Spectral Characterization, Antioxidant, Antibacterial Activity, and Molecular Dynamics Simulation of a New Bis-benzimidazole Molecule, 1,5-Bis(1H-benzimidazol-2-yl)pentan-3-one

Abstract Objective: Bis-benzimidazoles are an interesting class of compounds due to their chelating characteristics, various biological effects, and fluorescence properties. Methods: In this research, a new symmetric bis-benzimidazole derivative including a ketone group, 1,5-bis(1H-benzimidazol-2-yl)pentan-3-one (PBB), was synthesized and characterized. Antibacterial activity of PBB was tested against Gram-negative and Gram-positive bacteria. The total antioxidant capacity (as TEAC value) and free radical scavenging activity of (PBB) was determined by ferric reducing antioxidant power (FRAP) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) methods. Molecular modeling methods have been conducted in order to study the relationship between electronic characteristics and antioxidant activity. Results and Discussion: Molecular modelling techniques and approaches were used to ensure that (PBB) synthesized in this study could be a reliable drug-like ligand, ligand-protein interactions were studied in detail with molecular dynamic (MD) simulation techniques applied at the molecular level, and trajectory analyses after MD were discussed. The total antioxidant capacity (as TEAC value) and free radical scavenging activity results revealed that (PBB) has a moderate inhibition with a SC50 = 1.8686 ± 0.0030 mg/mL value and the FRAP value is 108.89 ± 1.92 μM TEAC. Conclusions: According to the molecular modelling calculations, the antioxidant and antibacterial activities of (PBB) result from the electrophilic and nucleophilic interactions of its electron-rich C=N nitrogen atoms and electron-withdrawing carbon atoms adjacent to the C=O group with the proteins of the target molecules.