Molecular Docking Approach of Natural Compound from Herbal Medicine in Java against Severe Acute Respiratory Syndrome Coronavirus-2 Receptor
DOI:
https://doi.org/10.3889/oamjms.2021.6963Keywords:
Natural compound, Herbal medicine, Angiotensin-converting enzyme-2 receptor, Severe acute respiratory syndrome coronavirus-2, Molecular dockingAbstract
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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Copyright (c) 2021 Yuyun Yueniwati, Mokhamad Fahmi Rizki Syaban, Icha Farihah Deniyati Faratisha, Khadijah Cahya Yunita, Dedy Budi Kurniawan, Gumilar Fardhani Ami Putra, Nabila Erina Erwan (Author)
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