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

Acta Pharmaceutica

Volumn 64, Issue 2, 2014, Pages 157-172

  Tambunan, Usman Sumo Friend ^a   Parikesit, Arli Aditya ^a   Dephinto, Yonaniko ^a   Sipahutar, Feimmy Ruth Pratiwi ^a  

^a UNIVERSITY OF INDONESIA   (Indonesia)

Author keywords

Cyclic peptide disulfide; H1N1; Molecular docking; Molecular dynamics; Neuraminidase 1

Indexed keywords

ANTIVIRUS AGENT; CYSTYLARGINYLASPARGYLPHENYLALANYLPROLYLCYSTEINE; CYSTYLARGINYLMETHIONYLTYROSYLPROLYLCYSTEINE; NEURAMINIDASE 1; SIALIDASE INHIBITOR; UNCLASSIFIED DRUG; VIRUS SIALIDASE; ENZYME INHIBITOR; LIGAND; PROTEIN BINDING; SIALIDASE;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; CARCINOGENICITY; CONFORMATIONAL TRANSITION; DRUG BIOAVAILABILITY; DRUG DESIGN; ENZYME INHIBITION; HYDROGEN BOND; INFLUENZA VIRUS A H1N1; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR DYNAMICS; MUTAGENICITY; NUCLEOTIDE SEQUENCE; PROTEIN CONFORMATION; ANTAGONISTS AND INHIBITORS; CHEMICAL STRUCTURE; CHEMISTRY; DRUG EFFECTS; PROCEDURES;

ANTIVIRAL AGENTS; DRUG DESIGN; ENZYME INHIBITORS; HYDROGEN BONDING; INFLUENZA A VIRUS, H1N1 SUBTYPE; LIGANDS; MODELS, MOLECULAR; MOLECULAR DOCKING SIMULATION; NEURAMINIDASE; PROTEIN BINDING;

EID: 84904181001     PISSN: 13300075     EISSN: 18469558     Source Type: Journal    
DOI: 10.2478/acph-2014-0015     Document Type: Article

References (30)

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
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
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
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
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
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
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. 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
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. 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
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
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
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
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
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. 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
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
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
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
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
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
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
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
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. 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
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
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
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
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
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.