In vitro activity: UNC669, as a low μM binder of L3MBTL1, provides new directions for optimization of MBT inhibitors to improve potency and selectivity.

Kinase Assay: A histone peptide consisting of residues 1-15 of the H3 histone tail containing an N-terminal fluorescein, a 6-aminohexanoic acid linker, and monomethyl lysine at position 9 (FAM-H3K9Me1) was used as the fluorescent probe to bind L3MBTL1 in the FP displacement assay (FAM-AHA-ARTKQTARK(Me)STGGKA-CO2H). Binding assays were carried out in 20 mM Tris-HCl (pH 8.), 25 mM NaCl, and 2 mM β-mercaptoethanol in black 384-well microplates (Corning, non-binding surface) with a final volume of 30 μL per well. To each well, 20 μL of a 150 nM stock solution of H3 FAM-K9Me was added to give a final concentration of 100 nM, followed by 5 μL of a 120 μM stock solution of L3MBTL1 to give a final protein concentration of 20 μM. Serial dilutions were prepared of inhibitor UNC669 (14) and added (5 μL) to give a final concentration range of 0-400 μM. Plates were incubated for 20 min at room temperature prior to analysis. FP measurements (mP) were made on an AcQuest (LJL BioSystems) plate reader at room temperature, with an excitation wavelength of 485 nm and the emission collected at 530 nm. The G factor was determined to be 0.92 from a standard solution of fluorescein and corrected for by the instrument software. All measurements were made in triplicate with 10 readings collected in each measurement.

Cell Assay: Purified protein was obtained using methods established previously for the three-MBT repeat (3MBT) domain of human L3MBTL1 (residues 200-522). Crystallization was performed using a protein sample concentrated to 10 mg/mL and pre-incubated with 1 mM compound 14 (UNC669). Initial screening was carried out by sitting drop vapor diffusion at room temperature using an in-house sparse-matrix crystallization screen, yielding needles which appeared after four days in a condition containing 25% PEG 3350, 0.1 M ammonium sulfate, and 0.1 M Bis-Tris buffer pH 5.5. The crystals belong to the trigonal space group P32 with unit cell dimensions of a = b = 106.3 A, and c = 90.1 A, containing three molecules in the asymmetric unit. A single crystal was cryoprotected by soaking in well solution with 18% glycerol (v/v) for 60 s before flash freezing in liquid nitrogen.

J Med Chem. 2011 Apr 14;54(7):2504-11.