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 | ||||||
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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: |
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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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