An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study

Abstract

A new strain of a novel infectious disease affecting millions of people, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently been declared as a pandemic by the World Health Organization (WHO). Currently, several clinical trials are underway to identify specific drugs for the treatment of this novel virus. The inhibition of the SARS-CoV-2 main protease is necessary for the blockage of the viral replication. Here, in this study, we have utilized a blind molecular docking approach to identify the possible inhibitors of the SARS-CoV-2 main protease, by screening a total of 33 molecules which includes natural products, anti-virals, anti-fungals, anti-nematodes and anti-protozoals. All the studied molecules could bind to the active site of the SARS-CoV-2 protease (PDB: 6Y84), out of which rutin (a natural compound) has the highest inhibitor efficiency among the 33 molecules studied, followed by ritonavir (control drug), emetine (anti-protozoal), hesperidin (a natural compound), lopinavir (control drug) and indinavir (anti-viral drug). All the molecules, studied out here could bind near the crucial catalytic residues, HIS41 and CYS145 of the main protease, and the molecules were surrounded by other active site residues like MET49, GLY143, HIS163, HIS164, GLU166, PRO168, and GLN189. As this study is based on molecular docking, hence being particular about the results obtained, requires extensive wet-lab experimentation and clinical trials under in vitro as well as in vivo conditions.

Communicated by Ramaswamy H. Sarma

Keywords:

• SARS-CoV-2 M^pro
• molecular docking
• natural products
• anti-virals
• anti-fungals

Acknowledgements

The authors are grateful to National Institute of Technology Meghalaya for providing research platform. SD and SS thank TEQIP III, National Institute of Technology Meghalaya for their fellowship. The study was not supported by any funding authority. The authors thank the reviewers for their valuable suggestions to increase the scientific quality of the manuscript.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Authors declaration

The authors declared that no competing conflict of interest exists. All authors have read and approved this version of the article.

Authors contribution

Sourav Das Conceptualization, Methodology, Investigation, Writing - original draft.

Sharat Sarmah Conceptualization, Methodology, Investigation, Writing - original draft.

Sona Lyndem Conceptualization, Methodology, Investigation, Writing - original draft.

Atanu Singha Roy Conceptualization, Methodology, Investigation, Writing-reviewing and editing.