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Selection of Peptide Inhibitors for Double-Stranded RNA-Dependent Protein Kinase PKR

M.-J. Du1#, H.-K. Zhang2#, A.-J. He3, Y.-S. Chang1, Y. Yang1, Y. Wang1, C.-Z. Zhang1*, and Y. Cao1*

1Key Laboratory of Microbial Functional Genomics of the Ministry of Education, College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, P. R. China; fax: (8622) 2350-0808; E-mail: caoyj@nankai.edu.cn; dumjnk@126.com; changyunsong1026@126.com; yangy@mail.nankai.edu.cn; yuwang0805@126.com; czz912@yahoo.com.cn

2Department of Molecular Biology, Scripps Research Institute, La Jolla, CA, 92037, USA; fax: (858) 784-2729; E-mail: hongkai@scripps.edu

3Tianjin Second Business College, Tianjin, 300193, P. R. China; E-mail: h_aj2005@126.com

# These authors contributed equally to the paper.

* To whom correspondence should be addressed.

Received April 25, 2013; Revision received June 28, 2013
Protein kinase inhibitors have been developed and applied as antitumor drugs. The majority of these inhibitors are derived from ATP analogs with limited specificity towards the kinase target. Here we present our proof-of-principle study on peptide inhibitors for kinases. Two peptides were selected by phage display against double-stranded RNA-dependent protein kinase (PKR). In vitro assay revealed that these peptides exhibit an inhibitory effect on PKR-catalyzed phosphorylation of the alpha subunit of eukaryotic initiation factor 2 (eIF2α). The peptides also interrupt PKR activity in cells infected by viruses, as PKR activation is one of the hallmarks of host response to viral infection. Kinetic study revealed that one of the peptides, named P1, is a competitive inhibitor for PKR, while the other, named P2, exhibits a more complicated pattern of inhibition on PKR activity. Fragment-based docking of the PKR–peptide complex suggests that P1 occupies the substrate pocket of PKR and thus inhibits the binding between PKR and eIF2α, whereas P2 sits near the substrate pocket. The computational model of PKR–peptide complex agrees with their kinetic behavior. We surmise that peptide inhibitors for kinases have higher specificity than ATP analogs, and that they provide promising leads for the optimization of kinase inhibitors.
KEY WORDS: fragment-based docking, kinase inhibitors, PKR, phage display, peptides

DOI: 10.1134/S0006297913110059