Presented in three parts - Introduction to Epigenetics, General Aspects and Methodologies, and Epigenetic Target Classes - it covers everything any drug researcher would need in order to know about targeting epigenetic mechanisms of disease.
Epigenetic Drug Discovery is an important resource for medicinal chemists, pharmaceutical researchers, biochemists, molecular biologists, and molecular geneticists.
Table of Contents
Part I Introduction - Epigenetics 1
1 Epigenetics:Moving Forward 3
Lucia Altucci
1.1 Why This Enormously Increased Interest? 4
1.2 Looking Forward to New Avenues of Epigenetics 5
Acknowledgments 7
References 7
Part II General Aspects/Methodologies 11
2 Structural Biology of Epigenetic Targets: Exploiting Complexity 13
Martin Marek, Tajith B. Shaik, and Christophe Romier
2.1 Introduction 13
2.2 DNA Methylases:The DNMT3A-DNMT3L-H3 and DNMT1-USP7 Complexes 14
2.3 Histone Arginine Methyltransferases:The PRMT5-MEP50 Complex 16
2.4 Histone Lysine Methyltransferases:The MLL3-RBBP5-ASH2L and the PRC2 Complexes 17
2.5 Histone Lysine Ubiquitinylases: The PRC1 Complex 21
2.6 Histone Lysine Deubiquitinylases: The SAGA Deubiquitination Module 22
2.7 Histone Acetyltransferases:The MSL1 and NUA4 Complexes 24
2.8 Histone Deacetylases: HDAC1-MTA1 and HDAC3-SMRT Complexes and HDAC6 26
2.9 Histone Variants and Histone Chaperones: A Complex and Modular Interplay 28
2.10 ATP-Dependent Remodelers: CHD1, ISWI, SNF2, and the SNF2-Nucleosome Complex 31
2.11 Epigenetic Readers: Histone Crotonylation Readers and the 53BP1-Nucleosome (H2AK15Ub-H4K20me2) Complex 35
2.12 Conclusions 37
Acknowledgments 38
References 38
3 Computer-based Lead Identification for Epigenetic Targets 45
Chiara Luise, Tino Heimburg, Berin Karaman, Dina Robaa, andWolfgang Sippl
3.1 Introduction 45
3.2 Computer-based Methods in Drug Discovery 46
3.2.1 Pharmacophore-based Methods 46
3.2.2 QSAR 47
3.2.3 Docking 47
3.2.4 Virtual Screening 48
3.2.5 Binding Free Energy Calculation 49
3.3 Histone Deacetylases 49
3.3.1 Zinc-Dependent HDACs 49
3.3.2 Sirtuins 54
3.4 Histone Methyltransferases 58
3.5 Histone Demethylases 61
3.5.1 LSD1 (KDM1A) 62
3.5.2 Jumonji Histone Demethylases 64
3.6 Summary 66
Acknowledgments 66
References 67
4 Mass Spectrometry and Chemical Biology in Epigenetics Drug Discovery 79
Christian Feller, DavidWeigt, and Carsten Hopf
4.1 Introduction: Mass Spectrometry Technology Used in Epigenetic Drug Discovery 79
4.1.1 Mass SpectrometryWorkflows for the Analysis of Proteins 80
4.1.2 Mass Spectrometry Imaging 83
4.2 Target Identification and Selectivity Profiling: Chemoproteomics 85
4.2.1 Histone Deacetylase and Acetyltransferase Chemoproteomics 87
4.2.2 Bromodomain Chemoproteomics 88
4.2.3 Demethylase Chemoproteomics 88
4.2.4 Methyltransferase Chemoproteomics 89
4.3 Characterization of Epigenetic Drug Target Complexes and Reader Complexes Contributing to Drug’s Mode of Action 89
4.3.1 Immunoaffinity Purification of Native Protein Complexes 89
4.3.2 Immunoaffinity Purification with Antibodies against Epitope Tags 90
4.3.3 Affinity Enrichment Using Histone Tail Peptides as Bait 91
4.4 Elucidation of a Drug’s Mode of Action: Analysis of Histone Posttranslational Modifications by MS-Based Proteomics 91
4.4.1 Histone Modification MS Workflows 92
4.4.2 Application of Histone MS Workflows to Characterize Epigenetic Drugs 95
4.5 Challenges and New Trends 97
4.5.1 Challenges and Trends in MS Analysis of Histone PTMs 97
4.5.2 High-Throughput Mass Spectrometry-Based Compound Profiling in Epigenetic Drug Discovery 98
4.5.3 Mass Spectrometry Imaging of Drug Action 98
Acknowledgments 99
References 99
5 PeptideMicroarrays for Epigenetic Targets 107
Alexandra Schutkowski, Diana Kalbas, Ulf Reimer, andMike Schutkowski
5.1 Introduction 107
5.2 Applications of Peptide Microarrays for Epigenetic Targets 110
5.2.1 Profiling of Substrate Specificities of Histone CodeWriters 110
5.2.2 Profiling of Substrate Specificities of Histone Code Erasers 114
5.2.3 Profiling of Binding Specificities of PTM-specific Antibodies and Histone Code Readers 117
5.2.3.1 Profiling of Specificities of PTM-specific Antibodies 118
5.2.3.2 Profiling of Binding Specificities of Histone Code Readers 119
5.2.4 Peptide Microarray-based Identification of Upstream Kinases and Phosphorylation Sites for Epigenetic Targets 121
5.3 Conclusion and Outlook 124
Acknowledgment 124
References 124
6 Chemical Probes 133
Amy Donner, Heather King, Paul E. Brennan, MosesMoustakim, andWilliam J. Zuercher
6.1 Chemical Probes Are Privileged Reagents for Biological Research 133
6.1.1 Best Practices for the Generation and Selection of Chemical Probes 134
6.1.2 Best Practices for Application of Chemical Probes 136
6.1.3 Cellular Target Engagement 137
6.1.3.1 Fluorescence Recovery after Photobleaching (FRAP) 138
6.1.3.2 Affinity Bead-Based Proteomics 138
6.1.3.3 Cellular Thermal Shift Assay (CETSA) 139
6.1.3.4 Bioluminescence Resonance Energy Transfer 139
6.2 Epigenetic Chemical Probes 141
6.2.1 Histone Acetylation and Bromodomain Chemical Probes 141
6.2.1.1 CBP/p300 Bromodomain Chemical Probes 144
6.2.1.2 Future Applications of Bromodomain Chemical Probes 147
6.3 Summary 147
References 148
Part III Epigenetic Target Classes 153
7 Inhibitors of the Zinc-Dependent Histone Deacetylases 155
Helle M. E. Kristensen, Andreas S. Madsen, and Christian A. Olsen
7.1 Introduction: Histone Deacetylases 155
7.2 Histone Deacetylase Inhibitors 158
7.2.1 Types of Inhibitors 158
7.2.2 HDAC Inhibitors in Clinical Use and Development 160
7.3 Targeting of HDAC Subclasses 169
7.3.1 Class I Inhibitors 169
7.3.1.1 HDAC1-3 Inhibitors 170
7.3.1.2 HDAC Inhibitors Targeting HDAC8 173
7.3.2 Class IIa Inhibitors 174
7.3.3 Class IIb 176
7.4 Perspectives 177
References 179
8 Sirtuins as Drug Targets 185
Clemens Zwergel, Dante Rotili, Sergio Valente, and Antonello Mai
8.1 Introduction 185
8.2 Biological Functions of Sirtuins in Physiology and Pathology 185
8.3 SIRT Modulators 188
8.3.1 SIRT Inhibitors 188
8.3.1.1 Small Molecules 188
8.3.1.2 Peptides and Pseudopeptides 191
8.3.2 SIRT Activators 191
8.4 Summary and Conclusions 192
References 193
9 Selective Small-Molecule Inhibitors of Protein Methyltransferases 201
H. Ümit Kaniskan and Jian Jin
9.1 Introduction 201
9.2 Protein Methylation 201
9.3 Lysine Methyltransferases (PKMTs) 202
9.4 Inhibitors of PKMTs 202
9.4.1 Inhibitors of H3K9 Methyltransferases 202
9.4.2 Inhibitors of H3K27 Methyltransferases 204
9.4.3 Inhibitors of H3K4 and H3K36 Methyltransferases 206
9.4.4 Inhibitors of H4K20 Methyltransferases 208
9.4.5 Inhibitors of H3K79 Methyltransferases 210
9.5 Protein Arginine Methyltransferases (PRMTs) 211
9.5.1 Inhibitors of PRMT1 211
9.5.2 Inhibitors of PRMT3 212
9.5.3 Inhibitors of CARM1 213
9.5.4 Inhibitors of PRMT5 214
9.5.5 Inhibitors of PRMT6 214
9.6 Concluding Remarks 215
References 215
10 LSD (Lysine-Specific Demethylase): A Decade-Long Trip from Discovery to Clinical Trials 221
Adam Lee, M. Teresa Borrello, and A. Ganesan
10.1 Introduction 221
10.2 LSDs: Discovery and Mechanistic Features 223
10.3 LSD Substrates 225
10.4 LSD Function and Dysfunction 229
10.5 LSD Inhibitors 232
10.5.1 Irreversible Small Molecule LSD Inhibitors from MAO Inhibitors 233
10.5.2 Reversible Small Molecule LSD Inhibitors 241
10.5.3 Synthetic Macromolecular LSD Inhibitors 248
10.6 Summary 251
References 253
11 JmjC-domain-Containing Histone Demethylases 263
Christoffer Højrup, Oliver D. Coleman, John-Paul Bukowski, Rasmus P. Clausen, and Akane Kawamura
11.1 Introduction 263
11.1.1 The LSD and JmjC Histone Lysine Demethylases 263
11.1.2 Histone Lysine Methylation and the JmjC-KDMs 265
11.1.3 The JmjC-KDMs in Development and Disease 266
11.2 KDM Inhibitor Development Targeting the JmjC Domain 272
11.2.1 2-Oxoglutarate Cofactor Mimicking Inhibitors 273
11.2.1.1 Emulation of the Chelating α-Keto AcidMoiety in 2OG 273
11.2.1.2 Bioisosteres of the Conserved 2OG C5-Carboxylic Acid-Binding Motif 273
11.2.2 Histone Substrate-Competitive Inhibitors 275
11.2.2.1 Small-Molecule Inhibitors 276
11.2.2.2 Peptide Inhibitors 276
11.2.3 Allosteric Inhibitors 276
11.2.4 Inhibitors Targeting KDM Subfamilies 277
11.2.4.1 KDM4 Subfamily-Targeted Inhibitors 277
11.2.4.2 KDM4/5 Subfamily-Targeted Inhibitors 279
11.2.4.3 KDM5 Subfamily-Targeted Inhibitors 280
11.2.4.4 KDM6 Subfamily-Targeted Inhibitors 281
11.2.4.5 KDM2/7- and KDM3-Targeted Inhibitors 282
11.2.4.6 Generic JmjC-KDM Inhibitors 282
11.2.5 Selectivity and Potency of JmjC-KDM Inhibition in Cells 283
11.3 KDM Inhibitors Targeting the Reader Domains 284
11.3.1 Plant Homeodomain Fingers (PHD Fingers) 284
11.3.2 Tudor Domains 286
11.4 Conclusions and Future Perspectives 286
Acknowledgments 287
References 287
12 Histone Acetyltransferases: Targets and Inhibitors 297
Gianluca Sbardella
12.1 Introduction 297
12.2 Acetyltransferase Enzymes and Families 298
12.3 The GNAT Superfamily 299
12.3.1 KAT2A/GCN5 and KAT2B/PCAF 301
12.3.2 KAT1/Hat1 303
12.3.3 GCN5L1 304
12.4 KAT3A/CBP and KAT3B/p300 Family 304
12.5 MYST Family 306
12.5.1 KAT5/Tip60 306
12.5.2 KAT6A/MOZ, KAT6B/MORF, and KAT7/HBO1 307
12.5.3 KAT8/MOF 307
12.5.4 SAS2 and SAS3 308
12.5.5 ESA1 308
12.5.6 Other KATs 308
12.6 KATs in Diseases 309
12.7 KAT Modulators 312
12.7.1 Bisubstrate Inhibitors 313
12.7.2 Natural Products and Synthetic Analogues and Derivatives 315
12.7.3 Synthetic Compounds 321
12.7.4 Compounds Targeting Protein-Protein Interaction Domains 328
12.8 Conclusion 333
References 334
13 Bromodomains: Promising Targets for Drug Discovery 347
Mehrosh Pervaiz, PankajMishra, and Stefan Günther
13.1 Introduction 347
13.2 The Human Bromodomain Family 348
13.2.1 Structural Features of the Human BRD Family 348
13.2.1.1 The Kac Binding Site 348
13.2.1.2 Druggability of the Human BRD Family 350
13.2.2 Functions of Bromodomain-containing Proteins 352
13.3 Bromodomains and Diseases 353
13.3.1 The BET Family 354
13.3.2 Non-BET Proteins 356
13.4 Methods for the Identification of Bromodomain Inhibitors 357
13.4.1 High-throughput Screening (HTS) 357
13.4.2 Fragment-based Lead Discovery 359
13.4.3 Structure-based Drug Design 359
13.4.4 Virtual Screening 362
13.4.4.1 Structure-based Virtual Screening 362
13.4.4.2 Ligand-based Virtual Screening 362
13.4.4.3 Pharmacophore Modeling 363
13.4.4.4 Substructure and Similarity Search 363
13.5 Current Bromodomain Inhibitors 364
13.6 Multi-target Inhibitors 365
13.6.1 Dual Kinase-Bromodomain Inhibitors 365
13.6.2 Dual BET/HDAC Inhibitors 369
13.7 Proteolysis Targeting Chimeras (PROTACs) 369
13.8 Conclusions 371
Acknowledgments 372
References 372
14 Lysine Reader Proteins 383
Johannes Bacher, Dina Robaa, Chiara Luise,Wolfgang Sippl, and Manfred Jung
14.1 Introduction 383
14.2 The Royal Family of Epigenetic Reader Proteins 385
14.2.1 The MBT Domain 385
14.2.2 The PWWP Domain 390
14.2.3 The Tudor Domain 392
14.2.4 The Chromodomain 395
14.3 The PHD Finger Family of Epigenetic Reader Proteins 400
14.4 TheWD40 Repeat Domain Family 402
14.5 Conclusion and Outlook 409
Acknowledgment 409
References 409
15 DNA-modifying Enzymes 421
Martin Roatsch, Dina Robaa,Michael Lübbert,Wolfgang Sippl, and Manfred Jung
15.1 Introduction 421
15.2 DNA Methylation 422
15.3 Further Modifications of Cytosine Bases 424
15.4 DNA Methyltransferases: Substrates and Structural Aspects 426
15.5 Mechanism of Enzymatic DNA Methylation 430
15.6 Physiological Role of DNA Methylation 431
15.7 DNA Methylation in Disease 432
15.8 DNMT Inhibitors 433
15.8.1 Nucleoside-mimicking DNMT Inhibitors 433
15.8.2 Non-nucleosidic DNMT Inhibitors 436
15.9 Therapeutic Applications of DNMT Inhibitors 441
15.10 Conclusion 442
Acknowledgment 443
References 443
16 Parasite Epigenetic Targets 457
Raymond J. Pierce and Jamal Khalife
16.1 Introduction: The Global Problem of Parasitic Diseases and the Need for New Drugs 457
16.2 Parasite Epigenetic Mechanisms 458
16.2.1 DNA Methylation 459
16.2.2 Histone Posttranslational Modifications 460
16.2.3 Histone-modifying Enzymes in Parasites 462
16.2.4 HMEs Validated as Therapeutic Targets 462
16.2.5 Structure-based Approaches for Defining Therapeutic Targets 464
16.3 Development of Epi-drugs for Parasitic Diseases 465
16.3.1 Repurposing of Existing Epi-drugs 466
16.3.2 Candidates from Phenotypic or High-throughput Screens 467
16.3.3 Structure-based Development of Selective Inhibitors 467
16.4 Conclusions 468
Acknowledgments 469
References 469
Index 477
