In silico screening of breadfruit (Artocarpus altilis) prenylated flavonoids identify potential SARS-CoV inhibitors

Nisha Govender, . and Siti Nur Athirah Mohd Kaspi, . and Thennavan Krishnan, . and Zeti Azura Mohamed Hussein, . (2023) In silico screening of breadfruit (Artocarpus altilis) prenylated flavonoids identify potential SARS-CoV inhibitors. Pertanika Journal of Science & Technology (Malaysia), 31 (5). 2145 -2159. ISSN 2231-8526

Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global health threat. Traditional herbals and dietary plants with medicinal values have a long antiviral history and, thus, are extensively studied in COVID-19 therapeutics development. Breadfruit (Artocarpus altilis) is a food crop with rich nutrient composition. This study screened selected breadfruit prenylated flavonoids for their potential inhibitory activities against the SARS-CoV family receptors using molecular docking and molecular dynamics (MD) simulation. The A. altilis prenylated flavonoids were selected as target ligands (artocarpin, artoindonesianin V, artonin M, cudraflavone A and cycloartobiloxanthone) and molecular targets from the SARS-CoV family were designated as receptors. Molecular docking was applied with the Lamarckian Genetic algorithm to measure the receptor-ligand orientation using AutoDock Vina software. The structural interactions of the receptor-ligand complexes were visualised using the Biovia Discovery Studio 4.5. Under all possible receptor-ligand combinations, the complexes’ minimum binding affinities (MBA) ranged from -5.5 to -9.1 kcal/mol and held by hydrophobic interactions, hydrogen bonds and electrostatic attractions. Receptor-ligand complexes with the least MBA (<-6.0 kcal/mol) along with strong structural interactions were validated by MD simulation using the GROMACS software. The 5RE4-artocarpin and 5RE4-artoindonesianin V showed the highest hydrophobic interactions at MBA=-6.6 kcal/mol and -6.4 kcal/mol, respectively. The trajectory analysis of 5RE4-artocarpin and 5RE4-artoindonesianin V complexes was fairly stable throughout a 50 ns MD simulation run. The findings conclude that artocarpin and artoindonesianin V are good potential SARS-CoV family receptor inhibitors.

Full text available from: Official URL: http://www.pertanika.upm.edu.my/resources/files/Pe...

Abstract

Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global health threat. Traditional herbals and dietary plants with medicinal values have a long antiviral history and, thus, are extensively studied in COVID-19 therapeutics development. Breadfruit (Artocarpus altilis) is a food crop with rich nutrient composition. This study screened selected breadfruit prenylated flavonoids for their potential inhibitory activities against the SARS-CoV family receptors using molecular docking and molecular dynamics (MD) simulation. The A. altilis prenylated flavonoids were selected as target ligands (artocarpin, artoindonesianin V, artonin M, cudraflavone A and cycloartobiloxanthone) and molecular targets from the SARS-CoV family were designated as receptors. Molecular docking was applied with the Lamarckian Genetic algorithm to measure the receptor-ligand orientation using AutoDock Vina software. The structural interactions of the receptor-ligand complexes were visualised using the Biovia Discovery Studio 4.5. Under all possible receptor-ligand combinations, the complexes’ minimum binding affinities (MBA) ranged from -5.5 to -9.1 kcal/mol and held by hydrophobic interactions, hydrogen bonds and electrostatic attractions. Receptor-ligand complexes with the least MBA (<-6.0 kcal/mol) along with strong structural interactions were validated by MD simulation using the GROMACS software. The 5RE4-artocarpin and 5RE4-artoindonesianin V showed the highest hydrophobic interactions at MBA=-6.6 kcal/mol and -6.4 kcal/mol, respectively. The trajectory analysis of 5RE4-artocarpin and 5RE4-artoindonesianin V complexes was fairly stable throughout a 50 ns MD simulation run. The findings conclude that artocarpin and artoindonesianin V are good potential SARS-CoV family receptor inhibitors.

[error in script]

Item Type:	Article
AGROVOC Term:	Artocarpus altilis
AGROVOC Term:	COVID-19
AGROVOC Term:	severe acute respiratory syndrome coronavirus 2
AGROVOC Term:	traditional medicines
AGROVOC Term:	computer applications
AGROVOC Term:	simulation models
AGROVOC Term:	human health
Geographical Term:	Malaysia
Depositing User:	Ms. Azariah Hashim
Date Deposited:	16 Jan 2025 01:29
Last Modified:	27 Jan 2025 02:49
URI:	http://webagris.upm.edu.my/id/eprint/1971

Actions (login required)

View Item