Structure, mechanism, and inhibition of AlkB homologues

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DESCRIPTION (provided by applicant): DNA repair is considered the double-edged sword of tumor biology. While the biochemical machinery that repairs DNA damage plays a central role in maintaining genomic integrity and thereby preventing cancer in normal cells, it also limits the efficacy of the DNA-damaging agents that represent some of the most widely used and successful chemotherapeutic drugs in clinical oncology. Therefore, a detailed understanding of the enzymatic reaction mechanisms and physiological functions of DNA repair enzymes represents essential basic knowledge concerning the function of normal cells and the systems that protect them from oncogenic transformation. However, this knowledge is also practically important in efforts to improve cancer therapy because inhibitors of DNA repair enzymes can potentiate the potency of other therapeutic agents. Recently, there has been an explosion of knowledge concerning the molecular function of the DNA repair enzymes in the AlkB superfamily, which are present in all eubacteria and all higher eukaryotes. These enzymes have been shown to catalyze direct repair of adenine and cytosine bases that have been alkylated on endocyclic ring nitrogen atoms, a toxic DNA modification that is mediated by both endogenous and environmental mutagens. Elucidation of the chemical reaction catalyzed by AlkB has enabled rapid progress to be made in understanding their physiological function, which includes repair of damaged mRNA and tRNA molecules that reduce translation efficiency in addition to repair of mutagenic lesions in DNA. However, numerous features of AlkB superfamily enzymes remain to be characterized, including the structural mechanisms enabling promiscuous recognition of different substrates, the details of their catalytic reaction mechanism, and the biological function of the 8 distinct sequence homologues that are conserved in mammalian organisms. We plan to apply a combination of biophysical, chemical, and molecular biological techniques to answer these fundamental questions concerning the biochemistry of AlkB-family DNA repair enzymes.