Unbiased and biased chemical libraries for chemical genetics

Diversity-oriented organic synthesis offers the promise of advancing chemical genetics, where small molecules are used to explore biology. Small molecules that modulate the circuitry of biological networks can be discovered using either phenotypic or protein-binding screens.; The discovery of small molecule ligands to proteins for which no structural or mechanistic information is available requires the structurally unbiased design of many small molecules. These molecules should be easily synthesized in large numbers and then tested in phenotypic or protein-binding screens to identify molecules that elicit a desired response. Alternatively, protein families for which some structural or mechanistic information is available can be the targets of chemical libraries that are structurally biased towards a feature of that protein family. These libraries can be used to identify selective activating or inactivating small molecule ligands for specific proteins within the protein family.; Herein is described the development of an approach to split-pool synthesis that enables synthesis of a target-unbiased collection of 1,3-dioxane molecules as individual stock solutions, each of which is sufficient for hundreds of phenotypic and protein-binding screens. These stock solutions have been used in phenotypic assays and also covalently attached to glass slides to generate small molecule microarrays for protein-binding assays. Use of these small molecule microarrays for protein-binding assays with the Saccharomyces cerevisiae Ure2p protein has led to the discovery of the selective small molecule modulator, uretupamine.; Also discussed is the adaptation of the synthetic route to unbiased 1,3-dioxane diversity structures for the discovery of paralog-selective inhibitors of the histone deacetylase protein family. The split-pool synthesis and post-synthetic analysis of a histone deacetylase-biased collection of 7200 small molecules reminiscent of the natural products trichostatin A and trapoxin is reported.