Preprint / Version 2

Immunoinformatics Patterns and Characteristic of Epitope-Based Peptide Vaccine candidates against COVID-19

Authors

DOI:

https://doi.org/10.21467/preprints.164

Abstract

Vaccination as defined by the WHO is “the administration of agent-specific, but safe, antigenic components that in vaccinated individuals can induce protective immunity against the corresponding infectious agent”. Regardless of their debated history, the standard vaccine approaches have been unsuccessful in providing vaccines for numerous infectious organisms. In the recent three decades, an enormous amount of immunological data was retrieved from clinical studies  due to the advancement in human genome sequencing. These data are being deposited in databases and numerous scientific literature. The development of several bioinformatics tools to analyze this rapidly increasing immunological databank has given rise to the field of immunoinformatics. This approach allows the selection of immunogenic residues from the pathogen genomes. The ideal residues could be industrialized as vaccine candidates to provide protective immune responses in the hosts. This methodology will significantly decrease the time and cost needed for the vaccine development.  This review focus on  published articles that proposed as vaccine candidates through immunoinformatics analysis. The reviewed  Published immunoinformatics studies provided vaccine peptide candidates against SARS-COV-2, which is based on functional and non functional immunogenic proteins like open reading frame , spike protein, envelope protein and membranous protein .All of which  are designed by unique strategies like reverse vaccinology . Spike protein was the most common used target with different suggeststed B and T cell peptides  due to the difference in methodology between the findings.

Keywords:

COVID-19 vaccine canididates, Peptides, Immunoinformatics

Downloads

Download data is not yet available.

References

T. Hampton, "Bats may be SARS reservoir," (in eng), Jama, vol. 294, no. 18, p. 2291, Nov 9 2005.

A. Banerjee, K. Kulcsar, V. Misra, M. Frieman, and K. Mossman, "Bats and Coronaviruses," (in eng), Viruses, vol. 11, no. 1, Jan 9 2019.

W. Li et al., "Bats are natural reservoirs of SARS-like coronaviruses," (in eng), Science, vol. 310, no. 5748, pp. 676-9, Oct 28 2005.

Q. Ye et al., "Epidemiological analysis of COVID-19 and practical experience from China," (in eng), J Med Virol, Apr 1 2020.

R. Lu et al., "Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding," (in eng), Lancet, vol. 395, no. 10224, pp. 565-574, Feb 22 2020.

S. A. Meo, T. Al-Khlaiwi, A. M. Usmani, A. S. Meo, D. C. Klonoff, and T. D. Hoang, "Biological and Epidemiological Trends in the Prevalence and Mortality due to Outbreaks of Novel Coronavirus COVID-19," (in eng), J King Saud Univ Sci, Apr 9 2020.

World Health Organization. (2020, 29/6). Coronavirus disease (COVID-19) Situation Report – 159. Available: https://www.who.int/docs/default-source/coronaviruse/situation-reports/20200627-covid-19-sitrep-159.pdf?sfvrsn=93e027f6_2

F. Carinci, "Covid-19: preparedness, decentralisation, and the hunt for patient zero," BMJ, vol. 368, p. bmj.m799, 02/28 2020.

C. Xiong, L. Jiang, Y. Chen, and Q. Jiang, "Evolution and variation of 2019-novel coronavirus," bioRxiv, p. 2020.01.30.926477, 2020.

W.-B. Yu, G.-d. Tang, L. Zhang, and R. Corlett, Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2) using the whole genomic data. 2020.

N. Zhu et al., "A Novel Coronavirus from Patients with Pneumonia in China, 2019," (in eng), N Engl J Med, vol. 382, no. 8, pp. 727-733, Feb 20 2020.

P. Zhou et al., "A pneumonia outbreak associated with a new coronavirus of probable bat origin," Nature, vol. 579, 03/01 2020.

S. Weiss and J. Leibowitz, "Coronavirus Pathogenesis," Advances in virus research, vol. 81, pp. 85-164, 12/31 2011.

A. de Wilde, E. Snijder, M. Kikkert, and M. Hemert, "Host Factors in Coronavirus Replication," Current topics in microbiology and immunology, vol. 419, 06/23 2017.

M. I. Abdelmageed et al., "Design of a Multiepitope-Based Peptide Vaccine against the E Protein of Human COVID-19: An Immunoinformatics Approach," BioMed Research International, vol. 2020, p. 2683286, 2020/05/11 2020.

M. Enayatkhani et al., "Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study," (in eng), J Biomol Struct Dyn, pp. 1-19, Apr 15 2020.

M. Bhattacharya et al., "Development of epitope-based peptide vaccine against novel coronavirus 2019 (SARS-COV-2): Immunoinformatics approach," (in eng), J Med Virol, Feb 28 2020.

V. Baruah and S. Bose, "Immunoinformatics-aided identification of T cell and B cell epitopes in the surface glycoprotein of 2019-nCoV," (in eng), J Med Virol, vol. 92, no. 5, pp. 495-500, May 2020.

B. Cao et al., "A Trial of Lopinavir-Ritonavir in Adults Hospitalized with Severe Covid-19," (in eng), N Engl J Med, Mar 18 2020.

M. Hoffmann et al., "SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor," (in eng), Cell, vol. 181, no. 2, pp. 271-280.e8, Apr 16 2020.

Z. Wang and X. Xu, "scRNA-seq Profiling of Human Testes Reveals the Presence of the ACE2 Receptor, A Target for SARS-CoV-2 Infection in Spermatogonia, Leydig and Sertoli Cells," (in eng), Cells, vol. 9, no. 4, Apr 9 2020.

F. Sallusto, A. Lanzavecchia, K. Araki, and R. Ahmed, "From vaccines to memory and back," (in eng), Immunity, vol. 33, no. 4, pp. 451-63, Oct 29 2010.

A. Jackson, "Acute viral infections," Current opinion in neurology, vol. 8, pp. 170-4, 07/01 1995.

T. Guo et al., "Cardiovascular Implications of Fatal Outcomes of Patients With Coronavirus Disease 2019 (COVID-19)," (in eng), JAMA Cardiol, Mar 27 2020.

P. Choe et al., "MERS-CoV antibody responses 1 year after symptom onset, South Korea, 2015," Emerging Infectious Diseases, vol. 23, 06/19 2017.

N. Okba et al., "Sensitive and Specific Detection of Low-Level Antibody Responses in Mild Middle East Respiratory Syndrome Coronavirus Infections," Emerging Infectious Diseases, vol. 25, 08/19 2019.

A. Alshukairi et al., "Recovery from the Middle East respiratory syndrome is associated with antibody and T-cell responses," Science Immunology, vol. 2, p. eaan5393, 08/04 2017.

K. A. Callow, H. Parry, M. Sergeant, and D. Tyrrell, "The time course of the immune response to experimental Coronavirus infection of man," Epidemiology and infection, vol. 105, pp. 435-46, 11/01 1990.

S. Crotty, "T Follicular Helper Cell Biology: A Decade of Discovery and Diseases," Immunity, vol. 50, pp. 1132-1148, 05/01 2019.

A. Grifoni et al., "Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals," Cell, 05/01 2020.

J. Ramana and K. Mehla, "Immunoinformatics and Epitope Prediction," vol. 2131, 2020, pp. 155-171.

N. Tomar and R. K. De, "Immunoinformatics: a brief review," (in eng), Methods Mol Biol, vol. 1184, pp. 23-55, 2014.

N. Kumar, S. Bhatia, R. Sood, A. Pateriya, and Y. Malik, "Immunoinformatics: Where Immunology Meets Bioinformatics," vol. 21, p. 55, 12/01 2019.

A. Nandy, S. Manna, and S. C. Basak, "Computational Methodology for Peptide Vaccine Design for Zika Virus: A Bioinformatics Approach," (in eng), Methods Mol Biol, vol. 2131, pp. 17-30, 2020.

R. A. Tahir, H. Wu, M. A. Rizwan, T. H. Jafar, S. Saleem, and S. A. Sehgal, "Immunoinformatics and molecular docking studies reveal potential epitope-based peptide vaccine against DENV-NS3 protein," (in eng), J Theor Biol, vol. 459, pp. 162-170, Dec 14 2018.

N. Khairkhah, A. Namvar, K. Kardani, and A. Bolhassani, "Prediction of cross-clade HIV-1 T-cell epitopes using immunoinformatics analysis," Proteins, vol. 86, no. 12, pp. 1284-1293, Dec 2018.

S. S. Bappy et al., "Extensive immunoinformatics study for the prediction of novel peptide-based epitope vaccine with docking confirmation against envelope protein of Chikungunya virus: a computational biology approach," J Biomol Struct Dyn, pp. 1-16, Feb 24 2020.

M. A. Hasan, M. Hossain, and M. J. Alam, "A computational assay to design an epitope-based Peptide vaccine against saint louis encephalitis virus," (in eng), Bioinform Biol Insights, vol. 7, pp. 347-55, 2013.

C. E. Bounds et al., "An immunoinformatics-derived DNA vaccine encoding human class II T cell epitopes of Ebola virus, Sudan virus, and Venezuelan equine encephalitis virus is immunogenic in HLA transgenic mice," Hum Vaccin Immunother, vol. 13, no. 12, pp. 2824-2836, Dec 2 2017.

N. Lohia and M. Baranwal, "An Immunoinformatics Approach in Design of Synthetic Peptide Vaccine Against Influenza Virus," Methods Mol Biol, vol. 2131, pp. 229-243, 2020.

S. F. O. Tosta et al., "Multi-epitope based vaccine against yellow fever virus applying immunoinformatics approaches," J Biomol Struct Dyn, pp. 1-17, Jan 6 2020.

S. Ahmed, A. A. Quadeer, and M. McKay, "Preliminary identification of potential vaccine targets for the COVID-19 Coronavirus (SARS-CoV-2) Based on SARS-CoV Immunological Studies," Viruses, vol. 12, p. 254, 02/25 2020.

A. Joshi, B. Joshi, M. A.-u. Mannan, and V. Kaushik, "Epitope based vaccine prediction for SARS-COV-2 by deploying immuno-informatics approach," p. 100338, 04/30 2020.

B. Sarkar, M. A. Ullah, F. T. Johora, M. Taniya, and Y. Araf, "Immunoinformatics-guided designing of epitope-based subunit vaccine against the SARS Coronavirus-2 (SARS-CoV-2)," Immunobiology, p. 151955, 05/01 2020.

A. Peele, T. Srihansa, S. Krupanidhi, V. S. Ayyagari, and T. C. Vekateswarulu, "Design of multi-epitope vaccine candidate against SARS-CoV-2: a in-silico study Design of multi-epitope vaccine candidate against SARS-CoV-2: a in-silico study," Journal of biomolecular Structure & Dynamics, 06/01 2020.

M. Bhattacharya et al., "Development of epitope?based peptide vaccine against novel Coronavirus 2019 (SARS?COV?2): Immunoinformatics approach," Journal of Medical Virology, 02/01 2020.

M. Enayatkhani et al., "Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study," Journal of Biomolecular Structure and Dynamics, pp. 1-19, 04/15 2020.

A. A. Mo?sa and E. F. Kolesanova, "[Synthetic peptide vaccines]," (in rus), Biomed Khim, vol. 57, no. 1, pp. 14-30, Jan-Feb 2011.

E. Raoufi et al., "Epitope Prediction by Novel Immunoinformatics Approach: A State-of-the-art Review," International Journal of Peptide Research and Therapeutics, vol. 26, no. 2, pp. 1155-1163, 2020/06/01 2020.

S. B. Sayed, Z. Nain, M. S. A. Khan, F. Abdulla, R. Tasmin, and U. K. Adhikari, "Exploring Lassa Virus Proteome to Design a Multi-epitope Vaccine Through Immunoinformatics and Immune Simulation Analyses," International Journal of Peptide Research and Therapeutics, 2020/01/02 2020.

H. Wang et al., "In silico simulation of a clinical trial with anti-CTLA-4 and anti-PD-L1 immunotherapies in metastatic breast cancer using a systems pharmacology model," (in eng), R Soc Open Sci, vol. 6, no. 5, p. 190366, May 2019.

M. Khan et al., "Immunoinformatics approaches to explore Helicobacter Pylori proteome (Virulence Factors) to design B and T cell multi-epitope subunit vaccine," Scientific Reports, vol. 9, no. 1, p. 13321, 2019/09/16 2019.

A. S. De Groot, L. Moise, J. A. McMurry, and W. Martin, "Epitope-Based Immunome-Derived Vaccines: A Strategy for Improved Design and Safety," (in eng), Clinical Applications of Immunomics, vol. 2, pp. 39-69, 2008.

A. W. Purcell, J. McCluskey, and J. Rossjohn, "More than one reason to rethink the use of peptides in vaccine design," Nature Reviews Drug Discovery, vol. 6, no. 5, pp. 404-414, 2007/05/01 2007.

M. Larché, "T cell epitope-based allergy vaccines," (in eng), Curr Top Microbiol Immunol, vol. 352, pp. 107-19, 2011.

J. Fan, A. Fu, and L. Zhang, "Progress in molecular docking," Quantitative Biology, 05/08 2019.

C. Schönbach and V. Brusic, Immunoinformatics. 2007.

N. London, B. Raveh, and O. Schueler-Furman, "Peptide docking and structure-based characterization of peptide binding: From knowledge to know-how," Current opinion in structural biology, vol. 23, 10/15 2013.

M. Chung et al., "CT Imaging Features of 2019 Novel Coronavirus (2019-nCoV)," Radiology, vol. 295, p. 200230, 02/04 2020.

R. Vita et al., "The Immune Epitope Database (IEDB): 2018 update," (in eng), Nucleic Acids Res, vol. 47, no. D1, pp. D339-d343, Jan 8 2019.

J. E. Larsen, O. Lund, and M. Nielsen, "Improved method for predicting linear B-cell epitopes," (in eng), Immunome Res, vol. 2, p. 2, Apr 24 2006.

H. Singh and G. Raghava, "ProPred: prediction of HLA-DR binding sites," Bioinformatics, vol. 17, pp. 1236-1237, 12/01 2001.

H. Singh and G. Raghava, "ProPred1: Prediction of promiscuous MHC Class-I binding sites," Bioinformatics (Oxford, England), vol. 19, pp. 1009-14, 06/01 2003.

I. Doytchinova and D. Flower, "VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics 8:4," BMC bioinformatics, vol. 8, p. 4, 02/01 2007.

D. Schneidman, Y. Inbar, R. Nussinov, and H. Wolfson, "PatchDock and SymmDock: Servers for Rigid and Symmetric Docking," Nucleic acids research, vol. 33, pp. W363-7, 08/01 2005.

R. Karuppasamy, S. Veerappapillai, and R. Sethumadhavan, "In Silico Identification of Catalytic Residues in Azobenzene Reductase from Bacillus Subtilis and Its Docking Studies with Azo Dyes," Interdisciplinary sciences, computational life sciences, vol. 1, pp. 290-7, 12/01 2009.

A. Lavi et al., "Detection of peptide-binding sites on protein surfaces: The first step toward the modeling and targeting of peptide-mediated interactions," Proteins, vol. 81, 07/01 2014.

X. Lu et al., Patient-derived mutations impact pathogenicity of SARS-CoV-2. 2020.

P. Venkatagopalan, S. M. Daskalova, L. A. Lopez, K. A. Dolezal, and B. G. Hogue, "Coronavirus envelope (E) protein remains at the site of assembly," (in eng), Virology, vol. 478, pp. 75-85, Apr 2015.

T. R. Ruch and C. E. Machamer, "A single polar residue and distinct membrane topologies impact the function of the infectious bronchitis coronavirus E protein," (in eng), PLoS Pathog, vol. 8, no. 5, p. e1002674, 2012.

J. Walker and M. Slifka, "Longevity of T-Cell Memory following Acute Viral Infection," Advances in experimental medicine and biology, vol. 684, pp. 96-107, 01/01 2010.

A. Grifoni et al., "Targets of T Cell Responses to SARS-CoV-2 Coronavirus in Humans with COVID-19 Disease and Unexposed Individuals," Cell, vol. 181, no. 7, pp. 1489-1501.e15, 2020.

R. C. Hardison, "Comparative genomics," (in eng), PLoS Biol, vol. 1, no. 2, p. E58, Nov 2003.

T. Carver, K. Rutherford, M. Berriman, M.-A. Rajandream, B. Barrell, and J. Parkhill, "ACT: The Artemis comparison tool," Bioinformatics (Oxford, England), vol. 21, pp. 3422-3, 09/01 2005.

"Issues with SARS-CoV-2 sequencing data," 2020.

A. Kanampalliwar, R. Soni, A. Girdhar, and A. Tiwari, "Reverse Vaccinology: Basics and Applications," The Open Vaccine Journal, vol. 4, pp. 1-5, 07/20 2013.

G. Weng et al., "HawkDock: a web server to predict and analyze the protein-protein complex based on computational docking and MM/GBSA," Nucleic acids research, vol. 47, 05/20 2019.

P. Reche and E. Reinherz, "Prediction of Peptide-MHC Binding Using Profiles," Methods in molecular biology (Clifton, N.J.), vol. 409, pp. 185-200, 02/01 2007.

J. Ponomarenko, N. Papangelopoulos, D. Zajonc, B. Peters, A. Sette, and P. Bourne, "IEDB-3D: Structural data within the immune epitope database," Nucleic acids research, vol. 39, pp. D1164-70, 10/01 2010.

A. Wieser et al., "A multiepitope subunit vaccine conveys protection against extraintestinal pathogenic Escherichia coli in mice," (in eng), Infect Immun, vol. 78, no. 8, pp. 3432-42, Aug 2010.

M. Agallou, E. Athanasiou, O. Koutsoni, E. Dotsika, and E. Karagouni, "Experimental Validation of Multi-Epitope Peptides Including Promising MHC Class I- and II-Restricted Epitopes of Four Known Leishmania infantum Proteins," (in English), Original Research vol. 5, no. 268, 2014-June-10 2014.

Downloads

Posted

2020-07-10 — Updated on 2020-07-19

Versions

Section

Coronavirus

Categories