Molecular Docking Studies : Activity of Natural Compounds as SAR-CoV-2 Inhibitors in Papain-like protease (PL pro)

Abstract

SARS-CoV-2 is a respiratory virus often referred to as COVID-19. The challenge of finding SARS-CoV-2 antivirals also attracted many researchers, one of which was by utilizing natural compounds. The purpose of this study was to analyze the potential activity of herbal plants in Indonesia as anti-COVID-19, specifically tasked with inhibiting the target protein, PLpro using the in-silico method. This research is an insilico approach with molecular docking studies. Docking simulation in this study was used to analyze the activity of natural herbal plant compounds against the target protein, namely PLpro. In addition, the docking method is also able to examine the interaction of compounds contained in plants with target receptors seen from a computational-based visual approach. So, the results obtained in this study are that when viewed from the value of the gibbs energy produced, the compound that has the best activity to inhibit the PLpro target protein (SARS CoV-2) is Luteolin. The Gibbs energy generated in the Luteolin docking simulation is -7.3 kcal/mol. The Gibbs energy value produced by the Luteolin ligand is the most negative or the smallest value of the 14 tested ligands. This means that the bond formed between the Papain-like protease (PLpro) protein and the Luteolin ligand is the most stable among the others. In addition to the Luteonin compound, there are also several compounds that have quite good potential when viewed from the amount of gibbs energy owned, namely Mangostin, quercetin compounds and Myricetin compounds with gibbs energy values of -7.1 kcal / mol, -7.0 kcal / mol and -7.0 kcal / mol. Based on these results, it can be concluded that several compounds from typical Indonesian plants such as Luteolin compounds (Compounds found in Celery plants (Apium graveolens)), Mangostin compounds (Compounds found in Mangosteen plants (Garcinia mangostana)), Quercetin compounds (Compounds found in Citrus plants (Citrus aurantium)) and Myricetin compounds (Compounds found in Clove plants (Syzygium aromaticum)) have the potential to be developed as anti-COVID-19.