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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
Volume106
Issue12
Pages4617-22
Date Published2009 Mar 24
ISSN1091-6490
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
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.

URLhttp://www.pnas.org/cgi/pmidlookup?view=long&pmid=19255428
DOI10.1073/pnas.0900191106
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/19255428?dopt=Abstract

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