| Abstract
| - Uracil DNA glycosylase (UNG) is an important DNA repair enzyme that recognizes and excisesuracil bases in DNA using an extrahelical recognition mechanism. It is emerging as a desirable target forsmall-molecule inhibitors given its key role in a wide range of biological processes including the generationof antibody diversity, DNA replication in a number of viruses, and the formation of DNA strand breaksduring anticancer drug therapy. To accelerate the discovery of inhibitors of UNG we have developed auracil-directed ligand tethering strategy. In this efficient approach, a uracil aldehyde ligand is tethered viaalkyloxyamine linker chemistry to a diverse array of aldehyde binding elements. Thus, the mechanism ofextrahelical recognition of the uracil ligand is exploited to target the UNG active site, and alkyloxyaminelinker tethering is used to randomly explore peripheral binding pockets. Since no compound purification isrequired, this approach rapidly identified the first small-molecule inhibitors of human UNG with micromolarto submicromolar binding affinities. In a surprising result, these uracil-based ligands are found not only tobind to the active site but also to bind to a second uncompetitive site. The weaker uncompetitive site suggeststhe existence of a transient binding site for uracil during the multistep extrahelical recognition mechanism.This very general inhibitor design strategy can be easily adapted to target other enzymes that recognizenucleobases, including other DNA repair enzymes that recognize other types of extrahelical DNA bases.
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