Metabolomic and molecular insights into adenosine triphosphate synthase inhibitors from <i>Micromonospora</i> sp. as novel antimicrobial agents against multidrug-resistant Gram-negative pathogens of enteric origin

The overuse of antibiotics has accelerated the emergence of antibiotic-resistant bacteria, necessitating alternative treatment options. Micromonospora spp., known for producing bioactive metabolites, is a promising source of novel antimicrobials. This study evaluated the antimicrobial potential of metabolic ethyl-acetate extracts from three Micromonospora strains against multidrug-resistant (MDR) Gram-negative clinical isolates of enteric origin. Using the Kirby-Bauer modified disc diffusion method, following Clinical and Laboratory Standards Institute guidelines, the extract from Micromonospora strain 65SH exhibited the most potent activity, with minimum inhibitory concentrations of 25 µg/ml against Enterobacter aerogenes and 12.5 µg/ml against Escherichia coli. 16S rRNA gene sequencing identified the strain as closely related to Micromonospora fluminis (99.6% similarity). Further analysis using LC-QTOF-MS/MS non-targeted metabolomics identified six bioactive compounds-melibiose, oligomycin A, queuine, heptelidic acid, diethyl phthalate, and 2'-deoxyguanosine-linked to the inhibition of bacterial enzymes essential for proliferation. Molecular modeling suggested that these compounds disrupt E. coli ATP synthase and inhibit ATP-dependent bacterial topoisomerases. This study integrates metabolomics, molecular docking, and genomics, offering robust mechanistic insights into ATP synthase inhibition. Future research will include fecal isolate testing, detailed structural elucidation using nuclear magnetic resonance (NMR) spectroscopy, and experimental validation to explore the therapeutic potential of Micromonospora-derived compounds.