QM/MM description of platinum–DNA interactions: comparison of binding and DNA distortion of five drugs

Abstract

Hybrid QM/MM calculations on adducts of five platinum-based anti-cancer drugs, namely cisplatin, oxaliplatin, lobaplatin, and heptaplatin are reported. Starting from the NMR structure of a cisplatin–DNA octamer complex (PDB entry 1AU5), we compare DNA binding of drugs that differ in their carrier ligands, and hence in their potential interactions with DNA. It is shown that all drugs induce broadly similar changes to the regular helical structure of DNA, but that variations in ligand lead to subtle differences in complex geometry, with cisplatin exhibiting notably different properties to other drugs. Cisplatin is also the most weakly bound of drugs considered here, and heptaplatin the most strongly bound. Differences in binding appear to be due to changes in the pattern of non-covalent interactions between drug and DNA, especially hydrogen bonding to oxygen in guanine and phosphate groups. Despite adopting very similar geometries, two isomers of lobaplatin (RRS and SSS) are found to have quite different binding energies, the latter being bound by up to 30 kcal mol⁻¹ more than the former.