Selection of small-molecule mediators of the RNA regulation of PKR, the RNA-dependent protein kinase

Coby B. Carlson, Richard J. Spanggord, Peter A. Beal

Research output: Contribution to journalArticle

18 Citations (Scopus)

Abstract

The RNA-dependent protein kinase (PKR) is a component of the interferon antiviral response and a member of the class of RNA-binding proteins with a double-stranded RNA binding motif. PKR is activated when it binds to double-stranded RNA (dsRNA) or viral replicative intermediates that comprise dsRNA and this activation results in the inhibition of protein synthesis. Some viruses circumvent this activity through the synthesis of highly structured decoy RNAs that bind PKR and block activation. Small-molecule mediators of the binding of PKR to these RNA inhibitors would be useful tools to further define the importance of specific PKR-RNA complexes in vivo and may possess antiviral activity. Here we investigate the ability of a library of structurally diverse peptide-acridine conjugates (PACs) to target a complex formed between the dsRNA binding domain (dsRBD) of PKR and a viral RNA inhibitor. We used a novel screening method based on the cleavage of RNA ligands with ethylenediaminetetraacetic acid · Fe modified protein. The selection revealed a PAC (9-anilinoacridine-4-Hyp-Nap-Nap, where Hyp is trans-4-hydroxyproline and Nap is 1-napthylalanine), able to inhibit the binding of the PKR dsRBD to RNA with an IC50 value of 10±51 μm. Furthermore, the structural requirements for inhibition by the selected PAC were substantiated in an independent PKR activation assay. We found that the potency of inhibition by an intercalating ligand can be increased by the introduction of a substituent that does not increase the overall charge of the molecule. This result is important for the design of inhibitors of PKR-RNA binding that function inside living cells.

Original languageEnglish (US)
Pages (from-to)859-865
Number of pages7
JournalChemBioChem
Volume3
Issue number9
DOIs
StatePublished - 2002
Externally publishedYes

Fingerprint

eIF-2 Kinase
Acridines
Double-Stranded RNA
RNA
Molecules
Peptides
Antiviral Agents
Chemical activation
RNA Cleavage
Intercalating Agents
RNA-Binding Proteins
Hydroxyproline
Viral RNA
Edetic Acid
Interferons
Inhibitory Concentration 50
Proteins
Ligands
Viruses
Assays

Keywords

  • Antiviral agents
  • Bioorganic chemistry
  • Combinatorial chemistry
  • Peptides
  • RNA recognition

ASJC Scopus subject areas

  • Drug Discovery
  • Organic Chemistry
  • Biochemistry, Genetics and Molecular Biology(all)

Cite this

Selection of small-molecule mediators of the RNA regulation of PKR, the RNA-dependent protein kinase. / Carlson, Coby B.; Spanggord, Richard J.; Beal, Peter A.

In: ChemBioChem, Vol. 3, No. 9, 2002, p. 859-865.

Research output: Contribution to journalArticle

Carlson, Coby B. ; Spanggord, Richard J. ; Beal, Peter A. / Selection of small-molecule mediators of the RNA regulation of PKR, the RNA-dependent protein kinase. In: ChemBioChem. 2002 ; Vol. 3, No. 9. pp. 859-865.
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