Combining an OSMAC approach and untargeted metabolomics to profile compounds exhibiting anti-HIV-1 activities in an endophytic fungus, Penicillium Rubens P03MB2

Abstract

The persistent burden of HIV-1 in Sub-Saharan Africa underscores the need for innovative treatments, as current antiretroviral therapies cannot eliminate latent proviral reservoirs and face challenges from multidrug-resistant strains. This study investigates the potential of Penicillium rubens P03MB2, an endophytic fungus from the Albizia adianthifolia plant, as a source of novel anti-HIV-1 compounds. The fungus was cultivated in various media (malt extract broth, oats, and rice), with oat media yielding crude extracts exhibiting significant anti-HIV-1 activity. Active fractions were further analyzed using an untargeted metabolomics and molecular networking approach, revealing clusters of secondary metabolites, including coumarins and other anti-HIV-1-associated compounds. A virtual screening workflow was employed to assess the binding affinities of these metabolites against HIV-1 protease. Furthermore, molecular dynamics simulations were used to analyze ligand-protein complex stability. Binding free energy calculations highlighted diosgenin as a promising candidate, with a binding free energy of -34.59 kcal/mol, outperforming the co-crystallized ligand ORV. This research demonstrates the potential of secondary metabolites from Penicillium rubens as novel anti-HIV-1 agents, offering a foundation for further developing effective antiviral therapies.