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 ($\Delta {\mathrm{G}}_{\mathrm{m}}^{\mathrm{o}}$) -(23.93 ± 0.23) kJ mol⁻¹, enthalpy change (${\Delta }_{\mathrm{vH}}{\mathrm{H}}_{\mathrm{m}}^{\mathrm{o}}$) -(50.84 ± 0.19) kJ mol⁻¹ and entropy change ($\Delta {\mathrm{S}}_{\mathrm{m}}^{\mathrm{o}}$) -(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.

Highlights

• Altretamine binds CT-DNA which is enthalpically driven with K_a of the order of 10³

• Insignificant conformational change is observed due to DNA-altretamine complexation

• Altretamine binds favorably with A-T rich sequences in the minor groove of CT-DNA

• Mechanistic insights obtained based on thermodynamic signatures

Communicated by Ramaswamy H. Sarma

Keywords:

• Altretamine
• calf thymus DNA
• spectroscopy
• viscosity
• molecular docking
• groove binding
• binding thermodynamics

Acknowledgments

The authors are grateful to Indian Institute of Technology Bombay, Mumbai for the financial support.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

The authors are grateful to Indian Institute of Technology Bombay, Mumbai for the financial support.