PMID- 35441904
OWN - NLM
STAT- PubMed-not-MEDLINE
LR  - 20230328
IS  - 2090-5920 (Electronic)
IS  - 1687-157X (Print)
IS  - 1687-157X (Linking)
VI  - 20
IP  - 1
DP  - 2022 Apr 20
TI  - Immunoinformatics approach of epitope prediction for SARS-CoV-2.
PG  - 60
LID - 10.1186/s43141-022-00344-1 [doi]
LID - 60
AB  - BACKGROUND: The novel coronavirus (SARS-CoV-2) caused lethal infections worldwide 
      during an unprecedented pandemic. Identification of the candidate viral epitopes 
      is the first step in the design of vaccines against the viral infection. Several 
      immunoinformatic approaches were employed to identify the SARS-CoV-2 epitopes 
      that bind specifically with the major histocompatibility molecules class I 
      (MHC-I). We utilized immunoinformatic tools to analyze the whole viral protein 
      sequences, to identify the SARS-CoV-2 epitopes responsible for binding to the 
      most frequent human leukocyte antigen (HLA) alleles in the Egyptian population. 
      These alleles were also found with high frequency in other populations worldwide. 
      RESULTS: Molecular docking approach showed that using the co-crystallized MHC-I 
      and T cell receptor (TCR) instead of using MHC-I structure only, significantly 
      enhanced docking scores and stabilized the conformation, as well as the binding 
      affinity of the identified SARS-CoV-2 epitopes. Our approach directly predicts 7 
      potential vaccine subunits from the available SARS-CoV-2 spike and ORF1ab protein 
      sequence. This prediction has been confirmed by published experimentally 
      validated and in silico predicted spike epitope. On the other hand, we predicted 
      novel epitopes (RDLPQGFSA and FCLEASFNY) showing high docking scores and 
      antigenicity response with both MHC-I and TCR. Moreover, antigenicity, 
      allergenicity, toxicity, and physicochemical properties of the predicted 
      SARS-CoV-2 epitopes were evaluated via state-of-the-art bioinformatic approaches, 
      showing high efficacy of the proposed epitopes as a vaccine candidate. 
      CONCLUSION: Our predicted SARS-CoV-2 epitopes can facilitate vaccine development 
      to enhance the immunogenicity against SARS-CoV-2 and provide supportive data for 
      further experimental validation. Our proposed molecular docking approach of 
      exploiting both MHC and TCR structures can be used to identify potential epitopes 
      for most microbial pathogens, provided the crystal structure of MHC 
      co-crystallized with TCR.
CI  - (c) 2022. The Author(s).
FAU - Awad, Nourelislam
AU  - Awad N
AD  - Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City 
      of Science and Technology, Giza, Egypt.
AD  - Center of Informatics Sciences, Nile University, Giza, Egypt.
FAU - Mohamed, Rania Hassan
AU  - Mohamed RH
AD  - Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City 
      of Science and Technology, Giza, Egypt.
AD  - Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, 
      Egypt.
FAU - Ghoneim, Nehal I
AU  - Ghoneim NI
AD  - Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City 
      of Science and Technology, Giza, Egypt.
FAU - Elmehrath, Ahmed O
AU  - Elmehrath AO
AD  - Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City 
      of Science and Technology, Giza, Egypt.
AD  - Faculty of Medicine, Cairo University, Cairo, Egypt.
FAU - El-Badri, Nagwa
AU  - El-Badri N
AD  - Center of Excellence for Stem Cells and Regenerative Medicine (CESC), Zewail City 
      of Science and Technology, Giza, Egypt. nelbadri@zewailcity.edu.eg.
LA  - eng
PT  - Journal Article
DEP - 20220420
PL  - Netherlands
TA  - J Genet Eng Biotechnol
JT  - Journal, genetic engineering & biotechnology
JID - 101317150
EIN - J Genet Eng Biotechnol. 2022 May 9;20(1):69. PMID: 35534710
PMC - PMC9019534
OTO - NOTNLM
OT  - Immunoinformatics
OT  - MHC class I epitopes
OT  - ORF1ab protein
OT  - SARS-CoV-2
OT  - Spike protein
COIS- The authors declare that they have no competing interests.
EDAT- 2022/04/21 06:00
MHDA- 2022/04/21 06:01
PMCR- 2022/04/20
CRDT- 2022/04/20 12:04
PHST- 2021/08/10 00:00 [received]
PHST- 2022/03/30 00:00 [accepted]
PHST- 2022/04/20 12:04 [entrez]
PHST- 2022/04/21 06:00 [pubmed]
PHST- 2022/04/21 06:01 [medline]
PHST- 2022/04/20 00:00 [pmc-release]
AID - 10.1186/s43141-022-00344-1 [pii]
AID - 344 [pii]
AID - 10.1186/s43141-022-00344-1 [doi]
PST - epublish
SO  - J Genet Eng Biotechnol. 2022 Apr 20;20(1):60. doi: 10.1186/s43141-022-00344-1.