Synthesis, characterization and biological evaluation of novel benzimidazole derivatives

Abstract

In search of achieving less toxic and more potent chemotherapeutics, three novel heterocyclic benzimidazole derivatives: 2-(1H-benzo[d]imidazol-2-yl)-4-chlorophenol (BM1), 4-chloro-2-(6-methyl-1H-benzo[d]imidazol-2-yl)phenol (BM2) and 4-chloro-2-(6-nitro-1H-benzo[d]imidazol-2-yl)phenol (BM3) with DNA-targeting properties, were synthesized and fully characterized by important physicochemical techniques. The DNA binding properties of the compounds were investigated by UV–Visible absorption titrations and thermal denaturation experiments. These molecules exhibited a good binding propensity to fish sperm DNA (FS-DNA), as evident from the high binding constants (K_b) values: 1.9 × 10⁵, 1.39 × 10⁵ and 1.8 × 10⁴ M^‒1 for BM1, BM2 and BM3, respectively. Thermal melting studies of DNA further validated the absorption titration results and best interaction was manifested by BM1 with ΔT_m = 4.96 °C. The experimental DNA binding results were further validated theoretically by molecular docking study. It was confirmed that the molecules (BM1–BM3) bind to DNA via an intercalative and groove binding mode. The investigations showed a correlation between binding constants and energies obtained experimentally and through molecular docking, indicating a binding preference of benzimidazole derivatives with the minor groove of DNA. BM1 was the preferential candidate for DNA binding because of its flat structure, π–π interactions and less steric hindrance. To complement the DNA interaction, antimicrobial assays (antibacterial & antifungal) were performed. It was observed that compound BM2 showed promising activity against all bacterial strains (Micrococcus luteus, Staphylococcus aureus, Enterobacter aerogenes and Escherichia coli) and fungi (Aspergillus flavus, Aspergillus fumigatus and Fusarium solani), while rest of the compounds were active against selective strains. The MIC values of BM2 were found to be in the range of 12.5 ± 2.2–25 ± 1.5 µg/mL. Thus, the compound BM2 was found to be the effective DNA binding antimicrobial agent. Furthermore, the preliminary cytotoxic properties of synthesized compounds were evaluated by brine shrimps lethality assay to check their nontoxic nature towards healthy normal cells.

Communicated by Ramaswamy H. Sarma

Highlights

• New heterocyclic benzimidazole molecules were synthesized and characterized.

• FT–IR, ¹H and ¹³C NMR, GC–MS, TOF–MS and single crystal X-ray diffraction and elemental analysis were used for structure elucidation.

• DNA binding propensity was assessed by spectroscopic and computational methods.

• Antibacterial and cytotoxic activities were also investigated.

Keywords:

• Benzimidazoles
• DNA interaction
• molecular docking
• antimicrobial
• cytotoxicity

Acknowledgements

We acknowledge the valuable input from Ms. Sadaf Ikram for the interpretation of molecular docking.

Additional information

Funding

Khalid Mahmood is highly thankful to HEC Pakistan for providing financial support under Indigenous 5000 Ph.D. Fellowship Program and for International Research Support Initiative Program (IRSIP). The funding from Quaid-i-Azam University, Islamabad, Pakistan under University Research Fund (URF) is also greatly acknowledged.