Chemical genomic profiling to identify intracellular targets of a multiplex kinase inhibitor

The identification of the kinase or kinases targeted by protein kinase inhibitors is a critical challenge in validating their use as therapeutic agents or molecular probes. Here, to address this problem, we describe a chemical genomics strategy that uses a direct comparison between microarray transc...

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Bibliographic Details
Published in:	Proceedings of the National Academy of Sciences - PNAS Vol. 102; no. 10; pp. 3587 - 3592
Main Authors:	Kung, C, Kenski, D.M, Dickerson, S.H, Howson, R.W, Kuyper, L.F, Madhani, H.D, Shokat, K.M
Format:	Journal Article
Language:	English
Published:	United States National Academy of Sciences 08-03-2005 National Acad Sciences
Subjects:	Alleles Biochemistry Biological Sciences CDC2 Protein Kinase - antagonists & inhibitors Cell growth Cell lines chemical genetics chemical genomics Comparative analysis cyclin-dependent kinase Cyclin-Dependent Kinases - antagonists & inhibitors Drug interactions enzyme inhibitors gene expression Gene Expression Profiling Genes genetic techniques and protocols Genomics messenger RNA microarray technology Molecules Oligonucleotide Array Sequence Analysis Pharmacology Phosphorylation Physical Sciences Plasmids polarized cell growth Protease inhibitors Protein Kinase Inhibitors - pharmacology Proteins Saccharomyces cerevisiae Saccharomyces cerevisiae Proteins - antagonists & inhibitors Yeast Yeasts
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Summary:	The identification of the kinase or kinases targeted by protein kinase inhibitors is a critical challenge in validating their use as therapeutic agents or molecular probes. Here, to address this problem, we describe a chemical genomics strategy that uses a direct comparison between microarray transcriptional signatures elicited by an inhibitor of unknown specificity and those elicited by highly specific pharmacological inhibition of engineered candidate kinase targets. By using this approach, we have identified two cyclin-dependent kinases, Cdk1 and Pho85, as the targets of the inhibitor GW400426 in Saccharomyces cerevisiae. We demonstrate that simultaneous inhibition of Cdk1 and Pho85, and not inhibition of either kinase alone, by GW400426 controls the expression of specific transcripts involved in polarized cell growth, thus revealing a cellular process that is uniquely sensitive to the multiplex inhibition of these two kinases. Our results suggest that the cellular responses induced by multiplex protein kinase inhibitors may be an emergent property that cannot be understood fully by considering only the sum of individual inhibitor-kinase interactions.
Bibliography:	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 23 ObjectType-Article-1 ObjectType-Feature-2 To whom correspondence should be addressed at: Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Box 2280, Genentech Hall, Room N512D, San Francisco, CA 94143-2280. E-mail: shokat@cmp.ucsf.edu. This paper was submitted directly (Track II) to the PNAS office. Author contributions: C.K., L.F.K., H.D.M., and K.M.S. designed research; C.K., D.M.K., S.H.D., and R.W.H. performed research; C.K. and D.M.K. analyzed data; and C.K. wrote the paper. Edited by Susan S. Taylor, University of California at San Diego, La Jolla, CA Abbreviations: CDK, cyclin-dependent kinase; ESR, environmental stress–response.
ISSN:	0027-8424 1091-6490
DOI:	10.1073/pnas.0407170102