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