Molecular Docking Evaluation of Some Indonesian’s Popular Herbals for a Possible COVID-19 Treatment

Abstract

Indonesia’s rich tropical biodiversity offers many possible options for fighting the unprecedented outbreak of coronavirus disease 2019 (COVID-19). In this paper, we evaluate the in silico (molecular docking) performance of some popular herbal supplements and natural remedies, which are usually consumed by Indonesian people and compare them to the docking performance of the control ligand (N3 inhibitor) and some protease-inhibitor drugs. The tested active compounds were grouped based on their popularity in the market, i.e., honey, black seed (Nigella sativa), Javanese turmeric (Curcuma xanthorriza roxb), and mangosteen, which usually served in the form of encapsulated oil or powder. The results show that most of the tested active compounds perform better than N3 inhibitor and protease inhibitor drugs (lopinavir and darunavir) in inhibiting the main protease of SARS-CoV-2 virus of COVID-19 (C19MP). Based on the combined scores of binding affinity, the similarity of active sites (SAS), and the drug-likeness properties of the ligand, gamma mangostin turns out to be the best possible C19MP inhibitor as compared to other ligands. The active site analysis also reveals that His41, Met49, Leu141, and Asn142 are among the most important amino acids that play a significant role in the protein-ligand binding due to their frequent occurrence in the docking simulation.