Natural Compounds as Inhibitors of SARS-CoV-2 Main Protease (3CLpro): A Molecular Docking and Simulation Approach to Combat COVID-19.

Current Pharmaceutical Design
Md Tabish RehmanAfzal Hussain

Abstract

The emergence and dissemination of SARS-CoV-2 has caused high mortality and enormous economic loss. Rapid development of new drug molecules is the need of hour to fight COVID-19. However, the conventional approaches of drug development are time consuming and expensive. Here, we have adopted a computational approach to identify lead molecules from nature. Ligands from natural compounds library available at Selleck Inc (L1400) have been screened for their ability to bind and inhibit the main protease (3CLpro) of SARS-CoV-2. The natural compounds library of Selleck Inc. (Catalog No. L1400) were retrieved from www.selleckchem.com. It contains 2230 compounds in sdf format, curated from natural sources. Prior to molecular docking, all the ligands were prepared by adding hydrogen atoms and merging them with non-polar hydrogen atoms. Gasteiger partial charges were added, rotatable bonds were defined, and the energies were minimized using MMFF94 forcefield (11,12). The three-dimensional coordinates of the main protease (Mpro), also known as 3C-like protein (3CLpro), was downloaded from the protein databank available at https://www.rcsb.org/structure/6LU7. The structure was solved to a resolution of 2.16 Å and is bound with a peptide-lik...Continue Reading

Citations

Apr 4, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Caterina VicidominiGiovanni N Roviello

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