Fragment-based Approaches in Drug Discovery

by Jahnke, Wolfgang; Erlanson, Daniel A.; Mannhold, Raimund; Kubinyi, Hugo; Folkers, Gerd

• ISBN13: 9783527312917
• ISBN10: 3527312919
• Edition: 1st
• Format: Hardcover
• Copyright: 2006-09-11
• Publisher: Wiley-VCH

Summary

Recent successes in the modular design of pharmacologically active ligands show how the concept of fragment-based ligand design is quickly pervading research departments throughout the drug industry. Fragment-based ligand design combines high-throughput screening with structure-based design to form a powerful new tool in drug discovery.

Author Biography

Wolfgang Jahnke studied Chemistry at the University of Tübingen (Germany) and obtained a Ph.D. degree from the University of M? with Horst Kessler in 1994.
He then joined the pharmaceutical industry and is currently head of a drug discovery group at Novartis Pharma AG in Basel (Switzerland). His main expertise is on the application of NMR spectroscopy for drug discovery. In recent years, this has included the development of novel methods for fragment-based ligand design and the characterization of protein-ligand interactions.

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	(8)
Daniel A. Erlanson and Wolfgang Jahnke
1.1 Introduction	3	(1)
1.2 Starting Small: Key Features of Fragment-based Ligand Design	4	(2)
1.2.1 FBS Samples Higher Chemical Diversity	4	(1)
1.2.2 FBS Leads to Higher Hit Rates	5	(1)
1.2.3 FBS Leads to Higher Ligand Efficiency	6	(1)
1.3 Historical Development	6	(1)
1.4 Scope and Overview of this Book	7	(2)
References	9	(2)
2 Multivalency in Ligand Design	11	(44)
Vijay M. Krishnamurthy, Lora A. Estroff and George M. Whitesides
2.1 Introduction and Overview	11	(1)
2.2 Definitions of Terms	12	(4)
2.3 Selection of Key Experimental Studies	16	(3)
2.3.1 Trivalency in a Structurally Simple System	17	(1)
2.3.2 Cooperativity (and the Role of Enthalpy) in the "Chelate Effect"	18	(1)
2.3.3 Oligovalency in the Design of Inhibitors to Toxins	18	(1)
2.3.4 Bivalency at Well Defined Surfaces (Self-assembled Monolayers, SAMs)	18	(1)
2.3.5 Polyvalency at Surfaces of Viruses, Bacteria, and SAMs	18	(1)
2.4 Theoretical Considerations in Multivalency	19	(7)
2.4.1 Survey of Thermodynamics	19	(1)
2.4.2 Additivity and Multivalency	19	(3)
2.4.3 Avidity and Effective Concentration (Ceff)	22	(2)
2.4.4 Cooperativity is Distinct from Multivalency	24	(1)
2.4.5 Conformational Entropy of the Linker between Ligands	25	(1)
2.4.6 Enthalpy/Entropy Compensation Reduces the Benefit of Multivalency	26	(1)
2.5 Representative Experimental Studies	26	(6)
2.5.1 Experimental Techniques Used to Examine Multivalent Systems	26	(1)
2.5.1.1 Isothermal Titration Calorimetry	26	(1)
2.5.1.2 Surface Plasmon Resonance Spectroscopy	27	(1)
2.5.1.3 Surface Assays Using Purified Components (Cell-free Assays)	27	(1)
2.5.1.4 Cell-based Surface Assays	27	(1)
2.5.2 Examination of Experimental Studies in the Context of Theory	28	(1)
2.5.2.1 Trivalency in Structurally Simple Systems	28	(1)
2.5.2.2 Cooperativity (and the Role of Enthalpy) in the "Chelate Effect"	29	(1)
2.5.2.3 Oligovalency in the Design of Inhibitors of Toxins	29	(1)
2.5.2.4 Bivalency in Solution and at Well Defined Surfaces (SAMs)	30	(1)
2.5.2.5 Polyvalency at Surfaces (Viruses, Bacteria, and SAMs)	31	(1)
2.6 Design Rules for Multivalent Ligands	32	(7)
2.6.1 When Will Multivalency Be a Successful Strategy to Design Tight-binding Ligands?	32	(1)
2.6.2 Choice of Scaffold for Multivalent Ligands	33	(1)
2.6.2.1 Scaffolds for Oligovalent Ligands	33	(1)
2.6.2.2 Scaffolds for Polyvalent Ligands	35	(1)
2.6.3 Choice of Linker for Multivalent Ligands	36	(1)
2.6.3.1 Rigid Linkers Represent a Simple Approach to Optimize Affinity	36	(1)
2.6.3.2 Flexible Linkers Represent an Alternative Approach to Rigid Linkers to Optimize Affinity	37	(1)
2.6.4 Strategy for the Synthesis of Multivalent Ligands	37	(1)
2.6.4.1 Polyvalent Ligands: Polymerization of Ligand Monomers	38	(1)
2.6.4.2 Polyvalent Ligands: Functionalization with Ligands after Polymerization	38	(1)
2.7 Extensions of Multivalency to Lead Discovery	39	(5)
2.7.1 Hetero-oligovalency Is a Broadly Applicable Concept in Ligand Design	39	(1)
2.7.2 Dendrimers Present Opportunities for Multivalent Presentation of Ligands	40	(1)
2.7.3 Bivalency in the Immune System	40	(2)
2.7.4 Polymers Could Be the Most Broadly Applicable Multivalent Ligands	42	(2)
2.8 Challenges and Unsolved Problems in Multivalency	44	(1)
2.9 Conclusions	44	(1)
Acknowledgments	45	(1)
References	45	(10)
3 Entropic Consequences of Linking Ligands	55	(12)
Christopher W. Murray and Marcel L. Verdonk
3.1 Introduction	55	(1)
3.2 Rigid Body Barrier to Binding	55	(2)
3.2.1 Decomposition of Free Energy of Binding	55	(1)
3.2.2 Theoretical Treatment of the Rigid Body Barrier to Binding	56	(1)
3.3 Theoretical Treatment of Fragment Linking	57	(2)
3.4 Experimental Examples of Fragment Linking Suitable for Analysis	59	(2)
3.5 Estimate of Rigid Body Barrier to Binding	61	(1)
3.6 Discussion	62	(2)
3.7 Conclusions	64	(1)
References	65	(2)
4 Location of Binding Sites on Proteins by the Multiple Solvent Crystal Structure Method	67	(24)
Dagmar Ringe and Carla Mattos
4.1 Introduction	67	(1)
4.2 Solvent Mapping	68	(1)
4.3 Characterization of Protein–Ligand Binding Sites	69	(2)
4.4 Functional Characterization of Proteins	71	(1)
4.5 Experimental Methods for Locating the Binding Sites of Organic Probe Molecules	71	(1)
4.6 Structures of Elastase in Nonaqueous Solvents	72	(1)
4.7 Organic Solvent Binding Sites	73	(2)
4.8 Other Solvent Mapping Experiments	75	(3)
4.9 Binding of Water Molecules to the Surface of a Protein	78	(1)
4.10 Internal Waters	79	(1)
4.11 Surface Waters	80	(1)
4.12 Conservation of Water Binding Sites	81	(1)
4.13 General Properties of Solvent and Water Molecules on the Protein	82	(1)
4.14 Computational Methods	83	(2)
4.15 Conclusion	85	(1)
Acknowledgments	85	(1)
References	85	(6)
Part 2: Fragment Library Design and Computional Approaches
5 Cheminformatics Approaches to Fragment-based Lead Discovery	91	(22)
Tudor I. Oprea and Jeffrey M. Blaney
5.1 Introduction	91	(1)
5.2 The Chemical Space of Small Molecules (Under 300 a.m.u.)	92	(2)
5.3 The Concept of Lead-likeness	94	(2)
5.4 The Fragment-based Approach in Lead Discovery	96	(3)
5.5 Literature-based Identification of Fragments: A Practical Example	99	(8)
5.6 Conclusions	107	(2)
Acknowledgments	109	(1)
References	109	(4)
6 Structural Fragments in Marketed Oral Drugs	113	(12)
Michal Vieth and Miles Siegel
6.1 Introduction	113	(1)
6.2 Historical Look at the Analysis of Structural Fragments of Drugs	113	(2)
6.3 Methodology Used in this Analysis	115	(3)
6.4 Analysis of Similarities of Different Drug Data Sets Based on the Fragment Frequencies	118	(5)
6.5 Conclusions	123	(1)
Acknowledgments	124	(1)
References	124	(1)
7 Fragment Docking to Proteins with the Multi-copy Simultaneous Search Methodology	125	(24)
Collin M. Stultz and Martin Karplus
7.1 Introduction	125	(1)
7.2 The MCSS Method	125	(7)
7.2.1 MCSS Minimizations	126	(1)
7.2.2 Choice of Functional Groups	126	(1)
7.2.3 Evaluating MCSS Minima	127	(5)
7.3 MCSS in Practice: Functionality Maps of Endothiapepsin	132	(3)
7.4 Comparison with GRID	135	(2)
7.5 Comparison with Experiment	137	(1)
7.6 Ligand Design with MCSS	138	(3)
7.6.1 Designing Peptide-based Ligands to Ras	138	(2)
7.6.2 Designing Non-peptide Based Ligands to Cytochrome P450	140	(1)
7.6.3 Designing Targeted Libraries with MCSS	140	(1)
7.7 Protein Flexibility and MCSS	141	(2)
7.8 Conclusion	143	(1)
Acknowledgments	144	(1)
References	144	(5)
Part 3: Experimental Techniques and Applications
8 NMR-guided Fragment Assembly	149	(32)
Daniel S. Sem
8.1 Historical Developments Leading to NM R-based Fragment Assembly	149	(1)
8.2 Theoretical Foundation for the Linking Effect	150	(2)
8.3 NMR-based Identification of Fragments that Bind Proteins	152	(11)
8.3.1 Fragment Library Design Considerations	152	(2)
8.3.2 The "SHAPES" NMR Fragment Library	154	(2)
8.3.3 The "SAR by NMR" Fragment Library	156	(4)
8.3.4 Fragment-based Classification of protein Targets	160	(3)
8.4 NMR-based Screening for Fragment Binding	163	(4)
8.4.1 Ligand-based Methods	163	(2)
8.4.2 Protein-based Methods	165	(2)
8.4.3 High-throughput Screening: Traditional and TINS	167	(1)
8.5 NMR-guided Fragment Assembly	167	(4)
8.5.1 SAR by NMR	167	(2)
8.5.2 SHAPES	169	(1)
8.5.3 Second-site Binding Using Paramagnetic Probes	169	(1)
8.5.4 NMR-based Docking	170	(1)
8.6 Combinatorial NMR-based Fragment Assembly	171	(5)
8.6.1 NMR SOLVE	171	(2)
8.6.2 NMR ACE	173	(3)
8.7 Summary and Future Prospects	176	(1)
References	177	(4)
9 SAR by NMR: An Analysis of Potency Gains Realized Through Fragment-linking and Fragment-elaboration Strategies for Lead Generation	181	(12)
Philip J. Hajduk, Jeffrey R. Huth, and Chaohong Sun
9.1 Introduction	181	(1)
9.2 SAR by NMR	182	(1)
9.3 Energetic Analysis of Fragment Linking Strategies	183	(4)
9.4 Fragment Elaboration	187	(1)
9.5 Energetic Analysis of Fragment Elaboration Strategies	188	(2)
9.6 Summary	190	(1)
References	191	(2)
10 Pyramid: An Integrated Platform for Fragment-based Drug Discovery	193	(1)
Thomas G. Davies, Rob L.M. van Montfort, Glyn Williams, and Harren Jhoti
10.1 Introduction	193	(1)
10.2 The Pyramid Process	194	(13)
10.2.1 Introduction	194	(1)
10.2.2 Fragment Libraries	195	(1)
10.2.2.1 Overview	195	(1)
10.2.2.2 Physico-chemical Properties of Library Members	196	(1)
10.2.2.3 Drug Fragment Library	197	(1)
10.2.2.4 Privileged Fragment Library	197	(1)
10.2.2.5 Targeted Libraries and Virtual Screening	197	(1)
10.2.2.6 Quality Control of Libraries	201	(1)
10.2.3 Fragment Screening	201	(1)
10.2.4 X-ray Data Collection	202	(1)
10.2.5 Automation of Data Processing	203	(2)
10.2.6 Hits and Diversity of Interactions	205	(1)
10.2.6.1 Example 1: Compound 1 Binding to CDK2	205	(1)
10.2.6.2 Example 2: Compound 2 Binding to p38a	207	(1)
10.2.6.3 Example 3: Compound 3 Binding to Thrombin	207	(1)
10.3 Pyramid Evolution – Integration of Crystallography and NMR	207	(4)
10.3.1 NMR Screening Using Water-LOGSY	208	(2)
10.3.2 Complementarity of X-ray and NMR Screening	210	(1)
10.4 Conclusions	211	(1)
Acknowledgments	211	(1)
References	212	(3)
11 Fragment-based Lead Discovery and Optimization Using X-Ray Crystallography, Computational Chemistry, and High-throughput Organic Synthesis	215	(1)
Jeff Blaney, Vicki Nienaber, and Stephen K. Burley
11.1 Introduction	215	(2)
11.2 Overview of the SGX Structure-driven Fragment-based Lead Discovery Process	217	(1)
11.3 Fragment Library Design for Crystallographic Screening	218	(3)
11.3.1 Considerations for Selecting Fragments	218	(1)
11.3.2 SGX Fragment Screening Library Selection Criteria	219	(1)
11.3.3 SGX Fragment Screening Library Properties	220	(1)
11.3.4 SGX Fragment Screening Library Diversity: Theoretical and Experimental Analyses	220	(1)
11.4 Crystallographic Screening of the SGX Fragment Library	221	(9)
11.4.1 Overview of Crystallographic Screening	222	(2)
11.4.2 Obtaining the Initial Target Protein Structure	224	(1)
11.4.3 Enabling Targets for Crystallographic Screening	225	(1)
11.4.4 Fragment Library Screening at SGX-CAT	225	(1)
11.4.5 Analysis of Fragment Screening Results	226	(2)
11.4.6 Factor VIIa Case Study of SGX Fragment Library Screening	228	(2)
11.5 Complementary Biochemical Screening of the SGX Fragment Library	230	(2)
11.6 Importance of Combining Crystallographic and Biochemical Fragment Screening	232	(1)
11.7 Selecting Fragments Hits for Chemical Elaboration	233	(1)
11.8 Fragment Optimization	234	(9)
11.8.1 Spleen Tyrosine Kinase Case Study	234	(6)
11.8.2 Fragment Optimization Overview	240	(1)
11.8.3 Linear Library Optimization	241	(1)
11.8.4 Combinatorial Library Optimization	242	(1)
11.9 Discussion and Conclusions	243	(2)
11.10 Postscript: SGX Oncology Lead Generation Program	245	(1)
References	245	(4)
12 Synergistic Use of Protein Crystallography and Solution-phase NMR Spectroscopy in Structure-based Drug Design: Strategies and Tactics	249	(1)
Cele Abad-Zapatero, Geoffrey F. Stamper, and Vincent S. Stoll
12.1 Introduction	249	(3)
12.2 Case 1: Human Protein Tyrosine Phosphatase	252	(9)
12.2.1 Designing and Synthesizing Dual-site Inhibitors	252	(1)
12.2.1.1 The Target	252	(1)
12.2.1.2 Initial Leads	252	(1)
12.2.1.3 Extension of the Initial Fragment	254	(1)
12.2.1.4 Discovery and Incorporation of the Second Fragment	256	(1)
12.2.1.5 The Search for Potency and Selectivity	257	(1)
12.2.2 Finding More "Drug-like" Molecules	258	(1)
12.2.2.1 Decreasing Polar Surface Area on Site 2	258	(1)
12.2.2.2 Monoacid Replacements on Site 1	258	(1)
12.2.2.3 Core Replacement	259	(2)
12.3 Case 2: MurF	261	(2)
12.3.1 Pre-filtering by Solution-phase NMR for Rapid Co-crystal Structure Determinations	261	(1)
12.3.1.1 The Target	261	(1)
12.3.1.2 Triage of Initial Leads	261	(1)
12.3.1.3 Solution-phase NMR as a Pre-filter for Co-crystallization Trials	262	(1)
12.4 Conclusion	263	(1)
Acknowledgments	264	(1)
References	264	(3)
13 Ligand SAR Using Electrospray Ionization Mass Spectrometry	267	(1)
Richard H. Griffey and Eric E. Swayze
13.1 Introduction	267	(1)
13.2 ES I-M S of Protein and RNA Targets	268	(3)
13.2.1 ESI-MS Data	268	(1)
13.2.2 Signal Abundances	268	(3)
13.3 Ligands Selected Using Affinity Chromatography	271	(4)
13.3.1 Antibiotics Binding Bacterial Cell Wall Peptides	272	(1)
13.3.2 Kinases and GPCRs	272	(1)
13.3.3 Src Homology 2 Domain Screening	273	(1)
13.3.4 Other Systems	274	(1)
13.4 Direct Observation of Ligand–Target Complexes	275	(7)
13.4.1 Observation of Enzyme–Ligand Transition State Complexes	276	(1)
13.4.2 Ligands Bound to Structured RNA	276	(1)
13.4.3 PSI-MS for Linking Low-affinity Ligands	277	(5)
13.5 Unique Features of ESI-MS Information for Designing Ligands	282	(1)
References	282	(3)
14 Tethering	285	(1)
Daniel A. Erlanson, Marcus D. Ballinger, and James A. Wells
14.1 Introduction	285	(1)
14.2 Energetics of Fragment Selection in Tethering	286	(3)
14.3 Practical Considerations	289	(1)
14.4 Finding Fragments	289	(4)
14.4.1 Thymidylate Synthase : Proof of Principle	289	(3)
14.4.2 Protein Tyrosine Phosphatase 1B: Finding Fragments in a Fragile, Narrow Site	292	(1)
14.5 Linking Fragments	293	(7)
14.5.1 Interleukin-2: Use of Tethering to Discover Small Molecules that Bind to a Protein–Protein Interface	293	(3)
14.5.2 Caspase-3: Finding and Combining Fragments in One Step	296	(3)
14.5.3 Caspase-1	299	(1)
14.6 Beyond Traditional Fragment Discovery	300	(6)
14.6.1 Caspase-3: Use of Tethering to Identify and Probe an Allosteric Site	300	(3)
14.6.2 GPCRs: Use of Tethering to Localize Hits and Confirm Proposed Binding Models	303	(3)
14.7 Related Approaches	306	(2)
14.7.1 Disulfide Formation	306	(1)
14.7.2 Imine Formation	307	(1)
14.7.3 Metal-mediated	307	(1)
14.8 Conclusions	308	(1)
Acknowledgments	308	(1)
References	308	(5)
Part 4: Emerging Technologies in Chemistry
15 Click Chemistry for Drug Discovery	313	(52)
Stefanie Röper and Hartmuth C. Kolb
15.1 Introduction	313	(1)
15.2 Click Chemistry Reactions	314	(2)
15.3 Click Chemistry in Drug Discovery	316	(9)
15.3.1 Lead Discovery Libraries	316	(1)
15.3.2 Natural Products Derivatives and the Search for New Antibiotics	317	(3)
15.3.3 Synthesis of Neoglycoconjugates	320	(1)
15.3.4 HIV Protease Inhibitors	321	(2)
15.3.5 Synthesis of Fucosyltranferase Inhibitor	323	(1)
15.3.6 Glycoarrays	324	(1)
15.4 In Situ Click Chemistry	325	(3)
15.4.1 Discovery of Highly Potent AChE by In Situ Click Chemistry	325	(3)
15.5 Bioconjugation Through Click Chemistry	328	(6)
15.5.1 Tagging of Live Organisms and Proteins	328	(2)
15.5.2 Activity-based Protein Profiling	330	(2)
15.5.3 Labeling of DNA	332	(1)
15.5.4 Artificial Receptors	333	(1)
15.6 Conclusion	334	(1)
References	335	(6)
16 Dynamic Combinatorial Diversity in Drug Discovery	341	(1)
Matthias Hochgürtel and Jean-Marie Lehn
16.1 Introduction	341	(1)
16.2 Dynamic Combinatorial Chemistry –The Principle	342	(1)
16.3 Generation of Diversity: DCC Reactions and Building Blocks	343	(3)
16.4 DCC Methodologies	346	(1)
16.5 Application of DCC to Biological Systems	347	(12)
16.5.1 Enzymes as Targets	349	(6)
16.5.2 Receptor Proteins as Targets	355	(2)
16.5.3 Nucleotides as Targets	357	(2)
16.6 Summary and Outlook	359	(2)
References	361	(4)
Index	365