegfried Reich
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4 - NMR in fragment-based drug discovery
pp 41-58
- By Christopher A. Lepre, Peter J. Connolly, Jonathan M. Moore
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PART II - COMPUTATIONAL CHEMISTRY METHODOLOGY
pp 59-60
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5 - Free-energy calculations in structure-based drug design
pp 61-86
- By Michael R. Shirts, David L. Mobley, Scott P. Brown
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6 - Studies of drug resistance and the dynamic behavior of HIV-1 protease through molecular dynamics simulations
pp 87-97
- By Fangyu Ding, Carlos Simmerling
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7 - Docking: a domesday report
pp 98-119
- By Martha S. Head
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8 - The role of quantum mechanics in structure-based drug design
pp 120-136
- By Kenneth M. Merz, Jr.
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9 - Pharmacophore methods
pp 137-150
- By Steven L. Dixon
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10 - QSAR in drug discovery
pp 151-164
- By Alexander Tropsha
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11 - Predicting ADME properties in drug discovery
pp 165-178
- By William J. Egan
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PART III - APPLICATIONS TO DRUG DISCOVERY
pp 179-180
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12 - Computer-aided drug design: a practical guide to protein-structure-based modeling
pp 181-196
- By Charles H. Reynolds
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13 - Structure-based drug design case study: p38
pp 197-208
- By Arthur M. Doweyko
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14 - Structure-based design of novel P2-P4 macrocyclic inhibitors of hepatitis C NS3/4A protease
pp 209-214
- By M. Katharine Holloway, Nigel J. Liverton
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15 - Purine nucleoside phosphorylases as targets for transition-state analog design
pp 215-247
- By Andrew S. Murkin, Vern L. Schramm
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16 - GPCR 3D modeling
pp 248-256
- By Frank U. Axe
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17 - Structure-based design of potent glycogen phosphorylase inhibitors
pp 257-264
- By Qiaolin Deng
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Index
pp 265-274
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Drug Design

Structure- and Ligand-Based Approaches

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Contents

Frontmatter
pp i-iv

Contents
pp v-vi

Contributors
pp vii-viii

Preface
pp ix-x

DRUG DESIGN
pp xi-xii

1 - Progress and issues for computationally guided lead discovery and optimization
pp 1-14

PART I - STRUCTURAL BIOLOGY
pp 15-16

2 - X-ray crystallography in the service of structure-based drug design
pp 17-29

3 - Fragment-based structure-guided drug discovery: strategy, process, and lessons from human protein kinases
pp 30-40

4 - NMR in fragment-based drug discovery
pp 41-58

PART II - COMPUTATIONAL CHEMISTRY METHODOLOGY
pp 59-60

5 - Free-energy calculations in structure-based drug design
pp 61-86

6 - Studies of drug resistance and the dynamic behavior of HIV-1 protease through molecular dynamics simulations
pp 87-97

7 - Docking: a domesday report
pp 98-119

8 - The role of quantum mechanics in structure-based drug design
pp 120-136

9 - Pharmacophore methods
pp 137-150

10 - QSAR in drug discovery
pp 151-164

11 - Predicting ADME properties in drug discovery
pp 165-178

PART III - APPLICATIONS TO DRUG DISCOVERY
pp 179-180

12 - Computer-aided drug design: a practical guide to protein-structure-based modeling
pp 181-196

13 - Structure-based drug design case study: p38
pp 197-208

14 - Structure-based design of novel P2-P4 macrocyclic inhibitors of hepatitis C NS3/4A protease
pp 209-214

15 - Purine nucleoside phosphorylases as targets for transition-state analog design
pp 215-247

16 - GPCR 3D modeling
pp 248-256

17 - Structure-based design of potent glycogen phosphorylase inhibitors
pp 257-264

Index
pp 265-274

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Structure- and Ligand-Based Approaches

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