MOLECULAR DOCKING OF CYMBOPOGON NARDUS (L.) RENDLE COMPOUNDS AS A PROTEASE INHIBITOR OF SARS-COV-2

Abstract

Objective: The study aimed to obtain active compounds from Cymbopogon nardus as candidates for protease inhibitor of SARS-CoV-2 virus by assessing the ligand-binding affinity in the binding pocket of SARS-CoV-2 main protease protein. Methods: Molecular docking as a protease inhibitor of SARS-CoV-2 was carried using computational software Molegro Virtual Docker (MVD); computational docking was carried using receptors with Protein Data Bank (PDB) were also used to compare the affinity strength of the test compounds against the protease receptor (code of 5R81). The compounds of Cymbopogon nardus were optimized before docking using ChemDraw and minimized energy using Chem3D. Visualization of the docking result by using Discovery Studio and pkCSM was utilized to perform a pharmacokinetic and toxicological analysis (ADMET). Results: The result showed geranyl acetate, elemol, citronellal, and citronellyl acetate compounds from Cymbopogon nardus has a rerank score more negative than native ligand from 5R81 receptor as a protease inhibitor of SARS-CoV-2. Conclusion: Cymbopogon nardus can be developed as an antivirus with the mechanism of a protease inhibitor of SARS-CoV-2 candidates after further experimental tests.