Unraveling the molecular interaction of Larotrectinib with calf thymus DNA: A comprehensive study using multi-spectroscopic, thermodynamic, and computational techniques

Abstract

The study of the interaction between small molecules and biological macromolecules is a critical area of research with significant implications across various scientific fields. Larotrectinib, a tropomyosin kinase inhibitor, is used to treat patients with solid tumors harboring neurotrophic tyrosine receptor kinase (NTRK) gene fusions. In this investigation, the interaction between larotrectinib and calf thymus DNA (ctDNA) was thoroughly examined using a combination of techniques, including UV–Vis spectrophotometry, spectrofluorimetry, viscosity measurements, ionic strength variation, thermodynamic analysis, molecular dynamics simulations, and docking studies. The results demonstrated a strong binding interaction between larotrectinib and ctDNA, with the drug primarily binding to the minor groove of ctDNA. This binding mode was established through competitive binding assays using ethidium bromide and rhodamine B, as well as UV–Vis spectroscopy and viscosity analysis. The binding constant (K_b) at 298 K, determined using the Benesi-Hildebrand equation, was found to be 4.4 × 10⁵ M⁻¹, pointing out a high binding affinity between larotrectinib and ctDNA. Thermodynamic analysis revealed that the interaction is driven mainly by hydrophobic forces and hydrogen bonding, as evidenced by the calculated enthalpy (ΔH⁰) and entropy (ΔS⁰) changes. Molecular docking studies further supported these findings, showing that larotrectinib binds preferentially to the AT-rich regions of the B-DNA minor groove. This was validated by molecular dynamics studies, which provided additional confirmation of the binding mechanism. Overall, these findings provide valuable understanding into the molecular interactions and pharmacological mechanisms of larotrectinib, contributing to a deeper insight of its role as a potent anticancer agent.