Evaluating the carcinogenic potential of trazodone hydrochloride via duplex DNA targeting: Molecular interaction, binding mechanism and affinity assessment via structural calculations.

Trazodone Hydrochloride (TRZ) is a selective serotonin antagonist reuptake inhibitor (SARI) antidepressant that is widely prescribed to treat depression. In this study, we have observed that TRZ disturbs the duplex DNA structure around the binding site causing base flip in the major groove and disrupting sequence readout. TRZ binds in the minor groove, yet it disturbs the DNA structure significantly, causing problems in sequence readout. Therefore, it would be interesting to investigate the interaction between duplex DNA. DNA binding study was conducted using multi-spectroscopic methods coupled with molecular simulations. Fluorescence investigations revealed a static quenching mechanism between TRZ and CT-DNA with a moderate binding strength (2.7 ×104 LM-1 at 288 K, 1.1 ×104 LM-1 at 298 K, 5.2 ×103 LM-1 at 308 K). The thermodynamic parameters suggested that the complexation was spontaneous, enthalpy-driven (-69.006 kJ/mol), with an entropy of -0.168 kJ/mol and Gibbs free energy ranging between -18.93 to -16.03 kJ/mol. Complexation was primarily facilitated by the formation of hydrogen bonds and Van der Waals forces which corroborated by the MM/PBSA findings. Detailed assessment of the binding mode and interaction mechanism through Molecular Docking and Molecular Dynamics Simulations (150 ns) indicated TRZ's affinity for the minor groove of CT-DNA which was further validated experimentally through displacement study with the known minor groove binder, DAPI. CD spectroscopy of CT-DNA in the absence and presence of TRZ revealed minor variations in the negative and positive bands indicative of groove binding. The structural variations of TRZ observed during binding indicated minor conformational adjustments and repositioning, especially at piperazine and chlorophenyl ring, providing stable interactions in the form of stacking forces leading to better fit within the binding site, particularly within the AT region of the CT-DNA's minor groove. The findings from this study will enhance our understanding of the interaction between TRZ and CT-DNA, adding depth to existing knowledge in the field.