Potency of three brown seaweeds species as the inhibitor of RNA-dependent RNA polymerase of SARS-CoV-2

Abstract

The objective of this study was to evaluate the binding activity of bioactive compounds from three brown seaweed on RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 by docking method. The bioactive identification of Sargassum cristaefolium, S. echinocarpum, and Padina australis was carried out using HPLC-HRMS. The ligand structures in PDB format were obtained from the PubChem website and the RdRp from the RCSB website. The binding affinity of the interaction of bioactive components with the RdRp Covid-19 was determined by docking method using AutoDock Vina on PyRx software. The visualization of 2D and 3D interactions between ligands and macromolecules were carried out with the Biovia Discovery Studio and PyMol software. The decoction of S. cristaefolium, S. echinocarpum, and P. australis contained ninety one compounds, and there were twenty compounds with a strong affinity for RdRp. Rhamnetin was a compound of the Sargassum species have the strongest binding affinity of -7.6 kcal/mol. Its affinity bonds were hydrogen bonds in Val315, Arg349, Phe396, Asn628, and hydrophobic bonds in the form of bonds to π-ε and π-alkyl from Pro461. Taribavirin bound to RdRp in hydrogen bonds at Thr393, Thr394, and Phe396 and bound hydrophobically to π-alkyl from Cys395. Rhamnetin has the same binding affinity region as taribavirin, which was the subdomain finger of the RdRp. In conclusion, rhamnetin is a compound of Sargassum sp that can inhibit the replication and transcription of RdRp SARS-CoV-2 and further studies using the molecular dynamics method on the mechanism of interaction between rhamnetin and the viral RdRp of SARS-CoV-2 are mandatory.