Chemical Biology

CHEMICAL BIOLOGY Approaches to Drug Discovery and Development to Targeting Disease Edited by NATANYA CIVJAN A JOHN WILEY & SONS, INC., PUBLICATION CHEMICAL BIOLOGY CHEMICAL BIOLOGY Approaches to Drug Discovery and Development to Targeting Disease Edited by NATANYA CIVJAN A JOHN WILEY & SONS, INC., PUBLICATION Copyright © 2012 by John Wiley & Sons, Inc. 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ISBN 978-1-118-10118-6 (hardback) 1. Biochemistry. I. Title. QP514.2.C58 2012 572–dc23 2012012322 Printed in the United States of America 10987654321 CONTENTS Preface ix Contributors xi PART I DRUG DISCOVERY AND DEVELOPMENT 1 1 The Role of Chemical Biology in Drug Discovery 3 Andrew J. Pope 2 Computational Approaches to Drug Discovery and Development 23 Honglin Li, Mingyue Zheng, Xiaomin Luo, Weiliang Zhu, and Hualiang Jiang 3 Design and Selection of Small Molecule Inhibitors 41 Jianwei Che, Yi Liu, and Nathanael S. Gray 4 Lead Optimization in Drug Discovery 65 Craig W. Lindsley, David Weaver, Thomas M. Bridges, and J. Phillip Kennedy 5 Pharmacokinetics of Drug Candidates 83 Ronald E. White v vi CONTENTS 6 ADME Properties of Drugs 101 Li Di and Edward H. Kerns 7 Drug Transport in Living Systems 115 Yael Elbaz and Shimon Schuldiner 8 Blood-Brain Barrier: Considerations in Drug Development and Delivery 133 David S. Miller and Brian T. Hawkins 9 Pharmacokinetic Considerations: Methods and Systems of Controlled Drug Delivery 147 Zhong Zuo and Vincent H. L. Lee 10 Pharmaceuticals: Natural Products and Natural Product Models 165 Sheo B. Singh PART II CHEMICAL BIOLOGY TO UNDERSTAND AND TARGET DISEASE 203 11 The Role of Chemical Biology in Understanding and Treating Disease—Are Small Molecule “Correctors” the Way of the Future? 205 David Selwood 12 Anxiety Disorders 215 Miklos Toth 13 Chronic Obstructive Pulmonary Disease (COPD) 245 Peter J. Barnes 14 Depression 267 Glen B. Baker and Nicholas D. Mitchell 15 Osteoarthritis 293 Marjolaine Gosset, Jérémie Sellam, Claire Jacques, and Francis Berenbaum 16 Human Immunodeficiency Virus (HIV) 331 Joseph P. Vacca CONTENTS vii 17 Allergy and Asthma 341 Garry M. Walsh 18 Schizophrenia 357 Ferenc Martenyi 19 Protein Misfolding and Disease 379 Johanna C. Scheinost, Grant E. Boldt, and Paul Wentworth 20 Protein Trafficking Diseases 401 Heidi M. Sampson and David Y. Thomas 21 Metabolic Diseases 419 Cynthia M. Arbeeny 22 Mitochondrial Medicine 445 Richard J. T. Rodenburg and Jan A. M. Smeitink 23 Lysosomal Disorders 461 Doug A. Brooks and Maria Fuller Index 483 PREFACE Chemical biology is a cross-disciplinary science at the interface of chemistry, biology, and medicine. Chemical biology aims at the elucidation of the chemical mechanisms of living systems and is important to drug discovery, playing a key role in the development of novel agents for the prevention, diagnosis, and treatment of diseases. Containing carefully selected reprints from the award-winning Wiley Encyclo- pedia of Chemical Biology, which published in 2008, as well as new contribu- tions, this book features a collection of chapters on topics of interest to scientists working in the areas of drug discovery and development. Chapters in Part I of this book cover a range of topics on the design, development, and optimization of drug candidates, the pharmacokinetics and properties of drugs, and drug transport and delivery. Part II covers the mechanisms of particular diseases and the strategies used to understand, target, and treat these diseases. Written by prominent scholars, this book will be of interest to advanced stu- dents and researchers, both in academia and industry, in the field of chemical biology or related fields such as biochemistry, medicine, and pharmaceutical sciences, with particular interest in drug discovery and development. Natanya Civjan ix CONTRIBUTORS Cynthia M. Arbeeny, Endocrine and Metabolic Diseases, Genzyme Corporation, Framingham, Massachusetts Glen B. Baker, Neurochemical Research Unit, Department of Psychiatry, University of Alberta, Edmonton, Alberta, Canada Peter J. Barnes, National Heart and Lung Institute, Imperial College, London, United Kingdom Francis Berenbaum, Paris Universitas APHP Saint-Antoine Hospital, Paris, France Grant E. Boldt, University of Oxford, Oxford, United Kingdom and The Scripps Research Institute, La Jolla, California Thomas M. Bridges, Department of Pharmacology, Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee Doug A. Brooks, Molecular Medicine Sector, Sansom Institute, University of South Australia, Adelaide, Australia Jianwei Che, Genomics Institute of the Novartis Research Foundation, San Diego, California Li Di, Wyeth Research, Princeton, New Jersey Yael Elbaz, Department of Biologic Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel xi xii CONTRIBUTORS Maria Fuller, Lysosomal Diseases Research Unit, Department of Genetic Medicine, Women’s and Children’s Hospital, Adelaide, Australia Marjolaine Gosset, Paris Universitas, Paris, France Nathanael S. Gray, Harvard Medical School, Dana Farber Cancer Institute, Biological Chemistry and Molecular Pharmacology, Boston Brian T. Hawkins, Laboratory of Pharmacology, NIH/NIEHS, Research Triangle Park, North Carolina Claire Jacques, Paris Universitas, Paris, France Hualiang Jiang, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China J. Phillip Kennedy, Department of Chemistry, Vanderbilt University, Nashville, Tennessee Edward H. Kerns, Wyeth Research, Princeton, New Jersey Vincent H. L. Lee, School of Pharmacy, The Chinese University of Hong Kong, Hong Kong SAR Honglin Li, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China Craig W. Lindsley, Departments of Pharmacology and Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee Yi Liu, Genomics Institute of the Novartis Research Foundation, San Diego, California Xiaomin Luo, Shanghai Institute of Materia Medica, Chinese Academy of Sci- ences, Shanghai, China Ferenc Martenyi, Lilly Research Laboratories, Indianapolis, Indiana David S. Miller, Laboratory of Pharmacology, NIH/NIEHS, Research Triangle Park, North Carolina Nicholas D. Mitchell, Neurochemical Research Unit, Department of Psychiatry, University of Alberta, Edmonton, Alberta, Canada Andrew J. Pope, Platform Technology & Science, GlaxoSmithKline, Collegeville, Pennsylvania, USA. Richard J.T. Rodenburg, Nijmegen Center for Mitochondrial Disorders, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands Heidi M. Sampson, McGill University, Quebec, Canada CONTRIBUTORS xiii Johanna C. Scheinost, University of Oxford, Oxford, United Kingdom and The Scripps Research Institute, La Jolla, California Shimon Schuldiner, Department of Biologic Chemistry, Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem,

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