Molecular dynamics–guided design of sulfadiazine-based α-aminophosphonates as DNA gyrase inhibitors with enhanced binding stability and antibacterial activity

A focused series of six sulfadiazine-based α-aminophosphonate derivatives (M1–M6) was synthesized via the Kabachnik–Fields three-component reaction and evaluated as potential DNA gyrase inhibitors against multidrug-resistant Staphylococcus aureus (MRSA) and Pseudomonas aeruginosa. Among the synthesized analogues, compound M3—a para-benzonitrile-substituted α-aminophosphonate derivative—emerged as the most promising candidate. Twenty-five-nanosecond molecular dynamics simulations combined with MM-GBSA free-energy calculations demonstrated that M3 forms a stable complex within the catalytic domain of bacterial DNA gyrase, exhibiting reduced conformational fluctuations and the most favorable binding energetics relative to the parent sulfadiazine. Detailed structural analyses include RMSD, RMSF, radius of gyration, solvent-accessible surface area, principal component analysis, and dynamic cross-correlation mapping confirmed sustained active-site stabilization. Experimentally, M3 displayed markedly reduced MIC values against both tested pathogens and induced significant oxidative stress, as evidenced by elevated reactive oxygen species generation and lipid peroxidation. Complementary quantum mechanical (DFT) analysis revealed that the para-benzonitrile substitution contributes to enhanced electrophilic character and electronic polarization, rationalizing the observed structure–activity relationship. Subsequent liposomal encapsulation preserved antibacterial performance while enabling tunable delivery properties. Collectively, this integrated experimental–computational framework highlights sulfadiazine-derived α-aminophosphonates—particularly the para-benzonitrile analogue M3—as promising DNA gyrase-targeting antibacterial candidates.