Molecular docking study of seventy-six phytomolecules from sixteen aromatics medicinal plants as promising inhibitors of five non-structural proteins of SARS-CoV-2

Since the identification of COVID-19 in China in December 2019, scientists and researchers have been continuously discovering and proposing drugs for this disease. Many efforts have been made to examine medicinal plants known for their benefits in treating infectious diseases and for their actions in boosting of the immune system. Repurposing of FDA-approved antiviral drugs has also been advanced. However, no effective antiviral drug specific to COVID-19 is currently available. To contribute in the search for drugs against this disease, the present study aims to identify secondary metabolites (or phytomolecules) possessing an inhibitory effect on the replication of SARS-CoV-2, the etiological agent of COVID-19.

76 secondary metabolites from 16 aromatics medicinal plants from Madagascar were uploaded to the PubChem server. Then, they were docked with 5 non-structural proteins (nsps) of SARS-CoV-2, including the main protease, the papain-type protease, the RNA-dependent RNA polymerase, the helicase and the 2'-O-methyltransferase, using the Autodock Vina program integrated in the PYRIX 0.8 software.

The results show that 5 secondary metabolites of Cinnamosma fragrans (Capsicodendrin, Ugandensolide, Cinnamolide, Tocotrienol and Pereniporin B) have good affinity with the 5 nsps of SARS-CoV-2 and can inhibit its functions in viral replication. Therefore, these phytomolecules could be used in the development of antiviral drugs against SARS-CoV-2 and COVID-19. Nevertheless, further in vitro and in vivo studies should be performed to valorize these results obtained by the in silico method.