New Amidino-Substituted Benzimidazole Derivatives as Human Dipeptidyl Peptidase III Inhibitors: Synthesis, In Vitro Evaluation, QSAR, and Molecular Docking Studies

Dipeptidyl peptidase III (DPP III) is a zinc-dependent enzyme that hydrolyses biologically active peptides by cleaving dipeptides from their amino terminus. While the fundamental role of this metallopeptidase remains incompletely understood, human DPP III (hDPP III) has been linked to several pathophysiological processes relevant to drug development. In this study, thirty-six amidino-substituted benzimidazole derivatives, including seven newly synthesized compounds, were examined for their activity against hDPP III by combining in vitro tests, in silico quantitative structure-activity relationship (QSAR) modelling, and molecular docking approaches. The experiments demonstrate that all compounds display inhibitory activity at a 30 µM concentration. A biochemical assay revealed that 2,2'-bithiophene, 4-trifluoromethylphenyl, 4-(<i>N,N</i>-diethylamino)phenyl, and 2,3,4-trihydroxyphenyl as substituents at position 2 of the benzimidazole core enhance inhibitor potency. Additionally, the type of substituent at positions 5(6) of the benzimidazole core influences enzyme inhibition, with effectiveness ranked as follows: 2-imidazolinyl > unsubstituted amidine > 2-tetrahydropyrimidine. A multiple linear regression QSAR model for hDPP III inhibition was developed using four Dragon descriptors (<i>Rww</i>, <i>Mats3e</i>, <i>BELe4</i>, and <i>nCs</i>), which can explain 82% of the inhibitory activity. Docking analysis of the semi-closed form of hDPP III in a complex with the most potent compounds indicates the structural features of the benzimidazole derivatives important for the binding at the hDPP III active site.