Fragment-based Approaches in Drug Discovery: (34 Methods & Principles in Medicinal Chemistry)

This first systematic summary of the impact of fragment-based approaches on the drug development process provides essential information that was previously unavailable. Adopting a practice-oriented approach, this represents a book by professionals for professionals, tailor-made for drug developers in the pharma and biotech sector who need to keep up-to-date on the latest technologies and strategies in pharmaceutical ligand design. The book is clearly divided into three sections on ligand design, spectroscopic techniques, and screening and drug discovery, backed by numerous case studies.

Table of Contents:
Preface xv A Personal Foreword xvii List of Contributors xix Part I: Concept and Theory 1 The Concept of Fragment-based Drug Discovery 3 Daniel A. Erlanson and Wolfgang Jahnke 1.1 Introduction 3 1.2 Starting Small: Key Features of Fragment-based Ligand Design 4 1.2.1 FBS Samples Higher Chemical Diversity 4 1.2.2 FBS Leads to Higher Hit Rates 5 1.2.3 FBS Leads to Higher Ligand Efficiency 6 1.3 Historical Development 6 1.4 Scope and Overview of this Book 7 References 9 2 Multivalency in Ligand Design 11 Vijay M. Krishnamurthy, Lara A. Estroff, and George M. Whitesides 2.1 Introduction and Overview 11 2.2 Definitions of Terms 12 2.3 Selection of Key Experimental Studies 16 2.3.1 Trivalency in a Structurally Simple System 17 2.3.2 Cooperativity (and the Role of Enthalpy) in the “Chelate Effect“ 18 2.3.3 Oligovalency in the Design of Inhibitors to Toxins 18 2.3.4 Bivalency at Well Defined Surfaces (Self-assembled Monolayers, SAMs) 18 2.3.5 Polyvalency at Surfaces of Viruses, Bacteria, and SAMs 18 2.4 Theoretical Considerations in Multivalency 19 2.4.1 Survey of Thermodynamics 19 2.4.2 Additivity and Multivalency 19 2.4.3 Avidity and Effective Concentration (Ceff) 22 2.4.4 Cooperativity is Distinct from Multivalency 24 2.4.5 Conformational Entropy of the Linker between Ligands 25 2.4.6 Enthalpy/Entropy Compensation Reduces the Benefit of Multivalency 26 2.5 Representative Experimental Studies 26 2.5.1 Experimental Techniques Used to Examine Multivalent Systems 26 2.5.1.1 Isothermal Titration Calorimetry 26 2.5.1.2 Surface Plasmon Resonance Spectroscopy 27 2.5.1.3 Surface Assays Using Purified Components (Cell-free Assays) 27 2.5.1.4 Cell-based Surface Assays 27 2.5.2 Examination of Experimental Studies in the Context of Theory 28 2.5.2.1 Trivalency in Structurally Simple Systems 28 2.5.2.2 Cooperativity (and the Role of Enthalpy) in the “Chelate Effect“ 29 2.5.2.3 Oligovalency in the Design of Inhibitors of Toxins 29 2.5.2.4 Bivalency in Solution and at Well Defined Surfaces (SAMs) 30 2.5.2.5 Polyvalency at Surfaces (Viruses, Bacteria, and SAMs) 31 2.6 Design Rules for Multivalent Ligands 32 2.6.1 When Will Multivalency Be a Successful Strategy to Design Tight-binding Ligands? 32 2.6.2 Choice of Scaffold for Multivalent Ligands 33 2.6.2.1 Scaffolds for Oligovalent Ligands 33 2.6.2.2 Scaffolds for Polyvalent Ligands 35 2.6.3 Choice of Linker for Multivalent Ligands 36 2.6.3.1 Rigid Linkers Represent a Simple Approach to Optimize Affinity 36 2.6.3.2 Flexible Linkers Represent an Alternative Approach to Rigid Linkers to Optimize Affinity 37 2.6.4 Strategy for the Synthesis of Multivalent Ligands 37 2.6.4.1 Polyvalent Ligands: Polymerization of Ligand Monomers 38 2.6.4.2 Polyvalent Ligands: Functionalization with Ligands after Polymerization 38 2.7 Extensions of Multivalency to Lead Discovery 39 2.7.1 Hetero-oligovalency is a Broadly Applicable Concept in Ligand Design 39 2.7.2 Dendrimers Present Opportunities for Multivalent Presentation of Ligands 40 2.7.3 Bivalency in the Immune System 40 2.7.4 Polymers Could Be the Most Broadly Applicable Multivalent Ligands 42 2.8 Challenges and Unsolved Problems in Multivalency 44 2.9 Conclusions 44 Acknowledgments 45 References 45 3 Entropic Consequences of Linking Ligands 55 Christopher W. Murray and Marcel L. Verdonk 3.1 Introduction 55 3.2 Rigid Body Barrier to Binding 55 3.2.1 Decomposition of Free Energy of Binding 55 3.2.2 Theoretical Treatment of the Rigid Body Barrier to Binding 56 3.3 Theoretical Treatment of Fragment Linking 57 3.4 Experimental Examples of Fragment Linking Suitable for Analysis 59 3.5 Estimate of Rigid Body Barrier to Binding 61 3.6 Discussion 62 3.7 Conclusions 64 References 65 4 Location of Binding Sites on Proteins by the Multiple Solvent Crystal Structure Method 67 Dagmar Ringe and Carla Mattos 4.1 Introduction 67 4.2 Solvent Mapping 68 4.3 Characterization of Protein–Ligand Binding Sites 69 4.4 Functional Characterization of Proteins 71 4.5 Experimental Methods for Locating the Binding Sites of Organic Probe Molecules 71 4.6 Structures of Elastase in Nonaqueous Solvents 72 4.7 Organic Solvent Binding Sites 73 4.8 Other Solvent Mapping Experiments 75 4.9 Binding of Water Molecules to the Surface of a Protein 78 4.10 Internal Waters 79 4.11 Surface Waters 80 4.12 Conservation of Water Binding Sites 81 4.13 General Properties of Solvent and Water Molecules on the Protein 82 4.14 Computational Methods 83 4.15 Conclusion 85 Acknowledgments 85 References 85 Part 2: Fragment Library Design and Computional Approaches 5 Cheminformatics Approaches to Fragment-based Lead Discovery 91 Tudor I. Oprea and Jeffrey M. Blaney 5.1 Introduction 91 5.2 The Chemical Space of Small Molecules (Under 300 a.m.u.) 92 5.3 The Concept of Lead-likeness 94 5.4 The Fragment-based Approach in Lead Discovery 96 5.5 Literature-based Identification of Fragments: A Practical Example 99 5.6 Conclusions 107 Acknowledgments 109 References 109 6 Structural Fragments in Marketed Oral Drugs 113 Michal Vieth and Miles Siegel 6.1 Introduction 113 6.2 Historical Look at the Analysis of Structural Fragments of Drugs 113 6.3 Methodology Used in this Analysis 115 6.4 Analysis of Similarities of Different Drug Data Sets Based on the Fragment Frequencies 118 6.5 Conclusions 123 Acknowledgments 124 References 124 7 Fragment Docking to Proteins with the Multi-copy Simultaneous Search Methodology 125 Collin M. Stultz and Martin Karplus 7.1 Introduction 125 7.2 The MCSS Method 125 7.2.1 MCSS Minimizations 126 7.2.2 Choice of Functional Groups 126 7.2.3 Evaluating MCSS Minima 127 7.3 MCSS in Practice: Functionality Maps of Endothiapepsin 132 7.4 Comparison with GRID 135 7.5 Comparison with Experiment 137 7.6 Ligand Design with MCSS 138 7.6.1 Designing Peptide-based Ligands to Ras 138 7.6.2 Designing Non-peptide Based Ligands to Cytochrome P450 140 7.6.3 Designing Targeted Libraries with MCSS 140 7.7 Protein Flexibility and MCSS 141 7.8 Conclusion 143 Acknowledgments 144 References 144 Part 3: Experimental Techniques and Applications 8 NMR-guided Fragment Assembly 149 Daniel S. Sem 8.1 Historical Developments Leading to NMR-based Fragment Assembly 149 8.2 Theoretical Foundation for the Linking Effect 150 8.3 NMR-based Identification of Fragments that Bind Proteins 152 8.3.1 Fragment Library Design Considerations 152 8.3.2 The “SHAPES” NMR Fragment Library 154 8.3.3 The “SAR by NMR“ Fragment Library 156 8.3.4 Fragment-based Classification of protein Targets 160 8.4 NMR-based Screening for Fragment Binding 163 8.4.1 Ligand-based Methods 163 8.4.2 Protein-based Methods 165 8.4.3 High-throughput Screening: Traditional and TINS 167 8.5 NMR-guided Fragment Assembly 167 8.5.1 SAR by NMR 167 8.5.2 SHAPES 169 8.5.3 Second-site Binding Using Paramagnetic Probes 169 8.5.4 NMR-based Docking 170 8.6 Combinatorial NMR-based Fragment Assembly 171 8.6.1 NMR SOLVE 171 8.6.2 NMR ACE 173 8.7 Summary and Future Prospects 176 References 177 9 SAR by NMR: An Analysis of Potency Gains Realized Through Fragmentlinking and Fragment-elaboration Strategies for Lead Generation 181 Philip J. Hajduk, Jeffrey R. Huth, and Chaohong Sun 9.1 Introduction 181 9.2 SAR by NMR 182 9.3 Energetic Analysis of Fragment Linking Strategies 183 9.4 Fragment Elaboration 187 9.5 Energetic Analysis of Fragment Elaboration Strategies 188 9.6 Summary 190 References 191 10 Pyramid: An Integrated Platform for Fragment-based Drug Discovery 193 Thomas G. Davies, Rob L. M. van Montfort, Glyn Williams, and Harren Jhoti 10.1 Introduction 193 10.2 The Pyramid Process 194 10.2.1 Introduction 194 10.2.2 Fragment Libraries 195 10.2.2.1 Overview 195 10.2.2.2 Physico-chemical Properties of Library Members 196 10.2.2.3 Drug Fragment Library 197 10.2.2.4 Privileged Fragment Library 197 10.2.2.5 Targeted Libraries and Virtual Screening 197 10.2.2.6 Quality Control of Libraries 201 10.2.3 Fragment Screening 201 10.2.4 X-ray Data Collection 202 10.2.5 Automation of Data Processing 203 10.2.6 Hits and Diversity of Interactions 205 10.2.6.1 Example 1: Compound 1 Binding to CDK2 205 10.2.6.2 Example 2: Compound 2 Binding to p38_ 207 10.2.6.3 Example 3: Compound 3 Binding to Thrombin 207 10.3 Pyramid Evolution – Integration of Crystallography and NMR 207 10.3.1 NMR Screening Using Water-LOGSY 208 10.3.2 Complementarity of X-ray and NMR Screening 210 10.4 Conclusions 211 Acknowledgments 211 References 212 11 Fragment-based Lead Discovery and Optimization Using X-Ray Crystallography, Computational Chemistry, and High-throughput Organic Synthesis 215 Jeff Blaney,Vicki Nienaber, and Stephen K. Burley 11.1 Introduction 215 11.2 Overview of the SGX Structure-driven Fragment-based Lead Discovery Process 217 11.3 Fragment Library Design for Crystallographic Screening 218 11.3.1 Considerations for Selecting Fragments 218 11.3.2 SGX Fragment Screening Library Selection Criteria 219 11.3.3 SGX Fragment Screening Library Properties 220 11.3.4 SGX Fragment Screening Library Diversity: Theoretical and Experimental Analyses 220 11.4 Crystallographic Screening of the SGX Fragment Library 221 11.4.1 Overview of Crystallographic Screening 222 11.4.2 Obtaining the Initial Target Protein Structure 224 11.4.3 Enabling Targets for Crystallographic Screening 225 11.4.4 Fragment Library Screening at SGX-CAT 225 11.4.5 Analysis of Fragment Screening Results 226 11.4.6 Factor VIIa Case Study of SGX Fragment Library Screening 228 11.5 Complementary Biochemical Screening of the SGX Fragment Library 230 11.6 Importance of Combining Crystallographic and Biochemical Fragment Screening 232 11.7 Selecting Fragments Hits for Chemical Elaboration 233 11.8 Fragment Optimization 234 11.8.1 Spleen Tyrosine Kinase Case Study 234 11.8.2 Fragment Optimization Overview 240 11.8.3 Linear Library Optimization 241 11.8.4 Combinatorial Library Optimization 242 11.9 Discussion and Conclusions 243 11.10 Postscript: SGX Oncology Lead Generation Program 245 References 245 12 Synergistic Use of Protein Crystallography and Solution-phase NMR Spectroscopy in Structure-based Drug Design: Strategies and Tactics 249 Cele Abad-Zapatero, Geoffrey F. Stamper, and Vincent S. Stoll 12.1 Introduction 249 12.2 Case 1: Human Protein Tyrosine Phosphatase 252 12.2.1 Designing and Synthesizing Dual-site Inhibitors 252 12.2.1.1 The Target 252 12.2.1.2 Initial Leads 252 12.2.1.3 Extension of the Initial Fragment 254 12.2.1.4 Discovery and Incorporation of the Second Fragment 256 12.2.1.5 The Search for Potency and Selectivity 257 12.2.2 Finding More “Drug-like” Molecules 258 12.2.2.1 Decreasing Polar Surface Area on Site 2 258 12.2.2.2 Monoacid Replacements on Site 1 258 12.2.2.3 Core Replacement 259 12.3 Case 2: MurF 261 12.3.1 Pre-filtering by Solution-phase NMR for Rapid Co-crystal Structure Determinations 261 12.3.1.1 The Target 261 12.3.1.2 Triage of Initial Leads 261 12.3.1.3 Solution-phase NMR as a Pre-filter for Co-crystallization Trials 262 12.4 Conclusion 263 Acknowledgments 264 References 264 13 Ligand SAR Using Electrospray Ionization Mass Spectrometry 267 Richard H. Griffey and Eric E. Swayze 13.1 Introduction 267 13.2 ESI-MS of Protein and RNA Targets 268 13.2.1 ESI-MS Data 268 13.2.2 Signal Abundances 268 13.3 Ligands Selected Using Affinity Chromatography 271 13.3.1 Antibiotics Binding Bacterial Cell Wall Peptides 272 13.3.2 Kinases and GPCRs 272 13.3.3 Src Homology 2 Domain Screening 273 13.3.4 Other Systems 274 13.4 Direct Observation of Ligand–Target Complexes 275 13.4.1 Observation of Enzyme–Ligand Transition State Complexes 276 13.4.2 Ligands Bound to Structured RNA 276 13.4.3 ESI-MS for Linking Low-affinity Ligands 277 13.5 Unique Features of ESI-MS Information for Designing Ligands 282 References 282 14 Tethering 285 Daniel A. Erlanson, Marcus D. Ballinger, and James A. Wells 14.1 Introduction 285 14.2 Energetics of Fragment Selection in Tethering 286 14.3 Practical Considerations 289 14.4 Finding Fragments 289 14.4.1 Thymidylate Synthase: Proof of Principle 289 14.4.2 Protein Tyrosine Phosphatase 1B: Finding Fragments in a Fragile, Narrow Site 292 14.5 Linking Fragments 293 14.5.1 Interleukin-2: Use of Tethering to Discover Small Molecules that Bind to a Protein–Protein Interface 293 14.5.2 Caspase-3: Finding and Combining Fragments in One Step 296 14.5.3 Caspase-1 299 14.6 Beyond Traditional Fragment Discovery 300 14.6.1 Caspase-3: Use of Tethering to Identify and Probe an Allosteric Site 300 14.6.2 GPCRs: Use of Tethering to Localize Hits and Confirm Proposed Binding Models 303 14.7 Related Approaches 306 14.7.1 Disulfide Formation 306 14.7.2 Imine Formation 307 14.7.3 Metal-mediated 307 14.8 Conclusions 308 Acknowledgments 308 References 308 Part 4: Emerging Technologies in Chemistry 15 Click Chemistry for Drug Discovery 313 Stefanie Röper and Hartmuth C. Kolb 15.1 Introduction 313 15.2 Click Chemistry Reactions 314 15.3 Click Chemistry in Drug Discovery 316 15.3.1 Lead Discovery Libraries 316 15.3.2 Natural Products Derivatives and the Search for New Antibiotics 317 15.3.3 Synthesis of Neoglycoconjugates 320 15.3.4 HIV Protease Inhibitors 321 15.3.5 Synthesis of Fucosyltranferase Inhibitor 323 15.3.6 Glycoarrays 324 15.4 In Situ Click Chemistry 325 15.4.1 Discovery of Highly Potent AChE by In Situ Click Chemistry 325 15.5 Bioconjugation Through Click Chemistry 328 15.5.1 Tagging of Live Organisms and Proteins 328 15.5.2 Activity-based Protein Profiling 330 15.5.3 Labeling of DNA 332 15.5.4 Artificial Receptors 333 15.6 Conclusion 334 References 335 16 Dynamic Combinatorial Diversity in Drug Discovery 341 Matthias Hochgürtel and Jean-Marie Lehn 16.1 Introduction 341 16.2 Dynamic Combinatorial Chemistry –The Principle 342 16.3 Generation of Diversity: DCC Reactions and Building Blocks 343 16.4 DCC Methodologies 346 16.5 Application of DCC to Biological Systems 347 16.5.1 Enzymes as Targets 349 16.5.2 Receptor Proteins as Targets 355 16.5.3 Nucleotides as Targets 357 16.6 Summary and Outlook 359 References 361 Index 365

About the Author :
Wolfgang Jahnke is a Senior Research Investigator at the Novartis Institutes for Biomedical Research in Basel, Switzerland, where he leads the Fragment-Based Screening technology platform. During his ten years at Novartis, he has received several honors, among them the appointment as Scientific Expert, and the Leading Scientist Award. Dr. Jahnke received his PhD from the TU Munchen, working with Horst Kessler on the development and application of novel NMR methods. He subsequently carried out research with Peter Wright at the Scripps Research Institute in La Jolla. Daniel A. Erlanson joined Sunesis Pharmaceuticals at its inception in 1998. He has been instrumental in inventing its drug-discovery technologies and using these to design leads against a variety of disease targets. Prior to Sunesis, Dr. Erlanson developed methods to conformationally constrain peptides as a post-doctoral fellow with James A. Wells at Genentech. Dr. Erlanson received his PhD in chemistry from Harvard University in the laboratory of Gregory L. Verdine, and his BA in chemistry from Carleton College, MN.

Review :
‘…this is indispensable reading for drug discovery researchers in the pharma and biotech sector.’ (Anticancer Research, 2007)