Deciphering the anti-COVID-19 compounds from Streptomyces isolated from the tea rhizosphere of Darjeeling Hills, India

Abstract

The outbreak of the novel coronavirus SARS-CoV-2, originating in China, has escalated into a global pandemic, causing severe health and socioeconomic impacts. Despite the development of vaccines, emerging variants continue to pose significant threats to human health. Therefore, the search for novel antiviral agents from natural sources remains a global priority. Streptomyces, a prolific producer of bioactive secondary metabolites, offers a promising avenue for discovering anti-COVID-19 compounds. Streptomyces strains were isolated from the tea rhizosphere soil of the Darjeeling hills, India. The bioactive metabolites produced by the selected strain were identified using Gas Chromatography–Mass Spectrometry (GC–MS). The anti-COVID-19 potential of these compounds was evaluated through in silico molecular docking and molecular dynamics (MD) simulation studies targeting the SARS-CoV-2 main protease (Mpro). Among the detected compounds, Vinylbital, Ergotaman, and Bis(2-ethylhexyl) phthalate exhibited strong binding affinities toward the active site of Mpro, suggesting their potential inhibitory effects. The stability of these ligand–protein complexes was further supported by RMSD and RMSF analyses during MD simulations, validating the reliability of the docking results. This study reports, for the first time, the discovery of Streptomyces-derived bioactive compounds from the tea rhizosphere of Darjeeling hills with promising in silico anti-COVID-19 activity. These findings highlight the potential of rhizospheric actinobacteria as a valuable source of antiviral metabolites and provide a foundation for future experimental validation and drug development efforts.