Buch, Englisch, 376 Seiten, Format (B × H): 170 mm x 244 mm, Gewicht: 930 g
Methods and Strategies for Drug Discovery
Buch, Englisch, 376 Seiten, Format (B × H): 170 mm x 244 mm, Gewicht: 930 g
Reihe: Methods and principles in medicinal chemistry
ISBN: 978-3-527-34529-8
Verlag: Wiley VCH Verlag GmbH
The modern drug developers? guide for making informed choices among the diverse target identification methods
Target Discovery and Validation: Methods and Strategies for Drug Discovery offers a hands-on review of the modern technologies for drug target identification and validation. With contributions from noted industry and academic experts, the book addresses the most recent chemical, biological, and computational methods. Additionally, the book highlights techologies that are applicable to ?difficult? targets and drugs directed at multiple targets, including chemoproteomics, activity-based protein profiling, pathway mapping, genome-wide association studies, and array-based profiling.
Throughout, the authors highlight a range of diverse approaches, and target validation studies reveal how these methods can support academic and drug discovery scientists in their target discovery and validation research. This resource:
-Offers a guide to identifying and validating targets, a key enabling technology without which no new drug development is possible
-Presents the information needed for choosing the appropriate assay method from the ever-growing range of available options
-Provides practical examples from recent drug development projects, e. g. in kinase inhibitor profiling
Written for medicinal chemists, pharmaceutical professionals, biochemists, biotechnology professionals, and pharmaceutical chemists, Target Discovery and Validation explores the current methods for the identification and validation of drug targets in one comrpehensive volume. It also includes numerous practical examples.
Fachgebiete
- Technische Wissenschaften Verfahrenstechnik | Chemieingenieurwesen | Biotechnologie Pharmazeutische Technologie
- Naturwissenschaften Biowissenschaften Zellbiologie
- Naturwissenschaften Chemie Chemie Allgemein Pharmazeutische Chemie, Medizinische Chemie
- Naturwissenschaften Biowissenschaften Molekularbiologie
- Medizin | Veterinärmedizin Medizin | Public Health | Pharmazie | Zahnmedizin Pharmazie
- Naturwissenschaften Biowissenschaften Angewandte Biologie Bioinformatik
Weitere Infos & Material
Preface xiii
A Personal Foreword xvii
1 Chemical Strategies for Evaluating New Drug Targets 1
Adrian J. Carter, Raina Seupel, Paul E. Brennan, Michael Sundström, Andrea Introini, and Anke Mueller-Fahrnow
1.1 Introduction 1
1.2 Use Cases and Case Studies for Chemogenomic Compounds and Chemical Probes 5
1.2.1 Chemogenomic Libraries 5
1.2.2 Inactive Control 6
1.2.3 Use of Biological Target Panels and Profiling 8
1.3 Development of Chemical Probes 10
1.3.1 From BIX01294 to EPZ035544: Development and Improvement of G9a/GLP Inhibitors 10
1.3.2 Development of BRD9 Inhibitors 12
1.4 Compound-Based Target Evaluation with Patient-Derived Cells 14
1.4.1 Compound-Based Target Evaluation 14
1.4.2 Patient-Derived Cell Assays 16
1.4.3 Target Evaluation Approach 16
1.4.4 Case Story: Inflammatory Bowel Disease (IBD) Tissue Platform 18
1.5 Summary and Outlook 19
References 20
2 Affinity-Based Chemoproteomics for Target Identification 25
Annika Jenmalm Jensen and Ivan Cornella Taracido
2.1 Introduction 25
2.2 Small Molecule Phenotypic Mechanism of Action Elucidation 29
2.3 Quantitative High-Resolution Mass Spectrometry as a Protein Detection Read-Out 30
2.4 In-Lysate Affinity-Based Chemical Proteomics 33
2.4.1 Design of the Affinity Probe 34
2.4.2 General Experimental Pulldown Workflow 36
2.4.3 Limitations 38
2.5 In-Cell Light-Activated Affinity-Based Chemoproteomics 39
2.5.1 Design of the Reactive Photoaffinity Probe (PAL Probe) 40
2.5.2 General Experimental Workflow 40
2.5.3 Limitations 43
2.6 Target Validation and Mode of Action 43
2.7 Concluding Remarks 45
References 46
3 Activity-Based Protein Profiling 51
Nattawadee Panyain, Cassandra R. Kennedy, Ryan T. Howard, and Edward W. Tate
3.1 Introduction 51
3.2 Activity-Based Probe (ABP) and Affinity-Based Probe (AfBP) Design 53
3.2.1 Warheads (Reactive Groups) 53
3.2.1.1 Electrophilic Warheads 55
3.2.1.2 Photocrosslinking Warheads 55
3.2.2 Reporter Tags 56
3.2.3 Linkers 56
3.2.4 Bioorthogonal Ligation Chemistry 57
3.2.4.1 Staudinger Ligation 58
3.2.4.2 Copper(I)-Catalysed Azide-Alkyne Cycloaddition (CuAAC) 58
3.2.4.3 Strain-Promoted Azide-Alkyne Cycloaddition (SPAAC) 59
3.2.4.4 Diels–Alder Reaction 59
3.3 Chemical Proteomic Workflow 60
3.3.1 Quantitative Proteomics by Mass Spectrometry 61
3.3.1.1 Label-Free Quantification (LFQ) 61
3.3.1.2 Chemical Labelling Quantification 61
3.3.1.3 Metabolic Labelling Quantification 63
3.4 ABPP Applications and Case Studies 63
3.4.1 Case Study 1: Activity-Based Protein Profiling as a Robust Method for Enzyme Identification and Screening in Extremophilic Archaea 65
3.4.2 Case Study 2: Failed Clinical Trial of a Fatty Acid Amide Hydrolase (FAAH) Inhibitor 68
3.4.3 Case Study 3: Target Identification of Small Molecule Inhibitors 71
3.4.3.1 New Target Profiling for Sulforaphane 71
3.4.3.2 Profiling USP Inhibitors in Human Cell Lines as Potential Therapeutic Molecules 73
3.4.4 Case Study 4: Fragment-Based Ligand Discovery Aided by Photoaffinity Labelling 74
3.4.5 Case Study 5: Quenched Fluorescent Activity-Based Probe (qABP) Design and Application in Protein Localization 80
3.5 Summary 82
References 83
4 Kinobeads: A Chemical Proteomic Approach for Kinase Inhibitor Selectivity Profiling and Target Discovery 97
Maria Reinecke, Stephanie Heinzlmeir, Mathias Wilhelm, Guillaume Médard, Susan Klaeger, and Bernhard Kuster
4.1 Kinase Inhibitor Target Deconvolution Using Chemical Proteomics 97
4.1.1 Polypharmacology of Small Molecule Kinase Inhibitors 97
4.1.2 Chemoproteomic Profiling of Kinase Inhibitors 100
4.1.3 Tips and Tricks Regarding Chemoproteomic Assay Development 103
4.2 Detailed Kinobeads Protocol 105
4.2.1 Cell or Tissue Lysate 107
4.2.2 Affinity Matrices 107
4.2.3 Kinobeads Competition Assay 110
4.2.4 Mass Spectrometry 111
4.2.5 Peptide and Protein Identification and Quantification 112
4.2.6 Data Analysis 112
4.3 Application Examples for Kinobeads 113
4.3.1 Expanding the Target Space of Kinobeads 113
4.3.2 Target Space Deconvolution of Small Molecule Kinase Inhibitors 116
4.3.3 Opportunities Arising from Inhibitor Polypharmacology: Drug Repositioning 120
4.3.4 Chemoproteomic-Guided Medicinal Chemistry 121
4.4 Kinobeads, Inhibitors, and Drug Discovery: Where are We Heading? 123
4.4.1 What is a Good Drug? 123
4.4.2 How Can We Discover New Drugs in the Future? 124
4.4.3 The Yin and Yang of Chemoproteomic-Guided Drug Discovery 124
Acknowledgments 125
References 125
5 Label-Free Techniques for Target Discovery and Validation 131
Daniel Martinez Molina and Michael Dabrowski
5.1 Introduction 131
5.2 CETSA: How It All Began 132
5.3 The CETSA Formats 136
5.3.1 CETSA Classics 136
5.3.2 CETSA HT 138
5.3.3 CETSA MS 140
5.4 Target Discovery 142
5.4.1 Generation of Active Hit Molecules 142
5.4.2 Tool Generation (Small Screens to Identify Tool Compounds) 143
5.4.3 Target Classes That are In and Out of Scope and Difficult Targets 143
5.4.4 Focused or Iterative Library Screening 144
5.4.5 Fragment Library Screening 144
5.4.6 Hit Confirmation 145
5.4.7 Phenotypic Hit Deconvolution to Discover Targets 145
5.5 Target Validation 147
5.5.1 Binding Modes 147
5.5.2 Selectivity, Specificity, and Safety 148
5.5.3 Translation Bench to Bedside (via Animals) 149
5.6 Conclusion 150
References 151
6 Reverse Translation to Support Efficient Drug Target Selection and Stratified Medicine 153
