The DOI matches its Crossref record; 32 of the 32 references it cites were found in a registry or an index.
Identifying the proteins to which small-molecule probes and drugs bind in cells
Open accessAbstract
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.
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Cites
The protein kinase complement of the human genome
Manning, G., Whyte, D. B., Martinez, R., Hunter, T., & Sudarsanam, S. (2002) · Science · doi:10.1126/science.1075762 · Cited by 8,145
Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955
Ong, S.-E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., & Mann, M. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200025-mcp200 · Cited by 5,574
Self-citationLamb, J., Crawford, E. D., Peck, D., Modell, J. W., Blat, I. C., Wrobel, M. J., Lerner, J., Brunet, J.-P., Subramanian, A., Ross, K. N., et al. (2006) · Science · doi:10.1126/science.1132939 · Cited by 5,257
Self-citationA mammalian protein targeted by G1-arresting rapamycin–receptor complex
Brown, E. J., Albers, M. W., Bum Shin, T., ichikawa, K., Keith, C. T., Lane, W. S., & Schreiber, S. L. (1994) · Nature · doi:10.1038/369756a0 · Cited by 2,053
Self-citationA small molecule–kinase interaction map for clinical kinase inhibitors
Fabian, M. A., Biggs, W. H., Treiber, D. K., Atteridge, C. E., Azimioara, M. D., Benedetti, M. G., Carter, T. A., Ciceri, P., Edeen, P. T., Floyd, M., et al. (2005) · Nature Biotechnology · doi:10.1038/nbt1068 · Cited by 1,892
A Planning Strategy for Diversity‐Oriented Synthesis
Burke, M. D., & Schreiber, S. L. (2004) · Angewandte Chemie International Edition · doi:10.1002/anie.200300626 · Cited by 1,493
Self-citationA receptor for the immuno-suppressant FK506 is a cis–trans peptidyl-prolyl isomerase
Harding, M. W., Galat, A., Uehling, D. E., & Schreiber, S. L. (1989) · Nature · doi:10.1038/341758a0 · Cited by 1,396
Self-citationActivity-Based Protein Profiling: From Enzyme Chemistry to Proteomic Chemistry
Cravatt, B. F., Wright, A. T., & Kozarich, J. W. (2008) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.75.101304.124125 · Cited by 1,270
Selective enzyme purification by affinity chromatography.
Cuatrecasas, P., Wilchek, M., & Anfinsen, C. B. (1968) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.61.2.636 · Cited by 1,223
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Lenalidomide Causes Selective Degradation of IKZF1 and IKZF3 in Multiple Myeloma Cells
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Self-citationQuantitative, High-Resolution Proteomics for Data-Driven Systems Biology
Cox, J., & Mann, M. (2011) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-061308-093216 · Cited by 685
Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes
Bantscheff, M., Hopf, C., Savitski, M. M., Dittmann, A., Grandi, P., Michon, A.-M., Schlegl, J., Abraham, Y., Becher, I., Bergamini, G., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1759 · Cited by 659
Target Identification for Small Bioactive Molecules: Finding the Needle in the Haystack
Ziegler, S., Pries, V., Hedberg, C., & Waldmann, H. (2013) · Angewandte Chemie International Edition · doi:10.1002/anie.201208749 · Cited by 466
Chemical inhibition of NAT10 corrects defects of laminopathic cells
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Metadata
- Authors
- Ong, S.-E., Schenone, M., Margolin, A. A., Li, X., Do, K., Doud, M. K., Mani, D. R., Kuai, L., Wang, X., Wood, J. L., Tolliday, N. J., Koehler, A. N., Marcaurelle, L. A., Golub, T. R., Gould, R. J., Schreiber, S. L., & Carr, S. A.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2009-03-24
- Volume
- 106
- Issue
- 12
- Pages
- 4617-4622
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2171525151
- Cited by
- 304
- References
- 32
- FWCI
- 16.36
- Type
- journal article
- Language
- en
- Open access
- green
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- Ong, S.-E., Schenone, M., Margolin, A. A., Li, X., Do, K., Doud, M. K., Mani, D. R., Kuai, L., Wang, X., Wood, J. L., Tolliday, N. J., Koehler, A. N., Marcaurelle, L. A., Golub, T. R., Gould, R. J., Schreiber, S. L., & Carr, S. A. (2009). Identifying the proteins to which small-molecule probes and drugs bind in cells. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.0900191106
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