1. Howard Hughes Medical Institute, Institute for Chemistry and Cell Biology, Bauer Center for Genomics Research, Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA
2. Department of Biophysics, Harvard University, Cambridge, Massachusetts 02138, USA
3. These authors contributed equally to this work.
4. Present address: Department of Chemistry, University of Illinois, Urbana, Illinois 61801, USA.

Correspondence to: Stuart L. Schreiber¹ Correspondence and requests for materials should be addressed to S.L.S. (e-mail: Email: sls@slsiris.harvard.edu).

Abstract

Small molecules that alter protein function provide a means to modulate biological networks with temporal resolution. Here we demonstrate a potentially general and scalable method of identifying such molecules by application to a particular protein, Ure2p, which represses the transcription factors Gln3p and Nil1p^{1, 2, 3}. By probing a high-density microarray of small molecules generated by diversity-oriented synthesis with fluorescently labelled Ure2p, we performed 3,780 protein-binding assays in parallel and identified several compounds that bind Ure2p. One compound, which we call uretupamine, specifically activates a glucose-sensitive transcriptional pathway downstream of Ure2p. Whole-genome transcription profiling and chemical epistasis demonstrate the remarkable Ure2p specificity of uretupamine and its ability to modulate the glucose-sensitive subset of genes downstream of Ure2p. These results demonstrate that diversity-oriented synthesis and small-molecule microarrays can be used to identify small molecules that bind to a protein of interest, and that these small molecules can regulate specific functions of the protein.