This laboratory is interested in the elucidation of the molecular mechanisms whereby potent enediyne antitumor antibiotics damage DNA by activation of the drug to a diradical species that directly and selectively attacks specific sites in nucleic acid sugars. These studies have enabled the development of such agents as specific probes of various nucleic acid structures. Upon activation of its highly strained bicyclo dodecadiyne moiety by thiol, neocarzinostatin chromophore is converted into a diradical species that abstracts hydrogen atoms from minor groove accessible sites at the C-5', C-4', and C-1' positions of deoxyribose on the complementary DNA strands, forming sequence-specific bistranded lesions containing both strand breaks and abasic sites. The chemistry of the DNA damage process and the three-dimensional structure of the DNA · active drug complex have been elucidated, and the biochemical and mutagenic consequences of lesion formation have been described in detail. This reaction has also been used to elucidate the chemical mechanism whereby nitro aromatic radiation sensitizers substitute for dioxygen by adduction at the carbon-centered radical on the DNA deoxyribose to form a nitroxylradical adduct intermediate, which undergoes novel cleavage of the sensitizer between its oxygen and nitrogen atoms and generation of an oxyradical on the DNA sugar. By a novel mechanism, the drug can also undergo base-catalyzed activation (without thiol) to a different diradical species that produces breaks selectively at nucleic acid bulge-specific sites. The chemical structure of the unique drug product of this reaction has been elucidated, and a mechanism for its formation has been proposed. This unusual mechanism implicates the DNA bulge conformation itself in the chemistry of drug transformation to its final product. Bulged structures in DNA and RNA have been proposed as binding motifs in a number of important biological processes, including slipped synthesis, leading to nucleotide repeat expansions in a number of neurodegenerative diseases and cancers. The solution structure of a two-base DNA bulge complexed with an analog of the cleaving species (radical) of the drug, in which the two drug rings stack with the base pairs above and below the bulge, has been determined. This structure clarifies the mechanism of bulge recognition and cleavage by the drug and provides insights into the design of bulge-specific nucleic acid binding molecules. We have initiated a synthetic effort to prepare bulge-specific, wedge-shaped, double-deckered molecules to study the usefulness of such agents as probes of such structures. We have been able to show that a designed spirocyclic mimic of the natural product binds specifically to DNA and RNA bulges and enhances DNA slipped synthesis in model systems containing nucleotide repeats. In addition, we have designed spirocyclic compounds capable of alkylation and cleavage reactions at the site of slippage. Other very potent enediynes (C-1027), with different DNA sequence requirements, are also being studied mechanistically. C-1027, the most potent anti-cancer agent known, has been found to generate novel interstrand cross-links, which in contrast to all other known agents covalently cross-links the deoxyribose moieties of the complementary DNA strands.
Xiao, Z., Zhang, N., Lin, Y., Jones, G.B., and Goldberg, I.H. Spirocyclic helical compounds as binding agents for bulged RNA, including HIV-2 TAR. Chem. Commun. (42), 4431-4433, 2006.
Battle of the bulge. Chem. Biol., (11), 25 October 2006 (Royal Society of Chemistry, www.rsc.org.)
Jones, G.B., Lin, Y., Ma, D., Xiao, Z., Hwang, G-S., Kappen, L., and Goldberg, I.H. Congeners of the enediyne neocarzinostatin chromophore: designed agents for bulged nucleic acid targets. Curr. Topics Med Chem. 8, 436-447. 2008.
Kappen, L.S., Lin, Y., Jones, G.B., and Goldberg, I.H. Probing DNA bulges with designed helical spirocyclic molecules. Biochemistry, 46, 561-567, 2007.
Zhang, N., Lin, Y., Xiao, Z., Jones, G.B., and Goldberg, I.H. Solution structure of a designed spirocyclic helical ligand binding at a two-base bulge site in DNA. Biochemistry, 46, 4793-4803, 2007.