MAPPING DRUG-INTERACTIONS AT THE COVALENT TOPOISOMERASE II-DNA COMPLEX BY BISANTRENE AMSACRINE CONGENERS/

To identify structural determinants for the sequence-specific recognit ion of covalent topoisomerase II-DNA complexes by anti-cancer drugs, w e investigated a number of bisantrene congeners, including a 10-azabio isoster, bearing one or two 4,5-dihydro-1H-imidazol-2-yl hydrazone sid e chains at positions 1, 4, or 9 of the anthracene ring system. The st udied bisantrene/amsacrine (m-AMSA) hybrid and bisantrene isomers were able to poison DNA topoisomerase II with an intermediate activity bet ween those of bisantrene and m-AMSA, Moving the side chain from the ce ntral to a lateral ring (from C-9 to C-1/C-4) only slightly modified t he drug DNA affinity, whereas it dramatically affected local base pref erences of poison-stimulated DNA cleavage. In contrast, switching the planar aromatic systems of bisantrene and m-AMSA did not substantially alter the sequence specificity of drug action. A computer-assisted st eric and electrostatic alignment analysis of the test compounds was in agreement with the experimental data, since a common pharmacophore wa s shared by bisantrene, m-AMSA, and 9-substituted analogs, whereas the 1-substituted isomer showed a radically changed pharmacophoric struct ure. Thus, the relative space occupancy and electron distribution of p utative DNA binding (aromatic rings) and enzyme binding (side chains) moieties are fundamental in directing the specific action of topoisome rase LI poisons and in determining the poison pharmacophore.