Small-molecule pyrimidine inhibitors of the cdc2-like (Clk) and dual specificity tyrosine phosphorylation-regulated (Dyrk) kinases: development of chemical probe ML315

Abstract

Substituted pyrimidine inhibitors of the Clk and Dyrk kinases have been developed, exploring structure-activity relationships around four different chemotypes. The most potent compounds have low-nanomolar inhibitory activity against Clk1, Clk2, Clk4, Dyrk1A and Dyrk1B. Kinome scans with 442 kinases using agents representing three of the chemotypes show these inhibitors to be highly selective for the Clk and Dyrk families. Further off-target pharmacological evaluation with ML315, the most selective agent, supports this conclusion.

Figure 1

Reported Clk and Dyrk kinase inhibitors

Figure 2

Quinazoline Clk/Dyrk kinase inhibitors

Figure 3

Three series of pyrimidine Clk4 inhibitors

Figure 4

IC₅₀ values (μM) against Clk4/Dyrk1A for matrix library pyrimidines (Kinase Glo (Promega) assay)

Figure 5

Dendrogram depiction of DiscoverRX^® KINOMEscan^® kinase binding selectivity analysis. Larger spheres represent <10% control at 10 μM and smaller spheres represent <30% control at 10 μM (% control refers to the percentage of kinase remaining bound to the anchored active-site ligand in the presence of a competitive inhibitor). Activity for 35: <10% = Clk1, Clk2, Clk4, Dyrk1A, PRKCE; <30% = CSNK1E, MAP3K1. Activity for 32: <10% = BIKE, Clk2, Dyrk1A; <30% = AAK1, Clk1, Clk4, GAK, LATS1, PIM1, PIP5K1A, PIP5K2B, RIOK3, SRPK3. Activity for 22: <10% = BIKE, CIT, Clk1, Clk2, Clk4, CSNK1D, CSNK1E, CSNK1G2, DRAK, Dyrk1A, Dyrk1B, Erk8, Flt3, HIPK3, KIT, MYLK4, PIP5K2C, PRKCE, PRKCH; <30% = BMPR2, Clk3, CSNK1A1, DDR2, Dyrk2, Erk5, GSK3B, HIPK4, HUNK, IGF1R, IKK-alpha, IRAK3, MAP3K1, PIP5K1A, PIP5K2B, RIOK1, RIOK2, RIOK3, ROCK1, SRPK3. (Dendrograms generated using the online tool at: http://tripod.nih.gov/?p=226)

Figure 6

Docking pose for compound 17 in Clk4 homology model: (a) Important hydrogen bond interactions with the hinge region of the enzyme; (b) surface representation showing hydrophobic pocket. (Graphics prepared using Pymol.)

Scheme 1

Synthesis of substituted aminopyrimidines