1. Identifying the proteins to which small-molecule probes and drugs bind in cells.
- Author
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Ong SE, Schenone M, Margolin AA, Li X, Do K, Doud MK, Mani DR, Kuai L, Wang X, Wood JL, Tolliday NJ, Koehler AN, Marcaurelle LA, Golub TR, Gould RJ, Schreiber SL, and Carr SA
- Subjects
- Carbazoles metabolism, HeLa Cells, Humans, Immunophilins chemistry, Immunophilins metabolism, Indole Alkaloids metabolism, Isotope Labeling, Ligands, Microspheres, Microtubule-Associated Proteins metabolism, Protein Kinase Inhibitors metabolism, Protein Kinases metabolism, Proteomics, Solubility, Molecular Probes metabolism, Pharmaceutical Preparations metabolism, Proteins metabolism
- Abstract
Most small-molecule probes and drugs alter cell circuitry by interacting with 1 or more proteins. A complete understanding of the interacting proteins and their associated protein complexes, whether the compounds are discovered by cell-based phenotypic or target-based screens, is extremely rare. Such a capability is expected to be highly illuminating--providing strong clues to the mechanisms used by small-molecules to achieve their recognized actions and suggesting potential unrecognized actions. We describe a powerful method combining quantitative proteomics (SILAC) with affinity enrichment to provide unbiased, robust and comprehensive identification of the proteins that bind to small-molecule probes and drugs. The method is scalable and general, requiring little optimization across different compound classes, and has already had a transformative effect on our studies of small-molecule probes. Here, we describe in full detail the application of the method to identify targets of kinase inhibitors and immunophilin binders.
- Published
- 2009
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