Abstract
Genome-wide association studies and genetic linkage studies have created a growing list of proteins related to disease. Small molecules can serve as useful probes of function for these proteins in a cellular setting or may serve as leads for therapeutic development. High-throughput and general binding assays may provide a path for discovering small molecules that target proteins for which little is known about structure or function or for which conventional functional assays have failed. One such binding assay involves small-molecule microarrays (SMMs) containing compounds that have been arrayed and immobilized onto a solid support. The SMMs can be incubated with a protein target of interest and protein–small molecule interactions may be detected using a variety of fluorescent readouts. Several suitable methods for manufacturing SMMs exist and different immobilization methods may be more or less preferable for any given application. Here, we describe protocols for covalent capture of small molecules using an isocyanate-coated glass surface and detection of binding using purified protein.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Vegas, A. J., Fuller, J. H., and Koehler, A. N. (2008) Small-molecule microarrays as tools in ligand discovery, Chem Soc Rev 37, 1385–1394.
Astle, J. M., Simpson, L.S., Huang, Y., Reddy, M.M., Wilson, R., Connell, S., Wilson, J., Kodadek, T. (2010) Seamless bead to microarray screening: rapid identification of the highest affinity protein ligands from large combinatorial libraries, Chem Biol 7 38–45.
Kwon, S. J., Lee, M. Y., Ku, B., Sherman, D. H., and Dordick, J. S. (2007) High-throughput, microarray-based synthesis of natural product analogues via in vitro metabolic pathway construction, ACS Chem Biol 2, 419–425.
Uttamchandani, M., Lee, W. L., Wang, J., and Yao, S. Q. (2007) Quantitative inhibitor fingerprinting of metalloproteases using small molecule microarrays, J Am Chem Soc 129, 13110–13117.
Vegas, A. J., Bradner, J. E., Tang, W., McPherson, O. M., Greenberg, E. F., Koehler, A. N., and Schreiber, S. L. (2007) Fluorous-based small-molecule microarrays for the discovery of histone deacetylase inhibitors, Angew Chem Int Ed Engl 46, 7960–7964.
Urbina, H. D., Debaene, F., Jost, B., Bole-Feysot, C., Mason, D. E., Kuzmic, P., Harris, J. L., and Winssinger, N. (2006) Self-assembled small-molecule microarrays for protease screening and profiling, Chembiochem 7, 1790–1797.
Koehler, A. N., Shamji, A. F., and Schreiber, S. L. (2003) Discovery of an inhibitor of a transcription factor using small molecule microarrays and diversity-oriented synthesis, J Am Chem Soc 125, 8420–8421.
Stanton, B. Z., Peng, L. F., Maloof, N., Nakai, K., Wang, X., Duffner, J. L., Taveras, K. M., Hyman, J. M., Lee, S. W., Koehler, A. N., Chen, J. K., Fox, J. L., Mandinova, A., and Schreiber, S. L. (2009) A small molecule that binds Hedgehog and blocks its signaling in human cells, Nat Chem Biol 5, 154–156.
Labuda, L. P., Pushechnikov, A., and Disney, M. D. (2009) Small molecule microarrays of RNA-focused peptoids help identify inhibitors of a pathogenic group I intron, ACS Chem Biol 4, 299–307.
Duffner, J. L., Clemons, P. A., and Koehler, A. N. (2007) A pipeline for ligand discovery using small-molecule microarrays, Curr Opin Chem Biol 11, 74–82.
Uttamchandani, M., Wang, J., and Yao, S. Q. (2006) Protein and small molecule microarrays: powerful tools for high-throughput proteomics, Mol Biosyst 2, 58–68.
Kohn, M., Wacker, R., Peters, C., Schroder, H., Soulere, L., Breinbauer, R., Niemeyer, C. M., and Waldmann, H. (2003) Staudinger ligation: a new immobilization strategy for the preparation of small-molecule arrays, Angew Chem Int Ed Engl 42, 5830–5834.
Bradner, J. E., McPherson, O. M., Mazitschek, R., Barnes-Seeman, D., Shen, J. P., Dhaliwal, J., Stevenson, K. E., Duffner, J. L., Park, S. B., Neuberg, D. S., Nghiem, P., Schreiber, S. L., and Koehler, A. N. (2006) A robust small-molecule microarray platform for screening cell lysates, Chem Biol 13, 493–504.
Bradner, J. E., McPherson, O. M., and Koehler, A. N. (2006) A method for the covalent capture and screening of diverse small molecules in a microarray format, Nature Protocols 1 2344–2352.
Miyazaki, I., Okumura, H., Simizu, S., Takahashi, Y., Kanoh, N., Muraoka, Y., Nonomura, Y., and Osada, H. (2009) Structure-affinity relationship study of bleomycins and Shble protein by use of a chemical array, Chembiochem 10, 845–852. 2
Acknowledgments
The authors would like to thank Michelle Palmer, Yan-Ling Zhang, Gil Walzer, Hong Chen, Jacob Asiedu, Lisa Marcaurelle, Michael Foley, James Bradner, Olivia McPherson, and Stuart Schreiber for materials, technical support, or advice that was relevant to developing this updated protocol. Work described herein was funded with Federal funds from the National Cancer Institute’s Initiative for Chemical Genetics, National Institutes of Health, under contract no. N01-CO-12400.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Casalena, D.E., Wassaf, D., Koehler, A.N. (2012). Ligand Discovery Using Small-Molecule Microarrays. In: Drewes, G., Bantscheff, M. (eds) Chemical Proteomics. Methods in Molecular Biology, vol 803. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-364-6_17
Download citation
DOI: https://doi.org/10.1007/978-1-61779-364-6_17
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-61779-363-9
Online ISBN: 978-1-61779-364-6
eBook Packages: Springer Protocols