Investigation of New Biologically Active Benzo[4,5]imidazo[1,2-a]pyrimidine Derivatives as Broad-Spectrum Antimicrobial Agents: Synthesis, Anti-Biofilm, ROS and in Silico Studies

A new series of biologically active benzo[4,5]imidazo[1,2-a]pyrimidine derivatives containing different substitutions such as thiophene, pyridine, pyrrole, and 3,4-dimethoxyphenyl at carbon 2 and, phenyl-pyrrolidinyl, -morpholinyl, -piperidinyl at carbon 4 were synthesized. The treatment of chalcone derivatives 5-16 with 2-aminobenzimidazole in DMF and drops of TEA afforded the targeted benzo[4,5]imidazo[1,2-a]pyrimidine derivatives (18-29) in good to excellent yields. These compounds were tested to evaluate their antimicrobial activity against different microbial pathogens such as Aspergillus niger, Candida albicans, Staphylococcus aureus and Salmonella typhimurium. Potently compounds 19 and 23 were contributed in a broad-spectrum inhibition process against all tested pathogens with lower MIC values ranging between 10 and 60 µg/mL. Furthermore, the efficiency of the potent compounds to inhibit the biofilm formation was moderately detected by compounds 18, 19 and 23. This study investigated the antimicrobial potential of synthesized compounds through experimental and computational approaches. Compounds 18, 19, 23, 25, and 28 demonstrated strong binding affinities to antimicrobial target proteins (1AD4, 2SIL, 4ZA5, and 5TZ1), suggesting their ability to inhibit key enzymes via diverse molecular interactions. Computational ADMET profiling confirmed their compliance with Lipinski's rules, indicating favorable drug-like properties. Molecular dynamics simulations further validated the stability of complexes formed by compounds 19 and 28, with stable RMSD values (0.17–0.45 nm), low RMSF fluctuations (0.10–0.7 nm), and consistent structural compactness (Rg: 1.45–1.75 nm). Solvent exposure (SASA: 120–220 nm²) varied across complexes. These results highlight the compounds’ potential as promising candidates for antimicrobial drug development, warranting further preclinical exploration.