Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics and<i>in silico</i>approaches

Qamar, Muhammad Tahir ul; Rehman, Abdur; Ashfaq, Usman Ali; Awan, Muhammad Qasim; Fatima, Israr; Shahid, Farah

doi:10.1101/2020.02.28.970343

Cited by 43 publications

(26 citation statements)

References 91 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Generally, a protein whose instability index is lesser than 40 are predicted to be stable and values above that predicts the protein as unstable [55]. The stability of the vaccine candidate in this study was found to be better than the recently published multiepitope vaccine candidate against SARS-CoV-2 in which instability index was found higher than the vaccine candidate of this study [56,57]. The theoretical pI of the vaccine was calculated to be 9.96.…”

Section: Immune Simulationmentioning

confidence: 65%

A Candidate multi-epitope vaccine against SARS-CoV-2

Narsaria

Basak

et al. 2020

Preprint

View full text Add to dashboard Cite

In the past two decades, 7 coronaviruses have infected the human population, with two major outbreaks caused by SARS-CoV and MERS-CoV in the year 2002 and 2012, respectively. Currently, the entire world is facing a pandemic of another coronavirus, SARS-CoV-2, with a high fatality rate. The spike glycoprotein of SARS-CoV-2 mediates entry of virus into the host cell and is one of the most important antigenic determinants, making it a potential candidate for a vaccine. In this study, we have computationally designed a multi-epitope vaccine using spike glycoprotein of SARS-CoV-2. The overall quality of the candidate vaccine was validated in silico and Molecular Dynamics Simulation confirmed the stabilityof the designed vaccine. Docking studies revealed stable interactions of the vaccine with Toll Like Receptors and MHC Receptors. Codon optimization was used to optimize high expression of the vaccine in E.coli K-12 strain. In silico cloning suggested efficient expression in pET-28a (+) vector. The efficiency of the candidate vaccine to trigger an effective immune response was assessed by an in silico immune simulation. The computational analyses suggest that the designed multi-epitope vaccine is structurally stable which can induce specific immune responses and thus, can be a potential vaccine candidate against SARS-CoV-2.Authors Tamalika Kar, Utkarsh Narsaria, Srijita Basak, and Debashrito Deb contributed equally to this work.

show abstract

Section: Immune Simulationmentioning

confidence: 65%

A Candidate multi-epitope vaccine against SARS-CoV-2

Narsaria

Basak

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…Several vaccines for virus diseases were designed based on these approaches that include effective vaccines on Human papilloma viridea (HPV) [23],Ebola [24], Zika[25]and MERS[26, 27]viruses. There are also few reports of a vaccine candidate for COVID19[28, 29]. These vaccines contained multiple cytotoxic T lymphocytes (CTL) and B cell epitopes against several proteins of SARS-CoV-2 virus.…”

Section: Introductionmentioning

confidence: 99%

Design an efficient multi-epitope peptide vaccine candidate against SARS-CoV-2: An in silico analysis

Yazdani

Rafiei

Yazdani

et al. 2020

Preprint

View full text Add to dashboard Cite

Background: To date, no specific vaccine or drug has been proven to be effective for SARS-CoV-2 infection. Therefore, we implemented immunoinformatics approach to design an efficient multi-epitopes vaccine against SARS-CoV-2.Results: The designed vaccine construct has several immunodominant epitopes from structural proteins of Spike, Nucleocapsid, Membrane and Envelope. These peptides promote cellular and humoral immunity and Interferon gamma responses. In addition, these epitopes have antigenicity ability and no allergenicity probability. To enhance the vaccine immunogenicity, we used three potent adjuvants; Flagellin, a driven peptide from high mobility group box 1 as HP-91 and human beta defensin 3 protein. The physicochemical and immunological properties of the vaccine structure were evaluated. Tertiary structure of the vaccine protein was predicted and refined by I-Tasser and galaxi refine and validated using Rampage and ERRAT. Results of Ellipro showed 242 residues from vaccine might be conformational B cell epitopes. Docking of vaccine with Toll-Like Receptors 3, 5 and 8 proved an appropriate interaction between the vaccine and receptor proteins. In silico cloning demonstrated that the vaccine can be efficiently expressed in Escherichia coli.Conclusions: The designed multi epitope vaccine is potentially antigenic in nature and has the ability to induce humoral and cellular immune responses against SARS-CoV-2. This vaccine can interact appropriately with the TLR3, 5, and 8. Also, this vaccine has high quality structure and suitable characteristics such as high stability and potential for expression in Escherichia coli.

show abstract

“…On the other hand, the multi-epitope vaccine involves fusion of multiple epitopes identified from the proteome of the SARS-CoV-2 by short peptide linkers. Several subunit and multi-epitope-based vaccine designs have been published claiming potential to activate CD4 and CD8 T-cell immune response driving long-term robust adaptive immunity in the vast majority of the population (Abdelmageed et al, 2020 ; Ahmed et al, 2020 ; Akhand et al, 2020 ; An et al, 2000 ; Banerjee et al, 2020 ; Baruah & Bose, 2020 ; Bhattacharya et al, 2020 ; Fast & Chen, 2020 ; Gragert et al, 2013 ; Gupta et al, 2020 ; Herst et al, 2020 ; Ismail et al, 2020 ; Khan et al, 2020 ; Lee & Koohy, 2020 ; Liu et al, 2020 ; Lu et al, 2014 ; Mitra et al, 2020 ; Nerli & Sgourakis, 2020 ; Poran et al, 2020 ; Ramaiah & Arumugaswami, 2020 ; Saha & Prasad, 2020 ; Sheikhshahrokh et al, 2020 ; Singh et al, 2020 ; Srivastava et al, 2020a ; 2020b ; Ul Qamar et al, 2020 ; Vashi et al, 2020 ; Yarmarkovich, Farrel et al, 2020; Yazdani et al, 2020 ). Numerous highly antigenic regions have also been reported from SARS-CoV-2 proteins, which have been recognized with a large population coverage by favorable binding with large number of HLA allele distributed among different ethnic human population across the world (Grifoni et al, 2020b ; Yarmarkovich, Warrington, et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch vaccines, designed by reverse epitomics approach, show potential to cover large ethnically distributed human population worldwide

Srivastava

Verma

Kamthania

et al. 2020

Journal of Biomolecular Structure and Dynamics

View full text Add to dashboard Cite

The SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is responsible for the COVID-19 outbreak. The highly contagious COVID-19 disease has spread to 216 countries in less than six months. Though several vaccine candidates are being claimed, an effective vaccine is yet to come. A novel reverse epitomics approach, ‘overlapping-epitope-clusters-to-patches’ method is utilized to identify the antigenic regions from the SARS-CoV-2 proteome. These antigenic regions are named as ‘Ag-Patch or Ag-Patches’, for Antigenic Patch or Patches. The identification of Ag-Patches is based on the clusters of overlapping epitopes rising from SARS-CoV-2 proteins. Further, we have utilized the identified Ag-Patches to design Multi-Patch Vaccines (MPVs), proposing a novel method for the vaccine design. The designed MPVs were analyzed for immunologically crucial parameters, physiochemical properties and cDNA constructs. We identified 73 CTL (Cytotoxic T-Lymphocyte) and 49 HTL (Helper T-Lymphocyte) novel Ag-Patches from the proteome of SARS-CoV-2. The identified Ag-Patches utilized to design MPVs cover 768 overlapping epitopes targeting 55 different HLA alleles leading to 99.98% of world human population coverage. The MPVs and Toll-Like Receptor ectodomain complex shows stable complex formation tendency. Further, the cDNA analysis favors high expression of the MPVs constructs in a human cell line. We identified highly immunogenic novel Ag-Patches from the entire proteome of SARS CoV-2 by a novel reverse epitomics approach and utilized them to design MPVs. We conclude that the novel MPVs could be a highly potential novel approach to combat SARS-CoV-2, with greater effectiveness, high specificity and large human population coverage worldwide.

show abstract

Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics andin silicoapproaches

Cited by 43 publications

References 91 publications

A Candidate multi-epitope vaccine against SARS-CoV-2

A Candidate multi-epitope vaccine against SARS-CoV-2

Design an efficient multi-epitope peptide vaccine candidate against SARS-CoV-2: An in silico analysis

Computationally validated SARS-CoV-2 CTL and HTL Multi-Patch vaccines, designed by reverse epitomics approach, show potential to cover large ethnically distributed human population worldwide

Contact Info

Product

Resources

About