The oxoguanine oxoG is arguably the most important
The 8-oxoguanine (8-oxoG) is arguably the most important muta-genic lesion in DNA. The oxidation potentials are highly dependent on the type of electrode and pH of the solution. With that in mind, it has been reported an 8-oxoG oxidation peak at + 0.25 and + 0.45 V, for neutral (Ferapontova, 2004) and acidic pH (Oliveira and Oliveira-Brett, 2010), respectively. In the present study, the presence of the 8-oxoG at E = +0.5 V (Fig. 4B, black line) after the interaction with the highest concentration of 7ESTAC01 (400 µM) with the dsDNA/GE biosensor, demonstrates a substantial DNA damage.
To understand the mechanism behind the observed increase in peak current signal from purine bases in the presence of 7ESTAC01 radicals, another double-stranded ctDNA was immobilized by non-covalent bonding on a glassy carbon electrode (GCE) (Supplementary informa-tion). The double-stranded ctDNA is a natural DNA from calf thymus widely used in studies of DNA binding anticancer compounds. The damage of the ctDNA in the presence of 7ESTAC01 radicals was in-vestigated in acetate buffer solution at pH 4.2 by DPV. Fig. S2 shows DPV peak potentials characteristic of the guanine and Sotrastaurin (AEB071) bases at the GCE (Li et al., 2010; Aydoğdu et al., 2014). In the presence of 7ESTAC01 in solution, the peak current recorded a significant increase of guanine and adenine bases at + 1.03 V and + 1.29 V, respectively, which could imply the opening of the double helix of ctDNA (Fig. S2).
Therefore, the increase in the signal, regardless of the electrode, in-dicates that the electron transfer through DNA increases in the presence of the 7ESTAC01 (oxidizing agent). It demonstrates that the 7ESTAC01 mechanism of intercalation into the DNA through electro-oxidation caused a substantial distortion of the double-stranded ctDNA. It also corroborates the imminent breaking of the double helix DNA, exposing the purine bases to the surface of the electrode as a result of the DPV current increase in the presence of 7ESTAC01. Finally, the blank signals upon oxidation of 7ESTAC01 were analyzed by DPV for both un-modified electrodes, GCE (Fig. S2) and the GE (Fig. S3) under the same working conditions. As recorded in Fig. S2 and Fig. S3, the blank re-sponse of the GE/GCE+7ESTAC01 does not show any peak.
3.6. Interaction of DNA with 7ESTAC01 by UV–Vis spectroscopy, molecular docking and density function theory (DFT) studies Elucidating the binding between 7ESTAC01 and DNA provides help in understanding drug-DNA interactions and consecutive DNA damage on the surface of the GE. The interaction of an anticancer drug 7ESTAC01 with double-stranded ctDNA was studied using various ap-proaches like UV–Vis spectroscopy, Molecular Docking, and Density Function Theory (DFT) studies. UV–Vis spectroscopy confirmed 7ESTAC01-DNA interaction. Importantly, as depicted in Fig. 5A, the presence of an isosbestic point developed at 297 nm in the 7ESTAC01-DNA spectra indicates inter-calation as a dominant binding mode. Moreover, UV–Vis showed a binding constant of Kb = 6.57 × 104 L mol−1 at 260 nm using the Wolfe-Shimer equation (Eq. (2)). The small molecules can interact with DNA involving a single mode of binding or mixed binding modes. Thus, the exact mode of interaction can be established merely by this tech-nique due to the presence of the isosbestic point; however, another kind of non- covalent interactions could be present.
Other types of non-covalent interactions were further studied by Molecular Docking and DFT studies. For these studies, the GoldScore was selected as the best algorithm to predict results without large de-viations between generated poses. Based on this, the GoldScore func-tion was employed to determine different thermodynamic parameters related to the 7ESTAC01 compound (see Table S in the Supplementary information). From this analysis, the most important type of interaction can be identified and, consequently, it is possible to determine their
Fig. 5. Interaction of DNA with 7ESTAC01 by UV–Vis Spectroscopy, and Molecular docking. (A) UV–Visible absorption spectra of 20 µM 7ESTAC01 in presence of different concentrations of DNA (μM): (a) 0.0; (b)2; (c)10; (d)12; (e)14; (f)16; (g)18; (h)20. (B) Molecular docking of 7ESTAC01 (forward of the mage) to ctDNA (background structure) sites, represented by H-bond at DA18. (C) The binding pose of ctDNA (orange helix) acting via intercalation mechanism between the aminothiophene and acridine domains of 7ESTAC01. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article).
contribution in kcal mol−1 (Kamal et al., 2010; Arshad et al., 2017; Kundu and Chattopadhyay, 2017; Veerashekhar Goud et al., 2017). According to the quantitative results from the Molecular Docking and DFT studies (Table S), it is observed that significant interactions from the 7ESTAC01-DNA complex are the contributions of Van der Walls, 46.35 kcal mol−1. In addition, it was observed that the 7ESTAC01 compound presented a significant external H-bond value of 1.2 kcal