全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用:99美元

查看量下载量

相关文章

更多...

Structure Elucidation of Coxsackievirus A16 in Complex with GPP3 Informs a Systematic Review of Highly Potent Capsid Binders to Enteroviruses

DOI: 10.1371/journal.ppat.1005165

Full-Text   Cite this paper   Add to My Lib

Abstract:

The replication of enterovirus 71 (EV71) and coxsackievirus A16 (CVA16), which are the major cause of hand, foot and mouth disease (HFMD) in children, can be inhibited by the capsid binder GPP3. Here, we present the crystal structure of CVA16 in complex with GPP3, which clarifies the role of the key residues involved in interactions with the inhibitor. Based on this model, in silico docking was performed to investigate the interactions with the two next-generation capsid binders NLD and ALD, which we show to be potent inhibitors of a panel of enteroviruses with potentially interesting pharmacological properties. A meta-analysis was performed using the available structural information to obtain a deeper insight into those structural features required for capsid binders to interact effectively and also those that confer broad-spectrum anti-enterovirus activity.

References

[1]  Zeng M, Li YF, Wang XH, Lu GP, Shen HG, et al. (2012) Epidemiology of hand, foot, and mouth disease in children in Shanghai 2007–2010. Epidemiol Infect 140: 1122–1130. doi: 10.1017/S0950268811001622. pmid:21878145
[2]  Wong SS, Yip CC, Lau SK, Yuen KY (2010) Human enterovirus 71 and hand, foot and mouth disease. Epidemiol Infect 138: 1071–1089. doi: 10.1017/S0950268809991555. pmid:20056019
[3]  Chen X, Tan X, Li J, Jin Y, Gong L, et al. (2013) Molecular epidemiology of coxsackievirus A16: intratype and prevalent intertype recombination identified. PLoS One 8: e82861. doi: 10.1371/journal.pone.0082861. pmid:24340064
[4]  Dang M, Wang X, Wang Q, Wang Y, Lin J, et al. (2014) Molecular mechanism of SCARB2-mediated attachment and uncoating of EV71. Protein Cell 5: 692–703. doi: 10.1007/s13238-014-0087-3. pmid:24986489
[5]  Wang X, Peng W, Ren J, Hu Z, Xu J, et al. (2012) A sensor-adaptor mechanism for enterovirus uncoating from structures of EV71. Nature structural & molecular biology 19: 424–429. doi: 10.1016/j.psychres.2015.09.034.
[6]  Ren J, Wang X, Hu Z, Gao Q, Sun Y, et al. (2013) Picornavirus uncoating intermediate captured in atomic detail. Nat Commun 4: 1929. doi: 10.1038/ncomms2889. pmid:23728514
[7]  Strauss M, Filman DJ, Belnap DM, Cheng N, Noel RT, et al. (2015) Nectin-Like Interactions between Poliovirus and Its Receptor Trigger Conformational Changes Associated with Cell Entry. Journal of virology 89: 4143–4157. doi: 10.1128/JVI.03101-14. pmid:25631086
[8]  De Colibus L, Wang X, Spyrou JAB, Kelly J, Ren J, et al. (2014) More-powerful virus inhibitors from structure-based analysis of HEV71 capsid-binding molecules. Nature structural & molecular biology 21: 282–288. doi: 10.1016/j.psychres.2015.09.034.
[9]  Axford D, Owen RL, Aishima J, Foadi J, Morgan AW, et al. (2012) In situ macromolecular crystallography using microbeams. Acta crystallographica Section D, Biological crystallography 68: 592–600. doi: 10.1107/S0907444912006749. pmid:22525757
[10]  Ren J, Wang X, Zhu L, Hu Z, Gao Q, et al. (2015) Structures of coxsackievirus A16 capsids with native antigenicity, implications for particle expansion, receptor binding and immunogenicity. J Virol.
[11]  Winn MD, Ballard CC, Cowtan KD, Dodson EJ, Emsley P, et al. (2011) Overview of the CCP4 suite and current developments. Acta crystallographica Section D, Biological crystallography 67: 235–242. doi: 10.1107/S0907444910045749. pmid:21460441
[12]  Cho AE, Guallar V, Berne BJ, Friesner R (2005) Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. J Comput Chem 26: 915–931. pmid:15841474
[13]  Miller ST, Hogle JM, Filman DJ (2001) Ab initio phasing of high-symmetry macromolecular complexes: successful phasing of authentic poliovirus data to 3.0 A resolution. J Mol Biol 307: 499–512. pmid:11254378
[14]  Lentz KN, Smith AD, Geisler SC, Cox S, Buontempo P, et al. (1997) Structure of poliovirus type 2 Lansing complexed with antiviral agent SCH48973: comparison of the structural and biological properties of three poliovirus serotypes. Structure 5: 961–978. pmid:9261087
[15]  Muckelbauer JK, Kremer M, Minor I, Tong L, Zlotnick A, et al. (1995) Structure determination of coxsackievirus B3 to 3.5 A resolution. Acta Crystallogr D Biol Crystallogr 51: 871–887. pmid:15299757
[16]  Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Macromolecular Crystallography, Pt A 276: 307–326.
[17]  French G.S. and Wilson K.S. (1978) On the treatment of negative intensity observations. Acta Cryst A34: 517–525.
[18]  Brunger AT, Adams PD, Clore GM, DeLano WL, Gros P, et al. (1998) Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallographica Section D-Biological Crystallography 54: 905–921.
[19]  Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallographica Section D-Biological Crystallography 66: 213–221.
[20]  Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of Coot. Acta Crystallographica Section D-Biological Crystallography 66: 486–501.
[21]  Schüttelkopf AW, van Aalten DMF (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr 1355–1363.
[22]  Kleywegt GJ (1995) Dictionaries for Heteros. CCP4/ESF-EACBM Newsletter on Protein Crystallography 45–50.
[23]  Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallographica Section D-Biological Crystallography 66: 12–21.
[24]  Krissinel E, Henrick K (2004) Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 60: 2256–2268. pmid:15572779
[25]  Pei J, Grishin NV (2007) PROMALS: towards accurate multiple sequence alignments of distantly related proteins. Bioinformatics 23: 802–808. pmid:17267437
[26]  Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, et al. (2005) ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 33: W299–302. pmid:15980475
[27]  Banks JLea (2005) Integrated modeling program, applied chemical theory (IMPACT). J Comput Chem: 1752–1780. pmid:16211539
[28]  Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, et al. (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47: 1739–1749. pmid:15027865
[29]  Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, et al. (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem 47: 1750–1759. pmid:15027866
[30]  Dubey KD, Chaubey AK, Ojha RP (2012) Role of polarization in ligand docking and binding affinity prediction for inhibitors of dengue virus. Medicinal Chemistry Research 21: 1030–1038.
[31]  Humphrey W, Dalke A, Schulten K (1996) VMD: Visual molecular dynamics. Journal of Molecular Graphics & Modelling 14: 33–38.

Full-Text

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133