Skip to main content
SpringerLink
Log in

Design and synthesis of novel protein kinase R (PKR) inhibitors

  • Original Article
  • Published:
Molecular Diversity Aims and scope Submit manuscript

Abstract

Protein kinase RNA-activated (PKR) plays an important role in a broad range of intracellular regulatory mechanisms and in the pathophysiology of many human diseases, including microbial and viral infections, cancer, diabetes and neurodegenerative disorders. Recently, several potent PKR inhibitors have been synthesized. However, the enzyme’s multifunctional character and a multitude of PKR downstream targets have prevented the successful transformation of such inhibitors into effective drugs. Thus, the need for additional PKR inhibitors remains. With the help of computer-aided drug-discovery tools, we designed and synthesized potential PKR inhibitors. Indeed, two compounds were found to inhibit recombinant PKR in pharmacologically relevant concentrations. One compound, 6-amino-3-methyl-2-oxo-N-phenyl-2,3-dihydro-1H-benzo[d]imidazole-1-carboxamide, also showed anti-apoptotic properties. The novel molecules diversify the existing pool of PKR inhibitors and provide a basis for the future development of compounds based on PKR signal transduction mechanism.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Scheme 1
Scheme 2
Fig. 1
Scheme 3
Scheme 4
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  1. Rothenburg S, Seo EJ, Gibbs JS, Dever TE, Dittmar K (2009) Rapid evolution of protein kinase PKR alters sensitivity to viral inhibitors. Nat Struct Mol Biol 16:63–70. doi:10.1038/nsmb.1529

    Article  CAS  PubMed  Google Scholar 

  2. Jammi NV, Whitby LR, Beal PA (2003) Small molecule inhibitors of the RNA-dependent protein kinase. Biochem Bioph Res Commun 308:50–57. doi:10.1016/S0006-291X(03)01318-4

    Article  CAS  Google Scholar 

  3. Berry MJ, Knutson GS, Lasky SR, Munemitsu SM, Samuel CE (1985) Mechanism of interferon action. Purification and substrate specificities of the double-stranded RNA-dependent protein kinase from untreated and interferon-treated mouse fibroblasts. J Biol Chem 260:11240–11247

    CAS  PubMed  Google Scholar 

  4. Garcia MA, Gil J, Ventoso I, Guerra S, Domingo E, Rivas C, Esteban M (2006) Impact of protein kinase PKR in cell biology: from antiviral to antiproliferative action. Microbiol Mol Biol Rev 70:1032–1060. doi:10.1128/MMBR.00027-06

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Eley HL, McDonald PS, Russell ST, Tisdale MJ (2009) Inhibition of activation of dsRNA-dependent protein kinase and tumour growth inhibition. Cancer Chemoth Pharm 63:651–659. doi:10.1007/s00280-008-0782-y

    Article  CAS  Google Scholar 

  6. Cohen P (2002) Protein kinases [mdash] the major drug targets of the twenty-first century? Nat Rev Drug Discov 1:309–315. doi:10.1038/nrd773

    Article  CAS  PubMed  Google Scholar 

  7. Shimazawa M, Hara H (2006) Inhibitor of double stranded RNA-dependent protein kinase protects against cell damage induced by ER stress. Neurosci Lett 409:192–195. doi:10.1016/j.neulet.2006.09.074

    Article  CAS  PubMed  Google Scholar 

  8. Chang RC, Suen KC, Ma CH, Elyaman W, Ng HK, Hugon J (2002) Involvement of double-stranded RNA-dependent protein kinase and phosphorylation of eukaryotic initiation factor-2alpha in neuronal degeneration. J Neurochem 83:1215–1225. doi:10.1046/j.1471-4159.2002.01237.x

    Article  CAS  PubMed  Google Scholar 

  9. Grant SK (2009) Therapeutic protein kinase inhibitors. Cell Mol Life Sci 66:1163–1177. doi:10.1007/s00018-008-8539-7

    Article  CAS  PubMed  Google Scholar 

  10. Taylor SS, Haste NM, Ghosh G (2005) PKR and eIF2alpha: integration of kinase dimerization, activation, and substrate docking. Cell 122:823–825. doi:10.1016/j.cell.2005.09.007

    Article  CAS  PubMed  Google Scholar 

  11. Dar AC, Dever TE, Sicheri F (2005) Higher-order substrate recognition of eIF2alpha by the RNA-dependent protein kinase PKR. Cell 122:887–900. doi:10.1016/j.cell.2005.06.044

    Article  CAS  PubMed  Google Scholar 

  12. Segev Y, Barrera I, Ounallah-Saad H, Wibrand K, Sporild I, Livne A, Rosenberg T, David O, Mints M, Bramham CR, Rosenblum K (2015) PKR inhibition rescues memory deficit and ATF4 overexpression in ApoE epsilon4 human replacement mice. J Neurosci 35:12986–12993. doi:10.1523/jneurosci.5241-14.2015

    Article  CAS  PubMed  Google Scholar 

  13. Segev Y, Michaelson DM, Rosenblum K (2013) ApoE epsilon4 is associated with eIF2alpha phosphorylation and impaired learning in young mice. Neurobiol Aging 34:863–872. doi:10.1016/j.neurobiolaging.2012.06.020

    Article  CAS  PubMed  Google Scholar 

  14. Kimball SR (1999) Eukaryotic initiation factor eIF2. Int J Biochem Cell Biol 31:25–29. doi:10.1016/S1357-2725(98)00128-9

    Article  CAS  PubMed  Google Scholar 

  15. Dever TE (2002) Gene-specific regulation by general translation factors. Cell 108:545–556. doi:10.1016/S0092-8674(02)00642-6

    Article  CAS  PubMed  Google Scholar 

  16. O’Connor T, Sadleir KR, Maus E, Velliquette RA, Zhao J, Cole SL, Eimer WA, Hitt B, Bembinster LA, Lammich S, Lichtenthaler SF, Hebert SS, De Strooper B, Haass C, Bennett DA, Vassar R (2008) Phosphorylation of the translation initiation factor eIF2alpha increases BACE1 levels and promotes amyloidogenesis. Neuron 60:988–1009. doi:10.1016/j.neuron.2008.10.047

    Article  PubMed  PubMed Central  Google Scholar 

  17. Donnelly N, Gorman AM, Gupta S, Samali A (2013) The eIF2alpha kinases: their structures and functions. Cell Mol Life Sci 70:3493–3511. doi:10.1007/s00018-012-1252-6

    Article  CAS  PubMed  Google Scholar 

  18. Takizawa T, Tatematsu C, Nakanishi Y (2002) Double-stranded RNA-activated protein kinase interacts with apoptosis signal-regulating kinase 1. Implications for apoptosis signaling pathways. Eur J Biochem 269:6126–6132. doi:10.1046/j.1432-1033.2002.03325.x

    Article  CAS  PubMed  Google Scholar 

  19. Cuddihy AR, Li S, Tam NW, Wong AH, Taya Y, Abraham N, Bell JC, Koromilas AE (1999) Double-stranded-RNA-activated protein kinase PKR enhances transcriptional activation by tumor suppressor p53. Mol Cell Biol 19:2475–2484

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Williams BR (1999) PKR; a sentinel kinase for cellular stress. Oncogene 18:6112–6120. doi:10.1038/sj.onc.1203127

    Article  CAS  PubMed  Google Scholar 

  21. Bando Y, Onuki R, Katayama T, Manabe T, Kudo T, Taira K, Tohyama M (2005) Double-strand RNA dependent protein kinase (PKR) is involved in the extrastriatal degeneration in Parkinson’s disease and Huntington’s disease. Neurochem Int 46:11–18. doi:10.1016/j.neuint.2004.07.005

    Article  CAS  PubMed  Google Scholar 

  22. Gkogkas C, Sonenberg N, Costa-Mattioli M (2010) Translational control mechanisms in long-lasting synaptic plasticity and memory. J Biol Chem 285:31913–31917. doi:10.1074/jbc.R110.154476

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  23. Costa-Mattioli M, Gobert D, Stern E, Gamache K, Colina R, Cuello C, Sossin W, Kaufman R, Pelletier J, Rosenblum K, Krnjevic K, Lacaille JC, Nader K, Sonenberg N (2007) eIF2alpha phosphorylation bidirectionally regulates the switch from short- to long-term synaptic plasticity and memory. Cell 129:195–206. doi:10.1016/j.cell.2007.01.050

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Ma T, Trinh MA, Wexler AJ, Bourbon C, Gatti E, Pierre P, Cavener DR, Klann E (2013) Suppression of eIF2alpha kinases alleviates Alzheimer’s disease-related plasticity and memory deficits. Nat Neurosci 16:1299–1305. doi:10.1038/nn.3486

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Rosenberg T, Gal-Ben-Ari S, Dieterich DC, Kreutz MR, Ziv NE, Gundelfinger ED, Rosenblum K (2014) The roles of protein expression in synaptic plasticity and memory consolidation. Front Mol Neurosci 7:86. doi:10.3389/fnmol.2014.00086

    Article  PubMed  PubMed Central  Google Scholar 

  26. Carlson CB, Spanggord RJ, Beal PA (2002) Selection of small-molecule mediators of the RNA regulation of PKR, the RNA-dependent protein kinase. ChemBioChem 3:859–865. doi:10.1002/1439-7633(20020902)3:9$<$859:AID-CBIC859$>$3.0.CO;2-J

    Article  CAS  PubMed  Google Scholar 

  27. Bryk R, Wu K, Raimundo BC, Boardman PE, Chao P, Conn GL, Anderson E, Cole JL, Duffy NP, Nathan C, Griffin JH (2011) Identification of new inhibitors of protein kinase R guided by statistical modeling. Bioorg Med Chem Lett 21:4108–4114. doi:10.1016/j.bmcl.2011.04.149

    Article  CAS  PubMed  Google Scholar 

  28. Couturier J, Paccalin M, Morel M, Terro F, Milin S, Pontcharraud R, Fauconneau B, Page G (2011) Prevention of the beta-amyloid peptide-induced inflammatory process by inhibition of double-stranded RNA-dependent protein kinase in primary murine mixed co-cultures. J Neuroinflamm 8:72. doi:10.1186/1742-2094-8-72

    Article  CAS  Google Scholar 

  29. Gray JS, Bae HK, Li JC, Lau AS, Pestka JJ (2008) Double-stranded RNA-activated protein kinase mediates induction of interleukin-8 expression by deoxynivalenol, Shiga toxin 1, and ricin in monocytes. Toxicol Sci 105:322–330. doi:10.1093/toxsci/kfn128

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Chen HM, Wang L, D’Mello SR (2008) A chemical compound commonly used to inhibit PKR, \(\{\)8-(imidazol-4-ylmethylene)-6H-azolidino[5,4-g] benzothiazol-7-one\(\}\), protects neurons by inhibiting cyclin-dependent kinase. Eur J Neurosci 28:2003–2016. doi:10.1111/j.1460-9568.2008.06491.x

    Article  PubMed  PubMed Central  Google Scholar 

  31. Islam Z, Hegg CC, Bae HK, Pestka JJ (2008) Satratoxin G-induced apoptosis in PC-12 neuronal cells is mediated by PKR and caspase independent. Toxicol Sci 105:142–152. doi:10.1093/toxsci/kfn110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Tronel C, Page G, Bodard S, Chalon S, Antier D (2014) The specific PKR inhibitor C16 prevents apoptosis and IL-1beta production in an acute excitotoxic rat model with a neuroinflammatory component. Neurochem Int 64:73–83. doi:10.1016/j.neuint.2013.10.012

    Article  CAS  PubMed  Google Scholar 

  33. Ingrand S, Barrier L, Lafay-Chebassier C, Fauconneau B, Page G, Hugon J (2007) The oxindole/imidazole derivative C16 reduces in vivo brain PKR activation. FEBS Lett 581:4473–4478. doi:10.1016/j.febslet.2007.08.022

    Article  CAS  PubMed  Google Scholar 

  34. Stern E, Chinnakkaruppan A, David O, Sonenberg N, Rosenblum K (2013) Blocking the eIF2alpha kinase (PKR) enhances positive and negative forms of cortex-dependent taste memory. J Neurosci 33:2517–2525. doi:10.1523/JNEUROSCI.2322-12.2013

    Article  CAS  PubMed  Google Scholar 

  35. Nakamura T, Arduini A, Baccaro B, Furuhashi M, Hotamisligil GS (2014) Small-molecule inhibitors of PKR improve glucose homeostasis in obese diabetic mice. Diabetes 63:526–534. doi:10.2337/db13-1019

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Levit A, Yarnitzky T, Wiener A, Meidan R, Niv MY (2011) Modeling of human prokineticin receptors: interactions with novel small-molecule binders and potential off-target drugs. PLoS One 6:e27990. doi:10.1371/journal.pone.0027990

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Saumitra RS NB, Muralidhara R (2012) 2, 4 - Diaminopyrimidine derivatives as protein kinase inhibitors. Indian Pat Appl, WO/059932

  38. Terrier F (1982) Rate and equilibrium studies in Jackson–Meisenheimer complexes. Chem Rev 82:77–152. doi:10.1021/cr00048a001

    Article  CAS  Google Scholar 

  39. Terpko MO, Heck RF (1980) Palladium-catalyzed triethylammonium formate reductions. 3. Selective reduction of dinitroaromatic compounds. J Org Chem 45:4992–4993. doi:10.1021/Jo01312a039

  40. Marvel CS, Helfrick MD, Belsley JP (1929) Identification of amines. IV. Methanesulfonamides. J Am Chem Soc 51:1272–1274. doi:10.1021/ja01379a043

    Article  CAS  Google Scholar 

  41. Fabian MA, Biggs WH 3rd, Treiber DK, Atteridge CE, Azimioara MD, Benedetti MG, Carter TA, Ciceri P, Edeen PT, Floyd M, Ford JM, Galvin M, Gerlach JL, Grotzfeld RM, Herrgard S, Insko DE, Insko MA, Lai AG, Lelias JM, Mehta SA, Milanov ZV, Velasco AM, Wodicka LM, Patel HK, Zarrinkar PP, Lockhart DJ (2005) A small molecule-kinase interaction map for clinical kinase inhibitors. Nat Biotechnol 23:329–336. doi:10.1038/nbt1068

    Article  CAS  PubMed  Google Scholar 

  42. Armstrong ME, Gantier M, Li L, Chung WY, McCann A, Baugh JA, Donnelly SC (2008) Small interfering RNAs induce macrophage migration inhibitory factor production and proliferation in breast cancer cells via a double-stranded RNA-dependent protein kinase-dependent mechanism. J Immunol 180:7125–7133

    Article  CAS  PubMed  Google Scholar 

  43. Reddy CN, Nayak VL, Mani GS, Kapure JS, Adiyala PR, Maurya RA, Kamal A (2015) Synthesis and biological evaluation of spiro[cyclopropane-1,3’-indolin]-2’-ones as potential anticancer agents. Bioorg Med Chem Lett 25:4580–4586. doi:10.1016/j.bmcl.2015.08.056

    Article  CAS  PubMed  Google Scholar 

  44. Alpert E, Altman H, Totary H, Gruzman A, Barnea D, Barash V, Sasson S (2004) 4-Hydroxy tempol-induced impairment of mitochondrial function and augmentation of glucose transport in vascular endothelial and smooth muscle cells. Biochem Pharmacol 67:1985–1995. doi:10.1016/j.bcp.2004.02.005

    Article  CAS  PubMed  Google Scholar 

  45. Atkinson NJ, Witteveldt J, Evans DJ, Simmonds P (2014) The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication. Nucleic Acids Res 42:4527–4545. doi:10.1093/nar/gku075

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Ohkubo K, Sakai Y, Inoue H, Akamine S, Ishizaki Y, Matsushita Y, Sanefuji M, Torisu H, Ihara K, Sardiello M, Hara T (2015) Moyamoya disease susceptibility gene RNF213 links inflammatory and angiogenic signals in endothelial cells. Sci Rep 5:13191. doi:10.1038/srep13191

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Flusberg DA, Sorger PK (2015) Surviving apoptosis: life-death signaling in single cells. Trends Cell Biol 25:446–458. doi:10.1016/j.tcb.2015.03.003

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Shalini S, Dorstyn L, Dawar S, Kumar S (2015) Old, new and emerging functions of caspases. Cell Death Differ 22:526–539. doi:10.1038/cdd.2014.216

    Article  CAS  PubMed  Google Scholar 

  49. Eckshtain-Levi M, Lavi R, Yufit DS, Daniel B, Green O, Fleker O, Richman M, Rahimipour S, Gruzman A, Benisvy L (2016) A versatile water-soluble chelating and radical scavenging platform. Chem Commun 52:2350–2353. doi:10.1039/c5cc08198j

    Article  CAS  Google Scholar 

  50. Kozlovsky N, Rudich A, Potashnik R, Bashan N (1997) Reactive oxygen species activate glucose transport in L6 myotubes. Free Radic Biol Med 23:859–869

    Article  CAS  PubMed  Google Scholar 

  51. Handler JA, Seed CB, Bradford BU, Thurman RG (1992) Induction of peroxisomes by treatment with perfluorooctanoate does not increase rates of \(\text{ H }_{2}\text{ O }_{2}\) production in intact liver. Toxicol Lett 60:61–68. doi:10.1016/0378-4274(92)90047-N

    Article  CAS  PubMed  Google Scholar 

  52. Systèmes BIOVIA DSME, San Diego, USA: Dassault Systèmes, 2016, (http://accelrys.com/products/collaborative-science/biovia-discovery-studio/)

  53. GraphPad Software IFA, Suite 230, La Jolla, CA 92037, USA (http://www.graphpad.com/quickcalcs/ttest1.cfm)

Download references

Acknowledgments

This study was partly supported by a Bar-Ilan-University new faculty Grant for A.G. This study was also supported by a KAMIN program grant (Israel Ministry of Industry, Trade and Labour) for M.Y.N. and K.R. We would like to thank Nechama-Sara Cohen for the English editing of the manuscript.

Author information

Authors and Affiliations

  1. Division of Medicinal Chemistry, Department of Chemistry, Faculty of Exact Sciences, Bar-Ilan University, 5290002, Ramat-Gan, Israel

    Sagiv Weintraub, Shirin Kahremany, Olga Viskind & Arie Gruzman

  2. Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, 7610001, Rehovot, Israel

    Tali Yarnitzky & Masha Y. Niv

  3. The Fritz Haber Research Center for Molecular Dynamics, The Hebrew University, 91904, Jerusalem, Israel

    Tali Yarnitzky & Masha Y. Niv

  4. Sagol Department of Neurobiology, Faculty of Natural Sciences and Center for Gene Manipulation in the Brain, University of Haifa, 3498838, Haifa, Israel

    Iliana Barrera & Kobi Rosenblum

Authors
  1. Sagiv Weintraub
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tali Yarnitzky
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Shirin Kahremany
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Iliana Barrera
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Olga Viskind
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Kobi Rosenblum
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Masha Y. Niv
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Arie Gruzman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Arie Gruzman.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (docx 14939 KB)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Weintraub, S., Yarnitzky, T., Kahremany, S. et al. Design and synthesis of novel protein kinase R (PKR) inhibitors. Mol Divers 20, 805–819 (2016). https://doi.org/10.1007/s11030-016-9689-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11030-016-9689-4

Keywords

Search

Navigation