Chromatin is the complex of histone proteins, RNA, and DNA that efficiently packages the genome within each human cell. The regulation of chromatin accessibility via post-translational modifications (PTM) of histones is of great current interest as opportunities for pharmacological intervention in the `writing', `reading' and `erasing' of PTMs are significant. The biological consequences of most PTMs result from their recruitment of regulatory machinery via protein-protein interactions directly facilitated by the PTM. The binding domains involved in PTM recognition on chromatin are referred to as ?readers?. Our understanding of chromatin regulation is in its infancy and chemical biology is poised to play a central role in advancing scientific knowledge and assessing therapeutic opportunities in this field. Specifically, cell penetrant, high-quality chemical probes that modulate the regulation of chromatin state are of great significance. The primary intent of a chemical probe is to establish the relationship between a molecular target, usually a protein whose function is modulated by the probe, and the biological consequences of that modulation. In order to fulfill this purpose, a chemical probe must be profiled for selectivity, mechanism of action, and cellular activity, as the cell is the minimal system in which `biology' can be explored. Fortuitously, the scientific community's interest in chromatin regulation and the appreciation for the role of chemical probes in driving biological understanding has intersected in an exciting and productive fashion over the last five years resulting in rapid translation of chromatin chemical probe-enabled biological hypotheses to clinical interventions. We have been focused on exploration of the druggability of readers of methyl-lysine (Kme) as this PTM plays a central role in chromatin regulation and more than 200 Kme reader domains within several protein families occur within the human proteome. Our prior work has begun to define the assays and chemical strategies for probe development in this target-class, as well as new directions required for future progress. The research proposed here is intended to overcome the key challenges we have identified utilizing new approaches toward chemical probes for chromatin readers within and beyond the Kme target-class. The overarching objectives of this program are to develop chemical probes of chromatin reader domains that exploit three distinct mechanisms of molecular recognition: 1) reader domains that function as dimers; 2) reader domains that operate via a dynamic, induced-fit recognition mechanism; and 3) multivalent reader domains. The probes developed in the course of this research will be made freely available to the academic community with no restrictions on use or intellectual property constraints. This prospective and purposeful creation of a set of tools placed in the public domain to advance science and drug discovery in a novel target- class area will enable academic biomedical research to contribute to more rapidly to translational science.
Multicellular organisms have evolved elaborate mechanisms to enable the differential and cell-type specific expression of genes. This capability permits specialization of function between cells even though each cell contains essentially the same genetic code. The creation of a `tool-kit' of potent, selective, well- characterized and cell-penetrant small molecule probes of chromatin regulation will permit biological hypotheses concerning chromatin-state to be tested with confidence in cell-based and animal models of human biology and disease.
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| Stuckey, Jacob I; Simpson, Catherine; Norris-Drouin, Jacqueline L et al. (2016) Structure-Activity Relationships and Kinetic Studies of Peptidic Antagonists of CBX Chromodomains. J Med Chem 59:8913-8923 |
| Pattenden, Samantha G; Simon, Jeremy M; Wali, Aminah et al. (2016) High-throughput small molecule screen identifies inhibitors of aberrant chromatin accessibility. Proc Natl Acad Sci U S A 113:3018-23 |
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| Barnash, Kimberly D; Lamb, Kelsey N; Stuckey, Jacob I et al. (2016) Chromodomain Ligand Optimization via Target-Class Directed Combinatorial Repurposing. ACS Chem Biol 11:2475-83 |
| Stuckey, Jacob I; Dickson, Bradley M; Cheng, Nancy et al. (2016) A cellular chemical probe targeting the chromodomains of Polycomb repressive complex 1. Nat Chem Biol 12:180-7 |
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