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Updated: May 1, 2026
Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions
Published on: August 2, 2015
New affinity probe targeting VEGF receptors for kinase inhibitor selectivity profiling by chemical proteomics
Xin Ku1, Stephanie Heinzlmeir, Dominic Helm
1Chair for Proteomics and Bioanalytics, Technische Universität München , Emil Erlenmeyer Forum 5, 85354 Freising, Germany.
Abstract:
Solid tumors are dependent for growth on nutrients and the supply of oxygen, which they often acquire via neoangiogenesis. Vascular endothelial growth factors and the corresponding receptors (VEGFRs) play central roles in this process, and consequently, the blockade of this pathway is one therapeutic strategy for cancer treatment. A number of small molecules inhibiting VEGFR inhibitors have been developed for clinical use, and a comprehensive view of target selectivity is important to assess the therapeutic as well as risk potential of a drug molecule. Recent advances in mass spectrometry-based chemical proteomics allow analyses of drug-target interactions under close-to-physiological conditions, and in this study, we report on the design, synthesis, and application of a small molecule affinity probe as a tool for the selectivity profiling of VEGFR and other kinase inhibitors. The probe is capable of binding >132 protein kinases, including angiokinases such as VEGFRs, PDGFRs, and c-KIT from lysates of cancer cell lines or human placenta tissue. Combining the new probe with Kinobeads in competitive binding assays, we were able to identify nanomolar off-targets of the VEGFR/PDGFR inhibitors pazopanib and axitinib. Because of its broad binding spectrum, the developed chemical tool can be generically used for the discovery of kinase inhibitor targets, which may contribute to a more comprehensive understanding of the mechanisms of action of such drugs.
Insights
Researchers developed a chemical probe to identify off-targets for VEGFR inhibitors, crucial for cancer drug development. This tool aids in understanding drug mechanisms and potential risks by profiling kinase inhibitor selectivity.
Area of Science:
- Biochemistry and Molecular Biology
- Chemical Biology and Proteomics
- Cancer Therapeutics
Background:
- Solid tumors rely on neoangiogenesis (new blood vessel formation) for growth, driven by vascular endothelial growth factors (VEGFs) and their receptors (VEGFRs).
- Blocking the VEGF/VEGFR pathway is a key cancer treatment strategy, with several small molecule VEGFR inhibitors in clinical use.
- Assessing the target selectivity of these inhibitors is vital for evaluating their therapeutic efficacy and potential risks.
Purpose of the Study:
- To design, synthesize, and apply a novel small molecule affinity probe for selectivity profiling of VEGFR and other kinase inhibitors.
- To investigate drug-target interactions under near-physiological conditions using advanced chemical proteomics techniques.
Main Methods:
- Development of a small molecule affinity probe for kinase inhibitor selectivity profiling.
- Application of the probe to analyze protein kinase binding from cancer cell line and human placenta tissue lysates.
- Utilizing competitive binding assays with Kinobeads to identify off-targets of specific VEGFR/PDGFR inhibitors.
Main Results:
- The developed probe demonstrated binding to over 132 protein kinases, including key angiokinases like VEGFRs, PDGFRs, and c-KIT.
- The probe successfully identified nanomolar off-targets for the VEGFR/PDGFR inhibitors pazopanib and axitinib.
- The broad binding spectrum of the probe highlights its utility in discovering kinase inhibitor targets.
Conclusions:
- The novel chemical probe serves as a valuable tool for comprehensive selectivity profiling of kinase inhibitors.
- This tool can facilitate the discovery of off-targets, contributing to a better understanding of drug mechanisms of action.
- The findings support the broader application of this chemical tool for generic kinase inhibitor target discovery in drug development.
