Binding of antitumor ruthenium complexes to DNA and proteins: a theoretical approach

The thermodynamics of the binding of the antitumor ammine, amine, and immine complexes of ruthenium(II) and ruthenium(III) to DNA and peptides was studied computationally using model molecules. We performed density functional calculations on several monofunctional ruthenium complexes of the formula [Ru(NH3)5B]z+, where B is an adenine, guanine, or cytosine nucleobase or an 4-methylimidazole, a dimethylthioether, or a dimethylphosphate anion and z = 2 and 3. The pentammineruthenium fragment has been intensively studied and also constitutes a good model for a wide class of antitumor ammine, amine, and imine complexes of Ru(II) and Ru(III), while the considered bases/ligands have been chosen as models for the main binding sites of DNA, nucleobases, and phosphate backbone and proteins, histidyl, and sulfur-containing residue such as methionine or cysteine. Bond dissociation enthalpies and free energies have been calculated for all the considered metal binding sites both in the gas phase and in solution and allow building a binding affinity order for the considered nucleic acid or protein binding sites. The binding of guanine to some bifunctional complexes, [Ru(NH3)(4)Cl2], [cis-RuCl(2)(bpy)2], and [cis-RuCl(2)(azpy)2], has also been considered to evaluate the effect of a second labile chloro or aquo ligand and more realistic polypyridyl and arylazopyridine ligands.