Original Article

In silico screening of potential compounds from begonia genus as 3CL protease (3Cl pro) SARS-CoV-2 inhibitors

Saipul Maulana, Tutik S. Wahyuni, Prihartini Widiyanti, Muhammad S. Zubair
Journal of Public Health in Africa | Vol 14, S 1 : 4th Joint Conference of UNAIR-USM, International Conference of Pharmacy and Health Sciences ICPHS| a109 | DOI: https://doi.org/10.4081/jphia.2023.2508 | © 2024 Saipul Maulana, Tutik S. Wahyuni, Prihartini Widiyanti, Muhammad S. Zubair | This work is licensed under CC Attribution 4.0
Submitted: 03 April 2024 | Published: 30 March 2023

About the author(s)

Saipul Maulana, Master Program of Department Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia
Tutik S. Wahyuni, Department Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia; and, Center for Natural Products Medicine Research and Development, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
Prihartini Widiyanti, Biomedical Engineering, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia; and, Institute of Tropical Disease (ITD), Universitas Airlangga, Surabaya, Indonesia
Muhammad S. Zubair, Faculty of Science, Department of Pharmacy, University of Tadulako, Palu, Indonesia

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Abstract

Background: The emergence of Coronavirus disease (COVID-19) has been declared a pandemic and made a medical emergency worldwide. Various attempts have been made, including optimizing effective treatments against the disease or developing a vaccine. Since the SARS-CoV-2 protease crystal structure has been discovered, searching for its inhibitors by in silico technique becomes possible. Objective: This study aims to virtually screen the potential of phytoconstituents from the Begonia genus as 3Cl pro-SARS-CoV- 2 inhibitors, based on its crucial role in viral replication, hence making these proteases “promising” for the anti-SARS-CoV-2 target. Methods: In silico screening was carried out by molecular docking on the web-based program DockThor and validated by a retrospective method. Predictive binding affinity (Dock Score) was used for scoring the compounds. Further molecular dynamics on Desmond was performed to assess the complex stability. Results: Virtual screening protocol was valid with the area under curve value 0.913. Molecular docking revealed only β-sitosterol-3-O-β-D-glucopyranoside with a lower docking score of - 9.712 kcal/mol than positive control of indinavir. The molecular dynamic study showed that the compound was stable for the first 30 ns simulations time with Root Mean Square Deviation <3 Å, despite minor fluctuations observed at the end of simulation times. Root Mean Square Fluctuation of catalytic sites HIS41 and CYS145 was 0.756 Å and 0.773 Å, respectively. Conclusions: This result suggests that β-sitosterol-3-O-β-D- glucopyranoside might be a prospective metabolite compound that can be developed as anti-SARS-CoV-2.

Keywords

Begonia; SARS-CoV-2; 3-Chymotrypsin-Like protease (3Clpro); Molecular docking; Molecular dynamics

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