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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 2.6x10 9  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

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