Epigenetic targets in drug discovery:
Gespeichert in:
| Format: | Buch |
|---|---|
| Sprache: | English |
| Veröffentlicht: |
Weinheim
Wiley-VCH
2009
|
| Schriftenreihe: | Methods and principles in medicinal chemistry
42 |
| Schlagworte: | |
| Online-Zugang: | Cover Inhaltstext Inhaltsverzeichnis |
| Beschreibung: | XXIII, 297 S. Ill., graph. Darst. |
| ISBN: | 9783527323555 |
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Titel: Epigenetic targets in drug discovery
Autor: Sippl, Wolfgang
Jahr: 2009
lv
Contents
List of Contributors XIII
Preface XVII
A Personal Foreword XXI
Part One General Aspects and Methodologies 1
1 New Frontiers in Epigenetic Modifications 3
Adam L Carske and John M. Denu
1.1 Introduction 3
1.2 DNA Methylation 3
1.3 Histone Modifications and the Histone Code Hypothesis 5
1.4 Origins of Specificity in Histone Binding Proteins/Modifying
Enzymes 7
1.5 Histone Modification Cross-talk 11
1.6 Inhibitors of DNMTs and HDACs 13
1.7 Conclusions 17
References 17
2 Structural Biology of Epigenetic Targets 23
Christophe Romier, Jean-Marie Wurtz, Jean-Paul Renaud,
and Jean Cavarelli
2.1 Introduction 23
2.2 Histone Acetyltransferases 24
2.2.1 Structures from the GNAT Family 24
2.2.2 Structures of HATs from the MYST Family 26
2.2.3 Structure of the p300 and RttlO9 HATs 26
2.2.4 Binding of Histone Substrates by HATs of the GNAT Family 27
2.2.5 Catalytic Mechanism of HATs 29
2.3 Histone Deacetylases 29
Epigenetic Targets in Drug Discovery. Edited by Wolfgang Sippl and Manfred Jung
Copyright © 2009 WILEY-VCH Verlag GmbH Co. KGaA, Weinheim
ISBN: 978-3-527-32355-5
VII Contents
2.3.1 Structure of HDACs 30
2.3.2 Binding of Acetylated Lysine by HDACs 32
2.3.3 Catalytic Mechanism of HDACs 32
2.3 .4 Structural Basis of Inhibition of HDACs 33
2.4 Sirtuins 34
2.4.1 Structure of Sirtuins 34
2.4.2 Catalytic Mechanism of Sirtuins 35
2.5 Histone Methylation Enzymes 35
2.5.1 Histone Lysine Methyltransferases 36
2.5.1.1 SET Domain of HKMTs 36
2.5.1.2 Dotl HKMTs 38
2.5.2 Histone Arginine Methyltransferases 39
2.6 Histone Demethylases 39
2.6.1 Lysine Histone Demethylases 41
2.6.1.1 LSD1 (KDM1) 41
2.6.1.2 The JmjC Family: Jumonji-C Domain Containing
Proteins 42
2.6.1.3 Lysine Demethylase JHDM1 (KDM2) 43
2.6.1.4 Lysine Demethylase JHDM3/JMJD2 (KDM4) 43
2.6.2 Arginine Demethylases 44
2.6.2.1 Histone Demethylimination 44
2.6.2.2 Histone Arginine Demethylase 45
2.7 DNA Methyltransferases 46
2.8 Concluding Remarks: the Challenge of Structural Studies of
Epigenetic Targets 47
References 49
3 Computer- and Structure-Based Lead Identification
for Epigenetic Targets 57
RalfHeinke, Urszula Uciechowska, and Wolfgang Sippl
3.1 Introduction 57
3.2 Computer-Based Methods in Drug Discovery 58
3.2.1 Pharmacophore-Based Methods 58
3.2.2 3D Quantitative Structure-Activity Relationship 59
3.2.3 Iigand Docking 59
3.2.4 Virtual Screening 60
3.2.5 Binding Free Energy Calculations 60
3.3 DNA Methyltransferases 61
3.4 Histone Deacetylases 62
3.4.1 Classic HDACs 62
3.4.1.1 Docking Studies Using X-Ray Structures and Homology
Models 63
3.4.1.2 3D-QSAR Studies 64
3.4.1.3 Virtual Screening Studies 64
3.4.2 Sirtuins 66
Contents VII
3.5 Histone Acetyltransferases 73
3.6 Histone Methyltransferases 74
3.7 Histone Demethylases 78
3.8 Summary 79
References 79
4 Histone Modification Analysis Using Mass Spectrometry 87
Ana Villar-Carea and Axel Imhof
4.1 Introduction 87
4.2 Histone Molecules 88
4.3 Capillary Electrophoresis 88
4.4 Reversed Phase Chromatography 89
4.5 Mass Spectrometry 89
References 94
5 In Vitro Assays for Histone-Modifying Enzymes 99
Alexander-Thomas Hauser and Manfred Jung
5.1 Introduction 99
5.2 Screening Hierarchy 99
5.3 General Principles of Screening for Histone-Modifying
Enzymes 100
5.4 Histone Deacetylases 101
5.4.1 Radioactive Assays 101
5.4.2 Fluorescent Assays 104
5.5 Histone Acetyltransferases 107
5.5.1 Radioactive Assays 107
5.5.2 Assays Based on CoA-SH Detection 107
5.5.3 Antibody-Based Assays 108
5.6 Histone Methyltransferases 110
5.6.1 Arginine Methyltransferases 110
5.6.2 Lysine Methyltransferases 110
5.7 Histone Demethylases 111
5.7.1 Lysine Demethylases 111
5.7.2 Arginine Demethylases 113
5.8 Conclusion ID
References 113
6 Epigenetic Targets in Drug Discovery: Cell-Based Assays
for HDAC Inhibitor Hit Validation 119
Mirajung, Kwon-Jeong Yong, Alfredo Velena, and Sung Lee
6.1 Introduction 119
6.2 In Vitro Assays for HDAC Inhibitors 120
6.2.1 In Vitro Enzymatic Assay and Substrate Specificity 120
6.2.2 In Vitro High-Throughput Assays 121
6.2.3 In Vitro Isoform-Spetificity Assays 121
VIII Contents
6.3 Cell-Based Assays 122
6.3.1 HDAC Activity Assays in Cultured Cells 123
6.3.2 Detection of Acetylated Histones and Nonhistone
Proteins 123
6.4 Biological Function-Based Assays 125
6.4.1 Cell Proliferation Assays 125
6.4.2 Reporter Systems 125
6.4.3 High-Throughput Gene Expression Analysis 126
6.4.4 Flow Cytometry Analysis 127
6.5 HDAC Isoform Functional Assays 128
6.5.1 Depletion of Target Genes in Cells 128
6.5.2 Knockout Animal Models 129
6.6 Anticancer Activity 129
6.6.1 Antiangiogenic Assays 129
6.6.2 Invasion Assay 130
6.6.3 Tumor Xenograft Models 130
6.7 Perspective 131
References 132
7 Chromatin Immunoprecipitation ChIP: Wet Lab Meets In Silico 139
Martin Seifert and Robert Schneider
7.1 Background and Overview 139
7.1.1 Chromatin and DNA Organization 139
7.1.2 Chromatin Immunoprecipitation as a Powerful Method to Study
Chromatin 140
7.2 The Basic Principle of ChIP 141
7.2.1 N-ChIP 142
7.2.2 X-ChIP 142
7.2.3 Choice of DNA Fragmentation Method 143
7.2.4 Choice of Antibodies 343
7.3 Different Variations of ChIP 144
7.3.1 ChlP-On-Chip 144
7.3.2 ChlPDSL 144
7.3.3 ChlP-Sequencing 145
7.3.4 Re-ChIP 145
7.3.5 ChlP-Chop 145
7.3.6 Methyl-DNA Immunoprecipitation (MeDIP) 146
7.4 Analysis of ChIP Data 146
7.4.1 Detection and Definition of Enriched Regions in ChlP-on-Chip
Experiments 146
7.4.2 Detection and Definition of Enriched Regions in ChlP-Seq
Experiments 146
7.4.3 Annotation of Enriched Regions 148
7.4.4 Analysis of Enriched Regions 148
7.5 Data Analysis Examples 149
Contents IX
7.6 The Future of ChIP 356
References 157
Part Two Epigenetic Target Classes and Inhibitor Development 161
8 DNA Methyhransferase Inhibitors 163
Wolfgang Sippl and Manfred Jung
8.1 Introduction 163
8.2 DNA Methylation 163
8.3 DNA Methyltransferases 165
8.4 Biochemical Mechanism of DNA Methylation 168
8.5 Physiological Role of DNA Methylation 168
8.6 DNA Methylation and Disease 169
8.7 DNMT Inhibitors 170
8.7.1 Covalent DNMT Inhibitors 170
8.7.2 Noncovalent DNMT Inhibitors 173
8.8 Therapeutic Applications of DNMT Inhibitors 175
8.9 Conclusion 176
References 176
9 Histone Deacetylase Inhibitors 185
Philip Jones
9.1 Introduction 185
9.2 Mechanism and X-Ray Crystal Structure 186
9.3 Histone Deacetylase Inhibitors 188
9.3.1 Short-Chain Fatty Acids 188
9.3.2 Hydroxamic Acids 190
9.3.2.1 Aliphatic Hydroxamic Acids 192
9.3.2.2 Cinnamic Hydroxamic Acids 194
9.3.2.3 Phenyl Hydroxamic Acids 197
9.3.2.4 Heterocyde Hydroxamic Acids 198
9.3.3 Aminoanilines 200
9.3.3.1 HDAC1 and 2 Selective Aminoanilines 204
9.3.4 Electrophilk Ketones 206
9.3.5 Natural Products 208
9.3.6 Hybrid Cyclic Tetrapeptides 212
9.3.7 Aliphatic Ketones 213
9.3.8 Thiols and Related HDAC Inhibitors 213
9.4 Conclusions 216
References 216
10 NAD-Dependent Deacetylases as Therapeutic Targets 225
Hongzhe Li, Julian Simon, and Antonio Bedalov
10.1 Historical Perspective and Functions of Sir2 in Yeast 225
S
X Contents
10.2 Sirtuin Enzymatic Activity and its Modulation by Endogenous
Molecules 226
10.3 Small Molecule Inhibitors of Sirtuins 228
10.4 Small Molecule Activators of Sirtuins 230
10.5 SIRT1 as a Therapeutic Target in Metabolic Syndrome and
Type 2 Diabetes 231
10.5.1 Sirtuins and Cancer 232
10.6 Neurological Diseases 234
10.7 Conclusion 235
References 236
11 Inhibitors of Histone AcetyKransferases: Discovery and Biomedical
Perspectives 243
Margarete von Wantoch Rekowski and Athanassios Ciannis
11.1 Introduction 243
11.2 HAT Inhibitors 245
11.3 Summary 248
References 249
12 Histone Methyitransferases as Novel Drug Targets 251
Manfred Jung
12.1 Introduction 251
12.2 Protein Methylation 251
12.2.1 Arginine Methylation 252
12.2.2 Lysine Methylation 253
12.3 Histone Demethylation 254
12 A Histone Methyitransferases 254
12A.I Arginine Methyitransferases 254
12.4.2 Lysine Methyitransferases 256
12.5 Histone Methyltransferase Inhibitors 257
12.5.1 Arginine Methyltransferase Inhibitors 257
12.5.2 Lysine Methyltransferase Inhibitors 260
12.6 Concluding Remarks 262
References 262
13 Histone Demethylases 269
Rasmus P. Clausen, Marianne T. Pedersen, and Kristian Helin
13.1 Introduction 269
13.2 Chromatin 269
13.3 Histone Methylation and Demethylation 270
13 A Histone Demethylases 271
13.5 LSD1/KDM1 273
13.5.1 Inhibitors of LSD1 274
13.6 JmjC Domain-Containing Demethylases 276
13.6.1 The FBXL/KDM2 Cluster 277
Contents XI
13.6.2 The JMJD1/KDM3 Cluster 279
13.6.3 The JMJD2/KDM4 Cluster 280
13.6.4 The JARID1/KDM5 Cluster 280
13.6.5 The UTX/JMJD3 (KDM6) Cluster 282
13.6.6 Inhibitors of JmjC Domain-Containing Demethylases 282
13.7 Summary 283
References 284
Index 291 |
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| spelling | Epigenetic targets in drug discovery ed. by Wolfgang Sippl ... Weinheim Wiley-VCH 2009 XXIII, 297 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Methods and principles in medicinal chemistry 42 Drug Discovery methods Epigenesis, Genetic Pharmacogenetics methods Pharmacogenomics Arzneimittelentwicklung (DE-588)4143176-5 gnd rswk-swf Pharmakogenetik (DE-588)4271255-5 gnd rswk-swf (DE-588)4143413-4 Aufsatzsammlung gnd-content Pharmakogenetik (DE-588)4271255-5 s Arzneimittelentwicklung (DE-588)4143176-5 s DE-604 Sippl, Wolfgang Sonstige oth Methods and principles in medicinal chemistry 42 (DE-604)BV035418617 42 DE-576;wiley image/jpeg http://swbplus.bsz-bw.de/bsz308071263cov.htm 20090701202116 Cover text/html http://deposit.dnb.de/cgi-bin/dokserv?id=3192482&prov=M&dok%5Fvar=1&dok%5Fext=htm Inhaltstext HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017730719&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Epigenetic targets in drug discovery Methods and principles in medicinal chemistry Drug Discovery methods Epigenesis, Genetic Pharmacogenetics methods Pharmacogenomics Arzneimittelentwicklung (DE-588)4143176-5 gnd Pharmakogenetik (DE-588)4271255-5 gnd |
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| title | Epigenetic targets in drug discovery |
| title_auth | Epigenetic targets in drug discovery |
| title_exact_search | Epigenetic targets in drug discovery |
| title_full | Epigenetic targets in drug discovery ed. by Wolfgang Sippl ... |
| title_fullStr | Epigenetic targets in drug discovery ed. by Wolfgang Sippl ... |
| title_full_unstemmed | Epigenetic targets in drug discovery ed. by Wolfgang Sippl ... |
| title_short | Epigenetic targets in drug discovery |
| title_sort | epigenetic targets in drug discovery |
| topic | Drug Discovery methods Epigenesis, Genetic Pharmacogenetics methods Pharmacogenomics Arzneimittelentwicklung (DE-588)4143176-5 gnd Pharmakogenetik (DE-588)4271255-5 gnd |
| topic_facet | Drug Discovery methods Epigenesis, Genetic Pharmacogenetics methods Pharmacogenomics Arzneimittelentwicklung Pharmakogenetik Aufsatzsammlung |
| url | http://swbplus.bsz-bw.de/bsz308071263cov.htm http://deposit.dnb.de/cgi-bin/dokserv?id=3192482&prov=M&dok%5Fvar=1&dok%5Fext=htm http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=017730719&sequence=000004&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| volume_link | (DE-604)BV035418617 |
| work_keys_str_mv | AT sipplwolfgang epigenetictargetsindrugdiscovery |