Molecular docking reveals the potential of Cleome amblyocarpa isolated compounds to inhibit COVID-19 virus main protease

Abstract

Nine flavonoids and one saponin were isolated from the aerial parts of Cleome amblyocarpa. Molecular docking of isolated compounds on COVID-19 virus main protease showed variable binding affinities with scores ranging from −8.63 to −6.08 compared to N3 inhibitor (−10.10) and binding modes better than N3 inhibitor in some of the isolated compounds. The descending order of the binding affinity of the tested drugs was as follows: N3 inhibitor (11, docked) > kaempferitrin (6) > isorhamnetin 3,7-O-α-L-dirhamnoside (3) > kaempferol 3-O-β-glucoside-7-O-α-rhamnoside (2) > soysaponin I (1) > isorhamnetin 7-O-α-L-rhamnoside (10) > genistein-8-C-glucoside (8) > tamarixetin 7-O-β-D-glucoside (4) > isoprunetin-7-glucoside (9) > genistin (5) > 5-O-methylgenistein (7). These results could be a good start for fast further examination of the isolated compounds in vitro and in vivo either alone or in combination for the treatment of the COVID-19 virus. Besides, this work gives an explanation of the SAR required for targeting the newly emerged SARS-CoV-2 protease and facilitates the future design and synthesis of new drugs targeting it as well.