MOLECULAR DOCKING OF CYMBOPOGON NARDUS (L.) RENDLE COMPOUNDS AS A PROTEASE INHIBITOR OF SARS-COV-2
Keywords:SARS-CoV-2, Main protease, Cymbopogon nardus, Molecular docking
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.
Boopathi S, Poma AB, Kolandaivel P. Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment. J Biomol Struct Dyn. 2021;39(9):3409-18. doi: 10.1080/07391102.2020.1758788. PMID 32306836.
The Food and Drug Supervisory Agency of the Republic of Indonesia. Informatorium of covid-19 drugs in. Indonesia; 2020.
Gupta MK, Vemula S, Donde R, Gouda G, Behera L, Vadde R. In silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel. J Biomol Struct Dyn. 2021;39(7):2617-27. doi: 10.1080/07391102.2020.1751300, PMID 32238078.
Elfiky AA. Anti-HCV, nucleotide inhibitors, repurposing against COVID-19. Life Sci. 2020;248:117477. doi: 10.1016/j.lfs.2020.117477. PMID 32119961.
Maier HJ, Bickerton E, Britton P. Preface coronaviruses. Methods Mol Biol. 2015;1282:v. doi: 10.1007/978-1-4939-2438-7. PMID 25870870.
Sanders JM, Monogue ML, Jodlowski TZ, Cutrell JB. Pharmacologic treatments for coronavirus disease 2019 (COVID-19): a review. JAMA. 2020;323(18):1824-36. doi: 10.1001/jama.2020.6019, PMID 32282022.
Purnomo H. Computational chemistry for pharmaceuticals and related sciences of insiliko tests and anticancer compounds. 1st ed. Yogyakarta: Student. Library; 2013.
da Silva LC, de Souza Perinotto WM, Sa FA, de Souza MAA, de Oliveira Barbosa Bitencourt R, Sanavria A. In vitro acaricidal activity of cymbopogon citratus, cymbopogon nardus and mentha arvensis against rhipicephalus microplus (Acari: Ixodidae). Exp Parasitol. 2020;216:107937. doi: 10.1016/j.exppara.2020.107937. PMID 32535114.
Zaidan S, Rahmat D, Djamil R, Mumpuni E. Activity of compounds in sargassum sp. as anti-atherosclerosis with ligand-receptor comparison HMG-CoA reductase-simvastatin (1HW9) and in silico toxicity test. Ilmu Kefarmasian Indones. 2019;17:120-5.
Santoso B, Tirtodiharjo MK, Artinda SA. Kajian docking 3-[(Asetiloksi)Metil-7- [(4-Hidroksi-3-Metoksifenil)Metilidin] Amino]-8-Okso-5-Thia-1-Azabisiklo[4.2.0]oct-Ene-Asam Karboksilat menggunakan. DOCK6. 2016:1-13.
How to Cite
Copyright (c) 2022 FAJRI RIFALDI, ESTI MUMPUNI, SHIRLY KUMALA, NOVI YANTIH, DESI NADYA AULENA, SAFIRA NAFISA
This work is licensed under a Creative Commons Attribution 4.0 International License.