The inhibitory performance of flavonoid cyanidin-3-sambubiocide against H274Y mutation in H1N1 influenza virus

References

• An, J., Lee, D. C., Law, A. H., Yang, C. L., Poon, L. L., Lau, A. S., & Jones, S. J. (2009). A novel small-molecule inhibitor of the avian influenza H5N1 virus determined through computational screening against the neuraminidase. Journal of Medicinal Chemistry, 52, 2667–2672. doi:10.1021/jm800455g
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., Gunsteren, W. F. V., & Hermans, J. (1981). Interaction models for water in relation to protein hydration. Intermolecular Forces, 14, 331–342. doi:10.1007/978-94-015-7658-1_21
   Google Scholar
• Berendsen, H. J. C., Postma, P. M., Gunsteren, W. F. V., DiNola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81, 3684–3690. doi:10.1063/1.448118
   Web of Science ®Google Scholar
• Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. F., Brice, M. D., Rodgers, J. R., … Tasumi, M. (1977). The protein data bank. A computer-based archival file for macromolecular structures. European Journal of Biochemistry, 80, 319–324. doi:10.1111/j.1432-1033.1977.tb11885.x
   PubMedGoogle Scholar
• Boys, S. F., & Bernardi, F. (1970). The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors. Molecular Physics, 19, 553–566. doi:10.1080/00268977000101561
   Web of Science ®Google Scholar
• Cheatham, T. E., Miller, J. L., Fox, T., Darden, T. A., & Kollman, P. A. (1995). Molecular dynamics simulations on solvated biomolecular systems: The particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. Journal of the American Chemical Society, 117, 4193–4194. doi:10.1021/ja00119a045
   Web of Science ®Google Scholar
• Colman, P. M., Varghese, J. N., & Laver, W. G. (1983). Structure of the catalytic and antigenic sites in influenza virus neuraminidase. Nature, 303, 41–44. doi:10.1038/303041a0
   PubMed Web of Science ®Google Scholar
• Ferraris, O., & Lina, B. (2008). Mutations of neuraminidase implicated in neuraminidase inhibitors resistance. Journal of Clinical Virology, 41, 13–19. doi:10.1016/j.jcv.2007.10.020
   PubMed Web of Science ®Google Scholar
• Frisch, G. W., Trucks, H. B., Schlegel, G. E., Scuseria, M. A., Robb, J. R., Chessman, G., … Fox, T. (2009). Gaussian 09 user’s reference. Wallingford, CT: Gaussian.
   Google Scholar
• Granadino-Roldan, J. M., Garzon, A., Garia, G., Pena-Ruiz, T., Fernandez-Liencres, M. P., Navarro, A., & Fernandez-Gomez, M. (2009). Theoretical study of the effect of ethynyl group on the structure and electrical properties of phenyl-thiadiazole systems as precursors of electron-conducting materials. The Journal of Chemical Physics, 130, 1–10. doi:10.1063/1.3149856
   Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18, 1463–1472. doi:10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
   Web of Science ®Google Scholar
• Hess, B., Kutzner, C., van der Spoel, D., & Lindahl, E. (2008). GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. Journal of Chemical Theory and Computation, 4, 435–447. doi:10.1021/ct700301q
   PubMed Web of Science ®Google Scholar
• Hockney, R. W., Goel, S. P., & Eastwood, J. W. (1974). Quiet high-resolution computer models of a plasma. Journal of Computational Physics, 14, 148–158. doi:10.1016/0021-9991(74)90010-2
   Web of Science ®Google Scholar
• Hohenstein, E. G., Chill, S. T., & Sherrill, C. D. (2008). Assessment of the performance of the M05-2X and M06-2X exchange-correlation functional for noncovalent interactions in biomolecules. Journal of Chemical Theory and Computation, 4, 1996–2000. doi:10.1021/ct800308k
   PubMed Web of Science ®Google Scholar
• Hurt, A. C., Deng, Y. M., Ernest, J., Caldwell, N., Leang, L., lannello, P., … Barr, I. G. (2011). Oseltamivir-resistant influenza viruses ciruculating during the first year of the influenza A (H1N1) 2009 pandemic in the Aia-Pacific region, March 2009 to March 2010. Euro Surveillance, 16, 1–8 http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19770
   Google Scholar
• Inoue, M., Barkham, T., Leo, Y. S., Chan, K. P., Chow, A., Wong, C. W., … Lin, C., (2010). Emergence of oseltamivir-resistant pandemic (H1N1) 2009 virus within 48 hours. Emerging Infectious Diseases, 16, 1633–1636. doi:10.3201/eid1610.100688
   PubMed Web of Science ®Google Scholar
• Jiande, G. U., Jing, W., & Jerzy, L. (2011). Stacking and H-bonding patterns of dGpdC and dGpdCpdG: Performance of the M05-2X and M06-2X Minnesota density functional for the single strand DNA. Chemical Physics Letters, 512, 108–112. doi:10.1016/j.cplett.2011.06.085
   Web of Science ®Google Scholar
• Jiang, J. L., Wu, Y. B., Wang, Z. X., & Wu, C. (2010). Assessing the performance of popular quantum mechanics and molecular mechanics methods and revealing the sequence-dependent energetic features using 100 tetrapeptide models. Journal of Chemical Theory and Computation, 6, 1199–1209. doi:10.1021/ct100008q
   Web of Science ®Google Scholar
• Johan, Ǻ., Carmen, M., & Jan-Erik, S. (1994). A new method for predicting binding affinity in computer-aided drug design. Protein Engineering, 7, 385–391. doi:10.1093/protein/7.3.385
   PubMedGoogle Scholar
• Kamali, A., & Holodniy, M. (2013). Influenza treatment and prophylaxis with neuraminidase inhibitors: A review. Journal of Infection and Drug Resistance, 6, 187–198. doi:10.2147/IDR.S36601
   PubMedGoogle Scholar
• Kannan, S., & Kolandaivel, P. (2016). Computational studies of pandemic 1918 and 2009 H1N1 hemaglutinins bound to avian and human receptor analogs. Journal of Biomolecular Structure and Dynamics, 34, 272–289. doi:10.1080/07391102.2015.1027737
   PubMed Web of Science ®Google Scholar
• Karelson, M., Lobanov, V. S., & Katritzky, A. R. (1996). Quantum-chemical descriptors in QSAR/QSPR studies. Chemical Reviews, 96, 1027–1044. doi:10.1021/cr950202r
   PubMed Web of Science ®Google Scholar
• Karthick, V., & Ramanathan, K. (2013). Computational investigation of oseltamivir resistance in influenza A (H5N1) virus. Medicinal Chemistry Research, 22, 5764–5771. doi:10.1007/s00044-013-0551-2
   Web of Science ®Google Scholar
• Karthick, V., & Ramanathan, K. (2014). Insight into the oseltamivir resistance R292k mutation in H5N1 influenza virus: A molecular docking and molecular dynamics approach. Cell Biochemistry and Biophysics, 68, 291–299. doi:10.1007/s12013-013-9709-2
   PubMed Web of Science ®Google Scholar
• Karthick, V., Shanthi, V., Rajasekaran, R., & Ramanathan, K. (2012). Exploring the cause of oseltamivir resistance against mutant H274Y neuraminidase by molecular simulation approach. Applied Biochemistry and Biotechnology, 167, 237–249. doi:10.1007/s12010-012-9687-7
   PubMed Web of Science ®Google Scholar
• Kinoshita, E., Hayashi, K., Katayama, H., Hayashi, T., & Obata, A. (2012). Anti-influenza virus effects of elderberry juice and its fractions. Bioscience, Biotechnology, and Biochemistry, 76, 1633–1638. doi:10.1271/bbb.120112
   PubMed Web of Science ®Google Scholar
• Krawitz, C., Mraheil, M. A., Stein, M., Imirzaliglu, C., Domann, E., Pleschka, S., & Hain, T. (2011). Inhibitory activity of a standardized elderberry liquid extract against clinically-relevant human respiratory bacterial pathogens and influenza A and B viruses. BMC Complementary and Alternative Medicine, 11, 11–16. doi:10.1186/1472-6882-11-16
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., Consortium, O. S. D. D., & Lynn, A (2014). g_mmpbsa- A GROMACS tool for high throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54, 1951–1962. doi:10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Li, Q., Qi, J., Zhang, W., Vavricka, C. J., Shi, Y., Wei, J., … Gao, G. F., (2010). The 2009 pandemic H1N1 neuraminidase N1 lacks the 150-cavity in its active site. Nature Structural and Molecular Biology, 17, 1266–1268. doi:10.1038/nsmb.1909
   PubMed Web of Science ®Google Scholar
• Li, L., Li, Y., Zhang, L., & Hou, T. (2012). Theoretical studies on the susceptibility of oseltamivir against variants of 2009 A/H1N1 influenza neuraminidase. Journal of Chemical Information and Modeling, 52, 2715–2729. doi:10.1021/ci300375 k
   PubMed Web of Science ®Google Scholar
• Manicassamy, B., Medina, R. A., Hai, R., Tsibane, T., Stertz, S., Nistal-Villan, E., … Garcia-Sastre, A. (2010). Protection of mice against lethal challenge with 2009 H1N1 influenza A virus by 1918- like and classical swine H1N1 based vaccines. PLoS Pathogens, 6, doi:10.1371/journal.ppat.1000745
   Web of Science ®Google Scholar
• Marco, A. C. N., Mark, Y., & Ruben, A. (2012). Unusual arginine formations in protein function and assembly: Rings, strings and stacks. Journal of Physical Chemistry B, 116, 7006–7013. doi:10.1021/jp3009699
   PubMed Web of Science ®Google Scholar
• Martha, C. D., Dobado, J. A., Jose, M. M., Pedro, S., Miquel, D., & Jose, L. V. (1999). Basis set superposition error-counterpoise corrected potential energy surfaces. Application to hydrogen peroxide…X=(X=F-, Cl-, Br-, Li+, Na+) complexes. The Journal of Chemical Physics, 110, 11806–11813. doi:10.1063/1.479166
   Web of Science ®Google Scholar
• McKimm-Breschkin, J. L. (2013). Influenza neuraminidase inhibitors: Antiviral action and mechanisms of resistance. Influenza and Other Respiratory Viruses, 7, 25–36. doi:10.1111/irv.12047
   PubMed Web of Science ®Google Scholar
• Ming, T., Jarek, M., & Xi, J. (2006). C-Terminal arginine cluster is essential for receptor binding of Norovirus capsid protein. Journal of Virology, 80, 7322–7331. doi:10.1128/JVI.00233-06
   PubMed Web of Science ®Google Scholar
• Nagai, T., Miyaichi, Y., Tomimori, T., Suzuki, Y., & Yamada, H. (1992). In vivo anti-influenza virus activity of plant flavonoids having inhibitory activity against influenza virus sialidase. Antiviral Research, 19, 207–217. doi:10.1016/0166-3542(92)90080-O
   PubMed Web of Science ®Google Scholar
• Oostenbrink, C., Villa, A., Mark, A. E., & Van Gunsteren, W. F. (2004). A biomolecular force field based on the free energy enthalpy of hydration and salvation: The GROMOS force-field parameter set 53A5 and 53A6. Journal of Computational Chemistry, 25, 1656–1676.10.1002/(ISSN)1096-987X
   PubMed Web of Science ®Google Scholar
• Park, J. W., & Jo, W. H. (2010). Computational design of novel, high-affinity neuraminidase inhibitors for H5N1 avian influenza virus. European Journal of Medicinal Chemistry, 45, 536–541. doi:10.1016/j.ejmech.2009.10.040
   PubMed Web of Science ®Google Scholar
• Parrinello, M., & Rahman, A. (1981). Ploymorphic transitions in single crystals: A new molecular dynamics method. Journal of Applied Physics, 52, 7182–7190. doi:10.1063/1.328693
   Web of Science ®Google Scholar
• Renaud, C., Pergam, S. A., Polyak, C., Jain, R., Kuypers, J., Englund, J. A., … Boeckh, M. J. (2010). Early emergence of an H275Y mutation in a hematopoietic cell transplant recipient treated with intravenous peramivir. Transplant Infectious Disease, 12, 513–517. doi:10.1111/j.1399-3062.2010.00582.x
   PubMed Web of Science ®Google Scholar
• Samson, M., Pizzorno, A., Abed, Y., & Boivin, G. (2013). Influenza virus resistance to neuraminidase inhibitors. Antiviral Research, 98, 174–185. doi:10.1016/j.antiviral.2013.03.014
   PubMed Web of Science ®Google Scholar
• Schüttelkopf, A. W., & van Aalten, D. M. (2004). PRODRG-a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60, 1355–1363. doi:10.1107/S0907444904011679
   PubMed Web of Science ®Google Scholar
• Swaminathan, K., Dyason, J. C., Maggioni, A., von Itzstein, M., & Downard, K. M. (2013). Binding of a natural anthocyanin inhibitor to influenza neuraminidase by mass spectrometry. Analytical and Bioanalytical Chemistry, 405, 6563–6572. doi:10.1007/s00216-013-7068-x
   PubMed Web of Science ®Google Scholar
• Swaminathan, K., Muller, P., & Downard, K. M. (2014). Substituent effects on the binding of natural product anthocyanidin inhibitors to influenza neuraminidase with mass spectrometry. Analytica Chimia Acta, 828, 61–69. doi:10.1016/j.aca.2014.04.021
   PubMed Web of Science ®Google Scholar
• Tan, H., Wei, K., Bao, J., & Zhou, X. (2013). In silico study on multidrug resistance conferred by I223R/H275Y double mutant neuraminidase. Molecular BioSystems, 9, 2764–2774. doi:10.1039/c3mb70253g
   PubMed Web of Science ®Google Scholar
• Thompson, M. A. (2004a). ArgusLab 4.0.1 Planaria Software, LLC, Seattle, WA. Retrieved from http://www.ArgusLab.com
   Google Scholar
• Thompson, M. A. (2004b). Poster presentation: Molecular docking using arguslab: An efficient shape-based search algorithm & the AScore scoring function. Fall ACS meeting Philadelphia.
   Google Scholar
• Thorlund, K., Awad, T., Boivin, G., & Thabane, L. (2011). Systematic review of influenza resistance to the neuraminidase inhibitors. BMC Infectious Diseases, 11, 795. doi:10.1186/1471-2334-11-134
   Web of Science ®Google Scholar
• Tomas, H., John, M., & Johan, Ǻ. (1998). Ligand binding affinity prediction by linear interaction energy methods. Journal of Computer-Aided Molecular Design, 12, 27–35.
   PubMed Web of Science ®Google Scholar
• Trott, O., & Olson A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. Journal of Computational Chemistry, 31, 455–461. doi:10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Valinotto, L. E., Diez, R. A., Barrero, P. R., Farías, J. A., López, E. L., & Mistchenko, A. S. (2010). Emergence of intratreatment resistance to oseltamivir in pandemic influenza A H1N1 2009 virus. Antiviral Therapy, 15, 923–927. doi:10.3851/IMP1635
   PubMed Web of Science ®Google Scholar
• Vergara-Jaque, A., Poblete, H., Lee, E. H., Schulten, K., González-Nilo, F., & Chipot, C. (2012). Molecular basis of drug resistance in A/H1N1 Virus. Journal of Chemical Information Modeling, 52, 2650–2656. doi:10.1021/ci300343w
   PubMed Web of Science ®Google Scholar
• Wang, S. Q., Cheng, X. C., Dong, W. L., Wang, R. L., & Chou, K. C. (2010). Three new powerful oseltamivir derivatives for inhibiting the neuraminidase of influenza virus. Biochemial Biophysical Research Communications, 401, 188–191. doi:10.1016/j.bbrc.2010.09.020
   PubMed Web of Science ®Google Scholar
• Woods, C. J., Malaisree, M., Pattarapongdilok, N., Sompornpisut, P., Hannongbua, S., & Mulholland, A. J. (2012). Long time scale GPU dynamics reveal the mechanism of drug resistance of the dual mutant I223R/H274Y neuraminidase from H1N2-2009 influenza virus. Biochemistry, 51, 4364–4375. doi:10.1021/bi300561n
   PubMed Web of Science ®Google Scholar
• Xu, R., McBride, R., Paulson, J. C., Basler, C. F., & Wilson, I. A. (2010). Structure, receptor and antigenicity of influenza virus hemagglutinins from the 1957 H2N2 pandemic. Journal of Virology, 84, 1715–1721. doi:10.1128/JVI.02162-09
   PubMed Web of Science ®Google Scholar
• Zakay-Rones, Z., Varsano, N., Zlotnik, M., Manor, O., Regev, L., Schlesinger, M., & Mumcuoglu, M. (1995). Inhibition of several strains of influenza virus in vitro and reduction of symptoms by an elderberry extract (Sambucas nigra L.) during an outbreak of influenza B Panama. Journal of Alternative and Complementary Medicine, 1, 361–369. doi:10.1089/acm.1995.1.361
   PubMedGoogle Scholar
• Zakay-Rones, Z., Thom, E., Wollan, T., & Wadstein, J. (2004). Randomized study of the efficacy and safety of oral elderberry extracts in the treatment of influenza A and B virus infections. Journal of International Medical Research, 32, 132–140. doi:10.1177/147323000403200205
   PubMed Web of Science ®Google Scholar
• Zhao, Y., & Truhlar, D. G. (2008). Exploring the limit of accuracy of the global hybrid meta density functional for main-group thermochemistry, kinetics, and noncovalent interactions. Journal of Chemical Theory and Computation, 4, 1849–1868. doi:10.1021/ct800246v
   PubMed Web of Science ®Google Scholar