Evaluation of the Interaction of Cinacalcet with Calf Thymus dsDNA: Use of Electrochemical, Spectrofluorimetric, and Molecular Docking Methods

Abstract

The binding of drugs to DNA plays a critical role in new drug discovery and is important for designing better drugs. In this study, the interaction and binding mode of calf-thymus double-stranded deoxyribonucleic acid (ct-dsDNA) with cinacalcet (CIN) from the calcimimetic drug that mimics the action of calcium on tissues group were investigated. The interaction of CIN with ct-dsDNA was observed by the differential pulse voltammetry (DPV) technique by following the decrease in electrochemical oxidation signals to deoxyguanosine and adenosine. A competitive study was performed on an indicator, methylene blue, to investigate the interaction of the drug with ct-dsDNA by fluorescence spectroscopy. Interaction studies have shown that the binding mode for the interaction of CIN with ct-dsDNA could be groove-binding. According to the results obtained, the binding constant values were found to be 6.30 × 10⁴ M^-1 and 3.16 × 10⁵ M^-1, respectively, at 25 °C as obtained from the cyclic voltammetry (CV) and spectroscopic techniques. Possible molecular interactions of CIN with dsDNA were explored via molecular docking experiments. The docked structure indicated that CIN could fit well into the minor groove of the DNA through H-bonding and π-π stacking contact with CIN.

Keywords: calf thymus double-stranded deoxyribonucleic acid; cinacalcet; electrochemistry; fluorescence spectroscopy; molecular docking.

Scheme 1

Molecular structure of CIN.

Figure 1

AFM topographical images (A) Clean glass surface, (B) Multilayer ct-dsDNA 3D view 4 × 4 μm scan size.

Figure 2

(A) DP voltammograms of the ct-dsDNA biosensor, 10 μg mL⁻¹ CIN, the ct-dsDNA biosensor after incubation in ABS (pH 4.7), the ct-dsDNA biosensor after incubation in 10 μg mL⁻¹ CIN, and the bare GCE in ABS (pH 4.7), (B) DP voltammograms of polyA biosensor, 10 μg mL⁻¹ CIN, the polyA biosensor after incubation in ABS (pH 4.7), the polyA biosensor after incubation in 10 μg mL⁻¹ CIN, and the bare GCE in ABS (pH 4.7).

Figure 3

(A) DP voltammograms and (B) the plot of the current of the dAdo peak vs. incubation time for the interaction of ct-dsDNA biosensor with 10 μg mL⁻¹ CIN, (C) DP voltammograms of the ct-dsDNA biosensor after interacting with various CIN concentrations, (D) Calibration plot for CIN determination based on the current of the dAdo peak.

Figure 4

(A) Cyclic voltammograms of 10 μg mL⁻¹ CIN and in the presence of ct-dsDNA in the range of 3.30 × 10⁻⁶ M–1.50 × 10⁻⁵ M, (B) Related plot of log (1/[DNA]) vs. log (I/(I₀ − I)).

Figure 5

(A) Fluorescence spectra of MB-ct-dsDNA titration, (B) CIN–MB+ct-dsDNA titration in ABS (pH 4.70), λexc: 665 nm, the concentration of MB: 50 µM, the concentration of the stock solution of ct-dsDNA: 100 µg mL⁻¹, (C) The Stern–Volmer curves at different temperatures, (D) Van’t Hoff plots of CIN-ct-dsDNA interactions.

Figure 6

The proposed binding mode of CIN represented as: (A) Yellow ball and stick mode; (B) CPK mode with dsDNA (represented as gray surface) (PDB: 1BNA) illustrating the interactions observed. Hydrogen bond and π-π contact are represented as: (A) Yellow and cyan dotted lines, respectively; (C) (in 2D-interaction map) Magenta and green lines, respectively.