Acridinecarboxamide topoisomerase poisons: Structural and kinetic studies of the DNA complexes of 5-substituted 9-amino-(N-(2-dimethylamino)ethyl)acridine-4-carboxamides

For a series of antitumor-active 5-substituted 9-aminoacridine-4-carboxamid e topoisomerase II poisons, we have used X-ray crystallography and stopped- flow spectrophotometry to explore relationships between DNA binding kinetic s, biological activity, and the structures of their DNA complexes. The stru cture of 5-F-9-amino-[N-(2-dimethylamino)ethyl]-acridine-4-carboxamide boun d to d(CGTACG)(2) has been solved to a resolution of 1.55 Angstrom in space group P6(4). A drug molecule intercalates between each of the CpG dinucleo tide steps, its protonated dimethylamino group partially occupying position s close to the N7 and O6 atoms of guanine G2 in the major groove. A water m olecule forms bridging hydrogen bonds between the 4-carboxamide NH and the phosphate group of the same guanine. Intercalation unwinds steps 1 and 2 by 12 degrees and 8 degrees, respectively compared with B-DNA, whereas the ce ntral TpA step is overwound by 10 degrees. Nonphenyl 5-substituents, on ave rage, decrease mean DNA dissociation rates by a factor of three, regardless of their steric, hydrophobic, H-bonding, or electronic properties. Cytotox icity is enhanced on average 4-fold and binding affinities rise by 3-fold, thus there is an apparent association between kinetics, affinity, and cytot oxicity. Taken together, the structural and kinetic studies imply that the main origin of this association is enhanced stacking interactions between t he 5-substituent and cytosine in the CpG binding site. Ligand-dependent per turbations in base pair twist angles and their consequent effects on base p air-base pair stacking interactions may also contribute to the stability of the intercalated complex. 5-Phenyl substituents modify dissociation rates without affecting affinities, and variations in their biological activity a re not correlated with DNA binding properties, which suggests that they int eract directly with the topoisomerase protein.