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Research Articles

The effect of genotype variation and M423 resistance mutations to the binding of phosphonomidate-based inhibitor IDX17119 with the thumb-II domain of Hepatitis C virus RdRp: an integrated molecular dynamics and binding free energy study

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Pages 164-174 | Received 18 Mar 2021, Accepted 03 Oct 2022, Published online: 27 Oct 2022

References

  • Bressanelli S, Tomei L, Roussel A, et al. Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus. Proc Natl Acad Sci USA. 1999;96:13034–13039. doi:10.1073/pnas.96.23.13034.
  • Chevaliez S, Pawlotsky PJ-M. HCV genome and life cycle. In: Tan SL, editor. Hepatitis C viruses: genomes and molecular biology. Norfolk: Horizon Biosciences; 2006. p. 5–47.
  • Huang Z, Murray MG, Secrist JA. Recent development of therapeutics for chronic HCV infection. Antiviral Res. 2006;71:351–362. doi:10.1016/j.antiviral.2006.06.001.
  • Koch U, Narjes F. Recent progress in the development of inhibitors of the hepatitis C virus RNA-dependent RNA polymerase. Curr Top Med Chem. 2007;7:1302–1329. doi:10.2174/156802607781212211.
  • 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. doi:10.1016/j.jhep.2014.07.027.
  • De Francesco R, Migliaccio G. Challenges and successes in developing new therapies for hepatitis C. Nature. 2005;436:953–960. doi:10.1038/nature04080.
  • Penin F, Dubuisson J, Rey FA, et al. Structural biology of hepatitis C virus. Hepatology. 2004;39:5–19. doi:10.1002/hep.20032.
  • Pierra Rouvière C, Amador A, Badaroux E, et al. Synthesis of potent and broad genotypically active NS5B HCV non-nucleoside inhibitors binding to the thumb domain allosteric site 2 of the viral polymerase. Bioorg Med Chem Lett. 2016;26:4536–4541. doi:10.1016/j.bmcl.2016.01.042.
  • Philip JFT, Marilyn L, Paul S, et al. Characterization of resistance to the nonnucleoside NS5B inhibitor filibuvir in hepatitis C virus-infected patients. Antimicrob Agents Chemother. 2012;56(3):1331–1341. doi:10.1128/AAC.05611-11.
  • Thomas K, Joerg T, Andrew B, et al. Naturally occurring dominant resistance mutations to hepatitis C virus protease and polymerase inhibitors in treatment-naïve patients. Hepatology. 2008;48(6):1769–1778. doi:10.1002/hep.22549.
  • Pingzu J, Weiwei X, Yulin S, et al. Understanding the drug resistance mechanism of hepatitis C virus NS5B to PF-00868554 due to mutations of the 423 site: a computational study. Mol Biosyst. 2014;10(4):767–777. doi:10.1039/c3mb70498j.
  • Frisch MJ, Trucks GW, Schlegel HB, et al. (2005). Gaussian 03, revision D.1.
  • Labanowski JK, Andzelm JW. Density functional methods in chemistry. New York (NY): Springer; 1991. doi:10.1007/978-1-4612-3136-3.
  • Parr RG, Yang W. Density functional theory of atoms and molecules. London: Oxford University Press; 1995.
  • Helen MB, John W, Zukang F, et al. The protein data bank. Nucleic Acids Res. 2000;28(1):235–242. doi:10.1093/nar/28.1.235.
  • Eswar N, Webb B, Marti-Renom MA, et al. Comparative protein structure modeling using modeller. Curr Protoc Bioinforma. 2006;15:5.6.1–5.6.30. doi:10.1002/0471250953.bi0506s15.
  • Delano WL. PyMol molecular graphics system; 2002.
  • 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. 2009. doi:10.1002/jcc.21334.
  • Pettersen EF, Goddard TD, Huang CC, et al. UCSF chimera? A visualization system for exploratory research and analysis. J Comput Chem. 2004;25:1605–1612. doi:10.1002/jcc.20084.
  • Case DA, Babin V, Berryman JT, et al. AMBER 14; n.d.
  • Harrach MF, Drossel B. Structure and dynamics of TIP3P, TIP4P, and TIP5P water near smooth and atomistic walls of different hydroaffinity. J Chem Phys. 2014;140:174501, doi:10.1063/1.4872239.
  • Yamamoto T, Miller WH. On the efficient path integral evaluation of thermal rate constants within the quantum instanton approximation. J Chem Phys. 2004;120:3086–3099. doi:10.1063/1.1641005.
  • Berendsen HJC, Postma JPM, van Gunsteren WF, et al. Molecular dynamics with coupling to an external bath. J Chem Phys. 1984;81:3684–3690. doi:10.1063/1.448118.
  • Essmann U, Perera L, Berkowitz ML, et al. A smooth particle mesh Ewald method. J Chem Phys. 1995;103:8577–8593. doi:10.1063/1.470117.
  • Ryckaert J-P, Ciccotti G, Berendsen HJ. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys. 1977;23:327–341. doi:10.1016/0021-9991(77)90098-5.
  • Roe DR, Cheatham TE. PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput. 2013;9:3084–3095. doi:10.1021/ct400341p.
  • Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph. 1996;14:33–38. doi:10.1016/0263-7855(96)00018-5.
  • Kollman PA, Massova I, Reyes C, et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res. 2000;33:889–897. doi:10.1021/ar000033j.
  • Charles CD, Donald JJ. Principal component analysis: a method for determining the essential dynamics of proteins. Methods Mol Biol. 2014;1084:193–226. doi:10.1007/978-1-62703-658-0_11.
  • Ndumiso NM, Mahasin E, Adam AS, et al. Dynamics of the thumb-finger regions in a GH11 xylanase bacillus circulans: comparison between the Michaelis and covalent intermediate. RSC Adv. 2015;5:82381–82394. doi:10.1039/C5RA16836H.
  • Ashona S, Mahmoud ES. Understanding the cross-resistance of oseltamivir to H1N1 and H5N1 influenza A neuraminidase mutations using multidimensional computational analyses. Drug Design, Develop Therapy. 2015;9:4137–4154. doi:10.2147/DDDT.S81934.
  • Imlimaong A, Pritish KV, Utkarsh R. Structural insights into conformational stability of both wild-type and mutant EZH2 receptor. 2016. Sci Rep. 2016; 6:34984. doi:10.1038/srep34984.

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