Deciphering the binding mechanism of tafamidis to calf thymus DNA: multimodal spectroscopic, thermodynamic, and computational perspectives

Abstract

The interaction between small molecules and biological macromolecules is a crucial area of research with significant implications across various scientific disciplines. Tafamidis is a clinically approved drug for transthyretin-mediated amyloidosis, yet its molecular interactions with biological macromolecules such as DNA remain unexplored. Investigating such interactions is crucial for understanding its broader pharmacodynamic profile and potential off-target effects. In this study, the binding interaction between tafamidis and calf thymus DNA (ct-DNA) was investigated, for the first time, using a combination of spectroscopic techniques, viscosity measurements, ionic strength studies, thermodynamic analysis, and computational modeling. The key binding parameters, including the binding constant, number of binding sites, binding forces, and binding mode were determined. UV-vis spectroscopic analysis revealed a binding constant on the order of 10⁵ M⁻¹, indicating a moderate-to-strong binding affinity between tafamidis and ct-DNA. Thermodynamic parameters (ΔH° > 0 and ΔS° > 0) suggested that hydrophobic interactions primarily drive the binding process. Fluorescence spectroscopy, viscosity measurements, and molecular modeling indicated that tafamidis preferentially binds to AT-rich regions of ct-DNA and acts as a minor groove binder. Ethidium bromide displacement assays showed no significant effect of tafamidis on the ethidium bromide–DNA complex, further supporting the groove binding mechanism. Molecular dynamics simulations corroborated these findings. Moreover, molecular dynamics simulations validated the dynamic behavior and stability of the tafamidis–ct-DNA complex, demonstrating its excellent structural stability. Overall, these results enhance the understanding of tafamidis by providing valuable insights into its pharmacological mechanisms and molecular interactions.