Molecular dynamics and docking reveal the potency of novel GTP derivatives against RNA dependent RNA polymerase of genotype 4a HCV

Life Sciences

Volumn 238, Issue , 2019, Pages

  Elfiky, Abdo A ^a   Ismail, Alaa ^a  

^a CAIRO UNIVERSITY   (Egypt)

Author keywords

HCV genotype 4a; Molecular dynamics simulation; Molecular modeling; Nucleotide inhibitors; Polymerase; Protein ligand docking

Indexed keywords

(2 HYDROXYPHENYL)OXIDANYL; (2,6 DIHYDROXYPHENYL)OXIDANYL; (3 FLUOROPHENYL)OXIDANYL; (3 HYDROXYPHENYL)OXIDANYL; (3 SULFANYLPHENYL)OXIDANYL; (3,5 DIHYDROXYPHENYL)OXIDANYL; (3,5 DISULFANYLPHENYL)OXIDANYL; (4 FLUOROPHENYL)OXIDANYL; ANTIVIRUS AGENT; GUANOSINE TRIPHOSPHATE; GUANOSINE TRIPHOSPHATE DERIVATIVE; IDX 184; MERICITABINE; NONSTRUCTURAL PROTEIN 5B; RIBAVIRIN; RNA POLYMERASE; SOFOSBUVIR; UNCLASSIFIED DRUG; NS-5 PROTEIN, HEPATITIS C VIRUS; VIRAL PROTEIN;

ARTICLE; BINDING ENERGY; CHEMICAL MODIFICATION; CONTROLLED STUDY; DRUG EFFICACY; DRUG POTENCY; DRUG PROTEIN BINDING; DRUG STRUCTURE; ENERGY; HEPATITIS C VIRUS GENOTYPE 4; HEPATITIS C VIRUS GENOTYPE 4A; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; CHEMISTRY; CLASSIFICATION; DRUG EFFECT; GENETICS; HEPACIVIRUS; HUMAN; METABOLISM; MOLECULAR MODEL; PROTEIN CONFORMATION;

ANTIVIRAL AGENTS; GUANOSINE TRIPHOSPHATE; HEPACIVIRUS; HUMANS; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; VIRAL NONSTRUCTURAL PROTEINS;

EID: 85073730795     PISSN: 00243205     EISSN: 18790631     Source Type: Journal    
DOI: 10.1016/j.lfs.2019.116958     Document Type: Article

References (34)

1. Choo QL, Kuo G, Weiner AJ, Overby LR, Bradley DW, Houghton M. Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome. Science (New York, NY). 1989;244:359-362.
2. 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 Research. 2003;58:1-16.
3. Elfiky AA, Elshemey WM, Gawad WA. 2′-Methylguanosine Prodrug (IDX-184), Phosphoramidate Prodrug (Sofosbuvir), Diisobutyryl Prodrug (R7128) Are Better Than Their Parent Nucleotides and Ribavirin in Hepatitis C Virus Inhibition: A Molecular Modeling Study. Journal of Computational and Theoretical Nanoscience. 2015;12:376-386.
4. Genovese D, Dettori S, Argentini C, Villano U, Chionne P, Angelico M, et al. Molecular epidemiology of hepatitis C virus genotype 4 isolates in Egypt and analysis of the variability of envelope proteins E1 and E2 in patients with chronic hepatitis. J Clin Microbiol. 2005;43:1902-1909.
5. Lemon SM, McKeating JA, Pietschmann T, Frick DN, Glenn JS, Tellinghuisen TL, et al. Development of novel therapies for hepatitis C. Antiviral Research. 2010;86:79-92.
6. Sarrazin C, Hezode C, Zeuzem S, Pawlotsky J-M. Antiviral strategies in hepatitis C virus infection. Journal of Hepatology. 2012;56:S88-S100.
7. Yang PL, Gao M, Lin K, Liu Q, Villareal VA. Anti-HCV drugs in the pipeline. Curr Opin Virol. 2011;1:607-616.
8. Bahgat MM, Ibrahim AA, Abd-Elshafy DN, Mesalam AA, Gewaid HE, Ismaeil AA, et al. Characterization of NS3 protease from an Egyptian HCV genotype 4a isolate. Arch Virol. 2009;154:1649-1657.
9. Elfiky AA, A. GW, M. EW. Hepatitis C Viral Polymerase Inhibition using Directly Acting Antivirals, A Computational Approach. In: A M, editor. Software and Techniques for Bio-Molecular Modeling. USA: Austin publishing group; 2016. p. 197.
10. Graham DJ, Stahlhut M, Flores O, Olsen DB, Hazuda DJ, LaFemina RL, et al. A genotype 2b NS5B polymerase with novel substitutions supports replication of a chimeric HCV 1b:2b replicon containing a genotype 1b NS3-5A background. Antiviral Research. 2006;69:24-30.
11. Asselah T. Daclatasvir plus sofosbuvir for HCV infection: an oral combination therapy with high antiviral efficacy. J Hepatol. 2014;61:435-438.
12. Gonzalez-Grande R, Jimenez-Perez M, Gonzalez Arjona C, Mostazo Torres J. New approaches in the treatment of hepatitis C. World J Gastroenterol. 2016;22:1421-1432.
13. Saleh NA, Ezat AA, Elfiky AA, Elshemey WM, Ibrahim M. Theoretical Study on Modified Boceprevir Compounds as NS3 Protease Inhibitors. Journal of Computational and Theoretical Nanoscience. 2015;12:371-375.
14. Yan S, Larson G, Wu JZ, Appleby T, Ding Y, Hamatake R, et al. Novel thiazolones as HCV NS5B polymerase allosteric inhibitors: Further designs, SAR, and X-ray complex structure. Bioorg Med Chem Lett. 2007;17:63-67.
15. Elfiky AA, Elshemey WM. IDX-184 is a superior HCV direct-acting antiviral drug: a QSAR study. Medicinal Chemistry Research. 2016a;25:1005-1008.
16. De Francesco R, Carfi A. Advances in the development of new therapeutic agents targeting the NS3-4A serine protease or the NS5B RNA-dependent RNA polymerase of the hepatitis C virus. Advanced Drug Delivery Reviews. 2007;59:1242-1262.
17. Elfiky AA. Zika viral polymerase inhibition using anti-HCV drugs both in market and under clinical trials. Journal of Medical Virology. 2016:n/a-n/a.
18. Yan S, Appleby T, Larson G, Wu JZ, Hamatake R, Hong Z, et al. Structure-based design of a novel thiazolone scaffold as HCV NS5B polymerase allosteric inhibitors. Bioorg Med Chem Lett. 2006;16:5888-5891.
19. Elfiky AA, Elshemey WM, Gawad WA, Desoky OS. Molecular modeling comparison of the performance of NS5b polymerase inhibitor (PSI-7977) on prevalent HCV genotypes. The protein journal. 2013;32:75-80.
20. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJE. The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protocols. 2015;10:845-858.
21. Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y. The I-TASSER Suite: protein structure and function prediction. Nat Methods. 2015;12:7-8.
22. Elshemey WM, Elfiky AA, Gawad WA. Correlation to protein conformation of Wide-angle X-ray Scatter parameters. Protein J. 2010;29:545-550.
23. Laskowski RA, MacArthur MW, Moss DS, Thornton JM. PROCHECK: a program to check the stereochemical quality of protein structures. Journal of Applied Crystallography. 1993;26:283-291.
24. Luthy R, Bowie JU, Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 1992;356:83-85.
25. Pontius J, Richelle J, Wodak SJ. Deviations from standard atomic volumes as a quality measure for protein crystal structures. J Mol Biol. 1996;264:121-136.
26. Zhang C, Liu S, Zhou H, Zhou Y. The dependence of all-atom statistical potentials on structural training database. Biophys. J.86:3349-3358.
27. Saleh NA, Elfiky AA, Ezat AA, Elshemey WM, Ibrahim M. The Electronic and Quantitative Structure Activity Relationship Properties of Modified Telaprevir Compounds as HCV NS3 Protease Inhibitors. Journal of Computational and Theoretical Nanoscience. 2014;11:544-548.
28. Summers KL, Mahrok AK, Dryden MD, Stillman MJ. Structural properties of metal-free apometallothioneins. Biochem Biophys Res Commun. 2012;425:485-492.
29. Lii JH, Allinger NL. Molecular mechanics. The MM3 force field for hydrocarbons. 3. The van der Waals' potentials and crystal data for aliphatic and aromatic hydrocarbons. Journal of the American Chemical Society. 1989;111:8576-8582.
30. Stewart JJP. Optimization of parameters for semiempirical methods. III Extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb, and Bi. Journal of Computational Chemistry. 1991;12:320-341.
31. Becke AD. Density-functional thermochemistry. III. The role of exact exchange. The Journal of Chemical Physics. 1993;98:5648-5652.
32. DeLano WL. PyMOL. 2002.
33. Release S. 1: Maestro. Schrodinger, LLC, New York, NY, USA. 2016.
34. Salentin S, Schreiber S, Haupt VJ, Adasme MF, Schroeder M. PLIP: fully automated protein-ligand interaction profiler. Nucleic Acids Res. 2015;43:W443-W447.