PROTEIN TARGETINGWITH SMALL MOLECULES

PROTEIN TARGETINGWITH SMALL MOLECULES

Chemical Biology Techniquesand Applications

Edited by

HIROYUKI OSADARIKEN Advanced Science InstituteWako, Saitama, Japan

A JOHN WILEY & SONS, INC., PUBLICATION

Copyright © 2009 by John Wiley & Sons, Inc. All rights reserved.

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Library of Congress Cataloging-in-Publication Data:

Protein targeting with small molecules : chemical biology techniques and applications /[edited by] Hiroyuki Osada.

p. ; cm.Includes bibliographical references and index.ISBN 978-0-470-12053-8 (cloth)

1. Protein binding. 2. Molecular probes. I. Osada, H. (Hiroyuki), 1954–[DNLM: 1. Protein Transport–physiology. 2. Proteins–metabolism. 3. Small Molecule

Libraries–metabolism. QU 55 P9690124 2009]QP517.P76P76 2009572′.633–dc22

2009007430

Printed in the United States of America

10 9 8 7 6 5 4 3 2 1

CONTENTS

Contributors vii

Preface ix

1 Chemical Biology Based on Small Molecule–Protein Interaction 1Hiroyuki Osada

2 Target Profiling of Small Molecules 11Leonid L. Chepelev and Michel Dumontier

3 Novel Applications of Affinity Beads 39Yasuaki Kabe, Mamoru Hatakeyama, Satoshi Sakamoto, Kosuke Nishio,and Hiroshi Handa

4 Recent Developments and Advances in Chemical Arrays 57Naoki Kanoh and Hiroyuki Osada

5 Use of the Phage Display Technique to Identify the TargetProtein 81Yoon Sun Cho and Ho Jeong Kwon

6 Development of Fluorescent Probes for Small Molecules 91Adrian P. Neal and Carsten Schultz

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vi CONTENTS

7 Development of Small-Molecule Ligands and Inhibitors 115Leonid L. Chepelev, Nikolai L. Chepelev, Hooman Shadnia,William G. Willmore, James S. Wright, and Michel Dumontier

8 Interaction of a Biological Response Modifier with Proteins 149Yuichi Hashimoto

9 Chemical Biology of Cell Motility Inhibitors 169Tatsuro Kawamura, Mitsuhiro Kitagawa, and Masaya Imoto

10 Chemical Biology of Cell Surface Oligosaccharides 189Prabhani U. Atukorale, Sean S. Choi, Udayanath Aich,Christopher T. Campbell, M. Adam Meledeo, and Kevin J. Yarema

11 Chemical Genomics Based on Yeast Genetics 223Shinichi Nishimura, Yoko Yashiroda, and Minoru Yoshida

12 Data on Small Molecules and Their Target Proteins 239Takeo Usui, Akiko Saito, and Hiroyuki Osada

Index 277

CONTRIBUTORS

Udayanath Aich, The Johns Hopkins University, Baltimore, Maryland

Prabhani U. Atukorale, The Johns Hopkins University, Baltimore, Maryland

Christopher T. Campbell, The Johns Hopkins University, Baltimore, Maryland

Leonid L. Chepelev, Carleton University, Ottawa, Ontario, Canada

Nikolai L. Chepelev, Carleton University, Ottawa, Ontario, Canada

Yoon Sun Cho, Yonsei University, Seoul, Republic of Korea

Sean S. Choi, The Johns Hopkins University, Baltimore, Maryland

Michel Dumontier, Carleton University, Ottawa, Ontario, Canada

Hiroshi Handa, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan

Yuichi Hashimoto, The University of Tokyo, Tokyo, Japan

Mamoru Hatakeyama, Tokyo Institute of Technology, Yokohama, Kanagawa,Japan

Masaya Imoto, Keio University, Yokohama, Kanagawa, Japan

Yasuaki Kabe, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan

Naoki Kanoh, Tohoku University, Sendai, Miyagi, Japan

Tatsuro Kawamura, Keio University, Yokohama, Kanagawa, Japan

Mitsuhiro Kitagawa, Keio University, Yokohama, Kanagawa, Japan

Ho Jeong Kwon, Yonsei University, Seoul, Republic of Korea

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viii CONTRIBUTORS

M. Adam Meledeo, The Johns Hopkins University, Baltimore, Maryland

Adrian P. Neal, European Molecular Biology Laboratory, Heidelberg, Germany

Shinichi Nishimura, RIKEN Advanced Science Institute, Wako, Saitama, Japan

Kosuke Nishio, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan

Hiroyuki Osada, RIKEN Advanced Science Institute, Wako, Saitama, Japan

Akiko Saito, RIKEN Advanced Science Institute, Wako, Saitama, Japan

Satoshi Sakamoto, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan

Carsten Schultz, European Molecular Biology Laboratory, Heidelberg, Germany

Hooman Shadnia, Carleton University, Ottawa, Ontario, Canada

Takeo Usui, University of Tsukuba, Tsukuba, Ibaraki, Japan

William G. Willmore, Carleton University, Ottawa, Ontario, Canada

James S. Wright, Carleton University, Ottawa, Ontario, Canada

Kevin J. Yarema, The Johns Hopkins University, Baltimore, Maryland

Yoko Yashiroda, RIKEN Advanced Science Institute, Wako, Saitama, Japan

Minoru Yoshida, RIKEN Advanced Science Institute, Wako, Saitama, Japan

PREFACE

Chemical biology is recognized as a new frontier research area between chemistryand biology. One of the goals of this research is to understand the complexbiological systems inspired by chemistry or chemical tools. Nowadays, researchin this field is highlighted because chemical biology is useful not only for basicresearch but also for drug discovery. The term “bandwagon effect” implies thatpeople often associate with the majority without deep consideration. The current“buzz” surrounding chemical biology may be like the bandwagon. If one does notpossess deep insight and a good grasp of the techniques, one will be discardedafter the boom is finished. It is very important to have one’s own opinion andtechnique in chemical biology.

This book offers you the contemporary knowledge and techniques necessaryto understand the entire research field of chemical biology. New technologies todissect the interactions between small molecules and proteins are introduced withsome examples of the identification of binding proteins of small molecules. Thefinal chapter will be useful to get a bird’s-eye view of recent progress on smallmolecules targeting proteins.

By offering an overview of chemical biology clarified by detailed examplesand descriptions of important techniques, it is the aim of this book to stimulateyoung chemical biologists and inform them of the opportunities to apply thepower of chemistry to important problems in biology.

Finally, I thank the members of my laboratory, especially Akiko Saito, fortheir assistance in the preparation of the book.

HIROYUKI OSADADirector of Chemical Biology DepartmentRIKEN Advanced Science InstituteFebruary 2009

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