Groove binding phenomenon of ajmalicine with HT DNA: An exothermic-entropy driven interaction involving hydrogen...

Many bioactive compounds target DNA, making ligand-DNA binding studies essential for developing new therapeutics. These interactions provide insight into how small molecules can bind to DNA and inhibit processes like replication and transcription, influencing gene-expression. Ajmalicine (AJM), while extensively studied for its pharmacological properties, has not been fully elucidated in its nucleic acid(s) binding mode. DNA binding of AJM can impact the structure, stability and function of the DNA leading to significant implications for drug development. In this study, we explored the interaction between AJM and Herring Testis (HT) DNA using both biophysical and in silico approaches. A hyperchromic shift in the fluorescence intensity indicated AJM-binding to HT-DNA. Scatchard plot analysis using the McGhee-von Hippel method revealed non-cooperative binding with affinities in the range of 10⁵ M^-1 with single preferred binding of AJM to DNA. Thermodynamic parameters calculated employing the fluorescence study data at varying temperatures indicate an exothermic binding, driven by positive entropic and negative enthalpic changes. Salt-dependent fluorescence indicated that non-polyelectrolytic forces govern the interaction between AJM and DNA. Iodide quenching, urea denaturation assays, dye displacement assays, and molecular docking studies suggested groove binding of AJM to HT-DNA. The spectra from circular dichroism showed minimal perturbation of HT-DNA upon AJM binding via the groove region. Molecular dynamics simulation also showed the stability of the HT-DNA upon AJM binding.