Insights on the interaction mechanism of sesquiterpene coumarin (7-geranyloxycoumarin) to double-strand DNA by multispectral techniques and molecular docking

• Published in: Journal of molecular structure 2024-06, Vol.1306, p.137830, Article 137830
• Main Authors: Dehghan, Bahar, Dehghan, Gholamreza, Shaghaghi, Masoomeh, Rashtbari, Samaneh, Yaghoubzad-Maleki, Mohammad, Iranshahi, Mehrdad
• Format: Article
• Language: English
• Subjects: Auraptene; DNA interactions; Groove binding; Molecular docking; Natural coumarins
• ISSN: 0022-2860; 1872-8014
• DOI: 10.1016/j.molstruc.2024.137830

•The binding ability of auraptene (AUR) with DNA has been evaluated for the first time.•The moderate fluorescence enhancement observed upon binding of AUR to DNA Fluorescence dynamic activation mechanism was prominent in AUR-DNA interaction.•Auraptene spontaneously binds to the minor groove of DNA.•Docking studies indicated that AUR fits into the minor groove via dodecamer base pairs. In this study, various spectroscopic methods, including UV-Vis spectrophotometry, fluorescence (competitive and non-competitive studies and binding thermodynamic parameters determine) and Fourier transform infrared (FT-IR) spectroscopies, viscometry, and molecular docking simulation, have been used to study the interaction of the bioactive 7-geranyloxycoumarin, auraptene (AUR), with calf thymus DNA (CT-DNA) as a model. According to the data, the AUR-CT-DNA association constant (Kb) is around 7.3×104 M−1, which is appropriate for the groove binding mode. Fluorescence experiments showed that the AUR-CT-DNA complex formation process has a dynamic fluorescence-enhancing mechanism. The observed thermodynamic values imply that a crucial part of the binding reaction between AUR and CT-DNA is played by hydrogen bonds. Additionally, a competitive MB binding experiment using fluorescence spectroscopy demonstrated that AUR binds to CT-DNA in a non-intercalative manner. Additionally, FT-IR investigations revealed that AUR attaches to backbone sugar molecules in a minor groove. Following the interaction of AUR with CT-DNA, minor alterations were noted based on viscosity measurement. According to experimental and molecular docking data, AUR is a powerful ligand with a high affinity for the minor groove of CT-DNA.