Molecular modelling of ligand–DNA intercalation interactions

Abstract

This paper reports the molecular modelling of one type of DNA–ligand interaction, namely intercalation, which is characterized by a planar moiety of the ligand inserting between adjacent DNA base-pairs. A series of molecular modelling studies demonstrate that it is possible to construct three-dimensional quantitative structure–activity relationships, 3D-QSARs, for both anticancer anthracycline and benzothiopyranoindazole analogues. The reaction specificities of dynemicin-A and benzo[α] pyrene-diol-epoxide isomers have also been shown to be consistent with particular molecular interaction mechanisms based upon molecular structure and simulation calculations.