Predicting Zika virus structural biology: Challenges and opportunities for intervention

Antiviral Chemistry and Chemotherapy

Volumn 24, Issue 3-4, 2015, Pages 118-126

  Cox, Bryan D ^a   Stanton, Richard A ^a   Schinazi, Raymond F ^a  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

drug discovery; flavivirus; homology modeling; vaccine design; Zika virus

Indexed keywords

AMINO ACID; GUANOSINE TRIPHOSPHATE; MEMBRANE PROTEIN; POLYPROTEIN; RNA DIRECTED RNA POLYMERASE; VACCINE; VIRAL PROTEIN; VIRUS ENVELOPE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; DENGUE VIRUS; GENE LOCUS; GENE MUTATION; NONHUMAN; PATHOGENESIS; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; SOFTWARE; STRUCTURAL HOMOLOGY; VIRUS GENE; VIRUS MORPHOLOGY; VIRUS STRAIN; WEST NILE VIRUS; ZIKA VIRUS; ALGORITHM; CHEMISTRY; MOLECULAR DYNAMICS;

ALGORITHMS; MOLECULAR DYNAMICS SIMULATION; SOFTWARE; VIRAL PROTEINS; ZIKA VIRUS;

EID: 84984999138     PISSN: 09563202     EISSN: None     Source Type: Journal    
DOI: 10.1177/2040206616653873     Document Type: Article

References (46)

1. M.K.KindhauserT.AllenV.Frank. Zika: the origin and spread of a mosquito-borne virus. Bull World Health Organ2016, pp. 171082,, http://icmr.nic.in/zika/publications/Zika%20the%20origin%20and%20spread%20of%20a%20mosquitoborne%20virus.pdf.
2. D.R.LuceyL.O.Gostin. The emerging Zika pandemic: enhancing preparedness. JAMA2016; 315: 865–866.
3. D.SirohiZ.ChenL.Sun. The 3.8 Å resolution cryo-EM structure of Zika virus. Science2016; 352: 467–470.
4. S.EkinsJ.LieblerB.J.Neves. Illustrating and homology modeling the proteins of the Zika virus. F1000Research2016; 5.
5. F.SieversA.WilmD.Dineen. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol2011; 7: 1–6.
6. H.McWilliamW.LiM.Uludag. Analysis tool web services from the EMBL-EBI. Nucleic Acids Res2013; 41: W597–W600.
7. R.GautierD.DouguetB.Antonny. HELIQUEST: a web server to screen sequences with specific α-helical properties. Bioinformatics2008; 24: 2101–2102.
8. M.BiasiniS.BienertA.Waterhouse. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res2014; 1: 1–7.
9. W.HumphreyA.DalkeK.Schulten. VMD: visual molecular dynamics. J Mol Graph1996; 14: 33–38.
10. B.GuyF.GuirakhooV.Barban. Preclinical and clinical development of YFV 17D-based chimeric vaccines against dengue, West Nile and Japanese encephalitis viruses. Vaccine2010; 28: 632–649.
11. V.B.RandolphG.WinklerV.Stollar. Acidotropic amines inhibit proteolytic processing of flavivirus prM protein. Virology1990; 174: 450–458.
12. L.LiS.-M.LokI.-M.Yu. The flavivirus precursor membrane-envelope protein complex: structure and maturation. Science2008; 319: 1830–1834.
13. Y.ModisS.OgataD.Clements. Variable surface epitopes in the crystal structure of dengue virus type 3 envelope glycoprotein. J Virol2005; 79: 1223–1231.
14. E.A.HenchalM.K.GentryJ.M.McCown. Dengue virus-specific and flavivirus group determinants identified with monoclonal antibodies by indirect immunofluorescence. Am J Trop Med Hyg1982; 31: 830–836.
15. Y.-Q.DengJ.-X.DaiG.-H.Ji. A broadly flavivirus cross-neutralizing monoclonal antibody that recognizes a novel epitope within the fusion loop of E protein. PLoS One2011; 6: e16059.
16. T.KampmannR.YennamalliP.Campbell. In silico screening of small molecule libraries using the dengue virus envelope E protein has identified compounds with antiviral activity against multiple flaviviruses. Antiviral Res2009; 84: 234–241.
17. R.S.LanciottiO.L.KosoyJ.J.Laven. Genetic and serologic properties of Zika virus associated with an epidemic, Yap State, Micronesia, 2007. Emerg Infect Dis2008; 14: 1232–1239.
18. A.D.HaddowA.J.SchuhC.Y.Yasuda. Genetic characterization of Zika virus strains: geographic expansion of the Asian lineage. PLoS Negl Trop Dis2012; 6: e1477.
19. T.J.ChambersM.HalevyA.Nestorowicz. West Nile virus envelope proteins: nucleotide sequence analysis of strains differing in mouse neuroinvasiveness. J Gen Virol1998; 79: 2375–2380.
20. H.TangC.HammackS.C.Ogden. Zika virus infects human cortical neural progenitors and attenuates their growth. Cell Stem Cell2016; 18.5: 587–590.
21. M.B.JohnsonP.P.WangK.D.Atabay. Single-cell analysis reveals transcriptional heterogeneity of neural progenitors in human cortex. Nat Neurosci2015; 18: 637–646.
22. D.A.MullerP.R.Young. The flavivirus NS1 protein: molecular and structural biology, immunology, role in pathogenesis and application as a diagnostic biomarker. Antiviral Res2013; 98: 192–208.
23. D.L.AkeyW.C.BrownS.Dutta. Flavivirus NS1 structures reveal surfaces for associations with membranes and the immune system. Science2014; 343: 881–885.
24. H.-J.ChengC.-F.LinH.-Y.Lei. Proteomic analysis of endothelial cell autoantigens recognized by anti-dengue virus nonstructural protein 1 antibodies. Exp Biol Med2009; 234: 63–73.
25. I.-J.LiuC.-Y.ChiuY.-C.Chen. Molecular mimicry of human endothelial cell antigen by autoantibodies to nonstructural protein 1 of dengue virus. J Biol Chem2011; 286: 9726–9736.
26. M.-C.ChenC.-F.LinH.-Y.Lei. Deletion of the C-terminal region of dengue virus nonstructural protein 1 (NS1) abolishes anti-NS1-mediated platelet dysfunction and bleeding tendency. J Immunol2009; 183: 1797–1803.
27. D.LuoS.G.VasudevanJ.Lescar. The flavivirus NS2B–NS3 protease–helicase as a target for antiviral drug development. Antiviral Res2015; 118: 148–158.
28. R.AssenbergE.MastrangeloT.S.Walter. Crystal structure of a novel conformational state of the flavivirus NS3 protein: implications for polyprotein processing and viral replication. J Virol2009; 83: 12895–12906.
29. S.KhadkaA.D.VangeloffC.Zhang. A physical interaction network of dengue virus and human proteins. Mol Cell Proteomics2011; 10. M111. 012187.
30. J.ZmurkoJ.NeytsK.Dallmeier. chameleon and jack-in-the-box roles in viral replication and pathogenesis, and a molecular target for antiviral intervention. Rev Med Virol2015; 25: 205–223.
31. S.MillerS.SparacioR.Bartenschlager. Subcellular localization and membrane topology of the dengue virus type 2 non-structural protein 4B. J Biol Chem2006; 281: 8854–8863.
32. A.G.PletnevR.PutnakJ.Speicher. West Nile virus/dengue type 4 virus chimeras that are reduced in neurovirulence and peripheral virulence without loss of immunogenicity or protective efficacy. Proc Natl Acad Sci2002; 99: 3036–3041.
33. D.W.BeasleyM.MorinA.R.Lamb. Adaptation of yellow fever virus 17D to Vero cells is associated with mutations in structural and non-structural protein genes. Virus Res2013; 176: 280–284.
34. J.A.WickerM.C.WhitemanD.W.Beasley. A single amino acid substitution in the central portion of the West Nile virus NS4B protein confers a highly attenuated phenotype in mice. Virology2006; 349: 245–253.
35. G.ZouF.Puig-BasagoitiB.Zhang. A single-amino acid substitution in West Nile virus 2K peptide between NS4A and NS4B confers resistance to lycorine, a flavivirus inhibitor. Virology2009; 384: 242–252.
36. X.XieQ.-Y.WangH.Y.Xu. Inhibition of dengue virus by targeting viral NS4B protein. J Virol2011; 85: 11183–11195.
37. C.G.PatkarM.LarsenM.Owston. Identification of inhibitors of yellow fever virus replication using a replicon-based high-throughput assay. Antimicrob Agents Chemother2009; 53: 4103–4114.
38. K.W.van CleefG.J.OverheulM.C.Thomassen. Identification of a new dengue virus inhibitor that targets the viral NS4B protein and restricts genomic RNA replication. Antiviral Res2013; 99: 165–171.
39. S.P.LimC.G.NobleP.-Y.Shi. The dengue virus NS5 protein as a target for drug discovery. Antiviral Res2015; 119: 57–67.
40. Y.ZhaoT.S.SohJ.Zheng. A crystal structure of the dengue virus NS5 protein reveals a novel inter-domain interface essential for protein flexibility and virus replication. PLoS Pathogens2015; 11: e1004682–e1004682.
41. S.P.LimL.S.SonntagC.Noble. Small molecule inhibitors that selectively block dengue virus methyltransferase. J Biol Chem2011; 286: 6233–6240.
42. K.Y.ChungH.DongA.T.Chao. Higher catalytic efficiency of N-7-methylation is responsible for processive N-7 and 2′-O methyltransferase activity in dengue virus. Virology2010; 402: 52–60.
43. M.BrecherH.ChenB.Liu. Novel broad spectrum inhibitors targeting the flavivirus methyltransferase. PLoS One2015; 10: e0130062.
44. H.MaletN.MasséB.Selisko. The flavivirus polymerase as a target for drug discovery. Antiviral Res2008; 80: 23–35.
45. T.C.ApplebyJ.K.PerryE.Murakami. Structural basis for RNA replication by the hepatitis C virus polymerase. Science2015; 347: 771–775.
46. J.YeB.ZhuZ.F.Fu. Immune evasion strategies of flaviviruses. Vaccine2013; 31: 461–471.