Login Register Cart 0
Generic placeholder image

Combinatorial Chemistry & High Throughput Screening

Editor-in-Chief

ISSN (Print): 1386-2073
ISSN (Online): 1875-5402

Back
Journal Home About Journal Editorial Board Journal Insight Current Issue Volumes/Issues
Subscribe
Research Article

T-cell Epitope-based Vaccine Design for Nipah Virus by Reverse Vaccinology Approach

Author(s): Praveen K.P. Krishnamoorthy*, Sekar Subasree, Udhayachandran Arthi, Mohammad Mobashir, Chirag Gowda and Prasanna D. Revanasiddappa

Volume 23, Issue 8, 2020

Page: [788 - 796] Pages: 9

DOI: 10.2174/1386207323666200427114343

Price: $65

Abstract

Aim and Objective: Nipah virus (NiV) is a zoonotic virus of the paramyxovirus family that sporadically breaks out from livestock and spreads in humans through breathing resulting in an indication of encephalitis syndrome. In the current study, T cell epitopes with the NiV W protein antigens were predicted.

Materials and Methods: Modelling of unavailable 3D structure of W protein followed by docking studies of respective Human MHC - class I and MHC - class II alleles predicted was carried out for the highest binding rates. In the computational analysis, epitopes were assessed for immunogenicity, conservation, and toxicity analysis. T – cell-based vaccine development against NiV was screened for eight epitopes of Indian - Asian origin.

Results: Two epitopes, SPVIAEHYY and LVNDGLNII, have been screened and selected for further docking study based on toxicity and conservancy analyses. These epitopes showed a significant score of -1.19 kcal/mol and 0.15 kcal/mol with HLA- B*35:03 and HLA- DRB1 * 07:03, respectively by using allele - Class I and Class II from AutoDock. These two peptides predicted by the reverse vaccinology approach are likely to induce immune response mediated by T – cells.

Conclusion: Simulation using GROMACS has revealed that LVNDGLNII epitope forms a more stable complex with HLA molecule and will be useful in developing the epitope-based Nipah virus vaccine.

Keywords: Nipah, vaccination, immunogenicity, conservation, toxicity, docking, simulation.

« Previous Next »
[1]
Yoneda, M.; Guillaume, V.; Ikeda, F.; Sakuma, Y.; Sato, H.; Wild, T.F.; Kai, C. Establishment of a Nipah virus rescue system. Proc. Natl. Acad. Sci. USA, 2006, 103(44), 16508-16513.
[http://dx.doi.org/10.1073/pnas.0606972103 ] [PMID: 17053073]
[2]
Singh, R.K.; Dhama, K.; Chakraborty, S.; Tiwari, R.; Natesan, S.; Khandia, R.; Munjal, A.; Vora, K.S.; Latheef, S.K.; Karthik, K.; Singh Malik, Y.; Singh, R.; Chaicumpa, W.; Mourya, D.T. Nipah virus: epidemiology, pathology, immunobiology and advances in diagnosis, vaccine designing and control strategies - a comprehensive review. Vet. Q., 2019, 39(1), 26-55.
[http://dx.doi.org/10.1080/01652176.2019.1580827 ] [PMID: 31006350]
[3]
Yu, J.; Lv, X.; Yang, Z.; Gao, S.; Li, C.; Cai, Y.; Li, J. The main risk factors of Nipah disease and its risk analysis in China. Viruses, 2018, 10(10), 572.
[http://dx.doi.org/10.3390/v10100572 ] [PMID: 30347642]
[4]
Raveendran, A.V.; Sadanandan, S.; Thulaseedharan, N.K.; Kg, S.K.; Pallivalappil, B.; As, A.K. Nipah Virus infection. J. Assoc. Physicians India, 2018, 66, 58.
[5]
Prarthana, M.S. Nipah virus in India: past, present, and future. Int. J. Community Med. Public Health, 2018, 5(9), 3653-3658.
[http://dx.doi.org/10.18203/2394-6040.ijcmph20183471]
[6]
Centers for Disease Control and Prevention (CDC). Update: outbreak of Nipah virus--Malaysia and Singapore, 1999. MMWR Morb. Mortal. Wkly. Rep., 1999, 48(16), 335-337.
[PMID: 10366143]
[7]
Gurley, E.S.; Montgomery, J.M.; Hossain, M.J.; Bell, M.; Azad, A.K.; Islam, M.R.; Molla, M.A.; Carroll, D.S.; Ksiazek, T.G.; Rota, P.A.; Lowe, L.; Comer, J.A.; Rollin, P.; Czub, M.; Grolla, A.; Feldmann, H.; Luby, S.P.; Woodward, J.L.; Breiman, R.F. Person-to-person transmission of Nipah virus in a Bangladeshi community. Emerg. Infect. Dis., 2007, 13(7), 1031-1037.
[http://dx.doi.org/10.3201/eid1307.061128 ] [PMID: 18214175]
[8]
Chua, K.B.; Bellini, W.J.; Rota, P.A.; Harcourt, B.H.; Tamin, A.; Lam, S.K.; Ksiazek, T.G.; Rollin, P.E.; Zaki, S.R.; Shieh, W.; Goldsmith, C.S.; Gubler, D.J.; Roehrig, J.T.; Eaton, B.; Gould, A.R.; Olson, J.; Field, H.; Daniels, P.; Ling, A.E.; Peters, C.J.; Anderson, L.J.; Mahy, B.W. Nipah virus: a recently emergent deadly paramyxovirus. Science, 2000, 288(5470), 1432-1435.
[http://dx.doi.org/10.1126/science.288.5470.1432 ] [PMID: 10827955]
[9]
Ang, B.S.P.; Lim, T.C.C.; Wang, L. Nipah virus infection. J. Clin. Microbiol., 2018, 56(6), e01875-e17.
[http://dx.doi.org/10.1128/JCM.01875-17 ] [PMID: 29643201]
[10]
Bever, L. Rare, Brain-damaging virus spreads panic in India as death toll rises. The Washington Post, 23 May 2018.
[11]
Narayan, V.A. Nipah virus outbreak in India: is it a bat-man conflict? Int. J. Community Med. Public Health, 2019, 6(4), 1826-1830.
[http://dx.doi.org/10.18203/2394-6040.ijcmph20191430]
[12]
Sun, B.; Jia, L.; Liang, B.; Chen, Q.; Liu, D. Phylogeography, transmission, and viral proteins of Nipah virus. Virol. Sin., 2018, 33(5), 385-393.
[http://dx.doi.org/10.1007/s12250-018-0050-1 ] [PMID: 30311101]
[13]
Ciancanelli, M.J.; Volchkova, V.A.; Shaw, M.L.; Volchkov, V.E.; Basler, C.F. Nipah virus sequesters inactive STAT1 in the nucleus via a P gene-encoded mechanism. J. Virol., 2009, 83(16), 7828-7841.
[http://dx.doi.org/10.1128/JVI.02610-08 ] [PMID: 19515782]
[14]
Shaw, M.L.; García-Sastre, A.; Palese, P.; Basler, C.F. Nipah virus V and W proteins have a common STAT1-binding domain yet inhibit STAT1 activation from the cytoplasmic and nuclear compartments, respectively. J. Virol., 2004, 78(11), 5633-5641.
[http://dx.doi.org/10.1128/JVI.78.11.5633-5641.2004 ] [PMID: 15140960]
[15]
Yoneda, M.; Guillaume, V.; Sato, H.; Fujita, K.; Georges-Courbot, M.C.; Ikeda, F.; Omi, M.; Muto-Terao, Y.; Wild, T.F.; Kai, C. The nonstructural proteins of Nipah virus play a key role in pathogenicity in experimentally infected animals. PLoS One, 2010, 5(9), e12709.
[http://dx.doi.org/10.1371/journal.pone.0012709 ] [PMID: 20856799]
[16]
Lo, M.K.; Peeples, M.E.; Bellini, W.J.; Nichol, S.T.; Rota, P.A.; Spiropoulou, C.F. Distinct and overlapping roles of Nipah virus P gene products in modulating the human endothelial cell antiviral response. PLoS One, 2012, 7(10), e47790.
[http://dx.doi.org/10.1371/journal.pone.0047790 ] [PMID: 23094089]
[17]
Satterfield, B.A.; Cross, R.W.; Fenton, K.A.; Borisevich, V.; Agans, K.N.; Deer, D.J.; Graber, J.; Basler, C.F.; Geisbert, T.W.; Mire, C.E. Nipah virus C and W proteins contribute to respiratory disease in ferrets. J. Virol., 2016, 90(14), 6326-6343.
[http://dx.doi.org/10.1128/JVI.00215-16 ] [PMID: 27147733]
[18]
Satterfield, B.A.; Cross, R.W.; Fenton, K.A.; Agans, K.N.; Basler, C.F.; Geisbert, T.W.; Mire, C.E. The immunomodulating V and W proteins of Nipah virus determine disease course. Nat. Commun., 2015, 6(1), 7483.
[http://dx.doi.org/10.1038/ncomms8483 ] [PMID: 26105519]
[19]
Uchida, S.; Horie, R.; Sato, H.; Kai, C.; Yoneda, M. Possible role of the Nipah virus V protein in the regulation of the interferon beta induction by interacting with UBX domain-containing protein1. Sci. Rep., 2018, 8(1), 7682.
[http://dx.doi.org/10.1038/s41598-018-25815-9 ] [PMID: 29769705]
[20]
Satterfield, B.A.; Borisevich, V.; Foster, S.L.; Rodriguez, S.E.; Cross, R.W.; Fenton, K.A.; Agans, K.N.; Basler, C.F.; Geisbert, T.W.; Mire, C.E. Antagonism of STAT1 by Nipah virus P gene products modulates disease course but not lethal outcome in the ferret model. Sci. Rep., 2019, 9(1), 16710.
[http://dx.doi.org/10.1038/s41598-019-53037-0 ] [PMID: 31723221]
[21]
Sharmin, R.; Islam, A.B.M.M.K. A highly conserved WDYPKCDRA epitope in the RNA directed RNA polymerase of human coronaviruses can be used as epitope-based universal vaccine design. BMC Bioinformatics, 2014, 15(1), 161.
[http://dx.doi.org/10.1186/1471-2105-15-161 ] [PMID: 24884408]
[22]
Purcell, A.W.; McCluskey, J.; Rossjohn, J. More than one reason to rethink the use of peptides in vaccine design. Nat. Rev. Drug Discov., 2007, 6(5), 404-414.
[http://dx.doi.org/10.1038/nrd2224 ] [PMID: 17473845]
[23]
Bairoch, A.; Apweiler, R.; Wu, C.H.; Barker, W.C.; Boeckmann, B.; Ferro, S.; Gasteiger, E.; Huang, H.; Lopez, R.; Magrane, M.; Martin, M.J.; Natale, D.A.; O’Donovan, C.; Redaschi, N.; Yeh, L.S. The universal protein resource (UniProt). Nucleic Acids Res., 2005, 33(Database issue), D154-D159.
[http://dx.doi.org/10.1093/nar/gki070 ] [PMID: 15608167]
[24]
Desai, D.V.; Kulkarni-Kale, U. T-cell epitope prediction methods: an overview. Immunoinformatics; Humana Press: New York, NY, 2014, pp. 333-364.
[http://dx.doi.org/10.1007/978-1-4939-1115-8_19]
[25]
Jurtz, V.; Paul, S.; Andreatta, M.; Marcatili, P.; Peters, B.; Nielsen, M. NetMHCpan-4.0: Improved peptide–MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data. J. Immunol., 2017, 199(9), 3360-3368.
[http://dx.doi.org/10.4049/jimmunol.1700893 ] [PMID: 28978689]
[26]
Stranzl, T.; Larsen, M.V.; Lundegaard, C.; Nielsen, M. NetCTLpan: pan-specific MHC class I pathway epitope predictions. Immunogenetics, 2010, 62(6), 357-368.
[http://dx.doi.org/10.1007/s00251-010-0441-4 ] [PMID: 20379710]
[27]
Vita, R.; Overton, J.A.; Greenbaum, J.A.; Ponomarenko, J.; Clark, J.D.; Cantrell, J.R.; Wheeler, D.K.; Gabbard, J.L.; Hix, D.; Sette, A.; Peters, B. The immune epitope database (IEDB) 3.0. Nucleic Acids Res., 2015, 43(Database issue), D405-D412.
[http://dx.doi.org/10.1093/nar/gku938 ] [PMID: 25300482]
[28]
Saha, C.K.; Mahbub Hasan, M.; Saddam Hossain, M.; Asraful Jahan, M.; Azad, A.K. In silico identification and characterization of common epitope-based peptide vaccine for Nipah and Hendra viruses. Asian Pac. J. Trop. Med., 2017, 10(6), 529-538.
[http://dx.doi.org/10.1016/j.apjtm.2017.06.016 ] [PMID: 28756915]
[29]
Calis, J.J.; Maybeno, M.; Greenbaum, J.A.; Weiskopf, D.; De Silva, A.D.; Sette, A.; Keşmir, C.; Peters, B. Properties of MHC class I presented peptides that enhance immunogenicity. PLOS Comput. Biol., 2013, 9(10), e1003266.
[http://dx.doi.org/10.1371/journal.pcbi.1003266 ] [PMID: 24204222]
[30]
Bui, H.H.; Sidney, J.; Li, W.; Fusseder, N.; Sette, A. Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics, 2007, 8(1), 361.
[http://dx.doi.org/10.1186/1471-2105-8-361 ] [PMID: 17897458]
[31]
Gupta, S.; Kapoor, P.; Chaudhary, K.; Gautam, A.; Kumar, R.; Raghava, G.P. Open Source Drug Discovery Consortium. In silico approach for predicting toxicity of peptides and proteins. PLoS One, 2013, 8(9), e73957.
[http://dx.doi.org/10.1371/journal.pone.0073957 ] [PMID: 24058508]
[32]
Lamiable, A.; Thévenet, P.; Rey, J.; Vavrusa, M.; Derreumaux, P.; Tufféry, P. PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex. Nucleic Acids Res., 2016, 44(W1), W449-54.
[http://dx.doi.org/10.1093/nar/gkw329 ] [PMID: 27131374]
[33]
Kelley, L.A.; Mezulis, S.; Yates, C.M.; Wass, M.N.; Sternberg, M.J. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc., 2015, 10(6), 845-858.
[http://dx.doi.org/10.1038/nprot.2015.053 ] [PMID: 25950237]
[34]
Trott, O.; Olson, A.J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem., 2010, 31(2), 455-461.
[PMID: 19499576]
[35]
Gangadharappa, B.S.; Sharath, R.; Revanasiddappa, P.D.; Chandramohan, V.; Balasubramaniam, M.; Vardhineni, T.P. Structural insights of metallo-beta-lactamase revealed an effective way of inhibition of enzyme by natural inhibitors. J. Biomol. Struct. Dyn., 2019, 1, 1-15.
[http://dx.doi.org/10.1080/07391102.2019.1667265 ] [PMID: 31514687]
[36]
Arunkumar, G.; Devadiga, S.; McElroy, A.K.; Prabhu, S.; Sheik, S.; Abdulmajeed, J.; Robin, S.; Sushama, A.; Jayaram, A.; Nittur, S.; Shakir, M.; Kumar, K.G.S.; Radhakrishnan, C.; Sakeena, K.; Vasudevan, J.; Reena, K.J.; Sarita, R.L.; Klena, J.D.; Spiropoulou, C.F.; Laserson, K.F.; Nichol, S.T. ’ Prabhu, S.’ Sheik, S.; Abdulmajeed, J.; Robin, S.; Sushama, A.; Jayaram, A.; Nittur, S.; Shakir, M. Adaptive immune responses in humans during Nipah virus acute and convalescent phases of infection. Clin. Infect. Dis., 2019, 69(10), 1752-1756.
[http://dx.doi.org/10.1093/cid/ciz010 ] [PMID: 30615097]
[37]
Altuvia, Y.; Margalit, H. A structure-based approach for prediction of MHC-binding peptides. Methods, 2004, 34(4), 454-459.
[http://dx.doi.org/10.1016/j.ymeth.2004.06.008 ] [PMID: 15542371]
[38]
Schönbach, C.; Nagashima, T.; Konagaya, A. Textmining in support of knowledge discovery for vaccine development. Methods, 2004, 34(4), 488-495.
[http://dx.doi.org/10.1016/j.ymeth.2004.06.009 ] [PMID: 15542375]
[39]
Pandey, B.; Singh, S.; Srivastava, S.; Sharma, N. In silico prediction of epitope-based peptides from proteome of nipah virus. Int. J. Sci. Innovative Res., 2015, 3(1), 75-79.
[40]
Mire, C.E.; Geisbert, J.B.; Agans, K.N.; Versteeg, K.M.; Deer, D.J.; Satterfield, B.A.; Fenton, K.A.; Geisbert, T.W. Use of single-injection recombinant vesicular stomatitis virus vaccine to protect nonhuman primates against lethal Nipah virus disease. Emerg. Infect. Dis., 2019, 25(6), 1144-1152.
[http://dx.doi.org/10.3201/eid2506.181620 ] [PMID: 31107231]
[41]
Keshwara, R.; Shiels, T.; Postnikova, E.; Kurup, D.; Wirblich, C.; Johnson, R.F.; Schnell, M.J. Rabies-based vaccine induces potent immune responses against Nipah virus. npj. Vaccines (Basel), 2019, 4(1), 1-10.
[42]
Walpita, P.; Cong, Y.; Jahrling, P.B.; Rojas, O.; Postnikova, E.; Yu, S.; Johns, L.; Holbrook, M.R. A VLP-based vaccine provides complete protection against Nipah virus challenge following multiple-dose or single-dose vaccination schedules in a hamster model. npj. Vaccines (Basel), 2017, 2(1), 1-9.
[43]
Broder, C.C.; Xu, K.; Nikolov, D.B.; Zhu, Z.; Dimitrov, D.S.; Middleton, D.; Pallister, J.; Geisbert, T.W.; Bossart, K.N.; Wang, L.F. A treatment for and vaccine against the deadly Hendra and Nipah viruses. Antiviral Res., 2013, 100(1), 8-13.
[http://dx.doi.org/10.1016/j.antiviral.2013.06.012 ] [PMID: 23838047]
[44]
Mire, C.E.; Satterfield, B.A.; Geisbert, J.B.; Agans, K.N.; Borisevich, V.; Yan, L.; Chan, Y.P.; Cross, R.W.; Fenton, K.A.; Broder, C.C.; Geisbert, T.W. Pathogenic differences between Nipah virus Bangladesh and Malaysia strains in primates: implications for antibody therapy. Sci. Rep., 2016, 6, 30916-30925.
[http://dx.doi.org/10.1038/srep30916 ] [PMID: 27484128]
[45]
Mire, C.E.; Chan, Y.P.; Borisevich, V.; Cross, R.W.; Yan, L.; Agans, K.N.; Dang, H.V.; Veesler, D.; Fenton, K.A.; Geisbert, T.W.; Broder, C.C. A Cross-Reactive humanized monoclonal antibody targeting fusion glycoprotein function protects ferrets against lethal nipah virus and hendra virus infection. J. Infect. Dis., 2019, 6, 1-9.
[PMID: 31686101]
[46]
Dang, H.V.; Chan, Y.P.; Park, Y.J.; Snijder, J.; Da Silva, S.C.; Vu, B.; Yan, L.; Feng, Y.R.; Rockx, B.; Geisbert, T.W.; Mire, C.E.; Broder, C.C.; Veesler, D. An antibody against the F glycoprotein inhibits Nipah and Hendra virus infections. Nat. Struct. Mol. Biol., 2019, 26(10), 980-987.
[http://dx.doi.org/10.1038/s41594-019-0308-9 ] [PMID: 31570878]

Rights & Permissions Print Cite
Article Metrics
35
1
© 2024 Bentham Science Publishers | Privacy Policy