In silico investigation of binding affinities between human leukocyte antigen class I molecules and SARS-CoV-2 virus spike and ORF1ab proteins

Aim: The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019, a global pandemic. There is hence an urgent need for effective approaches to understand the mechanism of viral interaction with immune cells that lead to viral elimination and sub...

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Autores principales:	Spyros A. Charonis, Effie-Photini Tsilibary, Apostolos P. Georgopoulos
Formato:	article
Lenguaje:	EN
Publicado:	Open Exploration Publishing Inc. 2021
Materias:	orf1ab sars-cov-2 sars-cov-2 spike glycoprotein protein human leukocyte antigen class i in silico investigation Immunologic diseases. Allergy RC581-607
Acceso en línea:	https://doaj.org/article/2eea781bd1cf4ce1aa7b4a88862f008d
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spelling	oai:doaj.org-article:2eea781bd1cf4ce1aa7b4a88862f008d2021-11-24T01:38:50ZIn silico investigation of binding affinities between human leukocyte antigen class I molecules and SARS-CoV-2 virus spike and ORF1ab proteins10.37349/ei.2021.000032768-6655https://doaj.org/article/2eea781bd1cf4ce1aa7b4a88862f008d2021-04-01T00:00:00Zhttps://www.explorationpub.com/Journals/ei/Article/10033https://doaj.org/toc/2768-6655Aim: The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019, a global pandemic. There is hence an urgent need for effective approaches to understand the mechanism of viral interaction with immune cells that lead to viral elimination and subsequent long-term immunity. The first, immediate response to the viral infection involves mobilization of native immunity and human leukocyte antigen (HLA) class I mechanisms to kill infected cells and eliminate the virus. The second line of defense involves the activation of HLA class II system for the production of antibodies against the virus which will add to the elimination of the virus and prevent future infections. In a previous study, investigated the relations between SARS-CoV-2 spike glycoprotein (S protein) and HLA class II alleles were investigaed; here report on the relations of the S protein and the open reading frame 1ab (ORF1ab) of SARS-CoV-2 to HLA class I alleles. Methods: An in silico sliding window approach was used to determine exhaustively the binding affinities of linear epitopes of 10 amino acid length (10-mers) to each of 61 common (global frequency ≥ 0.01) HLA class I molecules (17, 24 and 20 from gene loci A, B and C, respectively). A total of 8,354 epitopes were analyzed; 1,263 from the S protein and 7,091 from ORF1ab. Results: HLA-A genes were the most effective at binding SARS-CoV-2 epitopes for both spike and ORF1ab proteins. Good binding affinities were found for all three genes and were distributed throughout the length of the S protein and ORF1ab polyprotein sequence. Conclusions: Common HLA class I molecules, as a population, are very well suited to binding with high affinity to SARS-CoV-2 spike and ORF1ab proteins and hence should be effective in aiding the early elimination of the virus.Spyros A. CharonisEffie-Photini TsilibaryApostolos P. GeorgopoulosOpen Exploration Publishing Inc.articleorf1absars-cov-2sars-cov-2 spike glycoprotein proteinhuman leukocyte antigen class iin silico investigationImmunologic diseases. AllergyRC581-607ENExploration of Immunology, Vol 1, Iss 1, Pp 16-26 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	orf1ab sars-cov-2 sars-cov-2 spike glycoprotein protein human leukocyte antigen class i in silico investigation Immunologic diseases. Allergy RC581-607
spellingShingle	orf1ab sars-cov-2 sars-cov-2 spike glycoprotein protein human leukocyte antigen class i in silico investigation Immunologic diseases. Allergy RC581-607 Spyros A. Charonis Effie-Photini Tsilibary Apostolos P. Georgopoulos In silico investigation of binding affinities between human leukocyte antigen class I molecules and SARS-CoV-2 virus spike and ORF1ab proteins
description	Aim: The novel coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019, a global pandemic. There is hence an urgent need for effective approaches to understand the mechanism of viral interaction with immune cells that lead to viral elimination and subsequent long-term immunity. The first, immediate response to the viral infection involves mobilization of native immunity and human leukocyte antigen (HLA) class I mechanisms to kill infected cells and eliminate the virus. The second line of defense involves the activation of HLA class II system for the production of antibodies against the virus which will add to the elimination of the virus and prevent future infections. In a previous study, investigated the relations between SARS-CoV-2 spike glycoprotein (S protein) and HLA class II alleles were investigaed; here report on the relations of the S protein and the open reading frame 1ab (ORF1ab) of SARS-CoV-2 to HLA class I alleles. Methods: An in silico sliding window approach was used to determine exhaustively the binding affinities of linear epitopes of 10 amino acid length (10-mers) to each of 61 common (global frequency ≥ 0.01) HLA class I molecules (17, 24 and 20 from gene loci A, B and C, respectively). A total of 8,354 epitopes were analyzed; 1,263 from the S protein and 7,091 from ORF1ab. Results: HLA-A genes were the most effective at binding SARS-CoV-2 epitopes for both spike and ORF1ab proteins. Good binding affinities were found for all three genes and were distributed throughout the length of the S protein and ORF1ab polyprotein sequence. Conclusions: Common HLA class I molecules, as a population, are very well suited to binding with high affinity to SARS-CoV-2 spike and ORF1ab proteins and hence should be effective in aiding the early elimination of the virus.
format	article
author	Spyros A. Charonis Effie-Photini Tsilibary Apostolos P. Georgopoulos
author_facet	Spyros A. Charonis Effie-Photini Tsilibary Apostolos P. Georgopoulos
author_sort	Spyros A. Charonis
title	In silico investigation of binding affinities between human leukocyte antigen class I molecules and SARS-CoV-2 virus spike and ORF1ab proteins
title_short	In silico investigation of binding affinities between human leukocyte antigen class I molecules and SARS-CoV-2 virus spike and ORF1ab proteins
title_full	In silico investigation of binding affinities between human leukocyte antigen class I molecules and SARS-CoV-2 virus spike and ORF1ab proteins
title_fullStr	In silico investigation of binding affinities between human leukocyte antigen class I molecules and SARS-CoV-2 virus spike and ORF1ab proteins
title_full_unstemmed	In silico investigation of binding affinities between human leukocyte antigen class I molecules and SARS-CoV-2 virus spike and ORF1ab proteins
title_sort	in silico investigation of binding affinities between human leukocyte antigen class i molecules and sars-cov-2 virus spike and orf1ab proteins
publisher	Open Exploration Publishing Inc.
publishDate	2021
url	https://doaj.org/article/2eea781bd1cf4ce1aa7b4a88862f008d
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In silico investigation of binding affinities between human leukocyte antigen class I molecules and SARS-CoV-2 virus spike and ORF1ab proteins

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