Have a personal or library account? Click to login
Computational design of drug candidates for influenza A virus subtype H1N1 by inhibiting the viral neuraminidase-1 enzyme Cover

Computational design of drug candidates for influenza A virus subtype H1N1 by inhibiting the viral neuraminidase-1 enzyme

Open Access
|Jun 2014

References

  1. 1. J. K. Taubenberger and D. M. Morens, 1918 Influenza: the mother of all pandemic, Emerg. Infect. Dis. 12 (2006) 15-22; DOI: 10.3201/eid1201.050979.10.3201/eid1201.050979329139816494711
  2. 2. P. Auewarakul, O. Suptawiwat, A. Kongchanagul, C. Sangma, Y. Suzuki, K. Ungchusak, S. Louisirirotchanakul, H. Lerdsamran, P. Pooruk, A. Thitithanyanont, C. Pittayawonganon, C.-T. Guo, H. Hiramatsu, W. Jampangern, S. Chunsutthiwat and P. Puthavathana, An avian influenza H5N1 virus that binds to a human-type receptor, J. Virol. 81 (2007) 9950-9955; DOI: 10.1128/ JVI.00468-07.10.1128/JVI.00468-07204539817626098
  3. 3. I. V. Alymova, A. Portner, V. P. Mishin, J. A. McCullers, P. Freiden and G. L. Taylor, Receptor- -binding specificity of the human parainfluenza virus type 1 hemagglutinin-neuraminidase glycoprotein, Glycobiology 22 (2012) 174-180; DOI: 10.1093/glycob/cwr112.10.1093/glycob/cwr112325550521846691
  4. 4. S.-Q. Wang, Q.-S. Du, R.-B. Huang, D.-W. Zhang and K.-C. Chou, Insights from investigating the interaction of oseltamivir (Tamiflu) with neuraminidase of the 2009 H1N1 swine flu virus, Biochem. Biophys. Res. Commun. 386 (2009) 432-436; DOI: 10.1016/j.bbrc.2009.06.016.10.1016/j.bbrc.2009.06.01619523442
  5. 5. H. T. Nguyen, T. G. Sheu, V. P. Mishin, A. I. Klimov and L. V Gubareva, Assessment of pandemic and seasonal influenza A (H1N1) virus susceptibility to neuraminidase inhibitors in three enzyme activity inhibition assays, Antimicrob. Agents Chemother. 54 (2010) 3671-3677; DOI: 10.1128/ AAC.00581-10.10.1128/AAC.00581-10293494920585136
  6. 6. N. J. Dharan, L. V. Gubareva, J. J. Meyer, M. Okomo-Adhiambo, R. C. McClinton, S. A. Marshall, K. St George, S. Epperson, L. Brammer, A. I. Klimov, J. S. Bresee and A. M. Fry, Infections with oseltamivir-resistant influenza A(H1N1) virus in the United States, JAMA 301 (2009) 1034-1041; DOI: 10.1001/jama.2009.294.10.1001/jama.2009.29419255110
  7. 7. T. Kolomin, M. Shadrina, P. Slominsky, S. Limborska and N. Myasoedov, A new generation of drugs: Synthetic peptides based on natural regulatory peptides, Neurosci. Med. 4 (2013) 223-252; DOI: 10.4326/nm.2013.44035.
  8. 8. C. D. Fjell, J. A. Hiss, R. E. W. Hancock and G. Schneider, Designing antimicrobial peptides: form follows function, Nat. Rev. Drug Discov. 11 (2012) 37-51; DOI: 10.1038/nrd3591.10.1038/nrd359122173434
  9. 9. S. Riedl, D. Zweytick and K. Lohner, Membrane-active host defense peptides - challenges and perspectives for the development of novel anticancer drugs, Chem. Phys. Lipids 164 (2011) 766-781; DOI: 10.1016/j.chemphyslip.2011.09.004.10.1016/j.chemphyslip.2011.09.004322076621945565
  10. 10. P. Vlieghe, V. Lisowski, J. Martinez and M. Khrestchatisky, Synthetic therapeutic peptides: science and market, Drug. Disc. Today 15 (2010) 40-56; DOI: 10.1016/j.drudis.2009.10.009.10.1016/j.drudis.2009.10.00919879957
  11. 11. R. Benigni and C. Bossa, Structure alerts for carcinogenicity, and the Salmonella assay system: a novel insight through the chemical relational databases technology, Mutat. Res. 659 (2008) 248-261; DOI: 10.1016/j.mrrev.2008.05.003.10.1016/j.mrrev.2008.05.00318621573
  12. 12. U. S. F. Tambunan, N. Amri and A. A. Parikesit, In silico design of cyclic peptides as influenza virus, a subtype H1N1 neuraminidase inhibitor, African J. Biotechnol. 11 (2012) 11474-11491; DOI: 10.5897/AJB11.4094.10.5897/AJB11.4094
  13. 13. C. A. Lipinski, F. Lombardo, B. W. Dominy and P. J. Feeney, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Adv. Drug Deliv. Rev. 46 (2001) 3-26.10.1016/S0169-409X(00)00129-0
  14. 14. S.-L. Du, H. Pan, W.-Y. Lu, J. Wang, J. Wu and J.-Y. Wang, Cyclic Arg-Gly-Asp peptide-labeled liposomes for targeting drug therapy of hepatic fibrosis in rats, J. Pharmacol. Exp. Ther. 322 (2007) 560-568; DOI: 10.1124/jpet.107.122481.10.1124/jpet.107.12248117510318
  15. 15. T. R. White, C. M. Renzelman, A. C. Rand, T. Rezai, C. M. McEwen, V. M. Gelev, R. A. Turner, R. G. Linington, S. S. F. Leung, A. S. Kalgutkar, J. N. Bauman, Y. Zhang, S. Liras, D. A. Price, A. M. Mathiowetz, M. P. Jacobson and R. S. Lokey, On-resin N-methylation of cyclic peptides for discovery of orally bioavailable scaffolds, Nat. Chem. Biol. 7 (2011) 810-817; DOI: 10.1038/nchembio. 664.
  16. 16. M. Brvar, A. Perdih, M. Renko, G. Anderluh, D. Turk and T. Solmajer, Structure-based discovery of substituted 4,5’-bithiazoles as novel DNA gyrase inhibitors, J. Med. Chem. 55 (2012) 6413-6426; DOI: 10.1021/jm300395d.10.1021/jm300395d22731783
  17. 17. C. Liao, M. Sitzmann, A. Pugliese and M. C. Nicklaus, Software and resources for computational medicinal chemistry, Future Med. Chem. 3 (2011) 1057-1085; DOI: 10.4155/fmc.11.63.10.4155/fmc.11.63341332421707404
  18. 18. D. L. Wheeler, T. Barrett, D. A. Benson, S. H. Bryant, K. Canese, V. Chetvernin, D. M. Church, M. DiCuccio, R. Edgar, S. Federhen, L. Y. Geer, Y. Kapustin, O. Khovayko, D. Landsman, D. J. Lipman, T. L. Madden, D. R. Maglott, J. Ostell, K. D. Pruitt, G. D. Schuler, L. M. Schriml, E. Sequeira, S. T. Sherry, K. Sirotkin, A. Souvorov, G. Starchenko, T. O. Suzek, R. Tatusov, T. A. Tatusova, L. Wagner and E. Yaschenko, Database resources of the National Center for Biotechnology Information, Nucl. Acids Res. 35 (2007) D5-D12; DOI: 10.1093/nar/gkl1031.10.1093/nar/gkl1031178111317170002
  19. 19. U. S. F. Tambunan, R. Harganingtyas and A. A. Parikesit, In silico modification of (1R, 2R, 3R, 5S)-(-)-isopinocampheylamine as inhibitors of M2 proton channel in Influenza A virus subtype H1N1, using the molecular docking approach, Trends Bioinform. 5 (2012) 25-46; DOI: 10.3923/ tb.2012.25.46.10.3923/tb.2012.25.46
  20. 20. U. S. F. Tambunan, N. Bramantya and A. A. Parikesit, In silico modification of suberoylanilide hydroxamic acid (SAHA) as potential inhibitor for class II histone deacetylase (HDAC), BMC Bioinformatics 12 (Suppl. 13) (2011) S23-S38; DOI:10.1186/1471-2105-12-S13-S23.10.1186/1471-2105-12-S13-S23327884022373132
  21. 21. R. Benigni and C. Bossa, Structure alerts for carcinogenicity, and the Salmonella assay system: a novel insight through the chemical relational databases technology, Mutat. Res. 659 (2008) 248-261; DOI: 10.1016/j.mrrev.2008.05.003.10.1016/j.mrrev.2008.05.00318621573
  22. 22. T. Sander, J. Freyss, M. von Korff, J. R. Reich and C. Rufener, OSIRIS, an entirely in-house developed drug discovery informatics system, J. Chem. Inf. Model. 49 (2009) 232-246; DOI: 10.1021/ ci800305f.10.1021/ci800305f19434825
  23. 23. D. Lagorce, O. Sperandio, H. Galons, M. A. Miteva and B. O. Villoutreix, FAF-drugs2: free ADME/ tox filtering tool to assist drug discovery and chemical biology projects, BMC Bioinformatics 9 (2008) 396-405; DOI: 10.1186/1471-2105-9-396. 10.1186/1471-2105-9-396256105018816385
  24. 24. A. D. MacKerell, N. Banavali and N. Foloppe, Development and current status of the CHARMM force field for nucleic acids, Biopolymers 56 (2000) 257-265; DOI: 10.1002/1097-0282 (2000)56:4< 257::AID-BIP10029>3.0.CO;2-W.
  25. 25. Y. Shen, M. K. Gilson and B. Tidor, Charge optimization theory for induced-fit ligands, J. Chem. Theory Comput. 8 (2012) 4580-4592; DOI: 10.1021/ct200931c.10.1021/ct200931c349634623162383
  26. 26. J. R. Williams, A. L. Khandoga, P. Goyal, J. I. Fells, D. H. Perygin, W. Siess, A. L. Parrill, G. Tigyi and Y. Fujiwara, Unique ligand selectivity of the GPR92/LPA5 lysophosphatidate receptor indicates role in human platelet activation, J. Biol. Chem. 284 (2009) 17304-17319; DOI: 10.1074/jbc. M109.003194.10.1074/jbc
  27. 27. G. L. Warren, C. W. Andrews, A.-M. Capelli, B. Clarke, J. LaLonde, M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff and M. S. Head, A critical assessment of docking programs and scoring functions, J. Med. Chem.49 (2006) 5912-5931; DOI: 10.1021/jm050362n.10.1021/jm050362n17004707
  28. 28. Y. Modis, S. Ogata, D. Clements and S. C. Harrison, A ligand-binding pocket in the dengue virus envelope glycoprotein, Proc. Natl. Acad. Sci. USA 100 (2003) 6986-6991; DOI: 10.1073/pnas. 0832193100.10.1073/pnas
  29. 29. M. Takano, T. P. Terada and M. Sasai, Unidirectional Brownian motion observed in an in silico single molecule experiment of an actomyosin motor, Proc. Natl. Acad. Sci. USA 107 (2010) 7769-7774; DOI: 10.1073/pnas.0911830107.10.1073/pnas.0911830107286784720385833
  30. 30. S. Rogers, R. Wells and M. Rechsteiner, Amino acid sequences common to rapidly degraded proteins: the PEST hypothesis, Science 234 (1986) 364-368, DOI: 10.1126/science.2876518. 10.1126/science.28765182876518
DOI: https://doi.org/10.2478/acph-2014-0015 | Journal eISSN: 1846-9558 | Journal ISSN: 1330-0075
Language: English
Page range: 157 - 172
Accepted on: Jan 14, 2014
|
Published on: Jun 6, 2014
In partnership with: Paradigm Publishing Services
Publication frequency: 4 issues per year
Related subjects:

© 2014 Usman Sumo Friend Tambunan, Arli Aditya Parikesit, Yonaniko Dephinto, Feimmy Ruth Pratiwi Sipahutar, published by Croatian Pharmaceutical Society
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 3.0 License.