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. 2020 Dec 28;10(1):22387.
doi: 10.1038/s41598-020-79645-9.

In silico discovery of antigenic proteins and epitopes of SARS-CoV-2 for the development of a vaccine or a diagnostic approach for COVID-19

Hüseyin Can  1 , Ahmet Efe Köseoğlu  1 , Sedef Erkunt Alak  1 , Mervenur Güvendi  1 , Mert Döşkaya  2 , Muhammet Karakavuk  3 , Adnan Yüksel Gürüz  2 , Cemal Ün  4
Affiliations

In silico discovery of antigenic proteins and epitopes of SARS-CoV-2 for the development of a vaccine or a diagnostic approach for COVID-19

Hüseyin Can et al. Sci Rep. .

Abstract

In the genome of SARS-CoV-2, the 5'-terminus encodes a polyprotein, which is further cleaved into 15 non-structural proteins whereas the 3' terminus encodes four structural proteins and eight accessory proteins. Among these 27 proteins, the present study aimed to discover likely antigenic proteins and epitopes to be used for the development of a vaccine or serodiagnostic assay using an in silico approach. For this purpose, after the full genome analysis of SARS-CoV-2 Wuhan isolate and variant proteins that are detected frequently, surface proteins including spike, envelope, and membrane proteins as well as proteins with signal peptide were determined as probable vaccine candidates whereas the remaining were considered as possible antigens to be used during the development of serodiagnostic assays. According to results obtained, among 27 proteins, 26 of them were predicted as probable antigen. In 26 proteins, spike protein was selected as the best vaccine candidate because of having a signal peptide, negative GRAVY value, one transmembrane helix, moderate aliphatic index, a big molecular weight, a long-estimated half-life, beta wrap motifs as well as having stable, soluble and non-allergic features. In addition, orf7a, orf8, and nsp-10 proteins with signal peptide were considered as potential vaccine candidates. Nucleocapsid protein and a highly antigenic GGDGKMKD epitope were identified as ideal antigens to be used in the development of serodiagnostic assays. Moreover, considering MHC-I alleles, highly antigenic KLNDLCFTNV and ITLCFTLKRK epitopes can be used to develop an epitope-based peptide vaccine.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
(A) Predicted KWPWYIWLGF and KLNDLCFTNV epitopes docking to MHC-I alleles. (B) Docking results of epitopes with α chain of MHC-I alleles using ClusPro. (C) The snapshot representing the epitope docked in the pocket of molecular surface of the receptor (all the structures are visualised using Chimera 1.14).
Figure 2
Figure 2
(A) Predicted FLAFVVFLLV and LIFLWLLWPV epitopes docking to MHC-I alleles. (B) Docking results of epitopes with α chain of MHC-I alleles using ClusPro. (C) The snapshot representing the epitope docked in the pocket of molecular surface of the receptor (all the structures are visualised using Chimera 1.14).
Figure 3
Figure 3
(A) Predicted MEVTPSGTWL, FLIVAAIVFI and LEYHDVRVVL epitopes docking to MHC-I alleles. (B) Docking results of epitopes with α chain of MHC-I alleles using ClusPro. (C) The snapshot representing the epitope docked in the pocket of molecular surface of the receptor (all the structures are visualised using Chimera 1.14).
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