American Journal of Biomedical Research
ISSN (Print): 2328-3947 ISSN (Online): 2328-3955 Website: http://www.sciepub.com/journal/ajbr Editor-in-chief: Hari K. Koul
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American Journal of Biomedical Research. 2016, 4(3), 46-60
DOI: 10.12691/ajbr-4-3-1
Open AccessArticle

Highly Conserved Epitopes of ZIKA Envelope Glycoprotein May Act as a Novel Peptide Vaccine with High Coverage: Immunoinformatics Approach

Marwan Mustafa Badawi1, , Marwa Mohamed Osman1, Afra AbdElhamid Fadl Alla1, Ammar Mohammed Ahmedani1, Mohamed hamed Abdalla1, Mosab Mohamed Gasemelseed2, Ahmed Abubakar Elsayed3 and Mohamed Ahmed Salih1

1Department of Biotechnology, Africa city of Technology- Khartoum, Sudan

2Al Neelain University, Faculty of Medical Laboratory Sciences

3Department of Microbiology, Soba University Hospital, Khartoum-Sudan

Pub. Date: June 22, 2016

Cite this paper:
Marwan Mustafa Badawi, Marwa Mohamed Osman, Afra AbdElhamid Fadl Alla, Ammar Mohammed Ahmedani, Mohamed hamed Abdalla, Mosab Mohamed Gasemelseed, Ahmed Abubakar Elsayed and Mohamed Ahmed Salih. Highly Conserved Epitopes of ZIKA Envelope Glycoprotein May Act as a Novel Peptide Vaccine with High Coverage: Immunoinformatics Approach. American Journal of Biomedical Research. 2016; 4(3):46-60. doi: 10.12691/ajbr-4-3-1

Abstract

Zika virus (ZIKV) is positive sense single stranded RNA of Flavivirus genus belonging to the Flaviviridae family. It has neither drug nor protective vaccine, and considered to be in relatedness to neurological abnormalities such as Guillain Barre Syndrome and microcephaly of neonates. The aim of this study is to analyze envelope glycoprotein E of all Zika strains using in silico approaches looking for conservancy, which is further studied to predict all potential epitopes that can be used after in vitro and in vivo confirmation as a therapeutic peptide vaccine. A total of 50 Zikavirusvariants’(include 12from South America) polyproteins retrieved from NCBI database were aligned, and the conserved regions of Envelope Glycoprotein-E were selected for epitopes prediction. IEDB analysis resource was used to predict B and T cell epitopes and to calculate the population coverage. Epitopes with high scores in both B cell and T cell epitopes predicting tools were suggested. Three epitopes were proposed for international therapeutic peptide vaccine for B cell (AQDKP, TPNSPRAE and TPHWNNK) and two other epitopes designed especially for South America strains (LDKQSDTQYV and EVQYAGTDGPCK). For T cell epitopes, MMLELDPPF epitope was highly recommended as therapeutic peptide vaccine to interact with MHC class I along with three other epitopes (MAVLGDTAW, KEWFHDIPL and DTAWDFGSV) which showed very good population coverage against the whole world population. Three epitopes showed high affinity to interact with MHC class II alleles (FKSLFGGMS, LITANPVIT and VHTALAGAL) with excellent population coverage throughout the world and South America region. Herd immunity protocols can be achieved in countries with low population coverage percentage to minimize the active transmission of the virus, especially among pregnant women and other groups at risk.We recommendin vitro and in vivo proving the effectiveness of these proposed epitopes as a vaccine, as well as to be used as a diagnostic screening test.

Keywords:
Zika virus (ZIKV) arboviruses peptide vaccine Immune Epitope Database IEDB epitopes Herd immunity and Vaccine

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References:

[1]  Dick GW, Kitchen SF, Haddow AJ. Zika virus. I. Isolations and serological specificity. Trans R Soc Trop Med Hyg. 1952; 46(5): 509-20.
 
[2]  Hayes EB. Zika virus outside Africa. Emerg Infect Dis. 2009; 15(9): 1347-50.
 
[3]  Robert S. Lanciotti, Olga L. Kosoy, Janeen J. Laven, Jason O. Velez, Amy J. Lambert, Alison J. Johnson, Stephanie M. Stanfi eld, and Mark R. Duffy. Genetic and Serologic Properties of Zika Virus Associated with an Epidemic, Yap State,Micronesia, 2007.Emerging Infectious Diseases. 2008; 14 (8): 1232-39.
 
[4]  Dick GW. Zika virus pathogenicity and physical properties. Trans R Soc Trop Med Hyg. 1952; 46: 521-34.
 
[5]  Duffy MR, Chen TH, Hancock WT, Powers AM, Kool JL, et al. Zika virus outbreak on Yap Island, Federated States of Micronesia. N Engl J Med. 2009;360: 2536-2543.
 
[6]  Foy BD, Kobylinski KC, Chilson Foy JL, Blitvich BJ, Travassos da Rosa A, Haddow AD, et al. Probable nonvector-borne transmission of Zika virus, Colorado, USA. Emerg Infect Dis. 2011; 17(5): 880-2.
 
[7]  World Health Organization. ZIKA VIRUS MICROCEPHALY AND GUILLAIN-BARRÉ SYNDROME. 2016. Available at: http://portalsaude.saude.gov.br/images/pdf/2016/janeiro/22/microcefalia-protocolo-de-vigilancia-e-resposta-v1-3-22jan2016.pdf
 
[8]  World Health Organization. ZIKA SITUATION REPORT. 2016. Print.
 
[9]  Charrel RN, Leparc-Goffart I, Pas S, de Lamballerie X, Koopmans M & Reusken C. State of knowledge on Zika virus for an adequate laboratory response [Submitted]. Bull World Health Organ E-pub: 10 Feb 2016.
 
[10]  Services YSDoH. Zika virus. Information for clinicians and other health professionals. Federated States of Micronesia: Yap State Department of Health; 2007. p. 2.
 
[11]  Cerdeño-Tárraga AM, Efstratiou A, Dover LG, et al. The complete genome sequence and analysis of Corynebacterium diphtheriaeNCTC13129. Nucleic Acids Research. 2003; 31(22): 6516-6523.
 
[12]  Trent DW, Qureshi AA. Structural and nonstructural proteins of Saint Louis encephalitis virus. Journal of Virology. 1971; 7(3):379-88.
 
[13]  Global Research Collaboration for Infectious Disease Preparedness,. Zika Virus (ZIKV) Outbreak. 2015. Print.
 
[14]  Rezaul Islam, M Sadman Sakib & Aubhishek Zaman. A computational assay to design an epitope- based peptide vaccine against chokungunya virus. Future virol.2012 7(10): 1029-1042.
 
[15]  Arafat Rahman Oany, Tahmina Sharmin,Afrin Sultana Chowdhury,Tahmina Pervin Jyot and Md Anayet Hasan. Highly Conserved Reagions in Ebola Virus RNA dependent RNA polymerase may be act as a universal novel peptide vaccine target: a computational approach.Oany etal, In Silico Pharmacology(2015) 3:7.
 
[16]  Anayet Hasan, Mehjabeen Hossain and Md. Jibran Alam. A Computational Assay to Design an Epitope-Based Peptide Vaccine Against Saint Louis Encephalitis Virus. Bioinformatics and Biology Insights 2013:7 347-355.
 
[17]  Jens Erik Pontoppidan Larsen, Ole Lund and Morten Nielsen. Improved method for predicting linear B-cell epitopes. Immunome Res. 2006; 2: 2.
 
[18]  Emini EA, Hughes JV, Perlow DS, Boger J. 1985. Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol 55:836-839.
 
[19]  Kolaskar AS, Tongaonkar PC. 1990. A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett276:172-174.
 
[20]  Parker JM, Guo D, Hodges RS. 1986. New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry 25:5425-5432.
 
[21]  Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, Lundegaard C, Sette A, Lund O, Bourne PE, Nielsen M, Peters B. 2012. Immune epitope database analysis resource. NAR.
 
[22]  Nielsen M, Lundegaard C, Worning P, Lauemøller SL, Lamberth K, Buus S, Brunak S, Lund O. 2003. Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci 12:1007-1017.
 
[23]  Lundegaard C, Lamberth K, Harndahl M, Buus S, Lund O, and Nielsen M. 2008. NetMHC-3.0: Accurate web accessible predictions of Human, Mouse, and Monkey MHC class I affinities for peptides of length 8-11. NAR 36:W509-512.
 
[24]  Peters B, Sette A. 2005. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics 6:132.
 
[25]  Sidney J, Assarsson E, Moore C, Ngo S, Pinilla C, Sette A, Peters B. 2008. Quantitative peptide binding motifs for 19 human and mouse MHC class I molecules derived using positional scanning combinatorial peptide libraries. Immunome Res 4:2.
 
[26]  Kim Y, Ponomarenko J, Zhu Z, et al. Immune epitope database analysis resource. Nucleic Acids Research. 2012;40(Web Server issue):W525-W530.
 
[27]  Wang P, Sidney J, Dow C, Mothé B, Sette A, Peters B. 2008. A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol. 4(4):e1000048.
 
[28]  Wang P, Sidney J, Kim Y, Sette A, Lund O, Nielsen M, Peters B. 2010. Peptide binding predictions for HLA DR, DP and DQ molecules. BMC Bioinformatics. 11:568.
 
[29]  Pratik Narain Srivastava, Richa Jain, Shyam Dhar Dubey, Sharad Bhatnagar, Nabeel Ahmad. Prediction of Epitope-Based Peptides for Vaccine Development from Coat Proteins GP2 and VP24 of Ebola Virus Using Immunoinformatics, International Journal of Peptide Research and Therapeutics (2016) 22:119-133.
 
[30]  Zhang, Q., Wang, P., Kim, Y., Haste-Andersen, P., Beaver, J., Bourne, P. E. et al. (2008). Immune epitope database analysis resource (IEDB-AR).Nucleic Acids Research36(Web Server issue), W513-W518.
 
[31]  Bui HH,Sidney J, Dinh K, Southwood S, Newman MJ, Sette A. Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics. 2006 Mar 17;7:153.
 
[32]  The Phyre2 web portal for protein modeling, prediction and analysis Kelley LA et al. Nature Protocols 10, 845-858 (2015).
 
[33]  UCSF Chimera--a visualization system for exploratory research and analysis. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12.
 
[34]  Bachler, B.C.; Humbert, M.; Palikuqi, B.; Siddappa, N.B.; Lakhashe, S.K.; Rasmussen, R.A.; Ruprecht, R.M. Novel biopanning strategy to identify epitopes associated with vaccine protection. J. Virol. 2013, 87, 4403-4416.
 
[35]  Perrie, Y.; Kirby, D.; Bramwell, V.W.; Mohammed, A.R. Recent developments in particulate-based vaccines. Recent Pat. Drug Deliv. Formul. 2007, 1, 117-129.
 
[36]  Black, M.; Trent, A.; Tirrell, M.; Olive, C. Advances in the design and delivery of peptide subunit vaccines with a focus on toll-like receptor agonists. Expert Rev. Vaccines 2010, 9, 157-173.
 
[37]  Thompson, A.L.; Staats, H.F. Cytokines: The future of intranasal vaccine adjuvants. Clin. Dev. Immunol. 2011.
 
[38]  Petrovsky, N.; Aguilar, J.C. Vaccine adjuvants: Current state and future trends. Immunol. Cell Biol. 2004, 82, 488-496.
 
[39]  Sesardic, D. Synthetic peptide vaccines. J. Med. Microbiol. 1993, 39, 241-242.
 
[40]  Liu, Y.; McNevin, J.; Zhao, H.; Tebit, D.M.; Troyer, R.M.; McSweyn, M.; Ghosh, A.K.; Shriner, D.; Arts, E.J.; McElrath, M.J.; et al. Evolution of human immunodeficiency virus type 1 cytotoxic T-lymphocyte epitopes: Fitness-balanced escape. J. Virol. 2007, 81, 12179-12188.
 
[41]  Kolesanova, E.F.; Sanzhakov, M.A.; Kharybin, O.N. Development of the schedule for multiple parallel ―difficult Peptide synthesis on pins. Int. J. Pept. 2013.
 
[42]  Epstein, J.E.; Giersing, B.; Mullen, G.; Moorthy, V.; Richie, T.L. Malaria vaccines: Are we getting closer? Curr. Opin. Mol. Ther. 2007, 9, 12-24.
 
[43]  Volpina, O.M.; Gelfanov, V.M.; Yarov, A.V.; Surovoy, A.Y.; Chepurkin, A.V.; Ivanov, V.T. New virus-specific T-helper epitopes of foot-and-mouth disease viral VP1 protein. FEBS Lett. 1993, 333, 175-178.
 
[44]  Tarradas, J.; Monso, M.; Munoz, M.; Rosell, R.; Fraile, L.; Frías, M.T.; Domingo, M.; Andreu, D.; Sobrino, F.; Ganges, L. Partial protection against classical swine fever virus elicited by dendrimeric vaccine-candidate peptides in domestic pigs. Vaccine 2011, 29, 4422-4429.
 
[45]  Stanekova, Z.; Kiraly, J.; Stropkovska, A.; Mikušková, T.; Mucha, V.; Kostolanský, F.; Varečková, E. Heterosubtypic protective immunity against influenza a virus induced by fusion peptide of the hemagglutinin in comparison to ectodomain of M2 protein. Acta Virol. 2011, 55, 61-67.
 
[46]  Oscherwitz, J.; Yu, F.; Cease, K.B. A synthetic peptide vaccine directed against the 2ss2–2ss3 loop of domain 2 of protective antigen protects rabbits from inhalation anthrax. J. Immunol. 2010, 185, 3661-3668.
 
[47]  Solares, A.M.; Baladron, I.; Ramos, T.; Valenzuela, C.; Borbon, Z.; Fanjull, S.; Gonzalez, L.; Castillo, D.; Esmir, J.; Granadillo, M.; et al. Safety and immunogenicity of a human papillomavirus peptide vaccine (CIGB-228) in women with high-grade cervical intraepithelial neoplasia: first-in-human, proof-of-concept trial. ISRN Obstet. Gynecol. 2011.
 
[48]  Bernhardt, S.L.; Gjertsen, M.K.; Trachsel, S.; Møller, M.; Eriksen, J.A.; Meo, M.; Buanes, T.; Gaudernack, G. Telomerase peptide vaccination of patients with non-resectable pancreatic cancer: A dose escalating phase I/II study. Br. J. Cancer 2006, 95, 1474-1482.
 
[49]  Brunsvig, P.F.; Aamdal, S.; Gjertsen, M.K.; Kvalheim, G.; Markowski-Grimsrud, C.J.; Sve, I.; Dyrhaug, M.; Trachsel, S.; Møller, M.; Eriksen, J.A.; et al. Telomerase peptide vaccination: A phase I/II study in patients with non-small cell lung cancer. Cancer Immunol. Immunother. 2006, 55, 1553-1564.
 
[50]  Brunsvig, P.F.; Kyte, J.A.; Kersten, C.; Sundstrøm, S.; Møller, M.; Nyakas, M.; Hansen, G.L.; Gaudernack, G.; Aamdal, S. Telomerase peptide vaccination in NSCLC: A phase II trial in stage III patients vaccinated after chemoradiotherapy and an 8-year update on a phase I/II trial. Clin. Cancer Res. 2011, 17, 6847-6857.
 
[51]  Kyte, J.A.; Gaudernack, G.; Dueland, S.; Trachsel, S.; Julsrud, L.; Aamdal, S. Telomerase peptide vaccination combined with temozolomide: A clinical trial in stage IV melanoma patients. Clin. Cancer Res. 2011, 17, 4568-4580.
 
[52]  Greten, T.F.; Forner, A.; Korangy, F.; N’Kontchou, G.; Barget, N.; Ayuso, C.; Ormandy, L.A.; Manns, M.P.; Beaugrand, M.; Bruix, J. A phase II open label trial evaluating safety and efficacy of a telomerase peptide vaccination in patients with advanced hepatocellular carcinoma. BMC Cancer 2010, 10, e209.
 
[53]  Kyte, J.A.; Trachsel, S.; Risberg, B.; Thor, S.P.; Lislerud, K.; Gaudernack, G. Unconventional cytokine profiles and development of T cell memory in long-term survivors after cancer vaccination. Cancer Immunol. Immunother. 2009, 58, 1609-1626. 25.
 
[54]  Mohammad Mahfuz Ali Khan Shawan, Hafij Al Mahmud, Md. Mahmudul Hasan, Afroza Parvin, Md. Nazibur Rahman and S. M. Badier Rahman. In Silico Modeling and Immunoinformatics Probing Disclose the Epitope Based PeptideVaccine Against Zika Virus Envelope Glycoprotein. Indian J. Pharm. Biol. Res. 2014; 2(4):44-57.
 
[55]  Andrea J. Sant and Andrew McMichael. Revealing the role of CD4+ T cells in viral immunity. Journal of Experimental Medicine. 2012; 209(8): 1391-1395.
 
[56]  Paul S1, Weiskopf D, Angelo MA, Sidney J, Peters B, Sette A. HLA class I alleles are associated with peptide binding repertoires of different size, affinity and immunogenicity. Journal of Immunology. 2013; 191(12):5831-9.
 
[57]  A. Arnaiz-Villena, J. Moscoso, J.I. Serrano-Vela, J. Martinez-Laso. The uniqueness of amerindians according to HLA genes and the peopling of the Americas. Journal of Inmunología. 2006; 25: 13-24.
 
[58]  Lizcano Fernández, Francisco “Composición Étnica de las Tres Áreas Culturales del Continente Americano al Comienzo del Siglo XXI”.Convergencia (in Spanish) (Mexico: Universidad Autónoma del Estado de México, Centro de Investigación en Ciencias Sociales y Humanidades). 2005; 38: 185-232.
 
[59]  Zika virus infection outbreak, Brazil and the Pacific region”. Stockholm: European Centre for Disease Prevention and Control. 25 May 2015. p. 4. Retrieved 12 February 2016.
 
[60]  Testa, J.S.; Philip, R. Role of T-cell epitope-based vaccine in prophylactic and therapeutic applications. Future Virol. 2012, 7, 1077-1088. 28. Lanier, J.G.; Newman, M.J.; Lee, E.M.;
 
[61]  Sette, A.; Ahmed, R. Peptide vaccination using nonionic block copolymers induces protective anti-viral CTL responses. Vaccine 1999, 18, 549-557.