Multicellular organisms have evolved elaborate mechanisms to enable differential and cell-type specific expression of genes. Epigenetics refers to these heritable changes in how DNA is accessed in different cell-types and during development and differentiation. The template upon which the epigenome is written is chromatin - the complex of histone proteins, RNA and DNA that efficiently package the genome in an appropriately accessible state within each cell. The state of chromatin, and therefore access to the genetic code, is largely regulated by specific chemical modifications to histone proteins and DNA, and the recognition of these marks by other proteins and protein complexes. Our understanding of chromatin function is in its infancy and chemical biology can play a central role in advancing scientific knowledge and assessing therapeutic opportunities. Specifically, cell penetrant, high-quality chemical probes that modulate the regulation of chromatin state are of great significance in the fields of epigenetics, oncology, developmental biology, neurology, stem cell fate and regenerative medicine. The recognition of the methylation-state of lysine residues in histones is a critical event in chromatin regulation. For example, different lysine methylation marks (KMe) are associated with active (histone 3, lysine 4 dimethylation, i.e. - H3K4Me2) and repressed transcriptional states (H3K9Me2). The more than 200 methyl-lysine binding proteins in the human genome represent a relatively unexplored set of targets for intervention with small molecules. The overarching objectives of this program are to develop pharmacological probes of methyl-lysine binding domains to pioneer both the validation of specific domains and the assay framework in which issues of selectivity and mechanism of action can be assessed. We have discovered small molecule ligands for the methyl-lysine readers, L3MBTL3 and L3MBTL1, with low micro-molar to nanomolar Kd values (ITC). Ligands for L3MBTL3 also demonstrate effects on L3MBTL3- GFP protein localization in whole cells. We propose the optimization of these series to provide high quality chemical probes. The malignant brain tumor (MBT) repeat is a structural domain of ca. 100 amino acids and occurs in 9 human proteins that recognize mono- and dimethyl-lysine modifications of histones. There are no high-quality chemical probes for MBT domains, or indeed, any other methyl-lysine binding domain. Current understanding of the biological consequences of MBT domain antagonism would suggest that antagonists may be useful in de-differentiation, re-expression of silenced genes and cellular reprogramming, We will establish a firm connection between methyl-lysine reader in vitro antagonism, cell-based localization of the targeted reader, genome-wide selectivity finger-printing and biological consequences of reader antagonism. The probes developed in the course of this research would be made freely available to the academic community with no restrictions on use or intellectual property constraints.
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. This proposal specifically aims to develop potent antagonists of methyl-lysine recognition by human MBT domain containing proteins in order to permit exploration of the biological consequences of blocking this recognition in cell-based and in vivo models with relevance to normal and disease biology.
| Suh, Junghyun L; Watts, Brian; Stuckey, Jacob I et al. (2018) Quantitative Characterization of Bivalent Probes for a Dual Bromodomain Protein, Transcription Initiation Factor TFIID Subunit 1. Biochemistry 57:2140-2149 |
| Barnash, Kimberly D; James, Lindsey I; Frye, Stephen V (2017) Target class drug discovery. Nat Chem Biol 13:1053-1056 |
| Barnash, Kimberly D; The, Juliana; Norris-Drouin, Jacqueline L et al. (2017) Discovery of Peptidomimetic Ligands of EED as Allosteric Inhibitors of PRC2. ACS Comb Sci 19:161-172 |
| Gerken, Philip A; Wolstenhulme, Jamie R; Tumber, Anthony et al. (2017) Discovery of a Highly Selective Cell-Active Inhibitor of the Histone Lysine Demethylases KDM2/7. Angew Chem Int Ed Engl 56:15555-15559 |
| 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 |
| Zhou, Hao; Che, Xin; Bao, Guochen et al. (2016) Design, synthesis, and protein methyltransferase activity of a unique set of constrained amine containing compounds. Bioorg Med Chem Lett 26:4436-4440 |
| James, Lindsey I; Frye, Stephen V (2016) Chemical probes for methyl lysine reader domains. Curr Opin Chem Biol 33:135-41 |
| 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 |
| Baughman, Brandi M; Pattenden, Samantha G; Norris, Jacqueline L et al. (2016) The L3MBTL3 Methyl-Lysine Reader Domain Functions As a Dimer. ACS Chem Biol 11:722-8 |
Showing the most recent 10 out of 25 publications
