Epitope-Based Vaccine Design against Novel Coronavirus SARS-CoV-2 Envelope Protein

Dagur, Hanuman Singh

doi:10.14744/ejmo.2020.01978

Cited by 4 publications

(4 citation statements)

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“…To boost the low immunogenicity of peptides, CUK2 was used as an RNA adjuvant since we already have shown that it induces Th1 responses even in aged mice. Although T cell epitopes of SARS-CoV-2 have been predicted in several studies via in silico analysis (Dagur and Dhakar, 2020;Kiyotani et al, 2020;Wang et al, 2020), they have not been confirmed in vivo. In the present study, ST5, ST7, NT5, and NT6 peptides were found to induce T cell-mediated responses in vivo.…”

Section: Discussionmentioning

confidence: 99%

Peptides Derived From S and N Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 Induce T Cell Responses: A Proof of Concept for T Cell Vaccines

et al. 2021

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The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants that escape vaccine-induced neutralizing antibodies has indicated the importance of T cell responses against this virus. In this study, we highlight the SARS-CoV-2 epitopes that induce potent T cell responses and discuss whether T cell responses alone are adequate to confer protection against SARS-CoV-2 and describe the administration of 20 peptides with an RNA adjuvant in mice. The peptides have been synthesized based on SARS-CoV-2 spike and nucleocapsid protein sequences. Our study demonstrates that immunization with these peptides significantly increases the proportion of effector memory T cell population and interferon-γ (IFN-γ)-, interleukin-4 (IL-4)-, tumor necrosis factor-α (TNF-α)-, and granzyme B-producing T cells. Of these 20 peptides, four induce the generation of IFN-γ-producing T cells, elicit CD8+ T cell (CTL) responses in a dose-dependent manner, and induce cytotoxic T lymphocytes that eliminate peptide-pulsed target cells in vivo. Although it is not statistically significant, these peptide vaccines reduce viral titers in infected hamsters and alleviate pulmonary pathology in SARS-CoV-2-infected human ACE2 transgenic mice. These findings may aid the design of effective SARS-CoV-2 peptide vaccines, while providing insights into the role of T cells in SARS-CoV-2 infection.

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Section: Discussionmentioning

confidence: 99%

Peptides Derived From S and N Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 Induce T Cell Responses: A Proof of Concept for T Cell Vaccines

et al. 2021

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“…Therefore, this effort provides a quick starting point for wet-lab experiments to begin with, cutting the lead-time and costs by a significant amount, for vaccine design against any virus. Some comparative studies on peptide vaccine design against SARS-CoV-2 include (Durojaye et al 2020), which has used the main proteinase of the SARS-CoV-2 virus as the target protein and (Abdelmageed et al 2020 andDagur et al 2020) which have used the envelope E protein for the same. However, in the analysis presented here for SARS-CoV-2, it is the surface-situated spike glycoprotein of SARS-CoV-2 that has been exclusively studied.…”

Section: Introductionmentioning

confidence: 99%

“…In the context of the currently raging pandemic caused by SARS-CoV-2, there is a huge demand placed on the production of vaccines on a very urgent basis. In this regard, many researchers have adopted approaches towards peptide vaccine design as in Abdelmageed et al ( 2020 ), Slathia and Sharma ( 2020 ), Yazdani et al ( 2020 ), Dagur et al ( 2020 ), Kalita et al ( 2020 ) and Durojaye et al ( 2020 ).…”

Section: Introductionmentioning

confidence: 99%

New Computational Approach for Peptide Vaccine Design Against SARS-COV-2

Biswas

Manna

Nandy

et al. 2021

Int J Pept Res Ther

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The design for vaccines using in silico analysis of genomic data of different viruses has taken many different paths, but lack of any precise computational approach has constrained them to alignment methods and some alignment-free techniques. In this work, a precise computational approach has been established wherein two new mathematical parameters have been suggested to identify the highly conserved and surface-exposed regions which are spread over a large region of the surface protein of the virus so that one can determine possible peptide vaccine candidates from those regions. The first parameter, w, is the sum of the normalized values of the measure of surface accessibility and the normalized measure of conservativeness, and the second parameter is the area of a triangle formed by a mathematical model named 2D Polygon Representation. This method has been, therefore, used to determine possible vaccine targets against SARS-CoV-2 by considering its surfacesituated spike glycoprotein. The results of this model have been verified by a parallel analysis using the older approach of manually estimating the graphs describing the variation of conservativeness and surface-exposure across the protein sequence. Furthermore, the working of the method has been tested by applying it to find out peptide vaccine candidates for Zika and Hendra viruses respectively. A satisfactory consistency of the model results with pre-established results for both the test cases shows that this in silico alignment-free analysis proposed by the model is suitable not only to determine vaccine targets against SARS-CoV-2 but also ready to extend against other viruses.

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“…Thus, when choosing a target viral protein for vaccine design, mutations in amino acid sequences of different SARS-CoV-2 strains must be considered [19][20][21][22][23][24][25][26][27] . Different viral proteins of SARS-CoV-2 have been studied for the development of proposed vaccines against COVID-19, including surface glycoprotein [28,29] , spike protein [30] , envelop protein [31,32,33] , and nucleocapsid phosphoprotein [34] . In the GISAID database, hCoV-19/Wuhan/ WIV04/2019 (WIV04) is considered as a reference genome sequence because of its consensus with previously submitted sequences of the beta coronavirus responsible for COVID-19.…”

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confidence: 99%

Strategies for Vaccine Design for Corona Virus for All Variants of Concern Using Immunoinformatics Techniques

BASU

2022

IEM

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Aims: A short sequence of viral protein/ peptide could be used as a potential vaccine to treat coronavirus. Considering all variants of concern (VOC), designing a peptide vaccine for severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) is a challenging task for scientists. Materials & Methods: In this study, an epitope-containing vaccine peptide in nonstructural protein 4 (nsp4) of SARS-CoV-2 was predicted. Using a modified method for both B and T cell epitope prediction (verified by molecular docking studies), linear B and T cell epitopes of nsp4 protein were predicted. Predicted epitopes were analyzed with population coverage calculation and epitope conservancy analysis. Findings: The short peptide sequence 74 QRGGSYTNDKA 84 was selected as B-cell epitope by considering the scores of surface accessibility, hydrophilicity, and beta turn for each amino acid residue. Similarly, the peptide sequences 359 FLAHIQWMV 367 and 359 FLAHIQWVMFTPLV 373 were predicted as T cell epitopes for MHC-I and MHC-II molecules. These two potential epitopes could favor HLA-A*02:01 and HLA-DRB*01:01 as MHC allelic proteins with the lowest IC 50 values, respectively. No amino acid mutations were observed in GISAID (global initiative on sharing all influenza data) database for alpha, beta, gamma, and delta variants of concerns. Among seven amino acid point mutations in nsp4 protein of omicron variant, none were present in the peptide sequences of the predicted epitopes. Conclusion: Short peptide sequences could be predicted as vaccines to prevent infections caused by coronavirus variants of concerns.

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Epitope-Based Vaccine Design against Novel Coronavirus SARS-CoV-2 Envelope Protein

Cited by 4 publications

References 0 publications

Peptides Derived From S and N Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 Induce T Cell Responses: A Proof of Concept for T Cell Vaccines

Peptides Derived From S and N Proteins of Severe Acute Respiratory Syndrome Coronavirus 2 Induce T Cell Responses: A Proof of Concept for T Cell Vaccines

New Computational Approach for Peptide Vaccine Design Against SARS-COV-2

Strategies for Vaccine Design for Corona Virus for All Variants of Concern Using Immunoinformatics Techniques

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