Rational Drug Design Novel Methodology and

This book is an overview of current progress in drug design, applications of drug design, and new methodologies. It focuses on energetics of drug interactions with solvents and biomolecules, applications of traditional drug design methods, and related evolutionary algorithms. The volume concludes with a survey of recent successes and failures and describes outlooks for the future.

Preface

xi

Overview of Rational Drug Design

1

(11)

M. Rami Reddy

Abby L. Parrill

Conformational and Energetic Aspects of Receptor--Ligand Recognition

12

(25)

J. D. Hirst

B. Dominy

Z. Guo

M. Vieth

C. L. Brooks III

New Free Energy Calculation Methods for Structure-Based Drug Design and Prediction of Protein Stability

37

(16)

Lu Wang

Mats A. L. Eriksson

Jed Pitera

Peter A. Kollman

Binding Evaluation using the Finite Difference Solution to the Linearized Poisson--Boltzmann Equation and Solvation Entropy Correction

53

(17)

Jian Shen

SmoG: A Ligand Design Method Based on Knowledge-Based Parametrization of a Solvent Reorganization Model

70

(17)

Robert S. DeWitte

Eugene I. Shakhnovich

The Evaluation of Multi-Body Dynamics for Studying Ligand--Protein Interactions: Using MBO(N)D to Probe the unbinding Pathways of Cbz-Val-Phe-Phe-Val-Cbz from the Active Site of HIV-1 Protease

87

(20)

Donovan N. Chin

David N. Haney

Katya Delak

Hon M. Chun

Carlos E. Padilla

Calculation of Relative Hydration Free Energy Differences for Heteroaromatic Compounds: Use in the Design of AMP Deaminase Inhibitors

107

(14)

Mark D. Erion

M. Rami Reddy

New Tools for Rational Drug Design

121

(20)

Gregory D. Hawkins

Jiabo Li

Tianhai (Tony) Zhu

Candee C. Chambers

David J. Giesen

Daniel A. Liotard

Christopher J. Cramer

Donald G. Truhlar

Rational Approaches to Inhibition of Human Osteoclast Cathepsin K and Treatment of Osteoporosis

141

(12)

Sherin S. Abdel-Meguid

Baoguang Zhao

Ward W. Smith

Cheryl A. Hanson

Judith LaLonde

Thomas Carr

Karla D'Alessio

Michael S. McQueney

H.-J. Oh

Scott K. Thompson

Daniel F. Veber

Dennis S. Yamashita

Building a Hypothesis for Nucleotide Transport Inhibitors

153

(12)

K. Raghavan

Scott D. Kahn

John K. Buolamwini

Unified Pharmacophoric Model for Cannabinoids and Aminoalkylindoles Derived from Molecular Superimposition of CB1 Cannabinoid Receptor Agonists CP55244 and WIN55212-2

165

(20)

Joong-Youn Shim

Elizabeth R. Collantes

William J. Welsh

Allyn C. Howlett

Structure-Based Design of Novel Conformationally Restricted HIV Protease Inhibitors

185

(13)

B. G. Rao

C. T. Baker

J. T. Court

D. D. Deininger

J. P. Griffith

E. E. Kim

J. L. Kim

B. Li

S. Pazhanisamy

F. G. Salituro

W. C. Schairer

R. D. Tung

``New Tricks for an Old Dog'': Development and Application of Novel QSAR Methods for Rational Design of Combinatorial Chemical Libraries and Database Mining

198

(14)

A. Tropsha

S. J. Cho

W. Zheng

Molecular Hologram QSAR

212

(14)

Trevor W. Heritage

David R. Lowis

Adapting Structure-Based Drug Design in the paradigm of Combinatorial Chemistry and High-Throughput Screening: An Overview and New Examples with Important Caveats for Newcomers to Combinatorial Library Design Using pharmacophore Models or Multiple Copy Simultaneous Search Fragments

226

(13)

Arup K. Ghose

Vellarkad N. Viswanadhan

John J. Wendoloski

The Basic Shape Topology of Protein Interfaces

239

(16)

John Lawton

Melanie Tudor

W. Todd Wipke

Evolutionary Algorithms in Computer-Aided Molecular Design: A Review of Current Applications and a Look to the Future

255

(16)

David E. Clark

Further Development of a Genetic Algorithm for Ligand Docking and Its Application to Screening Combinatorial Libraries

271

(21)

Gareth Jones

Peter Willett

Robert C. Glen

Andrew R. Leach

Robin Taylor

Reduced Dimensionality in Ligand--Protein Structure Prediction: Covalent Inhibitors of Serine Proteases and Design of Site-Directed Combinatorial Libraries

292

(20)

Daniel K. Gehlhaar

Djamal Bouzida

Paul A. Rejto

Development and Validation of the EVA Descriptor for QSAR Studies

312

(18)

David B. Turner

Peter Willett

Allan M. Ferguson

Trevor W. Heritage

PRO_ANALOG: Automated Analog Building According to Principles of Medicinal Chemistry

330

(16)

Richard G. A. Bone

Michael A. Firth

Richard A. Sykes

Christopher W. Murray

Jin Li

Is Rational Design Good for Anything?

346

(11)

Donald B. Boyd

Author Index

357

(1)

Subject Index

358

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Rational Drug Design Novel Methodology and Practical Applications

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Table of Contents

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