Deciphering the groove-binding mode of dolutegravir with salmon sperm DNA through spectroscopic and molecular modelling approaches

Abstract

Abstract Understanding how small molecules interact with DNA opens new avenues for designing smarter, more selective therapies. These studies not only shed light on off-target effects that could cause side effects or influence treatment outcomes but also help predict a drug’s genotoxic potential, aiding long-term safety assessments. Dolutegravir (DGV) serves as a second-generation integrase inhibitor used as a first-line antiretroviral therapy for managing human immunodeficiency virus (HIV) infection. Recent studies have positioned DGV as a prospective lead compound for repositioning antiretrovirals as cancer treatments. Building on this perspective, the introduced protocol presents a detailed approach to exploring DGV’s genomic interactions using salmon sperm DNA (SS-DNA) as a reliable genomic surrogate, employing various biophysical methods, including spectroscopic analysis, viscosity profiling, ionic strength experiments, and molecular docking. UV-Visible results indicate that DGV binds to DNA grooves with a binding constant of 10 3 M⁻¹, as determined by the modified Benesi–Hildebrand equation. Fluorescent displacement assays with ethidium bromide and rhodamine B confirm the groove interaction mode with SS-DNA. Potassium iodide quenching of DGV yielded comparable quenching constants of 24.99 and 23.61 M⁻¹ in the presence and absence of DNA, respectively, giving a confirmatory sign for groove binding interaction. A constant viscosity profile after the addition of DGV provides strong evidence of the groove binding mechanism, while ionic strength assays ruled out any significant electrostatic contribution. In silico molecular docking further shows DGV’s preference for GC-rich regions of SS-DNA. Thermodynamic measurements taken at various temperatures indicate that the interaction is spontaneous (∆G° = -15.0 to -25.4 kJ mol − 1 ) and primarily driven by hydrogen bonds and van der Waals forces (∆H° = -198.51 kJ mol − 1 and ∆S° = -573.33 J mol − 1 K − 1 ). Overall, this work provides a foundational framework and a pioneering step for future clinical and pharmacological research, as well as genome integrity assessments, with the ultimate goal of developing DNA-targeted drugs with higher selectivity and effectiveness.