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Bioinformatics-based SARS-CoV-2 epitopes design and the impact of spike protein mutants on epitope humoral immunities.
Sun, Qi; Huang, Zhuanqing; Yang, Sen; Li, Yuanyuan; Ma, Yue; Yang, Fei; Zhang, Ying; Xu, Fenghua.
  • Sun Q; Pharmaceutical Sciences Research Division, Department of Pharmacy, Medical Supplies Centre of PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China.
  • Huang Z; Pharmaceutical Sciences Research Division, Department of Pharmacy, Medical Supplies Centre of PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China.
  • Yang S; Medical School of Chinese PLA, Beijing, China; Chinese People's Armed Police Force Hospital of Beijing, Beijing, China.
  • Li Y; Pharmaceutical Sciences Research Division, Department of Pharmacy, Medical Supplies Centre of PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China.
  • Ma Y; Pharmaceutical Sciences Research Division, Department of Pharmacy, Medical Supplies Centre of PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China.
  • Yang F; Pharmaceutical Sciences Research Division, Department of Pharmacy, Medical Supplies Centre of PLA General Hospital, Beijing, China; Medical School of Chinese PLA, Beijing, China.
  • Zhang Y; Pharmaceutical Sciences Research Division, Department of Pharmacy, Medical Supplies Centre of PLA General Hospital, Beijing, China.
  • Xu F; Pharmaceutical Sciences Research Division, Department of Pharmacy, Medical Supplies Centre of PLA General Hospital, Beijing, China. Electronic address: xufh@301hospital.com.cn.
Immunobiology ; 227(6): 152287, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-2105123
ABSTRACT

BACKGROUND:

Epitope selection is the key to peptide vaccines development. Bioinformatics tools can efficiently improve the screening of antigenic epitopes and help to choose the right ones.

OBJECTIVE:

To predict, synthesize and testify peptide epitopes at spike protein, assess the effect of mutations on epitope humoral immunity, thus provide clues for the design and development of epitope peptide vaccines against SARS-CoV-2.

METHODS:

Bioinformatics servers and immunological tools were used to identify the helper T lymphocyte, cytotoxic T lymphocyte, and linear B lymphocyte epitopes on the S protein of SARS-CoV-2. Physicochemical properties of candidate epitopes were analyzed using IEDB, VaxiJen, and AllerTOP online software. Three candidate epitopes were synthesized and their antigenic responses were evaluated by binding antibody detection.

RESULTS:

A total of 20 antigenic, non-toxic and non-allergenic candidate epitopes were identified from 1502 epitopes, including 6 helper T-cell epitopes, 13 cytotoxic T-cell epitopes, and 1 linear B cell epitope. After immunization with antigen containing candidate epitopes S206-221, S403-425, and S1157-1170 in rabbits, the binding titers of serum antibody to the corresponding peptide, S protein, receptor-binding domain protein were (415044, 2582, 209.3), (852819, 45238, 457767) and (357897, 10528, 13.79), respectively. The binding titers to Omicron S protein were 642, 12,878 and 7750, respectively, showing that N211L, DEL212 and K417N mutations cause the reduction of the antibody binding activity.

CONCLUSIONS:

Bioinformatic methods are effective in peptide epitopes design. Certain mutations of the Omicron would lead to the loss of antibody affinity to Omicron S protein.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Viral Vaccines / COVID-19 Type of study: Diagnostic study / Experimental Studies / Prognostic study Topics: Vaccines / Variants Limits: Animals / Humans Language: English Journal: Immunobiology Year: 2022 Document Type: Article Affiliation country: J.imbio.2022.152287

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Viral Vaccines / COVID-19 Type of study: Diagnostic study / Experimental Studies / Prognostic study Topics: Vaccines / Variants Limits: Animals / Humans Language: English Journal: Immunobiology Year: 2022 Document Type: Article Affiliation country: J.imbio.2022.152287