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Looking for inhibitors of the dengue virus NS5 RNA-dependent RNA-polymerase using a molecular docking approach. Galiano-Ibarra, V., Garcia-Valtanen, P., Micol, V., Encinar, J.A. Drug Design, Development and Therapy 2016, 10: 3163-3181.

  1. Weissenbock H, Hubalek Z, Bakonyi T, Nowotny N. Zoonotic mosquito-borne flaviviruses: worldwide presence of agents with proven pathogenicity and potential candidates of future emerging diseases. Vet Microbiol. 2010;140(3-4):271-280.
  2. Papageorgiou L, Loukatou S, Sofia K, Maroulis D, Vlachakis D. An updated evolutionary study of Flaviviridae NS3 helicase and NS5 RNA-dependent RNA polymerase reveals novel invariable motifs as potential pharmacological targets. Mol Biosyst. 2016;2(7):2080-2093.
  3. International Committee on Taxonomy of Viruses, King AMQ. Virus Taxonomy: Classification and Nomenclature of Viruses Ninth Report of the International Committee on Taxonomy of Viruses. London: Academic Press; 2012.
  4. Brady OJ, Gething PW, Bhatt S, et al. Refining the global spatial limits of dengue virus transmission by evidence-based consensus. PLoS Negl Trop Dis. 2012;6(8):e1760.
  5. Shepard DS, Undurraga EA, Halasa YA, Stanaway JD. The global economic burden of dengue: a systematic analysis. Lancet Infect Dis. 2016;16(8):935-941.
  6. Alagarasu K. Introducing dengue vaccine: implications for diagnosis in dengue vaccinated subjects. Vaccine. 2016;34(25):2759-2761.
  7. Mackenzie J. Wrapping things up about virus RNA replication. Traffic. 2005;6(11):967-977.
  8. Paul D, Bartenschlager R. Flaviviridae replication organelles: oh, what a tangled web we weave. Annu Rev Virol. 2015;2(1):289-310.
  9. Issur M, Geiss BJ, Bougie I, et al. The flavivirus NS5 protein is a true RNA guanylyltransferase that catalyzes a two-step reaction to form the RNA cap structure. RNA. 2009;15(12):2340-2350.
  10. Decroly E, Ferron F, Lescar J, Canard B. Conventional and unconventional mechanisms for capping viral mRNA. Nat Rev Microbiol. 2012;10(1):51-65.
  11. Zhao Y, Soh TS, Zheng J, et al. A crystal structure of the Dengue virus NS5 protein reveals a novel inter-domain interface essential for protein flexibility and virus replication. PLoS Pathog. 2015;11(3):e1004682.
  12. Yap TL, Xu T, Chen YL, et al. Crystal structure of the dengue virus RNA-dependent RNA polymerase catalytic domain at 1.85-angstrom resolution. J Virol. 2007;81(9):4753-4765.
  13. Bartholomeusz A, Thompson P. Flaviviridae polymerase and RNA replication. J Viral Hepat. 1999;6(4):261-270.
  14. You S, Falgout B, Markoff L, Padmanabhan R. In vitro RNA synthesis from exogenous dengue viral RNA templates requires long range interactions between 5'- and 3'-terminal regions that influence RNA structure. J Biol Chem. 2001;276(19):15581-15591.
  15. Malet H, Masse N, Selisko B, et al. The flavivirus polymerase as a target for drug discovery. Antiviral Res. 2008;80(1):23-35.
  16. De Clercq E, Neyts J. Antiviral agents acting as DNA or RNA chain terminators. Handb Exp Pharmacol. 2009(189):53-84.
  17. De Francesco R, Tomei L, Altamura S, Summa V, Migliaccio G. Approaching a new era for hepatitis C virus therapy: inhibitors of the NS3-4A serine protease and the NS5B RNA-dependent RNA polymerase. Antiviral Res. 2003;58(1):1-16.
  18. Yin Z, Chen YL, Schul W, et al. An adenosine nucleoside inhibitor of dengue virus. Proc Natl Acad Sci U S A. 2009;106(48):20435-20439.
  19. Kohler JJ, Lewis W. A brief overview of mechanisms of mitochondrial toxicity from NRTIs. Environ Mol Mutagen. 2007;48(3-4):166-172.
  20. Behnam MA, Nitsche C, Boldescu V, Klein CD. The medicinal chemistry of dengue virus. J Med Chem. 2016;59(12):5622-5649.
  21. Niyomrattanakit P, Chen YL, Dong H, Yin Z, Qing M, Glickman JF, Lin K, Mueller D, Voshol H, Lim JY, Nilar S, Keller TH, Shi PY. Inhibition of dengue virus polymerase by blocking of the RNA tunnel. J Virol. 2010;84(11): 5678-5686.
  22. Wang Y, Xiao J, Suzek TO, Zhang J, Wang J, Bryant SH. PubChem: a public information system for analyzing bioactivities of small molecules. Nucleic Acids Res. 2009;37(Web Server issue):W623-W633.
  23. Banerjee P, Erehman J, Gohlke BO, Wilhelm T, Preissner R, Dunkel M. Super Natural II - a database of natural products. Nucleic Acids Res. 2015; 43(Database issue):D935-D939.
  24. Zhao Y, Soh TS, Lim SP, et al. Molecular basis for specific viral RNA recognition and 2'-O-ribose methylation by the dengue virus nonstructural protein 5 (NS5). Proc Natl Acad Sci U S A. 2015;112(48): 14834-14839.
  25. Noble CG, Lim SP, Chen YL, et al. Conformational flexibility of the Dengue virus RNA-dependent RNA polymerase revealed by a complex with an inhibitor. J Virol. 2013;87(9):5291-5295.
  26. Lim SP, Koh JH, Seh CC, et al. A crystal structure of the dengue virus non-structural protein 5 (NS5) polymerase delineates interdomain amino acid residues that enhance its thermostability and de novo initiation activities. J Biol Chem. 2013;288(43):31105-31114.
  27. Biasini M, Bienert S, Waterhouse A, et al. SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 2014;42(Web Server issue):W252-W258.
  28. Encinar JA, Fernandez-Ballester G, Galiano-Ibarra V, Micol V. In silico approach for the discovery of new PPARgamma modulators among plant-derived polyphenols. Drug Des Devel Ther. 2015;9: 5877-5895.
  29. Morris GM, Huey R, Lindstrom W, et al. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem. 2009;30(16):2785-2791.
  30. Schymkowitz J, Borg J, Stricher F, Nys R, Rousseau F, Serrano L. The FoldX web server: an online force field. Nucleic Acids Res. 2005; 33(Web Server issue):W382-W388.
  31. Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem. 2010;31(2):455-461.
  32. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev. 2001; 46(1-3):3-26.
  33. Sander T, Freyss J, von Korff M, Rufener C. DataWarrior: an opensource program for chemistry aware data visualization and analysis. J Chem Inf Model. 2015;55(2):460-473.
  34. Cheng F, Li W, Zhou Y, et al. admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. J Chem Inf Model. 2012;52(11):3099-3105.
  35. Meng XY, Zhang HX, Mezei M, Cui M. Molecular docking: a powerful approach for structure-based drug discovery. Curr Comput Aided Drug Des. 2011;7(2):146-157.
  36. Jaghoori MM, Bleijlevens B, Olabarriaga SD. 1001 Ways to run AutoDock Vina for virtual screening. J Comput Aided Mol Des. 2016; 30(3):237-249.
  37. Moroy G, Martiny VY, Vayer P, Villoutreix BO, Miteva MA. Toward in silico structure-based ADMET prediction in drug discovery. Drug Discov Today. 2012;17(1-2):44-55.
  38. Merlot C. Computational toxicology - a tool for early safety evaluation. Drug Discov Today. 2010;15(1-2):16-22.
  39. Zhao YH, Abraham MH, Le J, et al. Rate-limited steps of human oral absorption and QSAR studies. Pharm Res. 2002;19(10):1446-1457.
  40. Anzenbacher P, Anzenbacherova E. Cytochromes P450 and metabolism of xenobiotics. Cell Mol Life Sci. 2001;58(5-6):737-747.
  41. Roche O, Trube G, Zuegge J, Pflimlin P, Alanine A, Schneider G. A virtual screening method for prediction of the HERG potassium channel liability of compound libraries. Chembiochem. 2002;3(5): 455-459.
  42. Daniele Mantione, Olatz Olaizola Aizpuru, Misal Giuseppe Memeo, Bruna Bovio, Paolo Quadrelli. 4-Heterosubstituted Cyclopentenone Antiviral Compounds: Synthesis, Mechanism, and Antiviral Evaluation. Eur. J. Org. Chem. 2016, 983–991.
  43. Powers CN, Setzer WN. An In-Silico Investigation of Phytochemicals as Antiviral Agents Against Dengue Fever. Comb Chem High Throughput Screen. 2016;19(7):516-36.
  44. Smee DF, Hurst BL, Evans WJ, Clyde N, Wright S, Peterson C, Jung KH, Day CW. Evaluation of Cell Viability Dyes in Antiviral Assays with RNA Viruses that Exhibit Different Cytopathogenic Properties. J Virol Methods. 2017. S0166-0934(17)30035-6.
  45. Oliveira AF, Teixeira RR, Oliveira AS, Souza AP, Silva ML, Paula SO. Potential Antivirals: Natural Products Targeting Replication Enzymes of Dengue and Chikungunya Viruses. Molecules. 2017; 22(3).