Antitargets

Prediction and Prevention of Drug Side Effects

Edited byRoy J. Vaz and Thomas Klabunde

InnodataFile Attachment9783527621477.jpg

Antitargets

Edited byRoy J. Vaz and Thomas Klabunde

Methods and Principles in Medicinal Chemistry

Edited by R. Mannhold, H. Kubinyi, G. Folkers

Editorial Board

H. Timmerman, J. Vacca, H. van de Waterbeemd, T. Wieland

Previous Volumes of this Series:

M. Hamacher, K. Marcus, K. Stühler,A. van Hall, B. Warscheid,H. E. Meyer (eds.)

Proteomics in Drug ResearchVol. 282006, ISBN: 978-3-527-31226-9

D. J. Triggle, M. Gopalakrishnan,D. Rampe, W. Zheng (eds.)

Voltage-Gated Ion Channelsas Drug TargetsVol. 292006, ISBN: 978-3-527-31258-0

D. Rognan (ed.)

Ligand Design for GProtein-coupled ReceptorsVol. 302006, ISBN: 978-3-527-31284-9

D. A. Smith, H. van de Waterbeemd,D. K. Walker

Pharmacokinetics andMetabolism in Drug Design,2nd Ed.Vol. 312006, ISBN: 978-3-527-31368-6

T. Langer, R. D. Hofmann (eds.)

Pharmacophores andPharmacophore SearchesVol. 322006, ISBN: 978-3-527-31250-4

E. Francotte, W. Lindner (eds.)

Chirality in Drug ResearchVol. 332006, ISBN: 978-3-527-31076-0

W. Jahnke, D. A. Erlanson (eds.)

Fragment-based Approachesin Drug DiscoveryVol. 342006, ISBN: 978-3-527-31291-7

J. Hüser (ed.)

High-Throughput Screeningin Drug DiscoveryVol. 352006, ISBN: 978-3-527-31283-2

K. Wanner, G. Höfner (eds.)

Mass Spectrometry inMedicinal ChemistryVol. 362007, ISBN: 978-3-527-31456-0

R. Mannhold (ed.)

Molecular Drug PropertiesVol. 372008, ISBN: 978-3-527-31755-4

Antitargets

Prediction and Prevention of Drug Side Effects

Edited byRoy J. Vaz and Thomas Klabunde

Series Editors

Prof. Dr. Raimund MannholdMolecular Drug Research GroupHeinrich-Heine-UniversitätUniversitätsstrasse 140225 DüsseldorfGermanymannhold@uni-duesseldorf.de

Prof. Dr. Hugo KubinyiDonnersbergerstrasse 967256 Weisenheim am SandGermanykubinyi@t-online.de

Prof. Dr. Gerd FolkersCollegium HelveticumSTW/ETH Zurich8092 ZurichSwitzerlandfolkers@collegium.ethz.ch

Volume Editors

Dr. Roy J. VazSanofi-AventisRoute 202-206Bridgewater, NJ 08807USARoy.Vaz@sanofi-aventis.com

Dr. Thomas KlabundeSanofi-Aventis DeutschlandIndustriepark Höchst G87865926 FrankfurtGermanyThomas.Klabunde@sanofi-aventis.com

Cover IllustrationThe cover shows a model of the hERG ion channelin the lower left (chapter 4), a CYP structure, lowerright (chapter 10), a pharmacophore model for thealpha1a adrenergic receptor, upper right (chapter 6)and a schematic of the intestinal epithelium withsome transporters, upper left (chapter 15).

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ISBN: 978-3-527-31821-6

Contents

List of Contributors XVPreface XIXA Personal Foreword XXI

I General Aspects 1

1 Why Drugs Fail – A Study on Side Effects in New Chemical Entities 3Daniela Schuster, Christian Laggner, Thierry Langer

1.1 Introduction 31.2 Drugs Withdrawn from the Market between 1992 and 2006

Listed Alphabetically 41.2.1 Amineptine 41.2.2 Aminophenazone (Aminopyrine) 51.2.3 Astemizole 51.2.4 Bromfenac Sodium 61.2.5 Cerivastatin 61.2.6 Chlormezanone 61.2.7 Fenfluramine and Dexfenfluramine 71.2.8 Flosequinan 71.2.9 Glafenine 71.2.10 Grepafloxacin 81.2.11 Levacetylmethadol 81.2.12 Mibefradil 91.2.13 Rapacuronium Bromide 91.2.14 Rofecoxib 101.2.15 Temafloxacin 101.2.16 Troglitazone 101.2.17 Ximelagatran 111.3 Borderline Cases 121.4 Investigational Drugs That Failed in Clinical Phases

from 1992 to 2002 12

V

1.4.1 A Case Study: Fialuridine 121.4.2 A Recent Case Study: Torcetrapib 141.4.3 General Reasons for Project Failing in Clinical Phases I–III 151.5 Strategies for Avoiding Failure 161.6 An Unusual Case: The Revival of Thalidomide 17

References 18

2 Use of Broad Biological Profiling as a Relevant Descriptor to Describeand Differentiate Compounds: Structure–In Vitro(Pharmacology-ADME)–In Vivo (Safety) Relationships 23Jonathan S. Mason, Jacques Migeon, Philippe Dupuis,Annie Otto-Bruc

2.1 Introduction 232.1.1 Biological Profiling/Fingerprints and Drug Discovery

Applications 232.1.2 Polypharmacology of Drugs 262.2 The BioPrint1 Approach 282.2.1 BioPrint1 – General 282.2.2 BioPrint1 Assay Selection and Profile Description 282.2.3 Compounds in BioPrint1 302.2.4 BioPrint1 In Vivo Data sets 312.2.4.1 Compound Details 312.2.4.2 ADR Data 312.2.4.3 Pharmacokinetics 312.2.4.4 Toxicity Data 322.3 Structure–In Vitro Relationships 322.3.1 Similarity, Chemotypes – What Is a Biologically Relevant

Descriptor? 322.3.2 Using Biological Fingerprints as a Meaningful Descriptor for

Drug Leads and Candidates 332.3.2.1 Differentiation of Leads 332.3.2.2 Analysis of Attrited Compounds 362.3.3 Structural versus Experimental Differentiation – Dependence

on Structure-Derived Descriptor Used 372.3.4 Predictive Models from Pharmacological Data 402.3.5 Predictive Models from ADME Data – BioPrint1 Learnings 412.4 Chemogenomic Analysis – Target–Target Relationships 412.5 In Vitro–In Vivo Relationships – Placing Drug Candidates in the

Context of BioPrint1 422.5.1 Analyzing Potential ADR Liabilities Based on

Individual Hits 432.5.2 Analyzing Potential ADR Liabilities Based on Profile

Similarity 492.6 A Perspective for the Future 50

References 50

VI Contents

II Antitargets: Ion Channels and GPCRs 53

3 Pharmacological and Regulatory Aspects of QT Prolongation 55Fabrizio De Ponti

3.1 Introduction 553.2 hERG: Target Versus Antitarget 573.3 Pharmacology of QT Prolongation 583.3.1 Multiple Mechanisms Leading to QT Prolongation 593.3.2 hERG as the Key Mechanism for the Drug-Induced Long

QT Syndrome 593.3.3 Pharmacogenetic Aspects 603.4 Significance of Drug-Induced QT Prolongation 613.4.1 Prolonged QT/QTc and Occurrence of TdP 613.4.2 Dose–Response Relationship for QT Prolongation 663.5 Regulatory Aspects of QT Prolongation 673.5.1 Regulatory Guidance Documents 673.5.2 Preclinical In Vitro and In Vivo Studies 683.5.3 Clinical Studies 723.6 Conclusions 76

References 77

4 hERG Channel Physiology and Drug-Binding Structure–ActivityRelationships 89Sarah Dalibalta, John S. Mitcheson

4.1 Introduction 894.2 hERG Channel Structure 904.3 hERG Potassium Channels and the Cardiac Action Potential 914.4 Mutations in hERG Are Associated with Cardiac Arrhythmias 934.5 Acquired Long QT Syndrome 944.6 Drug-Binding Site of hERG 954.7 Structural Basis for hERG Block 954.8 Alternative Mechanisms of Block 974.9 Role of Inactivation in hERG Block 984.10 Inhibition of hERG Trafficking by Pharmacological Agents 994.11 Computational Approaches to Predict hERG Kþ Channel

Block 994.12 Conclusions 101

References 102

5 QSAR and Pharmacophores for Drugs Involved in hERG Blockage 109Maurizio Recanatini, Andrea Cavalli

5.1 Introduction 1095.2 Ligand-Based Models for hERG-Blocking Activity 1105.2.1 3D QSAR 1115.2.2 2D QSAR 113

Contents VII

5.2.3 Classification Models 1165.3 Ligand-Derived Models in the Light of the hERG

Channel Structure 1195.4 Conclusions 121

References 123

6 GPCR Antitarget Modeling: Pharmacophore Models to AvoidGPCR-Mediated Side Effects 127Thomas Klabunde, Andreas Evers

6.1 Introduction: GPCRs as Antitargets 1276.2 In Silico Tools for GPCR Antitarget Modeling 1296.3 GPCR Antitarget Pharmacophore Modeling: The a1a

Adrenergic Receptor 1306.3.1 Generation of Cross-Chemotype Pharmacophore Models 1316.3.2 Description of Cross-Chemotype Pharmacophore Models 1316.3.3 Validation of Antitarget Pharmacophore Models 1326.3.3.1 Virtual Screening: Hit Rates and Yields 1326.3.3.2 Virtual Screening: Fit Values and Enrichment Factors 1346.3.4 Mapping of Pharmacophore Models into Receptor Site 1356.3.5 Guidance of Chemical Optimization to Avoid GPCR-Mediated

Side Effects 1386.4 Summary 139

References 140

7 The Emergence of Serotonin 5-HT2B Receptors asDRUG Antitargets 143Vincent Setola, Bryan L. Roth

7.1 Receptorome Screening to Identify Drug Targets and Antitargets 1447.2 Post-Receptorome Screening Data Implicate 5-HT2B Receptors

in Drug-Induced VHD and PH 1457.3 Drug Structural Classes and VHD/PH 1497.4 Conclusions 150

References 151

8 Computational Modeling of Selective Pharmacophores at thea1-Adrenergic Receptors 155Francesca Fanelli, Pier G. De Benedetti

8.1 Introduction 1558.2 Ligand-Based and Receptor-Based Pharmacophore Modeling

and QSAR Analysis 1588.3 The General �1-AR Pharmacophore 1618.3.1 Ligand-Based Pharmacophore and Virtual Screening 1618.3.1.1 Prazosin Analogues (2,4-Diamino-6,7-dimethoxyquinazoline

Derivatives) 1638.3.1.2 1,4-Benzodioxan (WB-4101) Related Compounds 166

VIII Contents

8.3.1.3 Arylpiperazine Derivatives 1678.3.1.4 Target and Antitarget Pharmacophore Modeling 1688.4 Modeling the a1-AR Subtype Selectivities of Different

Classes of Antagonists 1708.4.1 Supermolecule-Based Subtype Pharmacophore and

QSAR Models 1718.4.2 Ligand-Based Subtype Pharmacophores 1798.4.3 Receptor-Based Subtype Pharmacophore and Ligand–Target/

Antitarget Interaction-Based QSAR 1818.5 Antitarget Modeling of Biogenic Amine-Binding GPCRs:

Common Features and Subtle Differences 1828.6 Conclusions 1838.6.1 From Molecules to Pharmacophores to Descriptors to Models 1838.7 Perspectives 1848.7.1 Pharmacophore Combination Approach: From Lock and

Key to Passe–Partout Model 184References 186

III Antitargets: Cytochrome P450s and Transporters 195

9 Cytochrome P450s: Drug–Drug Interactions 197Dan Rock, Jan Wahlstrom, Larry Wienkers

9.1 Introduction 1979.1.1 CYP1A Subfamily 1999.1.2 CYP2C Subfamily 2009.1.3 CYP2D6 2019.1.4 CYP3A Subfamily 2019.2 Reversible Inhibition 2039.2.1 Bioanalytical Techniques 2049.2.2 Reagent Selection and Reaction Conditions 2069.2.3 Experimental Design 2139.3 Irreversible Inhibition 2179.3.1 Identification of Mechanism-Based Inhibitor 2209.3.2 Characterization of Mechanism-Based Inhibition 2229.3.3 Additional Mechanistic Tools for Investigating Mechanism-

Based Inhibition 2259.4 Conclusion 230

References 231

10 Site of Metabolism Predictions: Facts and Experiences 247Ismael Zamora

10.1 Introduction 24710.2 Factors That Influence the Site of Metabolism Prediction

by Cytochrome P450s 248

Contents IX

10.2.1 Chemical Reactivity 24910.2.2 Protein/Compound Interaction 24910.3 Methods to Predict the Site of Metabolism 25010.3.1 Knowledge-Based Methods 25110.3.2 From Protein Structure to Chemical Reactivity 25110.3.2.1 Docking 25110.3.2.2 MetaSite 25210.3.2.3 Quantum Chemistry 25210.4 The Influence of the Protein Structure on the Site of Metabolism 25310.4.1 ComparativeAnalysis Between theDifferentCYPCrystal Structures 25310.4.1.1 CYP1A2 25310.4.1.2 CYP2C5 25510.4.1.3 CYP2B4 25610.4.1.4 CYP2C9 25610.4.1.5 CYP2D6 25710.4.1.6 CYP3A4 25710.4.2 The Effect of the Structure in the Different Methods to Predict

the Site of Metabolism 25910.5 Conclusions 260

References 262

11 Irreversible Cytochrome P450 Inhibition: Common Substructuresand Implications for Drug Development 267Sonia M. Poli

11.1 Introduction 26711.2 Overview 26811.2.1 Characteristics of Irreversible CYP Inhibition 26811.2.2 Quantitative Prediction of Drug–Drug Interaction Caused by

Irreversible CYP Inhibitors 26911.2.3 Irreversible CYP Inhibition and Autoimmune Diseases 26911.3 Structural Features Often Responsible for Mechanism-Based

CYP Inhibition 27011.3.1 Terminal Acetylenes (o or o�1) 27111.3.2 Alkenes 27111.3.3 Furans and Thiophenes 27311.3.4 Secondary and Tertiary Amines 27311.3.5 Benzodioxoles (MDP) 27311.4 Conclusions 274

References 274

12 MetaSite: Understanding CYP Antitarget Modeling for EarlyToxicity Detection 277Yasmin Aristei, Gabriele Cruciani, Sergio Clementi, Emanuele Carosati,Riccardo Vianello, Paolo Benedetti

12.1 Introduction 277

X Contents

12.2 The CYPs as Antitarget Enzymes 27812.3 The UGTs as Antitarget Enzymes 27912.4 The MetaSite Technology 28212.4.1 Mechanism-Based Inhibitors 28512.4.2 Phase II Metabolism by UGTs 28712.4.3 The Flowchart of the Overall Method 28712.5 Conclusions 28912.6 Software Package 290

References 290

13 Orphan Nuclear Receptor PXR-Mediated Gene Regulation inDrug Metabolism and Endobiotic Homeostasis 293Jie Zhou, Yonggong Zhai, Wen Xie

13.1 Cloning and Initial Characterization of PXR 29313.2 PXR and Its Regulation of Drug-Metabolizing

Enzymes and Transporters 29513.2.1 PXR in Phase I CYP Enzyme Regulation 29513.2.2 PXR in Phase II Enzyme Regulation 29613.2.2.1 PXR in UGT Regulation 29613.2.2.2 PXR in SULT Regulation 29613.2.2.3 PXR in GST Regulation 29713.2.3 PXR in Drug Transporter Regulation 29813.3 Crosstalk Between PXR and Other Nuclear Receptors 29813.4 Implications of PXR-Mediated Gene Regulation for Drug

Metabolism and Pathophysiology 29913.4.1 PXR in Drug Metabolism and Drug–Drug Interactions 30013.4.1.1 PXR in Drug Metabolism 30013.4.1.2 PXR in Drug–Drug Interactions 30013.4.1.3 Enantiospecificity of PXR-Activating Drugs and its Implication

in Drug Development 30113.4.2 Endobiotic Function of PXR 30213.4.2.1 PXR in Bile Acid Detoxification and Cholestasis 30213.4.2.2 PXR in Bilirubin Detoxification and Clearance 30313.4.2.3 PXR in Adrenal Steroid Homeostasis and

Drug–Hormone Interactions 30313.4.2.4 PXR in Lipid Metabolism 30413.5 Species Specificity of PXR and the Creation of ‘‘Humanized’’

Mice 30413.5.1 Challenges of using Rodents as Drug Metabolism Models 30413.5.2 Species Specificity of the Rodent and Human PXR 30513.5.3 Creation and Characterization of the hPXR ‘‘Humanized’’ Mice 30513.5.4 Significance of Humanized Mice in Drug Metabolism

Studies and Drug Development 30713.6 Conclusions 307

References 310

Contents XI

14 Ligand Features Essential for Cytochrome P450 Induction 317Daniela Schuster, Theodora M.Steindl, Thierry Langer

14.1 Introduction 31714.2 Molecular Mechanisms Leading to P450 Induction 31814.2.1.1 Heteroactivation 31814.2.1.2 Activation of Nuclear Receptors 31914.2.2 Ligands Directly Inducing P450 Activity 31914.2.2.1 P450 2C9 Heteroactivators 31914.2.2.2 P450 3A4 Heteroactivators 32214.2.3 P450 Inducers Acting via Nuclear Receptors 32214.2.3.1 Pregnane X Receptor 32214.2.3.2 Constitutive Androstane Receptor 32514.2.3.3 Farnesoid X Receptor 32614.2.3.4 Liver X Receptors 32814.2.4 P450 Inducers Acting via Transcription Factors 33014.2.4.1 Aryl Hydrocarbon Receptor 33014.3 General Ligand Features Leading to NR Activation 332

References 333

15 Transporters and Drugs – An Overview 341Hartmut Glaeser, Martin F. Fromm, Jörg König

15.1 Introduction 34115.2 Organic Anion Transporting Polypeptides and

Drug Transport 34215.3 Multidrug Resistance Proteins and Drug Transport 34615.4 Role of P-Glycoprotein for Drug Disposition 34915.5 Vectorial Drug Transport 352

References 355

16 Computational Models for P-Glycoprotein Substrates andInhibitors 367Patrizia Crivori

16.1 P-Glycoprotein Structure, Expression, Mechanism of Transportand Role on Drug Pharmacokinetics 367

16.2 In Vitro Models for Studying P-gp Interacting Compounds 36916.3 Computational Models for Predicting P-gp Interacting

Compounds 37116.3.1 Ligand-Based Approach 37216.3.2 Protein and Ligand–Protein Interaction-Based

Approaches 38716.4 Computational Models for Other Important Drug

Transporters 38916.5 Conclusions 390

References 392

XII Contents

IV Case Studies of Drug Optimization Against Antitargets 399

17 Selective Dipeptidyl Peptidase IV Inhibitors for the Treatment ofType 2 Diabetes: The Discovery of JANUVIA2 (Sitagliptin) 401Scott D. Edmondson, Dooseop Kim

17.1 Introduction 40117.2 Selectivity of DPP-4 Inhibitors 40217.3 a-Amino Acid Amide Series 40617.3.1 Cyclohexylglycines and Related Derivatives 40617.3.2 b-Substituted Phenylalanines as Potent and Selective

DPP-4 Inhibitors 40717.4 Early b-Amino Acid Amide DPP-4 Inhibitors 41117.4.1 Discovery of JANUVIA2 (Sitagliptin) and Related

Structure–Activity Relationships 41317.5 Conclusions 416

References 417

18 Strategy and Tactics for hERG Optimizations 423Craig Jamieson, Elizabeth M. Moir, Zoran Rankovic, Grant Wishart

18.1 Introduction 42318.1.1 Classification of Optimization Literature 42318.1.1.1 Discrete Structural Modifications 42418.1.1.2 Formation of Zwitterions 42518.1.1.3 Control of log P 42518.1.1.4 Attenuation of pKa 42518.2 Survey of Strategies Used to Diminish hERG 42618.2.1 Discrete Structural Modifications 42618.2.2 Formation of Zwitterions 43418.2.3 Control of log P 44018.2.4 Attenuation of pKa 44418.3 Summary and Analysis 44818.3.1 Summary of Optimization Literature 44818.3.2 Global Analysis of Reported Optimizations 44818.3.3 Summary and Recommendations 44918.3.4 Future Directions 450

References 451

19 Structure-Based In Silico Driven Optimization: Discovery of theSelective 5-HT1A Agonist PRX-00023 457Oren M. Becker

19.1 Introduction 45719.2 Structure-Based In Silico Driven Multidimensional

Optimization Paradigm 45919.3 Clinical Candidate Selection Criteria 461

Contents XIII

19.4 Lead Identification 46119.5 Optimization Round 1: Reducing Off-Target Activities 46219.6 Optimization Round 2: Reducing Affinity to hERG 46819.7 Conclusion 471

References 472

Index 477

XIV Contents

List of Contributors

XV

Yasmin AristeiUniversity of PerugiaChemistry DepartmentLaboratory for Chemometricsand CheminformaticsVia Elce di Sotto 1006123 PerugiaItaly

Oren M. BeckerEpix Pharmaceuticals Ltd.3 Hayetzira St.Ramat Gan 52521Israel

Current address:Dynamix Pharmaceuticals12 Motza Ha-QetanaMevasserei Zion 90805Israel

Paolo BenedettiMolecular Discovery Ltd215 Marsh RoadPinner, MiddlesexHA5 5NE LondonUnited Kingdom

Emanuele CarosatiUniversity of PerugiaChemistry DepartmentLaboratory for Chemometricsand CheminformaticsVia Elce di Sotto 1006123 PerugiaItaly

Andrea CavalliDepartment of Pharmaceutical SciencesUniversity of BolognaVia Belmeloro 640126 BolognaItaly

Sergio ClementiUniversity of PerugiaChemistry DepartmentLaboratory for Chemometricsand CheminformaticsVia Elce di Sotto 1006123 PerugiaItaly

Patrizia CrivoriNerviano Medical SciencesAccelera, Pharmacokinetic & Modeling/ModelingViale Pasteur 1020014 NervianoItaly

Gabriele CrucianiUniversity of PerugiaChemistry DepartmentLaboratory for Chemometricsand CheminformaticsVia Elce di Sotto 1006123 PerugiaItaly

Sarah DalibaltaUniversity of LeicesterDepartment of Cell Physiology andPharmacologyMedical Sciences BuildingUniversity RoadLeicester LE1 9HNUnited Kingdom

Pier G. De BenedettiUniversity of Modena and Reggio EmiliaDepartment of Chemistry andAdvanced ScientificComputing LaboratoryVia Campi 18341100 ModenaItaly

Fabrizio De PontiUniversity of BolognaDepartment of PharmacologyVia Irnerio 4840126 Bologna BOItaly

Philippe DupuisCerep SALe bois l’Eveque86600 Celle L’EvescaultFrance

Scott D. EdmondsonMerck Research LaboratoriesDepartment of Medicinal ChemistryP.O. Box 2000, RY123-234Rahway, NJ 07065USA

Andreas EversSanofi-Aventis Deutschland GmbHChemical Analytical SciencesDrug DesignBuilding G83865926 Frankfurt am MainGermany

Francesca FanelliUniversity of Modena and Reggio EmiliaDulbecco Telethon Institute andDepartment of ChemistryVia Campi 18341100 ModenaItaly

Martin F. FrommUniversity of Erlangen-NurembergInstitute of Experimental and ClinicalPharmacology and ToxicologyFahrstr. 1791054 ErlangenGermany

Hartmut GlaeserUniversity of Erlangen-NurembergInstitute of Experimental and ClinicalPharmacology and ToxicologyFahrstr. 1791054 ErlangenGermany

Craig JamiesonOrganon Laboratories LtdMedicinal ChemistryNewhouseLanarkshireML1 5SHUnited Kingdom

Dooseop KimMerck Research LaboratoriesDepartment of Medicinal ChemistryP.O. Box 2000, RY800-C206Rahway, NJ 07065USA

XVI List of Contributors

Thomas KlabundeSanofi-Aventis Deutschland GmbHScience & Medical AffairsDrug DesignBuilding G87865926 Frankfurt am MainGermany

Jörg KönigUniversity of Erlangen-NurembergInstitute of Experimental and ClinicalPharmacology and ToxicologyFahrstr. 1791054 ErlangenGermany

Christian LaggnerUniversity of InnsbruckDepartment of PharmaceuticalChemistryCAMD GroupInnrain 52c6020 InnsbruckAustria

Thierry LangerUniversity of InnsbruckDepartment of PharmaceuticalChemistryCAMD GroupInnrain 52c6020 InnsbruckAustria

Jonathan S. MasonLundbeck ResearchOttiliavej 92500 ValbyDenmark

Jacques MigeonCerep SALe bois l’Eveque86600 Celle L’EvescaultFrance

John S. MitchesonUniversity of LeicesterDepartment of Cell Physiology andPharmacologyMedical Sciences BuildingUniversity RoadLeicester LE1 9HNUnited Kingdom

Elizabeth M. MoirOrganon Laboratories LtdMedicinal ChemistryNewhouseLanarkshireML1 5SHUnited Kingdom

Annie Otto-BrucCerep SALe bois l’Eveque86600 Celle L’EvescaultFrance

Sonia Maria PoliAddex PharmaNon-Clinical Development12, Chemin des Aulx1228 Plan-Les-Ouates – GESwitzerland

Zoran RankovicOrganon Laboratories LtdMedicinal ChemistryNewhouseLanarkshireML1 5SHUnited Kingdom

Maurizio RecanatiniUniversity of BolognaDepartment of Pharmaceutical SciencesVia Belmeloro 640126 BolognaItaly

List of Contributors XVII

Dan RockAmgen Inc.1201 Amgen Court WestSeattle, WA 98119USA

Bryan L. RothUNC Chapel Hill School of MedicineMedicinal ChemistryBurnett Womack Building; Room 8032UNC Chapel HillChapel Hill, NCUSA

Daniela SchusterUniversity of InnsbruckDepartment of PharmaceuticalChemistryCAMD GroupInnrain 52c6020 InnsbruckAustria

Vincent SetolaINSERMU616 Hôpital Pitié-SalpêtrièreParisFrance

Theodora M. SteindlInte:Ligand Softwareentwicklungs- undConsulting GmbHClemens-Maria-Hofbauer-G. 62344 Maria EnzersdorfAustria

Riccardo VianelloMolecular Discovery Ltd215 Marsh Road, PinnerMiddlesexHA5 5NE LondonUnited Kingdom

Jan WahlstromAmgen Inc.1201 Amgen Court WestSeattle, WA 98119USA

Larry WienkersAmgen Inc.1201 Amgen Court WestSeattle, WA 98119USA

Grant WishartOrganon Laboratories LtdMedicinal ChemistryNewhouseLanarkshireML1 5SHUnited Kingdom

Wen XieUniversity of PittsburghCenter for Pharmacogenetics633 Salk HallPittsburgh, PA 15216USA

Ismael ZamoraPompeu Fabra UniversityGRIB-IMIMDr Aiguader 80E080003 BarcelonaSpain

Yonggong ZhaiBeijing Normal UniversityBiomedicine Research Institute andCollege of Life ScienceBeijing 100875China

Jie ZhouUniversity of PittsburghCenter for Pharmacogenetics633 Salk HallPittsburgh, PA 15216USA

XVIII List of Contributors

Preface

When the hammer hits your thumb in addition to, or instead of the nail - this clearlyis an antitarget problem. In drug action and especially in drug-drug interactions, thesituation is much more serious. There are numerous targets which should not beactivated, induced, or inhibited by a drug. Adverse drug reactions (ADRs) areestimated to be one of the leading causes of morbidity and mortality in healthcare.Especially older patients receive up to 15 different medications, and evenmore, at thesame time – no wonder that unfavorable drug-drug interactions happen, consideringalso the poor physical condition of such patients. In January 2000, the Institute ofMedicine reported that in the US about 7000 deaths per year occur due to ADRs; thenumber may be even much larger, not to count the manyfold non-fatal side effects.In defining the term ‘‘antitarget’’ one runs into some problems. Let us start with

terfenadine, a non-sedating H1-antihistaminic. In its clinical studies it wasobviously safe, with only minor side effects. However, after its broad therapeuticuse it turned out to produce fatal arrhythmias. In addition to being anH1 antagonist,terfenadine is a potent hERG channel inhibitor. Under normal conditions, terfena-dine is already metabolized in the intestinal wall; no measurable plasma levels andno cardiac side effects are observed. If CYP inhibitors prevent terfenadine metabo-lism, cardiac toxicity results. Thus, in addition to its H1 receptor antagonism, thecompound inhibits the hERG channel, a most prominent antitarget. The terfena-dine problem could be circumvented by replacing the compound by its activemetabolite fexofenadine, which is not any longer a hERG channel inhibitor.Already around 1990, David Bailey discovered that grapefruit (but not orange)

juice significantly increases the bioavailability of some drugs, for example thecalcium channel blockers felodipine and nifedipine. After some problems to publishthis highly surprising observation, his manuscript was accepted by Lancet andmanyreports followed for other drugs. The whole story shall not be elaborated here indetail but it remains the question: is CYP3A4, which is inhibited by some flavonoidand furocoumarin constituents of grapefruit juice, an antitarget? It is: despite thefact that increase in bioavailability is a desirable effect, individual variation is toolarge to be of therapeutic value. Only in the case of clinically monitored drugs, forexample cyclosporin, the co-medication of a CYP3A4 inhibitor, for example ketoco-nazole, is used to reduce the dose of this expensive drug.

XIX

Recently it was discovered that grapefruit juice also induces the expression ofintestinal drug transporters. With fexofenadine, the safe replacement of terfenadine,the paradox situation results that bioavailability of this drug decreases (!) after intakeof grapefruit juice, due to induction of an efflux pump, the organic anion-transport-ing polypeptide 1A2 (OATP1A2). Kirby and Unadkat commented this paradox byasking the question ‘‘Grapefruit juice, a glass full of drug interactions?’’Not only food constituents but also OTC drugs may cause significant drug-drug

interactions. One of the well-known examples is St. John’s Wort (Hypericum perfor-atum L.) extract, supposed to be beneficial against mild depression. However, inaddition to the phototoxic agent hypericin, the plant contains hyperforin, thestrongest inducer of CYPs (especially CYP3A4) and drug transporters. In thismanner, self-medication with St. John’s Wort reduces the bioavailability and thusthe activity of several drugs, whereas doses of some drugs have to be reduced afterdiscontinuation of this extract because CYP and transporter levels return to normal.There are many more antitargets, prominent ones being several G protein-

coupled receptors. Thus, it is high time that a book on antitargets becomes availableand we, as Editors of the series Methods and Principles in Medicinal Chemistry, arevery much indebted to Roy Vaz and Thomas Klabunde, leading scientists in anti-target research, for editing such a monograph. The book starts with an introductionon the reasons why drugs fail in the clinics or after market introduction and achapter on ADME and side effects prediction. Themain two sections contain severalchapters on antitargets and side effects (hERG channel and GPCR antitargets) andon antitargets in ADME (CYPs and drug transporters). The book concludes withsome case studies of drug optimization against antitargets.We are very grateful to all chapter authors and we thank the publisherWiley-VCH,

especially Dr. FrankWeinreich, for the ongoing support of our series, and Dr. NicolaOberbeckmann-Winter for her contributions in the preparation of this volume.

October 2007 Raimund Mannhold, DüsseldorfHugo Kubinyi, Weisenheim am SandGerd Folkers, Zürich

XX Preface

A Personal Foreword

A single report of a drug reaction in a 39-year-old woman ultimately contributed tothe removal of the allergy drug Seldane (terfenadine) from the market in 1998 [1].Doctors at the National Naval Medical Center in Bethesda,Md., admitted the womanto the hospital because of fainting episodes. She had been prescribed Seldane(terfenadine) 10 days before. She also started using the prescription drug Nizoral(ketoconazole) for a vaginal yeast infection. That combination caused potentiallyfatal changes in her heart rhythm. The Food and Drug Administration (FDA) issuedwarnings indicating that ketoconazole interfered with terfenadine's metabolism,which resulted in increased levels of terfenadine in the blood and slowed itselimination from the body. The FDA also warned that a similar effect could occurif Seldane was taken with the antibiotic erythromycin.Thus the first awareness of antitargets was brought to the forefront with the

withdrawal of terfenadine. Ketoconazole is a strong inhibitor of CYP3A4, which isalso the primary enzyme responsible for the clearance of terfenadine. The inhibitionof CYP3A4 leads to the increase in concentration of terfenadine in the blood.Terfenadine itself is a blocker of the ion channel hERG (human ether-a-go-go relatedgene) and caused a prolongedQT, leading to Torsades de Pointes and possibly death.Also ketoconazole inhibits the efflux transporter P-glycoprotein (P-gp) or MDR1(multidrug resistance protein), for which terfenadine is a substrate. Hence when co-administered with ketoconazole, the concentration of terfenadine in blood would bemuch higher than if taken without other drugs such as ketoconazole. Thereforeinhibition of both P-gp and CYP3A4 could lead to drug-drug interactions andinhibition of hERG either by the compound itself or its metabolite.The example of terfenadine shows that toxic effects can be either induced

directly by the action of a drug or a drug metabolite on an antitarget like thehERG channel. In addition, certain transporters and metabolizing enzymes, likeP-gp and CYP3A4, need also be considered as antitargets as blocking their activitycan change the concentration of a co-administered drug or its metabolite in blood,thus causing drug-drug interactions and potential toxicity.Adverse drug reactions (ADRs) cost approximately one hundred and thirty nine

billion dollars annually [2–4] in the United States. This number is larger than the

XXI

cost of cardiovascular or diabetic care. ADRs cause 1 out of 5 injuries or deaths peryear to hospitalized patients and the mean length of stay, the cost and the mortalityfor patients admitted due to an ADR are double that for control patients. Many ADRsare due to off-target and antitarget interactions. Some of these have lead to with-drawal of the drug(s) from the marketplace.Since terfenadine, there have been other market withdrawals of drugs. As shown

in the first chapter of the book themain cause for the 16 drug withdrawals from 1992to 2002 was toxicity, mainly cardiovascular toxicity or hepatotoxicity. Only recentlyVioxx (rofecoxib) had to be withdrawn from the market. In contrast to terfenadine,where the molecular mechanism of its side effects has been fully understood, theunderlying mechanism by which rofecoxib, a selective cyclooxygenase 2 inhibitorthat exhibits cardiovascular effects is still unclear [5]. Pondimin (fenfluramine), aserotonergic anorectic, was withdrawn in 1997 due to the risk of development ofprimary pulmonary hypertension or valvular heart disease. The first case of fen-fluramine associated valvular heart disease discovered 7 years after discontinuationof treatment and requiring double valve replacement 2 years later has just beenreported [6]. For fenfluramine the mechanism by which it causes valvular heartdisease has recently been uncovered showing a causal association between agonismon the G-protein coupled receptor (GPCR) 5-HT2B and valvular heart disease(Chapter 7 in the book).According to FDA experts, discovering terfenadine’s interactions with other

drugs marked a significant advance. These and other discoveries improved theability of the FDA and drug manufacturers to test for drug interactions and toinvestigate risks of heart rhythm abnormalities and other toxicities before drugscould be marketed. In addition, unraveling the mechanism of drug toxicities andidentifying specific channels, receptors including nuclear receptors, transporters orenzymes as antitargets enabled establishment of in vitro test systems to monitorpotential antitarget mediated side effects and toxicity in the drug discovery phase.The list of antitargets is still being compiled but the events that have lead to thediscovery of the known antitargets has impacted the way research is conductedduring drug discovery today.In every family of biological targets there are antitargets. In this book, we have

avoided discussion of kinases, which are still controversial as non-oncology targetsand could probably command several chapters or volumes. Transporters and meta-bolizing enzymes like CYP450s that can mediate undesired drug-drug interactionshave been mentioned before. In the area of potassium voltage-gated ion channels,there are therapeutic targets such as Kv1.3 and Kv1.5 but at the same time there areantitargets such as hERG. GPCRs form a large protein family that plays an importantrole in many physiological and patho-physiological processes. Especially the sub-family of biogenic amine binding GPCRs has provided excellent drug targets for thetreatment of numerous diseases [7]. Although representing excellent therapeutictargets, the central role that many of the biogenic amine binding GPCRs play in cellsignaling also poses a risk on new drug candidates which reveal side-affinitiestowards these receptor sites: These candidates bear the risk to interfere with thephysiological signaling process and to cause undesired effects in preclinical or

XXII A Personal Foreword

clinical studies. Besides the 5-HT2B receptor mentioned before, the a1A adrenergicreceptor, being a drug target for the treatment of benign prostatic hypertrophy(BPH), has been suggested as an antitarget at the same time that mediates cardio-vascular side-effects of many drug candidates causing orthostatic hypotension,dizziness and fainting spells [8]. Other examples of GPCR antitargets are themuscarinic M1 receptor correlated with attention and memory deficits orthe serotonin 5-HT2C receptor associated with weight gain. As shown in one ofthe introductory chapters of this book, correlation between in vitro affinity and in vivoadverse effects can currently be recognized by profiling, hundreds of drugs withknown ADRs using large panels of pharmacological in vitro assays.There are several references made to both off-targets as well as antitargets in

the literature. In this book we will primarily be attempting to cover the topic ofantitargets. Off-target activity the way we interpret it, is activity for a particularcompound towards a target that was not anticipated, when it was synthesized orisolated. For example, compounds that are designed or synthesized for activitytowards serine proteases (not for thrombosis) are not expected to have any activitytowards serine protease targets such as thrombin or others in the coagulationpathway, which could be anti-thrombotic targets themselves. The term off-targetsincludes antitargets and the off-target activities could be beneficial or detrimental.Antitargets on the other hand are targets that are detrimental towards progression ofthe compound towards becoming a drug.Within recent years the understanding of the molecular interactions between

antitargets and drugs or drug candidates has tremendously increased allowingin silico antitarget models to be established. 3-dimensional structures of severalantitargets (often in complex with inhibitors) are now available either derived byhomologymodeling (e.g. the hERG channel or GPCRs) or by protein crystallography(e.g. cytochrome P450s). Structural chemical motifs often associated with antitargetinteractions (e.g. for cytochrome P450 binding or inhibition) have been captured inknowledge databases. Computational models like 3D-pharmacophore or 3D-QSARmodels (e.g. for GPCRs, hERG, CYPs, P-gp) have been established to not onlyrecognize antitarget affinities in chemical lead series but also to guide the chemicaloptimization of these leads towards development candidates lacking undesiredantitarget side affinities and thus potential side effects or toxicities. These modelsare captured – together with introductory chapters on the biological aspects – in thesecond (focusing on ion channels and GPCRs) and the third section of this book(describing antitargets mediating drug-drug interactions).Examples of optimization of selectivity towards the antitargets have been well

described in the recent literature such as illustrated in Gao et al. [9] and Kuduk et al.[10]. In the last section we have tried to include very specific case studies ofsuccessful drugs for which optimization of selectivity towards specific or generalantitargets were successfully negotiated, e.g. for Januvia (chapter 17), a recentlyreleased DPP4 inhibitor or for PRX-00023, a selective 5-HT1A agonist currently inphase IIb clinical trials (chapter 19).We would first thank the editors of the series for enabling this volume in the

Methods and Principles in Medicinal Chemistry series. We would like to sincerely

A Personal Foreword XXIII

thank all chapter authors for making this book a reality. We would like toacknowledge their great enthusiasm in preparing their manuscripts and the highquality of their contributions. It has been a pleasure working with each and every oneof them. The editors are also grateful to Frank Weinreich, Nicola Oberbeckmann-Winter and the staff of Wiley-VCH for their excellent support in the production ofthis book.We also thank the Sanofi-Aventis DiscoveryManagement for enabling thisbook. We thank our families for putting up with us during the last few months.

October 2007 Roy Vaz, BridgewaterThomas Klabundl, Frankfurt

References

1 Monahan, B.P., Ferguson, C.L.,Kileavy, E.S., Lloyd, B. K., Troy, J.,Cantilena, L.R. (1990) Torsades dePointes occurring in association withTerfenadine use. The Journal of theAmerican Medical Association, 264,2788–2790.

2 Johnson J.A., Bootman, J.L. (1995)Drug-related morbidity and mortality.A cost-of-illness model. Archives ofInternal Medicine, 155 (18), 1949–1956.

3 Leape, L.L., Brennan, T.A., Laird, N.,Lawthers, A.G., Localio, A.R., Barnes,B.A., Hebert, L., Newhouse, J.P.,Weiler, P.C., Hiatt, H.H. (1991) Thenature of Adverse events inhopitalized patients. Results of theHarvard Medical Practice Study II. TheNew Journal of Medicine, 324 (6),377–394.

4 Classen D.C., Pestotnik, S.L., Evans,R.S., Lloyd, J.F., Burke, J.P. (1997)Adverse drug events in hospitalizedpatients. Excess length of stay, extracosts, and attributable mortality. TheJournal of the American MedicalAssociation, 277 (4), 301–306.

5 Zarraga, I.G.E., Schwarz, E.R. (2007)Coxibs and Heart Disease. Journal ofthe American College of Cardiology, 49(1), 1–149.

6 Greffe, G., Chalabreysse, L., Mouly-Bertin, C., Lantelme, P., Thivolet, F.,Aulagner, G., Obadia, J-F. (2007)Valvular Heart Disease associated with

Fenfluramin Detected 7 Years afterDiscontinuation of Treatment. TheAnnals of Thoracic Surgery, 83, 1541–1543.

7 Klabunde, T., Hessler, G. (2002) Drugdesign strategies for targeting G-protein-coupled receptors. A EuropeanJournal of Chemical Biology, 3, 928–944.

8 Kehne, J.H., Baron, B.M., Carr, A. A.,Chaney, S. F., Elands, J., Feldman,D. J., Frank, R. A., van Giersbergen,P. L., McCloskey, T. C., Johnson, M.P.,McCarty, D. R., Poirot, M., Senyah, Y.,Siegel, B. W., Widmaier, C. (1996)Preclinical characterization of thepotential of the putative atypicalantipsychotic MDL 100,907 as a potent5-HT2A antagonist with a favorableCNS safety profile. The Journal ofPharmacology and ExperimentalTherapeutics, 277, 968–981.

9 Gao, Y.D., Olson, S.H., Balkovec, J.M.,Zhu, Y., Royo, I., Yabut, J., Evers, R.,Tan, E.Y., et al. (2007) Attenuatingpregnane X receptor (PXR) activation:A molecular modeling approach.Xenobiotica, 37 (2), 124–138.

10 Kuduk, S.D., DiMarco, C.N., Chang,R.K., Wood, M.R., Schirripa, K.M.,Kim, J.J., Wai, J.M.C., DiPardo, R.M.et al. (2007) Development of OrallyBio-available and CNS PenetrantBiphenyla-minocyclopropaneCarboxamide Bradykinin B1 ReceptorAntagonists. Journal of MedicinalChemistry, 50, 272–282.

XXIV A Personal Foreword

IGeneral Aspects

j1

1Why Drugs Fail – A Study on Side Effects in New Chemical EntitiesDaniela Schuster, Christian Laggner, Thierry Langer

1.1Introduction

Drug development is a long and cost-intensive business. Only after years of leadidentification, chemical optimization, in vitro and animal testing can the first clinicaltrials be conducted. Unfortunately, many projects still fail in this late stage ofdevelopment after a considerable amount of money has been spent. According toestimates, preapproval costs for a new drug exceed US$ 800 million [1].Approximately 10% of new chemical entities (NCEs) show serious adverse drug

reactions (ADRs) after market launch. Such events usually result in new black boxwarnings by the US Food and Drug Administration (FDA), label change or marketwithdrawal. The most common causes for these actions are hepatic toxicity, hema-tologic toxicity and cardiovascular toxicity [2]. Reasons for such ADRs, which areidentified only after NCEs are launched on themarket, include the narrow spectrumof clinical disorders and participating patient profiles in clinical studies as well as thefact that serious ADRs are often rare and that the number of patient exposuresrequired to identify such occurrences sometimes may range over a few millions [3].To avoid the occurrence of ADRs in the future, specific trials to detect them

should therefore be conducted before an NCE is launched on the market. Beforethis can be done, however, the major reasons leading to the withdrawal of drugs andtermination of NCE-to-drug development should be identified and analyzed.In this chapter, reasons why 17 drugs were withdrawn from the Western market

between 1992 and 2006 are discussed and facts on 63 terminated clinical developmentprojects presented, so as to identify themost common reasons for the failure of drugs inthis late stage of drug development. This analysis is then compared with two previousrelated studies published more than 18 years ago by Prentis et al. [4] and Kennedy [5].The study by Prentis et al. [4] included an analysis of 198 NCEs, developed between

1964 and 1985 by British pharmaceutical companies but had not been marketed forreasons presented in Figure 1.1. Kennedy [5] further analyzed these data and noticedthat a high number of anti-infective drug development projects were all terminated

1 j3

because of pharmacokinetic difficulties.He therefore excluded the anti-infectiveNCEsfrom the statistics and presented the facts as illustrated in Figure 1.2.

1.2Drugs Withdrawn from the Market between 1992 and 2006 Listed Alphabetically

1.2.1Amineptine

The atypical tricyclic antidepressant amineptine (Survector) is an indirect dopamineagonist, which selectively inhibits dopamine uptake and induces its release, withadditional stimulation of the adrenergic system. Its antidepressant effects are similarto those of other tricyclic antidepressant drugs. However, it acts more rapidly, is better

Figure 1.1 Reasons for drug development termination from 1964 to 1985 (n¼ 198).

Figure 1.2 Reasons for drug development termination, excluding anti-infectives (n¼ 121).

4j 1 Why Drugs Fail – A Study on Side Effects in New Chemical Entities