In silico prediction of natural compounds as potential multi-target inhibitors of structural proteins of SARS-CoV-2

Abstract

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a colossal loss to human health and lives and has deeply impacted socio-economic growth. Remarkable efforts have been made by the scientific community in containing the virus by successful development of vaccines and diagnostic kits. Initiatives towards drug repurposing and discovery have also been undertaken. In this study, we compiled the known natural anti-viral compounds using text mining of the literature and examined them against four major structural proteins of SARS-CoV-2, namely, spike (S) protein, nucleocapsid (N) protein, membrane (M) protein and envelope (E) protein. Following computational approaches, we identified fangchinoline and versicolactone C as the compounds to exhibit strong binding to the target proteins and causing structural deformation of three structural proteins (N, S and M). We recommend the inhibitory effects of these compounds from our study should be experimentally validated against SARS-CoV-2.

Communicated by Ramaswamy H. Sarma

Keywords:

• SARS-CoV-2
• natural antiviral compounds
• docking
• simulation
• COVID-19

Acknowledgements

We thank our lab members for their feedback and valuable comments. J.R. acknowledges Indian Council of Medical Research (ICMR) for Senior Research Fellowship. We acknowledge Acharya Narendra Dev College, University of Delhi, India and CSIR-IGIB (Institute of Genomics and Integrative Biology, India) for the infrastructural facilities. F.I.K. and D.L. acknowledge the China Postdoctoral Science Foundation (2020M673187), and the Sichuan Science and Technology Program (2021YFH0093)

Disclosure statement

The authors declare no competing financial interests.

Author’s contribution

The study was designed by U.B. and J.R. Data Collection and docking was done by J.R. and A.B. Simulation was done by J.R., A.B., F.I.K. and D.L. Data analysis was performed by J.R., A.B., U.B., F.I.K., D.L. and S.R. Manuscript written by J.R., U.B., F.I.K. and S.R. All authors have read and approved the manuscript for publication.