Molecular Docking Approach of Natural Compound from Herbal Medicine in Java against Severe Acute Respiratory Syndrome Coronavirus-2 Receptor

Authors

  • Yuyun Yueniwati Department of Radiology, Faculty of Medicine, Universitas Brawijaya, Dr. Saiful Anwar General Hospital Malang, Malang, Indonesia https://orcid.org/0000-0001-9932-2015
  • Mokhamad Fahmi Rizki Syaban Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia https://orcid.org/0000-0003-4287-2379
  • Icha Farihah Deniyati Faratisha Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia https://orcid.org/0000-0002-6767-5577
  • Khadijah Cahya Yunita Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia https://orcid.org/0000-0002-7641-5531
  • Dedy Budi Kurniawan Master Program in Biomedical Science, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia
  • Gumilar Fardhani Ami Putra Master Program in Biomedical Science, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia
  • Nabila Erina Erwan Master Program in Biomedical Science, Faculty of Medicine, Universitas Brawijaya, Malang, Indonesia

DOI:

https://doi.org/10.3889/oamjms.2021.6963

Keywords:

Natural compound, Herbal medicine, Angiotensin-converting enzyme-2 receptor, Severe acute respiratory syndrome coronavirus-2, Molecular docking

Abstract

Indonesia's diversity of natural resources presents an intriguing opportunity for the exploration of potential herbal medicines. Numerous compounds, both purified and crude, have been reported to exhibit antiviral activity. The ACE-2 receptor may be a therapeutic target for SARS-CoV-2 infection. We used a search engine to search for herbal medicines with ACE-2 inhibitory activity to predict the potential inhibition of natural compounds (i.e., theaflavin, deoxypodophyllotoxin, gallocatechin, allicin, quercetin, annonamine, Curcumin, 6-gingerol, and cucurbitacin B) to SARS-CoV2 – ACE-2 complex. We performed molecular docking analysis using the ACE-2 protein target from Protein Data Bank. Protein stabilization was carried out to adjust to the body's physiology, carried out using Pymol by removing water atoms and adding hydrogen atoms. Ligands of active compounds from natural resources were selected and downloaded from the PubChem database, then optimized by Pymol software. The complexes of the tested ligand compounds and ACE-2 receptors, which have a bond strength smaller than the control were selected for analysis.  Theaflavin, Deoxypodophyllotoxin, Gallocatechin, Curcumin, and Cucurbitacin B had a strong bond affinity than the control ligands. Based on our data, deoxypodophylotoxin and Curcumin had the same interaction amino acid residus compare to the control ligand. This study concludes that deoxypodophyllotoxin and Curcumin have the greatest potential to inhibit the formation of the SARS-Cov2-ACE-2 complex; additionally, these compounds exhibit favorable pharmacological and pharmacodynamic properties. It is suggested that additional research be conducted to determine the biological effects of deoxypodopyllotoxin and Curcumin on ACE-2 receptors.

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Published

2021-12-09

How to Cite

1.
Yueniwati Y, Rizki Syaban MF, Faratisha IFD, Yunita KC, Kurniawan DB, Putra GFA, Erwan NE. Molecular Docking Approach of Natural Compound from Herbal Medicine in Java against Severe Acute Respiratory Syndrome Coronavirus-2 Receptor. Open Access Maced J Med Sci [Internet]. 2021 Dec. 9 [cited 2024 Nov. 19];9(A):1181-6. Available from: https://oamjms.eu/index.php/mjms/article/view/6963