UNC1215

UNC1215 is a selective inhibitor of L3MBTL3 with IC50 value of 40 nM [1].
L3MBTL3 is a member of the MBT (malignant brain tumor) family of methyl-lysine reader proteins and is reported to play an important role in haematopoiesis and cancer biology. And it is reported that inhibition of L3MBTL3 can be regarded as a promising target used in clinic [2].  
UNC1215 is a potent L3MBTL3 inhibitor and has a more potent inhibitory ability than other MBT family members. When tested with HEK293 cells transfected with a GFP fusion protein of the 3 MBT domains of L3MBTL3, UNC1215 treatment decreased the recovery time in a dose responsive manner via binding and co-localizing L3MBTL3 [1]. Using AlphaScreen○R methylated histone peptide competition assay, UNC1215 showed high antagonism ability to L3MBTL3 with IC50 value of 24±7.6 nM [3]. As the first potent and selective inhibitor for methyl-lysine reader protein-L3MBTL3-UNC1215 showed highly selective inhibitor ability via antagonizing the mono- and dimethyl-lysine reading function of L3MBTL3 [2].
References:
1.    James, L.I., et al., Discovery of a chemical probe for the L3MBTL3 methyllysine reader domain. Nat Chem Biol, 2013. 9(3): p. 184-91.
2.    James, L.I., et al., Small-molecule ligands of methyl-lysine binding proteins: optimization of selectivity for L3MBTL3. J Med Chem, 2013. 56(18): p. 7358-71.
3.    Camerino, M.A., et al., The structure-activity relationships of L3MBTL3 inhibitors: flexibility of the dimer interface. Medchemcomm, 2013. 4(11): p. 1501-1507.

Developing Spindlin1 small-molecule inhibitors by using protein microarrays.[Pubmed:28504676]

Nat Chem Biol. 2017 Jul;13(7):750-756.

The discovery of inhibitors of methyl- and acetyl-binding domains has provided evidence for the 'druggability' of epigenetic effector molecules. The small-molecule probe UNC1215 prevents methyl-dependent protein-protein interactions by engaging the aromatic cage of MBT domains and, with lower affinity, Tudor domains. Using a library of tagged UNC1215 analogs, we screened a protein-domain microarray of human methyllysine effector molecules to rapidly detect compounds with new binding profiles with either increased or decreased specificity. Using this approach, we identified a compound (EML405) that acquired a novel interaction with the Tudor-domain-containing protein Spindlin1 (SPIN1). Structural studies facilitated the rational synthesis of SPIN1 inhibitors with increased selectivity (EML631-633), which engage SPIN1 in cells, block its ability to 'read' H3K4me3 marks and inhibit its transcriptional-coactivator activity. Protein microarrays can thus be used as a platform to 'target-hop' and identify small molecules that bind and compete with domain-motif interactions.

Small-molecule ligands of methyl-lysine binding proteins: optimization of selectivity for L3MBTL3.[Pubmed:24040942]

J Med Chem. 2013 Sep 26;56(18):7358-71.

Lysine methylation is a key epigenetic mark, the dysregulation of which is linked to many diseases. Small-molecule antagonism of methyl-lysine (Kme) binding proteins that recognize such epigenetic marks can improve our understanding of these regulatory mechanisms and potentially validate Kme binding proteins as drug-discovery targets. We previously reported the discovery of 1 (UNC1215), the first potent and selective small-molecule chemical probe of a methyl-lysine reader protein, L3MBTL3, which antagonizes the mono- and dimethyl-lysine reading function of L3MBTL3. The design, synthesis, and structure-activity relationship studies that led to the discovery of 1 are described herein. These efforts established the requirements for potent L3MBTL3 binding and enabled the design of novel antagonists, such as compound 2 (UNC1679), that maintain in vitro and cellular potency with improved selectivity against other MBT-containing proteins. The antagonists described were also found to effectively interact with unlabeled endogenous L3MBTL3 in cells.

The L3MBTL3 Methyl-Lysine Reader Domain Functions As a Dimer.[Pubmed:26317848]

ACS Chem Biol. 2016 Mar 18;11(3):722-8.

L3MBTL3 recognizes mono- and dimethylated lysine residues on histone tails. The recently reported X-ray cocrystal structures of the chemical probe UNC1215 and inhibitor UNC2533 bound to the methyl-lysine reading MBT domains of L3MBTL3 demonstrate a unique and flexible 2:2 dimer mode of recognition. In this study, we describe our in vitro analysis of L3MBTL3 dimerization via its MBT domains and additionally show that this dimerization occurs within a cellular context in the absence of small molecule ligands. Furthermore, mutations to the first and second MBT domains abrogated L3MBTL3 dimerization both in vitro and in cells. These observations are consistent with the hypothesis that L3MBTL3 engages methylated histone tails as a dimer while carrying out its normal function and provides an explanation for the presence of repeated MBT domains within L3MBTL3.

The structure-activity relationships of L3MBTL3 inhibitors: flexibility of the dimer interface.[Pubmed:24466405]

Medchemcomm. 2013 Nov;4(11):1501-1507.

We recently reported the discovery of UNC1215, a potent and selective chemical probe for the L3MBTL3 methyllysine reader domain. In this article, we describe the development of structure-activity relationships (SAR) of a second series of potent L3MBTL3 antagonists which evolved from the structure of the chemical probe UNC1215. These compounds are selective for L3MBTL3 against a panel of methyllysine reader proteins, particularly the related MBT family proteins, L3MBTL1 and MBTD1. A co-crystal structure of L3MBTL3 and one of the most potent compounds suggests that the L3MBTL3 dimer rotates about the dimer interface to accommodate ligand binding.

Methyllysine reader plant homeodomain (PHD) finger protein 20-like 1 (PHF20L1) antagonizes DNA (cytosine-5) methyltransferase 1 (DNMT1) proteasomal degradation.[Pubmed:24492612]

J Biol Chem. 2014 Mar 21;289(12):8277-87.

Inheritance of DNA cytosine methylation pattern during successive cell division is mediated by maintenance DNA (cytosine-5) methyltransferase 1 (DNMT1). Lysine 142 of DNMT1 is methylated by the SET domain containing lysine methyltransferase 7 (SET7), leading to its degradation by proteasome. Here we show that PHD finger protein 20-like 1 (PHF20L1) regulates DNMT1 turnover in mammalian cells. Malignant brain tumor (MBT) domain of PHF20L1 binds to monomethylated lysine 142 on DNMT1 (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. PHF20L1 knockdown by siRNA resulted in decreased amounts of DNMT1 on chromatin. Ubiquitination of DNMT1K142me1 was abolished by overexpression of PHF20L1, suggesting that its binding may block proteasomal degradation of DNMT1K142me1. Conversely, siRNA-mediated knockdown of PHF20L1 or incubation of a small molecule MBT domain binding inhibitor in cultured cells accelerated the proteasomal degradation of DNMT1. These results demonstrate that the MBT domain of PHF20L1 reads and controls enzyme levels of methylated DNMT1 in cells, thus representing a novel antagonist of DNMT1 degradation.

UNC1215 is a potent and selective inhibitor for the methyllysine (Kme) reading domain function of L3MBTL3 with a Kd value of 120 nM and an IC50 of 40 nM. UNC1215 has the potential to treat malignant brain tumor.

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