Department of Chemistry, National Institute of Technology Nagaland, Chumukedima 797103, Nagaland, India.
Genomics and Molecular Medicine Unit, Council of Scientific and Industrial Research-Institute of Genomics & Integrative Biology, New Delhi 110025, India.
J Phys Chem B. 2023 Jun 8;127(22):4966-4978. doi: 10.1021/acs.jpcb.3c00551. Epub 2023 May 24.
A variety of anticancer and antibacterial drugs target DNA as one of their primary intracellular targets. Understanding ligand-DNA interactions and developing new, promising bioactive molecules for clinical use are greatly aided by elucidating the interaction between small molecules and natural polymeric DNAs. Small molecules' ability to attach to and inhibit DNA replication and transcription provides more information on how drugs impact the expression of genes. Yohimbine has been broadly studied in pharmacological properties, while its binding mode to DNA has not been explicated so far. In this study, an attempt was made to explore the interaction between Yohimbine (YH) and calf thymus (CT-DNA) by using varying thermodynamics and approaches. Minor hypochromic and bathochromic shifts of fluorescence intensity were observed, suggesting the binding of YH to CT-DNA. The Scatchard plot analysis using the McGhee-von Hipple method revealed noncooperative binding and affinities in the range of 10 M. The binding stoichiometry value is 2:1 (2 molecules of YH were span by 1 base pair) and was determined by Job's plot. The thermodynamic parameters suggested exothermic binding, which was favored by negative enthalpy and positive entropy changes from both isothermal titration calorimetry and temperature-dependent fluorescence experiment. Salt-dependent fluorescence suggested that the interaction between the ligand and DNA was governed by nonpolyelectrolytic forces. Kinetics experiment confirmed the static type of quenching. The results of iodide quenching, urea denaturation assay, dye displacement, DNA melting, and molecular docking (MD) suggested groove binding of YH to CT-DNA. Circular dichroism spectra confirmed minimal perturbation of CT-DNA with YH binding via groove region. Therefore, the groove binding mechanism of interaction was validated by biophysical techniques and , MD approaches. The findings supported here may contribute to the development of new YH therapeutics possessing better efficacy and lesser side effects.
多种抗癌和抗菌药物将 DNA 作为其主要的细胞内靶点之一。阐明小分子与天然聚合 DNA 之间的相互作用，对于理解配体-DNA 相互作用以及开发新的、有前途的临床应用生物活性分子有很大帮助。小分子能够附着并抑制 DNA 复制和转录，这为药物如何影响基因表达提供了更多信息。育亨宾在药理学特性方面得到了广泛研究，但其与 DNA 的结合模式至今尚未阐明。在这项研究中，尝试通过使用不同的热力学和方法来探索育亨宾（YH）与小牛胸腺（CT-DNA）之间的相互作用。观察到荧光强度的轻微减色和红移，表明 YH 与 CT-DNA 的结合。使用 McGhee-von Hipple 方法的 Scatchard 图分析显示了非协同结合，亲和力在 10 M 的范围内。结合配位数的值为 2:1（2 个 YH 分子跨越 1 个碱基对），并通过 Job 图确定。热力学参数表明，由焓变和熵变的负值主导的是放热结合，这两个参数都来自等温滴定量热法和温度依赖荧光实验。盐依赖性荧光表明，配体与 DNA 之间的相互作用受非聚电解质力控制。动力学实验证实了静态猝灭类型。碘化物猝灭、尿素变性试验、染料置换、DNA 熔解和分子对接（MD）的结果表明，YH 与 CT-DNA 的结合方式为沟结合。圆二色性光谱证实了 CT-DNA 与 YH 结合后在沟区的微小扰动。因此，通过生物物理技术和 MD 方法验证了 YH 与 CT-DNA 的相互作用的沟结合机制。这里的研究结果可能有助于开发具有更好疗效和更少副作用的新型 YH 治疗药物。
