Integrated computational and experimental evaluation of natural products targeting PGM/AlgC and HisIE in multidrug-resistant respiratory pathogens

Abstract

Background The increasing prevalence of multidrug-resistant (MDR) Gram-negative respiratory pathogens has reduced the effectiveness of conventional antimicrobial therapies and created a need for antibacterial strategies targeting bacterial metabolic and virulence-associated functions. AlgC, a phosphomannomutase/phosphoglucomutase involved in cell-envelope and exopolysaccharide biosynthesis, and the bifunctional histidine-biosynthesis enzyme HisIE represent potentially relevant bacterial targets. Objective This study evaluated the antibacterial and enzyme-inhibitory activities of three natural products, 5-hydroxysophoranone, 10′-desmethoxystreptonigrin, and isoforsythiaside—and investigated their predicted interactions with AlgC and HisIE using an integrated computational and in vitro experimental approach. Methods Molecular docking was performed to examine the interactions of the selected compounds with the predicted catalytic or ligand-binding regions of AlgC and HisIE. Two lead protein–ligand complexes were subsequently evaluated using 500-ns molecular dynamics simulations and MM/GBSA analysis. Antibacterial activity against MDR respiratory isolates was assessed using broth dilution and disc-diffusion assays. Cytotoxicity was examined in A549 and BEAS-2B epithelial cells using the MTT assay. Cell-associated antibacterial activity, recombinant-enzyme inhibition, Western blotting, and quantitative real-time PCR were used to assess antibacterial effects and changes in selected metabolic and virulence-associated markers. Results The selected natural products showed favorable predicted interactions with the investigated AlgC and HisIE binding regions. Among the tested compounds, 10′-desmethoxystreptonigrin exhibited the strongest predicted interaction with AlgC and showed the lowest minimum inhibitory concentrations, the greatest reduction in cell-associated bacterial burden, and the strongest inhibition of the recombinant enzymes. The two simulated lead complexes retained generally stable protein–ligand interactions during the molecular dynamics trajectories. Treatment with the compounds was also associated with reduced expression of selected metabolic and virulence-associated markers, including pgm/algC, hisIE, lasR, pslA, and ompA. Isoforsythiaside demonstrated comparatively greater epithelial-cell compatibility, whereas 10′-desmethoxystreptonigrin showed greater antibacterial potency but lower host-cell tolerance. Conclusion The combined computational and experimental findings identify 10′-desmethoxystreptonigrin and 5-hydroxysophoranone as candidate natural-product scaffolds with antibacterial and recombinant AlgC/HisIE-inhibitory activities. The observed enzyme inhibition and changes in selected molecular markers are consistent with possible interference in AlgC- and HisIE-associated processes; however, they do not by themselves establish direct intracellular target engagement or pathway-specific causality. Further studies using target-engagement assays, genetically defined bacterial strains, broader clinical-isolate panels, biofilm and quorum-sensing assays, and in vivo respiratory-infection models are required to validate the proposed mechanism, safety, and translational potential.