Identification and Biological Evaluation of a Novel CLK4 Inhibitor Targeting Alternative Splicing in Pancreatic Cancer Using Structure‐Based Virtual Screening
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 progressio...
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| Format: | Article |
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Wiley
2025-05-01
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| Series: | Advanced Science |
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| Online Access: | https://doi.org/10.1002/advs.202416323 |
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| author | Chun‐Lin Yang Yi‐Wen Wu Huang‐Ju Tu Yun‐Hsuan Yeh Tony Eight Lin Tzu‐Ying Sung Mu‐Chun Li Shih‐Chung Yen Jui‐Hua Hsieh Ming‐Chin Yu Sen‐Yung Hsieh Hsing‐Pang Hsieh Shiow‐Lin Pan Kai‐Cheng Hsu |
| author_facet | Chun‐Lin Yang Yi‐Wen Wu Huang‐Ju Tu Yun‐Hsuan Yeh Tony Eight Lin Tzu‐Ying Sung Mu‐Chun Li Shih‐Chung Yen Jui‐Hua Hsieh Ming‐Chin Yu Sen‐Yung Hsieh Hsing‐Pang Hsieh Shiow‐Lin Pan Kai‐Cheng Hsu |
| author_sort | Chun‐Lin Yang |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-3a7ba31d767b4dd0acb99416eead9ced |
| institution | OA Journals |
| issn | 2198-3844 |
| language | English |
| publishDate | 2025-05-01 |
| publisher | Wiley |
| record_format | Article |
| series | Advanced Science |
| spelling | doaj-art-3a7ba31d767b4dd0acb99416eead9ced2025-08-20T02:26:18ZengWileyAdvanced Science2198-38442025-05-011219n/an/a10.1002/advs.202416323Identification and Biological Evaluation of a Novel CLK4 Inhibitor Targeting Alternative Splicing in Pancreatic Cancer Using Structure‐Based Virtual ScreeningChun‐Lin Yang0Yi‐Wen Wu1Huang‐Ju Tu2Yun‐Hsuan Yeh3Tony Eight Lin4Tzu‐Ying Sung5Mu‐Chun Li6Shih‐Chung Yen7Jui‐Hua Hsieh8Ming‐Chin Yu9Sen‐Yung Hsieh10Hsing‐Pang Hsieh11Shiow‐Lin Pan12Kai‐Cheng Hsu13Graduate Institute of Cancer Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei 110301 TaiwanGraduate Institute of Cancer Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei 110301 TaiwanGraduate Institute of Cancer Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei 110301 TaiwanGraduate Institute of Cancer Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei 110301 TaiwanGraduate Institute of Cancer Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei 110301 TaiwanGraduate Institute of Cancer Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei 110301 TaiwanInstitute of Biotechnology and Pharmaceutical Research National Health Research Institutes Miaoli County 350401 TaiwanWarshel Institute for Computational Biology School of Medicine The Chinese University of Hong Kong (Shenzhen) Shenzhen Guangdong 518172 ChinaDivision of Translational Toxicology National Institute of Environmental Health Sciences National Institutes of Health Durham NC 27709 USACollege of Medicine Chang Gung University Taoyuan 333323 TaiwanCollege of Medicine Chang Gung University Taoyuan 333323 TaiwanInstitute of Biotechnology and Pharmaceutical Research National Health Research Institutes Miaoli County 350401 TaiwanGraduate Institute of Cancer Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei 110301 TaiwanGraduate Institute of Cancer Biology and Drug Discovery College of Medical Science and Technology Taipei Medical University Taipei 110301 TaiwanAbstract 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.https://doi.org/10.1002/advs.202416323alternative splicingCLK4kinase inhibitorpancreatic cancerstructure‐based virtual screening |
| spellingShingle | Chun‐Lin Yang Yi‐Wen Wu Huang‐Ju Tu Yun‐Hsuan Yeh Tony Eight Lin Tzu‐Ying Sung Mu‐Chun Li Shih‐Chung Yen Jui‐Hua Hsieh Ming‐Chin Yu Sen‐Yung Hsieh Hsing‐Pang Hsieh Shiow‐Lin Pan Kai‐Cheng Hsu Identification and Biological Evaluation of a Novel CLK4 Inhibitor Targeting Alternative Splicing in Pancreatic Cancer Using Structure‐Based Virtual Screening Advanced Science alternative splicing CLK4 kinase inhibitor pancreatic cancer structure‐based virtual screening |
| title | Identification and Biological Evaluation of a Novel CLK4 Inhibitor Targeting Alternative Splicing in Pancreatic Cancer Using Structure‐Based Virtual Screening |
| title_full | Identification and Biological Evaluation of a Novel CLK4 Inhibitor Targeting Alternative Splicing in Pancreatic Cancer Using Structure‐Based Virtual Screening |
| title_fullStr | Identification and Biological Evaluation of a Novel CLK4 Inhibitor Targeting Alternative Splicing in Pancreatic Cancer Using Structure‐Based Virtual Screening |
| title_full_unstemmed | Identification and Biological Evaluation of a Novel CLK4 Inhibitor Targeting Alternative Splicing in Pancreatic Cancer Using Structure‐Based Virtual Screening |
| title_short | Identification and Biological Evaluation of a Novel CLK4 Inhibitor Targeting Alternative Splicing in Pancreatic Cancer Using Structure‐Based Virtual Screening |
| title_sort | identification and biological evaluation of a novel clk4 inhibitor targeting alternative splicing in pancreatic cancer using structure based virtual screening |
| topic | alternative splicing CLK4 kinase inhibitor pancreatic cancer structure‐based virtual screening |
| url | https://doi.org/10.1002/advs.202416323 |
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