Mode of interaction of altretamine with calf thymus DNA: biophysical insights

Abstract

Insights into drug-DNA interactions have importance in medicinal chemistry as it has a major role in the evolution of new therapeutic drugs. Therefore, binding studies of small molecules with DNA are of significant interest. Spectroscopy, coupled with measurements of viscosity and molecular docking studies were employed to obtain mechanistic insights into the binding of altretamine with calf thymus DNA (CT-DNA). The UV-visible spectroscopic measurements study confirmed altretamine-CT-DNA complex formation with affinity constant ([15.68 ± 0.04] × 10³ M^-1), a value associated with groove binding phenomenon. The associated thermodynamic signatures suggest enthalpically driven interactions. The values of standard molar free energy change ($\Delta G_m^o$) -(23.93 ± 0.23) kJ mol^-1, enthalpy change (${\Delta }_{\mathrm{vH}}{H}_m^o$) -(50.84 ± 0.19) kJ mol^-1 and entropy change ($\Delta S_m^o$) -(90.29 ± 0.12) JK^-1 mol^-1 indicate the binding is thermodynamically favorable and an important role of the hydrogen bonds and Van der Waals interactions in the binding of altretamine with CT-DNA. Circular dichroism spectroscopy indicated insignificant conformational changes in the DNA backbone upon interaction with altretamine suggesting no distortion and/or unstacking of the base pairs in the DNA helix. UV-melting study suggested that the thermal stability of the DNA backbone is not affected by the binding of the drug. Competitive displacement assays with ethidium bromide, Hoechst-33258 and DAPI established the binding of altretamine with CT-DNA in the minor groove. The mode of binding was further confirmed by viscosity and molecular docking studies. Molecular docking further ascertained binding of altretamine in the minor groove of the CT-DNA, preferably with the A-T rich sequences.[Formula: see text]HighlightsAltretamine binds CT-DNA which is enthalpically driven with K_a of the order of 10³Insignificant conformational change is observed due to DNA-altretamine complexationAltretamine binds favorably with A-T rich sequences in the minor groove of CT-DNAMechanistic insights obtained based on thermodynamic signaturesCommunicated by Ramaswamy H. Sarma.

Keywords: Altretamine; binding thermodynamics; calf thymus DNA; groove binding; molecular docking; spectroscopy; viscosity.