TG003

TG003 is a potent and selective inhibitor of Clk-family kinases with IC50 values of 15, 20, 200 nM and >10 μM for mClk4, 1, 2 and 3, respectively [1]. Also, TG003 is also an inhibitor of casein kinase 1 (CK1) [2].

Cdc2-like kinases (Clks) family consist of Clk1, 2, 3 and 4 and play an important role in mRNA splice site selection. Clks phosphorylate serine/arginine-rich proteins that involved in pre-mRNA processing and release them into the nucleoplasm.

TG003 is a potent and selective Clk-family kinases inhibitor. TG003 competed with ATP with Ki value of 0.01 μM on Clk1/Sty. In HeLa cytosolic S100 extract, TG003 inhibited Clk1/Sty-mediated phosphorylation of SF2/ASF, which played an important role in alternative splicing. Also, TG003 inhibited the splicing of β-globin pre-mRNA when complemented with rSF2/ASF. In HA-Clk1/Sty-overexpressing HeLa cells, TG003 (10 μM) reversibly inhibited phosphorylation of SR proteins and caused HA-Clk1/Sty localized in nuclear speckles [1].

In mice, TG003 inhibited the alteration of splicing site selection induced by Clk1/Sty and affected the alternative splicing of endogenous genes. In X. laevis embryo, TG003 (10μM) rescued the morphological abnormalities in the dorsal ectoderm and mesoderm induced by the overexpression of xClk kinase [1].

References:
[1].  Muraki M, Ohkawara B, Hosoya T, et al. Manipulation of alternative splicing by a newly developed inhibitor of Clks. J Biol Chem, 2004, 279(23): 24246-24254.
[2].  Kurihara T, Sakurai E, Toyomoto M, et al. Alleviation of behavioral hypersensitivity in mouse models of inflammatory pain with two structurally different casein kinase 1 (CK1) inhibitors. Mol Pain, 2014, 10: 17.

Deciphering targeting rules of splicing modulator compounds: case of TG003.[Pubmed:26400733]

BMC Mol Biol. 2015 Sep 24;16:16.

BACKGROUND: Recent advances in the development of small chemical compounds that can modulate RNA splicing brought excitement to the field of splicing-targeting therapy. Splicing-targeting therapy tries to ameliorate the disease by altering the exon combination of transcripts to reduce the undesired effect of genetic mutations. However, the knowledge and tools to understand factors contributing to splicing modulator compound sensitivity have been lacking. Our goal was to establish a method to characterize sequence features found in compound sensitive exons. RESULTS: Here we developed a comparative transcriptomic approach to explore features that make an exon sensitive to a chemical compound. In this study, we chose TG003, a potential drug for Duchenne muscular dystrophy, and performed RNA-sequencing on samples from human and mouse skeletal muscle cells, with and without TG003 treatments. We compared TG003 responsiveness between homologous exon pairs and identified 21 pairs in which human exons were skip-enhanced but not mouse exons. We compared the sequence features; splice site scores, number of splicing factor binding sites, and properties of branch sequence and polypyrimidine tracts, and found that polypyrimidine tracts were stronger (longer stretches and richer content of consecutive polypyrimidine) in the mouse TG003 insensitive exons. We also compared the features between TG003 skip-enhanced and insensitive exons within the species, and discovered that human TG003 skip-enhanced exons were shorter and had less splicing factor binding sites than the group of human TG003 insensitive exons. Mouse insensitive exons homologous to human TG003 skip-enhanced exons shared these properties. Our results suggested that these features are prerequisites for TG003 skip-enhanced exons and weak polypyrimidine tracts are defining features, which were supported by a decision tree analysis on all cassette exons in human. CONCLUSIONS: In this study we established a comparative transcriptomic approach, which shed lights on how small chemical compounds modulate RNA splicing. The results described here was the first attempt to decipher the targeting rules of a splicing modulator compound. We expect that this approach would contribute to the precise understanding of the mechanism of TG003-induced splicing modulation, expand target diseases of splicing modulators in general, as well as the development of new splicing modulators.

TG003 is a potent and ATP-competitive Cdc2-like kinase (Clk) inhibitor with IC50 of 20 nM, 200 nM, and 15 nM for Clk1, Clk2, and Clk4, respectively. No inhibitory effect on Clk3, SRPK1, SRPK2, or PKC.

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