In vitro and in silico docking studies of antibacterial compounds derived from endophytic Penicillium setosum

Occasionally, endophytic fungal species cognize as a hidden prospective source of plant secondary metabolites. In this study, a potent Penicillium setosum sp. nov. was explored for its detailed antibacterial action on Escherichia coli and Staphylococcus aureus through different in vitro and in silico assays. Fluorescence based viability assay determined increase in the number of dead cells in course of time with the continual exposure of extract during a 4 h period. Scanning electron micrographs reflect the distinguishable morphological changes in treated cells, namely shortening of size, bubbles, and blisters on the surface of E. coli, as well as open holes and deep craters on the surface of S. aureus, ultimately leading to rupture of cells. Significant intracellular changes in bacteria were remarkably noticed through different membrane permeabilization assays. The rate of Na⁺ and K⁺ leakage with respect to time, intracellular material and cytoplasmic β-galactosidase release were measured spectroscopically. The results indisputably prove that membrane disruption of S. aureus cells occurs within 2 h and in E.coli occurs in between 2 and 4 h of exposure. Crude extract of P. setosum was fractioned using semi-preparative HPLC and the separated antibacterial active fraction showed antibacterial efficacy with the minimum inhibitory concentration of 8 μg/mL against both organisms. Active fraction contains four well-known plant metabolite belongs to the polyphenolic group (Leucodelphinidin, dihydroquercetin, kaempferol, and quercetin) and one polyketide (patulin) familiar as fungal metabolite, identified through high resolution LC-MS. Interaction mechanisms of identified compounds with nine important antimicrobial drug targets showed highest binding affinity by leucodelphinidin followed by dihydroquercetin > kaempferol > quercetin. This is the first instance of using leucodelphinidin and dihydroquercetin for detailed interaction study with multiple targets, and it was found that they showed more effective interaction than quercetin, which was earlier utilized for antibacterial studies.