In silico screening of the effectiveness of natural compounds from algae as SARS-CoV-2 inhibitors: molecular docking, ADMT profile and molecular dynamic studies

Marine species are known as rich sources of metabolites largely involved in the pharmaceutical industry. This study aimed to evaluate in silico the effect of natural compounds identified in algae on the SARS-CoV-2 Main protease, RNA-dependent-RNA polymerase activity (RdRp), endoribonuclease (NSP15)...

Full description

Saved in:
Bibliographic Details
Published in:Journal of biomolecular structure & dynamics 2023-05, Vol.41 (7), p.3129-3144
Main Authors: Mohammed Ali, Hani S. H., Altayb, Hisham N., Bayoumi, Ahmed Atef Mohamed, El Omri, Abdelfatteh, Firoz, Ahmad, Chaieb, Kamel
Format: Article
Language:English
Subjects:
ADMT
Algae
antiviral
COVID-19
Humans
in silico study
molecular docking
Molecular Docking Simulation
molecular dynamics
Molecular Dynamics Simulation
RNA-Dependent RNA Polymerase
SARS-CoV-2
Spike Glycoprotein, Coronavirus
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Marine species are known as rich sources of metabolites largely involved in the pharmaceutical industry. This study aimed to evaluate in silico the effect of natural compounds identified in algae on the SARS-CoV-2 Main protease, RNA-dependent-RNA polymerase activity (RdRp), endoribonuclease (NSP15) as well as on their interaction with viral spike protein. A total of 45 natural compounds were screened for their possible interaction on SARS-CoV-2 target proteins using Maestro interface for molecular docking, molecular dynamic (MD) simulation to estimate compounds binding affinities. Among the algal compounds screened in this study, three (Laminarin, Astaxanthin and 4'-chlorostypotriol triacetate) exhibited the lowest docking energy and best interaction with SARS-CoV-2 viral proteins (Main protease, RdRp, Nsp15, and spike protein). The complex of the main protease with laminarin shows the most stable RMSD during a 150 ns MD simulation time. Which indicates their possible inhibitory activity on SARS-CoV-2. Communicated by Ramaswamy H. Sarma
ISSN:0739-1102
1538-0254
DOI:10.1080/07391102.2022.2046640