Synthesis, crystal structure, characterization, and electrochemical properties of 5-benzoyl-6-phenyl-pyrimidin-4-one-2-thione compound; voltammetric, spectrophotometric, and molecular docking studies of its interaction with DNA

A novel heterocyclic compound, 5-benzoyl-6-phenyl-pyrimidin-4-one-2-thione (PT), was synthesized from the cyclocondensation reaction of dibenzoyl acetic acid-N-carboxymethylamide with thiourea. Microanalysis, FT-IR, NMR, and API-ES mass techniques were used to characterize the structure of the pyrimidinethione compound. Cyclic voltammetric studies performed using a glassy carbon electrode in anhydrous medium revealed that the PT compound gave an irreversible reduction peak at -0.83 V, indicating electrochemical stability and irreversible redox behavior of the compound. The interaction of PT compound with DNA was investigated by spectrophotometric, voltammetric, and molecular docking methods. The interaction of PT with DNA in acetate as supporting electrolyte (pH 4.8) on a glassy carbon electrode was evaluated by the change in the anodic signal for guanine. The voltammetric analysis of the PT-DNA interaction calculated the binding free energy as -6.5 kcal/mol, while spectrophotometric studies supported the binding interactions with DNA. Molecular docking studies showed a stronger binding interaction with DNA and revealed a binding free energy of -8.12 kcal/mol. These results show that the compound performs a thermodynamically favorable binding process with DNA, and molecular docking provides important information about the binding mode and energy profile. The data obtained with all three techniques about the PT-DNA interaction supported each other, and the interaction occurred in the form of electrostatic and minor binding groove.