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

Journal of Public Health in Africa

Field Value
Title In silico screening of potential compounds from begonia genus as 3CL protease (3Cl pro) SARS-CoV-2 inhibitors
Creator Maulana, Saipul Wahyuni, Tutik S. Widiyanti, Prihartini Zubair, Muhammad S.
Subject — Begonia; SARS-CoV-2; 3-Chymotrypsin-Like protease (3Clpro); Molecular docking; Molecular dynamics
Description 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.
Publisher AOSIS
Date 2023-03-30
Type info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion — —
Format application/pdf
Identifier 10.4081/jphia.2023.2508
Source Journal of Public Health in Africa; Vol 14, S 1 (2023): 4th Joint Conference of UNAIR-USM, International Conference of Pharmacy and Health Sciences (ICPHS); 6 2038-9930 2038-9922
Language eng
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Rights Copyright (c) 2024 Saipul Maulana, Tutik S. Wahyuni, Prihartini Widiyanti, Muhammad S. Zubair