Özbağcı Duygu İnci, Erdağı Sevinç İlkar, Aydın Rahmiye
Department of Chemistry, Faculty of Arts and Sciences, Bursa Uludag University, 16059, Bursa, Türkiye.
Department of Chemistry, Faculty of Arts and Sciences, Kocaeli University, Umuttepe campus, 41380, Kocaeli, Türkiye.
J Fluoresc. 2025 Aug 18. doi: 10.1007/s10895-025-04455-z.
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.
伞形酮是香豆素家族的一员，是一种天然丰富的化合物，以其多样的药理和治疗特性而闻名。因此，为了深入了解其分子识别机制，我们计划通过光谱技术和计算建模相结合的方法，对其与小牛胸腺DNA（CT-DNA）和铜/锌超氧化物歧化酶（SOD1）的相互作用进行深入研究。由EB和Hoechst 33,258进行的竞争性置换实验结果，在分子对接分析的支持下，表明伞形酮优先结合到CT-DNA的小沟中。通过电子吸收光谱和荧光光谱，我们证实了伞形酮与SOD1之间的相互作用，表明形成了复合物。通过热力学研究证实了反应的自发性以及通过范德华力和氢键对复合物的稳定作用。研究表明能量转移高效发生，概率很高。伞形酮诱导了SOD1的微环境和构象变化，同步光谱、三维荧光图谱和傅里叶变换红外光谱分析证明了这一点。分子对接模拟表明，伞形酮优先结合到DNA的小沟中，形成多个氢键和范德华接触，而不会破坏螺旋结构。相比之下，该化合物与SOD1的非催化表面区域相互作用，远离金属配位活性位点，表明可能具有变构或稳定作用，而不是直接的酶抑制作用。计算得到的DNA结合亲和力为-6.32千卡/摩尔，SOD1的结合亲和力为-5.70千卡/摩尔。此外，计算机辅助的ADMET分析表明其具有高胃肠道吸收、血脑屏障通透性，并且一般具有良好的药代动力学特征，毒性限度可接受。这些发现支持了伞形酮作为一种沟结合DNA稳定剂和抗氧化酶的非共价调节剂的双重作用，突出了其在氧化应激相关病症中的治疗相关性。此外，通过DPPH测定法评估了伞形酮的抗氧化潜力，证明了其清除DPPH自由基的能力。
