Computational prediction of bioactive compounds as potential inhibitors of COVID-19 main protease (Mpro,) spike (S) glycoprotein receptor-binding domain (RBD) and RNA dependent RNA polymerase (RdRp).

Authors

  • SAMEER SHARMA Indian Academy Degree College - Autonomous

Keywords:

COVID-19 main protease (Mpro), RNA dependent RNA polymerase (RdRp), spike (S) glycoprotein receptor binding domain, Bioactive compounds

Abstract

The highly contagious COVID-19, firstly reported from China has spread worldwide in a very short span and the world has faced an unprecedented loss of lives. To find effective immunization and treatment strategies, continuous efforts have been made so far. The potential candidates which emerged as promising leads to control the infection displayed serious side effects. People are moving towards natural products such as immune boosters and antiviral agents with no definite drug around. 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. The study was based on a computational approach by 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.  22 ligands were selected in this study from different sources which includes three known inhibitors of the virus Remdesivir, Favipiravir and Nelfinavir. The bioactive compounds with suitable absorption, distribution, metabolism and excretion (ADME) properties were docked against the viral proteins and their binding energies were compared with known inhibitors. The docking results revealed that β-Carotene, piperine, and Cianidanol were best antagonists for Mpro, Isovitexin, Quercitin,  β-Carotene, piperine, and Cianidanol were 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. Among them piperine and,β-Carotene were the ones with lowest binding energies.  All of these bioactive compounds could be considered as 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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Published

11-06-2022

How to Cite

SHARMA, S. (2022). Computational prediction of bioactive compounds as potential inhibitors of COVID-19 main protease (Mpro,) spike (S) glycoprotein receptor-binding domain (RBD) and RNA dependent RNA polymerase (RdRp). Innovare Journal of Medical Sciences, 10(4). Retrieved from https://innovareacademics.in/journals/index.php/ijms/article/view/45115

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