Chemical Proteomics

Chemical proteomics are powerful mass spectrometry based approaches for identifying proteome-wide compound-target interactions. Chemical proteomics includes affinity capture approaches with: 1) compound-centric approaches using modified, tagged compounds as baits to identify target proteins that bind to them in a proteome-wide background; 2) activity based approaches, where irreversibly binding baits probe the activity status of broad pre-defined enzyme families. This method can elucidate target activity in vivo as well as in vitro in competitive binding assays. The interactions between the protein and drug compound can also be probed by thermal profiling. Thermal profiling exploits the fact that protein denaturation temperature is shifted upon ligand binding. Proteome-wide probing is performed by temperature series of quantitative proteomics analyses. Proteomics can also be used to probe the proteome wide effects of a drug treatment in a quantitative proteomics experiment. Moreover, the binding site of a drug of a particular protein can be probed by deuterium exchange experiments using mass spectrometry.

Support within chemical proteomics at BioMS include:

  • Target discovery:
    -Affinity capture using click chemistry based probes followed by MS-analysis, in collaboration with national drug development and chemical biology infrastructures (who can help with the organic synthesis of needed affinity probes).
    -Thermal profiling based target discovery
  • Target engagement studies:
    Kinetic profiling post compound exposure
    Thermal profiling proteomics
  • Target characterization by top-down proteomics
  • Interaction interface elucidation by deuterium exchange mass spectrometry assays