computational toxicology - risk assessment for pharmaceutical and environmental chemicals - s. ekins (wiley, 2007)

Pacifi co Library of Congress Cataloging-in-Publication Data: Computational toxicology : risk assessment for pharmaceutical and environmental chemicals / edited by Sean Ekins.. CONTENTS i

COMPUTATIONAL TOXICOLOGY

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

Published by John Wiley & Sons, Inc., Hoboken, New Jersey

Published simultaneously in Canada

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Wiley Bicentennial logo: Richard J Pacifi co

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

To Maggie

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 Mead

A mechanical account of poisons in several essays

2nd edition, London, 1708.

PART I INTRODUCTION TO TOXICOLOGY METHODS 1

1 An Introduction to Toxicology and Its Methodologies 3

Alan B Combs and Daniel Acosta Jr.

2 In vitro Toxicology: Bringing the In silico and In vivo

Jinghai J Xu

3 Physiologically Based Pharmacokinetic and Pharmacodynamic

Brad Reisfeld, Arthur N Mayeno, Michael A Lyons,

and Raymond S H Yang

4 Species Differences in Receptor-Mediated Gene Regulation 71

Edward L LeCluyse and J Craig Rowlands

5 Toxicogenomics and Systems Toxicology 99

Michael D Waters, Jennifer M Fostel, Barbara A Wetmore,

and B Alex Merrick

PART II COMPUTATIONAL METHODS 151

William J Welsh, Weida Tong, and Panos G Georgopoulos

7 Computational Approaches for Assessment of Toxicity:

A Historical Perspective and Current Status 183

Vijay K Gombar, Brian E Mattioni, Craig Zwickl, and J Thom Deahl

8 Current QSAR Techniques for Toxicology 217

Yu Zong Chen, Chun Wei Yap, and Hu Li

PART III APPLYING COMPUTERS TO TOXICOLOGY

11 QSAR Studies on Drug Transporters Involved in Toxicology 295

Gerhard F Ecker and Peter Chiba

12 Computational Modeling of Receptor-Mediated Toxicity 315

Markus A Lill and Angelo Vedani

13 Applications of QSAR Methods to Ion Channels 353

Alex M Aronov, Konstantin V Balakin, Alex Kiselyov,

Shikha Varma-O’Brien, and Sean Ekins

14 Predictive Mutagenicity Computer Models 391

Laura L Custer, Constantine Kreatsoulas, and Stephen K Durham

15 Novel Applications of Kernel–Partial Least Squares to

Modeling a Comprehensive Array of Properties for

Sean Ekins, Mark J Embrechts, Curt M Breneman, Kam Jim,

and Jean-Pierre Wery

16 Homology Models Applied to Toxicology 433

Stewart B Kirton, Phillip J Stansfeld, John S Mitcheson,

and Michael J Sutcliffe

17 Crystal Structures of Toxicology Targets 469

Frank E Blaney and Ben G Tehan

Philip N Judson

CONTENTS ix

19 Strategies for Using Computational Toxicology Methods in

Lutz Müller, Alexander Breidenbach, Christoph Funk,

Wolfgang Muster, and Axel Pähler

20 Application of Interpretable Models to ADME/TOX Problems 581

Tomoko Niwa and Katsumi Yoshida

PART IV APPLYING COMPUTERS TO TOXICOLOGY

21 The Toxicity and Risk of Chemical Mixtures 601

John C Lipscomb, Jason C Lambert, and Moiz Mumtaz

22 Environmental and Ecological Toxicology: Computational

Emilio Benfenati, Giovanna Azimonti, Domenica Auteri,

and Marco Lodi

23 Application of QSARs in Aquatic Toxicology 651

James Devillers

24 Dermatotoxicology: Computational Risk Assessment 677

Jim E Riviere

PART V NEW TECHNOLOGIES FOR TOXICOLOGY:

FUTURE AND REGULATORY PERSPECTIVES 693

25 Novel Cell Culture Systems: Nano and Microtechnology for

Mike L Shuler and Hui Xu

26 Future of Computational Toxicology: Broad Application into

Dale E Johnson, Amie D Rodgers, and Sucha Sudarsanam

27 Computational Tools for Regulatory Needs 751

Arianna Bassan and Andrew P Worth

SERIES INTRODUCTION

xi

This book is the fi rst in a series to be published by Wiley entitled Technologies

for the Pharmaceutical Industry The series aims to bring opinion leaders

together to address important topics for the industry, from their tion of technologies to current challenges The pharmaceutical industry is at

implementa-a criticimplementa-al juncture It is pressured by pimplementa-atients on one side wimplementa-anting 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 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

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, A

mechanical 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 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

con-of pharmaceutical research This may be just the tip con-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

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 PerspectivesThe 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 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

occupa-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

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 Ekins

Jenkintown, Pennsylvania

September 2006

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

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 der Drive Research Triangle Park, NC 27709-2233, USA

Alexan-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)

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

Jason C Lambert, Oak Ridge Institute for Science and Education, On

assign-ment to the US Environassign-mental 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, NaComputa-tional 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 graphics Laboratory 3R, Friendensgasse 35, 4056 Basel, Switzerland (mlill@pharmacy.purdue.edu)

Bio-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)

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, UniUni-versity Road, Leicester, LE1 7RH, UK

Lutz Müller, Hoffmann-La Roche, PRBN-T, Bldg 73/311B, CH-4070, Basel,

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, UniUni-versity 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 berg, Germany (itetko@vcclab.org)

Neuher-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 RWJMS) & Environmental Bioinformatics and Computational Toxicology Center (ebCTC) & the Informatics Institute of UMDNJ, Piscataway, NJ

(UMDNJ-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)

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

1.2 Where and Why Toxicological Knowledge Is Important 4

1.3 Indispensable Disciplines for the Science of Toxicology 4

1.4 Subdisciplines of Toxicology 5

1.5 Traditional Tools of Toxicology 6

1.6 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

1.7 In vitro Methodologies for Fields of Expertise within Toxicology 11

1.8 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 Ekins

Copyright © 2007 by John Wiley & Sons, Inc.

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 16

1.9 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 tational techniques are becoming so useful to the fi eld

compu-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 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

elec-1.3 INDISPENSABLE DISCIPLINES FOR

THE SCIENCE OF TOXICOLOGY

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

toxi-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 tion of the resulting data have become more and more essential and increas-ingly routine in toxicology

interpreta-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 regulatory

counterparts, 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 ism’s organization

organ-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 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

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

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

Vet-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 sures that are safe

expo-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

topic within the scientifi c or medical literature Not only is the extent of effort indicated by these numbers, but also the diffuse, diffi cult, intractable, and fractal nature of the fi eld.

Carcinogenesis is a multiple-step, progressive process Causes of such damage can include alkylating agents, active oxygen species, and radiation These causes of injury can also lead to genetic toxicology Much of the current mechanistic interest is centered on dysregulation of cellular growth control mechanisms [3]

1.6.2 Genetic Toxicology

There is a great degree of overlap between the topics of genetic toxicity and chemical carcinogenesis This is because many of the stepwise changes that occur during the development of neoplasia consist of somatic mutations that result in changes in growth regulation of the affected tissues

The fi eld more commonly thought of as genetic toxicology deals with changes in what might be termed legacy genes, those genes that are passed

from one generation to the next These changes occur as a result of unrepaired injury to the cellular DNA and the effects are almost always bad The safety screening required for carcinogenesis in drug and chemical discovery is exten-sive [4]

1.6.3 Developmental Toxicology/Reproductive Toxicology

The topic of teratogenesis as a disruption of the control of embryological development is covered later in this chapter Safety screening requires evaluation of developmental and reproductive toxicity of the compounds of interest [5]

1.6.4 Blood and Bone Marrow

Hematotoxicity is another area of active investigation Benzene is an excellent example of the extremes that can be caused by substances that are toxic to the bone marrow Chronic exposure to benzene can cause either leukemia, or bone marrow injury that can lead to aplastic anemia [6,7] Agranulocytosis and aplastic anemia are infrequent but deadly toxic effects of several drugs Anemias related to defi ciencies of each of the formed elements of the blood also are known, and some of these are toxicological in origin For example, thrombocytopenia is an established and potentially deadly adverse effect of heparin, though the etiology may be immunological [8]

1.6.5 The Immune System

The function of the immune system is to protect the internal environment of the body against external attack [9] Because the nature of the attack can be

so varied, bacterial, fungal, viral, and the presence of foreign proteins, the immune system has become one of great complexity Antibody-mediated immunity and cellularly mediated immunity both exist, and the stimulus–response characteristics of this system and the necessary control mechanisms are also very complex.

Decreased immunological competency can lead to susceptibility to tions, and it can also lead to cells that lack the capacity to control their growth

infec-In contrast, excess activity can cause the immune system to attack the host organism, itself Both of these adverse effects can result from xenobiotic exposure

Among the drugs that can decrease immunological competence are infl ammatory steroids, cyclosporine, and tacrolimus Certain of these com-pounds are used to prevent transplant rejection, but they simultaneously carry the risk of allowing infection to occur The aplastic anemia caused by the bone marrow toxicity of benzene was described above Lead and chlorinated aryl hydrocarbons such as hexachlorobenzene also can cause bone marrow suppression

anti-Inappropriate immunological activation has been known for a long time Anaphylaxis following sensitization is an example Another example is that untreated beta-hemolytic streptococcus infections can lead to rheumatic fever and damage to the heart valves This appears to occur because the streptococ-cus organism and our heart valves share a common antigen, and development

of immunity against the former leads to damage to the latter

Immunotoxicology is a discipline still in its infancy Perhaps, this is most clearly bourn out by the recent experience in Great Britain in which a mono-clonal antibody that was designed as an agonist to a receptor on T-lympho-cytes was fi rst given to six human volunteers The dose given was much lower (500 times) than that which had been safe in animals Nevertheless, the result was a massive release of cytokines leading to global organ failure At this time all have survived the event, though it was not certain for some time that this would happen This is an excellent example of species differences, and it is clear that much more work must be done to characterize human immunologi-cal responses when potential immunological stimulants are in the process of drug discovery [10,11]

1.6.6 The Liver

The liver has two main functions in the body [12] The fi rst is maintenance of internal nutritional homeostasis through facilitation of lipid absorption and intermediary metabolism As described later, the large metabolic capacity of the liver renders it vulnerable to heavy metals through binding of the metals

to and inactivation of electrophilic ligands

The second function of the liver is to deal with various endogenous strates and dietary xenobiotics through their metabolism and biliary excretion Several toxicities are associated with disturbances of this function One

sub-example is the oxidative dechlorination of carbon tetrachloride and other chlorinated hydrocarbons to free radical metabolites that bind to and destroy hepatic tissues Another example of toxicity by metabolic activation occurs with acetaminophen A trace metabolite of acetaminophen is a very reactive quinoneimine Under normal usage of this analgesic, this metabolite is not a problem because it is inactivated by binding to reduced glutathione However, when an overdose of acetaminophen is taken, the protective glutathione becomes depleted and the reactive metabolite covalently binds to and destroys hepatic parenchymal tissue.

Cirrhosis of the liver is one of the most well-known adverse effects of chronic alcohol abuse The cholesterol-lowering, life-prolonging statin drugs must be monitored routinely for hepatotoxicity and rhabdomyolosis A Google search on the terms “statins,” “hepatotoxicity,” and “review” produced over 22,000 hits indicating this is a very active fi eld of interest

1.6.7 The Kidney

For the same reasons as described for the liver, heavy metals and compounds converted to active metabolites can also be toxic to the kidney, which is very active metabolically [13,14] With certain quinones, reduced glutathione can enhance toxicity, rather than being protective [15]

Gentamycin and other aminoglycoside antibiotics are toxic to the kidney Use of these compounds necessitates repeated dosage adjustments according

to drug blood levels

1.6.8 The Respiratory System

As is the case with the skin, the lungs are in constant contact with the external environment [16] Exposure to the toxins in cigarette smoke is one of the most common causes of congestive, obstructive damage in the respiratory system Occupational exposure to asbestos and medically necessary exposure to drugs such as cyclophosphamide and carmustine can also cause lung injury Inhala-tions of coal dust and cotton fi bers are other occupational hazards to the lungs

1.6.9 The Nervous System

The central nervous system is one of the most complex organs in living systems [17] Neurotoxicity can be manifested rather globally, or very specifi cally, depending on the poison One example of a very specifi c toxicity occurs with MPTP, a notorious meperidine analogue that can destroy the substantia nigra and leads to a very severe Parkinson-like syndrome Another example of rather global neurotoxicity occurs with lead encephalopathy Other metals can also be highly neurotoxic

Developmental retardation occurs following exposure to metals, and this has been instrumental in decreasing the amount of lead used in gasoline and indoor paints Maternal alcohol drinking during pregnancy can also cause developmental retardation manifested as fetal alcohol syndrome Organo-phosphates can cause acute injury related to acetylcholine accumulation and certain ones such as triothocresylphosphate can cause delayed axonal degen-eration Picrotoxin, camphor, and strychnine are examples of powerful con-vulsants Anesthetics and analgesics can lead to respiratory depression and hypoxia Carbon monoxide and cyanide also cause general hypoxic damage

to the brain and to other high oxygen demand organs of the body The ture abounds with other examples of substances that are toxic to the nervous system

litera-1.6.10 Behavioral Toxicity

Many poisons can disturb mental and rational function leading to behavioral abnormalities Psychototoxins include phencyclidine, LSD, and fungal toxins Less commonly, stimulants such as cocaine and amphetamine can cause psy-chiatric problems Psychiatric effects of high doses of corticosteroids have also been described In addition to the developmental retardation, some investiga-tors believe that cognitive impairment, hyperactivity, and perhaps even anti-social behavior may be caused by childhood lead exposure Public discussion

of these subtle toxic effects is highly politicized because childhood exposure

to lead still occurs as a risk factor in slums and tenements

1.6.11 Cardiotoxicity

Compared to many of the other organs, the heart must continuously maintain beating activity [18] There is little energy storage capacity in the heart, which therefore must be producing the energy it uses in real time Drugs that decrease the capacity of the heart to use substrate and generate ATP can be very harmful to the heart Examples of toxicants believed to act by this mechanism include cyanide, glycolysis inhibitors such as emetine [19], and Krebs-cycle metabolism inhibitors such as the cardiotoxic anthracycline doxorubicin [18]

In addition to the necessity of continuous energy generation, the heart must maintain rhythmic function throughout its lifetime Substances such

as cocaine and cyclopropane that decrease the reuptake of norepinephrine after its release from noradrenergic neurons are prone to cause fatal arrhyth-mias Additionally drugs that modify plasma membrane ion channel function can also cause arrhythmias More recently cardiotoxicity from drugs that prolong the QT-interval has been reported Such drugs include several anti-microbial agents, antidepressants, and anti-migraine agents This broadly based toxicological effect has clear implications for the drug discovery process [20]

1.6.12 Dermal Toxicity

The skin is the primary organ of contact between the organism and its ronment There is extensive commercial interest in dermal toxicology and safety screening because of the many different products used topically for therapeutic and cosmetic purposes Similar comments can be made about ocular products

envi-Some of the toxic effects to the skin are allergic in nature The response to poison oak or poison ivy is an example Corrosive injury to the skin can occur following contact with many household products Cutaneous responses to certain drugs can include dangerous exfoliative dermatitis and the Stevens-Johnson syndrome [21,22]

1.6.13 The Reproductive Systems

In addition to chemical carcinogenesis, teratogenesis is a toxic effect that catches the public’s attention The public response to thalidomide was so great that it is still very diffi cult to get the drug approved for newer indications Once we know what a toxic effect can be, toxicologists are quite effective in developing animal tests that screen for that effect For example, the fetotoxic effects of compounds such as Accutane® and the angiotensin converting enzyme inhibitors are known from screening studies, and a large teratogenic disaster such as thalidomide should not happen, again It is a commentary on human nature that the fetal alcohol syndrome still continues to occur

1.6.14 Endocrine Systems

Toxic changes can be caused by endocrine agonists, antagonists, and tors There are estrogen active compounds such as diethylstilbesterol and dioxin Natural and synthetic thyroid antagonists such as propylthiouracil are known Agonists and antagonists for adrenocortical hormones have been described Oral contraceptives are risk factors for increased blood clotting and stroke Estrogens are risk factors for breast and uterine cancers, and there is much interest in the associated risks from environmental estrogen pollutants (e.g., the REACH initiative)

disrup-1.7 IN VITRO METHODOLOGIES FOR FIELDS OF EXPERTISE WITHIN TOXICOLOGY

Biomedical and toxicological research and safety screening require the use of animals [23] However, since the inception of the fi rst animal welfare organiza-tions, society’s use of animals has been a matter of concern and controversy [24] Because of this interest there has been much activity in the past few decades in fi nding alternative methods for doing research and screening The

“Three Rs” of Russell and Burch [25], replacement, reduction, and refi nement,

have been the goals of much of this work Many alternatives to animals have been suggested, and where the alternatives have been verifi ed to be useful, it

is appropriate that they be used One of the best examples of replacement is the current use of Limulus (horseshoe crab) serum to detect the presence of the gram-negative organism endotoxins known as pyrogens [26] Parenteral products must be sterile and pyrogen-free Limulus serum is more sensitive to the presence of these harmful proteins than the rabbits that were previously used Not many other alternatives have been so well verifi ed, however.The current all out attack mounted by animal activists on the societal use

of animals is a matter of extreme concern to toxicology and the other cal sciences Some of the best resources to inform ourselves and to counter these activists are the frequently asked questions (FAQ) detailed in the Animal Rights Myths FAQ [27]

biomedi-Cell culture is one of the primary methods being studied for animal ment Primary cultures of heart cells, liver, keratinocytes, corneal cells, and many other tissues are actively being studied [28] Much work has been done for decades in some cases to maintain the functions of the parent tissue close

replace-to those in vivo while the cells are in culture Eventually most differentiated function of the cells is lost The art is to maintain such function for as long as possible so that longer in vitro exposures can mimic in vivo dosing

Propagated cell lines are also widely used Such cells are immortalized by combination with neoplastic cells One problem with these cell lines is that they frequently do not express any of the differentiated functions of the parent cells, and therefore do not provide tissue specifi c responses

One of the failings of cell culture in predictive toxicology is that some examples of toxicity are multi-organ in nature Methanol toxicity, for example, occurs when the methanol is oxidized in the liver to formate The formate is transported by the blood to the retina and CNS where it produces its charac-teristic effects of blindness and brain damage To model methanol toxicity in cell culture would require co-cultures of liver and retinal cells Co-cultures are technically diffi cult, and it would be very diffi cult to predict which multiple cell types are needed in a co-culture to detect a previously unknown toxicity

It requires an intact organism to do this

Innumerable cell lines are used in studies trying to understand intracellular messengers and control processes Such models are particularly useful pro-vided that the cells remain viable as almost any desired genetic alteration can

be produced and studied

1.8 MECHANISMS OF TOXIC INJURY

Although many different cells and tissues can be injured by toxicants, there are not many different fundamental mechanisms by which injury can occur Each of these categories can be very broad, however Mechanisms of injury

include ligand binding by heavy metals, covalent binding, oxidative stress by

active oxygen species, antimetabolites, the extension of pharmacologic action,

dysregulation of cellular signaling, and a miscellaneous category, all of which

are now described in a little more detail

1.8.1 Ligand Binding by Heavy Metals

Electrophilic ligands such as sulfhydryls, amino groups, and hydroxyl groups are found at the active sites of many, if not most enzymes [29] These ligands have a high affi nity for many different metals (e.g., Hg, As, Pb, Sb), and the uptake of and binding of metals to these sites inactivates them The effect that occurs depends on the location and function of the enzymes in the tissue involved The more metabolically active a tissue is, the more it is likely to be adversely affected by metals The liver, kidneys, gastrointestinal mucosa, and central nervous system are particularly vulnerable because they are so meta-bolically active Teratology of the toxic metals is also an issue The major dif-ferences between the metals are more a matter of pharmacokinetics than fundamental differences in mechanisms of toxicity

The antidotes for heavy metals are called chelating agents, a picturesque term invoking an image of lobster claws (chelae) grabbing hold of the metal Such drugs are rich sources of the ligands to which metals readily bind, and these drugs are able to compete effectively for the metal against the endoge-nous tissue ligands

1.8.2 Covalent Binding to Biological Macromolecules

This toxic mechanism, which had its most active interest in the late 1970s and early 1980s, occurs when chemicals are metabolized to free radicals or other highly active molecules These radicals then covalently alkylate nearby mac-romolecules Such macromolecules can include proteins, cellular membranes (including plasma membranes, nuclear membranes, membranes of organelles, etc.), and genetic components such as DNA and RNA If metabolically critical areas of these large molecules become covalently bound to a metabolic product, they may become inactivated Specifi c toxic effects will depend on which biological macromolecules become inactivated An example is the case

of carbon tetrachloride that becomes oxidized by liver P450 enzymes to the trichloromethane free radical This active alkylating agent attaches itself to nearby liver parenchyma, resulting in the classic liver toxicity described for carbon tetrachloride Research interest in covalent binding as a mechanism of toxicity has decreased since the 1980s because it is very diffi cult to determine which of all the structures in the body that become alkylated is ultimately responsible for the toxicity produced

1.8.3 Oxidative Stress

Oxidative stress is a general term for the excessive production of active oxygen

species and the resulting biological responses [30] The various oxygen species

are depicted in the schematic of Figure 1.1 as a series of one-step electron reductions—starting with molecular oxygen and ending with the hydroxyl anion.

Active oxygen species are usually produced within cells as by-products of normal oxidative metabolism The location of these processes can include the cytochromes P450, mitochondria, lysosomes, and peroxisomes As was the case with damage by free radical metabolic remnants leading to covalent binding and injury, several of the active oxygen species can also cause damage

to biological macromolecules

In addition lipid peroxidation can result from action of active oxygen species This leads to destruction of metabolically necessary lipid molecules and damage to the structural integrity of cellular membranes Damage from oxidative stress can occur with excessive production of active oxygen species, inadequate protection against such species, or both Examples of toxicity from active oxygen species include the pancreatic beta-cell destruction by alloxan, the neurotoxicity of 6-hydroxydopamine, the cardiotoxicity of the anthracy-cline antibiotics, and the pulmonary toxicity of the herbicide paraquat.Singlet oxygen is a unique form of activated oxygen It is most commonly involved in phototoxic reactions Because of absorption of an energetic photon, one of the previously paired electrons of the molecule has been promoted to

an orbital of higher energy In the strictest sense it is not a free radical, but it can act as an active oxygen species Certain compounds such as tetracyclines

or amiodarone can trap photons upon exposure of the skin to the ultraviolet portion of the light spectrum These photon-activated compounds can pass their energy to molecular oxygen, converting it to singlet oxygen Singlet

Figure 1.1 Various valence states of oxygen as a function of increasing single-electron

reductions.

oxygen, in turn, passes its excess energy to dermal tissues, resulting in tissue damage and sunburn.

1.8.4 Antimetabolites

Antimetabolites compete with normal endogenous substrates and cause bition of the processes that require those substrates Examples include purine and pyrimidine antagonists, which prevent nucleic acid replication and cellular division in cancer chemotherapy Another example is methotrexate, which can inhibit folic acid metabolism

inhi-1.8.5 Denaturing Agents

Denaturing agents can destroy the tertiary structure of proteins Alcohol’s antiseptic action results from denaturing of bacterial proteins Corrosives can cause tissue damage upon accidental exposure

1.8.6 Extension of Pharmacology

This is a broad category of toxic action in which exaggeration of the tic effects of many drugs in overdose can lead to poisoning For example, general anesthetics are also respiratory depressants, and too high concentra-tions can cause fatalities Many antihypertensives cause potentially fatal vas-cular collapse and shock when taken in overdose Overdoses of certain antiarrhythmic drugs can themselves cause fatal arrhythmias, actions that are related to their action on ion channels

therapeu-1.8.7 Dysregulation of Cell Signaling

This is one of the currently most active areas of toxicological research interest, and it is one with many different research thrusts There is much current inter-est, for example, in the mechanisms of regulation of apoptosis, programmed cellular death Production of apoptosis when it should not occur, or its lack when it normally should occur, can each be mechanisms of toxicity Part of the adverse remodeling of cardiac and vascular tissue can occur because of hypertension-induced apoptosis of cardiac and vascular cells [31] Apoptotic processes also have been implicated in alcoholic hepatotoxicity [32]

Excessive infl ammatory responses may result from inappropriate cellular signaling On the other hand, infl ammation is normally a protective response, and its lack can lead to increased susceptibility to infections Dysregulation of cellular division can lead to neoplasia or aplasia Neoplastic changes refl ect

a dysregulation of cell growth, whether from failure of apoptosis or other mechanisms

Embryological development is a highly conserved, highly regulated sequence of events in which many processes must be activated or deactivated

in their proper sequence We are just in the infancy of discovering what are the messages and messengers controlling development of the embryo into a fetus and eventual birth Many substances perturb these processes and thus are fetotoxic teratogens The most common human teratogen is alcohol, the use of which during pregnancy can cause the developmental retardation known

as the fetal alcohol syndrome [33] Among the many other effects it causes,

angiotensin II is a growth regulator Disturbing angiotensin II action by angiotensin-converting enzyme inhibition, or by angiotensin receptor block can be used therapeutically to reduce the inappropriate growth and remodel-ing that occurs in congestive heart failure and hypertension However, these blocking actions also can result in severe fetotoxicity [34] Numerous other examples of teratogens are known Screening for these adverse effects is a necessary part of drug discovery

1.8.8 Miscellaneous Other Mechanisms of Toxicity

Addition of a miscellaneous category to any list adds completeness On the other hand, it is diffi cult to fi nd toxic effects that do not fi t into one or more

of the previous categories One example of such might be the necrosis of the mandible that appears to result from the use of bisphosphonates to prevent osteoporosis in postmenopausal women The mechanism of this unexpected effect is not known, but the toxicity certainly has become of great concern to our dental colleagues [35]

1.9 COMPUTATION IN TOXICOLOGY

The primary advantage of the computer is to deal with work that is so large and so complex that it cannot otherwise readily be possible One example of such a need is the highly complicated chemical/toxicological/biomedical litera-ture that exists A computer can search and mine the literature, and it can organize it into mutually relevant collections of articles Data clustering is one example of such an intelligent organization of the literature [36] Other exam-ples include directory searches, keyword searches, and database searches

(See types of search engines [37].)

There are several different clustered search engines available A case in point is Clusty.com’s Vivisimo [38] The default setting of this engine is to search the recent literature Repeated searches, say at monthly intervals, enables one to keep up with topics of interest A recent (June 2006) clustered search on “Computational Toxicology,” the topic of this book, gave the results described in Table 1.1

The relevance of these topics to computation and to toxicology is not trivial

Currently commercially available gene microarrays can characterize the

expression of thousands of genes of several different species [39], and this

information has great potential in the drug discovery process [40] Routines

to interpret and correlate these fi ndings are under active development, and the results are available on the internet through the NIH [41] In the case of

toxicogenomics, a subset of pharmacogenomics, several correlations between

an individual’s genome and susceptibility to particular toxicants are known Databases exist and people are working to develop toxicogenomic in vitro procedures that might be useful early in drug discovery, or in predictive toxi-cology [42,43,44]

The predictive toxicology cluster provided a group of articles related to

QSARs [45], bioinformatics [46], and expert systems [47] Pharmacokinetic data acquisition and interpretation have been heavily intertwined with com-putation since the early days of the discipline This hasn’t changed with the

more current fi eld of toxicokinetics.

The high-throughput data cluster appears to be related to using

computa-tional and statistical techniques to separate useful data signals from large amounts of irrelevant noise (e.g., see [48]) This important endeavor is just in its infancy

The connection between toxicology and dose–response relationships is

several hundreds of years old [2,49] In the pre-computational days these data were calculated by hand and nomogram [50] The sheer labor involved has been greatly eased by computational techniques Nevertheless, this author feels that working through such manual techniques at least once is very salu-tory for nacent pharmacologists and toxicologists

Predictions of drug receptor interactions and related QSARs are useful for

predictive toxicology and drug development Validation of computer

technol-ogy and predictions is another concern Many of these topics are covered in the following chapters of this book

TABLE 1.1 Results of a Clustered Search on “Computational Toxicology” as Divided by the Vivisimo Search Engine into Topic Clusters

Microarray, gene expression profi ling (13 articles)

Toxicogenomics (12 articles)

Protein, impact (13 articles)

Dose–response (11 articles)

Quantitative (8 articles)

Receptor, expression (7 articles)

Predict toxicity (7 articles)

Pharmacology and toxicology (6 articles)

Physiologically based pharmacokinetic (8 articles)

Properties (5 articles)

High-throughput data (3 articles)

Note: The search retrieved 105 articles Less frequent items are not included above.