Discovery of a chemical probe for the L3MBTL3 methyllysine 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, J Martin, 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: United States Nature Publishing Group 01.03.2013
• Subjects: Apoptosis; Benzamides - chemistry; Benzamides - metabolism; Benzamides - pharmacology; Binding, Competitive - drug effects; Biochemistry; Brain cancer; Brain tumors; Chromatin; Crystallography; Crystallography, X-Ray; Deoxyribonucleic acid; DNA; DNA-Binding Proteins - antagonists & inhibitors; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - metabolism; Dose-Response Relationship, Drug; Drug Discovery; HEK293 Cells; Humans; Lysine - analogs & derivatives; Lysine - antagonists & inhibitors; Lysine - chemistry; Lysine - metabolism; Models, Molecular; Molecular Probes - chemistry; Molecular Probes - metabolism; Molecular Probes - pharmacology; Molecular Structure; Peptides; Piperidines - chemistry; Piperidines - metabolism; Piperidines - pharmacology; Protein Structure, Tertiary; Proteins; Repressor Proteins - metabolism; Structure-Activity Relationship; Tumor Suppressor Proteins - metabolism; Tumors
• ISSN: 1552-4450; 1552-4469
• DOI: 10.1038/NCHEMBIO.1157

We describe the discovery of UNC1215, a potent and selective chemical probe for the methyllysine (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 dimethyllysine-containing peptides, and is greater than 50-fold more potent toward L3MBTL3 than other members of the MBT family while also demonstrating selectivity against more than 200 other reader domains examined. X-ray crystallography identified a unique 2:2 polyvalent mode of interaction between UNC1215 and L3MBTL3. In cells, UNC1215 is nontoxic and directly binds 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 on localization. Finally, UNC1215 was used to reveal a new Kme-dependent interaction of L3MBTL3 with BCLAF1, a protein implicated in DNA damage repair and apoptosis.