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

Abstract

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

Keywords:

• Algae
• antiviral
• SARS-CoV-2
• in silico study
• molecular docking
• ADMT
• molecular dynamics

Disclosure statement

No potential conflict of interest was reported by the authors.

Author contributions

HSH, HNA, KC, AAM, AF and AEO contribute to data collection experimental design, conceptualization, and manuscript writing, HNA and KC wrote the manuscript, all team critically reviewing the final version of the manuscript and project supervision, HNA, AF, KC did the bioinformatics analysis.

Additional information

Funding

This project was funded by the Deanship of Scientific Research (DSR) at King Abdulaziz University, Jeddah, under a grant (GCV19-31-1441). Therefore, the authors gratefully acknowledge technical and financial support from King Abdulaziz University, DSR, Jeddah, Saudi Arabia.