Medicinal Chemistry: An Introduction (Wiley, 2nd Edition) PDF

Medicinal Chemistry Second Edition Gareth Thomas University of Portsmouth Medicinal Chemistry Second Edition Medicinal Chemistry Second Edition Gareth Thomas University of Portsmouth Copyright # 2007 John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, W...

Medicinal Chemistry Second Edition Gareth Thomas University of Portsmouth Medicinal Chemistry Second Edition Medicinal Chemistry Second Edition Gareth Thomas University of Portsmouth Copyright # 2007 John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex PO19 8SQ, England Telephone (þ 44) 1243 779777 Email (for orders and customer service enquiries): [email protected] Visit our Home Page on www.wileyeurope.com or www.wiley.com All Rights Reserved. No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, scanning or otherwise, except under the terms of the Copyright, Designs and Patents Act 1988 or under the terms of a licence issued by the Copyright Licensing Agency Ltd, 90 Tottenham Court Road, London W1T 4LP, UK, without the permission in writing of the Publisher. 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Other Wiley Editorial Offices John Wiley & Sons Inc., 111 River Street, Hoboken, NJ 07030, USA Jossey-Bass, 989 Market Street, San Francisco, CA 94103-1741, USA Wiley-VCH Verlag GmbH, Boschstr. 12, D-69469 Weinheim, Germany John Wiley & Sons Australia Ltd, 33 Park Road, Milton, Queensland 4064, Australia John Wiley & Sons (Asia) Pte Ltd, 2 Clementi Loop #02-01, Jin Xing Distripark, Singapore 129809 John Wiley & Sons Canada Ltd, 6045 Freemont Blvd, Mississauga, Ontario, L5R 4J3 Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic books. Anniversary Logo Design: Richard J. Pacifico Library of Congress Cataloging-in-Publication Data Thomas, Gareth, Dr. Medicinal chemistry : an introduction / Gareth Thomas. – 2nd ed. p. ; cm. Includes bibliographical references and index. ISBN 978-0-470-02597-0 (cloth : alk. paper) – ISBN 978-0-470-02598-7 (pbk. : alk. paper) 1. Pharmaceutical chemistry. I. Title. [DNLM: 1. Chemistry, Pharmaceutical. 2. Drug Design. 3. Drug Evaluation. 4. Pharmacokinetics. QV 744 T4567m 2007] RS403.T447 2007 615’.19–dc22 2007026412 British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library ISBN 978-0-470-02597-0 (HB) 978-0-470-02598-7 (PB) Typeset in 10.5/13pt Times Roman by Thomson Digital Printed and bound in Great Britain by Antony Rowe Ltd., Chippenham., Wiltshire This book is printed on acid-free paper responsibly manufactured from sustainable forestry in which at least two trees are planted for each one used for paper production. Contents Preface to the First Edition xv Preface to the Second Edition xvii Acknowledgements xix Abbreviations xxi 1 An introduction to drugs, their action and discovery 1 1.1 Introduction 1 1.2 What are drugs and why do we need new ones? 1 1.3 Drug discovery and design: a historical outline 3 1.3.1 The general stages in modern-day drug discovery and design 7 1.4 Leads and analogues: some desirable properties 9 1.4.1 Bioavailability 9 1.4.2 Solubility 10 1.4.3 Structure 10 1.4.4 Stability 11 1.5 Sources of leads and drugs 14 1.5.1 Ethnopharmaceutical sources 15 1.5.2 Plant sources 15 1.5.3 Marine sources 17 1.5.4 Microorganisms 18 1.5.5 Animal sources 20 1.5.6 Compound collections, data bases and synthesis 20 1.5.7 The pathology of the diseased state 21 1.5.8 Market forces and ‘me-too drugs’ 21 1.6 Methods and routes of administration: the pharmaceutical phase 21 1.7 Introduction to drug action 24 1.7.1 The pharmacokinetic phase (ADME) 25 1.7.2 The pharmacodynamic phase 32 1.8 Classification of drugs 33 1.8.1 Chemical structure 33 1.8.2 Pharmacological action 34 1.8.3 Physiological classification 34 1.8.4 Prodrugs 35 1.9 Questions 35 vi CONTENTS 2 Drug structure and solubility 37 2.1 Introduction 37 2.2 Structure37 2.3 Stereochemistry and drug design 38 2.3.1 Structurally rigid groups 38 2.3.2 Conformation 39 2.3.3 Configuration 41 2.4 Solubility 44 2.4.1 Solubility and the physical nature of the solute 44 2.5 Solutions 46 2.6 The importance of water solubility 47 2.7 Solubility and the structure of the solute 49 2.8 Salt formation 50 2.9 The incorporation of water solubilising groups in a structure 52 2.9.1 The type of group 52 2.9.2 Reversible and irreversible groups 53 2.9.3 The position of the water solubilising group 53 2.9.4 Methods of introduction 54 2.9.5 Improving lipid solubility 59 2.10 Formulation methods of improving water solubility 59 2.10.1 Cosolvents 59 2.10.2 Colloidal solutions 59 2.10.3 Emulsions 60 2.11 The effect of pH on the solubility of acidic and basic drugs 61 2.12 Partition 63 2.12.1 Practical determination of partition coefficients 65 2.12.2 Theoretical determination of partition coefficients 66 2.13 Surfactants and amphiphiles 66 2.13.1 Drug solubilisation 69 2.13.2 Mixed micelles as drug delivery systems 71 2.13.3 Vesicles and liposomes 72 2.14 Questions 72 3 Structure–activity and quantitative structure relationships 75 3.1 Introduction 75 3.2 Structure–activity relationship (SAR) 76 3.3 Changing size and shape 77 3.3.1 Changing the number of methylene groups in chains and rings 77 3.3.2 Changing the degree of unsaturation 78 3.3.3 Introduction or removal of a ring system 78 3.4 Introduction of new substituents 80 3.4.1 Methyl groups 81 3.4.2 Halogen groups 83 3.4.3 Hydroxy groups 84 3.4.4 Basic groups 84 3.4.5 Carboxylic and sulphonic acid groups 85 3.4.6 Thiols, sulphides and other sulphur groups 85 3.5 Changing the existing substituents of a lead 86 3.6 Case study: a SAR investigation to discover potent geminal bisphosphonates 87 3.7 Quantitative structure–activity relationship (QSAR) 90 3.7.1 Regression analysis 93 3.7.2 The lipophilic parameters 94  CONTENTS vii 3.7.3 Electronic parameters 99 3.7.4 Steric parameters 102 3.8 Questions 110 4 Computer-aided drug design 113 4.1 Introduction 113 4.1.1 Models 114 4.1.2 Molecular modelling methods 115 4.1.3 Computer graphics 116 4.2 Molecular mechanics 117 4.2.1 Creating a molecular model using molecular mechanics 120 4.3 Molecular dynamics 123 4.3.1 Conformational analysis 124 4.4 Quantum mechanics 124 4.5 Docking 127 4.5.1 De novo design 128 4.6 Comparing three-dimensional structures by the use of overlays 130 4.6.1 An example of the use of overlays 132 4.7 Pharmacophores and some of their uses 133 4.7.1 High-resolution X-ray crystallography or NMR 133 4.7.2 Analysis of the structures of different ligands 134 4.8 Modelling protein structures 135 4.9 Three-dimensional QSAR 136 4.9.1 Advantages and disadvantages 140 4.10 Other uses of computers in drug discovery 141 4.11 Questions 143 5 Combinatorial chemistry 145 5.1 Introduction 145 5.1.1 The design of combinatorial syntheses 147 5.1.2 The general techniques used in combinatorial synthesis 148 5.2 The solid support method 148 5.2.1 General methods in solid support combinatorial chemistry 150 5.2.2 Parallel synthesis 152 5.2.3 Furka’s mix and split technique 155 5.3 Encoding methods 157 5.3.1 Sequential chemical tagging 157 5.3.2 Still’s binary code tag system 160 5.3.3 Computerised tagging 161 5.4 Combinatorial synthesis in solution 161 5.4.1 Parallel synthesis in solution 162 5.4.2 The formation of libraries of mixtures 163 5.4.3 Libraries formed using monomethyl polyethylene glycol (OMe-PEG) 164 5.4.4 Libraries produced using dendrimers as soluble supports 164 5.4.5 Libraries formed using fluorocarbon reagents 165 5.4.6 Libraries produced using resin-bound scavenging agents 166 5.4.7 Libraries produced using resin-bound reagents 168 5.4.8 Resin capture of products 168 5.5 Deconvolution 169 5.6 High-throughput screening (HTS) 170 5.6.1 Biochemical assays 171 5.6.2 Whole cell assays 173 5.6.3 Hits and hit rates 173 viii CONTENTS 5.7 Automatic methods of library generation and analysis 174 5.8 Questions 175 6 Drugs from natural sources 177 6.1 Introduction 177 6.2 Bioassays 179 6.2.1 Screening tests 180 6.2.2 Monitoring tests 183 6.3 Dereplication 185 6.4 Structural analysis of the isolated substance 186 6.5 Active compound development 188 6.6 Extraction procedures 189 6.6.1 General considerations 190 6.6.2 Commonly used methods of extraction 191 6.6.3 Cleaning up procedures 195 6.7 Fractionation methods 195 6.7.1 Liquid–liquid partition 196 6.7.2 Chromatographic methods 199 6.7.3 Precipitation 200 6.7.4 Distillation 200 6.7.5 Dialysis 202 6.7.6 Electrophoresis 202 6.8 Case history: the story of Taxol 202 6.9 Questions 206 7 Biological membranes 207 7.1 Introduction 207 7.2 The plasma membrane 208 7.2.1 Lipid components 209 7.2.2 Protein components 211 7.2.3 The carbohydrate component 213 7.2.4 Similarities and differences between plasma membranes in different cells 213 7.2.5 Cell walls 214 7.2.6 Bacterial cell exterior surfaces 217 7.2.7 Animal cell exterior surfaces 218 7.2.8 Virus 218 7.2.9 Tissue 219 7.2.10 Human skin 219 7.3 The transfer of species through cell membranes 220 7.3.1 Osmosis 220 7.3.2 Filtration 221 7.3.3 Passive diffusion 221 7.3.4 Facilitated diffusion 223 7.3.5 Active transport 223 7.3.6 Endocytosis 224 7.3.7 Exocytosis 225 7.4 Drug action that affects the structure of cell membranes and walls 225 7.4.1 Antifungal agents 226 7.4.2 Antibacterial agents (antibiotics) 230 7.4.3 Local anaesthetics 244 7.5 Questions 249  CONTENTS ix 8 Receptors and messengers 251 8.1 Introduction 251 8.2 The chemical nature of the binding of ligands to receptors 252 8.3 Structure and classification of receptors 254 8.4 General mode of operation 256 8.4.1 Superfamily Type 1 259 8.4.2 Superfamily Type 2 260 8.4.3 Superfamily Type 3 263 8.4.4 Superfamily Type 4 264 8.5 Ligand–response relationships 265 8.5.1 Experimental determination of ligand concentration–response curves 266 8.5.2 Agonist concentration–response relationships 267 8.5.3 Antagonist concentration–receptor relationships 268 8.5.4 Partial agonists 271 8.5.5 Desensitisation 272 8.6 Ligand–receptor theories 272 8.6.1 Clark’s occupancy theory 272 8.6.2 The rate theory 277 8.6.3 The two-state model 278 8.7 Drug action and design 279 8.7.1 Agonists 279 8.7.2 Antagonists 281 8.7.3 Citalopram, an antagonist antidepressant discovered by a rational approach 282 8.7.4 b-Blockers 285 8.8 Questions 289 9 Enzymes 291 9.1 Introduction 291 9.2 Classification and nomenclature 293 9.3 Active sites and catalytic action 295 9.3.1 Allosteric activation 297 9.4 Regulation of enzyme activity 298 9.4.1 Covalent modification 298 9.4.2 Allosteric control 298 9.4.3 Proenzyme control 300 9.5 The specific nature of enzyme action 300 9.6 The mechanisms of enzyme action 302 9.7 The general physical factors affecting enzyme action 302 9.8 Enzyme kinetics 303 9.8.1 Single substrate reactions 303 9.8.2 Multiple substrate reactions 305 9.9 Enzyme inhibitors 306 9.9.1 Reversible inhibitors 307 9.9.2 Irreversible inhibition 312 9.10 Transition state inhibitors 318 9.11 Enzymes and drug design: some general considerations 320 9.12 Examples of drugs used as enzyme inhibitors 321 9.12.1 Sulphonamides 321 9.12.2 Captopril and related drugs 323 9.12.3 Statins 326 9.13 Enzymes and drug resistance 329 9.13.1 Changes in enzyme concentration 330 x CONTENTS 9.13.2 An increase in the production of the substrate 331 9.13.3 Changes in the structure of the enzyme 331 9.13.4 The use of an alternative metabolic pathway 332 9.14 Ribozymes 332 9.15 Questions 332 10 Nucleic acids 335 10.1 Introduction 335 10.2 Deoxyribonucleic acid (DNA) 336 10.2.1 Structure 337 10.3 The general functions of DNA 338 10.4 Genes 339 10.5 Replication 340 10.6 Ribonucleic acid (RNA) 341 10.7 Messenger RNA (mRNA) 342 10.8 Transfer RNA (tRNA) 343 10.9 Ribosomal RNA (rRNA) 345 10.10 Protein synthesis 345 10.10.1 Activation 345 10.10.2 Initiation 346 10.10.3 Elongation 347 10.10.4 Termination 348 10.11 Protein synthesis in prokaryotic and eukaryotic cells 348 10.11.1 Prokaryotic cells 348 10.11.2 Eukaryotic cells 350 10.12 Bacterial protein synthesis inhibitors (antimicrobials) 350 10.12.1 Aminoglycosides 351 10.12.2 Chloramphenicol 355 10.12.3 Tetracyclines 356 10.12.4 Macrolides 359 10.12.5 Lincomycins 360 10.13 Drugs that target nucleic acids 362 10.13.1 Antimetabolites 362 10.13.2 Enzyme inhibitors 368 10.13.3 Intercalating agents 372 10.13.4 Alkylating agents 374 10.13.5 Antisense drugs 377 10.13.6 Chain cleaving agents 379 10.14 Viruses 380 10.14.1 Structure and replication 380 10.14.2 Classification 381 10.14.3 Viral diseases 383 10.14.4 Antiviral drugs 384 10.15 Recombinant DNA technology (genetic engineering) 389 10.15.1 Gene cloning 389 10.15.2 Medical applications 392 10.16 Questions 401 11 Pharmacokinetics 403 11.1 Introduction 403 11.1.1 General classification of pharmacokinetic properties 405 11.1.2 Drug regimens 405 11.1.3 The importance of pharmacokinetics in drug discovery 406 11.2 Drug concentration analysis and its therapeutic significance 407  CONTENTS xi 11.3 Pharmacokinetic models 409 11.4 Intravascular administration 411 11.4.1 Distribution 412 11.5 Extravascular administration 425 11.5.1 Dissolution 428 11.5.2 Absorption 429 11.5.3 Single oral dose 430 11.5.4 The calculation of tmax and Cmax 433 11.5.5 Repeated oral doses 434 11.6 The use of pharmacokinetics in drug design 435 11.7 Extrapolation of animal experiments to humans 435 11.8 Questions 436 12 Drug metabolism 439 12.1 Introduction 439 12.1.1 The stereochemistry of drug metabolism 439 12.1.2 Biological factors affecting metabolism 440 12.1.3 Environmental factors affecting metabolism 443 12.1.4 Species and metabolism 443 12.1.5 Enzymes and metabolism 443 12.2 Secondary pharmacological implications of metabolism 443 12.2.1 Inactive metabolites 444 12.2.2 Metabolites with a similar activity to the drug 444 12.2.3 Metabolites with a dissimilar activity to the drug 444 12.2.4 Toxic metabolites 445 12.3 Sites of action 445 12.4 Phase I metabolic reactions 446 12.4.1 Oxidation 446 12.4.2 Reduction 448 12.4.3 Hydrolysis 448 12.4.4 Hydration 449 12.4.5 Other Phase I reactions 449 12.5 Examples of Phase I metabolic reactions 449 12.6 Phase II metabolic routes 454 12.7 Pharmacokinetics of metabolites 457 12.8 Drug metabolism and drug design 458 12.9 Prodrugs 460 12.9.1 Bioprecursor prodrugs 461 12.9.2 Carrier prodrugs 462 12.9.3 Photoactivated prodrugs 464 12.9.4 The design of carrier prodrug systems for specific purposes 465 12.10 Questions 475 13 Complexes and chelating agents 477 13.1 Introduction 477 13.2 The shapes and structures of complexes 478 13.2.1 Ligands 479 13.2.2 Bridging ligands 483 13.2.3 Metal–metal bonds 483 13.2.4 Metal clusters 483 13.3 Metal–ligand affinities 485 13.3.1 Affinity and equilibrium constants 485 13.3.2 Hard and soft acids and bases 487 xii CONTENTS 13.3.3 The general medical significance of complex stability 488 13.4 The general roles of metal complexes in biological processes 488 13.5 Therapeutic uses 491 13.5.1 Metal poisoning 491 13.5.2 Anticancer agents 494 13.5.3 Antiarthritics 497 13.5.4 Antimicrobial complexes 498 13.5.5 Photoactivated metal complexes 499 13.6 Drug action and metal chelation 501 13.7 Questions 501 14 Nitric oxide 503 14.1 Introduction 503 14.2 The structure of nitric oxide 503 14.3 The chemical properties of nitric oxide 504 14.3.1 Oxidation 505 14.3.2 Salt formation 506 14.3.3 Reaction as an electrophile 507 14.3.4 Reaction as an oxidising agent 507 14.3.5 Complex formation 508 14.3.6 Nitric oxide complexes with iron 508 14.3.7 The chemical properties of nitric oxide complexes 510 14.3.8 The chemistry of related compounds 512 14.4 The cellular production and role of nitric oxide 514 14.4.1 General mode of action 516 14.4.2 Suitability of nitric oxide as a chemical messenger 518 14.4.3 Metabolism 518 14.5 The role of nitric oxide in physiological and pathophysiological states 519 14.5.1 The role of nitric oxide in the cardiovascular system 519 14.5.2 The role of nitric oxide in the nervous system 520 14.5.3 Nitric oxide and diabetes 522 14.5.4 Nitric oxide and impotence 522 14.5.5 Nitric oxide and the immune system 523 14.6 Therapeutic possibilities 524 14.6.1 Compounds that reduce nitric oxide generation 524 14.6.2 Compounds that supply nitric oxide 526 14.6.3 The genetic approach 529 14.7 Questions 529 15 An introduction to drug and analogue synthesis 531 15.1 Introduction 531 15.2 Some general considerations 532 15.2.1 Starting materials 532 15.2.2 Practical considerations 532 15.2.3 The overall design 532 15.2.4 The use of protecting groups 533 15.3 Asymmetry in syntheses 534 15.3.1 The use of non-stereoselective reactions to produce stereospecific centres 535 15.3.2 The use of stereoselective reactions to produce stereogenetic centres 535 15.3.3 General methods of asymmetric synthesis 541 15.3.4 Methods of assessing the purity of stereoisomers 547 15.4 Designing organic syntheses 548 15.4.1 An introduction to the disconnection approach 548  CONTENTS xiii 15.4.2 Convergent synthesis 554 15.5 Partial organic synthesis of xenobiotics 556 15.6 Questions 557 16 Drug development and production 559 16.1 Introduction 559 16.2 Chemical development 560 16.2.1 Chemical engineering issues 561 16.2.2 Chemical plant: health and safety considerations 562 16.2.3 Synthesis quality control 563 16.2.4 A case study 563 16.3 Pharmacological and toxicological testing 565 16.4 Drug metabolism and pharmacokinetics 569 16.5 Formulation development 570 16.6 Production and quality control 570 16.7 Patent protection 571 16.8 Regulation 572 16.9 Questions 573 Selected further reading 575 Answers to questions 579 Index 601 Preface to the First Edition This book is written for second, and subsequent, year undergraduates studying for degrees in medicinal chemistry, pharmaceutical chemistry, pharmacy, pharmacology and other related degrees. It assumes that the reader has a knowledge of chemistry at level one of a university life sciences degree. The text discusses the chemical principles used for drug discovery and design with relevant physiology and biology introduced as required. Readers do not need any previous knowledge of biological subjects. Chapter 1 is intended to give an overview of the subject and also includes some topics of peripheral interest to medicinal chemists that are not discussed further in the text. Chapter 2 discusses the approaches used to discover and design drugs. The remaining chapters cover the major areas that have a direct bearing on the discovery and design of drugs. These chapters are arranged, as far as is possible, in a logical succession. The approach to medicinal chemistry is kept as simple as possible. Each chapter has a summary of its contents in which the key words are printed in bold type. The text is also supported by a set of questions at the end of each chapter. Answers, sometimes in the form of references to sections of the book, are listed separately. A list of recommended further reading, classified according to subject, is also included. Gareth Thomas Preface to the Second Edition This book is written for second and subsequent year undergraduates studying for degrees in medicinal chemistry, pharmaceutical chemistry, pharmacy, pharmacology and other related degrees. It assumes that the reader has a knowledge of chemistry at Level 1 of a university life science degree. The text discusses the chemical principles used for drug discovery and design with relevant physiology and biology introduced as required. Readers do not need any previous knowledge of biological subjects. The second edition of Medicinal Chemistry, an Introduction has a new layout that I hope presents the subject in a more logical form. The main changes are that Chapter 2 has been rewritten as three separate chapters, namely, structure–activity and quantitative structure relationships, computer-aided drug design and combinatorial chemistry. Two new chapters entitled Drugs from Natural Sources and Drug Development and Production have been added. The text has been simplified and extended where appropriate with a number of case histories, new examples and topics. Among the new topics are a discussion of monoclonal antibodies and photodynamic drugs. The inclusion of the new chapters and new material has necessitated a reduction in the biological and chemical introductions to some topics and the omission of some material included in the first edition. Furthermore, the reader should be aware that there are many more drugs and targets than those discussed in this text. Chapter 1 introduces and gives an overview of medicinal chemistry. This is followed by chapters that discuss the principal methods used in drug design and the isolation of drugs from natural sources. Chapters 7–14 are concerned with a discussion of more specialised aspects of medicinal chemistry. The final two chapters outline drug and analogue synthesis, development and production. Appropriate chapters have an outline introduction to the relevant biology. Each chapter is supported by a set of questions. Answers to these questions, sometimes in the form of references to sections and figures in the book, are listed separately. An updated list of further reading, classified according to subject, is also included. Gareth Thomas Acknowledgements I wish to thank all my colleagues and students, past and present, whose help enabled this second edition of my book to be written. In particular I would like to rethank all those who helped me with the first edition. I would like particularly to thank the following for their help with the second edition: Dr L. Banting; Dr J. Brown for once again acting as my living pharmacology dictionary; Dr P. Cox for his advice on molecular modelling; Dr J. Gray for proofreading the sections on monoclonal antibodies; Dr P. Howard for bringing me up to date with advances in combinatorial chemistry and allowing me to use his lecture notes; Dr Tim Mason, Mr A. Barrow and Dr D. Brimage; Dr A. Sautreau for proofreading and correcting Chapter 6; Robin Usher and his colleagues at Mobile Library Link One for their help in obtaining research papers; Dr. G. White; and Professor D. Thurston for his support. My thanks are also due to Dr J. Fetzer of Tecan Deutschland GmbH, Crailsheim, Germany for the pictures of the equipment used in high-throughput screening. I also wish to acknowledge that the main source of the historical information given in the text is Drug Discovery, a History, by W. Sneader, published by John Wiley and Sons Ltd. I would like to offer a very special thanks to the dedicated NHS medical teams who have treated my myeloma over the past years. Without their excellent care I would not have been here to have written this book. I would particularly like to thank Dr R. Corser, Dr T. Cranfield and the other doctors of the Haematology Department at the Queen Alexandra Hospital, Portsmouth, the nurses and ancillary staff of Ward D16, Queen Alexandra Hospital, Portsmouth, Dr K. Orchard, Dr C. Ottensmier and their respective staff at Southampton General Hospital and the nurses and ancillary staff of Wards C3 and C6 at Southampton General Hospital. Finally, I would like to thank my wife for the cover design for the first Edition and the sketches included in this text. Her support through the years has been an essential contribution to my completing the text.  ABBREVIATIONS xxi Abbreviations A Adenine Abe Abequose AC Adenylate cyclase ACE Angiotensin-converting enzymes ACh Acetyl choline ADAPT Antibody-directed abzyme prodrug therapy ADEPT Antibody-directed enzyme prodrug therapy ADME Absorption, distribution, metabolism and elimination ADR Adverse drug reaction AIDS Acquired immuno deficiency syndrome Ala Alanine AMP Adenosine monophosphate Arg Arginine Asp Aspartate ATP Adenosine triphosphate AUC Area under the curve AZT Zidovudine BAL British anti-Lewisite BESOD Bovine erythrocyte superoxide dismutase C Cytosine CaM Calmodulin cAMP Cyclic adenosine monophosphate Cbz N-(Benzyloxycarbonyloxy)succinamide Cl Clearance CNS Central nervous system CoA Coenzyme A CoMFA Comparative molecular field analysis CYP-450 Cytochrome P-450 family Cys Cysteine Cx Concentration of x dATP Deoxyadenosine triphosphate d.e. Diastereoisomeric excess DHF Dihydrofolic acid DHFR Dihydrofolate reductase DMPK Drug metabolism and pharmacokinetics DNA Deoxyribonucleic acid dTMP Deoxythymidylate-50 -monophosphate dUMP Deoxyuridylate-50 -monophosphate EC Enzyme Commission EDRF Endothelium-derived relaxing factor xxii ABBREVIATIONS EDTA Ethylenediaminotetraacetic acid e.e. Enantiomeric excess ELF Effluent load factor EMEA European Medicines Evaluation Agency EPC European Patent Convention EPO European Patent Office Es Taft steric parameter F Bioavailability FAD Flavin adenine dinucleotide FDA Food and Drug Administration (USA) FdUMP 5-Fluoro-20 -deoxyuridyline monophosphate FGI Functional group interconversion FH4 Tetrahydrofolate FMO Flavin monooxygenases Fmoc 9-Fluorenylmethoxychloroformyl group FUdRP 5-Fluoro-20 -deoxyuridylic acid G Guanine GABA g-Aminobutyric acid GC Guanylyl cyclase GDEPT Gene-directed enzyme prodrug therapy GDP Guanosine diphosphate GI Gastrointestinal Gln Glutamine Glu Glutamatic acid Gly Glycine 50 -GMP Guanosine 50 -monophosphate GSH Glutathione GTP Guanosine triphosphate HAMA Human anti-mouse antibodies Hb Haemoglobin HbS Sickle cell haemoglobin His Histidine HIV Human immunodeficiency disease hnRNA Heterogeneous nuclear RNA HTS High-throughput screening IDDM Insulin-dependent diabetes mellitus Ig Immunoglobins Ile Isoleucine IP3 Inositol-1,4,5-triphosphate IV Intravenous IM Intramuscular KDO 2-Keto-3-deoxyoctanoate kx Reaction rate constant for reaction x LDA Lithium diisopropylamide  ABBREVIATIONS xxiii LDH Lactose dehydrogenase Leu Leucine Lys Lysine MA(A) Marketing authorisation (application) Mab Monoclonal antibody mACh Muscarinic cholinergic receptor MAO Monoamine oxidase MCA Medicines Control Agency MESNA 2-Mercaptoethanesulphonate Met Methionine MO Molecular orbital Moz 4-Methoxybenzyloxychloroformyl group MR Molar refractivity mRNA Messenger RNA nACh Nicotinic cholinergic receptor NAD þ Nicotinamide adenine dinucleotide (oxidised form) NADH Nicotinamide adenine dinucleotide (reduced form) NADP þ Nicotinamide dinucleotide phosphate (oxidised form) NADPH Nicotinamide dinucleotide phosphate (reduced form) NAG b-N-Acetylglucosamine NAM b-N-Acetylmuramic acid NCI National Cancer Institute (USA) NOS Nitric oxide synthase P-450 Cytochrome P-450 oxidase PABA p-Aminobenzoic acid PCT Patent Cooperation Treaty PDT Photodynamic therapy PEG Polyethyene glycol PG Prostaglandin Phe Phenylalanine PO Per os (by mouth) pre-mRNA Premessenger RNA Pro Proline ptRNA Primary transcript RNA QSAR Quantitative structure–activity relationship Qx Rate of blood flow for x RMM Relative molecular mass RNA Ribonucleic acid S Svedberg units SAM S-Adenosylmethionine SAR Structure–activity relationship Ser Serine SIN-1 3-Morpholino-sydnomine T Thymine xxiv ABBREVIATIONS TdRP Deoxythymidylic acid THF Tetrahydrofolic acid Thr Threonine tRNA Transfer RNA Tyr Tyrosine U Uracil UDP Uridine diphosphate UDPGA Uridine diphosphate glucuronic acid UdRP Deoxyuridylic acid Val Valine Vd Volume of distribution WHO World Health Organization 1 An introduction to drugs, their action and discovery 1.1 Introduction The primary objective of medicinal chemistry is the design and discovery of new compounds that are suitable for use as drugs. This process involves a team of workers from a wide range of disciplines such as chemistry, biology, biochemistry, pharmacology, mathematics, medicine and computing, amongst others. The discovery or design of a new drug not only requires a discovery or design process but also the synthesis of the drug, a method of administration, the development of tests and procedures to establish how it operates in the body and a safety assessment. Drug discovery may also require fundamental research into the biological and chemical nature of the diseased state. These and other aspects of drug design and discovery require input from specialists in many other fields and so medicinal chemists need to have an outline knowledge of the relevant aspects of these fields. 1.2 What are drugs and why do we need new ones? Drugs are strictly defined as chemical substances that are used to prevent or cure diseases in humans, animals and plants. The activity of a drug is its pharmaceutical effect on the subject, for example, analgesic or b-blocker, whereas its potency is the quantitative nature of that effect. Unfortunately the term drug is also used by the media and the general public to describe the substances taken for their psychotic rather than medicinal effects. However, this does not mean that these substances cannot be used as drugs. Heroin, for example, is a very effective painkiller and is used as such in the form of diamorphine in terminal cancer cases. Medicinal Chemistry, Second Edition Gareth Thomas # 2007 John Wiley & Sons, Ltd 2 CH1 AN INTRODUCTION TO DRUGS, THEIR ACTION AND DISCOVERY CH3COO Heroin O NCH 3 CH3COO Drugs act by interfering with biological processes, so no drug is completely safe. All drugs, including those non-prescription drugs such as aspirin and paracetamol (Fig. 1.1) that are commonly available over the counter, act as poisons if taken in excess. For example, overdoses of paracetamol can causes coma and death. Furthermore, in addition to their beneficial effects most drugs have non-beneficial biological effects. Aspirin, which is commonly used to alleviate headaches, can also cause gastric irritation and occult bleeding in some people The non-beneficial effects of some drugs, such as cocaine and heroin, are so undesirable that the use of these drugs has to be strictly controlled by legislation. These unwanted effects are commonly referred to as side effects. However, side effects are not always non-beneficial; the term also includes biological effects that are beneficial to the patient. For example, the antihistamine promethazine is licenced for the treatment of hayfever but also induces drowsiness, which may aid sleep. Figure 1.1 Aspirin and paracetamol Drug resistance or tolerance (tachyphylaxis) occurs when a drug is no longer effective in controlling a medical condition. It arises in people for a variety of reasons. For example, the effectiveness of barbiturates often decreases with repeated use because the body develops mixed function oxidases in the liver that metabolise the drug, which reduces its effectiveness. The development of an enzyme that metabolises the drug is a relatively common reason for drug resistance. Another general reason for drug resistance is the downregulation of receptors (see section 8.6.1). Downregulation occurs when repeated stimulation of areceptor results in the receptor being broken down. This results in the drug being less effective because there are fewer receptors available for it to act on. However, downregulating has been utilised therapeutically in a number of cases. The continuous use  1.3 DRUG DISCOVERY AND DESIGN: A HISTORICAL OUTLINE 3 of gonadotrophin releasing factor, for example, causes gonadotrophin receptors that control the menstrual cycle to be downregulated. This is why gonadotrophin-like drugs are used as contraceptives. Drug resistance may also be due to the appearance of a significantly high proportion of drug-resistant strains of microorganisms. These strains arise naturally and can rapidly multiply and become the currently predominant strain of that microorganism. Antimalarial drugs are proving less effective because of an increase in the proportion of drug-resistant strains of the malaria parasite. New drugs are constantly required to combat drug resistance even though it can be minimised by the correct use of medicines by patients. They are also required for improving the treatment of existing diseases, the treatment of newly identified diseases and the production of safer drugs by the reduction or removal of adverse side effects. 1.3 Drug discovery and design: a historical outline Since ancient times the peoples of the world have had a wide range of natural products that they use for medicinal purposes. These products, obtained from animal, vegetable and mineral sources, were sometimes very effective. However, many of the products were very toxic and it is interesting to note that the Greeks used the same word pharmakon for both poisons and medicinal products. Information about these ancient remedies was not readily available to users until the invention of the printing press in the fifteenth century. This led to the widespread publication and circulation of Herbals and Pharmacopoeias, which resulted in a rapid increase in the use, and misuse, of herbal and other remedies. Misuse of tartar emetic (antimony potassium tartrate) was the reason for its use being banned by the Paris parliament in 1566, probably the first recorded ban of its type. The usage of such remedies reached its height in the seventeenth century. However, improved communica- tions between practitioners in the eighteenth and nineteenth centuries resulted in the progressive removal of preparations that were either ineffective or too toxic from Herbals and Pharmacopoeias. It also led to a more rational development of new drugs. The early nineteenth century saw the extraction of pure substances from plant material. These substances were of consistent quality but only a few of the compounds isolated proved to be satisfactory as therapeutic agents. The majority were found to be too toxic although many, such as morphine and cocaine for example, were extensively prescribed by physicians. The search to find less toxic medicines than those based on natural sources resulted in the introduction of synthetic substances as drugs in the late nineteenth century and their widespread use in the twentieth century. This development was based on the structures of known pharmacologically active compounds, now referred to as leads. The approach adopted by most nineteenth century workers was to synthesise structures related to that of the lead and test these compounds for the required activity. These lead-related compounds are now referred to as analogues. The first rational development of synthetic drugs was carried out by Paul Ehrlich and Sacachiro Hata who produced arsphenamine in 1910 by combining synthesis with reliable 4 CH1 AN INTRODUCTION TO DRUGS, THEIR ACTION AND DISCOVERY biological screening and evaluation procedures. Ehrlich, at the beginning of the nineteenth century, had recognised that both the beneficial and toxic properties of a drug were important to its evaluation. He realised that the more effective drugs showed a greater selectivity for the target microorganism than its host. Consequently, to compare the effectiveness of different compounds, he expressed a drug’s selectivity and hence its effectiveness in terms of its chemotherapeutic index, which he defined as: Minimum curative dose Chemotherapeutic index ¼ ð1:1Þ Maximum tolerated dose At the start of the nineteenth century Ehrlich was looking for a safer antiprotozoal agent with which to treat syphilis than the then currently used atoxyl. He and Hata tested and catalogued in terms of his therapeutic index over 600 structurally related arsenic compounds. This led to their discovery in 1909 that arsphenamine (Salvarsan) could cure mice infected with syphilis. This drug was found to be effective in humans but had to be used with extreme care as it was very toxic. However, it was used up to the mid- 1940s when it was replaced by penicillin. OH HCl.NH 2 NH 2.HCl H 2N As O HO As A s OH ONa Atoxyl Arsphenamine (Salvarsan) Ehrlich’s method of approach is still one of the basic techniques used to design and evaluate new drugs in medicinal chemistry. However, his chemotherapeutic index has been updated to take into account the variability of individuals and is now defined as its reciprocal, the therapeutic index or ratio: LD50 Therapeutic index ¼ ð1:2Þ ED50 where LD50 is the lethal dose required to kill 50 per cent of the test animals and ED50 is the dose producing an effective therapeutic response in 50 per cent of the test animals. In theory, the larger a drug’s therapeutic index, the greater is its margin of safety. However, because of the nature of the data used in their derivation, therapeutic index values can only be used as a limited guide to the relative usefulness of different compounds. The term structure–activity relationship (SAR) is now used to describe Ehrlich’s approach to drug discovery, which consisted of synthesising and testing a series of structurally related compounds (see Chapter 3). Although attempts to quantitatively relate chemical structure to biological action were first initiated in the nineteenth century, it was not until the 1960s that Hansch and Fujita devised a method that successfully incorporated quantitative measurements into structure–activity relationship determinations (see section 3.4.4). The technique is referred to as QSAR (quantitative structure–activity relationship).  1.3 DRUG DISCOVERY AND DESIGN: A HISTORICAL OUTLINE 5 QSAR methods have subsequently been expanded by a number of other workers. One of the most successful uses of QSAR has been in the development in the 1970s of the antiulcer agents cimetidine and ranitidine. Both SAR and QSAR are important parts of the foundations of medicinal chemistry. H CH 3 NCN CHNO 2 N CH 2 SCH 2 CH 2 NHCNHCH 3 (CH 3) 2NCH 2 CH 2 SCH 2 CH 2 NHCNHCH 3 N O Cimetidine Ranitidine At the same time as Ehrlich was investigating the use of arsenical drugs to treat syphilis, John Langley formulated his theory of receptive substances. In 1905 Langley proposed that so-called receptive substances in the body could accept either a stimulating compound, which would cause a biological response, or a non-stimulating compound, which would prevent a biological response. These ideas have been developed by subsequent workers and the theory of receptors has become one of the fundamental concepts of medicinal chemistry. Receptor sites (see Chapter 8) usually take the form of pockets, grooves or other cavities in the surface of certain proteins and glycoproteins in the living organism. They should not be confused with active sites (see section 9.3), which are the regions of enzymes where metabolic chemical reactions occur. It is now accepted that the binding of a chemical agent, referred to as a ligand (see section 8.1), to a receptor sets in motion a series of biochemical events that result in a biological or physiological effect. Furthermore, a drug is most effective when its structure or a significant part of its structure, both as regards molecular shape and electron distribution (stereoelectronic structure), is complementary with the stereoelectronic structure of the receptor responsible for the desired biological action. Since most drugs are able to assume a number of different conformations, the conformation adopted when the drug binds to the receptor is known as its active conformation. The section of the structure of a ligand that binds to a receptor is known as its pharmacophore. The sections of the structure of a ligand that comprise a pharmacophore may or may not be some distance apart in that structure. They do not have to be adjacent to one another. For example, the quaternary nitrogens that are believed to form the pharmacophore of the neuromuscular blocking agent tubocrarine are separated in the molecule by a distance of 115.3 nm. O CH3 + CH3 N HO CH3 O H Tubocrarine CH3 H + O N OH CH3 OCH3 6 CH1 AN INTRODUCTION TO DRUGS, THEIR ACTION AND DISCOVERY The concept of receptors also gives a reason for side effects and a rational approach to ways of eliminating their worst effects. It is now believed that side effects can arise when the drug binds to either the receptor responsible for the desired biological response or to different receptors. The mid- to late twentieth century has seen an explosion of our understanding of the chemistry of disease states, biological structures and processes. This increase in knowledge has given medicinal chemists a clearer picture of how drugs are distributed through the body, transported across membranes, their mode of operation and metabolism. This knowledge has enabled medicinal chemists to place groups that influence its absorption, stability in a bio-system, distribution, metabolism and excretion into the molecular structure of a drug. For example, the in situ stability of a drug and hence its potency could be increased by rationally modifying the molecular structure of the drug. Esters and N-substituted amides, for example, have structures with similar shapes and electron distributions (Fig. 1.2a) but N-substituted amides hydrolyse more slowly than esters. Consequently, the replacement of an ester group by an N-substituted amide group may increase the stability of the drug without changing the nature of its activity. This could possibly lead to an increase in either the potency or time of duration of activity of a drug by improving its chances of reaching its site of action. However, changing a group or introducing a group may change the nature of the activity of the compound. For example, the change of the ester group in procaine to an amide (procainamide) changes the activity from a local anaesthetic to an antiarrhythmic (Fig. 1.2b)..... R O: R O: C C......O 1 N 1 R H R Ester group Amide group (a) H2 N COOCH2 CH2 N(C2 H5 )2 H2 N CONHCH 2 CH2 N(C2 H5)2 Procaine Procainamide (b) Figure 1.2 (a) The similar shapes and outline electronic structures (stereoelectronic structures) of amide and ester groups. (b) Procaine and procainamide Drugs normally have to cross non-polar lipid membrane barriers (see sections 7.2 and 7.3) in order to reach their site of action. As the polar nature of the drug increases it usually becomes more difficult for the compound to cross these barriers. In many cases drugs whose structures contain charged groups will not readily pass through membranes. Consequently, charged structures can be used to restrict the distribution of a drug. For example, quaternary ammonium salts, which are permanently charged, can be used as an alternative to an amine in a structure in order to restrict the passage of a drug across a membrane. The structure of the anticholinesterase neostigmine, developed from physostigmine, contains a quaternary  1.3 DRUG DISCOVERY AND DESIGN: A HISTORICAL OUTLINE 7 ammonium group that gives the molecule a permanent charge. This stops the molecule from crossing the blood–brain barrier, which prevents unwanted CNS activity. However, its analogue miotine can form the free base. As a result, it is able to cross lipid membranes and causes unwanted CNS side effects. CH3 OCONHCH 3 + Me3N OCONMe 2 N CH3 N CH3 Neostigmine Physostigmine Me + OCONHMe Me Me2 NH Bases OCONHMe Me2 N Acids Miotine Serendipity has always played a large part in the discovery of drugs. For example, the development of penicillin by Florey and Chain was only possible because Alexander Fleming noted the inhibition of staphylococcus by Penicillium notatum. In spite of our increased knowledge base, it is still necessary to pick the correct starting point for an investigation if a successful outcome is to be achieved and luck still plays a part in selecting that point. This state of affairs will not change and undoubtedly luck will also lead to new discoveries in the future. However, modern techniques such as computerised molecular modelling (see Chapter 4) and combinatorial chemistry (see Chapter 5) introduced in the 1970s and 1990s, respectively, are likely to reduce the number of intuitive discoveries. Two of the factors necessary for drug action are that the drug fits and binds to the target. Molecular modelling allows the researcher to predict the three-dimensional shapes of molecules and target. It enables workers to check whether the shape of a potential lead is complementary to the shape of its target. It also allows one to calculate the binding energy liberated when a molecule binds to its target (see section 4.6). Molecular modelling has reduced the need to synthesise every analogue of a lead compound. It is also often used retrospectively to confirm the information derived from other sources. Combinatorial chemistry originated in the field of peptide chemistry but has now been expanded to cover other areas. It is a group of related techniques for the simultaneous production of large numbers of compounds, known as libraries, for biological testing. Consequently, it is used for structure–activity studies and to discover new lead compounds. The procedures may be automated. 1.3.1 The general stages in modern-day drug discovery and design At the beginning of the nineteenth century drug discovery and design was largely carried out by individuals and was a matter of luck rather than structured investigation. Over the last century, a large increase in our general scientific knowledge means that today drug discovery 8 CH1 AN INTRODUCTION TO DRUGS, THEIR ACTION AND DISCOVERY requires considerable teamwork, the members of the team being specialists in various fields, such as medicine, biochemistry, chemistry, computerised molecular modelling, pharmaceu- tics, pharmacology, microbiology, toxicology, physiology and pathology. The approach is now more structured but a successful outcome still depends on a certain degree of luck. The modern approach to drug discovery/design depends on the objectives of the project. These objectives can range from changing the pharmacokinetics of an existing drug to discovering a completely new compound. Once the objectives of the project have been decided the team will select an appropriate starting point and decide how they wish to proceed. For example, if the objective is to modify the pharmacokinetics of an existing drug the starting point is usually that the drug and design team has to decide what structural modifications need to be investigated in order to achieve the desired modifications. Alternatively, if the objective is to find a new drug for a specific disease the starting point may be a knowledge of the biochemistry of the disease and/or the microorganism responsible for that disease (Fig. 1.3). This may require basic research into the biochemistry of the disease Basic research into the disease process and its causes Assessment of the biochemical and biological processes of the disease and/or its cause Team decides where intervention is most likely to bring about the desired result Team decides the structure of a suitable lead compound Design of the synthetic pathway to produce the lead compound Initial biological and toxicological testing Synthesis of analogues Selection of the analogue with the optimum activity Clinical trials and MAA Figure 1.3 The general steps in the discovery of a new drug for a specific disease state causing process before initiating the drug design investigation. The information obtained is used by the team to decide where intervention would be most likely to bring about the desired result. Once the point of intervention has been selected the team has to decide on the structure of a compound, referred to as a lead compound, that could possibly bring about the required change. A number of candidates are usually considered but the expense of producing drugs dictates that the team has to choose only one or two of these compounds to act as the lead compound. The final selection depends on the experience of the research team. Lead compounds are obtained from a variety of sources that range from extracting compounds from natural sources (see Chapter 6), synthesis using combinatorial chemistry  1.4 LEADS AND ANALOGUES: SOME DESIRABLE PROPERTIES 9 (see Chapter 5), searching data bases and compound collections (see section 1.5.6) for suitable candidates and ethnopharmacological sources (see section 1.5.1). However, whatever the objective and starting point, all investigations start with the selection of a suitable bioassay(s) (see section 6.2), which will indicate whether the compound is likely to be active against the diseased state and also if possible the potency of active compounds. These assays are often referred to as screening programmes. They may also be carried out at different stages in drug discovery in order to track active compounds. Once an active lead has been found, it is synthesised and its activity determined. SAR studies (see Chapter 3) are then carried out by synthesising and testing compounds, referred to as analogues, that are structurally related to the lead in order to find the structure with the optimum activity. These studies may make use of QSAR (see section 3.4) and computational chemistry (see Chapter 4) to help discover the nature of this optimum structure for activity. This analogue would, if economically viable, be developed and ultimately, if it met the MAA regulations, placed in clinical use (see Chapter 16). 1.4 Leads and analogues: some desirable properties 1.4.1 Bioavailability The activity of a drug is related to its bioavailability, which is defined as the fraction of the dose of a drug that is found in general circulation (see section 11.5). Consequently, for a compound to be suitable as a lead it must be bioavailable. In order to assess a compound’s bioavailability it must be either available off the shelf or be synthesised. Synthesis of a compound could result in the synthesis of an inactive compound, which could be expensive both in time and money. In order to avoid unnecessary work and expense in synthesising inactive molecules, Lipinski et al. proposed a set of four rules that would predict whether a molecule was likely to be orally bioavailable. These rules may be summarised as having:
a molecular mass less than 500;
a calculated value of log P less than 5;
less than ten hydrogen bond acceptor groups (e.g. -O- and -N-, etc.);
less than five hydrogen bond donor groups (e.g. NH and OH, etc.). where P is the calculated partition coefficient for the octanol/water system (see section 2.12.1). Any compound that fails to comply with two or more of the rules is unlikely to be bioavailable, that is, it is unlikely to be active. Lipinski’s rules are based on multiples of five and so are often referred to as the rule of fives. Other researchers have developed similar methods to assess the bioavailability of molecules prior to their synthesis. However, it should be realised that Lipinski’s and other similar rules are only guidelines. 10 CH1 AN INTRODUCTION TO DRUGS, THEIR ACTION AND DISCOVERY 1.4.2 Solubility Solubility is discussed in more detail in Chapter 2. However, a requirement for compounds that are potential drug candidates is that they are soluble to some extent in both lipids and water. Compounds that readily dissolve in lipid solvents are referred to as lipophilic or hydrophobic compounds. Their structures often contain large numbers of non-polar groups, such as benzene rings and ether and ester functional groups. Compounds that do not readily dissolve in lipids but readily dissolve in water are known as hydrophilic or lipophobic compounds. Their structures contain polar groups such as acid, amine and hydroxy functional groups. The balance between the polar and non-polar groups in a molecule defines its lipophilic character: compounds with a high degree of lipophilic character will have a good lipid solubility but a poor water solubility; conversely, compounds with a low degree of lipophilic character will tend to be poorly soluble in lipids but have a good solubility in water. It is desirable that leads and analogues have a balance between their water solubility and their lipophilicity. Most drugs are administered either as aqueous or solid preparations and so need to be water soluble in order to be transported through the body to its site of action. Consequently, poor water solubility can hinder or even prevent the development of a good lead or analogue. For example, one of the factors that hindered the development of the anticancer drug taxol was its poor water solubility. This made it difficult to obtain a formulation for administrationby intravenous infusion, the normal route for anticancer drugs (see section 6.8). However, careful design of the form in which the drug is administered (the dosage form) can in many instances overcome this lack of water solubility (see sections 2.13 and 6.8). Drugs also require a degree of lipid solubility in order to pass through membranes (see section 7.3.3). However, if it has too high a degree of lipophilicity it may become trapped in a membrane and so become ineffective. The lipophilicity of a compound is often represented by the partition coefficient of that compound in a defined solvent system (see section 2.12.1). 1.4.3 Structure The nature of the structures of leads and analogues will determine their ability to bind to receptors and other target sites. Binding is the formation, either temporary or permanent, of chemical bonds between the drug or analogue with the receptor (see sections 2.2 and 8.2). Their nature will influence the operation of a receptor. For example, the binding of most drugs or analogues takes the form of an equilibrium (see section 8.6.1) in which the drug or analogue forms weak, electrostatic bonds, such as hydrogen bonds and van der Waals’ forces, with the receptor. Ultimately the drug or analogue is removed from the vicinity of the receptor by natural processes and this causes the biological processes due to the receptor’s activity to stop. For example, it is thought that the local anaesthetic benzocaine (see section 7.4.3) acts in this manner. However, some drugs and analogues act by forming strong covalent bonds with the receptor and either prevent it operating or increase its  1.4 LEADS AND ANALOGUES: SOME DESIRABLE PROPERTIES 11 duration of operation. For example, melphalan, which is used to treat cancer, owes its action to the strong covalent bonds it forms with DNA (see section 10.13.4). Cl NH 2 HOOCCHCH 2 N Melphalan Cl A major consideration in the selection of leads and analogues is their stereochemistry. It is now recognised that the biological activities of the individual enantiomers and their racemates may be very different (see section 2.3 and Table 1.1). Consequently, it is necessary to pharmacologically evaluate individual enantiomers as well as any racemates. However, it is often difficult to obtain specific enantiomers in a pure state (see section 15.3). Both of these considerations make the production of optically active compounds expensive and so medicinal chemists often prefer to synthesise lead compounds that are not optically active. However, this is not always possible and a number of strategies exist to produce compounds with specific stereochemical centres (see sections 6.5 and 15.3). 1.4.4 Stability Drug stability can be broadly divided into two main areas: stability after administration and shelf-life. Stability after administration A drug will only be effective if, after administration, it is stable enough to reach its target site in sufficient concentration (see section 1.6) to bring about the desired effect. However, as soon as a drug is administered the body starts to remove it by metabolism (see section 1.7.1 and Chapter 12). Consequently, for a drug to be effective it must be stable long enough after administration for sufficient quantities of it to reach its target site. In other words, it must not be metabolised too quickly in the circulatory system. Three strategies are commonly used for improving a drug’s in situ stability, namely:
modifying its structure;
administering the drug as a more stable prodrug (see section 12.9.4);
using a suitable dosage form (see section 1.6). The main method of increasing drug stability in the biological system is to prepare a more stable analogue with the same pharmacological activity. For example, pilocarpine, 12 CH1 AN INTRODUCTION TO DRUGS, THEIR ACTION AND DISCOVERY Table 1.1 Variations in the biological activities of stereoisomers First stereoisomer Second stereoisomer Example Active Activity of same type The R and S isomers of the antimalarial and potency chloroquine have equal potencies Cl N NHCH(CH3 )CH2 CH2 CH2 N(C2 H5 )2 Active Activity of same type The E isomer of diethylstilbestrol, an oestrogen but weaker, is only 7% as active as the Z isomer C 2 H5 OH HO C2H5 Active Activity of a different type S-Ketamine is an anaesthetic whereas R-Ketamine has little anaesthetic action but is a psychotic agent O NHCH3 Ketamine Cl Active No activity S-a-Methyldopa is a hypertensive drug but the R isomer is inactive HO S- α -Methyldopa COOH HO CH 2 NH 2 CH 3 Active Active but different Thalidomide: the S isomer is a sedative and side effects has teratogenic side effects; the R isomer is also a sedative but has no teratogenic activity O S-Thalidomide H N O NH O O which is used to control glaucoma, rapidly loses it activity because the lactone ring readily opens under physiological conditions. Consequently, the lowering of intraocular pressure by pilocarpine lasts for about three hours, necessitating administration of 3–6 doses a day. However, the replacement of C-2 of pilocarpine by a nitrogen yields an isosteric carbamate  1.4 LEADS AND ANALOGUES: SOME DESIRABLE PROPERTIES 13 that has the same potency as pilocarpine but is more stable. Although this analogue was discovered in 1989 it has not been accepted for clinical use. C-2 N N N N N N N Hydrolysis HOOC O O O O HO Pilocarpine Carbamate analogue The in situ stability of a drug may also be improved by forming a complex with a suitable reagent. For example, complexing with hydroxypropyl-b-cyclodextrin is used to improve both the stability and solubility of thalidomide, which is used to inhibit rejection of bone marrow transplants in the treatment of leukaemia. The half-life of a dilute solution of the drug is increased from 2.1 to 4.1 hours while its aqueous solubility increases from 50 to 1700 mg ml.  1 Cyclodextrins are bottomless flower-pot-shaped cylindrical oligosaccharides consisting of about 6–8 glucose units. The exterior of the ‘flower-pot’ is hydrophilic in character whilst the interior has a hydrophobic nature. Cyclodextrins are able to form inclusion complexes in which part of the guest molecule is held within the flower-pot structure (Fig. 1.4). The hydrophobic nature of the interior of the cyclodextrin structure probably means that hydrophobic interaction plays a large part in the formation and stability of the complex. Furthermore, it has been found that the stability of a drug in situ is often improved when the active site of a drug lies within the cylinder and decreased when it lies outside the cylinder. In addition, it has been noted that the formation of these complexes may improve the water solubility, bioavailability and pharmacological action and reduce the side effects of some drugs. However, a high concentration of cyclodextrins in the blood stream can cause nephrotoxicity. COOH COOH COOH Figure 1.4 Schematic representations of the types of inclusion complexes formed by cyclodextrins and prostaglandins. The type of complex formed is dependent on the cavity size Prodrug formation can also be used to improve drug stability. For example, cyclopho- sphamide, which is used to treat a number of carcinomas and lymphomas, is metabolised in 14 CH1 AN INTRODUCTION TO DRUGS, THEIR ACTION AND DISCOVERY the liver to the corresponding phosphoramidate mustard, the active form of the drug. H N O H2 N O P CH2 CH2 Cl P CH2 CH2 Cl O N HO N CH2 CH2 Cl CH2 CH2 Cl Cyclophosphamide Phosphoramidate mustard The highly acidic gastric fluids can cause extensive hydrolysis of a drug in the gastrointestinal tract (GI tract). This will result in poor bioavailability. However, drug stability in the gastrointestinal tract can be improved by the use of enteric coatings, which dissolve only when the drug reaches the small intestine. In many cases, but not all (see sections 2.2 and 8.2), once a drug has carried out its function it needs to be removed from the body. This occurs by metabolism and excretion and so a potential drug should not be too stable that it is not metabolised. Furthermore, the drug should not accumulate in the body but be excreted. These aspects of drug stability should be investigated in the preclinical and clinical investigations prior to the drug’s release onto the market. Shelf-life Shelf-life is the time taken for a drug’s pharmacological activity to decline to an unacceptable level. This level depends on the individual drug and so there is no universal specification. However, 10 per cent decomposition is often taken as an acceptable limit provided that the decomposition products are not toxic. Shelf-life deterioration occurs through microbial degradation and adverse chemical interactions and reactions. Microbial deterioration can be avoided by preparing the dosage form in the appropriate manner and storage under sterile conditions. It can also be reduced by the use of antimicrobial excipients. Adverse chemical interactions between the components of a dosage form can also be avoided by the use of suitable excipients. Decomposition by chemical reaction is usually brought about by heat, light, atmospheric oxidation, hydrolysis by atmospheric moisture and racemisation. These may be minimised by correct storage with the use of refrigerators, light-proof containers, air-tight lids and the appropriate excipients. 1.5 Sources of leads and drugs Originally drugs and leads were derived from natural sources. These natural sources are still important sources of lead compounds and new drugs, however the majority of lead compounds are now discovered in the laboratory using a variety of sources, such as local folk remedies (ethnopharmacology), investigations into the biochemistry of the pathology  1.5 SOURCES OF LEADS AND DRUGS 15 of disease states and high-throughput screening of compound collections (see Chapter 5), databases and other literature sources of organic compounds. 1.5.1 Ethnopharmaceutical sources The screening of local folk remedies (ethnopharmacology) has been a fruitful source of lead compounds and many important therapeutic agents. For example, the antimalarial quinine from cinchona bark, the cardiac stimulants from foxgloves (Fig. 1.5) and the antidepressant reserpine isolated from Rauwolfia serpentina. Figure 1.5 Digitalis purpurea, the common foxglove. The leaves contain about 30 different cardioactive compounds. The major components of this mixture are glycosides, with aglycones of digitoxigenin, gitox- igenin and gitaloxigenin. Two series of compounds are known, those where R, the carbohydrate residue (glycone) of the glycoside, is either a tetrasaccharide or a trisaccharide chain. Many of the compounds isolated were formed by drying of the leaves prior to extraction. Digitoxin, a trisaccharide derivative of digitoxigenin, is the only compound to be used clinically to treat congestive heart failure and cardiac arrhythmias 1.5.2 Plant sources In medicinal chemistry, ‘plant’ includes trees, bushes, grasses, etc., as well as what one normally associates with the term plant. All parts of a plant, from roots to seed heads and flowers, can act as the source of a lead. However, the collecting of plant samples must be carried out with due consideration of its environmental impact. In order to be able to repeat 16 CH1 AN INTRODUCTION TO DRUGS, THEIR ACTION AND DISCOVERY the results of a collection and if necessary cultivate the plant to ensure supplies of the compounds produced by the plant, it is essential that a full botanical record of the plant is made if it does not already exist. This record should contain a description and pictures of the plant and any related species, where it was found (GPS coordinates) and its growing conditions. A detailed record of the collection of the samples taken must also be kept since the chemical constitution of a plant can vary with the seasons, the method used for its collection, its harvest site storage and method of preparation for onward transportation to the investigating laboratory. If the plant material is to be shipped to a distant destination it must be protected from decomposition by exposure to inappropriate environmental conditions, such as a damp atmosphere or contamination by insects, fungi and micro- organisms.. The drying of so-called green samples for storage and shipment can give rise to chemical constituent changes because of enzyme action occurring during the drying process. Consequently, extraction of the undried green sample is often preferred, especially as chemical changes due to enzyme action is minimised when the green sample is extracted with aqueous ethanol. Plant samples are normally extracted and put through screening programmes (see Chapter 6). Once screening shows that a material contains an active compound the problem becomes one of extraction, purification and assessment of the pharmacological activity. However, the isolation of a pure compound of therapeutic value can cause ecological problems. The anticancer agent Taxol (Fig. 1.6), for example, was isolated from the bark of O HO CH3 COO OH C6 H5 CONH O CH3 CH3 CH3 O H C6 H 5 NCH3 CH3 OH H O HO OH C6 H5 COO OCOCH3 Morphine OH Taxol N C 2 H5 CH3 H N N O N H N C2 H5 CH3 OOC H H O CH3 O N OCOCH3 CH3 H COOCH3 CHO OH Pilocarpine Vincristine Figure 1.6 Examples of some of the drugs in clinical use obtained from plants. Taxol and vincristine are anticancer agents isolated from Taxus breifolia and Vinca rosea Linn, respectively. Pilocarpine is used to treat glaucoma and is obtained from Pilocarpus jaborandi Holmes Rutaceae. Morphine, which is used as an analgesic, is isolated from the opium poppy  1.5 SOURCES OF LEADS AND DRUGS 17 the Pacific Yew tree (see section 6.8). Its isolation from this source requires the destruction of this slow-growing tree. Consequently, the production of large quantities of Taxol from the Pacific Yew could result in the wholesale destruction of the tree, a state of affairs that is ecologically unacceptable. A different approach to identifying useful sources is that used by Hostettmann and Marston, who deduced that owing to the climate African plants must be resistant to constant fungal attack because they contain biologically active constituents. This line of reasoning led them to discover a variety of active compounds (Fig. 1.7). OR O O OH