Design of a multi-epitope-based peptide vaccine against the S and N proteins of SARS-COV-2 using immunoinformatics approach

Rouzbahani, Arian Karimi; Kheirandish, Farnaz; Hosseini, Seyedeh Zeinab

doi:10.1186/s43042-022-00224-w

Cited by 15 publications

(10 citation statements)

References 70 publications

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“…The main benefit of using linkers in the context of multiple-epitope vaccine is that they prevent the formation of junctional antigens and improve the processing as well as presentation of antigens ( 92 ). CTL-HTL-B-cell epitopes were ordered in the putative vaccine construct in the same way as described in ( 93 ) and ( 94 ). In addition, considering ( 75 , 93 , 95 , 96 ), we used various linkers: GGGS, EAAAK, AAY, GPGPG, and KK.…”

Section: Discussionmentioning

confidence: 99%

“…CTL-HTL-B-cell epitopes were ordered in the putative vaccine construct in the same way as described in ( 93 ) and ( 94 ). In addition, considering ( 75 , 93 , 95 , 96 ), we used various linkers: GGGS, EAAAK, AAY, GPGPG, and KK. To provide structural rigidity, an EAAAK linker was used that can reduce the hindrance of other protein’s regions during the interaction of the adjuvant and its receptor ( 81 ).…”

Section: Discussionmentioning

confidence: 99%

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Immunoinformatics design of multivalent epitope vaccine against monkeypox virus and its variants using membrane-bound, enveloped, and extracellular proteins as targets

et al. 2023

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IntroductionThe current monkeypox (MPX) outbreak, caused by the monkeypox virus (MPXV), has turned into a global concern, with over 59,000 infection cases and 23 deaths worldwide.ObjectivesHerein, we aimed to exploit robust immunoinformatics approach, targeting membrane-bound, enveloped, and extracellular proteins of MPXV to formulate a chimeric antigen. Such a strategy could similarly be applied for identifying immunodominant epitopes and designing multi-epitope vaccine ensembles in other pathogens responsible for chronic pathologies that are difficult to intervene against.MethodsA reverse vaccinology pipeline was used to select 11 potential vaccine candidates, which were screened and mapped to predict immunodominant B-cell and T-cell epitopes. The finalized epitopes were merged with the aid of suitable linkers, an adjuvant (Resuscitation-promoting factor), a PADRE sequence (13 aa), and an HIV TAT sequence (11 aa) to formulate a multivalent epitope vaccine. Bioinformatics tools were employed to carry out codon adaptation and computational cloning. The tertiary structure of the chimeric vaccine construct was modeled via I-TASSER, and its interaction with Toll-like receptor 4 (TLR4) was evaluated using molecular docking and molecular dynamics simulation. C-ImmSim server was implemented to examine the immune response against the designed multi-epitope antigen.Results and discussionThe designed chimeric vaccine construct included 21 immunodominant epitopes (six B-cell, eight cytotoxic T lymphocyte, and seven helper T-lymphocyte) and is predicted non-allergen, antigenic, soluble, with suitable physicochemical features, that can promote cross-protection among the MPXV strains. The selected epitopes indicated a wide global population coverage (93.62%). Most finalized epitopes have 70%–100% sequence similarity with the experimentally validated immune epitopes of the vaccinia virus, which can be helpful in the speedy progression of vaccine design. Lastly, molecular docking and molecular dynamics simulation computed stable and energetically favourable interaction between the putative antigen and TLR4.ConclusionOur results show that the multi-epitope vaccine might elicit cellular and humoral immune responses and could be a potential vaccine candidate against the MPXV infection. Further experimental testing of the proposed vaccine is warranted to validate its safety and efficacy profile.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Immunoinformatics design of multivalent epitope vaccine against monkeypox virus and its variants using membrane-bound, enveloped, and extracellular proteins as targets

et al. 2023

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“…According to a survey, current vaccines can provoke a high amount of neutralizing antibody but do not stop the breakthrough infection. Recently, several studies were conducted to develop broad-spectrum COVID-19 vaccines to address the issue of immune surveillance escape, including using multiple T cell epitopes, multiple spike proteins loaded on virus-like particles, conserved regions outside RBD targeting epitopes or spike S2 domains as antigens 19,20,21,22 . Nearly 1 year after the COVID-19 pandemic, scientists noticed that T cell immunity played a critical protective role in COVID-19 convalescence patients and appealed to regulatory affairs that T cell immunity should be included in COVID-19 vaccine clinical trials 23 .…”

Section: Discussionmentioning

confidence: 99%

T cell immunity of the nonadjuvanted HLA-restricted peptide COVID-19 vaccine

Lee¹,

Liou²,

Liu³

et al. 2023

Preprint

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Recently, the cases of breakthrough infection and restored virus of COVID-19 have increased after full vaccination, which might be contributed by immune surveillance escape or rebound virus. Here, artificial linear 9-mer human leucocyte antigen (HLA)-restricted UC peptides are designed based on the well-conserved S2 region of the COVID-19 spike protein regardless of rapid mutation and glycosylation hindrance. Through HLA molecule presentation, UC peptides can activate cytotoxic T lymphocytes (CTLs), which elicit cytotoxic activity by recognizing COVID-19 spike-bearing cells and preferably secreting Th1 cytokines. The UC peptides showed immunogenicity and generated a specific antibody in mice either by intramuscular injection or oral delivery without an adjuvant formulation. In conclusion, the T cell vaccine could provide long-lasting protection against COVID-19 either during reinfection or during the rebound of COVID-19. With the eradication of COVID-19 virus-infected cells, the COVID-19 T cell vaccine might provide a solution to lower COVID-19 severity and long COVID.

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“…The main advantage of using linkers in a multi-epitope vaccine is that they avert the formation of junctional immunity and assist in the processing and presentation of antigens [ 61 ]. Following the literature [ 52 , 62 , 63 , 64 ], several linkers (EAAAK, GGGS, AAY, and GPGPG) were used to construct the chimeric vaccine. CTL and B-cell epitopes were connected using the AAY and GPGPG linker, as reported by Robert et al [ 65 ].…”

Section: Discussionmentioning

confidence: 99%

An Immunoinformatics Approach to Design a Potent Multi-Epitope Vaccine against Asia-1 Genotype of Crimean–Congo Haemorrhagic Fever Virus Using the Structural Glycoproteins as a Target

et al. 2022

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Crimean–Congo haemorrhagic fever (CCHF), caused by Crimean–Congo haemorrhagic fever virus (CCHFV), is a disease of worldwide importance (endemic yet not limited to Asia, Middle East, and Africa) and has triggered several outbreaks amounting to a case fatality rate of 10–40% as per the World Health Organization. Genetic diversity and phylogenetic data revealed that the Asia-1 genotype of CCHFV remained dominant in Pakistan, where 688 confirmed cases were reported between the 2012–2022 period. Currently, no approved vaccine is available to tackle the viral infection. Epitope-based vaccine design has gained significant attention in recent years due to its safety, timeliness, and cost efficiency compared to conventional vaccines. In the present study, we employed a robust immunoinformatics-based approach targeting the structural glycoproteins G1 and G2 of CCHFV (Asia-1 genotype) to design a multi-epitope vaccine construct. Five B-cells and six cytotoxic T-lymphocytes (CTL) epitopes were mapped and finalized from G1 and G2 and were fused with suitable linkers (EAAAK, GGGS, AAY, and GPGPG), a PADRE sequence (13 aa), and an adjuvant (50S ribosomal protein L7/L12) to formulate a chimeric vaccine construct. The selected CTL epitopes showed high affinity and stable binding with the binding groove of common human HLA class I molecules (HLA-A*02:01 and HLA-B*44:02) and mouse major histocompatibility complex class I molecules. The chimeric vaccine was predicted to be an antigenic, non-allergenic, and soluble molecule with a suitable physicochemical profile. Molecular docking and molecular dynamics simulation indicated a stable and energetically favourable interaction between the constructed antigen and Toll-like receptors (TLR2, TLR3, and TLR4). Our results demonstrated that innate, adaptive, and humoral immune responses could be elicited upon administration of such a potent muti-epitope vaccine construct. These results could be helpful for an experimental vaccinologist to develop an effective vaccine against the Asia-1 genotype of CCHFV.

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Design of a multi-epitope-based peptide vaccine against the S and N proteins of SARS-COV-2 using immunoinformatics approach

Cited by 15 publications

References 70 publications

Immunoinformatics design of multivalent epitope vaccine against monkeypox virus and its variants using membrane-bound, enveloped, and extracellular proteins as targets

Immunoinformatics design of multivalent epitope vaccine against monkeypox virus and its variants using membrane-bound, enveloped, and extracellular proteins as targets

T cell immunity of the nonadjuvanted HLA-restricted peptide COVID-19 vaccine

An Immunoinformatics Approach to Design a Potent Multi-Epitope Vaccine against Asia-1 Genotype of Crimean–Congo Haemorrhagic Fever Virus Using the Structural Glycoproteins as a Target

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