Isolation and In silico prediction of potential drug-like compounds with a new dimeric prenylated quinolone alkaloid from Zanthoxylum rhetsa (Roxb.) root extracts targeted against SARS-CoV-2 (Mpro)

Abstract

A new dimeric prenylated quinolone alkaloid, named 2,11-didemethoxy-vepridimerine A, was isolated from the root bark of Zanthoxylum rhetsa, together with thirteen known compounds. The structure of the new compound was elucidated on the basis of spectroscopic investigations (NMR and Mass). The interaction of the isolated compounds with the main protease of SARS-CoV-2 (Mpro) was evaluated using molecular docking followed by MD simulations. The result suggests that 2, 11-didemethoxy- vepridimerine A, the new compound has the highest negative binding affinity against the Mpro with free energy of binding of-8.5 Kcal/mol indicating interaction with the Mpro. This interaction was further validated with the help of MD simulation using remdesivir, one of the currently approved drugs against SARS-CoV-2, as a control.