Structure-Activity Relationship Studies of Novel 2-Substituted Benzimidazole Derivatives as Potential Broad-Spectrum Antimicrobial Agents: Synthesis, Molecular Docking, and In Vitro Biological Evaluation

Abstract

The benzimidazole scaffold — a fused bicyclic aromatic system comprising a benzene ring fused to an imidazole ring — occupies a privileged position in medicinal chemistry as a pharmacophore with documented biological activity across antimicrobial, antifungal, antiparasitic, antiviral, antihypertensive, and anticancer therapeutic domains, attributed to its planar aromatic architecture enabling intercalative and hydrogen-bond-mediated interactions with biological macromolecular targets. The escalating global crisis of antimicrobial resistance — including the WHO-declared critical priority pathogens methicillin-resistant Staphylococcus aureus (MRSA) and multidrug-resistant Pseudomonas aeruginosa — demands continuous innovation in antibacterial pharmacophore development beyond the established natural product-derived antibiotic classes. This study reports thesynthesis of five novel 2-substituted benzimidazole derivatives (BZ-1 to BZ-5), characterised by spectroscopic methods (IR, ¹H NMR, ¹³C NMR, and mass spectrometry), evaluated by in silico molecular docking at the E. coli DNA gyrase B and S. aureus topoisomerase IV binding sites using AutoDock Vina, and subjected to in vitro antimicrobial susceptibility testing by the broth microdilution method against MRSA, Escherichia coli ATCC 25922, and Pseudomonas aeruginosa ATCC 27853. BZ-3 emerged as the lead compound, exhibiting the lowest MIC values across all three organisms (MRSA 4 µg/mL, E. coli 8 µg/mL, P. aeruginosa 16 µg/mL) alongside the highest docking score (?10.84 kcal/mol at DNA gyrase B), with SARanalysis identifying the 4-fluorophenyl substituent at the C-2 position and asulfonamide linker as the key pharmacophoric elements driving enhancedantimicrobial potency. These findings establish BZ-3 as a promising lead for further optimisation toward a novel benzimidazole-based antibacterial agent.  KEYWORDS: Benzimidazole, Antimicrobial activity, Structure-activity relationship, Molecular docking, MIC, MRSA, Drug discovery, Rajasthan, DNA gyrase, Pharmaceutical chemistry