Binding stability of a cross-linked drug: Calculation of an anticancer drug cisplatin-DNA complex

One of the binding modes of anticancer and antibiotic drugs bound to DNA is the formation of a cross link, i.e., binding is made through the formation of covalent bonds between a binding drug and DNA. In this work we present a computational method to calculate the binding stability of a drug cross linked to DNA. Our method is based on the modified self-consistent harmonic approach in which the disruption probabil- ity of the cross-linked bonds as well as hydrogen bonds is calculated from a statistical analysis of micro- scopic thermal fluctuational motions. A Morse potential with appropriate parameters is used to model the cross-linked covalent bonds. Our method is applied to an anticancer drug cisplatin-DNA oligomer d(CTCTAGTGCTCAC){·}d(GTGAGCACTAGAG) complex. We calculated the equilibrium binding constant of a cisplatin bound to this DNA oligomer. Our method can also be used to analyze the effect of drug binding on DNA base-pair thermal stability. We find that, despite the disruption of certain interbase H bonds, the thermal fluctuational opening probability Pᵒᵖ of base pairs in the cisplatin binding region is enhanced by the formation of non-Watson-Crick H bonds as well as cross-linked covalent bonds. Although the entire DNA helix is bent by cisplatin binding, the stability of the base pairs outside the binding region is only slightly affected by this deformation.