Baseline dasabuvir resistance in Hepatitis C virus from the genotypes 1, 2 and 3 and modeling of the NS5B-dasabuvir complex by the in silico approach

References

• Miller RH, Purcell RH. Hepatitis C virus shares amino acid sequence similarity with pestiviruses and flaviviruses as well as members of two plant virus supergroups. Proc Natl Acad Sci U S A. 1990;87:1–10.
   Web of Science ®Google Scholar
• Gower E, Estes C, Blach S, et al. Global epidemiology and genotype distribution of the hepatitis C virus infection. J Hepatol. 2014;61:S45–S57.
   PubMed Web of Science ®Google Scholar
• Nakano T, Lau GMG, Lau GML, et al. An updated analysis of hepatitis C virus genotypes and subtypes based on the complete coding region. Liver Int. 2012;32:339–345.
   PubMed Web of Science ®Google Scholar
• Alberti A, Lacoin L, Morais E, et al. Literature review of the distribution of hepatitis C virus genotypes across Europe. J Med Virol. 2016;88:2157–2169.
   PubMed Web of Science ®Google Scholar
• Palanisamy N, Danielsson A, Kokkula C, et al. Implications of baseline polymorphisms for potential resistance to NS3 protease inhibitors in Hepatitis C virus genotypes 1a, 2b and 3a. Antiviral Res. 2013;99:12–17.
   PubMed Web of Science ®Google Scholar
• Hoffmann-La Roch. Antiviral drugs advisory committee Briefing document for Pegasys® in combination with CopegusTM. 2002 Nov 14 [cited 2018 Apr 18]. Available from: https://www.fda.gov/ohrms/dockets/ac/02/briefing/3909B1_01_Hoffman-LaRoche.pdf
   Google Scholar
• Sarrazin C. The importance of resistance to direct antiviral drugs in HCV infection in clinical practice. J Hepatol. 2016;64:486–504.
   PubMed Web of Science ®Google Scholar
• Sofia MJ, Chang W, Furman PA, et al. Nucleoside, nucleotide, and non-nucleoside inhibitors of hepatitis C virus NS5B RNA-dependent RNA-polymerase. J Med Chem. 2012;55:2481–2531.
   PubMed Web of Science ®Google Scholar
• Ferenci P, Bernstein D, Lalezari J, et al. ABT-450/r–ombitasvir and dasabuvir with or without ribavirin for HCV. New England J Med. 2014;370:1983–1992.
   PubMed Web of Science ®Google Scholar
• Gane EJ, Stedman CA, Hyland RH, et al. Nucleotide polymerase inhibitor sofosbuvir plus ribavirin for hepatitis C. New England J Med. 2013;368:34–44.
   PubMed Web of Science ®Google Scholar
• European medicines agency. European public assessment report. Exviera: ANNEX I, SUMMARY OF PRODUCT CHARACTERISTICS [Internet]. 2018 May [cited 2018 Aug 17]. Available from: http://www.ema.europa.eu/docs/en_GB/document_library/EPAR_-_Product_Information/human/003837/WC500182233.pdf.
   Google Scholar
• European medicines agency. European public assessment report. Viekirax: ANNEX I, SUMMARY OF PRODUCT CHARACTERISTICS [Internet]. 2018 Jul [cited 2018 Aug 17]. Available from: http://www.ema.europa.eu/docs/en_GB/document_library/EPAR_-_Product_Information/human/003839/WC500183997.pdf.
   Google Scholar
• Mantry PS, Dasabuvir PL. (ABT333) for the treatment of chronic HCV genotype I: a new face of cure, an expert review. Expert Rev Anti Infect Ther. 2016;14:157–165.
   PubMed Web of Science ®Google Scholar
• Ogata N, Alter HJ, Miller RH, et al. Nucleotide sequence and mutation rate of the H strain of hepatitis C virus. Proc Natl Acad Sci U S A. 1991;88:3392–3396.
   PubMed Web of Science ®Google Scholar
• Fridell RA, Wang C, Sun J-H, et al. Genotypic and phenotypic analysis of variants resistant to hepatitis C virus nonstructural protein 5A replication complex inhibitor BMS-790052 in humans: in vitro and in vivo correlations. Hepatology. 2011;54:1924–1935.
   PubMed Web of Science ®Google Scholar
• McCown MF, Rajyaguru S, Le Pogam S, et al. The hepatitis C virus replicon presents a higher barrier to resistance to nucleoside analogs than to nonnucleoside polymerase or protease inhibitors. Antimicrob Agents Chemother. 2008;52:1604–1612.
   PubMed Web of Science ®Google Scholar
• Wyles DL. Antiviral resistance and the future landscape of hepatitis C virus infection therapy. J Infect Dis. 2013;207:S33–S39.
   PubMed Web of Science ®Google Scholar
• Götte M. The distinct contributions of fitness and genetic barrier to the development of antiviral drug resistance. Curr Opin Virol. 2012;2:644–650.
   Web of Science ®Google Scholar
• Powdrill MH, Tchesnokov EP, Kozak RA, et al. Contribution of a mutational bias in hepatitis C virus replication to the genetic barrier in the development of drug resistance. Proc Natl Acad Sci U S A. 2011;108:20509–20513.
   PubMed Web of Science ®Google Scholar
• Kati W, Koev G, Irvin M, et al. In vitro activity and resistance profile of dasabuvir, a nonnucleoside hepatitis C virus polymerase inhibitor. Antimicrob Agents Chemother. 2015;59:1505–1511.
   PubMed Web of Science ®Google Scholar
• Feld JJ, Kowdley KV, Coakley E, et al. Treatment of HCV with ABT-450/r–ombitasvir and dasabuvir with ribavirin. New England J Med. 2014;370:1594–1603.
   PubMed Web of Science ®Google Scholar
• Poordad F, Hezode C, Trinh R, et al. ABT-450/r–ombitasvir and dasabuvir with ribavirin for hepatitis C with cirrhosis. New England J Med. 2014;370:1973–1982.
   PubMed Web of Science ®Google Scholar
• Zeuzem S, Jacobson IM, Baykal T, et al. Retreatment of HCV with ABT-450/r–ombitasvir and dasabuvir with ribavirin. New England J Med. 2014;370:1604–1614.
   PubMed Web of Science ®Google Scholar
• Lontok E, Harrington P, Howe A, et al. Hepatitis C virus drug resistance-associated substitutions: state of the art summary. Hepatology. 2015;62:1623–1632.
   PubMed Web of Science ®Google Scholar
• Schoenfeld RC, Bourdet DL, Brameld KA, et al. Discovery of a novel series of potent non-nucleoside inhibitors of hepatitis C virus NS5B. J Med Chem. 2013;56:8163–8182.
   PubMed Web of Science ®Google Scholar
• 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;31:455–461.
   PubMed Web of Science ®Google Scholar
• Yang J-M, Chen -C-C. GEMDOCK: a generic evolutionary method for molecular docking. Proteins. 2004;55:288–304.
   PubMed Web of Science ®Google Scholar
• Hess B, Kutzner C, van der Spoel D, et al. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008;4:435–447.
   PubMed Web of Science ®Google Scholar
• Lindorff-Larsen K, Piana S, Palmo K, et al. Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins. 2010;78:1950–1958.
   PubMed Web of Science ®Google Scholar
• Wang J, Wolf RM, Caldwell JW, et al. Development and testing of a general amber force field. J Comput Chem. 2004;25:1157–1174.
   PubMed Web of Science ®Google Scholar
• Wang J, Wang W, Kollman PA, et al. Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model. 2006;25:247–260.
   PubMed Web of Science ®Google Scholar
• Sousa da Silva AW, Vranken WF. ACPYPE - AnteChamber PYthon parser interfacE. BMC Res Notes. 2012;5:367.
   PubMedGoogle Scholar
• Bussi G, Donadio D, Parrinello M. Canonical sampling through velocity rescaling. J Chem Phys. 2007;126:014101.
   PubMed Web of Science ®Google Scholar
• Parrinello M, Rahman A. Polymorphic transitions in single crystals: a new molecular dynamics method. J Appl Phys. 1981;52:7182–7190.
   Web of Science ®Google Scholar
• Hess B. P-LINCS: a parallel linear constraint solver for molecular simulation. J Chem Theory Comput. 2008;4:116–122.
   PubMed Web of Science ®Google Scholar
• Verlet L. Computer “Experiments” on classical fluids. I. Thermodynamical properties of lennard-jones molecules. Phys Rev. 1967;159:98–103.
   Web of Science ®Google Scholar
• Darden T, York D, Pedersen L. Particle mesh Ewald: an N⋅log(N) method for Ewald sums in large systems. J Chem Phys. 1993;98:10089–10092.
   Web of Science ®Google Scholar
• Essmann U, Perera L, Berkowitz ML, et al. A smooth particle mesh Ewald method. J Chem Phys. 1995;103:8577–8593.
   Web of Science ®Google Scholar
• Liu Y, Lim BH, Jiang WW, et al. Identification of aryl dihydrouracil derivatives as palm initiation site inhibitors of HCV NS5B polymerase. Bioorg Med Chem Lett. 2012;22:3747–3750.
   PubMed Web of Science ®Google Scholar
• Deval J, D’Abramo CM, Zhao Z, et al. High resolution footprinting of the hepatitis C virus polymerase NS5B in complex with RNA. J Biol Chem. 2007;282:16907–16916.
   Web of Science ®Google Scholar
• Powers JP, Piper DE, Li Y, et al. SAR and mode of action of novel non-nucleoside inhibitors of hepatitis C NS5b RNA polymerase. J Med Chem. 2006;49:1034–1046.
   PubMed Web of Science ®Google Scholar
• Di Maio VC, Cento V, Mirabelli C, et al. Hepatitis C virus genetic variability and the presence of NS5B resistance-associated mutations as natural polymorphisms in selected genotypes could affect the response to NS5B inhibitors. Antimicrob Agents Chemother. 2014;58:2781–2797.
   PubMed Web of Science ®Google Scholar
• Ishii K, Tanaka Y, Yap CC, et al. Expression of hepatitis C virus NS5B protein: characterization of its RNA polymerase activity and RNA binding. Hepatology. 1999;29:1227–1235.
   PubMed Web of Science ®Google Scholar
• Bartlett SR, Grebely J, Eltahla AA, et al. Sequencing of hepatitis C virus for detection of resistance to direct-acting antiviral therapy: a systematic review. Hepatol Commun. 2017;1:379–390.
   PubMed Web of Science ®Google Scholar
• Patiño-Galindo JÁ, Salvatierra K, González-Candelas F, et al. Comprehensive screening for naturally occurring hepatitis C virus resistance to direct-acting antivirals in the NS3, NS5A, and NS5B genes in worldwide isolates of viral genotypes 1 to 6. Antimicrob Agents Chemother. 2016;60:2402–2416.
   PubMed Web of Science ®Google Scholar
• Palanisamy N, Kalaghatgi P, Akaberi D, et al. (2018) Worldwide prevalence of baseline resistance-associated polymorphisms and resistance mutations in HCV against current direct-acting antivirals. Antivir Ther. Advance online publication. Doi:10.3851/IMP3237.
   Web of Science ®Google Scholar
• Boyce SE, Tirunagari N, Niedziela-Majka A, et al. Structural and regulatory elements of HCV NS5B polymerase–β-loop and C-terminal tail–are required for activity of allosteric thumb site II inhibitors. PLoS ONE. 2014;9:e84808.
   Web of Science ®Google Scholar
• Feld JJ, Moreno C, Trinh R, et al. Sustained virologic response of 100% in HCV genotype 1b patients with cirrhosis receiving ombitasvir/paritaprevir/r and dasabuvir for 12weeks. J Hepatol. 2016;64:301–307.
   PubMed Web of Science ®Google Scholar
• Welzel TM, Asselah T, Dumas EO, et al. Ombitasvir, paritaprevir, and ritonavir plus dasabuvir for 8 weeks in previously untreated patients with hepatitis C virus genotype 1b infection without cirrhosis (GARNET): a single-arm, open-label, phase 3b trial. Lancet Gastroenterol Hepatol. 2017;2:494–500.
   PubMed Web of Science ®Google Scholar
• Wedemeyer H, Craxí A, Zuckerman E, et al. Real-world effectiveness of ombitasvir/paritaprevir/ritonavir±dasabuvir±ribavirin in patients with hepatitis C virus genotype 1 or 4 infection: a meta-analysis. J Viral Hepat. 2017;24:936–943.
   PubMed Web of Science ®Google Scholar