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. 2021 May;63(5):389-409.
doi: 10.1007/s12033-021-00303-0. Epub 2021 Feb 24.

Bioinformatics Analysis of SARS-CoV-2 to Approach an Effective Vaccine Candidate Against COVID-19

Seyed Mehdi Sadat  1 , Mohammad Reza Aghadadeghi  2 , Masoume Yousefi  1 , Arezoo Khodaei  1 , Mona Sadat Larijani  1 , Golnaz Bahramali  3
Affiliations

Bioinformatics Analysis of SARS-CoV-2 to Approach an Effective Vaccine Candidate Against COVID-19

Seyed Mehdi Sadat et al. Mol Biotechnol. 2021 May.

Abstract

The emerging Coronavirus Disease 2019 (COVID-19) pandemic has posed a serious threat to the public health worldwide, demanding urgent vaccine provide. According to the virus feature as an RNA virus, a high rate of mutations imposes some vaccine design difficulties. Bioinformatics tools have been widely used to make advantage of conserved regions as well as immunogenicity. In this study, we aimed at immunoinformatic evaluation of SARS-CoV-2 proteins conservancy and immunogenicity to design a preventive vaccine candidate. Spike, Membrane and Nucleocapsid amino acid sequences were obtained, and four possible fusion proteins were assessed and compared in terms of structural features and immunogenicity, and population coverage. MHC-I and MHC-II T-cell epitopes, the linear and conformational B-cell epitopes were evaluated. Among the predicted models, the truncated form of Spike in fusion with M and N protein applying AAY linker has high rate of MHC-I and MCH-II epitopes with high antigenicity and acceptable population coverage of 82.95% in Iran and 92.51% in Europe. The in silico study provided truncated Spike-M-N SARS-CoV-2 as a potential preventive vaccine candidate for further in vivo evaluation.

Keywords: COVID-19; In silico; Protein; SARS-CoV-2; Vaccine design.

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Conflict of interest statement

The authors declare no potential conflict of interest that could negatively influence the study.

Figures

Fig. 1
Fig. 1
Schematic view of the applied methods in the study
Fig. 2
Fig. 2
Schematic view of predicted constructs with the flexible spacer (AAY)
Fig. 3
Fig. 3
Graphical representation of B cell epitopes prediction by a Parker hydrophilicity prediction (threshold: 1.474), b Emini surface accessibility prediction (threshold: 1.000), c Karplus and Schulz flexibility prediction (threshold: 0.999), d Chou and Fasman beta turn prediction (threshold: 1.004) and e Kolaskar and Tongaonkar Antigenicity (threshold: 1.0). The yellow regions above the threshold (red line) are supposed to be a part of B cell epitope whereas the green areas are not (Color figure online)
Fig.4
Fig.4
Sequence and structural analysis of Model 4. a Secondary structure by SOPMA tool, b Three dimensional structure by PyMOL and c Ramachandran Plot generated to validate the modeled 3 structure of model 4 protein which indicates that 91.7% of residues are in the favored region
See this image and copyright information in PMC

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