Alternative splicing is a nearly ubiquitous versatile process that controls gene expression and creates numerous
protein isoforms with different functions from a single gene. The significance of alternative splicing has been confirmed by the increasing number of human diseases that are caused by misregulation of splicing events. Very few compounds, however, have been reported to act as inhibitors of alternative splicing, and their potential clinical use needs to be evaluated. Here, we report that
CX-4945, a previously well-characterized inhibitor of
casein kinase 2 (CK2) and a molecule currently in clinical trials (Phase II) for
cancer treatment, regulates splicing in mammalian cells in a CK2-independent manner. Transcriptome-wide analysis using exon array also showed a widespread alteration in alternative splicing of numerous genes. We found that
CX-4945 potently inhibits the Cdc2-like
kinases (Clks) in vitro and in turn, leads to suppression of the phosphorylation of
serine/
arginine-rich (SR)
proteins in mammalian cells. Surprisingly, the overall efficacy of
CX-4945 on Clks (IC50 = 3-90 nM) was stronger than that of
TG-003, the strongest inhibitor reported to date. Of the Clks, Clk2 was most strongly inhibited by
CX-4945 in an
ATP-competitive manner. Our research revealed an unexpected activity of the
drug candidate
CX-4945 as a potent splicing modulator and also suggested a potential application for
therapy of diseases caused by abnormal splicing.