Structure activity relationships of topoisomerase inhibitors

Topoisomerases have become increasingly important both in understanding the dynamics of DNA structure in vivo and in cancer chemotherapy. Topoisomerases are proteins that convert super-coiled DNA to the relaxed state, either by nicking one strand and passing the other strand through the break (type I enzymes), or by causing a double stranded break, through which a duplex segment is moved (type II enzymes). The enzymes then reseal the DNA after strand passage. This activity is required for many cellular processes, and is elevated in many cancer cells.; Research in the last decade has revealed that several important anticancer agents inhibit topoisomerases. Camptothecin, an isoquinoline alkaloid, reversibly inhibits topoisomerase I by stabilizing the transiently nicked covalent complex, which can be detected by rapid denaturation of the enzyme. Daunomycin, an intercalating anthracycline antibiotic, stabilizes the analogous cleavable complex arising from topoisomerase II-mediated DNA relaxation, also in a reversible manner.; This thesis details the study of analogs of these two families of medicinal agents. Chapter 2 shows that position 14 of camptothecin must remain unencumbered, that planarity of the western zone of the drug is important, that the A ring of the drug is not necessary for activity against topo I, and that the E ring lactone is important. Chapter 3 shows that DNA binding agents like daunomycin, as well as daunomycins with modified carbohydrates, are able to inhibit topo I solely by competing for binding sites on the DNA, and not by stabilizing the cleavable complex. Chapter 4 details the ability of the synthetic anthracyclines to inhibit topoisomerase II, the major target of the parent compound, daunomycin. Finally, Chapter 5 discusses native gel electrophoresis of the noncovalent complex of DNA and topo II and the attempts to use this technique to footprint the complex.