In silico Design of Discontinuous Peptides Representative of B and T-cell Epitopes from HER2-ECD as Potential Novel Cancer Peptide Vaccines

  • Manijeh, Mahdavi (Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences) ;
  • Mehrnaz, Keyhanfar (Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan) ;
  • Violaine, Moreau (UMR 3145 SysDiag CNRS/Bio-Rad) ;
  • Hassan, Mohabatkar (Department of Biotechnology, Faculty of Advanced Sciences and Technologies, University of Isfahan) ;
  • Abbas, Jafarian (Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences) ;
  • Mohammad, Rabbani (Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences)
  • Published : 2013.10.30


At present, the most common cause of cancer-related death in women is breast cancer. In a large proportion of breast cancers, there is the overexpression of human epidermal growth factor receptor 2 (HER2). This receptor is a 185 KDa growth factor glycoprotein, also known as the first tumor-associated antigen for different types of breast cancers. Moreover, HER2 is an appropriate cell-surface specific antigen for passive immunotherapy, which relies on the repeated application of monoclonal antibodies that are transferred to the patient. However, vaccination is preferable because it would stimulate a patient's own immune system to actively respond to a disease. In the current study, several bioinformatics tools were used for designing synthetic peptide vaccines. PEPOP was used to predict peptides from HER2 ECD subdomain III in the form of discontinuous-continuous B-cell epitopes. Then, T-cell epitope prediction web servers MHCPred, SYFPEITHI, HLA peptide motif search, Propred, and SVMHC were used to identify class-I and II MHC peptides. In this way, PEPOP selected 12 discontinuous peptides from the 3D structure of the HER2 ECD subdomain III. Furthermore, T-cell epitope prediction analyses identified four peptides containing the segments 77 (384-391) and 99 (495-503) for both B and T-cell epitopes. This work is the only study to our knowledge focusing on design of in silico potential novel cancer peptide vaccines of the HER2 ECD subdomain III that contain epitopes for both B and T-cells. These findings based on bioinformatics analyses may be used in vaccine design and cancer therapy; saving time and minimizing the number of tests needed to select the best possible epitopes.


HER2 receptor;discontinuous B cell epitope;T-cell epitope;bioinformatics;peptide vaccine


  1. Bian H, Reidhaar-Olson JF, Hammer J (2003). The use of bioinformatics for identifying class II-restricted T-cell epitopes. Meth, 29, 299-309.
  2. Alvarenga L, Moreau V, Felicori L, et al (2010). Design of antibody-reactive peptides from discontinuous parts of scorpion toxins. Vaccine, 28, 970-80.
  3. Ansari HR, Raghava GP (2010). Identification of conformational B-cell Epitopes in an antigen from its primary sequence. Immunol Res, 6, 6.
  4. Arensa R, Hallb TV, van der Burgb SH (2013). Prospects of combinatorial synthetic peptide vaccine-based immunotherapy against cancer. Sem Immunol, 25, 182-90.
  5. Awada A, Bozovic-Spasojevic I, Chow L (2012). New therapies in HER2-positive breast cancer: a major step towards a cure of the disease? Cancer Treatment Reviews, 38, 494-504.
  6. Axelsena TV, Holma A, Christiansena G, Birkelund S (2011). Identification of the shortest AB-peptide generating highly specific antibodies against the C-terminal end of amyloid-B42. Vaccine, 29, 3260-9.
  7. Calabrich A, Fernandes GS, Katz A (2008). Trastuzumab: mechanisms of resistance and therapeutic opportunities. Oncol, 22, 1250-8.
  8. Chen P, Rayner S, Hu KH (2011). Advances of bioinformatics tools applied in virus epitopes prediction. Virologica Sinica, 26, 1.
  9. Chen SW, Van Regenmortel MH, Pellequer JL (2009). Structure-activity relationships in peptide-antibody complexes: implications for epitope prediction and development of synthetic peptide vaccines. Curr Med Chem, 16, 953.
  10. Cho HS, Mason K, Ramyar KX, et al (2003). Structure of the extracellular region of HER2 alone and in complex with the herceptin fab. Nature, 421, 756-60.
  11. Correa I, Plunkett T (2001). Update on HER-2 as a target for cancer therapy HER2/neu peptides as tumour vaccines for T cell recognition. Breast Cancer Res, 3, 399-403.
  12. Disis M, Schiffman K (2001). Cancer vaccines targeting the HERZ/neu oncogenic protein. Sem Oncol, 28, 12-20.
  13. Dakappagari NK, Douglas DB, Triozzi PL, et al (2000). Prevention of mammary tumors with a chimeric Her-2 B-cell epitope peptide vaccine. Cancer Res, 60, 3782-9.
  14. Dakappagari NK, Pyles J, Parihar R, et al (2003). Multi-human epidermal growth factor receptor-2 B cell epitope peptide vaccine mediates superior antitumor responses. J Immunol, 170, 4242-53.
  15. De Groot AS, Cohen T, Ardito M, et al (2010). Use of bioinformatics to predict MHC ligands and T-cell epitopes: application to epitope-driven vaccine design. Methods Microbiol, 37, 35-66.
  16. Donnes P, Elofsson A (2002). Prediction of MHC class I binding peptides, using SVMHC. BMC Bioinformatics, 3, 25.
  17. Doytchinova IA, Flower DR (2002). Quantitative approaches to computational vaccinology. Immunol Cell Biol, 80, 270-9.
  18. Firat H, Garcia-Pons F, Tourdot S, et al (1999). H-2 class I knockout, HLA-A2.1-transgenic mice: a versatile animal model for preclinical evaluation of antitumor immunotherapeutic strategies. Eur J Immunol, 29, 3112.<3112::AID-IMMU3112>3.0.CO;2-Q
  19. Fisher RD, Ultsch M, Lingel A, et al (2010). Structure of the complex between HER2 and an antibody paratope formed by side chains from tryptophan and serine. J Mol Biol, 402, 217.
  20. Franklin MC, Carey KD, Vajdos FF, et al (2004). Insights into ErbB signaling from the structure of the ErbB2-pertuzumab complex. Cancer Cell, 5, 317-28.
  21. Gritzapis AD, Fridmanb A, Pereza SA, et al (2010). HER-2/neu (657-665) represents an immunogenic epitope of HER-2/neu oncoprotein with potent antitumor properties. Vaccine, 28, 162-70.
  22. Gangwara RS, Shil P, Sapkala GN, Khanc SA, Gore MM (2012). Induction of virus-specific neutralizing immune response against West Nile and Japanese encephalitis viruses by chimeric peptides representing T-helper and B-cell epitopes. Vir Res, 163, 40-50.
  23. Garrett JT, Kaumaya P, Pei D, Dalbey R, Magliery T (2007). Peptide based B cell epitope vaccines targeting HER-2/Neu. PhD thesis. Ohio State University, Ohio, USA.
  24. Goede A, Jaeger IS, Preissner R (2005). SUPERFICIAL-Surface mapping of proteins via structure-based peptide library design. BMC Bioinformatics, 6, 223.
  25. Gritzapis AD, Voutsas IF, Lekka E, et al (2008). Identification of a novel immunogenic HLA-A*0201-binding epitope of HER-2/neu with potent antitumor properties. J Immunol, 181, 146-54.
  26. Guan P, Doytchinova IA, Zygouri C, Flower DR (2003). MHCPred: a server for quantitative prediction of peptide-MHC binding. Nucleic Acids Res, 31, 3621-4.
  27. Haste Andersen P, Nielsen M, Lund O (2006). Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci, 15, 2558-67.
  28. Jacot W, Fiche M, Zaman K (2013). The HER2 amplicon in breast cancer: topoisomerase IIA and beyond. Biochim Biophys Acta (BBA), 1836, 146-57.
  29. Kageyama S, Kitano S, Hirayama M, et al (2008). Humoral immune responses in patients vaccinated with 1-146 HER2 protein complexed with cholesteryl pullulan nanogel. Cancer Sci, 99, 601.
  30. Kobayashi H, Wood M, Song Y, Appella E, Celis E (2000). Defining promiscuous MHC class II helper T-cell epitopes for the HER2/neu tumor antigen. Cancer Res, 60, 5228-36.
  31. Kastenmuller W, Gasteiger G, Gronau JH, et al (2007). Cross-competition of CD8+T cells shapes the immunodominance hierarchy during boost vaccination. J Exp Med, 204, 2187.
  32. Kennedy R, Celis E (2008). Multiple roles for CD4+ T cells in antitumor immune responses, Immunol Rev, 222, 129.
  33. Kobayashi H, Celis E (2008). Peptide epitope identification for tumorreactive CD4 T cells. Cur Opin Immunol, 20, 221.
  34. Kulkarni-Kale U, Bhosle S, Kolaskar AS (2005). CEP: a conformational epitope prediction server. Nucleic Acids Res, 33, 168-71.
  35. Kumar S, Hinks JA, Maman JC, et al (2011). p185, an immunodominant epitope, is an autoantigen mimotope. J Bio Chem, 286, 26220.
  36. Lax I (1988). Localization of a major receptor-binding domain for epidermal growth factor by affinity labeling. Mol Cell Biol, 8, 1831-4.
  37. Lebreton A, Moreau V, Lapalud P, et al (2011). Discontinuous epitopes on the C2 domain of coagulation Factor VIII mapped by computer-designed synthetic peptides. Bri J Haematol, 155, 487-97.
  38. Li GF, Wang Y, Zhang ZS (2005). Identification of immunodominant Th1-type T cell epitopes from Schistosoma japonicum 28 kDa glutathione-Stransferase, a vaccine candidate. Acta Biochim Biophys Sin, 37, 751-8.
  39. Mahdavi M, Mohabatkar H, Keyhanfar M, Jafarian Dehkordi A, Rabbani M (2012). Linear and conformational B cell epitope prediction of HER 2 ECD-subdomain III by in silico methods. Asian Pac J Cancer Prev, 13, 3053.
  40. Nair S, Kukreja N, Singh BP, Arora N (2011). Identification of B cell epitopes of alcohol dehydrogenase allergen of Curvularia lunata. PLoS ONE, 6, 20020.
  41. Maupetit J, Derreumaux P, Tuffery P (2009). PEP-FOLD: an online resource for de novo peptide structure prediction. Nucleic Acids Res, 37, 498-503.
  42. Miyako H, Kametani Y, Katano I, et al (2011). Antitumor effect of new HER2 peptide vaccination based on B cell epitope. Anticancer Res, 31, 3361-8.
  43. Moreau V, Fleury C, Piquer D, et al (2008). PEPOP: computational design of immunogenic peptides. BMC Bioinformatics, 9, 71.
  44. Noguchi M, Sasada T (2013). Personalized peptide vaccination: a new approach for advanced cancer as therapeutic cancer vaccine. Cancer Immunol Immunother, 62, 919-29.
  45. Parker KC, Bednarek MA, Coligan JE (1994). Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J Immunol, 152, 163.
  46. Pellequer JL, Westhof E, Van Regenmortel MH (1994). Epitope prediction from primary structure of proteins. In Peptide Antigens: A Practical Approach. GB Wisdow ed. Oxford, IRL Press.
  47. Rammensee HG, Bachmann J, Emmerich NN, Bachor OA, Stevanovic S (1999). SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics, 50, 213-9.
  48. Ripoll DR (1992). Conformational study of a peptide epitope shows large preferences for beta-turn conformations. Int J Pept Protein Res, 40, 575-81.
  49. Roggen EL (2008). B-cell epitope engineering: a matter of recognizing protein features and motives. Drug Discovery Today: Technologies, 5, 49-55.
  50. Singh H, Raghava GPS (2001). ProPred: Prediction of HLA-DR binding sites. Bioinformatics, 17, 1236-7.
  51. Rosenberg S (2001). Progress in human tumor immunology and immunotherapy. Nature, 411, 380-4.
  52. Senpuku H, Kato H, Takeuchi H, Noda A, Nisizawa T (1997). Identification of core B cell epitope in the synthetic peptide inducing cross inhibiting antibodies to surface protein antigen of streptococcus mutans. Immunol invest, 26, 531-48.
  53. Singh AK, Rathb SK, Misraa K (2011). Identification of epitopes in Indian human papilloma virus 16 E6: A bioinformatics approach. J Vir Methods, 177, 26-30.
  54. Siyi H, Zhiqiang Z, Liangwei L, et al (2008). Epitope mapping and structural analysis of an anti-ErbB2 antibody A21: Molecular basis for tumor inhibitory mechanism. Proteins, 70, 938-49.
  55. Tai W, Mahato R, Cheng K (2010). The role of HER2 in cancer therapy and targeted drug delivery. J Control Rel, 146, 264-75.
  56. Thompson JD, Higgins DG, Gibson TJ (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res, 22, 4673.
  57. Van Regenmortel MH (1996). Mapping epitope structure and activity: from onedimensional prediction to four-dimensional description of antigenic specificity. Meth, 9, 465.
  58. Vita R, Zarebski L, Greenbaum JA, et al (2010). The immune epitope database 2.0. Nucleic Acids Res, 38, 854-62.
  59. Wallecha A, Ramos K, Malinina I, Singh R (2012). Listeria monocytogenes-based bivalent Lm-LLO immunotherapy for the treatment of HER2/neu positive and triple negative breast cancer and its impact on immunosuppression. Cancer Research, 72, 4-5.
  60. Zaks TZ, Rosenberg SA (1998). Immunization with a peptide epitope from HER-2/neu leads to peptide-specific cytotoxic T lymphocytes that fail to recognize HER-2/neu+ tumors. Cancer Res, 58, 4902-8.
  61. Wang B, Kaumaya PTP, Cohn DE (2010). Immunization with synthetic VEGF peptides in ovarian cancer. Gyn Oncol, 119, 564-70.
  62. Weber CA, Mehta PJ, Ardito M, et al (2009). T cell epitope: friend or foe? Immunogenicity of biologics in context. Adv Drug Delivery Rev, 61, 965-76.
  63. Wiwanitkit V (2007). Predicted epitopes of Lig A of Leptospira interrogans by bioinformatics method: a clue for further vaccine development. Vaccine, 25, 2768-70.

Cited by

  1. Breast cancer immunotherapy: monoclonal antibodies and peptide-based vaccines vol.10, pp.7, 2014,
  2. Immunization with a novel chimeric peptide representing B and T cell epitopes from HER2 extracellular domain (HER2 ECD) for breast cancer vol.35, pp.12, 2014,
  3. Production and Characterization of New Anti-HER2 Monoclonal Antibodies vol.34, pp.3, 2015,
  4. In Silico Analysis of Synaptonemal Complex Protein 1 (SYCP1) and Acrosin Binding Protein (ACRBP) Antigens to Design Novel Multiepitope Peptide Cancer Vaccine Against Breast Cancer pp.1573-3904, 2018,