DNA binding by pixantrone

Abstract

The binding of the anticancer drug pixantrone (6,9-bis[(2-aminoethyl)amino]benzo[g]isoquinoline-5,10-dione dimaleate) to the octanucleotide duplexes d(ACGATCGT)₂ and the corresponding C-5 methylated cytosine (^5MeC) analogue d(A^5MeCGAT^5MeCGT)₂ has been studied by NMR spectroscopy and molecular modelling. The large upfield shifts observed for the resonances from the aromatic protons of pixantrone upon addition to either d(ACGATCGT)₂ or the corresponding ^5MeC analogue is consistent with the drug binding the octanucleotides by intercalation. The selective reduction in the sequential NOEs between the C₂-G₃ and C₆-G₇ nucleotides in NOESY spectra of either octanucleotide with added pixantrone confirms the intercalative binding mechanism. Strong NOEs from the side-chain ethylene protons of pixantrone to the H5 protons and the 5-CH₃ protons of the C₂ and C₆ residues of d(ACGATCGT)₂ and d(A^5MeCGAT^5MeCGT)₂, respectively, indicate that pixantrone predominantly intercalates from the DNA major groove at the 5′-CG and 5′-^5MeCG sites. Simple molecular models based on the conclusions from the NMR experiments indicated that the ^5MeC groups do not represent a steric barrier to intercalation from the major groove. However, the observation of weak NOEs from the ethylene protons of pixantrone to a variety of minor groove protons from either octanucleotide suggests that the drug can also associate in the minor groove.