VinSpinIn A chemical probe for the Spin family proteins

The SYPRO Orange thermal shift assay was employed to screen VinSpinIn and VinSpinIC against a panel of methyl binding domains (MBDs), which included four of the five Spin family members (Table 1). VinSpinIn induced a large shift in thermal stability of Spin1, Spin2B, Spin3, Spin4. No other significant shift in thermal stability was observed for VinSpinIn or the inactive VinSpinIC.

Table 1: Screening on a panel of MBDs.^a protein = 0.05 to 0.2 mg/ml, compound = 200 µM; ^b protein = 2 µM, compound = 20 µM; ^c Intrinsic tryptophan fluorescence used

A fluorescence polarization displacement assays was employed to screen the compounds against L3MBTL1 and L3MBTL3 (MBT methyl lysine readers), which gave respective K_disp.s of 27 and 8 µM for VinSpinIn, and 28 and 14 µM for the inactive VinSpinIC. Therefore, VinSpinIn is approximately 267 times less potent towards L3MBTL1 than Spin1.

Selectivity screening was also performed against a panel of methyl transferases domains (MTDs) including protein, DNA and RNA methyltransferases using a Scintillation Proximity Assay (SPA) (Figure 1).

Figure 1: (Top) Methyltransferase activity in presence of VinSpinIn at 10 & 50 µM
(Bottom) Methyltransferase activity in presence of VinSpinIC at 10 and 50 µM.

For selected targets IC₅₀s were determined (Table 2). The lowest IC₅₀ of VinSpinIn (PRMT4) was approximately 300 times greater than the AlphaScreen IC₅₀ on Spin1.

Table 2: IC₅₀s of selected methyltransferases.^a Not determined

Materials and Methods

Effects of VinSpinIn  and VinSpinIC on methyltransferase activity of G9a, GLP, SUV39H1, SUV39H2, SETDB1, SETD8, SUV420H1, SUV420H2, SETD7, MLL1 trimeric complex, MLL3 pentameric complex, EZH2 trimeric complex, PRMT1, PRMT3, PRMT4, PRMT5-MEP50 complex, PRMT6, PRMT7, PRMT8, PRMT9, PRDM9, SETD2, SMYD2, SMYD3, and DNMT1 was assessed by monitoring the incorporation of tritium-labeled methyl group to lysine or arginine residues of peptide substrates using Scintillation Proximity Assay (SPA) as previously described¹⁴.  Assays were performed in a 10 µl reaction mixture containing ³H-SAM (Cat.# NET155V250UC; Perkin Elmer; www.perkinelmer.com) at substrate concentrations close to K_m values for each enzyme.  Two concentrations (10µM and 50 µM) of VinSpinIn or  VinSpinIC  were used in all selectivity assays.  To stop the enzymatic reactions, 10 µl of 7.5 M guanidine hydrochloride was added, followed by 180 µl of buffer (20 mM Tris, pH 8.0), mixed and then transferred to a FlashPlate (Cat.# SMP103; Perkin Elmer; www.perkinelmer.com). After mixing, the reaction mixtures in Flash plates were incubated for 2 hours and the CPM were measured using Topcount plate reader (Perkin Elmer, www.perkinelmer.com). The CPM counts in the absence of compound for each data set were defined as 100% activity. In the absence of the enzyme, the CPM counts in each data set were defined as background (0%).

For DOT1L, NSD1, NSD2, NSD3, ASH1L, DNMT3A/3L, and DNMT3B/3L, a filter-based assay was used. In this assay, 10 µl of reaction mixtures were incubated at 23 ^oC for 1 hour, 50 µl of 10% trichloroacetic acid (TCA) was added, mixed and transferred to filter-plates (Millipore; cat.# MSFBN6B10; www.millipore.com). Plates were centrifuged at 2000 rpm (Allegra X-15R - Beckman Coulter, Inc.) for 2 min followed by 2 additional 10% TCA wash and one ethanol wash followed by centrifugation. Plates were dried and 30 µl MicroO (MicroScint-O; Cat.# 6013611, Perkin Elmer; www.perkinelmer.com) was added to each well, centrifuged and removed. 50 µl of MicroO was added again and CPM was measured using Topcount plate reader.

IC₅₀ Determinations:
IC₅₀ values were determined for inhibition of methyltransferase activity of the following enzymes:

• PRMT4 (20 nM PRMT4, 1 µM of biotinlated-H3 1-25, 2 µM of ³H-SAM)
• SETD2 (150 nM SETD2, 0.5 µM of biotinylated-H3 21-44, 5 µM of ³H-SAM)
• PRMT7 (25 nM PRMT7, 0.3 µM of biotinylated-H2B(23-37), 1 µM of ³H-SAM)
• SUV39H1 (20 nM SUV30H1, 0.2 µM of biotinlated-H3 1-25, 5 µM of ³H-SAM)
• PRMT6 (20 nM PRMT6, 1 µM of biotinlated-H4 1-24, 2 µM of ³H-SAM)
• PRC2 (20 nM PRC2, 1 µM of biotinlated-H3 21-44, 2 µM of ³H-SAM)
• SMYD2 (30 nM SMYD2, 3 µM of biotinlated-P⁵³peptide, 0.3 µM of ³H-SAM)
• PRDM9 (5 nM PRDM9, 4 µM of biotinlated-H3 1-25, 71 µM of SAM)
• PRMT1 (15 nM PRMT1, 0.13 µM of biotinlated-H4 1-24, 5 µM of ³H-SAM)
• PRMT8 (20 nM PRMT8, 1 µM of biotinlated-H4 1-24, 2 µM of ³H-SAM)
• DNMT3A/3L (20 nM DNMT3A/3L, 0.5 µM of poly DI-DC, 1 µM of ³H-SAM)
• DNMT3B/3L (50 nM DNMT3B/3L, 0.5 µM of poly DI-DC, 1 µM of ³H-SAM)
• G9a (5 nM G9A, 0.8 µM of biotinlated-H3 1-25, 10 µM of SAM)
• GLP (5 nM Glp, 0.8 µM of biotinlated-H3 1-25, 10 µM of SAM).

To stop the enzymatic reactions, 7.5 M Guanidine hydrochloride was added, followed by 180 µL of buffer (20 mM Tris, pH 8.0), mixed and then transferred to a FlashPlate (Cat.# SMP103; Perkin Elmer; www.perkinelmer.com). After mixing, the reaction mixtures in Flash plate were incubated for 2 hour and the CPM counts were measured using Topcount plate reader (Perkin Elmer, www.perkinelmer.com). The CPM counts in the absence of compound for each data set were defined as 100% activity. In the absence of the enzyme, the CPM counts in each data set were defined as background (0%). The IC₅₀ values were calculated using GraphPad Prism 7 software.