Ligand Discovery Using Small-Molecule Microarrays

  • Dominick E. Casalena
  • Dina Wassaf
  • Angela N. KoehlerEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 803)


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.

Key words

Small-molecule microarrays Ligand discovery Isocyanate Rapamycin FK506 FKBP12 



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.


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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Dominick E. Casalena
    • 1
  • Dina Wassaf
    • 1
  • Angela N. Koehler
    • 1
    Email author
  1. 1.Chemical Biology PlatformThe Broad Institute of MIT and HarvardCambridgeUSA

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