Bending of DNA upon binding of ecteinascidin 743 and phthalascidin 650 studied by unrestrained molecular dynamics simulations

Recognition of DNA sequence information by the natural antitumor agent ecteinascidin 743 (ET743) has been proposed to operate through a direct readout mechanism involving specific hydrogen bonding interactions between the drug and the DNA minor groove prior to covalent alkylation of a guanine base. 5'-AGC and 5'-CGG are examples of high-reactivity target triplets whereas 5'-CGA is a low-reactivity sequence. Molecular dynamics computer simulations were first used to explore the stability and behavior of the pre-covalent complex between ET743 and a DNA nonamer containing the 5'-AGC binding site in the central region. The pre-covalent complex was stable, and some unreported distinctive features were observed that may not be amenable to direct experimental verification. A similar simulation with ET743 bound to another nonamer containing a central 5'-CGA triplet did not result in a stable association supporting the proposed role of a hydrogen bonding network in the stabilization of these complexes. The covalent complexes between ET743 and the nonamers containing the 5'-AGC and 5'-CGG target sites were then simulated. In each case the drug displayed the predicted binding mode and gave rise to a widening of the minor groove. In addition, we show that as a consequence of ET743 binding to the target sequences, positive roll is introduced that results in smooth bending of the helix toward the major groove, in agreement with results from gel electrophoresis experiments. Similar results were obtained with the synthetic compound phthalascidin, which presents a biological profile almost indistinguishable from that of ET743. The local bending elements in AGC and CGG were found to be different, and the distinct behavior of these sequences in the absence of bound drugs was in consonance with their intrinsic bending propensities.