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. 2020 Oct 15;15(10):e0240577.
doi: 10.1371/journal.pone.0240577. eCollection 2020.

Design of novel multiepitope constructs-based peptide vaccine against the structural S, N and M proteins of human COVID-19 using immunoinformatics analysis

Affiliations

Design of novel multiepitope constructs-based peptide vaccine against the structural S, N and M proteins of human COVID-19 using immunoinformatics analysis

Niloofar Khairkhah et al. PLoS One. .

Abstract

The causative agent of severe acute respiratory syndrome (SARS) reported by the Chinese Center for Disease Control (China CDC) has been identified as a novel Betacoronavirus (SARS-CoV-2). A computational approach was adopted to identify multiepitope vaccine candidates against SARS-CoV-2 based on S, N and M proteins being able to elicit both humoral and cellular immune responses. In this study, the sequence of the virus was obtained from NCBI database and analyzed with in silico tools such as NetMHCpan, IEDB, BepiPred, NetCTL, Tap transport/proteasomal cleavage, Pa3P, GalexyPepDock, I-TASSER, Ellipro and ClusPro. To identify the most immunodominant regions, after analysis of population coverage and epitope conservancy, we proposed three different constructs based on linear B-cell, CTL and HTL epitopes. The 3D structure of constructs was assessed to find discontinuous B-cell epitopes. Among CTL predicted epitopes, S257-265, S603-611 and S360-368, and among HTL predicted epitopes, N167-181, S313-330 and S1110-1126 had better MHC binding rank. We found one putative CTL epitope, S360-368 related to receptor-binding domain (RBD) region for S protein. The predicted epitopes were non-allergen and showed a high quality of proteasomal cleavage and Tap transport efficiency and 100% conservancy within four different clades of SARS-CoV-2. For CTL and HTL epitopes, the highest population coverage of the world's population was calculated for S27-37 with 86.27% and for S196-231, S303-323, S313-330, S1009-1030 and N328-349 with 90.33%, respectively. We identified overall 10 discontinuous B-cell epitopes for three multiepitope constructs. All three constructs showed strong interactions with TLRs 2, 3 and 4 supporting the hypothesis of SARS-CoV-2 susceptibility to TLRs 2, 3 and 4 like other Coronaviridae families. These data demonstrated that the novel designed multiepitope constructs can contribute to develop SARS-CoV-2 peptide vaccine candidates. The in vivo studies are underway using several vaccination strategies.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. The suggested epitope constructs: a) the schematic diagram of the LBL epitope construct derived from the S and N proteins of the SARS-CoV-2 linked by KK linker; b) the schematic diagram of the CTL epitope construct derived from the S, M and N proteins of the SARS-CoV-2 linked by AAY linker; c) the schematic diagram of the HTL epitope construct derived from the S, M and N proteins of the SARS-CoV-2 linked by GPGPG linker.
Fig 2
Fig 2. The tertiary structure of the predicted LBL construct: a) 3D prediction of LBL multiepitope construct, b) sequence prediction and conformation scores of each amino acid in LBL multiepitope construct.
Fig 3
Fig 3. The tertiary structure of the predicted CTL construct: a) 3D prediction of CTL multi-epitope construct, b) sequence prediction and conformation scores of each amino acid in CTL multiepitope construct.
Fig 4
Fig 4. The tertiary structure of the predicted HTL construct: a) 3D prediction of HTL multiepitope construct, b) sequence prediction and conformation scores of each amino acid in HTL multiepitope construct.
Fig 5
Fig 5. Refined characteristics of LBL multiepitope construct: a) Refined 3D prediction of LBL multiepitope construct, b) overall quality of refinement, c) Ramachandran plot.
Fig 6
Fig 6. Refined characteristics of CTL multiepitope construct: a) Refined 3D prediction of CTL multiepitope construct, b) overall quality of refinement, c) Ramachandran plot.
Fig 7
Fig 7. Refined characteristics of HTL multiepitope construct: a) Refined 3D prediction of HTL multiepitope construct, b) overall quality of refinement, c) Ramachandran plot.
Fig 8
Fig 8. The peptide-protein docking between LBL construct and TLRs 2, 3 and 4: a) LBL-TLR2 complex with participated residues in interaction, b) LBL-TLR3 complex with participated residues in interaction, c) LBL-TLR4 complex with participated residues in interaction.
Fig 9
Fig 9. The peptide-protein docking between CTL construct and TLRs 2, 3 and 4: a) CTL-TLR2 complex with participated residues in interaction, b) CTL-TLR3 complex with participated residues in interaction, c) CTL-TLR4 complex with participated residues in interaction.
Fig 10
Fig 10. The peptide-protein docking between HTL construct and TLRs 2, 3 and 4: a) HTL-TLR2 complex with participated residues in interaction, b) HTL-TLR3 complex with participated residues in interaction, c) HTL-TLR4 complex with participated residues in interaction.

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The author(s) received no specific funding for this work.