Structural and functional parameters of the flaviviral protease: A promising antiviral drug target

Future Virology

Volumn 5, Issue 5, 2010, Pages 593-606

  Shiryaev, Sergey A ^a   Strongin, Alex Y ^a  

^a BURNHAM INSTITUTE   (United States)

Author keywords

Dengue virus; flavivirus; helicase; NS2B; NS3; NS4A; protease; West Nile virus

Indexed keywords

GENOMIC RNA; HELICASE; NONSTRUCTURAL PROTEIN 2; NONSTRUCTURAL PROTEIN 3; NONSTRUCTURAL PROTEIN 4A;

AMINO TERMINAL SEQUENCE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CONFORMATIONAL TRANSITION; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME SPECIFICITY; NONHUMAN; PRECURSOR; PRIORITY JOURNAL; PROTEIN CLEAVAGE; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; REVIEW; RNA TRANSLATION; SEQUENCE ALIGNMENT; WEST NILE FLAVIVIRUS;

DENGUE VIRUS; FLAVIVIRUS; WEST NILE VIRUS;

EID: 77957295779     PISSN: 17460794     EISSN: None     Source Type: Journal    
DOI: 10.2217/fvl.10.39     Document Type: Review

References (121)

1. van der Meulen KM, Pensaert MB, Nauwynck HJ: West Nile virus in the vertebrate world. Arch. Virol. 150(4), 637-657 (2005).
2. Madden K: West Nile virus infection and its neurological manifestations. Clin. Med. Res. 1(2), 145-150 (2003).
3. Wang T, Town T, Alexopoulou L, Anderson JF, Fikrig E, Flavell RA: Toll-like receptor 3 mediates West Nile virus entry into the brain causing lethal encephalitis. Nat. Med. 10(12), 1366-1373 (2004).
4. Rice CM, Lenches EM, Eddy SR, Shin SJ, Sheets RL, Strauss JH: Nucleotide sequence of yellow fever virus: implications for flavivirus gene expression and evolution. Science 229(4715), 726-733 (1985).
5. Mackow E, Makino Y, Zhao BT et al.: The nucleotide sequence of dengue type 4 virus: analysis of genes coding for nonstructural proteins. Virology 159(2), 217-228 (1987).
6. Zhao B, Mackow E, Buckler-White A et al.: Cloning full-length dengue type 4 viral DNA sequences: analysis of genes coding for structural proteins. Virology 155(1), 77-88 (1986).
7. Hahn YS, Galler R, Hunkapiller T, Dalrymple JM, Strauss JH, Strauss EG: Nucleotide sequence of dengue 2 RNA and comparison of the encoded proteins with those of other flaviviruses. Virology 162(1), 167-180 (1988).
8. Yaegashi T, Vakharia VN, Page K, Sasaguri Y, Feighny R, Padmanabhan R: Partial sequence analysis of cloned dengue virus type 2 genome. Gene 46 (2-3), 257-267 (1986).
9. Irie K, Mohan PM, Sasaguri Y, Putnak R, Padmanabhan R: Sequence analysis of cloned dengue virus type 2 genome (New Guinea-C strain). Gene 75(2), 197-211 (1989).
10. Deubel V, Kinney RM, Trent DW: Nucleotide sequence and deduced amino acid sequence of the nonstructural proteins of dengue type 2 virus, Jamaica genotype: comparative analysis of the full-length genome. Virology 165(1), 234-244 (1988).
11. Coia G, Parker MD, Speight G, Byrne ME, Westaway EG: Nucleotide and complete amino acid sequences of Kunjin virus: definitive gene order and characteristics of the virus-specified proteins. J. Gen. Virol. 69 (Pt 1), 1-21 (1988).
12. Castle E, Leidner U, Nowak T, Wengler G: Primary structure of the West Nile flavivirus genome region coding for all nonstructural proteins. Virology 149(1), 10-26 (1986).
13. Chambers TJ, Hahn CS, Galler R, Rice CM: Flavivirus genome organization, expression, and replication. Annu. Rev. Microbiol. 44, 649-688 (1990).
14. Chambers TJ, Weir RC, Grakoui A et al.: Evidence that the N-terminal domain of nonstructural protein NS3 from yellow fever virus is a serine protease responsible for site-specific cleavages in the viral polyprotein. Proc. Natl Acad. Sci. USA 87(22), 8898-8902 (1990). □□ The first publication that identifies the N-terminal domain of flaviviral NS3 as a serine protease.
15. Crawford GR, Wright PJ: Characterization of novel viral polyproteins detected in cells infected by the flavivirus Kunjin and radiolabeled in the presence of the leucine analog hydroxyleucine. J. Gen. Virol. 68 (Pt 2), 365-376 (1987).
16. Preugschat F, Strauss JH: Processing of nonstructural proteins NS4A and NS4B of dengue 2 virus in vitro and in vivo. Virology 185(2), 689-697 (1991).
17. Yamshchikov VF, Trent DW, Compans RW: Up regulation of signalase processing and induction of prM-E secretion by the flavivirus NS2B-NS3 protease: roles of protease components. J. Virol. 71(6), 4364-4371 (1997).
18. Thomas G: Furin at the cutting edge: from protein traffic to embryogenesis and disease. Nat. Rev. Mol. Cell. Biol. 3(10), 753-766 (2002). □ A comprehensive review on the furin-like proprotein convertases.
19. Mukhopadhyay S, Kuhn RJ, Rossmann MG: A structural perspective of the flavivirus life cycle. Nat. Rev. Microbiol. 3(1), 13-22 (2005).
20. Padmanabhan R, Mueller N, Reichert e et al.: Multiple enzyme activities of flavivirus proteins. Novartis Found Symp. 277, 74-84; discussion 84-76, 251-253 (2006).
21. Li H, Clum S, You S, Ebner KE, Padmanabhan R: 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(4), 3108-3116 (1999).
22. Gorbalenya AE, Koonin EV, Donchenko AP, Blinov VM: Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res. 17(12), 4713-4730 (1989).
23. Wengler G, Wengler G: The NS 3 nonstructural protein of flaviviruses contains an RNA triphosphatase activity. Virology 197(1), 265-273 (1993).
24. Mastrangelo E, Milani M, Bollati M et al.: Crystal structure and activity of Kunjin virus NS3 helicase; protease and helicase domain assembly in the full length NS3 protein. J. Mol. Biol. 372(2), 444-455 (2007). □ Structural analysis of the Kunjin virus full-length NS3 protein.
25. Cui T, Sugrue RJ, Xu Q, Lee AK, Chan YC, Fu J: Recombinant dengue virus type 1 NS3 protein exhibits specific viral RNA binding and NTPase activity regulated by the NS5 protein. Virology 246(2), 409-417 (1998).
26. Borowski P, Niebuhr A, Mueller O et al.: Purification and characterization of West Nile virus nucleoside triphosphatase (NTPase)/helicase: evidence for dissociation of the NTPase and helicase activities of the enzyme. J. Virol. 75(7), 3220-3229 (2001).
27. Luo D, Xu T, Hunke C, Gruber G, Vasudevan SG, Lescar J: Crystal structure of the NS3 protease-helicase from dengue virus. J. Virol. 82(1), 173-183 (2008).
28. Luo D, Xu T, Watson RP et al.: Insights into RNA unwinding and ATP hydrolysis by the flavivirus NS3 protein. EMBO J. 27(23), 3209-3219 (2008). □□ Structural analysis of the dengue virus serotype-4 NS3 helicase at several stages along the catalytic pathway, including bound to single-stranded RNA, to an ATP analog, to a transition-state analog and to an ATP hydrolysis product.
29. Frick DN: Helicases as antiviral drug targets. Drug News Perspect. 16(6), 355-362 (2003).
30. Dahl G, Sandstrom A, Akerblom E, Danielson UH: Effects on protease inhibition by modifying of helicase residues in hepatitis C virus nonstructural protein 3. FEBS J. 274(22), 5979-5986 (2007).
31. Chappell KJ, Stoermer MJ, Fairlie DP, Young PR: West Nile Virus NS2B/NS3 protease as an antiviral target. Curr. Med. Chem. 15(27), 2771-2784 (2008). □ Review paper on the NS3 protease from the drug design perspective.
32. Yusof R, Clum S, Wetzel M, Murthy HM, Padmanabhan R: Purified NS2B/NS3 serine protease of dengue virus type 2 exhibits cofactor NS2B dependence for cleavage of substrates with dibasic amino acids in vitro. J. Biol. Chem. 275(14), 9963-9969 (2000).
33. Aleshin AE, Shiryaev SA, Strongin AY, Liddington RC: Structural evidence for regulation and specificity of flaviviral proteases and evolution of the Flaviviridae fold. Protein Sci. 16(5), 795-806 (2007). □□ Describes in detail the structure of the two-component NS2B-NS3 West Nile virus protease.
34. Erbel P, Schiering N, DArcy A et al.: Structural basis for the activation of flaviviral NS3 proteases from dengue and West Nile virus. Nat. Struct. Mol. Biol. 13(4), 372-373 (2006). □□ Describes the structure of the two-component NS2B-NS3 dengue virus protease.
35. Luking A, Stahl U, Schmidt U: The protein family of RNA helicases. Crit. Rev. Biochem. Mol. Biol. 33(4), 259-296 (1998).
36. 2+-dependent and require a functional Walker B motif in the helicase catalytic core. Virology 328(2), 208-218 (2004).
37. Maga G, Gemma S, Fattorusso C et al.: Specific targeting of hepatitis C virus NS3 RNA helicase. Discovery of the potent and selective competitive nucleotide-mimicking inhibitor QU663. Biochemistry 44(28), 9637-9644 (2005).
38. Nall TA, Chappell KJ, Stoermer MJ et al.: Enzymatic characterization and homology model of a catalytically active recombinant West Nile virus NS3 protease. J. Biol. Chem. 279(47), 48535-48542 (2004).
39. Johnston PA, Phillips J, Shun TY et al.: HTS identifies novel and specific uncompetitive inhibitors of the twocomponent NS2B-NS3 proteinase of West Nile virus. Assay Drug Dev. Technol. 5(6), 737-750 (2007).
40. Ray D, Shi PY: Recent advances in flavivirus antiviral drug discovery and vaccine development. Recent Patents Antiinfect. Drug Disc. 1(1), 45-55 (2006).
41. Keller TH, Chen YL, Knox JE et al.: Finding new medicines for flaviviral targets. Novartis Found Symp. 277, 102-114; discussion 114-109, 251-103 (2006).
42. Sampath A, Xu T, Chao A, Luo D, Lescar J, Vasudevan SG: Structure-based mutational analysis of the NS3 helicase from dengue virus. J. Virol. 80(13), 6686-6690 (2006).
43. Xu T, Sampath A, Chao A et al.: Towards the design of flavivirus helicase/NTPase inhibitors: crystallographic and mutagenesis studies of the dengue virus NS3 helicase catalytic domain. Novartis Found Symp. 277, 87-97; discussion 97-101, 251-103 (2006).
44. Kapoor M, Zhang L, Ramachandra M, Kusukawa J, Ebner KE, Padmanabhan R: Association between NS3 and NS5 proteins of dengue virus type 2 in the putative RNA replicase is linked to differential phosphorylation of NS5. J. Biol. Chem. 270(32), 19100-19106 (1995).
45. Kapoor M, Zhang L, Mohan PM, Padmanabhan R: Synthesis and characterization of an infectious dengue virus type-2 RNA genome (New Guinea C strain). Gene 162(2), 175-180 (1995).
46. Lindenbach B: Flaviviridae: the viruses and their replication. In: Fields Virology. Bernard N, Fields DMK, Howley PM (Eds). Lippincott Williams & Wilkins, PA, USA 1101 (2007).
47. Lindenbach BD, Pragai BM, Montserret R et al.: The C terminus of hepatitis C virus NS4A encodes an electrostatic switch that regulates NS5A hyperphosphorylation and viral replication. J. Virol. 81(17), 8905-8918 (2007).
48. Liu WJ, Sedlak PL, Kondratieva N, Khromykh AA: Complementation analysis of the flavivirus Kunjin NS3 and NS5 proteins defines the minimal regions essential for formation of a replication complex and shows a requirement of NS3 in cis for virus assembly. J. Virol. 76(21), 10766-10775 (2002).
49. Uchil PD, Kumar AV, Satchidanandam V: Nuclear localization of flavivirus RNA synthesis in infected cells. J. Virol. 80(11), 5451-5464 (2006).
50. Brooks AJ, Johansson M, John AV, Xu Y, Jans DA, Vasudevan SG: The interdomain region of dengue NS5 protein that binds to the viral helicase NS3 contains independently functional importin β 1 and importin α/β-recognized nuclear localization signals. J. Biol. Chem. 277(39), 36399-36407 (2002).
51. Amberg SM, Nestorowicz A, McCourt DW, Rice CM: NS2B-3 proteinase-mediated processing in the yellow fever virus structural region: in vitro and in vivo studies. J. Virol. 68(6), 3794-3802 (1994).
52. Arias CF, Preugschat F, Strauss JH: Dengue 2 virus NS2B and NS3 form a stable complex that can cleave NS3 within the helicase domain. Virology 193(2), 888-899 (1993).
53. Chambers TJ, Grakoui A, Rice CM: 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(11), 6042-6050 (1991).
54. Jan LR, Yang CS, Trent DW, Falgout B, Lai CJ: Processing of Japanese encephalitis virus non-structural proteins: NS2B-NS3 complex and heterologous proteases. J. Gen. Virol. 76 (Pt 3), 573-580 (1995).
55. Lin C, Amberg SM, Chambers TJ, Rice CM: Cleavage at a novel site in the NS4A region by the yellow fever virus NS2B-3 proteinase is a prerequisite for processing at the downstream 4A/4B signalase site. J. Virol. 67(4), 2327-2335 (1993).
56. Lin C, Chambers TJ, Rice CM: Mutagenesis of conserved residues at the yellow fever virus 3/4A and 4B/5 dibasic cleavage sites: effects on cleavage efficiency and polyprotein processing. Virology 192(2), 596-604 (1993).
57. Wengler G, Czaya G, Farber PM, Hegemann JH: In vitro synthesis of West Nile virus proteins indicates that the aminoterminal segment of the NS3 protein contains the active centre of the protease which cleaves the viral polyprotein after multiple basic amino acids. J. Gen. Virol. 72 (Pt 4), 851-858 (1991).
58. Wengler G, Wengler G: 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(2), 707-715 (1991).
59. Zhang L, Mohan PM, Padmanabhan R: Processing and localization of dengue virus type 2 polyprotein precursor NS3-NS4A-NS4B-NS5. J. Virol. 66(12), 7549-7554 (1992).
60. Falgout B, Pethel M, Zhang YM, Lai CJ: Both nonstructural proteins NS2B and NS3 are required for the proteolytic processing of dengue virus nonstructural proteins. J. Virol. 65(5), 2467-2475 (1991).
61. Falgout B, Miller RH, Lai CJ: Deletion analysis of dengue virus type 4 nonstructural protein NS2B: identification of a domain required for NS2B-NS3 protease activity. J. Virol. 67(4), 2034-2042 (1993).
62. Chambers TJ, Nestorowicz A, Amberg SM, Rice CM: Mutagenesis of the yellow fever virus NS2B protein: effects on proteolytic processing, NS2B-NS3 complex formation, and viral replication. J. Virol. 67(11), 6797-6807 (1993).
63. Leung D, Schroder K, White H et al.: 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(49), 45762-45771 (2001).
64. Chappell KJ, Nall TA, Stoermer MJ et al.: Site-directed mutagenesis and kinetic studies of the West Nile Virus NS3 protease identify key enzyme-substrate interactions. J. Biol. Chem. 280(4), 2896-2903 (2005).
65. Cahour A, Falgout B, Lai CJ: Cleavage of the dengue virus polyprotein at the NS3/NS4A and NS4B/NS5 junctions is mediated by viral protease NS2B-NS3, whereas NS4A/NS4B may be processed by a cellular protease. J. Virol. 66(3), 1535-1542 (1992).
66. Miller S, Kastner S, Krijnse-Locker J, Buhler S, Bartenschlager R: 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(12), 8873-8882 (2007).
67. Beran RK, Lindenbach BD, Pyle AM: The NS4A protein of hepatitis C virus promotes RNA-coupled ATP hydrolysis by the NS3 helicase. J. Virol. 83(7), 3268-3275 (2009). □ Determines that NS4A plays a cofactor role for the NS3 helicase from HCV.
68. Shiryaev SA, Chernov AV, Aleshin AE, Shiryaeva TN, Strongin AY: NS4A regulates the ATPase activity of the NS3 helicase: a novel cofactor role of the non-structural protein NS4A from West Nile virus. J. Gen. Virol. 90 (Pt 9), 2081-2085 (2009). □ Reports on the cofactor function of NS4A.
69. Shiryaev SA, Aleshin AE, Ratnikov BI, Smith JW, Liddington RC, Strongin AY: Expression and purification of a twocomponent flaviviral proteinase resistant to autocleavage at the NS2B-NS3 junction region. Protein Expr. Purif. 52(2), 334-339 (2007).
70. Chappell KJ, Stoermer MJ, Fairlie DP, Young PR: Generation and characterization of proteolytically active and highly stable truncated and full-length recombinant West Nile virus NS3. Protein Expr. Purif. 53(1), 87-96 (2007).
71. Shiryaev SA, Ratnikov BI, Chekanov AV et al.: Cleavage targets and the d-argininebased inhibitors of the West Nile virus NS3 processing proteinase. Biochem J. 393 (Pt 2), 503-511 (2006).
72. Niyomrattanakit P, Winoyanuwattikun P, Chanprapaph S, Angsuthanasombat C, Panyim S, Katzenmeier G: Identification of residues in the dengue virus type 2 NS2B cofactor that are critical for NS3 protease activation. J. Virol. 78(24), 13708-13716 (2004).
73. Chappell KJ, Stoermer MJ, Fairlie DP, Young PR: Mutagenesis of the West Nile virus NS2B cofactor domain reveals two regions essential for protease activity. J. Gen. Virol. 89 (Pt 4), 1010-1014 (2008).
74. Radichev I, Shiryaev SA, Aleshin AE et al.: Structure-based mutagenesis identifies important novel determinants of the NS2B cofactor of the West Nile virus twocomponent NS2B-NS3 proteinase. J. Gen. Virol. 89 (Pt 3), 636-641 (2008).
75. Chandramouli S, Joseph JS, Daudenarde S, Gatchalian J, Cornillez-Ty C, Kuhn P: Serotype-specific structural differences in the protease-cofactor complexes of the dengue virus family. J. Virol. 84(6), 3059-3067 (2010). □ First report on serotype-specific structural element in the dengue virus NS3 protease.
76. Pasternak A, Ringe D, Hedstrom L: Comparison of anionic and cationic trypsinogens: the anionic activation domain is more flexible in solution and differs in its mode of BPTI binding in the crystal structure. Protein Sci. 8(1), 253-258 (1999).
77. Robin G, Chappell K, Stoermer MJ et al.: Structure of West Nile virus NS3 protease: ligand stabilization of the catalytic conformation. J. Mol. Biol. 385(5), 1568-1577 (2009).
78. Koshland DE: Application of a theory of enzyme specificity to protein synthesis. Proc. Natl Acad. Sci. USA 44(2), 98-104 (1958).
79. Matusan AE, Kelley PG, Pryor MJ, Whisstock JC, Davidson AD, Wright PJ: Mutagenesis of the dengue virus type 2 NS3 proteinase and the production of growthrestricted virus. J. Gen. Virol. 82 (Pt 7), 1647-1656 (2001).
80. Matusan AE, Pryor MJ, Davidson AD, Wright PJ: Mutagenesis of the dengue virus type 2 NS3 protein within and outside helicase motifs: effects on enzyme activity and virus replication. J. Virol. 75(20), 9633-9643 (2001).
81. Otlewski J, Jaskolski M, Buczek O et al.: Structure-function relationship of serine protease-protein inhibitor interaction. Acta Biochim. Pol. 48(2), 419-428 (2001).
82. Hedstrom L: Serine protease mechanism and specificity. Chem Rev. 102(12), 4501-4524 (2002).
83. Perona JJ, Craik CS: Structural basis of substrate specificity in the serine proteases. Protein Sci. 4(3), 337-360 (1995).
84. Valle RP, Falgout B: Mutagenesis of the NS3 protease of dengue virus type 2. J. Virol. 72(1), 624-632 (1998).
85. Remacle AG, Shiryaev SA, Oh ES et al.: Substrate cleavage analysis of furin and related proprotein convertases. A comparative study. J. Biol. Chem. 283(30), 20897-20906 (2008). □ In-depth analysis of the cleavage preferences of the individual proteinases from the proprotein convertase family.
86. Seidah NG: Unexpected similarity between the cytosolic West Nile virus NS3 and the secretory furin-like serine proteinases. Biochem. J. 393 (Pt 2), E1-E3 (2006).
87. Li J, Lim SP, Beer D et al.: Functional profiling of recombinant NS3 proteases from all four serotypes of dengue virus using tetrapeptide and octapeptide substrate libraries. J. Biol. Chem. 280(31), 28766-28774 (2005). □ Extensive analysis of the cleavage preferences of the dengue NS3 protease.
88. Shiryaev SA, Kozlov IA, Ratnikov BI, Smith JW, Lebl M, Strongin AY: Cleavage preference distinguishes the two-component NS2B-NS3 serine proteinases of dengue and West Nile viruses. Biochem J. 401(3), 743-752 (2007). □ Extensive analysis of the relative cleavage preferences of the dengue and West Nile virus NS3 proteases.
89. Shiryaev SA, Ratnikov BI, Aleshin AE et al.: Switching the substrate specificity of the two-component NS2B-NS3 flavivirus proteinase by structure-based mutagenesis. J. Virol. 81(9), 4501-4509 (2007). □ First instance of engineering a viral protease with switched substrate cleavage preferences.
90. Chappell KJ, Stoermer MJ, Fairlie DP, Young PR: Insights to substrate binding and processing by West Nile virus NS3 protease through combined modeling, protease mutagenesis, and kinetic studies. J. Biol. Chem. 281(50), 38448-38458 (2006).
91. Gouvea IE, Izidoro MA, Judice WA et al.: 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(2), 187-196 (2007).
92. Khumthong R, Angsuthanasombat C, Panyim S, Katzenmeier G: In vitro determination of dengue virus type 2 NS2B-NS3 protease activity with fluorescent peptide substrates. J. Biochem. Mol. Biol. 35(2), 206-212 (2002).
93. Khumthong R, Niyomrattanakit P, Chanprapaph S, Angsuthanasombat C, Panyim S, Katzenmeier G: Steady-state cleavage kinetics for dengue virus type 2 NS2B-NS3 (pro) serine protease with synthetic peptides. Protein Pept. Lett. 10(1), 19-26 (2003).
94. Mueller NH, Yon C, Ganesh VK, Padmanabhan R: Characterization of the West Nile virus protease substrate specifcity and inhibitors. Int. J. Biochem. Cell. Biol. 39(3), 606-614 (2007).
95. Patel SS, Donmez I: Mechanisms of helicases. J. Biol. Chem. 281(27), 18265-18268 (2006).
96. Andersen CB, Ballut L, Johansen JS et al.: Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA. Science 313(5795), 1968-1972 (2006).
97. Bono F, Ebert J, Lorentzen E, Conti E: The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA. Cell 126(4), 713-725 (2006).
98. Sengoku T, Nureki O, Nakamura A, Kobayashi S, Yokoyama S: Structural basis for RNA unwinding by the DEAD-box protein Drosophila vasa. Cell 125(2), 287-300 (2006).
99. Assenberg R, Mastrangelo E, Walter TS et al.: Crystal structure of a novel conformational state of the flavivirus NS3 protein: implications for polyprotein processing and viral replication. J. Virol. 83(24), 12895-12906 (2009). □ Indicates the alternating relative folds of the protease and the helicase in the full-length NS3 protein.
100. Chernov AV, Shiryaev SA, Aleshin AE et al.: The two-component NS2B-NS3 proteinase represses DNA unwinding activity of the West Nile virus NS3 helicase. J. Biol. Chem. 283(25), 17270-17278 (2008).
101. Dahl G, Arenas OG, Danielson UH: Hepatitis C virus NS3 protease is activated by low concentrations of protease inhibitors. Biochemistry 48(48), 11592-11602 (2009).
102. Yang W, Zhao Y, Fabrycki J et al.: Selection of replicon variants resistant to ACH-806, a novel hepatitis C virus inhibitor with no cross-resistance to NS3 protease and NS5B polymerase inhibitors. Antimicrob. Agents Chemother. 52(6), 2043-2052 (2008).
103. Wyles DL, Kaihara KA, Schooley RT: Synergy of a hepatitis C virus (HCV) NS4A antagonist in combination with HCV protease and polymerase inhibitors. Antimicrob. Agents Chemother. 52(5), 1862-1864 (2008).
104. Ekonomiuk D, Su XC, Ozawa K et al.: Discovery of a non-peptidic inhibitor of West Nile virus NS3 protease by high-throughput docking. PLoS Negl. Trop. Dis. 3(1), e356 (2009).
105. Ganesh VK, Muller N, Judge K, Luan CH, Padmanabhan R, Murthy KH: Identification and characterization of nonsubstrate based inhibitors of the essential dengue and West Nile virus proteases. Bioorg. Med. Chem. 13(1), 257-264 (2005).
106. Lescar J, Luo D, Xu T et al.: Towards the design of antiviral inhibitors against flaviviruses: the case for the multifunctional NS3 protein from dengue virus as a target. Antiviral Res. 80(2), 94-101 (2008).
107. Mueller NH, Pattabiraman N, Ansarah-Sobrinho C, Viswanathan P, Pierson TC, Padmanabhan R: Identifcation and biochemical characterization of small-molecule inhibitors of West Nile virus serine protease by a high-throughput screen. Antimicrob. Agents Chemother. 52(9), 3385-3393 (2008).
108. Sampath A, Padmanabhan R: Molecular targets for flavivirus drug discovery. Antiviral Res. 81(1), 6-15 (2009).
109. Sidique S, Shiryaev SA, Ratnikov BI et al.: 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(19), 5773-5777 (2009).
110. Su XC, Ozawa K, Yagi H et al.: NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease. FEBS J. 276(15), 4244-4255 (2009).
111. Tomlinson SM, Malmstrom RD, Russo A, Mueller N, Pang y P, Watowich SJ: Structurebased discovery of dengue virus protease inhibitors. Antiviral Res. 82(3), 110-114 (2009).
112. Zuo Z, Liew OW, Chen G et al.: Mechanism of NS2B-mediated activation of NS3pro in dengue virus: molecular dynamics simulations and bioassays. J. Virol. 83(2), 1060-1070 (2009).
113. Chanprapaph S, Saparpakorn P, Sangma C et al.: Competitive inhibition of the dengue virus NS3 serine protease by synthetic peptides representing polyprotein cleavage sites. Biochem. Biophys. Res. Commun. 330(4), 1237-1246 (2005).
114. Ekonomiuk D, Su XC, Ozawa K et al.: Flaviviral protease inhibitors identified by fragment-based library docking into a structure generated by molecular dynamics. J. Med. Chem. 52(15), 4860-4868 (2009).
115. Kiat TS, Pippen R, Yusof R, Ibrahim H, Khalid N, Rahman NA: Inhibitory activity of cyclohexenyl chalcone derivatives and flavonoids of fingerroot, Boesenbergia rotunda (L.), towards dengue-2 virus NS3 protease. Bioorg. Med. Chem. Lett. 16(12), 3337-3340 (2006).
116. Knox JE, Ma NL, Yin Z et al.: Peptide inhibitors of West Nile NS3 protease: SAR study of tetrapeptide aldehyde inhibitors. J. Med. Chem. 49(22), 6585-6590 (2006). (Pubitemid 44657452)
117. Stoermer MJ, Chappell KJ, Liebscher S et al.: Potent cationic inhibitors of West Nile virus NS2B/NS3 protease with serum stability, cell permeability and antiviral activity. J. Med. Chem. 51(18), 5714-5721 (2008).
118. Yin Z, Patel SJ, Wang WL et al.: Peptide inhibitors of dengue virus NS3 protease. Part 2: SAR study of tetrapeptide aldehyde inhibitors. Bioorg. Med. Chem. Lett. 16(1), 40-43 (2006). (Pubitemid 41625637)
119. Yin Z, Patel SJ, Wang WL et al.: Peptide inhibitors of dengue virus NS3 protease. Part 1: warhead. Bioorg. Med. Chem. Lett. 16(1), 36-39 (2006).
120. Shiryaev SA, Radichev IA, Ratnikov BI et al.: Isolation and characterization of selective and potent human Fab inhibitors directed to the active-site region of the two-component NS2B-NS3 proteinase of West Nile virus. Biochem. J. 427(3), 369-376 (2010).
121. Bollati M, Alvarez K, Assenberg R et al.: Structure and functionality in flavivirus NS-proteins: perspectives for drug design. Antiviral Res. 87(2), 125-148 (2010).