Molecular Docking for Computer-Aided Drug Design

Fundamentals, Techniques, Resources and Applications

1st Edition - February 17, 2021
Imprint: Academic Press
Editor: Mohane S. Coumar
Language: English
Paperback ISBN:
9 7 8 - 0 - 1 2 - 8 2 2 3 1 2 - 3
eBook ISBN:
9 7 8 - 0 - 1 2 - 8 2 2 3 1 3 - 0

Molecular Docking for Computer-Aided Drug Design: Fundamentals, Techniques, Resources and Applications offers in-depth coverage on the use of molecular docking for drug design… Read more

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Molecular Docking for Computer-Aided Drug Design: Fundamentals, Techniques, Resources and Applications offers in-depth coverage on the use of molecular docking for drug design. The book is divided into three main sections that cover basic techniques, tools, web servers and applications. It is an essential reference for students and researchers involved in drug design and discovery.

Cover image
Title page
Table of Contents
Copyright
Dedication
List of Contributors
Preface
Acknowledgments
Part I. Foundations and Basic Techniques of Docking
Chapter 1. Modern Tools and Techniques in Computer-Aided Drug Design
1. Overview of Computer-Aided Drug Design
2. Chemical Libraries
3. Structure-Based Approaches and Screening
4. Ligand-Based Approaches and Screening
5. Applications of CADD in Drug Discovery
6. Conclusions
Chapter 2. Biomolecular Talks—Part 1: A Theoretical Revisit on Molecular Modeling and Docking Approaches
1. Biomolecules and Their Interactions
2. Computational Approaches to Study Biomolecular Interactions
3. Molecular Docking
4. Conclusion
Chapter 3. Post-processing of Docking Results: Tools and Strategies
1. Introduction
2. Scoring Functions
3. Representation of Ligand–receptor Complexes
4. Post-processing Strategies
5. Conclusions
Chapter 4. Best Practices for Docking-Based Virtual Screening
1. Introduction
2. Docking-Based Virtual Screening
3. Best Practices in Molecular Docking for Virtual Screening
4. Incorporating Protein Flexibility
5. Molecular Docking in Fragment-Based Drug Discovery
6. Case Studies of DBVS
7. Concluding Remarks and Future Directions
Chapter 5. Virtual Libraries for Docking Methods: Guidelines for the Selection and the Preparation
1. Introduction
2. Data Collection Within the Vast Chemical Space
3. Database Preparation
4. Conclusion
List of Abbreviations
Part II. Methods For Generating 3d Structures of Targets
Chapter 6. 3D Structural Determination of Macromolecules Using X-ray Crystallography Methods
1. Introduction
2. Protein Purification
3. Protein Crystallization
4. X-ray, Synchrotron, and XFELS
5. Data Collection and Processing
6. Solving Phases in MR, SIR/MIR, and SAD/MAD Methods
7. Structure Solution
8. Structure Refinement and Model Building
9. Characterization and Cross-Validation of Solved 3D Structures
10. Structure Validation
11. Conclusion
Chapter 7. Electron Microscopy and Single Particle Analysis for Solving Three-Dimensional Structures of Macromolecules
1. Introduction
2. The Major Techniques in Structural Biology
3. Electron Microscope
4. Outline of Single Particle Analysis
5. Remarkable Results From Single Particle Analysis
6. Single Particle Analysis and Drug Discovery
7. Conclusions and Future Directions
Chapter 8. Computational Modeling of Protein Three-Dimensional Structure: Methods and Resources
1. Introduction
2. Protein Structural Organization
3. Sequence–Structure–Function Relationship
4. Experimental Approaches to Determine Structures
5. Computational Approaches for Predicting Protein Structures
6. Case Study and Resources for Modeling Protein Structures
7. Conclusions and Future Directions
Part III. Tools, Web Servers, Resources, and a Step-By-Step Guide for Docking
Chapter 9. Resources for Docking-Based Virtual Screening
1. Drug Discovery
2. A Brief View of Docking and Its Use
3. Resources for Docking
4. Conclusion
Chapter 10. Do It Yourself—Dock It Yourself: General Concepts and Practical Considerations for Beginners to Start Molecular Ligand–Target Docking Simulations
1. Introduction
2. Selecting the Docking Program and Associated Tools
3. Installing and Launching ADV, ADT, SPDBV, and Vega ZZ
4. Creating the Virtual Docking Laboratory
5. Preparing the Input Structures of the Target Proteins
6. Preparing the Small Organic Compound Ligands
7. Generating the Search Space and Running the Docking Simulations
8. Analyzing the Graphical Docking Results
9. Analyzing the Numerical Docking Results
10. Synopsis of the Input, Processing, and Output Steps for ADV Docking
11. Solutions for Problems With the Programs (Trouble Shooting)
12. Applicability of the Presented Docking Procedures
13. Conclusion
Part IV. Applications and Case Studies of Docking
Chapter 11. Use of Molecular Docking as a Decision-Making Tool in Drug Discovery
1. Introduction
2. Molecular Docking Simulation
3. Integrated Computational Methods Involving Molecular Docking
4. Conclusion and Outlook
Chapter 12. Biomolecular Talks—Part 2: Applications and Challenges of Molecular Docking Approaches
1. Introduction
2. Applications of Molecular Docking
3. Challenges in Molecular Docking Studies
4. Computational Tools/Servers Available for Docking
5. Conclusion
Chapter 13. Application of Docking for Lead Optimization
1. Introduction
2. Approaches to Lead Optimization
3. Structure-Based Lead Optimization
4. Molecular Docking for Lead Optimization
5. Methods for Calculating Binding Affinities for Lead Optimization
6. Machine Learning–Based Lead Optimization
7. Limitations of Molecular Docking for Lead Optimization
8. Predictive Toxicity Using Docking and Machine Learning
9. Case Studies
10. Conclusion
Chapter 14. Multi-Target Drugs as Master Keys to Complex Diseases: Inverse Docking Strategies and Opportunities
1. Introduction
2. Computational Strategies for Multi-Target Drug Design
3. Case Examples
4. Concluding Remarks and Future Perspectives
Chapter 15. Drug Repositioning: Principles, Resources, and Application of Structure-Based Virtual Screening for the Identification of Anticancer Agents
1. Introduction
2. Computer-Aided Virtual Screening
3. Drug Repositioning
4. Conclusion
Chapter 16. Design and Discovery of Kinase Inhibitors Using Docking Studies
1. Introduction
2. Protein Kinases as Drug Targets
3. Structure of Protein Kinases
4. Dynamics of Protein Kinases
5. Types of Inhibitors
6. Molecular Docking in Design and Discovery of Kinase Inhibitors
7. Structure-Guided Strategies for Overcoming Kinase Inhibitors Resistance
8. Molecular Dynamics in Design and Discovery of Kinase Inhibitors
9. Molecular Dynamics Approaches to Enhance Docking
10. Application of Molecular Dynamics to Describe Allostery
11. Machine Learning Approaches to Enhance Docking
12. Conclusion
Chapter 17. Docking Approaches Used in Epigenetic Drug Investigations
1. Epigenetics
2. Epigenetics and Diseases
3. Drug Discovery of Epigenetic Modulators with Docking
4. Conclusion and Future Perspectives
Chapter 18. Molecular Docking for Natural Product Investigations: Pitfalls and Ways to Overcome Them
1. Introduction
2. Peculiarities in Natural Product Investigations
3. Molecular Docking for Natural Product Investigations
4. Other Computational Methods for Natural Product Investigations
5. Recent Examples of Docking in Natural Product Research
6. Conclusions
Chapter 19. Advances in Docking-Based Drug Design for Microbial and Cancer Drug Targets
1. Introduction
2. Structure-Based Drug Design
3. Ligand-Based Virtual Screening
4. In Silico Fragment-Based Drug Design
5. In Silico Drug Repurposing
6. Reverse or Inverse Drug Designing
7. Antibiotic Resistance and Drug Designing Through Docking
8. Conclusion
Chapter 20. Role of Bioinformatics in Subunit Vaccine Design
1. Introduction
2. Basics of Vaccine
3. Properties of an Ideal Vaccine and Its Components
4. Bioinformatics in Vaccine Design
5. Computational Design of Vaccine Constructs
6. Computational Prediction of Physicochemical Properties of Designed Vaccine Construct/s
7. Structure Prediction, Protein–Protein Interactions, and Complex Stability Analysis
8. An Overview of Successful Vaccine Design Using Bioinformatics
9. Conclusion
Chapter 21. Computational Approaches Toward Development of Topoisomerase I Inhibitor: A Clinically Validated Target
1. Introduction
2. Structure of Human Topoisomerase I
3. Inhibitors of Human Topoisomerase I
4. Computational Approaches for the Discovery of Topoisomerase I Inhibitors
5. Conclusion
Chapter 22. Docking-Based Virtual Screening Using PyRx Tool: Autophagy Target Vps34 as a Case Study
1. Introduction
2. PyRx 0.8 as a Docking-Based Virtual Screening Tool
3. Case Study: DBVS to Identify Small Molecule Inhibitors of Vps34
4. Discussion
5. Conclusion
Chapter 23. Molecular Docking: A Contemporary Story About Food Safety
1. Introduction
2. Food Safety
3. Databases and Big Data in Food Safety
4. In silico Methods
5. Case Studies
6. Conclusions
Index

Life Sciences

Physical Sciences & Engineering

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Molecular Docking for Computer-Aided Drug Design

Fundamentals, Techniques, Resources and Applications

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Mohane S. Coumar

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