Probing the interaction of an antiviral drug 8-methoxy-3-nitro-2-(4-methoxyphenyl)-2H-chromene (MNC) with DNA by experimental and computational approach

Abstract

Deoxyribonucleic acid (DNA) is a major target in research pertaining to antiviral and anticancer therapies since it is the principal genetic material that controls vital biological functions. The complex relationship between calf thymus DNA (ct-DNA) and 8-Methoxy-3-nitro-2-(4-methoxyphenyl)-2H-chromene (MNC), an anticancer drug derivative of 2-aryl-3-nitro-2H-chromenes, is explored in this work. Using various spectroscopic methods such as fluorescence, circular dichroism (CD), UV–visible, isothermal titration calorimetry (ITC) experiment, and molecular docking calculations, this study elucidates the binding characteristics and affinity between MNC and ct-DNA. Through predominant groove binding and moderate intercalation, MNC demonstrates a complicated binding pattern with DNA at the minor groove, as shown by the UV–Vis spectra and emission-based dye displacement investigations. DNA undergoes a little conformational change that MNC induces, as shown by CD spectroscopy. The thermodynamics parameters such as the binding constant, binding enthalpy, and binding free energy of DNA-MNC interaction, as calculated by the ITC experiment, were approximately ∼ 104 M−1, −26 kcal mol−1, and 6 kcal/mol, respectively. The binding process is enthalpy driven implying a stabilizing contact of MNC with DNA and the entropic penalty (−TΔS = +20.1 kcal mol−1) points to a reduction in the degree of freedom of movement. The molecular docking investigation also estimates the similar interaction energy and binding locations of MNC with DNA. Interestingly, MNC attaches to the surface of the DNA via electrostatic interactions; a stronger attachment through van der Waals and hydrophobic contacts within the minor groove follows this. These studies are anticipated to provide researchers with important direction for designing new drug molecules for further biomolecular investigations.