Peer Review #3 of "Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2, the etiologic agent of COVID-19 pandemic: an in silico approach (v0.1)"

With different countries facing multiple waves, with some SARS-CoV-2 variants more deadly and virulent, the COVID-19 pandemic is becoming more dangerous by the day and the world is facing an even more dreadful extended pandemic with exponential positive cases and increasing death rates. There is an urgent need for more efficient and faster methods of vaccine development against SARS-CoV-2. Compared to experimental protocols, the opportunities to innovate are very high in immunoinformatics/in silico approaches especially with the recent adoption of structural bioinformatics in peptide vaccine design. In recent times, multi-epitope-based peptide vaccine candidates (MEBPVCs) have shown extraordinarily high humoral and cellular responses to immunization. Most of the publications claim that respective reported MEBPVC(s) assembled using a set of in silico predicted epitopes, to be the computationally validated potent vaccine candidate(s) ready for experimental validation. However, in this article, for a given set of predicted epitopes, it is shown that the published MEBPVC is one among the many possible variants and there is high likelihood of finding more potent MEBPVCs than the published candidate. To test the same, a methodology is developed where novel MEBP variants are derived by changing the epitope order of the published MEBPVC. Further, to overcome the limitations of current qualitative methods of assessment of MEBPVC, to enable quantitative comparison, ranking, and the discovery of more potent MEBPVCs, novel predictors, Percent Epitope Accessibility (PEA), Receptor specific MEBP vaccine potency(RMVP), MEBP vaccine potency(MVP) are introduced. The MEBP variants indeed showed varied MVP scores indicating varied immunogenicity. When the MEBP variants were ranked in descending order of their MVP scores, the published MEBPVC had the least MVP score. Further, the MEBP variants with IDs, SPVC_387 and SPVC_206, had the highest MVP scores indicating these variants to be more potent MEBPVCs than the published MEBPVC and hence should be prioritized for experimental testing and validation. Through this method, more vaccine candidates will be available for experimental validation and testing. This study also opens the opportunity to develop new software tools for designing more potent MEBPVCs in less time. The computationally validated top-ranked MEBPVCs must be experimentally tested, validated, and verified. The differences and deviations between experimental results and computational predictions provide an opportunity for improving and developing more efficient algorithms and reliable scoring schemes and software.

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Epitope-Based Peptide Vaccine Design against Mokola Rabies Virus Glycoprotein G Utilizing In Silico Approaches

Immunome Research ◽

10.4172/1745-7580.1000144 ◽

2017 ◽

Vol 13 (3) ◽

Cited By ~ 5

Author(s):

Mohammed AA ◽

Hashim O ◽

Elrahman KAA ◽

Hamdi A ◽

Hassan MA

Keyword(s):

Rabies Virus ◽

In Silico ◽

Peptide Vaccine ◽

Vaccine Design ◽

Rabies Virus Glycoprotein ◽

Virus Glycoprotein ◽

Glycoprotein G

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An in silico epitope-based peptide vaccine design against the 2019-nCoV

Egyptian Journal of Medical Human Genetics ◽

10.1186/s43042-020-00071-7 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Olanrewaju Ayodeji Durojaye ◽

Talifhani Mushiana ◽

Samuel Cosmas ◽

Glory Omini Ibiang ◽

Mercy Omini Ibiang

Keyword(s):

In Silico ◽

Peptide Vaccine ◽

Vaccine Design

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In Silico Approach for Peptide Vaccine Design for CoVID 19

10.3390/mol2net-06-06787 ◽

2020 ◽

Cited By ~ 2

Author(s):

Subhamoy Biswas ◽

Shreyans Chatterjee ◽

Tathagata Dey ◽

Sumanta Dey ◽

Smarajit Manna ◽

...

Keyword(s):

In Silico ◽

Peptide Vaccine ◽

Vaccine Design

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Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach

PeerJ ◽

10.7717/peerj.9572 ◽

2020 ◽

Vol 8 ◽

pp. e9572 ◽

Cited By ~ 10

Author(s):

M. Shaminur Rahman ◽

M. Nazmul Hoque ◽

M. Rafiul Islam ◽

Salma Akter ◽

ASM Rubayet-Ul-Alam ◽

...

Keyword(s):

Immune Response ◽

Tertiary Structure ◽

Peptide Vaccine ◽

Etiologic Agent ◽

Dynamics Simulation ◽

World Health ◽

Primary Immune Response ◽

World Population ◽

E Proteins ◽

Chimeric Vaccine

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiologic agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19), a public health emergency of international concerns declared by the World Health Organization (WHO). An immuno-informatics approach along with comparative genomics was applied to design a multi-epitope-based peptide vaccine against SARS-CoV-2 combining the antigenic epitopes of the S, M, and E proteins. The tertiary structure was predicted, refined and validated using advanced bioinformatics tools. The candidate vaccine showed an average of ≥90.0% world population coverage for different ethnic groups. Molecular docking and dynamics simulation of the chimeric vaccine with the immune receptors (TLR3 and TLR4) predicted efficient binding. Immune simulation predicted significant primary immune response with increased IgM and secondary immune response with high levels of both IgG1 and IgG2. It also increased the proliferation of T-helper cells and cytotoxic T-cells along with the increased IFN-γ and IL-2 cytokines. The codon optimization and mRNA secondary structure prediction revealed that the chimera is suitable for high-level expression and cloning. Overall, the constructed recombinant chimeric vaccine candidate demonstrated significant potential and can be considered for clinical validation to fight against this global threat, COVID-19.

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