CellEKT: A Robust Chemical Proteomics Workflow to Profile Cellular Target Engagement of Kinase Inhibitors
The human genome encodes 518 protein kinases that are pivotal for drug discovery in various therapeutic areas, such as cancer and autoimmune disorders. The majority of kinase inhibitors target the conserved ATP-binding pocket, making it difficult to develop selective inhibitors. To characterize and prioritize kinase-inhibiting drug candidates, efficient methods are desired to determine target engagement (TE) across the cellular kinome. In this study, we present CellEKT (Cellular Endogenous Kinase Targeting), an optimized and robust chemical proteomics platform for investigating cellular TE of endogenously expressed kinases using the sulfonyl fluoride-based probe XO44 and two new probes ALX005 and ALX011. The optimized workflow enabled the determination of the kinome interaction landscape of covalent and noncovalent drugs across over 300 kinases, expressed as IC<sub>50</sub>, which were validated using distinct platforms like phosphoproteomics and NanoBRET. With CellEKT, TE profiles were linked to their substrate space. CellEKT has the ability to decrypt drug actions and to guide the discovery and development of drugs.
Authors
- Bogdan I. Florea (ORCID: https://orcid.org/0000-0001-7114-2266)
- Stephan Kirchner
- Berend Gagestein (ORCID: https://orcid.org/0000-0002-0993-6812)
- Jitao David Zhang (ORCID: https://orcid.org/0000-0002-3085-0909)
- Jan Paul Medema (ORCID: https://orcid.org/0000-0003-3045-2924)
- Alex A. Henneman (ORCID: https://orcid.org/0000-0002-3746-4410)
- Uwe Grether (ORCID: https://orcid.org/0000-0002-3164-9270)
- Marielle van der Peet (ORCID: https://orcid.org/0000-0001-8155-1485)
- Michael S. Boutkan (ORCID: https://orcid.org/0000-0001-9189-1897)
- Antonius P. A. Janssen (ORCID: https://orcid.org/0000-0003-4203-261X)
- Paul Westwood
- Mario van der Stelt (ORCID: https://orcid.org/0000-0002-1029-5717)
- Andreas Topp (ORCID: https://orcid.org/0009-0002-5511-2870)
- Arne C. Rufer (ORCID: https://orcid.org/0000-0001-5092-7478)
- Connie R. Jiménez (ORCID: https://orcid.org/0000-0002-3103-4508)
- Patricia M. Gomez Barila (ORCID: https://orcid.org/0000-0003-3878-3373)
- Alexandra Valeanu
- Haiyan Wang (ORCID: https://orcid.org/0000-0001-8617-6848)
- Joel Rüegger (ORCID: https://orcid.org/0000-0002-4201-4676)
- Bigna Woersdoerfer
- Remo Hochstrasser
- Alger Lazo Mori
Institutions
- Roche (Switzerland) (CH)
- Leiden University (NL)
- Oncode Institute (NL)
- Cancer Center Amsterdam (NL)
- University of Amsterdam (NL)
- Amsterdam UMC Location Vrije Universiteit Amsterdam (NL)
Publication Details
- Journal
- Molecular & Cellular Proteomics
- Published
- 2025-04-06
- DOI
- https://doi.org/10.1016/j.mcpro.2025.100961
- Citations
- 4
- Primary Topic
- Cell Image Analysis Techniques
- Type
- article
- Field-Weighted Citation Impact
- 6.54
Funders
- F. Hoffmann-La Roche
- Radboud Universiteit
- Radboud Universitair Medisch Centrum
- Oncode Institute