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Identification of Unique Peptides for SARS-CoV-2 Diagnostics and Vaccine Development by an In Silico Proteomics Approach

Kesarwani, Veerbhan and Gupta, Rupal and Vetukuri, Ramesh and Kushwaha, Sandeep Kumar and Gandhi, Sonu (2021). Identification of Unique Peptides for SARS-CoV-2 Diagnostics and Vaccine Development by an In Silico Proteomics Approach. Frontiers in Immunology. 12 , 725240
[Research article]

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Abstract

Ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus strains is posing new COVID-19 diagnosis and treatment challenges. To help efforts to meet these challenges we examined data acquired from proteomic analyses of human SARS-CoV-2-infected cell lines and samples from COVID-19 patients. Initially, 129 unique peptides were identified, which were rigorously evaluated for repeats, disorders, polymorphisms, antigenicity, immunogenicity, toxicity, allergens, sequence similarity to human proteins, and contributions from other potential cross-reacting pathogenic species or the human saliva microbiome. We also screened SARS-CoV-2-infected NBHE and A549 cell lines for presence of antigenic peptides, and identified paratope peptides from crystal structures of SARS-CoV-2 antigen-antibody complexes. We then selected four antigen peptides for docking with known viral unbound T-cell receptor (TCR), class I and II peptide major histocompatibility complex (pMHC), and identified paratope sequences. We also tested the paratope binding affinity of SARS-CoV T- and B-cell peptides that had been previously experimentally validated. The resultant antigenic peptides have high potential for generating SARS-CoV-2-specific antibodies, and the paratope peptides can be directly used to develop a COVID-19 diagnostics assay. The presented genomics and proteomics-based in-silico approaches have apparent utility for identifying new diagnostic peptides that could be used to fight SARS-CoV-2.

Authors/Creators:Kesarwani, Veerbhan and Gupta, Rupal and Vetukuri, Ramesh and Kushwaha, Sandeep Kumar and Gandhi, Sonu
Title:Identification of Unique Peptides for SARS-CoV-2 Diagnostics and Vaccine Development by an In Silico Proteomics Approach
Series Name/Journal:Frontiers in Immunology
Year of publishing :2021
Volume:12
Article number:725240
Number of Pages:14
ISSN:1664-3224
Language:English
Publication Type:Research article
Article category:Scientific peer reviewed
Version:Published version
Copyright:Creative Commons: Attribution 4.0
Full Text Status:Public
Subjects:(A) Swedish standard research categories 2011 > 3 Medical and Health Sciences > 301 Basic Medicine > Immunology in the medical area
Keywords:SARS-CoV-2, COVID-19 vaccines, diagnostic peptides, docking, paratopes, TCR, MHC
URN:NBN:urn:nbn:se:slu:epsilon-p-113620
Permanent URL:
http://urn.kb.se/resolve?urn=urn:nbn:se:slu:epsilon-p-113620
Additional ID:
Type of IDID
DOI10.3389/fimmu.2021.725240
Web of Science (WoS)000705061200001
ID Code:25976
Faculty:LTV - Fakulteten för landskapsarkitektur, trädgårds- och växtproduktionsvetenskap
Department:(LTJ, LTV) > Department of Plant Breeding (from 130101)
Deposited By: SLUpub Connector
Deposited On:27 Oct 2021 15:25
Metadata Last Modified:27 Oct 2021 15:31

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