Joel Rüegger, Berend Gagestein, Antonius P A Janssen, Alexandra Valeanu, Alger Lazo Mori, Marielle van der Peet, Michael S Boutkan, Bogdan I Florea, Alex A Henneman, Remo Hochstrasser, Haiyan Wang, Paul Westwood, Andreas Topp, Patricia M Gomez Barila, Jan Paul Medema, Connie R Jimenez, Bigna Woersdoerfer, Stephan Kirchner, Jitao David Zhang, Uwe Grether, Arne C Rufer, Mario van der Stelt
{"title":"celllekt：一个强大的化学蛋白质组学工作流程，以分析激酶抑制剂的细胞靶标参与。","authors":"Joel Rüegger, Berend Gagestein, Antonius P A Janssen, Alexandra Valeanu, Alger Lazo Mori, Marielle van der Peet, Michael S Boutkan, Bogdan I Florea, Alex A Henneman, Remo Hochstrasser, Haiyan Wang, Paul Westwood, Andreas Topp, Patricia M Gomez Barila, Jan Paul Medema, Connie R Jimenez, Bigna Woersdoerfer, Stephan Kirchner, Jitao David Zhang, Uwe Grether, Arne C Rufer, Mario van der Stelt","doi":"10.1016/j.mcpro.2025.100961","DOIUrl":null,"url":null,"abstract":"<p><p>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 across the cellular kinome. 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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 across the cellular kinome. In this study, we present CellEKT (Cellular Endogenous Kinase Targeting), an optimized and robust chemical proteomics platform for investigating cellular target engagement 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 non-covalent drugs across over 300 kinases, expressed as half maximum inhibitory concentration (IC50), which were validated using distinct platforms like phosphoproteomics and NanoBRET. With CellEKT, target engagement profiles were linked to their substrate space. CellEKT has the ability to decrypt drug actions and to guide the discovery and development of drugs.
期刊介绍：
The mission of MCP is to foster the development and applications of proteomics in both basic and translational research. MCP will publish manuscripts that report significant new biological or clinical discoveries underpinned by proteomic observations across all kingdoms of life. Manuscripts must define the biological roles played by the proteins investigated or their mechanisms of action.
The journal also emphasizes articles that describe innovative new computational methods and technological advancements that will enable future discoveries. Manuscripts describing such approaches do not have to include a solution to a biological problem, but must demonstrate that the technology works as described, is reproducible and is appropriate to uncover yet unknown protein/proteome function or properties using relevant model systems or publicly available data.
Scope:
-Fundamental studies in biology, including integrative "omics" studies, that provide mechanistic insights
-Novel experimental and computational technologies
-Proteogenomic data integration and analysis that enable greater understanding of physiology and disease processes
-Pathway and network analyses of signaling that focus on the roles of post-translational modifications
-Studies of proteome dynamics and quality controls, and their roles in disease
-Studies of evolutionary processes effecting proteome dynamics, quality and regulation
-Chemical proteomics, including mechanisms of drug action
-Proteomics of the immune system and antigen presentation/recognition
-Microbiome proteomics, host-microbe and host-pathogen interactions, and their roles in health and disease
-Clinical and translational studies of human diseases
-Metabolomics to understand functional connections between genes, proteins and phenotypes
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