DOI: https://doi.org/10.14710/jksa.26.5.166-177

The potential of Myricitrin, a Flavonoid Compound in Eugenia polyantha from Indonesia, as an Antiviral Drug for SARS-Cov-2 through the Molecular Docking Analysis

1Department of Biochemistry, Faculty of Mathematics and Natural Sciences, IPB University, Kampus IPB Darmaga, Bogor, Jawa Barat, Indonesia

2Department of Biochemistry, Faculty of Mathematics and Natural Sciences, IPB University, Bogor, 16680, Indonesia

3Department of Applied Biosciences, Faculty of Agriculture, Ehime University, Ehime, Japan

Received: 18 Oct 2022; Revised: 9 Jun 2023; Accepted: 22 Jun 2023; Published: 31 Jul 2023.
Open Access Copyright 2023 Jurnal Kimia Sains dan Aplikasi under http://creativecommons.org/licenses/by-sa/4.0.

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Abstract

A Flavonoid glycoside compound, isolated and identified from E. polyantha as myricitrin, was analyzed as a ligand for its molecular binding activity against SARS-CoV-2 protein (receptor binding domain on Spike/RBD, main protease/nsp5, EndoRNAse, RNA-dependent-RNA-polymerase/RdRp), and its receptor, ACE2, and computationally assessed via molecular docking method. This study aims to determine the potential of myricitrin in E. polyantha from Indonesia as an antiviral drug for SARS-CoV-2 through molecular docking and molecular dynamic simulation analysis. The results showed that the myricitrin had the strongest binding affinity energy towards the three important SARS-CoV-2 proteins, namely endoRNAse, main protease (3CLpro), and RdRp with ∆G values of −9.60 kcal/mol, −8.40 kcal/mol, and −8.30 kcal/mol, respectively. These values are stronger than the comparator ligands of favipiravir (−5.60 kcal/mol), atazanavir (−7.20 kcal/mol), and remdesivir (−7.70 kcal/mol). This indicated that the compound has the potential as an inhibitor against 3CLpro, endoRNAse, and RdRp of SARS-CoV-2 proteins. This result was supported by the prediction made according to the Molprobity and PASS Online web servers, which showed that myricitrin has high bioactivity potential as an enzyme inhibitor (with a score of 0.38) and antiviral (with a score of 0.704).

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Keywords: Eugenia polyantha; molecular docking; myricitrin; SARS-CoV-2
Funding: Deputy for Strengthening Research and Development, Ministry of Research and Technology of the Republic of Indonesia-Research and Innovation Agency (Kemenristek-BRIN)

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