COMPUTATIONALTOXICOLOGY

Risk Assessment for Pharmaceutical and Environmental Chemicals

Edited by

SEAN EKINS

WILEY-INTERSCIENCE

A JOHN WILEY & SONS, INC., PUBLICATION

Innodata9780470145883.jpg

COMPUTATIONAL TOXICOLOGY

COMPUTATIONALTOXICOLOGY

Risk Assessment for Pharmaceutical and Environmental Chemicals

Edited by

SEAN EKINS

WILEY-INTERSCIENCE

A JOHN WILEY & SONS, INC., PUBLICATION

Cover design/concept by Sean Ekins using images from Chapters 13, 16, and 19.

Copyright © 2007 by John Wiley & Sons, Inc. All rights reserved

Published by John Wiley & Sons, Inc., Hoboken, New JerseyPublished simultaneously in Canada

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Library of Congress Cataloging-in-Publication Data:

Computational toxicology : risk assessment for pharmaceutical and environmental chemicals / edited by Sean Ekins. p. ; cm. – (Wiley series on technologies for the pharmaceutical industry) Includes bibliographical references and index. ISBN 978-0-470-04962-4 (cloth) 1. Toxicology – Mathematical models. 2. Toxicology – Computer simulation. 3. QSAR (Biochemistry) I. Ekins, Sean. II. Series. [DNLM: 1. Toxicology – methods. 2. Computer Simulation. 3. Drug Toxicity. 4. Environmental Pollutants – toxicity. 5. Risk Assessment. QV 602 C738 2007] RA1199.4.M37C66 2007 615.9001′5118–dc22

2006100242

Printed in the United States of America

10 9 8 7 6 5 4 3 2 1

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To Maggie

It is very evident, that all other methods of improving medicine have been found ineffectual, by the stand it has been at these two or three thousand years; and that since of late mathematicians have set themselves to the study of it, men do already begin to talk intelligibly and comprehensibly, even about abstruse matters, that it may be hop’d in a short time, if those who are designed for this profession are early, while their minds and bodies are patient of labour and toil, initiated in the knowledge of numbers and geometry, that mathematical learning will be the distinguishing mark of a physician from a quack: and that he who wants this necessary qualifi cation, will be as ridiculous as one without Greek or Latin.

Richard MeadA mechanical account of poisons in several essays

2nd edition, London, 1708.

CONTENTS

vii

SERIES INTRODUCTION xi

PREFACE xiii

ACKNOWLEDGMENTS xv

CONTRIBUTORS xvii

PART I INTRODUCTION TO TOXICOLOGY METHODS 1

1 An Introduction to Toxicology and Its Methodologies 3Alan B. Combs and Daniel Acosta Jr.

2 In vitro Toxicology: Bringing the In silico and In vivo Worlds Closer 21Jinghai J. Xu

3 Physiologically Based Pharmacokinetic and Pharmacodynamic Modeling 33Brad Reisfeld, Arthur N. Mayeno, Michael A. Lyons, and Raymond S. H. Yang

4 Species Differences in Receptor-Mediated Gene Regulation 71Edward L. LeCluyse and J. Craig Rowlands

5 Toxicogenomics and Systems Toxicology 99Michael D. Waters, Jennifer M. Fostel, Barbara A. Wetmore, and B. Alex Merrick

viii CONTENTS

PART II COMPUTATIONAL METHODS 151

6 Toxicoinformatics: An Introduction 153William J. Welsh, Weida Tong, and Panos G. Georgopoulos

7 Computational Approaches for Assessment of Toxicity: A Historical Perspective and Current Status 183Vijay K. Gombar, Brian E. Mattioni, Craig Zwickl, and J. Thom Deahl

8 Current QSAR Techniques for Toxicology 217Yu Zong Chen, Chun Wei Yap, and Hu Li

PART III APPLYING COMPUTERS TO TOXICOLOGY ASSESSMENT: PHARMACEUTICAL 239

9 The Prediction of Physicochemical Properties 241Igor V. Tetko

10 Applications of QSAR to Enzymes Involved in Toxicology 277Sean Ekins

11 QSAR Studies on Drug Transporters Involved in Toxicology 295Gerhard F. Ecker and Peter Chiba

12 Computational Modeling of Receptor-Mediated Toxicity 315Markus A. Lill and Angelo Vedani

13 Applications of QSAR Methods to Ion Channels 353Alex M. Aronov, Konstantin V. Balakin, Alex Kiselyov, Shikha Varma-O’Brien, and Sean Ekins

14 Predictive Mutagenicity Computer Models 391Laura L. Custer, Constantine Kreatsoulas, and Stephen K. Durham

15 Novel Applications of Kernel–Partial Least Squares to Modeling a Comprehensive Array of Properties for Drug Discovery 403Sean Ekins, Mark J. Embrechts, Curt M. Breneman, Kam Jim, and Jean-Pierre Wery

16 Homology Models Applied to Toxicology 433Stewart B. Kirton, Phillip J. Stansfeld, John S. Mitcheson, and Michael J. Sutcliffe

17 Crystal Structures of Toxicology Targets 469Frank E. Blaney and Ben G. Tehan

18 Expert Systems 521Philip N. Judson

CONTENTS ix

19 Strategies for Using Computational Toxicology Methods in Pharmaceutical R&D 545Lutz Müller, Alexander Breidenbach, Christoph Funk, Wolfgang Muster, and Axel Pähler

20 Application of Interpretable Models to ADME/TOX Problems 581Tomoko Niwa and Katsumi Yoshida

PART IV APPLYING COMPUTERS TO TOXICOLOGY ASSESSMENT: ENVIRONMENTAL 599

21 The Toxicity and Risk of Chemical Mixtures 601John C. Lipscomb, Jason C. Lambert, and Moiz Mumtaz

22 Environmental and Ecological Toxicology: Computational Risk Assessment 625Emilio Benfenati, Giovanna Azimonti, Domenica Auteri, and Marco Lodi

23 Application of QSARs in Aquatic Toxicology 651James Devillers

24 Dermatotoxicology: Computational Risk Assessment 677Jim E. Riviere

PART V NEW TECHNOLOGIES FOR TOXICOLOGY: FUTURE AND REGULATORY PERSPECTIVES 693

25 Novel Cell Culture Systems: Nano and Microtechnology for Toxicology 695Mike L. Shuler and Hui Xu

26 Future of Computational Toxicology: Broad Application into Human Disease and Therapeutics 725Dale E. Johnson, Amie D. Rodgers, and Sucha Sudarsanam

27 Computational Tools for Regulatory Needs 751Arianna Bassan and Andrew P. Worth

INDEX 777

SERIES INTRODUCTION

xi

This book is the fi rst in a series to be published by Wiley entitled Technologiesfor the Pharmaceutical Industry. The series aims to bring opinion leaders together to address important topics for the industry, from their implementa-tion of technologies to current challenges. The pharmaceutical industry is at a critical juncture. It is pressured by patients on one side wanting effective treatments for diseases and governments trying to curtail health care spending while on the other side limited patent life and competition from generics all compound the issue. New technologies are one of the keys to maintaining competitiveness and minimizing the time for an idea coming from the bench to the bedside. Importantly these volumes will also describe how key technolo-gies are likely to impact the direction in discovery and development for the future and will be accessible to readers both inside and outside the industry. Signifi cant emphasis will also be put on the application rather than theory presented from both industrial and academic perspectives. At the time of going to press, two books are in preparation on in vitro–in vivo correlations, and biomarkers, with others in the pipeline. To ensure that the topics pub-lished are timely and relevant, an editorial board has been established and is listed in the front of this book. I gratefully acknowledge this team of scientists and those preparing the fi rst volumes in the series for their time and willing-ness to assist me in this endeavor as we begin the series here.

PREFACE

xiii

It would have been unusual to mention the importance of mathematics to physicians in a book on poisons in the eighteenth century (Richard Mead, Amechanical account of poisons in several essays, second edition published in 1708), but nearly 300 years later mathematical and computational (in silico) methods are valuable assets for toxicology as they are in many other areas of science. From such a vantage point no one would have foreseen the broad impact and importance of toxicology itself, let alone its entwined relationship with pharmaceutical and environmental research. Now is the time for an assessment of the convergence of toxicology and computational methods in these areas and to outline where they will go in the future.

In pharmaceutical drug discovery and development, processes are in con-stant fl ux as new technologies are continually devised, tested, validated, and implemented. However, we have seen in the recent white paper from the US FDA on innovation stagnation in toxicology, that this is not always the case. Areas key to the overall development continue to use old technologies and processes and are not keeping pace with other developments in disparate fi elds of pharmaceutical research. This may be just the tip of the iceberg. If this industry is to improve its ability to rapidly identify and test therapeutics clini-cally with a high probability of success, it needs to discover and embrace new technologies early on.

Currently many companies, academics, regulatory authorities, and global organizations have or are evaluating the use of new predictive tools to improve human hazard assessment, (drug toxicity, P450 mediated drug metabolism etc.). For example the interaction of molecules can be predicted by using computer-based tools utilizing X-ray crystal structures, homology, receptor, pharmacophore, and QSAR models of human enzymes, transporters, nuclear

xiv PREFACE

receptors, ion channels, as well as other physicochemical properties and complex endpoints. In silico modeling for toxicology may therefore provide effective pre-screening for chemicals in pharmaceutical discovery and the chemical industry in general, and their effects on the environment may also be predicted. The criteria for the validation of computational toxicology models and other requirements for regulatory acceptance have not yet been widely discussed. This book addresses all of the above-mentioned areas and many more, presenting computational toxicology from an international and holistic perspective that differs signifi cantly from recently published papers and books in the computational toxicology fi eld.

The book is split into fi ve key sections:

I. Introduction to Toxicology Methods II. Computational Methods III. Applying Computers to Toxicology Assessment: Pharmaceutical IV. Applying Computers to Toxicology Assessment: Environmental V. New Technologies for Toxicology: Future and Regulatory Perspectives

The book includes a comprehensive discussion on the state of the art of cur-rently available molecular-modeling software for toxicology and their role in testing strategies for different types of toxicity when used alongside in vitro and in vivo models. The publication of this book comes at a critical time as we are now seeing REACH legislation coming into effect whose goal is to increase the amount of toxicological data required on tens of thousands of manufactured chemicals in order to predict the effect of chemicals on human health and their environmental impact. Naturally there has to be some means to prioritize in vitro and in vivo testing, and computational toxicology will be critical. The role of these computational approaches in addressing environmental and occupa-tional toxicity is therefore covered broadly in this book, as well as new technolo-gies and thoughts on the past, present, and future of computational toxicology and its applicability to chemical design. Each chapter is written by one or more leading expert in the fi eld from industry, academe, or regulatory authorities, and each chapter has been edited to ensure consistency. Extensive use of explanatory fi gures is made, and all chapters include extensive key references for readers to delve deeper into topics at their own leisure.

This book is not aimed solely at laboratory toxicologists, as scientists of all disciplines in the pharmaceutical, chemical industries, and environmental sci-ences will fi nd it of value. In particular, those researchers involved in ADMET, drug discovery, systems biology, and software development should benefi t greatly from reading this book. The accessibility to the general reader with some scientifi c background should enable this volume to serve as an educa-tional tool that inspires readers to pursue further the technologies presented. I hope you enjoy this book and benefi t from the insights offered by the variety of contributing authors, as we take you on a tour of computational toxicology and go beyond—in silico.

ACKNOWLEDGMENTS

xv

I am extremely grateful to Jonathan Rose at John Wiley who initiated this project and provided considerable assistance for initial chapter ideas and author suggestions. Thank you for getting me involved and allowing me to edit it. In addition I would like to thank all the team at Wiley for their assis-tance and in particular, Danielle Lacourciere for patiently putting the book together. My anonymous proposal reviewers are kindly acknowledged for their helpful suggestions, and along with other scientists who provided numer-ous ideas for additional authors, they greatly helped bring the book closer to its fi nal format. Thank you!

I am immensely grateful to the many outstanding authors of the chapters for agreeing to contribute their valuable time, sharing their latest work and ideas, while patiently putting up with my editorial changes. This book repre-sents their considerable talents. Although we have referenced many groups in these chapters, I acknowledge the many others that may have been omitted due to lack of space.

I would also like to take this opportunity to thank The Othmer Library at the Chemical Heritage Foundation in Philadelphia and, in particular, Ms. Ashley Augustyniak, Assistant Librarian, for providing access to a copy of the historic Mead text.

My studies in computational toxicology owe a great deal to collaboration with colleagues in both industry and academia, and several of these are con-tributors here. I acknowledge them all for letting me participate in stimulating science with them.

My parents and family have been incredibly supportive over what has been a tumultuous year. I dedicate this book to all my family in the United Kingdom

and the United States, and to Maggie, in particular, for her continued steadfast support, valuable advice, and general encouragement to continue in the face of all adversity, this is for you.

Sean EkinsJenkintown, Pennsylvania

September 2006

xvi ACKNOWLEDGMENTS

CONTRIBUTORS

Daniel Acosta Jr., College of Pharmacy, University of Cincinnati, 3225 Eden Avenue, Cincinnati, OH 45267, USA. (daniel.acosta@uc.edu)

Alex M. Aronov, Vertex Pharmaceuticals Inc., 130 Waverly Street, Cam-bridge, MA 02139-4242, USA. (alex_aronov@vrtx.com)

Domenica Auteri, International Centre for Pesticides and Health Risk Pre-vention, Milano, Italy.

Giovanna Azimonti, International Centre for Pesticides and Health Risk Prevention, Milano, Italy.

Konstantin V. Balakin, ChemDiv, Inc. 11558 Sorrento Valley Road, Suite 5, San Diego, CA 92121, USA. (kvb@chemdiv.com)

Arianna Bassan, European Chemicals Bureau, Joint Research Centre, Euro-pean Commission, Ispra, 21020 (VA), Italy.

Emilio Benfenati, Laboratory of Environmental Chemistry and Toxicol-ogy, Istituto di Ricerche Farmacologiche “Mario Negri,” Milano, Italy. (benfenati@marionegri.it)

Frank E. Blaney, Computational, Analytical and Structural Sciences, Glaxo-SmithKline Medicines Research, NFSP (North), Third Avenue, Harlow, Essex CM19 5AW, UK. (frank.e.blaney@gsk.com)

Alexander Breidenbach, Hoffmann-La Roche, PRBN-T, Bldg. 73/311B, CH-4070, Basel, Switzerland.

xvii

xviii CONTRIBUTORS

Curt M. Breneman, Department of Chemistry, Rensselaer Polytechnic Insti-tute, 110 Eighth Street, Troy, NY 12180, USA.

Yu Zong Chen, Bioinformatics and Drug Design Group, Department of Computational Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543. (yzchen@cz3.nus.edu.sg)

Peter Chiba, Institute of Medical Chemistry, Medical University Vienna, Waehringerstrasse 10, A-1090 Wien, Austria.

Alan B. Combs, College of Pharmacy, 2409 University Avenue, A2925 Austin, TX 78712, USA. (acombs@mail.utexas.edu)

Laura L. Custer, Drug Safety Evaluation, Bristol-Myers Squibb Pharmaceuti-cal Research Institute, Syracuse, NY, USA. (laura.custer@bms.com)

J. Thom Deahl, Lilly Research Laboratories, Division of Eli Lilly and Company, Toxicology and Drug Disposition, Greenfi eld, IN 46140, USA.

James Devillers, CTIS, 3 Chemin de la Gravière, 69140 Rillieux La Pape, France. (j.devillers@ctis.fr)

Stephen K. Durham, Charles River Laboratories, 587 Dunn Circle, Sparks, NV 89431, USA. (stephen.durham@us.crl.com)

Gerhard F. Ecker, Emerging Field Pharmacoinformatics, Department of Medicinal Chemistry, University of Vienna, Althanstraße 14, A-1090 Wien, Austria. (gerhard.f.ecker@univie.ac.at)

Sean Ekins, ACT LLC, 1 Penn Plaza–36th Floor, New York, NY 10119, USA. (ekinssean@yahoo.com)

Mark J. Embrechts, Department of Decision Sciences and Engineering Systems, Rensselaer Polytechnic Institute, CII 5217, Troy, NY 12180, USA. (embrem@rpi.edu)

Jennifer M. Fostel, National Center for Toxicogenomics, National Institute of Environmental Health Sciences, PO Box 12233, MD F1-05, 111 Alexan-der Drive Research Triangle Park, NC 27709-2233, USA.

Christoph Funk, Hoffmann-La Roche, PRBN-T, Bldg. 73/311B, CH-4070, Basel, Switzerland.

Panos G. Georgopoulos, Department of Environmental and Occupational Medicine & Environmental and Occupational Health Sciences Institute, UMDNJ-RWJMS and Rutgers, the State University of New Jersey & Envi-ronmental Bioinformatics and Computational Toxicology Center (ebCTC), Piscataway, NJ 08854, USA.

Vijay K. Gombar, Lilly Research Laboratories, Division of Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA. (Gombar_Vijay_Kumar@Lilly.com)

CONTRIBUTORS xix

Kam Jim, 5 Donald Avenue, Kendall Park, NJ 08824, USA. (kamcjim@gmail.com)

Dale E. Johnson, Emiliem, Inc., 6027 Christie Avenue, Emeryville, CA 94608, USA. (daleejohnson@sbcglobal.net)

Philip N. Judson, Judson Consulting Service, Heather Lea, Bland Hill, Norwood, Harrogate HG3 1TE, UK. (philip.judson@blubberhouses.net)

Stewart B. Kirton, NCE Discovery Ltd, 418 Science Park, Cambridge, CB24 0PZ, UK.

Alex Kiselyov, ChemDiv, Inc. 11558 Sorrento Valley Road, Suite 5, San Diego, CA 92121, USA.

Constantine Kreatsoulas, Merck Research Laboratories, Merck and Co. Inc., Rahway, NJ, USA.

Jason C. Lambert, Oak Ridge Institute for Science and Education, On assign-ment to the US Environmental Protection Agency, Cincinnati, OH, USA.

Edward L. LeCluyse, CellzDirect, 480 Hillsboro Street, Suite 130 Pittsboro, NC 27312, USA. (edl@cellzdirect.com)

Hu Li, Bioinformatics and Drug Design Group, Department of Computa-tional Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543.

Markus A. Lill, Institute of Molecular Pharmacy, Pharmacenter, Univer-sity of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland and Bio-graphics Laboratory 3R, Friendensgasse 35, 4056 Basel, Switzerland. (mlill@pharmacy.purdue.edu)

John C. Lipscomb, US Environmental Protection Agency, National Center for Environmental Assessment, 26 West Martin Luther King Drive (MS-190), Cincinnati, OH 45268, USA. (lipscomb.john@epa.gov)

Marco Lodi, Laboratory of Environmental Chemistry and Toxicology, Isti-tuto di Ricerche Farmacologiche “Mario Negri,” Milano, Italy.

Michael A. Lyons, Department of Environmental and Radiological Health Sciences Colorado State University, 1681 Campus Delivery, Fort Collins, CO 80523-1681, USA (lyonsm@lamar.ColoState.edu)

Brian E. Mattioni, Lilly Research Laboratories, Division of Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA.

Arthur N. Mayeno, Department of Environmental and Radiological Health Sciences Colorado State University, 1681 Campus Delivery, Fort Collins, CO 80523-1681, USA. (arthur.mayeno@colostate.edu)

xx CONTRIBUTORS

B. Alex Merrick, National Center for Toxicogenomics, National Institute of Environmental Health Sciences, PO Box 12233, MD F1-05, 111 Alexander Drive Research Triangle Park, NC 27709-2233, USA.

John S. Mitcheson, Department of Cell Physiology and Pharmacology, Uni-versity of Leicester, University Road, Leicester, LE1 7RH, UK.

Lutz Müller, Hoffmann-La Roche, PRBN-T, Bldg. 73/311B, CH-4070, Basel, Switzerland. (lutz.mueller@roche.com)

Moiz Mumtaz, Agency for Toxic Substances and Disease Registry, Atlanta, GA, USA.

Wolfgang Muster, Hoffmann-La Roche, PRBN-T, Bldg. 73/311B, CH-4070, Basel, Switzerland.

Tomoko Niwa, Discovery Research Laboratories, Nippon Shinyaku Co., Ltd. 14, Nishinosho-Monguchi-cho, Kisshoin, Minami-ku Kyoto, 601-8550, Japan. (t.niwa@po.nippon-shinyaku.co.jp)

Axel Pähler, Hoffmann-La Roche, PRBN-T, Bldg. 73/311B, CH-4070, Basel, Switzerland.

Brad Reisfeld, Department of Chemical and Biological Engineering and Department of Environmental and Radiological Health Sciences, Colorado State University, 1370, Campus Delivery, Fort Collins, CO 80523-1370, USA. (brad.reisfeld@colostate.edu)

Jim E. Riviere, Center for Chemical Toxicology Research and Pharmacoki-netics Biomathematics Program, Carolina State University, Raleigh, NC, USA. (Jim_Riviere@ncsu.edu)

Amie D. Rodgers, Emiliem, Inc., 6027 Christie Avenue, Emeryville, CA 94608, USA.

J. Craig Rowlands, The Dow Chemical Company, Toxicology and Environ-mental Research and Consulting, 1803 Building, Midland, MI 48674, USA. (jcrowlands@dow.com)

Mike L. Shuler, Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA. (mls50@cornell.edu)

Phillip J. Stansfeld, Department of Cell Physiology and Pharmacology, Uni-versity of Leicester, University Road, Leicester, LE1 7RH, UK.

Sucha Sudarsanam, Emiliem, Inc., 6027 Christie Ave, Emeryville, CA 94608, USA.

Michael J. Sutcliffe, Manchester Interdisciplinary Biocentre & School of Chemical Engineering and Analytical Science, University of Manchester, 131 Princess Street, Manchester, M1 7ND, UK. (michael.sutcliffe@manchester.ac.uk)

CONTRIBUTORS xxi

Ben G. Tehan, Computational, Analytical and Structural Sciences, Glaxo-SmithKline Medicines Research, NFSP (North), Third Avenue, Harlow, Essex CM19 5AW, UK.

Igor V. Tetko, Institute for Bioinformatics, GSF–National Research Centre for Environment and Health, Ingolstädter Landstraße 1, D-85764 Neuher-berg, Germany. (itetko@vcclab.org)

Weida Tong, Center for Toxicoinformatics, US Food and Drug Administra-tion–National Center for Toxicological Research (US FDA-NCTR), Jefferson, AR 72079, USA.

Shikha Varma-O’Brien, Accelrys, Inc., 10188 Telesis Court, Suite 100, San Diego CA, 92121, USA.

Angelo Vedani, Institute of Molecular Pharmacy, Pharmacenter, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland and Biographics Laboratory 3R, Friendensgasse 35, 4056 Basel, Switzerland. (angelo@biograf.ch)

Michael D. Waters, Integrated Laboratory Systems, Inc., PO Box 13501, Research Triangle Park, NC 27709, USA. (mwaters@ils-inc.com)

William J. Welsh, Department of Pharmacology, University of Medicine & Dentistry of New Jersey-Robert Wood Johnson Medical School (UMDNJ-RWJMS) & Environmental Bioinformatics and Computational Toxicology Center (ebCTC) & the Informatics Institute of UMDNJ, Piscataway, NJ 08854, USA. (welshwj@umdnj.edu)

Jean-Pierre Wery, INCAPS, 351 West 10th Street, Suite 350, Indianapolis, IN 46202, USA. (jwery@indianacaps.com)

Barbara A. Wetmore, National Center for Toxicogenomics, National Insti-tute of Environmental Health Sciences, PO Box 12233, MD F1-05, 111 Alexander Drive Research Triangle Park, NC 27709-2233, USA.

Andrew P. Worth, European Chemicals Bureau, Joint Research Centre, European Commission, Ispra, 21020 (VA), Italy. (andrew.worth@jrc.it)

Hui Xu, Department of Biomedical Engineering, Cornell University, Ithaca, NY, USA. (hx28@cornell.edu)

Jinghai J. Xu, Pfi zer Inc., Research Technology Center, 620 Memorial Drive, Rm. 367, Cambridge, MA 02139, USA. (jim.xu@pfi zer.com)

Raymond S. H. Yang, Department of Environmental and Radiological Health Sciences, Colorado State University, 1681 Campus Delivery, Fort Collins, CO 80523-1681, USA. (raymond.yang@colostate.edu)

xxii CONTRIBUTORS

Chun Wei Yap, Bioinformatics and Drug Design Group, Department of Computational Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543.

Katsumi Yoshida, Discovery Research Laboratories, Nippon Shinyaku Co., Ltd. 14, Nishinosho-Monguchi-cho, Kisshoin, Minami-ku Kyoto, 601-8550, Japan.

Craig Zwickl, Lilly Research Laboratories, Division of Eli Lilly and Company, Toxicology and Drug Disposition, Greenfi eld, IN 46140, USA.

PART I

INTRODUCTION TO TOXICOLOGY METHODS

1AN INTRODUCTION TO TOXICOLOGY AND ITS METHODOLOGIES

Alan B. Combs and Daniel Acosta Jr.

Contents1.1 Overview 41.2 Where and Why Toxicological Knowledge Is Important 41.3 Indispensable Disciplines for the Science of Toxicology 41.4 Subdisciplines of Toxicology 51.5 Traditional Tools of Toxicology 61.6 Fields of Expertise within Toxicology 6 1.6.1 Chemical Carcinogenesis 6 1.6.2 Genetic Toxicology 7 1.6.3 Developmental Toxicology/Reproductive Toxicology 7 1.6.4 Blood and Bone Marrow 7 1.6.5 The Immune System 7 1.6.6 The Liver 8 1.6.7 The Kidney 9 1.6.8 The Respiratory System 9 1.6.9 The Nervous System 9 1.6.10 Behavioral Toxicity 10 1.6.11 Cardiotoxicity 10 1.6.12 Dermal Toxicity 11 1.6.13 The Reproductive Systems 11 1.6.14 Endocrine Systems 111.7 In vitro Methodologies for Fields of Expertise within Toxicology 111.8 Mechanisms of Toxic Injury 12 1.8.1 Ligand Binding by Heavy Metals 13 1.8.2 Covalent Binding to Biological Macromolecules 13

3

Computational Toxicology: Risk Assessment for Pharmaceutical and Environmental Chemicals,Edited by Sean EkinsCopyright © 2007 by John Wiley & Sons, Inc.

4 AN INTRODUCTION TO TOXICOLOGY AND ITS METHODOLOGIES

1.8.3 Oxidative Stress 13 1.8.4 Antimetabolites 15 1.8.5 Denaturing Agents 15 1.8.6 Extension of Pharmacology 15 1.8.7 Dysregulation of Cell Signaling 15 1.8.8 Miscellaneous Other Mechanisms of Toxicity 161.9 Computation in Toxicology 16 References 18

1.1 OVERVIEW

Toxicology in the broadest sense is the study of the adverse effects of drugs or chemicals on living systems. The questions asked by this discipline include what things are toxic, how and why toxicity is manifested, and how might toxicity be predicted, treated, or prevented. It is the purpose of this chapter to give a broad introduction to toxicology and to show how modern compu-tational techniques are becoming so useful to the fi eld.

1.2 WHERE AND WHY TOXICOLOGICAL KNOWLEDGE IS IMPORTANT

Our modern industrial society is highly dependent on chemical entities for its very existence. Useful chemicals cover the gamut from the building materials that make up our dwellings and machines, to the fertilizers and pesticides used in our production of food, to the chemicals used in our manufacture of elec-tronics and communications. These chemicals include the drugs and materials used in medicine and health care. Many new biologically active and useful compounds result from the activity of our pharmaceutical industry in areas of biotechnology. The production of each of these materials leads to industrial waste and the potential for environmental pollution. Because we become exposed to all of these things, prudence and regulations dictate that their potentials for toxic risk must be determined. Toxicologists are involved in all facets of this risk evaluation. The purpose of this chapter is to introduce the endeavors used to evaluate risk in the fi eld of toxicology and to indicate why instrumentation and computation are necessary.

1.3 INDISPENSABLE DISCIPLINES FOR THE SCIENCE OF TOXICOLOGY

It has long been a matter of honor and pride that pharmacologists and toxi-cologists must be highly conversant with so many different sciences. The

disciplines needed for toxicology include many of the life sciences, mainly biology, zoology, botany, physiology, genetics, pharmacology, biochemistry, histology, and pathology. Analytically related methodologies used in toxicol-ogy include analytical chemistry, fl ow cytometry [1], the techniques and tools of modern genetics, and molecular biology. Statistics is involved in study design, data analysis, and interpretation. In effect, the topic of this book, the use of computation in the gathering of the massive amounts of data generated by modern toxicology, the documentation of these efforts, and the interpreta-tion of the resulting data have become more and more essential and increas-ingly routine in toxicology.

Biology, zoology, and physiology predict the normal responses of living systems, whose deviations can help defi ne the effects of toxic substances on these systems. Toxic effects may produce adverse changes at the biochemical, tissue, organ, and organism levels. Again, perturbations from normal function or anatomy can help defi ne toxic effects. Histology is the study of normal microanatomy, and pathology describes what happens to these microstruc-tures when they become injured by toxicants. Many different sophisticated analytical techniques are used in the most advanced studies.

1.4 SUBDISCIPLINES OF TOXICOLOGY

In its role of explaining, predicting, preventing, and treating the adverse effects of drugs and chemicals, toxicologists are working in many subdisciplines. They are involved in drug and chemical safety screening and in their regulatorycounterparts, the EPA, FDA, and USDA in the United States. They are involved in occupational and industrial toxicology and in their own particular scientifi c and regulatory counterparts, NIOSH and OSHA. In addition there are people specializing in forensic, veterinary, and clinical toxicology. Finally there are scientists involved in mechanistic studies at all levels of the organ-ism’s organization.

The whole idea behind toxicological testing and safety screening is the potential benefi t to humans and animals that will accrue. This entails defi ning the risk of exposure to drugs and chemicals, understanding the risk when it exists, and preventing the risk. This concept holds whether one is doing drug discovery, environmental, or regulatory toxicology.

As described, toxicologists in chemical and pharmaceutical industries work to defi ne the risk associated with new drugs and chemicals. Such safety evalu-ation is part of the art and science of toxicology, though much of the method-ology is codifi ed in the law. Regulatory toxicologists acting for the general public welfare work to create and ensure adherence to safety regulations. The process of discovery is part collegial and part adversarial as investigators and regulators strive to fi ll their co-dependent function.

Forensic toxicology combines analytical chemistry, knowledge of toxicol-ogy, and detective work to determine the causes of those cases of poisoning

SUBDISCIPLINES OF TOXICOLOGY 5

6 AN INTRODUCTION TO TOXICOLOGY AND ITS METHODOLOGIES

that have become of interest to law enforcement or regulatory agencies. Vet-erinary toxicology and human clinical toxicology deal with the evaluation and treatment of poisoning.

1.5 TRADITIONAL TOOLS OF TOXICOLOGY

Epistemology is the undertaking of how we know what we know, or the study of knowledge and the basis of its validity. Toward this end in toxicology we bring all the tools of our science and our rationality. This entails the appropri-ate gathering of information and its proper evaluation and interpretation.

Properly designed and interpreted animal studies are the primary tools of safety screening and predictive toxicology. Among the basic techniques used by toxicologists are dose–response studies. Articulated fi rst by Paracelsus [2] is the idea that it is the dose that makes the poison. All things are dangerous in large enough doses and all things are safe if exposure is small enough. Additionally the demonstration of a dose–response relationship between a tested substance and the effect it is suspected to produce provides strong evi-dence that a cause–effect relationship exists between them. As the basis for regulatory toxicology, the existence of a threshold dose, the dose below which no adverse effect occurs, provides the basis for recommended maximal expo-sures that are safe.

Many of the fi elds of study and types of toxicology are described below. These efforts are very broad and entail the use of many disciplines.

1.6 FIELDS OF EXPERTISE WITHIN TOXICOLOGY

Toxicology can be classifi ed according to the effects on the organ systems damaged. Alternatively, it can be classifi ed according to the mechanisms of toxicity. Almost anything that can go wrong with almost any tissue in the body will occur. Each of these areas comprises its own realm of toxicological exper-tise. We will fi rst examine several examples of organ-based toxicity. In some cases there will be extensive overlap between categories. One of the important questions is why there frequently is specifi c target organ toxicity. We will examine some aspects of this question. Most frequently the answer relates to the specifi c biological characteristics of the tissues.

1.6.1 Chemical Carcinogenesis

Because of the intense public interest that exists in cancer prevention and the resulting political interest, chemical carcinogenesis is a gigantic and relatively well-funded fi eld. Amazon.com (as of June 2006) lists nearly 80 books in print on the topic. Google.com lists over 200,000 hits on the topic. The National Library of Medicine’s Medline lists nearly the same number of articles on the