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Journal of Computer-Aided Molecular Design

, Volume 33, Issue 4, pp 387–404 | Cite as

AZT acts as an anti-influenza nucleotide triphosphate targeting the catalytic site of A/PR/8/34/H1N1 RNA dependent RNA polymerase

  • Nataraj Sekhar PagadalaEmail author
Article
  • 173 Downloads

Abstract

To develop potent drugs that inhibit the activity of influenza virus RNA dependent RNA polymerase (RdRp), a set of compounds favipiravir, T-705, T-1105 and T-1106, ribavirin, ribavirin triphosphate viramidine, 2FdGTP (2′-deoxy-2′-fluoroguanosine triphosphate) and AZT-TP (3′-Azido-3′-deoxy-thymidine-5′-triphosphate) were docked with a homology model of IAV RdRp from the A/PR/8/34/H1N1 strain. These compounds bind to four pockets A-D of the IAV RdRp with different mechanism of action. In addition, AZT-TP also binds to the PB1 catalytic site near to the tip of the priming loop with a highest ΔG of − 16.7 Kcal/mol exhibiting an IC50 of 1.12 µM in an in vitro enzyme transcription assay. This shows that AZT-TP mainly prevents the incorporation of incoming nucleotide involved in initiation of vRNA replication. Conversely, 2FdGTP used as a positive control binds to pocket-B at the end of tunnel-II with a highest ΔG of − 16.3 Kcal/mol inhibiting chain termination with a similar IC50 of 1.12 µM. Overall, our computational results in correlation with experimental studies gives information for the first time about the binding modes of the known influenza antiviral compounds in different models of vRNA replication by IAV RdRp. This in turn gives new structural insights for the development of new therapeutics exhibiting high specificity to the PB1 catalytic site of influenza A viruses.

Keywords

RNA dependent RNA polymerase Catalytic site Docking Nucleotide triphosphates 

Notes

Supplementary material

10822_2019_189_MOESM1_ESM.docx (4.3 mb)
Supplementary material 1 (DOCX 4358 KB)

References

  1. 1.
    Fodor E (2013) The RNA polymerase of influenza a virus: mechanisms of viral transcription and replication. Acta Virol 57(2):113–122CrossRefGoogle Scholar
  2. 2.
    Resa-Infante P, Jorba N, Coloma R, Ortin J (2011) The influenza virus RNA synthesis machine: advances in its structure and function. RNA Biol 8(2):207–215CrossRefGoogle Scholar
  3. 3.
    Hengrung N, El Omari K, Serna Martin I, Vreede FT, Cusack S, Rambo RP, Vonrhein C, Bricogne G, Stuart DI, Grimes JM, Fodor E (2015) Crystal structure of the RNA-dependent RNA polymerase from influenza C virus. Nature 527(7576):114–117.  https://doi.org/10.1038/nature15525 CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Pflug A, Guilligay D, Reich S, Cusack S (2014) Structure of influenza A polymerase bound to the viral RNA promoter. Nature 516(7531):355–360.  https://doi.org/10.1038/nature14008 CrossRefPubMedGoogle Scholar
  5. 5.
    Reich S, Guilligay D, Pflug A, Malet H, Berger I, Crepin T, Hart D, Lunardi T, Nanao M, Ruigrok RW, Cusack S (2014) Structural insight into cap-snatching and RNA synthesis by influenza polymerase. Nature 516(7531):361–366.  https://doi.org/10.1038/nature14009 CrossRefPubMedGoogle Scholar
  6. 6.
    Appleby TC, Perry JK, Murakami E, Barauskas O, Feng J, Cho A, Fox D III, Wetmore DR, McGrath ME, Ray AS, Sofia MJ, Swaminathan S, Edwards TE (2015) Viral replication. Structural basis for RNA replication by the hepatitis C virus polymerase. Science 347(6223):771–775.  https://doi.org/10.1126/science.1259210 CrossRefPubMedGoogle Scholar
  7. 7.
    Butcher SJ, Grimes JM, Makeyev EV, Bamford DH, Stuart DI (2001) A mechanism for initiating RNA-dependent RNA polymerization. Nature 410(6825):235–240.  https://doi.org/10.1038/35065653 CrossRefPubMedGoogle Scholar
  8. 8.
    Tao Y, Farsetta DL, Nibert ML, Harrison SC (2002) RNA synthesis in a cage–structural studies of reovirus polymerase lambda3. Cell 111(5):733–745CrossRefGoogle Scholar
  9. 9.
    Te Velthuis AJ, Robb NC, Kapanidis AN, Fodor E (2016) The role of the priming loop in Influenza A virus RNA synthesis. Nat Microbiol 1 (5).  https://doi.org/10.1038/nmicrobiol.2016.29
  10. 10.
    Babar MM, Zaidi NU, Tahir M (2014) Global geno-proteomic analysis reveals cross-continental sequence conservation and druggable sites among influenza virus polymerases. Antiviral Res 112:120–131.  https://doi.org/10.1016/j.antiviral.2014.10.013 CrossRefPubMedGoogle Scholar
  11. 11.
    Furuta Y, Takahashi K, Shiraki K, Sakamoto K, Smee DF, Barnard DL, Gowen BB, Julander JG, Morrey JD (2009) T-705 (favipiravir) and related compounds: novel broad-spectrum inhibitors of RNA viral infections. Antiviral Res 82(3):95–102.  https://doi.org/10.1016/j.antiviral.2009.02.198 CrossRefPubMedGoogle Scholar
  12. 12.
    Tisdale M, Ellis M, Klumpp K, Court S, Ford M (1995) Inhibition of influenza virus transcription by 2′-deoxy-2′-fluoroguanosine. Antimicrob Agents Chemother 39(11):2454–2458CrossRefGoogle Scholar
  13. 13.
    Sidwell RW, Bailey KW, Wong MH, Barnard DL, Smee DF (2005) In vitro and in vivo influenza virus-inhibitory effects of viramidine. Antiviral Res 68(1):10–17.  https://doi.org/10.1016/j.antiviral.2005.06.003 CrossRefPubMedGoogle Scholar
  14. 14.
    Ghanem A, Mayer D, Chase G, Tegge W, Frank R, Kochs G, Garcia-Sastre A, Schwemmle M (2007) Peptide-mediated interference with influenza A virus polymerase. J Virol 81(14):7801–7804.  https://doi.org/10.1128/JVI.00724-07 CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Reich S, Guilligay D, Cusack S (2017) An in vitro fluorescence based study of initiation of RNA synthesis by influenza B polymerase. Nucleic Acids Res 45(6):3353–3368.  https://doi.org/10.1093/nar/gkx043 CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Tomassini J, Selnick H, Davies ME, Armstrong ME, Baldwin J, Bourgeois M, Hastings J, Hazuda D, Lewis J, McClements W et al (1994) Inhibition of cap (m7GpppXm)-dependent endonuclease of influenza virus by 4-substituted 2,4-dioxobutanoic acid compounds. Antimicrob Agents Chemother 38(12):2827–2837CrossRefGoogle Scholar
  17. 17.
    Kowalinski E, Zubieta C, Wolkerstorfer A, Szolar OH, Ruigrok RW, Cusack S (2012) Structural analysis of specific metal chelating inhibitor binding to the endonuclease domain of influenza pH1N1 (2009) polymerase. PLoS Pathog 8(8):e1002831.  https://doi.org/10.1371/journal.ppat.1002831 CrossRefPubMedPubMedCentralGoogle Scholar
  18. 18.
    Tomassini JE, Davies ME, Hastings JC, Lingham R, Mojena M, Raghoobar SL, Singh SB, Tkacz JS, Goetz MA (1996) A novel antiviral agent which inhibits the endonuclease of influenza viruses. Antimicrob Agents Chemother 40(5):1189–1193CrossRefGoogle Scholar
  19. 19.
    Parkes KE, Ermert P, Fassler J, Ives J, Martin JA, Merrett JH, Obrecht D, Williams G, Klumpp K (2003) Use of a pharmacophore model to discover a new class of influenza endonuclease inhibitors. J Med Chem 46(7):1153–1164.  https://doi.org/10.1021/jm020334u CrossRefPubMedGoogle Scholar
  20. 20.
    Byrn RA, Jones SM, Bennett HB, Bral C, Clark MP, Jacobs MD, Kwong AD, Ledeboer MW, Leeman JR, McNeil CF, Murcko MA, Nezami A, Perola E, Rijnbrand R, Saxena K, Tsai AW, Zhou Y, Charifson PS (2015) Preclinical activity of VX-787, a first-in-class, orally bioavailable inhibitor of the influenza virus polymerase PB2 subunit. Antimicrob Agents Chemother 59(3):1569–1582.  https://doi.org/10.1128/AAC.04623-14 CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Hayden FG, Sugaya N, Hirotsu N, Lee N, de Jong MD, Hurt AC, Ishida T, Sekino H, Yamada K, Portsmouth S, Kawaguchi K, Shishido T, Arai M, Tsuchiya K, Uehara T, Watanabe A, Baloxavir Marboxil Investigators G (2018) Baloxavir Marboxil for uncomplicated influenza in adults and adolescents. N Engl J Med 379(10):913–923.  https://doi.org/10.1056/NEJMoa1716197 CrossRefPubMedGoogle Scholar
  22. 22.
    Muratore G, Goracci L, Mercorelli B, Foeglein A, Digard P, Cruciani G, Palu G, Loregian A (2012) Small molecule inhibitors of influenza A and B viruses that act by disrupting subunit interactions of the viral polymerase. Proc Natl Acad Sci USA 109(16):6247–6252.  https://doi.org/10.1073/pnas.1119817109 CrossRefPubMedGoogle Scholar
  23. 23.
    Obayashi E, Yoshida H, Kawai F, Shibayama N, Kawaguchi A, Nagata K, Tame JR, Park SY (2008) The structural basis for an essential subunit interaction in influenza virus RNA polymerase. Nature 454(7208):1127–1131.  https://doi.org/10.1038/nature07225 CrossRefPubMedGoogle Scholar
  24. 24.
    Massari S, Nannetti G, Goracci L, Sancineto L, Muratore G, Sabatini S, Manfroni G, Mercorelli B, Cecchetti V, Facchini M, Palu G, Cruciani G, Loregian A, Tabarrini O (2013) Structural investigation of cycloheptathiophene-3-carboxamide derivatives targeting influenza virus polymerase assembly. J Med Chem 56(24):10118–10131.  https://doi.org/10.1021/jm401560v CrossRefPubMedGoogle Scholar
  25. 25.
    Lepri S, Nannetti G, Muratore G, Cruciani G, Ruzziconi R, Mercorelli B, Palu G, Loregian A, Goracci L (2014) Optimization of small-molecule inhibitors of influenza virus polymerase: from thiophene-3-carboxamide to polyamido scaffolds. J Med Chem 57(10):4337–4350.  https://doi.org/10.1021/jm500300r CrossRefPubMedGoogle Scholar
  26. 26.
    Loregian A, Coen DM (2006) Selective anti-cytomegalovirus compounds discovered by screening for inhibitors of subunit interactions of the viral polymerase. Chem Biol 13(2):191–200.  https://doi.org/10.1016/j.chembiol.2005.12.002 CrossRefPubMedGoogle Scholar
  27. 27.
    Muratore G, Mercorelli B, Goracci L, Cruciani G, Digard P, Palu G, Loregian A (2012) Human cytomegalovirus inhibitor AL18 also possesses activity against influenza A and B viruses. Antimicrob Agents Chemother 56(11):6009–6013.  https://doi.org/10.1128/AAC.01219-12 CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Fukuoka M, Minakuchi M, Kawaguchi A, Nagata K, Kamatari YO, Kuwata K (2012) Structure-based discovery of anti-influenza virus A compounds among medicines. Biochim Biophys Acta 1820(2):90–95.  https://doi.org/10.1016/j.bbagen.2011.11.003 CrossRefPubMedGoogle Scholar
  29. 29.
    Kessler U, Castagnolo D, Pagano M, Deodato D, Bernardini M, Pilger B, Ranadheera C, Botta M (2013) Discovery and synthesis of novel benzofurazan derivatives as inhibitors of influenza A virus. Bioorg Med Chem Lett 23(20):5575–5577.  https://doi.org/10.1016/j.bmcl.2013.08.048 CrossRefPubMedGoogle Scholar
  30. 30.
    Li L, Chang SH, Xiang JF, Li Q, Liang HH, Tang YL, Liu YF (2012) NMR identification of anti-influenza lead compound targeting at PA(C) subunit of H5N1 polymerase. Chinese Chem Lett 23(1):89–92.  https://doi.org/10.1016/j.cclet.2011.09.006 CrossRefGoogle Scholar
  31. 31.
    Nakazawa M, Kadowaki SE, Watanabe I, Kadowaki Y, Takei M, Fukuda H (2008) PA subunit of RNA polymerase as a promising target for anti-influenza virus agents. Antiviral Res 78(3):194–201.  https://doi.org/10.1016/j.antiviral.2007.12.010 CrossRefPubMedGoogle Scholar
  32. 32.
    Giannecchini S, Wise HM, Digard P, Clausi V, Del Poggetto E, Vesco L, Puzelli S, Donatelli I, Azzi A (2011) Packaging signals in the 5′-ends of influenza virus PA, PB1, and PB2 genes as potential targets to develop nucleic-acid based antiviral molecules. Antiviral Res 92(1):64–72.  https://doi.org/10.1016/j.antiviral.2011.06.013 CrossRefPubMedGoogle Scholar
  33. 33.
    Tado M, Abe T, Hatta T, Ishikawa M, Nakada S, Yokota T, Takaku H (2001) Inhibitory effect of modified 5′-capped short RNA fragments on influenza virus RNA polymerase gene expression. Antivir Chem Chemother 12(6):353–358.  https://doi.org/10.1177/095632020101200605 CrossRefPubMedGoogle Scholar
  34. 34.
    Cianci C, Colonno RJ, Krystal M (1997) Differential effect of modified capped RNA substrates on influenza virus transcription. Virus Res 50(1):65–75CrossRefGoogle Scholar
  35. 35.
    Sali A, Blundell TL (1993) Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 234(3):779–815.  https://doi.org/10.1006/jmbi.1993.1626 CrossRefPubMedGoogle Scholar
  36. 36.
    Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410.  https://doi.org/10.1016/S0022-2836(05)80360-2 CrossRefPubMedGoogle Scholar
  37. 37.
    Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48(3):443–453CrossRefGoogle Scholar
  38. 38.
    Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673–4680CrossRefGoogle Scholar
  39. 39.
    Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions. Protein Sci 2(9):1511–1519.  https://doi.org/10.1002/pro.5560020916 CrossRefPubMedPubMedCentralGoogle Scholar
  40. 40.
    Guex N, Peitsch MC (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 18(15):2714–2723.  https://doi.org/10.1002/elps.1150181505 CrossRefPubMedGoogle Scholar
  41. 41.
    Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S (1998) Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins 33(1):1–17CrossRefGoogle Scholar
  42. 42.
    Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S (1998) Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins 33(1):18–29CrossRefGoogle Scholar
  43. 43.
    Goto J, Kataoka R, Hirayama N (2004) Ph4Dock: pharmacophore-based protein-ligand docking. J Med Chem 47(27):6804–6811.  https://doi.org/10.1021/jm0493818 CrossRefPubMedGoogle Scholar
  44. 44.
    Clark M, Cramer RD, Vanopdenbosch N (1989) Validation of the general-purpose tripos 5.2 force-field. J Comput Chem 10(8):982–1012.  https://doi.org/10.1002/jcc.540100804 CrossRefGoogle Scholar
  45. 45.
    Mackerell AD Jr, Feig M, Brooks CL III (2004) Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem 25(11):1400–1415.  https://doi.org/10.1002/jcc.20065 CrossRefPubMedGoogle Scholar
  46. 46.
    Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 21(6):1087–1092.  https://doi.org/10.1063/1.1699114 CrossRefGoogle Scholar
  47. 47.
    Sangawa H, Komeno T, Nishikawa H, Yoshida A, Takahashi K, Nomura N, Furuta Y (2013) Mechanism of action of T-705 ribosyl triphosphate against influenza virus RNA polymerase. Antimicrob Agents Chemother 57(11):5202–5208.  https://doi.org/10.1128/AAC.00649-13 CrossRefPubMedPubMedCentralGoogle Scholar
  48. 48.
    Barauskas O, Xing W, Aguayo E, Willkom M, Sapre A, Clarke M, Birkus G, Schultz BE, Sakowicz R, Kwon H, Feng JY (2017) Biochemical characterization of recombinant influenza A polymerase heterotrimer complex: Polymerase activity and mechanisms of action of nucleotide analogs. PLoS ONE 12(10):e0185998.  https://doi.org/10.1371/journal.pone.0185998 CrossRefPubMedPubMedCentralGoogle Scholar
  49. 49.
    Furuta Y, Takahashi K, Kuno-Maekawa M, Sangawa H, Uehara S, Kozaki K, Nomura N, Egawa H, Shiraki K (2005) Mechanism of action of T-705 against influenza virus. Antimicrob Agents Chemother 49(3):981–986.  https://doi.org/10.1128/AAC.49.3.981-986.2005 CrossRefPubMedPubMedCentralGoogle Scholar
  50. 50.
    Sleeman K, Mishin VP, Deyde VM, Furuta Y, Klimov AI, Gubareva LV (2010) In vitro antiviral activity of favipiravir (T-705) against drug-resistant influenza and 2009 A(H1N1) viruses. Antimicrob Agents Chemother 54(6):2517–2524.  https://doi.org/10.1128/AAC.01739-09 CrossRefPubMedPubMedCentralGoogle Scholar
  51. 51.
    Graci JD, Cameron CE (2006) Mechanisms of action of ribavirin against distinct viruses. Rev Med Virol 16(1):37–48.  https://doi.org/10.1002/rmv.483 CrossRefPubMedGoogle Scholar
  52. 52.
    Cheung PP, Watson SJ, Choy KT, Fun Sia S, Wong DD, Poon LL, Kellam P, Guan Y, Malik Peiris JS, Yen HL (2014) Generation and characterization of influenza A viruses with altered polymerase fidelity. Nat Commun 5:4794.  https://doi.org/10.1038/ncomms5794 CrossRefPubMedPubMedCentralGoogle Scholar
  53. 53.
    Zamyatkin DF, Parra F, Alonso JM, Harki DA, Peterson BR, Grochulski P, Ng KK (2008) Structural insights into mechanisms of catalysis and inhibition in Norwalk virus polymerase. J Biol Chem 283(12):7705–7712.  https://doi.org/10.1074/jbc.M709563200 CrossRefPubMedGoogle Scholar
  54. 54.
    Biswas SK, Nayak DP (1994) Mutational analysis of the conserved motifs of influenza A virus polymerase basic protein 1. J Virol 68(3):1819–1826PubMedPubMedCentralGoogle Scholar
  55. 55.
    Te Velthuis AJ, Robb NC, Kapanidis AN, Fodor E (2016) The role of the priming loop in influenza A virus RNA synthesis. Nat Microbiol 1:16029.  https://doi.org/10.1038/nmicrobiol.2016.29 CrossRefPubMedPubMedCentralGoogle Scholar
  56. 56.
    Nilsson BE, Te Velthuis AJ, Fodor E (2017) Role of the PB2 627 domain in influenza A virus polymerase function. J Virol.  https://doi.org/10.1128/JVI.02467-16 CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonCanada
  2. 2.Li Ka Shing Applied Virology InstituteUniversity of AlbertaEdmontonCanada
  3. 3.Department of Medical Microbiology and ImmunologyUniversity of AlbertaEdmontonCanada
  4. 4.Medical Microbiology and Immunology, Li Ka Shing Institute of VirologyUniversity of AlbertaEdmontonCanada

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