Epi-Informatics

Chapter 1. Introduction of Epigenetic Targets in Drug Discovery and Current Status of Epi-Drugs and Epi-Probes

• 1. Introduction

Chapter 2. Overview of Computer-Aided Drug Design for Epigenetic Targets

• 1. Introduction
• 2. Ligand-Based Drug Design
• 3. Structure-Based Drug Design
• 4. Combining Methods
• 5. Concluding Remarks

Chapter 3. Structure-Guided Optimization of DNA Methyltransferase Inhibitors

• 1. Introduction to DNA Methyltransferases
• 2. Drug Discovery
• 3. Further Promising Perspectives

Chapter 4. Discovery and Development of Small Molecules Targeting Epigenetic Enzymes with Computational Methods

• 1. Introduction
• 2. Writer
• 3. Readers
• 4. Erasers
• 5. Protein–Protein Interactions
• 6. Future Directions

Chapter 5. In Silico Optimization of the First DNA-Independent Mechanism-Based Inhibitor of Mammalian DNA Methyltransferase DNMT1

• 1. Introduction
• 2. Lead Structure for the Mechanism-Based Transition-State Analog
• 3. Evaluation of the Proposed Lead Compound as a Mechanism-Based Inhibitor of DNMT1
• 4. Optimization of Binding Interactions at Multiple Sites on the Lead Compound
• 5. Binding of the Mechanism-Based Inhibitor to Different Conformations of DNMT1
• 6. Conclusions and Future Directions
• 7. Methodology
• Appendix tables

Chapter 6. Structure-Based Modeling of Histone Deacetylases Inhibitors

• 1. Introduction
• 2. SBDD Studies on Zn-Based HDAC Inhibitors
• 3. SB Modeling for NAD-HDAC (Sirtuins)
• 4. Conclusions

Chapter 7. Searching Histone Deacetylase Inhibitors under Computational Procedures

• 1. Introduction
• 2. Histones
• 3. Targeting Histones
• 4. General Steps for Development of New Drugs
• 5. Developing New Strategies to Get Selective Compounds on Histones
• 6. Developing New Strategies to Multitarget Compounds Including Histones
• 7. Conclusions

Chapter 8. Current Development of Protein Arginine Methyltransferase Inhibitors

• 1. Introduction
• 2. Protein Arginine Methyltransferases
• 3. Catalytic Activity of PRMTs
• 4. Pharmacological Significance
• 5. PRMT Inhibitors
• 6. Conclusion
• List of Acronyms and Abbreviations

Chapter 9. Molecular Design of Compounds Targeting Histone Methyltransferases

• 1. Introduction
• 2. Protein Methyltransferases
• 3. Clinicopathological Role of PKMTs
• 4. Drug Discovery of New Epi-Drugs for Histone Methyltransferases
• 5. Conclusions

Chapter 10. Computational Chemical Biology of Methyllysine Histone Effectors

• 1. Introduction
• 2. Lysine Methylation: Chemistry and Biology
• 3. Methyllysine Effectors
• 4. What Role for Computational Approaches?
• 5. Elucidation of Effector-Substrate Recognition
• 6. Chemical Probes: Identification and Design
• 7. Structural Mechanics of Methyllysine Signaling
• 8. Conclusions and Perspectives

Chapter 11. Structure-Based Design and Computational Studies of Sirtuin Inhibitors

• 1. Introduction
• 2. Sirtuins, Insights into Their Chemical Mechanism, Characteristic Features, and Substrates
• 3. Crystal Structures of Sirtuins with Inhibitors and Activators
• 4. Computational Studies of Sirtuin Modulators
• 5. Conclusion

Chapter 12. Drug Repurposing for Epigenetic Targets Guided by Computational Methods

• 1. Introduction
• 2. Drug Repurposing Strategies
• 3. Drug Repurposing in Epigenetics
• 4. Conclusions

Chapter 13. Computational Structure–Activity Relationship Studies of Epigenetic Target Inhibitors

• 1. Introduction
• 2. Computational Methods to Study Structure–Activity Relationships
• 3. Analyzing SARs of Epigenetic Targets Using Computational Tools
• 4. Overcoming Selectivity Challenges in the Computational Design of Epi-Drugs
• 5. Conclusions

Chapter 14. Role of Nutrition in Epigenetics and Recent Advances of In Silico Studies

• 1. Nutritional Genomics
• 2. Diet and Health
• 3. Diseases Related to Epigenetic Changes
• 4. Computational Studies on Nutrigenomics and Food Chemicals

Chapter 15. The Road Ahead of the Epi-Informatics Field

• 1. Introduction
• 2. Promising Computational Approaches in Epigenetic Drug Discovery
• 3. Epi-Informatics: The Road Ahead
• 4. Conclusions