A holistic evolutionary and structural study of flaviviridae provides insights into the function and inhibition of HCV helicase

PeerJ

Volumn 2013, Issue 1, 2013, Pages

  Vlachakis, Dimitrios ^a   Koumandou, Vassiliki Lila ^a   Kossida, Sophia ^a  

^a BIOMEDICAL RESEARCH FOUNDATION   (Greece)

Author keywords

Antiviral bioinformatics; Hepatitis C; Molecular dynamics; Structure based drug design

Indexed keywords

NONSTRUCTURAL PROTEIN 3; RNA HELICASE;

AMINO ACID SEQUENCE; ARTICLE; ENZYME ACTIVITY; ENZYME CONFORMATION; FLAVIVIRUS; GENOTYPE; HEPATITIS C VIRUS; IC 50; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MOLECULAR MODEL; NONHUMAN; PHYLOGENETIC TREE; PHYLOGENY; PREDICTION; SEQUENCE ALIGNMENT; SIMULATION;

EID: 84881495337     PISSN: None     EISSN: 21678359     Source Type: Journal    
DOI: 10.7717/peerj.74     Document Type: Article

References (41)

1. Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105.
2. Brancale A, Vlachaki C, Vlachakis D. 2008. Molecular modelling study of the 3D structure of the bovine viral diarrhea virus (BVDV) helicase. In Silico Biology 8(5-6):461-469.
3. Calisher CH, Gould EA. 2003. Taxonomy of the virus family Flaviviridae. Advances in Virus Research 59:1-19.
4. Chen R, Li L,Weng Z. 2003. ZDOCK: an initial-stage protein-docking algorithm. Proteins 52:80-87.
5. Cook S, Holmes EC. 2006. A multigene analysis of the phylogenetic relationships among the flaviviruses (Family: Flaviviridae) and the evolution of vector transmission. Archives of Virology 151:309-325.
6. Cook S,Moureau G, Kitchen A, Gould EA, de Lamballerie X, Holmes EC, Harbach RE. 2012. Molecular evolution of the insect-specific flaviviruses. Journal of General Virology 93:223-234.
7. Daly M,Ward F. 2003. Liver disease. In: Walker R, Edwards C, eds. Clinical pharmacy and therapeutics. 3rd ed. Churchill Livingstone, 209-228.
8. Diana G, Bailey T. 1997. Compounds, compositions and methods for treatment of hepatitis C. United States Patent No. 5,633,388.
9. Degos F. 1994. Epidemiology of hepatitis C virus in Europe. FEMS Microbiology Reviews 14(3):267-271.
10. DeLano WL. 2002. The PyMOL user's manual San Carlos. CA, USA: DeLano Scientific.
11. Duan Y,Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J,Wang J, Kollman P. 2003. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Journal of Computational Chemistry 24:1999-2012.
12. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792-1797.
13. Eisenberg D, Luthy R, Bowie JU. 1997. VERIFY3D: assessment of protein models with threedimensional profiles. Methods in Enzymology 277:396-404.
14. Ferron F, Bussetta C, Dutartre H, Canard B. 2005. The modeled structure of the RNA dependent RNA polymerase of GBV-C virus suggests a role for motif E in Flaviviridae RNA polymerases. BMC Bioinformatics 6:255.
15. Guex N, Peitsch MC. 1997. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18:2714-2723.
16. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52:696-704.
17. Guzmán MG, Kourí G. 2004. Dengue diagnosis, advances and challenges. International Journal of Infectious Diseases 8(2):69-80.
18. Hess B, Kutzner C, van der Spoel D, Lindahl E. 2008. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation 4:435-447.
19. Kadare G, Haenni AL. 1997. Virus-encoded RNA helicases. Journal of Virology 71:2583-2590.
20. Kandil S, Biondaro S, Vlachakis D, Cummins AC, Coluccia A, Berry C, Leyssen P, Neyts J, Brancale A. 2009. Discovery of a novel HCV helicase inhibitor by a de novo drug design approach. Bioorganic & Medicinal Chemistry Letters 19(11):2935-2937.
21. Kim JL,Morgenstern KA, Griffith JP, Dwyer MD, Thomson JA,Murcko MA, Lin C, Caron PR. 1998. Hepatitis C virus NS3 RNA helicase domain with a bound oligonucleotide: the crystal structure provides insights into the mode of unwinding. Structure 6(1):89-100.
22. Laskowski RA, Rullmann JA,MacArthur MW, Kaptein R, Thornton JM. 1996. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. Journal of Biomolecular NMR 8:477-486.
23. Li L, Chen R,Weng Z. 2003. RDOCK: refinement of rigid-body protein docking predictions. Proteins 53:693-707.
24. Lobo FP,Mota BE, Pena SD, Azevedo V,Macedo AM, Tauch A,Machado CR, Franco GR. 2009. Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts. PLoS ONE 4:e6282.
25. Maddison WP,Maddison DR. 1989. Interactive analysis of phylogeny and character evolution using the computer program MacClade. Folia Primatol (Basel) 53:190-202.
26. Neyts J, Leyssen P, De Clercq E. 1999. Infections with flaviviridae. Verhandelingen - Koninklijke Academie Voor Geneeskunde Van Belgie 61(6):661-697. discussion 697-9.
27. Nulf CJ, Corey D. 2004. Intracellular inhibition of hepatitis C virus (HCV)internal ribosomal entry site (IRES)-dependent translation by peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). Nucleic Acids Research 32(13):3792-3798.
28. Pasta L,Marrone C, D'amico M, Bevacqua EA, D'Amico G, Pagliaro L. 2005. Familial clustering of HCV-related liver cirrhosis and hepatocellular carcinoma. Digestive and Liver Disease 37(9):716-717.
29. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM,Meng EC, Ferrin TE. 2004. UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry 25:1605-1612.
30. Pickett BE, Sadat EL, Zhang Y, Noronha JM, Squires RB, Hunt V, Liu M, Kumar S, Zaremba S, Gu Z, Zhou L, Larson CN, Dietrich J, KlemEB, Scheuermann RH. 2012. ViPR: an open bioinformatics database and analysis resource for virology research. Nucleic Acids Research 40:D593-D598.
31. Phoon C, Ng P, Ting A, Yeo S, Sim M. 2001. Biological evaluation of hepatitis C virus helicase inhibitors. Bioorganic & Medicinal Chemistry Letters 11:1647-1650.
32. Poynard T, Bedossa P, Opolon P. 1997. Natural history of liver fibrosis progression in patients with chronic hepatitis C. Lancet 349:825-832.
33. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
34. Rosenberg S. 2001. Recent advances in the molecular biology of hepatitis C virus. Journal of Molecular Biology 313:451-464.
35. Shepard CW, Finelli L, Alter MJ. 2005. Global epidemiology of hepatitis C virus infection. The Lancet Infectious Diseases 5(9):558-567.
36. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
37. Sellis D, Vlachakis D, Vlassi M. 2009. Gromita: a fully integrated graphical user interface to gromacs 4. Bioinformatics and Biology Insights 3:99-102.
38. Thompson B, Finch R. 2005. Hepatitis C virus infection. Clinical Microbiology and Infection 11(2):86-94.
39. Vlachakis D. 2009. Theoretical study of the Usutu virus helicase 3D structure, by means of computer-aided homology modelling. Theoretical Biology and Medical Modelling 25(6):9.
40. Vlachakis D, Brancale A. 2007. The 3D structure of the Japanese Encephalitis helicase, using homology based molecular modelling techniques. Online Journal of Bioinformatics 8(2):154-164.
41. Waterhouse AM, Procter JB,Martin DM, Clamp M, Barton GJ. 2009. Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25:1189-1191