Synthesis and Antibacterial Evaluation of Novel Ketoprofen Derivatives as Bacterial Transpeptidase Inhibitors via Combined <i>In Silico</i> and <i>In Vitro</i> Approaches

Ten ketoprofen derivatives were synthesized in two steps, producing six Schiff base derivatives from ketoprofen hydrazide and four hydrazine carbothioamide derivatives. Structural confirmation was achieved via FTIR, 1H-, and 13C-NMR spectroscopy. The prepared compounds were tested for their ability to kill bacteria against two types of Gram-positive bacteria, Staphylococcus aureus and Streptococcus pyogenes, and two types of Gram-negative bacteria, Escherichia coli and Klebsiella pneumoniae, using the resazurin broth test. In silico studies were also conducted to calculate the binding energies of the synthesized compounds against a key antimicrobial target, followed by molecular dynamics simulation and ADME prediction. Molecular docking studies revealed that 2-(3-benzoylphenyl)-N'-(4-hydroxy-3,5-dimethylbenzylidene)propane hydrazide (RAF1) had the strongest binding to the 3UDI domain (ΔG = –8.19 kcal/mol), while molecular dynamics simulation confirmed the stability of the ligand–receptor complexes with acceptable RMSD and RMSF values. 2-(2-(3-benzoylphenyl)propanoyl)-N-(4-chlorophenyl)hydrazine-1-carbothioamide (RAF9) exhibited a significantly reduced minimum inhibitory concentration against S. aureus compared to penicillin G. Furthermore, 2-(3-benzoylphenyl)-N'-(4-(benzyloxy)benzylidene)propane hydrazide (RAF5) exhibits superior zone inhibition against S. pyogenes compared to penicillin G. These results suggest that ketoprofen derivatives exhibit promising activity as bacterial transpeptidase inhibitors and warrant further optimization.