Molecular Interaction of the Coumarin Derivative Umbelliferone with Cu/Zn-SOD1 and DNA: Insights into Binding Mode and Antioxidant Mechanism.

Abstract

A member of the coumarin family, umbelliferone is a naturally abundant compound known for its diverse pharmacological and therapeutic properties. Therefore, to gain insight into its molecular recognition mechanism, we plan to conduct an in-depth investigation of its interactions with calf thymus DNA (CT-DNA) and Cu/Zn superoxide dismutase enzyme (SOD1) through a combination of spectroscopic techniques and computational modeling. Results from competitive displacement experiments with EB and Hoechst 33,258, supported by molecular docking analyses, indicate that the umbelliferone preferentially binds to the minor groove of CT-DNA. Using electronic absorption and fluorescence spectroscopy, we confirmed the interaction between the umbelliferone and SOD1, indicating complex formation. The spontaneous nature of the reaction and the stabilization of the complex via van der Waals forces and hydrogen bonding were confirmed through thermodynamic studies. The study revealed that energy transfer takes place efficiently, with a high probability. Microenvironmental and conformational changes in SOD1 were induced by the umbelliferone, as demonstrated by synchronous spectra, 3D fluorescence maps and FTIR analysis. Molecular docking simulations revealed that the umbelliferone preferentially bind to the minor groove of DNA, forming several hydrogen bonds and van der Waals contacts without disrupting the helical structure. In contrast, the compound interacted with a non-catalytic surface region of SOD1, away from the metal-coordinating active site, suggesting a potential allosteric or stabilizing effect rather than direct enzymatic inhibition. The binding affinities were calculated as - 6.32 kcal/mol for DNA and - 5.70 kcal/mol for SOD1. Furthermore, in silico ADMET analyses indicated high gastrointestinal absorption, blood-brain barrier permeability, and a generally favourable pharmacokinetic profile with acceptable toxicity limits. These findings support the dual role of the umbelliferone as a groove-binding DNA stabilizer and a non-covalent modulator of antioxidant enzymes, highlighting its therapeutic relevance in oxidative stress-related conditions. Additionally, the umbelliferone's antioxidant potential was evaluated through the DPPH assay, demonstrating its capacity to scavenge DPPH free radicals.