Structural Bioinformatics: Applications in Preclinical Drug Discovery Process

1. Front Matter

   Pages i-xii

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2. Free Energy-Based Methods to Understand Drug Resistance Mutations

   • Elvis A. F. Martis, Evans C. Coutinho

   Pages 1-24

3. Pharmacophore Modelling and Screening: Concepts, Recent Developments and Applications in Rational Drug Design

   • Chinmayee Choudhury, G. Narahari Sastry

   Pages 25-53

4. Analysis of Protein Structures Using Residue Interaction Networks

   • Dmitrii Shcherbinin, Alexander Veselovsky

   Pages 55-69

5. Combinatorial Drug Discovery from Activity-Related Substructure Identification

   • Md. Imbesat Hassan Rizvi, Chandan Raychaudhury, Debnath Pal

   Pages 71-108

6. In Silico Structure-Based Prediction of Receptor–Ligand Binding Affinity: Current Progress and Challenges

   • Shailesh Kumar Panday, Indira Ghosh

   Pages 109-175

7. Structure-Based Drug Design of PfDHODH Inhibitors as Antimalarial Agents

   • Shweta Bhagat, Anuj Gahlawat, Prasad V. Bharatam

   Pages 177-220

8. Recent Advancements in Computing Reliable Binding Free Energies in Drug Discovery Projects

   • N. Arul Murugan, Vasanthanathan Poongavanam, U. Deva Priyakumar

   Pages 221-246

9. Integrated Chemoinformatics Approaches Toward Epigenetic Drug Discovery

   • Saurabh Loharch, Vikrant Karmahapatra, Pawan Gupta, Rethi Madathil, Raman Parkesh

   Pages 247-269

10. Structure-Based Drug Design with a Special Emphasis on Herbal Extracts

    • D. Velmurugan, N. H. V. Kutumbarao, V. Viswanathan, Atanu Bhattacharjee

    Pages 271-305

11. Impact of Target-Based Drug Design in Anti-bacterial Drug Discovery for the Treatment of Tuberculosis

    • Anju Choorakottayil Pushkaran, Raja Biswas, C. Gopi Mohan

    Pages 307-346

12. Turbo Analytics: Applications of Big Data and HPC in Drug Discovery

    • Rajendra R. Joshi, Uddhavesh Sonavane, Vinod Jani, Amit Saxena, Shruti Koulgi, Mallikarjunachari Uppuladinne et al.

    Pages 347-374

13. Single-Particle cryo-EM as a Pipeline for Obtaining Atomic Resolution Structures of Druggable Targets in Preclinical Structure-Based Drug Design

    • Ramanathan Natesh

    Pages 375-400

14. Back Matter

    Pages 401-406

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This book reviews the advances and challenges of structure-based drug design in the preclinical drug discovery process, addressing various diseases, including malaria, tuberculosis and cancer. Written by internationally recognized researchers, this edited book discusses how the application of the various in-silico techniques, such as molecular docking, virtual screening, pharmacophore modeling, molecular dynamics simulations, and residue interaction networks offers insights into pharmacologically active novel molecular entities. It presents a clear concept of the molecular mechanism of different drug targets and explores methods to help understand drug resistance. In addition, it includes chapters dedicated to natural-product- derived medicines, combinatorial drug discovery, the CryoEM technique for structure-based drug design and big data in drug discovery.


The book offers an invaluable resource for graduate and postgraduate students, as well as forresearchers in academic and industrial laboratories working in the areas of chemoinformatics, medicinal and pharmaceutical chemistry and pharmacoinformatics.

• Structural Bioinformatics
• Drug Discovery Process
• Drug Discovery and Development
• Computer Aided Drug Design
• Predictive Chemoinformatics
• Virtual Screening of Drugs
• In Silico Molecular Modeling
• Molecular Docking
• Structure Based Drug Design
• Structure-activity Relationships
• Structure-function Relationships
• Pharmacoinformatics and Drug Discovery
• Predictive Models Drug Discovery
• Protein-ligand Interactions
• Computer-aided Molecular Design
• Biomolecular Interactions Drug Design
• Hydrogen Bonding and Protein Active Site
• Rational Drug Design
• Pharmaceutical Design
• Ligand Based Drug Design

• Amrita Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences and Research Centre, Kochi, India

  C. Gopi Mohan

Dr. C. Gopi Mohan is an Associate Professor at the Center for Nanosciences and Molecular Medicine, specializing in the areas of structural bioinformatics, structure-based drug design, protein crystallography, and nanoinformatics. He graduated from Banaras Hindu University with a PhD in Physics and gained experience as a postdoctoral researcher at the Indian Institute of Science, Bangalore (India), as a research officer at the University of Bath (UK) and as an associate researcher at the University Henri Poincare, Nancy (France). Further, he worked as a member of the faculty at the National Institute of Pharmaceutical Education & Research (NIPER), Mohali, Punjab. Dr. Gopi Mohan has published more than 70 research papers in refereed journals and was cited as an internationally recognized expert in the field of Structural Bioinformatics and Chemoinformatics by Synergix Ltd. (UK) founded by Dr. N.C. Cohen, a pioneer of rational drug design. Recently he was awarded the ICMR Senior Biomedical Scientist International Fellowship to visit US laboratories for research collaborations.

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