Virologica Sinica

, Volume 28, Issue 6, pp 326–336 | Cite as

The flavivirus protease as a target for drug discovery

  • Matthew Brecher
  • Jing Zhang
  • Hongmin LiEmail author


Many flaviviruses are significant human pathogens causing considerable disease burdens, including encephalitis and hemorrhagic fever, in the regions in which they are endemic. A paucity of treatments for flaviviral infections has driven interest in drug development targeting proteins essential to flavivirus replication, such as the viral protease. During viral replication, the flavivirus genome is translated as a single polyprotein precursor, which must be cleaved into individual proteins by a complex of the viral protease, NS3, and its cofactor, NS2B. Because this cleavage is an obligate step of the viral life-cycle, the flavivirus protease is an attractive target for antiviral drug development. In this review, we will survey recent drug development studies targeting the NS3 active site, as well as studies targeting an NS2B/NS3 interaction site determined from flavivirus protease crystal structures.


Flavivirus Inhibitor Protease 


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  1. Ackermann M, and Padmanabhan R. 2001. De novo synthesis of RNA by the dengue virus RNA-dependent RNA polymerase exhibits temperature dependence at the initiation but not elongation phase. J Biol Chem, 276: 39926–39937.PubMedGoogle Scholar
  2. Aleshin A, Shiryaev S, Strongin A, and Liddington R. 2007. Structural evidence for regulation and specificity of flaviviral proteases and evolution of the Flaviviridae fold. Protein Sci., 16: 795–806.PubMedGoogle Scholar
  3. Aravapalli S, Lai H, Teramoto T, Alliston K R, Lushington G H, Ferguson E L, Padmanabhan R, and Groutas W C. 2012. Inhibitors of Dengue virus and West Nile virus proteases based on the aminobenzamide scaffold. Bioorg Med Chem, 20: 4140–4148.PubMedCentralPubMedGoogle Scholar
  4. Arias C F, Preugschat F, and Strauss J H. 1993. Dengue 2 virus NS2B and NS3 form a stable complex that can cleave NS3 within the helicase domain. Virology, 193: 888–899.PubMedGoogle Scholar
  5. Ashour J, Laurent-Rolle M, Shi P Y, and Garcia-Sastre A. 2009. NS5 of dengue virus mediates STAT2 binding and degradation. J Virol, 83: 5408–5418.PubMedCentralPubMedGoogle Scholar
  6. Asnis D S, Conetta R, Waldman G, and Teixeira A A. 2001. The West Nile virus encephalitis outbreak in the United States (1999–2000): from Flushing, New York, to beyond its borders. Ann N Y Acad Sci, 951: 161–171.PubMedGoogle Scholar
  7. Asnis D S, Conetta R, Teixeira A A, Waldman G, and Sampson B A. 2000. The West Nile Virus outbreak of 1999 in New York: the Flushing Hospital experience. Clin Infect Dis, 30: 413–418.PubMedGoogle Scholar
  8. Assenberg R, Mastrangelo E, Walter T S, Verma A, Milani M, Owens R J, Stuart D I, Grimes J M, and Mancini E J. 2009. Crystal structure of a novel conformational state of the flavivirus NS3 protein: implications for polyprotein processing and viral replication. J Virol, 83: 12895–12906.PubMedCentralPubMedGoogle Scholar
  9. Bazan J F, and Fletterick R J. 1989. Detection of a trypsin-like serine protease domain in flaviviruses and pestiviruses. Virology, 171: 637–639.PubMedGoogle Scholar
  10. Best S M, Morris K L, Shannon J G, Robertson S J, Mitzel D N, Park G S, Boer E, Wolfinbarger J B, and Bloom M E. 2005. Inhibition of interferon-stimulated JAK-STAT signaling by a tick-borne flavivirus and identification of NS5 as an interferon antagonist. J. Virol., 79: 12828–12839.PubMedCentralPubMedGoogle Scholar
  11. Bodenreider C, Beer D, Keller T H, Sonntag S, Wen D, Yap L, Yau Y H, Shochat S G, Huang D, Zhou T, Caflisch A, Su X C, Ozawa K, Otting G, Vasudevan S G, Lescar J, and Lim S P. 2009. A fluorescence quenching assay to discriminate between specific and nonspecific inhibitors of dengue virus protease. Anal Biochem, 395: 195–204.PubMedGoogle Scholar
  12. Bressanelli S, Stiasny K, Allison S L, Stura E A, Duquerroy S, Lescar J, Heinz F X, and Rey F A. 2004. Structure of a flavivirus envelope glycoprotein in its low-pH-induced membrane fusion conformation. EMBO J., 23: 728–738.PubMedGoogle Scholar
  13. Brinton M A. 1981. Isolation of a replication-efficient mutant of West Nile virus from a persistently infected genetically resistant mouse cell culture. J Virol, 39: 413–421.PubMedCentralPubMedGoogle Scholar
  14. Brinton M A. 2002. THE MOLECULAR BIOLOGY OF WEST NILE VIRUS: A New Invader of the Western Hemisphere. Annu Rev Microbiol, 56: 371–402.PubMedGoogle Scholar
  15. Burke D S, and Monath T P. 2001. Flaviviruses. Lippincott William & Wilkins.Google Scholar
  16. Chambers T J, Grakoui A, and Rice C M. 1991. Processing of the yellow fever virus nonstructural polyprotein: a catalytically active NS3 proteinase domain and NS2B are required for cleavages at dibasic sites. J. Virol., 65: 6042–6050.PubMedCentralPubMedGoogle Scholar
  17. Chambers T J, Hahn C S, Galler R, and Rice C M. 1990. Flavivirus genome organization, expression, and replication. Annu Rev Microbiol, 44: 649–688.PubMedGoogle Scholar
  18. Chambers T J, Nestorowicz A, Amberg S M, and Rice C M. 1993. Mutagenesis of the yellow fever virus NS2B protein: effects on proteolytic processing, NS2B-NS3 complex formation, and viral replication. J Virol, 67: 6797–6807.PubMedCentralPubMedGoogle Scholar
  19. Chambers T J, Droll D A, Tang Y, Liang Y, Ganesh V K, Murthy K H, and Nickells M. 2005. Yellow fever virus NS2B-NS3 protease: characterization of charged-to-alanine mutant and revertant viruses and analysis of polyprotein-cleavage activities. J Gen Virol, 86: 1403–1413.PubMedGoogle Scholar
  20. Chandramouli S, Joseph J S, Daudenarde S, Gatchalian J, Cornillez-Ty C, and Kuhn P. 2010. Serotype-specific structural differences in the protease-cofactor complexes of the dengue virus family. J Virol, 84: 3059–3067.PubMedCentralPubMedGoogle Scholar
  21. Chanprapaph S, Saparpakorn P, Sangma C, Niyomrattanakit P, Hannongbua S, Angsuthanasombat C, and Katzenmeier G. 2005. Competitive inhibition of the dengue virus NS3 serine protease by synthetic peptides representing polyprotein cleavage sites. Biochem Biophys Res Commun, 330: 1237–1246.PubMedGoogle Scholar
  22. Chappell K J, Stoermer M J, Fairlie D P, and Young P R. 2006. Insights to substrate binding and processing by West Nile Virus NS3 protease through combined modeling, protease mutagenesis, and kinetic studies. J Biol Chem, 281: 38448–38458.PubMedGoogle Scholar
  23. Chappell K J, Stoermer M J, Fairlie D P, and Young P R. 2008. West Nile Virus NS2B/NS3 protease as an antiviral target. Curr Med Chem, 15: 2771–2784.PubMedGoogle Scholar
  24. Chappell K J, Stoermer M J, Fairlie D P, and Young P R. 2008. Mutagenesis of the West Nile virus NS2B cofactor domain reveals two regions essential for protease activity. J Gen Virol, 89: 1010–1014.PubMedGoogle Scholar
  25. Cleaves G R, and Dubin D T. 1979. Methylation status of intracellular dengue type 2 40 S RNA. Virology, 96: 159–165.PubMedGoogle Scholar
  26. Cregar-Hernandez L, Jiao G S, Johnson A T, Lehrer A T, Wong T A, and Margosiak S A. 2011. Small molecule pan-dengue and West Nile virus NS3 protease inhibitors. Antivir Chem Chemother, 21: 209–217.PubMedCentralPubMedGoogle Scholar
  27. Daffis S, Szretter K J, Schriewer J, Li J, Youn S, Errett J, Lin T Y, Schneller S, Zust R, Dong H, Thiel V, Sen G C, Fensterl V, Klimstra W B, Pierson T C, Buller R M, Gale M, Jr., Shi P Y, and Diamond M S. 2010. 2′-O methylation of the viral mRNA cap evades host restriction by IFIT family members. Nature, 468: 452–456.PubMedCentralPubMedGoogle Scholar
  28. Deng J, Li N, Liu H, Zuo Z, Liew O W, Xu W, Chen G, Tong X, Tang W, Zhu J, Zuo J, Jiang H, Yang C G, Li J, and Zhu W. 2012. Discovery of novel small molecule inhibitors of dengue viral NS2B-NS3 protease using virtual screening and scaffold hopping. J Med Chem, 55: 6278–6293.PubMedGoogle Scholar
  29. Dong H, Chang D C, Hua M H, Lim S P, Chionh Y H, Hia F, Lee Y H, Kukkaro P, Lok S M, Dedon P C, and Shi P Y. 2012. 2′-O methylation of internal adenosine by flavivirus NS5 methyltransferase. PLoS pathogens, 8: e1002642.PubMedCentralPubMedGoogle Scholar
  30. Egloff M P, Benarroch D, Selisko B, Romette J L, and Canard B. 2002. An RNA cap (nucleoside-2′-O-)-methyltransferase in the flavivirus RNA polymerase NS5: crystal structure and functional characterization. Embo J, 21: 2757–2768.PubMedGoogle Scholar
  31. Ekonomiuk D, Su X C, Ozawa K, Bodenreider C, Lim S P, Otting G, Huang D, and Caflisch A. 2009. Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics. J Med Chem, 52: 4860–4868.PubMedGoogle Scholar
  32. Ekonomiuk D, Su X C, Ozawa K, Bodenreider C, Lim S P, Yin Z, Keller T H, Beer D, Patel V, Otting G, Caflisch A, and Huang D. 2009. Discovery of a non-peptidic inhibitor of west nile virus NS3 protease by high-throughput docking. PLoS Negl Trop Dis, 3: e356.PubMedCentralPubMedGoogle Scholar
  33. Erbel P, Schiering N, D’Arcy A, Renatus M, Kroemer M, Lim S, Yin Z, Keller T, Vasudevan S, and Hommel U. 2006. Structural basis for the activation of flaviviral NS3 proteases from dengue and West Nile virus. Nat. Struct. Mol. Biol., 13: 372–373.PubMedGoogle Scholar
  34. Ezgimen M, Lai H, Mueller N H, Lee K, Cuny G, Ostrov D A, and Padmanabhan R. 2012. Characterization of the 8-hydroxyquinoline scaffold for inhibitors of West Nile virus serine protease. Antiviral Res, 94: 18–24.PubMedCentralPubMedGoogle Scholar
  35. Falgout B, Miller R H, and Lai C J. 1993. Deletion analysis of dengue virus type 4 nonstructural protein NS2B: identification of a domain required for NS2B-NS3 protease activity. J Virol, 67: 2034–2042.PubMedCentralPubMedGoogle Scholar
  36. Falgout B, Bray M, Schlesinger J J, and Lai C J. 1990. Immunization of mice with recombinant vaccinia virus expressing authentic dengue virus nonstructural protein NS1 protects against lethal dengue virus encephalitis. J Virol, 64: 4356–4363.PubMedCentralPubMedGoogle Scholar
  37. Falgout B, Pethel M, Zhang Y M, and Lai C J. 1991. Both nonstructural proteins NS2B and NS3 are required for the proteolytic processing of dengue virus nonstructural proteins. J Virol, 65: 2467–2475.PubMedCentralPubMedGoogle Scholar
  38. Ganesh V K, Muller N, Judge K, Luan C H, Padmanabhan R, and Murthy K H. 2005. Identification and characterization of nonsubstrate based inhibitors of the essential dengue and West Nile virus proteases. Bioorg Med Chem, 13: 257–264.PubMedGoogle Scholar
  39. Gao Y, Cui T, and Lam Y. 2010. Synthesis and disulfide bond connectivity-activity studies of a kalata B1-inspired cyclopeptide against dengue NS2B-NS3 protease. Bioorg Med Chem, 18: 1331–1336.PubMedGoogle Scholar
  40. Gao Y, Samanta S, Cui T, and Lam Y. 2013. Synthesis and in vitro Evaluation of West Nile Virus Protease Inhibitors Based on the 1,3,4,5-Tetrasubstituted 1H-Pyrrol-2(5H)-one Scaffold. ChemMedChem, 8: 1554–1560.PubMedGoogle Scholar
  41. Gouvea I E, Izidoro M A, Judice W A, Cezari M H, Caliendo G, Santagada V, dos Santos C N, Queiroz M H, Juliano M A, Young P R, Fairlie D P, and Juliano L. 2007. Substrate specificity of recombinant dengue 2 virus NS2B-NS3 protease: influence of natural and unnatural basic amino acids on hydrolysis of synthetic fluorescent substrates. Arch Biochem Biophys, 457: 187–196.PubMedGoogle Scholar
  42. Grant D, Tan G K, Qing M, Ng J K, Yip A, Zou G, Xie X, Yuan Z, Schreiber M J, Schul W, Shi P Y, and Alonso S. 2011. A Single Amino Acid in Nonstructural Protein NS4B Confers Virulence to Dengue Virus in AG129 Mice through Enhancement of Viral RNA Synthesis. J Virol, 85: 7775–7787.PubMedCentralPubMedGoogle Scholar
  43. Guirakhoo F, Bolin R A, and Roehrig J T. 1992. The Murray Valley encephalitis virus prM protein confers acid resistance to virus particles and alters the expression of epitopes within the R2 domain of E glycoprotein. Virology, 191: 921–931.PubMedGoogle Scholar
  44. Guo J, Hayashi J, and Seeger C. 2005. West nile virus inhibits the signal transduction pathway of alpha interferon. J. Virol., 79: 1343–1350.PubMedCentralPubMedGoogle Scholar
  45. Guyatt K J, Westaway E G, and Khromykh A A. 2001. Expression and purification of enzymatically active recombinant RNA-dependent RNA polymerase (NS5) of the flavivirus Kunjin. J Virol Methods, 92: 37–44.PubMedGoogle Scholar
  46. Hammamy M Z, Haase C, Hammami M, Hilgenfeld R, and Steinmetzer T. 2013. Development and characterization of new peptidomimetic inhibitors of the West Nile virus NS2B-NS3 protease. ChemMedChem, 8: 231–241.PubMedGoogle Scholar
  47. Issur M, Geiss B J, Bougie I, Picard-Jean F, Despins S, Mayette J, Hobdey S E, and Bisaillon M. 2009. The flavivirus NS5 protein is a true RNA guanylyltransferase that catalyzes a two-step reaction to form the RNA cap structure. Rna, 15: 2340–2350.PubMedGoogle Scholar
  48. Jia F, Zou G, Fan J, and Yuan Z. 2010. Identification of palmatine as an inhibitor of West Nile virus. Arch Virol, 155: 1325–1329.PubMedGoogle Scholar
  49. Johnston P A, Phillips J, Shun T Y, Shinde S, Lazo J S, Huryn D M, Myers M C, Ratnikov B I, Smith J W, Su Y, Dahl R, Cosford N D, Shiryaev S A, and Strongin A Y. 2007. HTS identifies novel and specific uncompetitive inhibitors of the two-component NS2B-NS3 proteinase of West Nile virus. Assay Drug Dev Technol, 5: 737–750.PubMedGoogle Scholar
  50. Kiat T S, Pippen R, Yusof R, Ibrahim H, Khalid N, and Rahman N A. 2006. Inhibitory activity of cyclohexenyl chalcone derivatives and flavonoids of fingerroot, Boesenbergia rotunda (L.), towards dengue-2 virus NS3 protease. Bioorg Med Chem Lett, 16: 3337–3340.PubMedGoogle Scholar
  51. Knehans T, Schuller A, Doan D N, Nacro K, Hill J, Guntert P, Madhusudhan M S, Weil T, and Vasudevan S G. 2011. Structure-guided fragment-based in silico drug design of dengue protease inhibitors. J Comput Aided Mol Des, 25: 263–274.PubMedGoogle Scholar
  52. Knox J E, Ma N L, Yin Z, Patel S J, Wang W L, Chan W L, Ranga Rao K R, Wang G, Ngew X, Patel V, Beer D, Lim S P, Vasudevan S G, and Keller T H. 2006. Peptide inhibitors of West Nile NS3 protease: SAR study of tetrapeptide aldehyde inhibitors. J Med Chem, 49: 6585–6590.PubMedGoogle Scholar
  53. Koonin E V. 1993. Computer-assisted identification of a putative methyltransferase domain in NS5 protein of flaviviruses and lambda 2 protein of reovirus. J Gen Virol, 74: 733–740.PubMedGoogle Scholar
  54. Kramer L D, and Bernard K A. 2001. West Nile virus infection in birds and mammals. Ann N Y Acad Sci, 951: 84–93.PubMedGoogle Scholar
  55. Kramer L D, Li J, and Shi P Y. 2007. West Nile virus. Lancet Neurol, 6: 171–181.PubMedGoogle Scholar
  56. Kummerer B M, and Rice C M. 2002. Mutations in the yellow fever virus nonstructural protein NS2A selectively block production of infectious particles. J. Virol., 76: 4773–4784.PubMedCentralPubMedGoogle Scholar
  57. Lai H, Sridhar Prasad G, and Padmanabhan R. 2013. Characterization of 8-hydroxyquinoline derivatives containing aminobenzothiazole as inhibitors of dengue virus type 2 protease in vitro. Antiviral Res, 97: 74–80.PubMedCentralPubMedGoogle Scholar
  58. Lai H, Dou D, Aravapalli S, Teramoto T, Lushington G H, Mwania T M, Alliston K R, Eichhorn D M, Padmanabhan R, and Groutas W C. 2013. Design, synthesis and characterization of novel 1,2-benzisothiazol-3(2H)-one and 1,3,4-oxadiazole hybrid derivatives: potent inhibitors of Dengue and West Nile virus NS2B/NS3 proteases. Bioorg Med Chem, 21: 102–113.PubMedCentralPubMedGoogle Scholar
  59. Leung D, Schroder K, White H, Fang N-X, Stoermer M, Abbenante G, Martin J, PR Y, and Fairlie D. 2001. Activity of recombinant dengue 2 virus NS3 protease in the presence of a truncated NS2B co-factor, small peptide substrates, and inhibitors. J. Biol. Chem., 276: 45762–45771.PubMedGoogle Scholar
  60. Leung J Y, Pijlman G P, Kondratieva N, Hyde J, Mackenzie J M, and Khromykh A A. 2008. Role of nonstructural protein NS2A in flavivirus assembly. J Virol, 82: 4731–4741.PubMedCentralPubMedGoogle Scholar
  61. Li H, Clum S, You S, Ebner K E, and Padmanabhan R. 1999. The serine protease and RNA-stimulated nucleoside triphosphatase and RNA helicase functional domains of dengue virus type 2 NS3 converge within a region of 20 amino acids. J Virol, 73: 3108–3116.PubMedCentralPubMedGoogle Scholar
  62. Li J, Lim S P, Beer D, Patel V, Wen D, Tumanut C, Tully D C, Williams J A, Jiricek J, Priestle J P, Harris J L, and Vasudevan S G. 2005. Functional profiling of recombinant NS3 proteases from all four serotypes of dengue virus using tetrapeptide and octapeptide substrate libraries. J Biol Chem, 280: 28766–28774.PubMedGoogle Scholar
  63. Li L, Lok S M, Yu I M, Zhang Y, Kuhn R J, Chen J, and Rossmann M G. 2008. The flavivirus precursor membrane-envelope protein complex: structure and maturation. Science, 319: 1830–1834.PubMedGoogle Scholar
  64. Lin C, Kwong A D, and Perni R B. 2006. Discovery and development of VX-950, a novel, covalent, and reversible inhibitor of hepatitis C virus NS3.4A serine protease. Infect Disord Drug Targets, 6: 3–16.PubMedGoogle Scholar
  65. Lin K, Perni R B, Kwong A D, and Lin C. 2006. VX-950, a novel hepatitis C virus (HCV) NS3-4A protease inhibitor, exhibits potent antiviral activities in HCv replicon cells. Antimicrob Agents Chemother, 50: 1813–1822.PubMedCentralPubMedGoogle Scholar
  66. Lindenbach B D, and Rice C M. 1997. trans-Complementation of yellow fever virus NS1 reveals a role in early RNA replication. J. Virol., 71: 9608–9617.PubMedCentralPubMedGoogle Scholar
  67. Lindenbach B D, and Rice C M. 1999. Genetic interaction of flavivirus nonstructural proteins NS1 and NS4A as a determinant of replicase function. J Virol, 73: 4611–4621.PubMedCentralPubMedGoogle Scholar
  68. Lindenbach B D, Thiel H J, and Rice C M. 2007. Flaviviridae: The Virus and Their Replication, Fourth ed. Lippincott William & Wilkins.Google Scholar
  69. Luo D, Xu T, Hunke C, Gruber G, Vasudevan S G, and Lescar J. 2008. Crystal structure of the NS3 protease-helicase from dengue virus. J Virol, 82: 173–183.PubMedCentralPubMedGoogle Scholar
  70. Luo D, Wei N, Doan D N, Paradkar P N, Chong Y, Davidson A D, Kotaka M, Lescar J, and Vasudevan S G. 2010. Flexibility between the protease and helicase domains of the dengue virus NS3 protein conferred by the linker region and its functional implications. J Biol Chem, 285: 18817–18827.PubMedGoogle Scholar
  71. Luo D, Xu T, Watson R P, Scherer-Becker D, Sampath A, Jahnke W, Yeong S S, Wang C H, Lim S P, Strongin A, Vasudevan S G, and Lescar J. 2008. Insights into RNA unwinding and ATP hydrolysis by the flavivirus NS3 protein. Embo J, 27: 3209–3219.PubMedGoogle Scholar
  72. Mangano D T, Tudor I C, and Dietzel C. 2006. The risk associated with aprotinin in cardiac surgery. N Engl J Med, 354: 353–365.PubMedGoogle Scholar
  73. Mangano D T, Miao Y, Vuylsteke A, Tudor I C, Juneja R, Filipescu D, Hoeft A, Fontes M L, Hillel Z, Ott E, Titov T, Dietzel C, and Levin J. 2007. Mortality associated with aprotinin during 5 years following coronary artery bypass graft surgery. JAMA, 297: 471–479.PubMedGoogle Scholar
  74. Marianneau P, Steffan A M, Royer C, Drouet M T, Jaeck D, Kirn A, and Deubel V. 1999. Infection of primary cultures of human Kupffer cells by Dengue virus: no viral progeny synthesis, but cytokine production is evident. J Virol, 73: 5201–5206.PubMedCentralPubMedGoogle Scholar
  75. Menendez-Arias L. 2010. Molecular basis of human immunodeficiency virus drug resistance: an update. Antiviral Res, 85: 210–231.PubMedGoogle Scholar
  76. Miller S, Kastner S, Krijnse-Locker J, Buhler S, and Bartenschlager R. 2007. The non-structural protein 4A of dengue virus is an integral membrane protein inducing membrane alterations in a 2K-regulated manner. J Biol Chem, 282: 8873–8882.PubMedGoogle Scholar
  77. Modis Y, Ogata S, Clements D, and Harrison S C. 2004. Structure of the dengue virus envelope protein after membrane fusion. Nature, 427: 313–319.PubMedGoogle Scholar
  78. Mueller N H, Yon C, Ganesh V K, and Padmanabhan R. 2007. Characterization of the West Nile virus protease substrate specificity and inhibitors. Int J Biochem Cell Biol, 39: 606–614.PubMedGoogle Scholar
  79. Mueller N H, Pattabiraman N, Ansarah-Sobrinho C, Viswanathan P, Pierson T C, and Padmanabhan R. 2008. Identification and biochemical characterization of small-molecule inhibitors of west nile virus serine protease by a high-throughput screen. Antimicrob Agents Chemother, 52: 3385–3393.PubMedCentralPubMedGoogle Scholar
  80. Munoz-Jordan J L, Sanchez-Burgos G G, Laurent-Rolle M, and Garcia-Sastre A. 2003. Inhibition of interferon signaling by dengue virus. Proc. Natl. Acad. Sci. USA, 100: 14333–14338.PubMedGoogle Scholar
  81. Munoz-Jordan J L, Laurent-Rolle M, Ashour J, Martinez-Sobrido L, Ashok M, Lipkin W I, and Garcia-Sastre A. 2005. Inhibition of Alpha/Beta Interferon Signaling by the NS4B Protein of Flaviviruses. J. Virol., 79: 8004–8013.PubMedCentralPubMedGoogle Scholar
  82. Muylaert I R, Galler R, and Rice C M. 1997. Genetic analysis of the yellow fever virus NS1 protein: identification of a temperature-sensitive mutation which blocks RNA accumulation. J. Virol., 71: 291–298.PubMedCentralPubMedGoogle Scholar
  83. Nall T A, Chappell K J, Stoermer M J, Fang N X, Tyndall J D, Young P R, and Fairlie D P. 2004. Enzymatic characterization and homology model of a catalytically active recombinant West Nile virus NS3 protease. J Biol Chem, 279: 48535–48542.PubMedGoogle Scholar
  84. Nitsche C, Steuer C, and Klein C D. 2011. Arylcyanoacrylamides as inhibitors of the Dengue and West Nile virus proteases. Bioorg Med Chem, 19: 7318–7337.PubMedGoogle Scholar
  85. Nitsche C, Behnam M A, Steuer C, and Klein C D. 2012. Retro peptide-hybrids as selective inhibitors of the Dengue virus NS2B-NS3 protease. Antiviral Res, 94: 72–79.PubMedGoogle Scholar
  86. Niyomrattanakit P, Winoyanuwattikun P, Chanprapaph S, Angsuthanasombat C, Panyim S, and Katzenmeier G. 2004. Identification of residues in the dengue virus type 2 NS2B cofactor that are critical for NS3 protease activation. J Virol, 78: 13708–13716.PubMedCentralPubMedGoogle Scholar
  87. Noble C G, Seh C C, Chao A T, and Shi P Y. 2012. Ligand-bound structures of the dengue virus protease reveal the active conformation. Journal of Virology, 86: 438–446.PubMedCentralPubMedGoogle Scholar
  88. Noble C G, Chen Y L, Dong H, Gu F, Lim S P, Schul W, Wang Q Y, and Shi P Y. 2010. Strategies for development of Dengue virus inhibitors. Antiviral Res, 85: 450–462.PubMedGoogle Scholar
  89. Pambudi S, Kawashita N, Phanthanawiboon S, Omokoko M D, Masrinoul P, Yamashita A, Limkittikul K, Yasunaga T, Takagi T, Ikuta K, and Kurosu T. 2013. A Small Compound Targeting the Interaction between Nonstructural Proteins 2B and 3 Inhibits Dengue Virus Replication. Biochem Biophys Res Commun: in press (doi: 10.1016/j.bbrc.2013.1009.1078).Google Scholar
  90. Phong W Y, Moreland N J, Lim S P, Wen D, Paradkar P N, and Vasudevan S G. 2011. Dengue protease activity: the structural integrity and interaction of NS2B with NS3 protease and its potential as a drug target. Bioscience reports.Google Scholar
  91. Radichev I, Shiryaev S A, Aleshin A E, Ratnikov B I, Smith J W, Liddington R C, and Strongin A Y. 2008. Structure-based mutagenesis identifies important novel determinants of the NS2B cofactor of the West Nile virus two-component NS2B-NS3 proteinase. J Gen Virol, 89: 636–641.PubMedGoogle Scholar
  92. Ray D, Shah A, Tilgner M, Guo Y, Zhao Y, Dong H, Deas T, Zhou Y, Li H, and Shi P. 2006. West nile virus 5′-cap structure is formed by sequential guanine N-7 and ribose 2′-O methylations by nonstructural protein 5. J. Virol., 80: 8362–8370.PubMedCentralPubMedGoogle Scholar
  93. Rice C M, Lenches E M, Eddy S R, Shin S J, Sheets R L, and Strauss J H. 1985. Nucleotide sequence of yellow fever virus: implications for flavivirus gene expression and evolution. Science, 229: 726–733.PubMedGoogle Scholar
  94. Robin G, Chappell K, Stoermer M J, Hu S H, Young P R, Fairlie D P, and Martin J L. 2009. Structure of West Nile virus NS3 protease: ligand stabilization of the catalytic conformation. J Mol Biol, 385: 1568–1577.PubMedGoogle Scholar
  95. Romano K P, Ali A, Royer W E, and Schiffer C A. 2010. Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding. Proc Natl Acad Sci U S A, 107: 20986–20991.PubMedCentralPubMedGoogle Scholar
  96. Roosendaal J, Westaway E G, Khromykh A, and Mackenzie J M. 2006. Regulated cleavages at the West Nile virus NS4A-2K-NS4B junctions play a major role in rearranging cytoplasmic membranes and Golgi trafficking of the NS4A protein. J Virol, 80: 4623–4632.PubMedCentralPubMedGoogle Scholar
  97. Rothan H A, Han H C, Ramasamy T S, Othman S, Rahman N A, and Yusof R. 2012. Inhibition of dengue NS2B-NS3 protease and viral replication in Vero cells by recombinant retrocyclin-1. BMC Infect Dis, 12: 314.PubMedCentralPubMedGoogle Scholar
  98. Samanta S, Cui T, and Lam Y. 2012. Discovery, synthesis, and in vitro evaluation of West Nile virus protease inhibitors based on the 9,10-dihydro-3H,4aH-1,3,9,10a-tetraazaphenanthren-4-one scaffold. ChemMedChem, 7: 1210–1216.PubMedGoogle Scholar
  99. Sarrazin C, Rouzier R, Wagner F, Forestier N, Larrey D, Gupta S K, Hussain M, Shah A, Cutler D, Zhang J, and Zeuzem S. 2007. SCH 503034, a novel hepatitis C virus protease inhibitor, plus pegylated interferon alpha-2b for genotype 1 nonresponders. Gastroenterology, 132: 1270–1278.PubMedGoogle Scholar
  100. Schuller A, Yin Z, Brian Chia C S, Doan D N, Kim H K, Shang L, Loh T P, Hill J, and Vasudevan S G. 2011. Tripeptide inhibitors of dengue and West Nile virus NS2B-NS3 protease. Antiviral Res, 92: 96–101.PubMedGoogle Scholar
  101. Shi P Y, Tilgner M, and Lo M K. 2002. Construction and characterization of subgenomic replicons of New York strain of West Nile virus. Virology, 296: 219–233.PubMedGoogle Scholar
  102. Shi P Y, Tilgner M, Lo M K, Kent K A, and Bernard K A. 2002. Infectious cDNA clone of the epidemic west nile virus from New York City. J Virol, 76: 5847–5856.PubMedCentralPubMedGoogle Scholar
  103. Shi P Y, Kauffman E B, Ren P, Felton A, Tai J H, Dupuis A P, 2nd, Jones S A, Ngo K A, Nicholas D C, Maffei J, Ebel G D, Bernard K A, and Kramer L D. 2001. High-throughput detection of West Nile virus RNA. J Clin Microbiol, 39: 1264–1271.PubMedCentralPubMedGoogle Scholar
  104. Shiryaev S, Ratnikov B, Chekanov A, Sikora S, Rozanov D, Godzik A, Wang J, Smith J, Huang Z, Lindberg I, Samuel M, Diamond M, and Strongin A. 2006. Cleavage targets and the D-arginine-based inhibitors of the West Nile virus NS3 processing proteinase. Biochem J., 393: 503–511.PubMedGoogle Scholar
  105. Sidique S, Shiryaev S A, Ratnikov B I, Herath A, Su Y, Strongin A Y, and Cosford N D. 2009. Structure-activity relationship and improved hydrolytic stability of pyrazole derivatives that are allosteric inhibitors of West Nile Virus NS2B-NS3 proteinase. Bioorg Med Chem Lett, 19: 5773–5777.PubMedCentralPubMedGoogle Scholar
  106. Steuer C, Gege C, Fischl W, Heinonen K H, Bartenschlager R, and Klein C D. 2011. Synthesis and biological evaluation of alpha-ketoamides as inhibitors of the Dengue virus protease with antiviral activity in cell-culture. Bioorg Med Chem, 19: 4067–4074.PubMedGoogle Scholar
  107. Stoermer M J, Chappell K J, Liebscher S, Jensen C M, Gan C H, Gupta P K, Xu W J, Young P R, and Fairlie D P. 2008. Potent cationic inhibitors of West Nile virus NS2B/NS3 protease with serum stability, cell permeability and antiviral activity. J Med Chem, 51: 5714–5721.PubMedGoogle Scholar
  108. Tan B H, Fu J, Sugrue R J, Yap E H, Chan Y C, and Tan Y H. 1996. Recombinant dengue type 1 virus NS5 protein expressed in Escherichia coli exhibits RNA-dependent RNA polymerase activity. Virology, 216: 317–325.PubMedGoogle Scholar
  109. Tassaneetrithep B, Burgess T H, Granelli-Piperno A, Trumpfheller C, Finke J, Sun W, Eller M A, Pattanapanyasat K, Sarasombath S, Birx D L, Steinman R M, Schlesinger S, and Marovich M A. 2003. DC-SIGN (CD209) mediates dengue virus infection of human dendritic cells. J Exp Med, 197: 823–829.PubMedCentralPubMedGoogle Scholar
  110. Tiew K C, Dou D, Teramoto T, Lai H, Alliston K R, Lushington G H, Padmanabhan R, and Groutas W C. 2012. Inhibition of Dengue virus and West Nile virus proteases by click chemistry-derived benz[d]isothiazol-3(2H)-one derivatives. Bioorg Med Chem, 20: 1213–1221.PubMedCentralPubMedGoogle Scholar
  111. Tomlinson S M, and Watowich S J. 2011. Anthracene-based inhibitors of dengue virus NS2B-NS3 protease. Antiviral Res, 89: 127–135.PubMedCentralPubMedGoogle Scholar
  112. Tomlinson S M, and Watowich S J. 2012. Use of parallel validation high-throughput screens to reduce false positives and identify novel dengue NS2B-NS3 protease inhibitors. Antiviral Res, 93: 245–252.PubMedCentralPubMedGoogle Scholar
  113. Tomlinson S M, Malmstrom R D, Russo A, Mueller N, Pang Y P, and Watowich S J. 2009. Structure-based discovery of dengue virus protease inhibitors. Antiviral Res, 82: 110–114.PubMedCentralPubMedGoogle Scholar
  114. Umareddy I, Chao A, Sampath A, Gu F, and Vasudevan S G. 2006. Dengue virus NS4B interacts with NS3 and dissociates it from single-stranded RNA. J Gen Virol, 87: 2605–2614.PubMedGoogle Scholar
  115. USGS. 2010. Disease Maps 2010. Scholar
  116. Warrener P, Tamura J K, and Collett M S. 1993. RNA-stimulated NTPase activity associated with yellow fever virus NS3 protein expressed in bacteria. J Virol, 67: 989–996.PubMedCentralPubMedGoogle Scholar
  117. Wegzyn C M, and Wyles D L. 2012. Antiviral drug advances in the treatment of human immunodeficiency virus (HIV) and chronic hepatitis C virus (HCV). Curr Opin Pharmacol, 12: 556–561.PubMedGoogle Scholar
  118. Wengler G. 1981. Terminal sequences of the genome and replicative-from RNA of the flavivirus West Nile virus: absence of poly(A) and possible role in RNA replication. Virology, 113: 544–555.PubMedGoogle Scholar
  119. Wengler G. 1991. The carboxy-terminal part of the NS 3 protein of the West Nile flavivirus can be isolated as a soluble protein after proteolytic cleavage and represents an RNA-stimulated NTPase. Virology, 184: 707–715.PubMedGoogle Scholar
  120. Westaway E G, Brinton M A, Gaidamovich S Y, Horzinek M C, Igarashi A, Kaariainen L, Lvov D K, Porterfield J S, Russell P K, and Trent D W. 1985. Flaviviridae. Intervirol., 24: 183–192.Google Scholar
  121. WHO. 2009. Immunization, vaccines and biologicals: Japanese encephalitis. 〈〉.Google Scholar
  122. Wyles D L. 2012. Beyond telaprevir and boceprevir: resistance and new agents for hepatitis C virus infection. Top Antivir Med, 20: 139–145.PubMedGoogle Scholar
  123. Wyles D L. 2013. Antiviral resistance and the future landscape of hepatitis C virus infection therapy. J Infect Dis, 207Suppl 1: S33–39.PubMedGoogle Scholar
  124. Xu S, Li H, Shao X, Fan C, Ericksen B, Liu J, Chi C, and Wang C. 2012. Critical effect of peptide cyclization on the potency of peptide inhibitors against Dengue virus NS2B-NS3 protease. J Med Chem, 55: 6881–6887.PubMedGoogle Scholar
  125. Yang C C, Hsieh Y C, Lee S J, Wu S H, Liao C L, Tsao C H, Chao Y S, Chern J H, Wu C P, and Yueh A. 2011. Novel dengue virus-specific NS2B/NS3 protease inhibitor, BP2109, discovered by a high-throughput screening assay. Antimicrob Agents Chemother, 55: 229–238.PubMedCentralPubMedGoogle Scholar
  126. Yin Z, Patel S J, Wang W L, Wang G, Chan W L, Rao K R, Alam J, Jeyaraj D A, Ngew X, Patel V, Beer D, Lim S P, Vasudevan S G, and Keller T H. 2006. Peptide inhibitors of Dengue virus NS3 protease. Part 1: Warhead. Bioorg Med Chem Lett, 16: 36–39.PubMedGoogle Scholar
  127. Yin Z, Patel S J, Wang W L, Chan W L, Ranga Rao K R, Wang G, Ngew X, Patel V, Beer D, Knox J E, Ma N L, Ehrhardt C, Lim S P, Vasudevan S G, and Keller T H. 2006. Peptide inhibitors of dengue virus NS3 protease. Part 2: SAR study of tetrapeptide aldehyde inhibitors. Bioorg Med Chem Lett, 16: 40–43.PubMedGoogle Scholar
  128. Zhang Y, Corver J, Chipman P R, Zhang W, Pletnev S V, Sedlak D, Baker T S, Strauss J H, Kuhn R J, and Rossmann M G. 2003. Structures of immature flavivirus particles. EMBO J., 22: 2604–2613.PubMedGoogle Scholar
  129. Zhou Y, Ray D, Zhao Y, Dong H, Ren S, Li Z, Guo Y, Bernard K A, Shi P Y, and Li H. 2007. Structure and function of flavivirus NS5 methyltransferase. J Virol, 81: 3891–3903.PubMedCentralPubMedGoogle Scholar

Copyright information

© Wuhan Institute of Virology, CAS and Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Wadsworth CenterNew York State Department of HealthAlbanyUSA
  2. 2.Department of Biomedical Sciences, School of Public HealthState University of New YorkAlbanyUSA

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