You are here

Proc Natl Acad Sci U S A DOI:10.1073/pnas.0900191106

Identifying the proteins to which small-molecule probes and drugs bind in cells.

Publication TypeJournal Article
Year of Publication2009
AuthorsOng, S-E, 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, Carr, SA
JournalProc Natl Acad Sci U S A
Date Published2009 Mar 24
KeywordsCarbazoles, HeLa Cells, Humans, Immunophilins, Indole Alkaloids, Isotope Labeling, Ligands, Microspheres, Microtubule-Associated Proteins, Molecular Probes, Pharmaceutical Preparations, Protein Kinase Inhibitors, Protein Kinases, Proteins, Proteomics, Solubility

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.


Alternate JournalProc. Natl. Acad. Sci. U.S.A.
PubMed ID19255428
PubMed Central IDPMC2649954
Grant ListUL1RR024924 / RR / NCRR NIH HHS / United States
RL1HG004671 / HG / NHGRI NIH HHS / United States
RL1CA133834 / CA / NCI NIH HHS / United States
RL1GM084437 / GM / NIGMS NIH HHS / United States
UL1 RR024924 / RR / NCRR NIH HHS / United States
RL1 GM084437 / GM / NIGMS NIH HHS / United States
N01CO12400 / CA / NCI NIH HHS / United States
RL1 HG004671 / HG / NHGRI NIH HHS / United States
RL1 CA133834 / CA / NCI NIH HHS / United States
N01-CO-12400 / CO / NCI NIH HHS / United States