Exploring the out of sight antigens of SARS-CoV-2 to design a candidate multi-epitope vaccine by utilizing immunoinformatics approaches

Safavi, Ashkan; Kefayat, Amirhosein; Mahdevar, Elham; Abiri, Ardavan; Ghahremani, Fatemeh

doi:10.1016/j.vaccine.2020.10.016

Cited by 101 publications

(85 citation statements)

References 118 publications

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“…The physicochemical properties of the vaccine, including instability index, grand average of hydropathicity (GRAVY), molecular weight, theoretical pI (isoelectric point), aliphatic index, and in vivo and in vitro half-life, were investigated using the ProtParam online server (http://web.expasy.org/protparam/) [38]. The immunodominant epitopes of SYCP1 and ACRBP antigen (C1) were used in the multiepitope vaccine [39], and the SARS-CoV-2 multi-epitope vaccine candidate (C2) [40] was used as positive control for comparing the polyvalent construct's properties. For predicting proteasomal processing, the NetChop (http://tools.iedb.org/netchop/) was used [38].…”

Section: Prediction Of Physicochemical Properties and Proteasomalmentioning

confidence: 99%

“…Solubility is a vital physiochemical property for protein expression and, as a result, manufacturability. Proteins with insufficient hydrophilicity may have a substantial impact on their expression, efficacy, and manufacturability [40]. Furthermore, after overexpression in E. coli, the peptide solubility likelihood was 0.753713.…”

Section: Molecular Modeling Of Epitopesmentioning

confidence: 99%

“…Antigenicity, Allergenicity, Cell Localization, and Immune System Response. The antigenicity scores of the polyvalent are constructed by Vaxijen 2.0 (threshold value: 0.5), Antigenpro (threshold value: 0.3) [46], and Secret-AAR [40]. Our construct showed an antigenicity score above the threshold value and considered antigenic.…”

Section: Molecular Modeling Of Epitopesmentioning

confidence: 99%

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Designing of Potential Polyvalent Vaccine Model for Respiratory Syncytial Virus by System Level Immunoinformatics Approaches

Naqvi

Yasmeen

Ismail

et al. 2021

BioMed Research International

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Background. Respiratory syncytial virus (RSV) infection is a public health epidemic, leading to around 3 million hospitalization and about 66,000 deaths each year. It is a life-threatening condition exclusive to children with no effective treatment. Methods. In this study, we used system-level and vaccinomics approaches to design a polyvalent vaccine for RSV, which could stimulate the immune components of the host to manage this infection. Our framework involves data accession, antigenicity and subcellular localization analysis, T cell epitope prediction, proteasomal and conservancy evaluation, host-pathogen-protein interactions, pathway studies, and in silico binding affinity analysis. Results. We found glycoprotein (G), fusion protein (F), and small hydrophobic protein (SH) of RSV as potential vaccine candidates. Of these proteins (G, F, and SH), we found 9 epitopes for multiple alleles of MHC classes I and II bear significant binding affinity. These potential epitopes were linked to form a polyvalent construct using AAY, GPGPG linkers, and cholera toxin B adjuvant at N-terminal with a 23.9 kDa molecular weight of 224 amino acid residues. The final construct was a stable, immunogenic, and nonallergenic protein containing cleavage sites, TAP transport efficiency, posttranslation shifts, and CTL epitopes. The molecular docking indicated the optimum binding affinity of RSV polyvalent construct with MHC molecules (-12.49 and -10.48 kcal/mol for MHC classes I and II, respectively). This interaction showed that a polyvalent construct could manage and control this disease. Conclusion. Our vaccinomics and system-level investigation could be appropriate to trigger the host immune system to prevent RSV infection.

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Section: Prediction Of Physicochemical Properties and Proteasomalmentioning

confidence: 99%

Section: Molecular Modeling Of Epitopesmentioning

confidence: 99%

Section: Molecular Modeling Of Epitopesmentioning

confidence: 99%

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Designing of Potential Polyvalent Vaccine Model for Respiratory Syncytial Virus by System Level Immunoinformatics Approaches

Naqvi

Yasmeen

Ismail

et al. 2021

BioMed Research International

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“…Other studies have also demonstrated the influential role of TLR4 in inducing immune responses against coronavirus [ [99] , [100] , [101] ]. Consequently, TLR4 was selected as the immune receptor for molecular docking in the present study, such as studies by Yang et al [ 102 ] and Safavi et al [ 103 ]. The molecular docking analysis showed that our vaccine has the ability to bind TLR4 and induce a strong immune response.…”

Section: Discussionmentioning

confidence: 99%

Exploring SARS-COV-2 structural proteins to design a multi-epitope vaccine using immunoinformatics approach: An in silico study

Sanami

Alizadeh

Nosrati

et al. 2021

Computers in Biology and Medicine

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In December 2019, a new virus called SARS-CoV-2 was reported in China and quickly spread to other parts of the world. The development of SARS-COV-2 vaccines has recently received much attention from numerous researchers. The present study aims to design an effective multi-epitope vaccine against SARS-COV-2 using the reverse vaccinology method. In this regard, structural proteins from SARS-COV-2, including the spike (S), envelope (E), membrane (M), and nucleocapsid (N) proteins, were selected as target antigens for epitope prediction. A total of five helper T lymphocytes (HTL) and five cytotoxic T lymphocytes (CTL) epitopes were selected after screening the predicted epitopes for antigenicity, allergenicity, and toxicity. Subsequently, the selected HTL and CTL epitopes were fused via flexible linkers. Next, the cholera toxin B-subunit (CTxB) as an adjuvant was linked to the N-terminal of the chimeric structure. The proposed vaccine was analyzed for the properties of physicochemical, antigenicity, and allergenicity. The 3D model of the vaccine construct was predicted and docked with the Toll-like receptor 4 (TLR4). The molecular dynamics (MD) simulation was performed to evaluate the stable interactions between the vaccine construct and TLR4. The immune simulation was also conducted to explore the immune responses induced by the vaccine. Finally, in silico cloning of the vaccine construct into the pET-28 (+) vector was conducted. The results obtained from all bioinformatics analysis stages were satisfactory; however, in vitro and in vivo tests are essential to validate these results.

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“…These results highlight the importance of pre-existing and induced SARS-CoV-2-specific CD8+ and CD4+ T cell responses for immune protection in mild SARS-CoV-2 infection. Since then, studies suggested the inclusion of specific peptides to elicit T cell response in vaccine design and in silico analysis of SARS-CoV-2 proteins has detected candidate epitopes specific for protective T CD4+ or CD8+ and B responses with low risks of allergy or autoimmunity (17)(18)(19)(20) . In fact, approved vaccines induce T cell response in addition to the production of neutralizing antibodies for immunization against SARS-CoV-2 (21)(22)(23) .…”

Section: Introductionmentioning

confidence: 99%

New SARS-CoV-2 lineages could evade CD8+ T-cells response

Pretti

Galvani

Farias

et al. 2021

Preprint

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Background: Many SARS-CoV-2 variants of concern have emerged since the Covid-19 outburst, notably the lineages detected in the UK, South Africa, and Brazil. Their increased transmissibility and higher viral load put them in the spotlight. Much has been investigated on the ability of those new variants to evade antibody recognition. However, not enough attention has been given to pre-existing and induced SARS-CoV-2-specific CD8+ T cell responses during the natural course of infection by new lineages. Methods: In this work, we investigated the SARS-CoV-2-specific CD8+ T cell epitopes from the main variants of concern and the potential of associated mutations to trigger or hinder CD8+ T-cells response. We also estimated the population's coverage of these different lineages, considering peptide binding predictions to class I HLA alleles from 29 countries to investigate differences in the fraction of individuals expected to respond to a given epitope set from new and previous lineages. Results: We observed a lower populational coverage for 20B/S.484K (P2 lineage) in contrast to an increased coverage found for 20H/501Y.V2 (B.1.351 Lineage) and 20J/501Y.V3 (P1 lineage) compared to a reference lineage. Moreover, mutations such as Spike N501Y and Nucleocapsid T205I were predicted to have an overall higher affinity through HLA-I than the reference sequence. Conclusions: In summary, the data in this work provided evidence for the existence of potentially immunogenic and conserved epitopes across new SARS-CoV-2 variants, but also highlights the reduced populational's coverage for the Brazilian lineage P.1, suggesting its potential to evade from CD8+ T-cell responses. Our results also may guide efforts to characterize and validate relevant peptides to trigger CD8+ T-cell responses, and design new universal T-cell-inducing vaccine candidates that minimize detrimental effects of viral diversification and at the same time induce responses to a broad human population.

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Exploring the out of sight antigens of SARS-CoV-2 to design a candidate multi-epitope vaccine by utilizing immunoinformatics approaches

Cited by 101 publications

References 118 publications

Designing of Potential Polyvalent Vaccine Model for Respiratory Syncytial Virus by System Level Immunoinformatics Approaches

Designing of Potential Polyvalent Vaccine Model for Respiratory Syncytial Virus by System Level Immunoinformatics Approaches

Exploring SARS-COV-2 structural proteins to design a multi-epitope vaccine using immunoinformatics approach: An in silico study

New SARS-CoV-2 lineages could evade CD8+ T-cells response

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