Synthesis, Characterization, and Biological Evaluation of Benzimidazole Derivatives: In Vitro and In Silico Investigations

Abstract

ABSTRACT In this study, a series of benzimidazole derivatives was synthesized and characterized using FT‐IR, NMR, and mass spectrometry, followed by density functional theory (DFT) and molecular docking analyses to elucidate their structural, electronic, and biological properties. DFT calculations at the B3LYP/6‐311++G(d,p) level revealed HOMO‐LUMO energy gaps ranging from 3.46 to 4.52 eV, indicating moderate electronic reactivity and stability, while electrophilicity (ω = 3.14–6.80 eV) and dipole moment (μ = 3.03–7.30 D) values highlighted their potential for polar and nucleophilic interactions. The antibacterial evaluation demonstrated that BI 2 and BI 3 exhibited the most potent inhibitory effects, with minimum inhibitory concentrations (MICs) of 0.5–0.7 mg/mL against Staphylococcus aureus and Klebsiella pneumoniae , and 0.18–0.45 mg/mL against Pseudomonas aeruginosa and Escherichia coli . Antibiofilm assays further confirmed strong inhibition at concentrations as low as 0.4 mg/mL. Molecular docking simulations against E. coli targets, RecQ helicase, DNA gyrase B, PBP3, and OXA‐1 β‐lactamase, showed that BI 2 and BI 3 had the most favorable binding affinities (−8.3 to −7.7 kcal/mol) and formed stable hydrogen bonds with key catalytic residues. The combined experimental and theoretical results reveal that electronic softness, moderate Δ E gap, and high dipole moments contribute to effective ligand‐protein interactions.