Proefschrift
CellEKT: a chemical proteomics platform to study the kinome
Kinase inhibitors are key therapeutic agents, particularly in oncology, yet their clinical efficacy is often hampered by off-target effects and limited understanding of their cellular target profiles.
- Auteur
- J. Rüegger
- Datum
- 04 juli 2025
- Links
- Thesis in Leiden Repository
This PhD project focused on developing a robust chemical proteomics platform, CellEKT (Cellular Endogenous Kinase Targeting), to systematically profile kinase–inhibitor interactions in intact cells. CellEKT leverages cell-permeable, broad-spectrum kinase probes that covalently bind the conserved lysine residue in the ATP-binding pocket, enabling enrichment of endogenous kinases for identification and quantification via mass spectrometry.A major advancement was the design and validation of novel chemical probes that significantly expanded kinome coverage, enabling detection of over 90% of expressed kinases in cell lines such as HEK293T and MV4-11. This enhanced coverage allowed for in-depth mapping of drug–kinase interactions and improved selectivity profiling of clinically relevant kinase inhibitors. Furthermore, CellEKT was applied to characterize the cellular response to therapies inducing senescence, uncovering kinases with potential roles in this phenotype that had not been previously linked to senescence pathways.Together, these developments provide a scalable and physiologically relevant platform to interrogate drug–target engagement, guide kinase inhibitor development, and uncover mechanistic insights into disease-relevant signaling networks.