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A combination of docking
approaches, scoring functions, molecular dynamic simulation, and literature
mining have been employed to screen readily available natural products (unique
27256 chemical entities, 598435 unique compounds), which can inhibit the
SARS-CoV-2 main protease. Theaflavin digallate, a major constituent of black
tea, has been observed to be as three top hits after the virtual screening of
598435 unique compounds. The main protease-theaflavin digallate complex
appeared to be in the metastable stage and interact with critical active site
residues of the main protease during molecular dynamics simulation for 200 ns. Invitro evidence on main protease
inhibition of 2003 SARS-CoV by theaflavin digallate is available in the
scientific literature. As evident by the dynamics of intermolecular
interactions, theaflavin digallate, forms approximately three hydrogen bonds
with Glu166 of main protease, mostly through hydroxyl groups in the benzene
ring of benzo(7) annulen-6-one. Glu166 is the most critical amino acid for main
protease dimerization, which in turn, is necessary for catalytic activity.We have employed chloroquine and epigallocatechin
gallate (green tea component) as a control set. Based on computational
molecular interaction and data available in scientific literature, theaflavin
digallate can inhibit the main protease of SARS-CoV-2.