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Identification and Biological Evaluation of a Novel CLK4 Inhibitor Targeting Alternative Splicing in Pancreatic
Chun-Lin Yang1, Yi-Wen Wu1, Huang-Ju Tu1
1Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, 110301, Taiwan.
Abstract:
Pancreatic cancer is an aggressive malignancy with a poor prognosis and limited treatment options. Cdc-like kinase 4 (CLK4), a kinase that regulates alternative splicing by phosphorylating spliceosome components, is implicated in aberrant splicing events driving pancreatic cancer progression. In this study, we established a computational model that integrates pharmacological interactions of CLK4 inhibitors with an improved hit rate. Through this model, we identified a novel CLK4 inhibitor, compound 150441, with a 50% inhibitory concentration (IC50) value of 21.4 nm. Structure-activity relationship analysis was performed to investigate key interactions and functional groups. Kinase profiling revealed that compound 150441 is selective for CLK4. Subsequent in vitro assays demonstrated that this inhibitor effectively suppressed cell growth and viability of pancreatic cancer cells. In addition, it inhibited the phosphorylation of key splicing factors, including serine- and arginine-rich splicing factor (SRSF) 4 and SRSF6. Cell cycle analysis further indicated that the compound induced G2/M arrest, leading to apoptosis. RNA-seq analysis revealed that the compound induced significant changes in alternative splicing and key biological pathways, including RNA processing, DNA replication, DNA damage, and mitosis. These findings suggest that compound 150441 has promising potential for further development as a novel pancreatic cancer treatment.
Insights
A novel compound, 150441, effectively inhibits CDC-like kinase 4 (CLK4) and suppresses pancreatic cancer cell growth. This CLK4 inhibitor shows promise for developing new pancreatic cancer treatments by targeting aberrant splicing.
Area of Science:
- Oncology
- Molecular Biology
- Drug Discovery
Background:
- Pancreatic cancer is an aggressive malignancy with limited treatment options.
- Aberrant alternative splicing, regulated by CDC-like kinase 4 (CLK4), drives pancreatic cancer progression.
Purpose of the Study:
- To develop a computational model for identifying CLK4 inhibitors.
- To identify and characterize a novel CLK4 inhibitor for pancreatic cancer treatment.
Main Methods:
- Established a computational model for CLK4 inhibitor screening.
- Identified compound 150441 and performed structure-activity relationship analysis.
- Conducted in vitro assays, kinase profiling, cell cycle analysis, and RNA-seq analysis.
Main Results:
- Compound 150441 demonstrated potent and selective inhibition of CLK4 (IC50 = 21.4 nM).
- The inhibitor suppressed pancreatic cancer cell growth, viability, and phosphorylation of splicing factors (SRSF4, SRSF6).
- Compound 150441 induced G2/M cell cycle arrest, apoptosis, and significant alterations in alternative splicing and key biological pathways.
Conclusions:
- Compound 150441 is a novel, selective CLK4 inhibitor with significant anti-pancreatic cancer activity.
- The compound's ability to modulate alternative splicing and induce apoptosis suggests therapeutic potential.
- Compound 150441 warrants further investigation for pancreatic cancer treatment development.
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