Inhibitory activity of marine sponge metabolites on SARS-CoV-2 RNA dependent polymerase: virtual screening and molecular dynamics simulation

Abstract

Marine species are known as rich sources of metabolites involved mainly in the pharmaceutical industry. This study aimed to evaluate the effect of biologically active compounds in the marine sponge on the SARS-CoV-2 RNA-dependent-RNA polymerase protein (RdRp) using the in-silico method. A total of 51 marine compounds were checked for their possible interaction with SARS-CoV-2 RdRp using Maestro interface for molecular docking, molecular dynamic (MD) simulation, and MM/GBSA method to estimate compounds binding affinities. Among the 51 compounds screened in this study, two (mycalamide A, and nakinadine B) exhibited the lowest docking energy and best interaction. Among these compounds, mycalamide A was identified as a potent inhibitor of SARS-CoV-2 RdRp that showed the best and stable interaction during molecular dynamic simulation, with residues (Asp760 and Asp761) found in the catalytic domain of RdRp. The analysis through MM/GBSA for molecular dynamic simulation results revealed binding energy −59.7 ± 7.18 for Mycalamide A and −56 ± 10.55 for Nakinadine B. These results elucidate the possible use of mycalamide A for treating coronavirus disease.

Communicated by Ramaswamy H. Sarma

Keywords:

• Marine compounds
• sponge
• antiviral
• SARS-CoV-2
• in-silico
• molecular docking
• molecular dynamics
• MM/GBSA

Disclosure statement

No potential conflict of interest was reported by the authors.

Correction Statement

This article has been republished with minor changes. These changes do not impact the academic content of the article.

Additional information

Funding

This project was funded by the Deanship of Scientific Research (DSR) at King Abdulaziz University, Jeddah, under a grant (GCV19-31-1441). Therefore, the authors gratefully acknowledge technical and financial support from King Abdulaziz University, DSR, Jeddah, Saudi Arabia.