Anthramycin-DNA binding explored by molecular simulations.

Abstract

The anticancer drug anthramycin inhibits replication and transcription processes by covalently binding to DNA. Here, we use molecular simulations to investigate the interaction between this ligand and the dodecanucleotide d[GCCAACGTTGGC](2). We start from the X-ray structure of the adduct anthramycin-d[CCAACGTTG*G](2), in which the drug binds covalently to guanine.1 We focus on the noncovalent complexes between the oligonucleotide and the anhydro and hydroxy forms of the drug. Molecular dynamics (MD) simulations show that only the hydroxy form lies in front of the reactive center for the whole simulation ( approximately 20 ns), while the anhydro form moves inside the minor groove to the nearest base pair after approximately 10 ns. This sliding process is associated to both energetic and structural relaxations of the complex. The accuracy of our computational setup is established by performing MD simulations of the covalent adduct and of a 14-mer complexed with anhydro-anthramycin. The MD simulations are complemented by hybrid Car-Parrinello quantum mechanics/molecular mechanics (QM/MM) simulations. These show that in the noncovalent complexes the electric field due to DNA polarizes the hydroxy and, even more, the anhydro form of the drug as to favor a nucleophilic attack by the alkylating guanine. This suggests that the binding process may be characterized by a multistep pathway, catalyzed by the electric field of DNA.