Discovery of a chemical probe for the L3MBTL3 methyl-lysine reader domain

• Published in: Nature chemical biology Vol. 9; no. 3; pp. 184 - 191
• Main Authors: James, Lindsey I., Barsyte-Lovejoy, Dalia, Zhong, Nan, Krichevsky, Liubov, Korboukh, Victoria K., Herold, Martin J., MacNevin, Christopher J., Norris, Jacqueline L., Sagum, Cari A., Tempel, Wolfram, Marcon, Edyta, Guo, Hongbo, Gao, Cen, Huang, Xi-Ping, Duan, Shili, Emili, Andrew, Greenblatt, Jack F., Kireev, Dmitri B., Jin, Jian, Janzen, William P., Brown, Peter J., Bedford, Mark T., Arrowsmith, Cheryl H., Frye, Stephen V.
• Format: Journal Article
• Language: English
• Published: 06.01.2013
• ISSN: 1552-4450; 1552-4469
• DOI: 10.1038/nchembio.1157

We describe the discovery of UNC1215, a potent and selective chemical probe for the methyl-lysine (Kme) reading function of L3MBTL3, a member of the malignant brain tumor (MBT) family of chromatin interacting transcriptional repressors. UNC1215 binds L3MBTL3 with a K d of 120 nM, competitively displacing mono- or dimethyl-lysine containing peptides, and is greater than 50-fold selective versus other members of the MBT family while also demonstrating selectivity against more than 200 other reader domains examined. X-ray crystallography identified a novel 2:2 polyvalent mode of interaction. In cells, UNC1215 is non-toxic and binds directly to L3MBTL3 via the Kme-binding pocket of the MBT domains. UNC1215 increases the cellular mobility of GFP-L3MBTL3 fusion proteins and point mutants that disrupt the Kme binding function of GFP-L3MBTL3 phenocopy the effects of UNC1215. Finally, UNC1215 demonstrates a novel Kme-dependent interaction of L3MBTL3 with BCLAF1, a protein implicated in DNA damage repair and apoptosis.