Endophytic Klebsiella pasteurii from Alliaria petiolata L. Produces DNA Gyrase-Inhibiting Metabolites with Broad-Spectrum Antibacterial Activity

The escalating threat of antimicrobial resistance underscores the urgent need for novel antibacterial agents. In this study, we investigated the secondary metabolites produced by Klebsiella pasteurii strain AP5, an endophyte isolated from the flowers of the understudied plant Alliaria petiolata L., for their antibacterial activity and potential mechanism of action. Gas chromatography–mass spectrometry analysis of the crude extract revealed 12 bioactive compounds, with predominant constituents including pyrrolo[1,2-a]pyrazine-1,4-dione,hexahydro-3-(2-methyl)- (28.59%), Z-3-methyl-2-decene (21.34%), and pyrrolidino[1,2-a]piperazine-3,6-dione (18.70%). The extract demonstrated statistically significant antibacterial activity (p < 0.05), exhibiting inhibition zones against Pseudomonas aeruginosa (23.0 ± 2.82 mm), Escherichia coli (30.5 ± 0.70 mm), Salmonella typhi (28.5 ± 2.12 mm), Enterobacter sp. (28.5 ± 2.12 mm), Klebsiella pneumoniae (20.5 ± 0.70 mm), and Staphylococcus aureus (26.5 ± 2.12 mm). In silico molecular docking analysis further supported the antibacterial potential of the identified compounds by predicting their strong binding affinities at the active site of bacterial DNA gyrase. These findings highlight the potential of endophytic K. pasteurii from A. petiolata as a promising source of novel antibacterial agents and suggest a mechanistic basis for their activity.