Identification of amentoflavone as a potent SARS-CoV-2 Mpro inhibitor: a combination of computational studies and in vitro biological evaluation.

Abstract

Small-molecule inhibitors of SARS-CoV-2 M^pro that block the active site pocket of the viral main protease have been considered potential therapeutics for the development of drugs against SARS-CoV-2. Here, we report the identification of amentoflavone (a biflavonoid) through docking-based virtual screening of a library comprised of 231 compounds consisting of flavonoids and isoflavonoids. The docking results were further substantiated through extensive analysis of the data obtained from all-atom 150 ns MD simulation. End-state effective free energy calculations using MM-PBSA calculations further suggested that (R_a)-amentoflavone (C3'-C8''-atropisomer) may show a greater binding affinity towards the M^pro than (S_a)-amentoflavone. In vitro cytotoxicity assay established that amentoflavone showed a high CC₅₀ value indicating much lower toxicity. Further, potent inhibition of the M^pro by amentoflavone was established by studying the effect on HEK293T cells treated with SARS-CoV-2 M^pro expressing plasmid.