Design, Synthesis, Spectroscopic Characterization, and in Vitro Pharmacological Evaluation of Novel 2-(5-Alkoxybenzimidazol-2-ylthio)-N-arylacetamide Derivatives as Antimicrobial and Antioxidant Agents

Abstract

Background: Benzimidazole represents one of the most pharmacologically significant nitrogen-containing heterocyclic scaffolds in medicinal chemistry. Its structural resemblance to purine nucleobases enables effective interaction with diverse biological macromolecules, providing a broad therapeutic spectrum. Antimicrobial resistance (AMR) has emerged as a critical global threat, necessitating continuous discovery of novel antimicrobial agents. Methods: Nineteen novel 2-(benzimidazol-2-ylthio)-N-arylacetamide derivatives (SS1–SS19) were designed and synthesized via a three-step route: preparation of 5-methoxy-and 5-ethoxy-2-mercapto-benzimidazole intermediates, synthesis of N-chloroacetyl arylamine intermediates (A1–A11), and SN2 thioether-forming coupling. Compounds were characterized using melting point determination, TLC, FT-IR, ¹H-NMR, ¹³C-NMR, mass spectrometry, and CHN elemental analysis. Antimicrobial activity was evaluated against five bacterial and five fungal strains by broth microdilution; anti-tubercular activity against Mycobacterium tuberculosis H37Rv by the Loöwenstein–Jensen slope method; antioxidant capacity by DPPH radical scavenging; and computational binding affinity by molecular docking against Cyclopropane-fatty-acylphospholipid synthase (PDB: 1KPG and 1KPI). Results: All compounds were isolated in moderate to good yields (49–68%) and comprehensively characterized. Nitro-substituted derivatives SS9 and SS10, as well as halogen-bearing compounds SS5, SS6, SS16, and SS17, exhibited the lowest MIC values (12.5–50 µg/mL) against bacterial and fungal pathogens. Methoxy-substituted compounds SS8, SS18, and SS19 demonstrated the strongest DPPH radical scavenging activity (IC₅₀ = 62.3–72.1 µg/mL). Molecular docking confirmed SS15 and SS5 as the strongest binders to 1KPG and 1KPI (binding energy −6.2 kcal/mol each), surpassing the co-crystallized reference ligand. Conclusions: Structure-activity relationship (SAR) analysis confirmed that electron-withdrawing N-aryl substituents enhance antimicrobial potency, while electron-donating groups improve antioxidant capacity. The 5-ethoxy series (SS12–SS19) generally outperformed the 5-methoxy series (SS1–SS11) in antimicrobial efficacy. These findings establish the synthesized derivatives as pharmacologically promising lead compounds warranting further preclinical optimization.