A closer look at the mode of binding of drug pemetrexed with CT-DNA

Abstract

The interaction of antifolate drug Pemetrexed (PEM) with CT-DNA has been studied by UV-Vis, fluorescence and circular dichroism spectroscopic techniques. The results of these spectroscopic studies in combination with viscosity measurements, voltammetric and KI quenching studies suggested a less-common mode of binding of PEM with CT-DNA i.e. neither intercalation nor groove binding. Thus, metadynamic (MD) simulation is utilized to decipher the nature of binding of PEM with CT-DNA. Analysis of free energy surfaces obtained in MD simulation, reveals that PEM binds to the 3’- and 5’-ends of the DNA molecule. The thermodynamics of the interaction has been investigated by isothermal titration calorimetric experiment. The analysis shows that PEM binds with CT-DNA strongly with a binding constant of 2.6x10⁹ M⁻¹ and the process is found to be spontaneous (ΔG − 12.84 kcal/mol). Further, positive values of enthalpy (ΔH 6.09 cal/mol) and entropy (ΔS 43.1 cal/mol) changes indicate that the binding is an enthalpically unfavourable and, instead, entropically driven process.

Communicated by Ramaswamy H. Sarma

Keywords:

• DNA binding
• pemetrexed
• simulation
• ITC

Acknowledgment

The authors thank the Central Research Facility, Indian Institute of Technology, Kharagpur for providing Isothermal Titration Calorimetry facility.