Protein kinases regulate numerous cellular processes, including cell growth, metabolism and cell death. Because the primary sequence and the three-dimensional structure of many kinases are highly similar, the development of selective inhibitors for only one kinase is challenging. Furthermore, many protein kinases are pleiotropic, mediating diverse and sometimes even opposing functions by phosphorylating multiple protein substrates. Here, we set up to develop an inhibitor of a selective protein kinase phosphorylation of only one of its substrates. Focusing on the pleiotropic delta protein kinase C (δPKC), we used a rational approach to identify a distal docking site on δPKC for its substrate, pyruvate dehydrogenase kinase (PDK). We reasoned that an inhibitor of PDK's docking should selectively inhibit the phosphorylation of only PDK without affecting phosphorylation of the other δPKC substrates. Our approach identified a selective inhibitor of PDK docking to δPKC with an in vitro Kd of ~50 nM and reducing cardiac injury IC 50 of ~5 nM. This inhibitor, which did not affect the phosphorylation of other δPKC substrates even at 1 µM, demonstrated that PDK phosphorylation alone is critical for δPKC-mediated injury by heart attack. The approach we describe is likely applicable for the identification of other substrate-specific kinase inhibitors.
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*Corresponding Author. mochly@stanford.edu. ASSOCIATED CONTENT Supporting Information. Experimental details, additional figures and data are available free of charge via the Internet at http:// pubs.acs.org.
Author ContributionsAll authors have given approval to the final version of the manuscript.The authors declare that no competing interests exist.
HHS Public AccessAuthor manuscript J Am Chem Soc. Author manuscript; available in PMC 2016 October 14.
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INTORDUCTIONThe protein kinases super family accounts for approximately 2% of the eukaryotic genes and about 518 protein kinases are predicted in the human kinome. 1 Protein kinases catalyzed phosphorylation, the transfer of the γ-phosphoryl group from adenosine triphosphate (ATP) to the hydroxyl group of defined amino acid, which regulated many biological processes, including metabolism, transcription, cell cycle progression, and differentiation. Phosphorylation is the most widespread type of post-translational modification in signal transduction with over 500,000 potential phosphorylation sites for any given kinase in the human proteome and 25,000 phosphorylation events described for 7,000 human proteins. 2,3 Phosphorylation is mediated by the catalytic domain that consists of a small N-terminal lobe of β-sheets, a larger C-terminal lobe of α-helices, and the ATP binding site in a cleft between the two lobes. 4 Many kinase inhibitors target the highly conserved ATP-binding pocket. 5 However, since the catalytic domain of most eukaryotic kinases is structurally similar, developing specific protein kinase inhibitors that target the c...