COMPUTATIONAL PREDICTION OF BIOACTIVE COMPOUNDS AS POTENTIAL INHIBITORS OF COVID-19 MAIN PROTEASE, SPIKE GLYCOPROTEIN RECEPTOR-BINDING DOMAIN, AND RNA-DEPENDENT RNA POLYMERASE

RUCHIKA SHARMA; VAEESHNAVI BUWA

doi:10.22159/ijms.2022.v10i4.45115

Authors

RUCHIKA SHARMA Government College for Women, Parade Ground, Jammu, Jammu and Kashmir, India.
VAEESHNAVI BUWA Department of Bioinformatics, BioNome, Bengaluru, India.

DOI:

https://doi.org/10.22159/ijms.2022.v10i4.45115

Keywords:

COVID-19 main protease, RNA-dependent RNA polymerase, Spike glycoprotein receptor-binding domain, Bioactive compounds

Abstract

Objectives: It has been known for ages that natural products have potent antiviral activity and hence show inhibitory effects on SARS-CoV-2 infections. In this study, some promising bioactive compounds from natural sources for drug development against SARS-CoV-2 were studied.

Methods: The study was based on a computational approach using different phytochemicals for evaluating their potential against non-structural (main protease [MPro], RNA-dependent RNA polymerase [RdRp], and structural [spike [S] glycoprotein receptor-binding domain]) viral proteins. Molecular docking was conducted systematically using PyRx and AutoDock 4.2 to determine the binding affinities between bioactive compounds and Mpro, spike RBD, and RdRp. Twenty-two ligands were selected in this study from different sources including three known inhibitors of the virus remdesivir, favipiravir, and nelfinavir. The pharmacological assessment of the ligands was achieved using ADMET filters.

Results: The docking results revealed that β-carotene, piperine, and cianidanol were the best antagonists for Mpro, isovitexin, quercitin, β-carotene, piperine, and cianidanol were the best antagonists for RdRp, and in case of the spike RBD, capsaicin, cianidanol, curcumin, gingerol, isovitexin, piperine, quercitin, rhapontin, and riboflavin were found to be best.

Conclusion: All of these bioactive compounds could be considered potential drug candidates for COVID-19 inhibition due to their promising binding affinities with the viral structural and non-structural proteins.

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