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.

Public Health Relevance

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.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
1R01GM100919-01
Application #
8270684
Study Section
Synthetic and Biological Chemistry B Study Section (SBCB)
Program Officer
Fabian, Miles
Project Start
2012-05-01
Project End
2016-01-31
Budget Start
2012-05-01
Budget End
2013-01-31
Support Year
1
Fiscal Year
2012
Total Cost
$281,200
Indirect Cost
$91,200
Name
University of North Carolina Chapel Hill
Department
Pharmacology
Type
Schools of Pharmacy
DUNS #
608195277
City
Chapel Hill
State
NC
Country
United States
Zip Code
27599
James, Lindsey I; Korboukh, Victoria K; Krichevsky, Liubov et al. (2013) Small-molecule ligands of methyl-lysine binding proteins: optimization of selectivity for L3MBTL3. J Med Chem 56:7358-71
James, Lindsey I; Barsyte-Lovejoy, Dalia; Zhong, Nan et al. (2013) Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain. Nat Chem Biol 9:184-91