Vol. 54, Issue 6, 1036-1045, December 1998

DNA-Binding Preferences of Bisantrene Analogues: Relevance to the Sequence Specificity of Drug-Mediated Topoisomerase II Poisoning

Claudia Sissi, Loretta Bolgan, Stefano Moro, Giuseppe Zagotto, Christian Bailly, Ernesto Menta, Giovanni Capranico, and Manlio Palumbo

Department of Pharmaceutical Sciences, University of Padova, 35131 Padova, Italy (C.S., L.B., S.M., G.Z., M.P.), INSERM U124 and Laboratoire de Pharmacologie Antitumorale Moléculaire, Centre Oscar Lambret, 59045 Lille, France (C.B.), Boehringer Mannheim Italia, 20052 Monza, Italy (E.M.), and Division of Experimental Oncology B, Istituto Nazionale per lo Studio e la Cura dei Tumori, 20133 Milan, Italy (G.C.)

To elucidate structure-activity relationships for drugs that are able to poison or inhibit topoisomerase II, we investigated the thermodynamics and stereochemistry of the DNA binding of a number of anthracene derivatives bearing one or two 4,5-dihydro-1H-imidazol-2-yl-hydrazone side chains (characteristic of bisantrene) at different positions of the planar aromatic system. An aza-bioisostere, which can be considered a bisantrene-amsacrine hybrid, was also tested. The affinity for nucleic acids in different sequence contexts was evaluated by spectroscopic techniques, using various experimental conditions. DNA-melting and DNase I footprinting experiments were also performed. The location and number of the otherwise identical side chains dramatically affected the affinity of the test compounds for the nucleic acid. In addition, the new compounds exhibited different DNA sequence preferences, depending on the locations of the dihydroimidazolyl-hydrazone groups, which indicates a major role for the side-chain position in generating specific contacts with the nucleic acid. Molecular modeling studies of the intercalative binding of the 1- or 9-substituted isomers to DNA fully supported the experimental data, because a substantially more favorable recognition of A-T steps, compared with G-C steps, was found for the 9-substituted derivative, whereas a much closer energy balance was found for the 1-substituted isomer. These results compare well with the alteration of base specificity found for the topoisomerase II-mediated DNA cleavage stimulated by the isomeric drugs. Therefore, DNA-binding specificity appears to represent an important determinant for the recognition of the topoisomerase-DNA cleavable complex by the drug, at least for poisons belonging to the amsacrine-bisantrene family.