<i>In silico</i> Characterization and Selection of Epitope-based Peptide Vaccines Against Ebola Viruses

Sameer Sharma; Sudhakar Malla

doi:doi:10.11648/j.ijhnm.20200601.11

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In silico Characterization and Selection of Epitope-based Peptide Vaccines Against Ebola Viruses

Sameer Sharma, Sudhakar Malla

Published in International Journal of Homeopathy & Natural Medicines (Volume 6, Issue 1)

Received: 20 February 2020 Accepted: 3 March 2020 Published: 24 March 2020

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Abstract

Background & Objective: To analyze the mutual B and T cell epitope related vaccine which can evoke the immune response against Ebola hemorrhagic fever. Ebola virus is pathogenic in nature which is associated with a systemic disease in man and apes. Ebola virus disease is advised to be zoonotic with random spillovers to human beings, particularly animals, and apes. These viruses can affect on immune suppression, abnormal inflammatory responses and high mortality. Methodology: In this study, membrane proteins NP, VP35, VP40, sGP, ssGP, VP30, and VP24 of Ebola virus were retrieved from the protein databases and subjected to many bioinformatics related tools to identify the antigenic B and T-cell epitopes using antigenicity analysis. The selected epitopes were subjected to molecular docking simulation along with HLA-DR to affirm their antigenicity in silico. Result & Conclusion: The data present in our study exposed that the epitopes from NP, VP35, VP40, sGP, ssGP, VP30, and VP24 proteins might be the specific target for Ebola virus based on the best binding affinity and molecular docking score. The biochemical analysis and various characterization is also mandatory to evaluate the correlation of epitopes solely with the MHC molecules.

Published in	International Journal of Homeopathy & Natural Medicines (Volume 6, Issue 1)
DOI	10.11648/j.ijhnm.20200601.11
Page(s)	1-5
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2020. Published by Science Publishing Group

Keywords

Ebola Virus, Peptide Vaccine, TMHMM, BCpreds, Propred, AutoDock

References

[1]	Lo TQ, Marston BJ, Dahl BA, De Cock KM, 2017. Ebola: anatomy of an epidemic. Annu Rev Med, 68: 359–70.
[2]	Emanuel J, Marzi A, Feldmann H, 2018. Filoviruses: ecology, molecular biology, and evolution. Adv Virus Res, 100: 189–221.
[3]	Hira S, Piot P, 2016. The counter effects of the Ebola epidemic on control and treatment of HIV/AIDS, tuberculosis, and malaria in West Africa. AIDS, 30: 2555–59.
[4]	Parpia AS, Ndeffo-Mbah ML, Wenzel NS, Galvani AP, 2016. Effects of response to 2014–2015 Ebola outbreak on deaths from malaria, HIV/AIDS, and tuberculosis, west Africa. Emerg Infect Dis, 22: 433–41.
[5]	Aregawi M, Smith SJ, Sillah-Kanu M, et al, 2016. Impact of the mass drug administration for malaria in response to the Ebola outbreak in Sierra Leone. Malar J, 15: 480.
[6]	Plucinski MM, Guilavogui T, Sidikiba S, et al, 2015. Effect of the Ebola-virus-disease epidemic on malaria case management in Guinea, 2014: a cross-sectional survey of health facilities. Lancet Infect Dis, 15: 1017–23.
[7]	Bekolo CE, Diallo A, Philips M, et al, 2017. Six-monthly appointment spacing for clinical visits as a model for retention in HIV care in Conakry-Guinea: a cohort study. BMC Infect Dis, 17: 766.
[8]	Tattevin P, Baysah MK, Raguin G, et al, 2015. Retention in care for HIV-infected patients in the eye of the Ebola storm: lessons from Monrovia, Liberia. AIDS, 29: N1–2.
[9]	Ansumana R, Keitell S, Roberts GM, et al, 2017. Impact of infectious disease epidemics on tuberculosis diagnostic, management, and prevention services: experiences and lessons from the 2014–2015 Ebola virus disease outbreak in west Africa. Int J Infect Dis, 56: 101–04.
[10]	Camara M, Ouattara E, Duvignaud A, et al, 2017. Impact of the Ebola outbreak on Trypanosoma brucei gambiense infection medical activities in coastal Guinea, 2014–2015: a retrospective analysis from the Guinean national Human African Trypanosomiasis control program. PLoS Negl Trop Dis, 11: e0006060.
[11]	Doytchinova IA, Flower DR, 2007. VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinform, 8 (1): 4.
[12]	Krogh A, Larsson B, Von Heijne G, Sonnhammer EL, 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol, 305 (3): 567-80.
[13]	EL-Manzalawy Y, Dobbs D, Honavar V, 2008. Predicting linear B-cell epitopes using string kernels. J Mol Recognit, 21 (4): 243-55.
[14]	Singh H, Raghava G, 2003. ProPred1: prediction of promiscuous MHC Class-I binding sites. Bioinformatics, 19 (8): 1009-14.
[15]	Singh H, Raghava G, 2001. ProPred: prediction of HLA-DR binding sites. Bioinformatics, 17 (12): 1236-37.
[16]	Sturniolo T, Bono E, Ding J, Raddrizzani L, Tuereci O, Sahin U, et al, 1999. Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat Biotechnol, 17 (6): 555-61.
[17]	Guan P, Doytchinova IA, Zygouri C, Flower DR, 2003. MHCPred: a server for quantitative prediction of peptide–MHC binding. Nucleic Acids Res, 31 (13): 3621-4.
[18]	Kangueane P, Sakharkar MK, 2005. T-Epitope designer: a HLA-peptide binding prediction server. Bioinformation, 1 (1): 21.
[19]	Totrov M, Abagyan R, 1997. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins, 29 (s1): 215-20.
[20]	Schwede T, Kopp J, Guex N, Peitsch MC, 2003. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res, 31 (13): 3381-5.
[21]	Patronov A, Dimitrov I, Flower DR, Doytchinova I, 2011. Peptide binding prediction for the human class II MHC allele HLA-DP2: a molecular docking approach. BMC Struct Biol, 11 (1): 32.
[22]	Garske T, Cori A, Ariyarajah A, et al, 2017. Heterogeneities in the case fatality ratio in the West African Ebola outbreak 2013–2016. Philos Trans R Soc Lond B Biol Sci, 372.
[23]	Briand S, Bertherat E, Cox P, et al, 2014. The international Ebola emergency. N Engl J Med, 371: 1180–83.
[24]	Houlihan CF, McGowan CR, Dicks S, et al, 2017. Ebola exposure, illness experience, and Ebola antibody prevalence in international responders to the west African Ebola epidemic 2014–2016: a cross-sectional study. PLoS Med, 14: e1002300.

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APA Style

Sameer Sharma, Sudhakar Malla. (2020). In silico Characterization and Selection of Epitope-based Peptide Vaccines Against Ebola Viruses. International Journal of Homeopathy & Natural Medicines, 6(1), 1-5. https://doi.org/10.11648/j.ijhnm.20200601.11

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ACS Style

Sameer Sharma; Sudhakar Malla. In silico Characterization and Selection of Epitope-based Peptide Vaccines Against Ebola Viruses. Int. J. Homeopathy Nat. Med. 2020, 6(1), 1-5. doi: 10.11648/j.ijhnm.20200601.11

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AMA Style

Sameer Sharma, Sudhakar Malla. In silico Characterization and Selection of Epitope-based Peptide Vaccines Against Ebola Viruses. Int J Homeopathy Nat Med. 2020;6(1):1-5. doi: 10.11648/j.ijhnm.20200601.11

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@article{10.11648/j.ijhnm.20200601.11,
  author = {Sameer Sharma and Sudhakar Malla},
  title = {In silico Characterization and Selection of Epitope-based Peptide Vaccines Against Ebola Viruses},
  journal = {International Journal of Homeopathy & Natural Medicines},
  volume = {6},
  number = {1},
  pages = {1-5},
  doi = {10.11648/j.ijhnm.20200601.11},
  url = {https://doi.org/10.11648/j.ijhnm.20200601.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijhnm.20200601.11},
  abstract = {Background & Objective: To analyze the mutual B and T cell epitope related vaccine which can evoke the immune response against Ebola hemorrhagic fever. Ebola virus is pathogenic in nature which is associated with a systemic disease in man and apes. Ebola virus disease is advised to be zoonotic with random spillovers to human beings, particularly animals, and apes. These viruses can affect on immune suppression, abnormal inflammatory responses and high mortality. Methodology: In this study, membrane proteins NP, VP35, VP40, sGP, ssGP, VP30, and VP24 of Ebola virus were retrieved from the protein databases and subjected to many bioinformatics related tools to identify the antigenic B and T-cell epitopes using antigenicity analysis. The selected epitopes were subjected to molecular docking simulation along with HLA-DR to affirm their antigenicity in silico. Result & Conclusion: The data present in our study exposed that the epitopes from NP, VP35, VP40, sGP, ssGP, VP30, and VP24 proteins might be the specific target for Ebola virus based on the best binding affinity and molecular docking score. The biochemical analysis and various characterization is also mandatory to evaluate the correlation of epitopes solely with the MHC molecules.},
 year = {2020}
}

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TY  - JOUR
T1  - In silico Characterization and Selection of Epitope-based Peptide Vaccines Against Ebola Viruses
AU  - Sameer Sharma
AU  - Sudhakar Malla
Y1  - 2020/03/24
PY  - 2020
N1  - https://doi.org/10.11648/j.ijhnm.20200601.11
DO  - 10.11648/j.ijhnm.20200601.11
T2  - International Journal of Homeopathy & Natural Medicines
JF  - International Journal of Homeopathy & Natural Medicines
JO  - International Journal of Homeopathy & Natural Medicines
SP  - 1
EP  - 5
PB  - Science Publishing Group
SN  - 2472-2316
UR  - https://doi.org/10.11648/j.ijhnm.20200601.11
AB  - Background & Objective: To analyze the mutual B and T cell epitope related vaccine which can evoke the immune response against Ebola hemorrhagic fever. Ebola virus is pathogenic in nature which is associated with a systemic disease in man and apes. Ebola virus disease is advised to be zoonotic with random spillovers to human beings, particularly animals, and apes. These viruses can affect on immune suppression, abnormal inflammatory responses and high mortality. Methodology: In this study, membrane proteins NP, VP35, VP40, sGP, ssGP, VP30, and VP24 of Ebola virus were retrieved from the protein databases and subjected to many bioinformatics related tools to identify the antigenic B and T-cell epitopes using antigenicity analysis. The selected epitopes were subjected to molecular docking simulation along with HLA-DR to affirm their antigenicity in silico. Result & Conclusion: The data present in our study exposed that the epitopes from NP, VP35, VP40, sGP, ssGP, VP30, and VP24 proteins might be the specific target for Ebola virus based on the best binding affinity and molecular docking score. The biochemical analysis and various characterization is also mandatory to evaluate the correlation of epitopes solely with the MHC molecules.
VL  - 6
IS  - 1
ER  -

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Author Information

Sameer Sharma

Department of Biotechnology, Indian Academy Degree College, Bangalore, India
Sudhakar Malla

Department of Biotechnology, Indian Academy Degree College, Bangalore, India

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Plain Text BibTeX RIS

APA Style

Sameer Sharma, Sudhakar Malla. (2020). In silico Characterization and Selection of Epitope-based Peptide Vaccines Against Ebola Viruses. International Journal of Homeopathy & Natural Medicines, 6(1), 1-5. https://doi.org/10.11648/j.ijhnm.20200601.11

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ACS Style

Sameer Sharma; Sudhakar Malla. In silico Characterization and Selection of Epitope-based Peptide Vaccines Against Ebola Viruses. Int. J. Homeopathy Nat. Med. 2020, 6(1), 1-5. doi: 10.11648/j.ijhnm.20200601.11

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AMA Style

Sameer Sharma, Sudhakar Malla. In silico Characterization and Selection of Epitope-based Peptide Vaccines Against Ebola Viruses. Int J Homeopathy Nat Med. 2020;6(1):1-5. doi: 10.11648/j.ijhnm.20200601.11

Copy | Download

@article{10.11648/j.ijhnm.20200601.11,
  author = {Sameer Sharma and Sudhakar Malla},
  title = {In silico Characterization and Selection of Epitope-based Peptide Vaccines Against Ebola Viruses},
  journal = {International Journal of Homeopathy & Natural Medicines},
  volume = {6},
  number = {1},
  pages = {1-5},
  doi = {10.11648/j.ijhnm.20200601.11},
  url = {https://doi.org/10.11648/j.ijhnm.20200601.11},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijhnm.20200601.11},
  abstract = {Background & Objective: To analyze the mutual B and T cell epitope related vaccine which can evoke the immune response against Ebola hemorrhagic fever. Ebola virus is pathogenic in nature which is associated with a systemic disease in man and apes. Ebola virus disease is advised to be zoonotic with random spillovers to human beings, particularly animals, and apes. These viruses can affect on immune suppression, abnormal inflammatory responses and high mortality. Methodology: In this study, membrane proteins NP, VP35, VP40, sGP, ssGP, VP30, and VP24 of Ebola virus were retrieved from the protein databases and subjected to many bioinformatics related tools to identify the antigenic B and T-cell epitopes using antigenicity analysis. The selected epitopes were subjected to molecular docking simulation along with HLA-DR to affirm their antigenicity in silico. Result & Conclusion: The data present in our study exposed that the epitopes from NP, VP35, VP40, sGP, ssGP, VP30, and VP24 proteins might be the specific target for Ebola virus based on the best binding affinity and molecular docking score. The biochemical analysis and various characterization is also mandatory to evaluate the correlation of epitopes solely with the MHC molecules.},
 year = {2020}
}

Copy | Download

TY  - JOUR
T1  - In silico Characterization and Selection of Epitope-based Peptide Vaccines Against Ebola Viruses
AU  - Sameer Sharma
AU  - Sudhakar Malla
Y1  - 2020/03/24
PY  - 2020
N1  - https://doi.org/10.11648/j.ijhnm.20200601.11
DO  - 10.11648/j.ijhnm.20200601.11
T2  - International Journal of Homeopathy & Natural Medicines
JF  - International Journal of Homeopathy & Natural Medicines
JO  - International Journal of Homeopathy & Natural Medicines
SP  - 1
EP  - 5
PB  - Science Publishing Group
SN  - 2472-2316
UR  - https://doi.org/10.11648/j.ijhnm.20200601.11
AB  - Background & Objective: To analyze the mutual B and T cell epitope related vaccine which can evoke the immune response against Ebola hemorrhagic fever. Ebola virus is pathogenic in nature which is associated with a systemic disease in man and apes. Ebola virus disease is advised to be zoonotic with random spillovers to human beings, particularly animals, and apes. These viruses can affect on immune suppression, abnormal inflammatory responses and high mortality. Methodology: In this study, membrane proteins NP, VP35, VP40, sGP, ssGP, VP30, and VP24 of Ebola virus were retrieved from the protein databases and subjected to many bioinformatics related tools to identify the antigenic B and T-cell epitopes using antigenicity analysis. The selected epitopes were subjected to molecular docking simulation along with HLA-DR to affirm their antigenicity in silico. Result & Conclusion: The data present in our study exposed that the epitopes from NP, VP35, VP40, sGP, ssGP, VP30, and VP24 proteins might be the specific target for Ebola virus based on the best binding affinity and molecular docking score. The biochemical analysis and various characterization is also mandatory to evaluate the correlation of epitopes solely with the MHC molecules.
VL  - 6
IS  - 1
ER  -

Copy | Download