Eukaryotic protein kinases catalyze the phosphorylation of tyrosine, serine, and threonine residues and regulate essentially all cellular processes. Protein kinases are therefore important therapeutic targets for a variety of human diseases. The human genome encodes approximately 500 protein kinases, all of which share a highly conserved ATP binding site. Nearly all known small-molecule kinase inhibitors target this site, a deep hydrophobic cleft containing all of the essential catalytic residues. Thus, a central problem in the chemical biology of protein kinases concerns the development of selective inhibitors that discriminate among these similar binding sites. This proposal describes a structural bioinformatics approach for the design of selective, irreversible kinase inhibitors. Beginning with a sequence alignment of all protein kinase domains in the human genome, we identified a small subset that possess a cysteine residue in a unique location within the ATP binding site. The location of this cysteine, predicted by our analysis of multiple crystal structures, forms the starting point for the design of novel, electrophilic inhibitors. We hypothesize that an electrophilic substituent appended to an appropriate scaffold will rapidly alkylate the cysteine, thereby blocking the ATP binding site and irreversibly inhibiting the enzyme. The long-term goal of this project is to develop highly selective, cell-permeable inhibitors to unravel the precise cellular roles of these protein kinases, thought to regulate processes as diverse as transcription, apoptosis, chromosome segregation, and cytokinesis.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM071434-03
Application #
7219453
Study Section
Bio-Organic and Natural Products Chemistry Study Section (BNP)
Program Officer
Fabian, Miles
Project Start
2005-04-01
Project End
2009-03-31
Budget Start
2007-04-01
Budget End
2008-03-31
Support Year
3
Fiscal Year
2007
Total Cost
$270,409
Indirect Cost
Name
University of California San Francisco
Department
Pharmacology
Type
Schools of Medicine
DUNS #
094878337
City
San Francisco
State
CA
Country
United States
Zip Code
94143
Rodríguez-Molina, Juan B; Tseng, Sandra C; Simonett, Shane P et al. (2016) Engineered Covalent Inactivation of TFIIH-Kinase Reveals an Elongation Checkpoint and Results in Widespread mRNA Stabilization. Mol Cell 63:433-44
Bradshaw, J Michael; McFarland, Jesse M; Paavilainen, Ville O et al. (2015) Prolonged and tunable residence time using reversible covalent kinase inhibitors. Nat Chem Biol 11:525-31
Heo, Kyung-Sun; Le, Nhat-Tu; Cushman, Hannah J et al. (2015) Disturbed flow-activated p90RSK kinase accelerates atherosclerosis by inhibiting SENP2 function. J Clin Invest 125:1299-310
Krishnan, Shyam; Miller, Rand M; Tian, Boxue et al. (2014) Design of reversible, cysteine-targeted Michael acceptors guided by kinetic and computational analysis. J Am Chem Soc 136:12624-30
Miller, Rand M; Taunton, Jack (2014) Targeting protein kinases with selective and semipromiscuous covalent inhibitors. Methods Enzymol 548:93-116
Nishino, Mari; Choy, Jonathan W; Gushwa, Nathan N et al. (2013) Hypothemycin, a fungal natural product, identifies therapeutic targets in Trypanosoma brucei [corrected]. Elife 2:e00712
Le, Nhat-Tu; Heo, Kyung-Sun; Takei, Yuichiro et al. (2013) A crucial role for p90RSK-mediated reduction of ERK5 transcriptional activity in endothelial dysfunction and atherosclerosis. Circulation 127:486-99
Li, Dan; Jin, Lingtao; Alesi, Gina N et al. (2013) The prometastatic ribosomal S6 kinase 2-cAMP response element-binding protein (RSK2-CREB) signaling pathway up-regulates the actin-binding protein fascin-1 to promote tumor metastasis. J Biol Chem 288:32528-38
Jin, Lingtao; Li, Dan; Lee, Jong Seok et al. (2013) p90 RSK2 mediates antianoikis signals by both transcription-dependent and -independent mechanisms. Mol Cell Biol 33:2574-85
Miller, Rand M; Paavilainen, Ville O; Krishnan, Shyam et al. (2013) Electrophilic fragment-based design of reversible covalent kinase inhibitors. J Am Chem Soc 135:5298-301

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