Abstract
Small molecules interact with proteins to perturb their functions, a property that has been exploited both for research applications and to produce therapeutic agents for disease treatment. Commonly utilized approaches for identifying the target proteins for a small molecule have limitations in terms of throughput and resource consumption and lack a mechanism to broadly assess the selectivity profile of the small molecule. Here we describe how protein microarray technology can be applied to the study of small molecule-protein interactions using tritiated small molecules. Protein arrays comprising thousands of full-length functional proteins facilitate target identification for those small molecules discovered in cell-based phenotypic assays and both target validation and off-target binding assessment for compounds discovered in target-based screens. The assays are highly reproducible, sensitive, and scalable, and provide an enabling technology for small molecule selectivity profiling in the context of drug development.
Key words
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Predki PF (2004) Functional protein microarrays: ripe for discovery. Curr Opin Chem Biol 8:8-13
Boyle SN, Michaud GA, Schweitzer B, Predki PF, Koleske AJ (2007) A critical role for cortactin phosphorylation by Abl-family kinases in PDGF-induced dorsal-wave formation. Curr Biol 17:1-7
Gupta R, Kus B, Fladd C, Wasmuth J, Tonikian R, Sidhu S, Krogan NJ, Parkinson J, Rotin D (2007) Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast. Mol Systems Biol 3(116):1-12
Hudson ME, Pozdnyakova I, Haines K, Mor G, Snyder M (2007) Identification of differentially expressed proteins in ovarian cancer using high-density protein microarrays. Proc Natl Acad Sci USA 104:17494-17499
Satoh J, Obayashi S, Misawa T, Sumiyoshi K, Oosumi K, Abunoki H (2008) Protein microarray analysis identifies human cellular prion protein interactors. Neuropathol Appl Neurobiol 35:16-35
Schnack C, Hengerer B, Gillardon F (2008) Identification of novel substrates for Cdk5 and new targets for Cdk5 inhibitors using high-density protein microarrays. Proteomics 8:1980-6
MacBeath G, Schreiber SL (2000) Printing proteins as microarrays for high-throughput function determination. Science 289:1760-3
Ge H (2000) UPA, a universal protein array system for quantitative detection of protein-protein, protein-DNA, protein-RNA, and protein-ligand interactions. Nucleic Acids Res 28:e3
Fang Y, Frutos AG, Lahiri J (2002) Membrane protein microarrays. J Am Chem Soc 124:2394-5
Schweitzer B, Predki P, Snyder M (2003) Microarrays to characterize protein interactions on a whole-proteome scale. Proteomics 3:2190-9
Huang J, Zhu H, Haggarty SJ, Spring DR, Hwang H, Jin F, Snyder M, Schreiber SL (2004) Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc Natl Acad Sci USA 101:16594-9
Singh J, Salcius M, Liu S-W, Staker BL, Mishra R, Thurmond J, Michaud G, Mattoon DR, Printen J, Christensen J, Bjornsson JM, Pollok BA, Kiledjian M, Stewart L, Jarecki J, Gurney ME (2008) DcpS as a therapeutic target for Spinal Muscular Atrophy. ACS Chem Biol 3:711-22
Zhang J-H, Chung TDY, Oldenburg KR (2000) Confirmation of primary active substances from high-throughput screening of chemical and biological populations: A statistical approach and practical considerations. J Com Chem 2:258-265
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2010 Humana Press, a part of Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Kraus, P.R., Meng, L., Freeman-Cook, L. (2010). Small Molecule Selectivity and Specificity Profiling Using Functional Protein Microarrays. In: Chittur, S.V. (eds) Microarray Methods for Drug Discovery. Methods in Molecular Biology, vol 632. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-60761-663-4_16
Download citation
DOI: https://doi.org/10.1007/978-1-60761-663-4_16
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-60761-662-7
Online ISBN: 978-1-60761-663-4
eBook Packages: Springer Protocols