Structure-Based Virtual Screening of a Natural Product Database to Identify Several Possible SARS-CoV-2 Main Protease Inhibitors

A novel coronavirus (SARS-CoV-2) has been the cause of a recent pandemic of respiratory illness known as COVID-19. The lack of anti-viral drugs or vaccines to control the infection has resulted in an enormous number of seriously ill patients requiring hospitalization. In the absence of an effective vaccine, there is an urgent need for therapies which can fight COVID-19 infection. Readily available compounds in foods and plants may be one source of anti-viral compounds. Here, natural product chemicals from the Nuclei of Bioassays, Ecophysiology and Biosynthesis of Natural Products Database (NuBBE_DB) were screened against the main protease (Mpro) of SARS-CoV-2. This protease was chosen as a target due to its importance in the replication of SARS-CoV-2. Molecular docking was used to screen the natural products against Mpro to identify potential candidates. The identified candidates were further filtered using molecular dynamics simulation investigation. Nine natural compounds were identified for experimental validation, with carlinoside and quercetin 3-o-sophoroside being the top candidates.