Main description:

This essential volume explores a variety of tools and protocols of structure-based (homology modeling, molecular docking, molecular dynamics, protein-protein interaction network) and ligand-based (pharmacophore mapping, quantitative structure-activity relationships or QSARs) drug design for ranking and prioritization of candidate molecules in search of effective treatment strategy against coronaviruses. Beginning with an introductory section that discusses coronavirus interactions with humanity and COVID-19 in particular, the book then continues with sections on tools and methodologies, literature reports and case studies, as well as online tools and databases that can be used for computational anti-coronavirus drug research. Written for the Methods in Pharmacology and Toxicology series, chapters include the kind of practical detail and implementation advice that ensures high quality results in the lab.
Comprehensive and timely, In Silico Modeling of Drugs Against Coronaviruses: Computational Tools and Protocols is an ideal reference for researchers working on the development of novel anti-coronavirus drugs for SARS-CoV-2 and for coronaviruses that will likely appear in the future.

Contents:

Section I: Introduction

1. History and Recent Advances in Coronavirus Discovery

Sora Abdul-Fattah, Aman Pal, Nagham Kaka, and Pramath Kakodkar

2. The Origin, Transmission, and Clinical Therapies in the Management of Coronavirus Diseases

Nagham Kaka, Aman Pal, Sora Abdul-Fattah, and Pramath Kakodkar

3. Transmission, Medical Consequences, and Prevention/Treatment of COVID-19 Infection

Suliman Khan, Rabeea Siddique, and Aigerim Bizhanova

4. Molecular-Level Targets for Development of Therapies Against Coronavirus Diseases

Qiongqiong Angela Zhou, Roger Granet, and Linda V. Garner

5. Candidate Drugs for the Potential Treatment of Coronavirus Diseases

Thanigaimalai Pillaiyar, Manoj Manickam, Sangeetha Meenakshisundaram, and Ajith Jerome Benjamine

Section II: Tools and Methodologies

6. Ligand-Based Approaches for Development of Drugs Against SARS-CoV-2

Ekampreet Singh, Rameez Jabeer Khan, Rajat Kumar Jha, Gizachew Muluneh Amera, Monika Jain, Rashmi Prabha Singh, Jayaraman Muthukumaran, and Amit Kumar Singh

7. Computational Drug Repurposing for Development of Drugs Against Coronaviruses

Ekampreet Singh, Rameez Jabeer Khan, Rajat Kumar Jha, Gizachew Muluneh Amera, Monika Jain, Rashmi Prabha Singh, Jayaraman Muthukumaran, and Amit Kumar Singh

8. Computational Methods and Tools for Repurposing of Drugs Against Coronaviruses

Sohini Chakraborti, Sneha Bheemireddy, and Narayanaswamy Srinivasan

9. Molecular Multi-Target Approach on COVID-19 for Designing Novel Chemicals

Pawan Kumar and Indira Ghosh

10. Structural Bioinformatics to Unveil Weaknesses of Coronavirus Spike Glycoprotein Stability

Pietro Bongini, Alfonso Trezza, Monica Bianchini, Ottavia Spiga, and Neri Niccolai

11. Protein-Protein Interaction Network for Identification of New Targets Against Novel Coronavirus

Suresh Kumar

12. Nonequilibrium Alchemical Simulations for the Development of Drugs Against COVID-19

Marina Macchiagodena, Maurice Karrenbrock, Marco Pagliai, Guido Guarnieri, Francesco Iannone, and Piero Procacci

13. Therapeutic and Vaccine Strategies for Stopping the COVID-19 Pandemic Based on Structural and Molecular Modelling Studies of Virus-Ganglioside Interactions

Jacques Fantini

14. Discovery of Covalent Drugs Targeting the Key Enzymes of SARS-CoV-2 Using SCARdock

Qi Song, Zhiying Wang, and Sen Liu

15. Machine Learning Techniques for Development of Drugs Against Coronavirus-2019 (COVID-19): A Case Study Protocol

Saurabh Sharma, Ajay Prakash, Phulen Sarma, and Bikash Medhi

Section III: Case Studies and Literature Reports

16. Dissecting the Drug Development Strategies Against SARS-CoV-2 Through Diverse Computational Modeling Techniques

Nilanjan Adhikari, Sk. Abdul Amin, and Tarun Jha

17. Recent Perspectives on COVID-19 and Computer-Aided Virtual Screening of Natural Compounds for the Development of Therapeutic Agents towards SARS-CoV-2

Dharshini Gopal and Sinosh Skariyachan

18. Computational Modeling of Protease Inhibitors for the Development of Drugs Against Coronaviruses

Joseph T. Ortega, Beata Jastrzebska, and Hector R. Rangel

19. Computational Modeling of ACE2-Mediated Cell Entry Inhibitors for the Development of Drugs Against Coronaviruses

Priyanka De and Kunal Roy

20. Computational Modeling of RdRp Inhibitors for the Development of Drugs Against Novel Coronavirus (nCoV)

Vinay Kumar and Kunal Roy

21. Computational Modeling of Chloroquine Analogues for Development of Drugs Against Novel Coronavirus (nCoV)

Vinay Kumar and Kunal Roy

22. Computational Modeling of ACE2 Inhibitors for Development of Drugs Against Coronaviruses

Rupa Joshi, Seema Bansal, Deepti Malik, Rubal Singla, Abhishek Mishra, Ajay Prakash, and Bikash Medhi

23. Deep Learning-Based Drug Screening for COVID-19 and Case Studies

Konda Mani Saravanan, Haiping Zhang, Md. Tofazzal Hossain, Md. Selim Reza, and Yanjie Wei

24. Virtual Screening of Natural Compounds Targeting Proteases of Coronaviruses and Picornaviruses

Sirin Theerawatanasirikul and Porntippa Lekcharoensuk

25. Molecular Simulation Driven Drug Repurposing for Identification of Inhibitors Against Non-Structural Proteins of SARS-CoV-2

Amita Pathak, Bhumika Singh, Dheeraj Kumar Chaurasia, and B. Jayaram

Section IV: Online Tools and Databases

26. Online Tools and Antiviral Databases for the Development of Drugs Against Coronaviruses

Rahul Balasaheb Aher and Dhiman Sarkar

27. Online Resource and Tools for the Development of Drugs Against Novel Corona Virus

Suresh Kumar

28. Drug Databases for Development of Therapeutics Against Coronaviruses

Supratik Kar and Jerzy Leszczynski