Conserved envelope protein of nCoV2 as the possible target to design polytope vaccine

Aim: The envelope protein of novel coronavirus 2 (nCoV2) was reported to be highly conserved compared to its spike (S) protein which was shown to undergo several alterations in their amino acid sequences in the span of one year (2020–2021). Therefore, it is aimed to consider highly conserved structu...

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Autor principal:	Krupanidhi Sreerama
Formato:	article
Lenguaje:	EN
Publicado:	Open Exploration Publishing Inc. 2021
Materias:	severe acute respiratory syndrome novel coronavirus 2 envelope protein polytope vaccine design south indian asians Immunologic diseases. Allergy RC581-607
Acceso en línea:	https://doaj.org/article/b8d65bfdff09433d8607aafa13480af4
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spelling	oai:doaj.org-article:b8d65bfdff09433d8607aafa13480af42021-11-24T06:09:53ZConserved envelope protein of nCoV2 as the possible target to design polytope vaccine10.37349/ei.2021.000122768-6655https://doaj.org/article/b8d65bfdff09433d8607aafa13480af42021-08-01T00:00:00Zhttps://www.explorationpub.com/Journals/ei/Article/100312https://doaj.org/toc/2768-6655Aim: The envelope protein of novel coronavirus 2 (nCoV2) was reported to be highly conserved compared to its spike (S) protein which was shown to undergo several alterations in their amino acid sequences in the span of one year (2020–2021). Therefore, it is aimed to consider highly conserved structural protein of nCov2 namely envelope (E) protein to design the polytope for the formulation of the vaccine against coronavirus disease 2019 (Covid-19). Methods: Online in silico tools were employed to decipher the conservancy and antigenicity of E-protein of nCoV2. They are: to evaluate the molecular affinities among the chosen representatives of alpha and beta coronaviruses, the Molecular Evolutionary Genetics Analysis (MEGA) X 10.1.1 was used. Immune Epitope Database (IEDB)-NetMHCpan (ver. 4.1) tool was used to predict the epitopes of E protein binding to the frequently distributed major histocompatibility complex (MHC) I alleles. ProtParam, VaxJen, ToxinPred and AllerTop online tools were used to assess the physicochemical features, antigenicity, non-toxin and non-allergen aspects of constructed polytope. Secondary structure analysis and homology modelling validation of polytope were done using Phyre2 online tool. Discontinuous and linear epitopes of the designed polytope were predicted through IEDB Ellipro tool. Population coverage of epitopes of the polytope was performed using IEDB online tool with the frequent distribution of human leukocyte antigen (HLA) I alleles in the South Indian Asian population. Results: The phylogeny of envelope proteins of chosen representatives of Coronaviridae confirmed its conservancy and possible origin of nCoV2 from alpha coronaviruses through vampire CoV2. The designed polytope of E-protein was with 53 amino acid residues. The same was developed by linking with cysteine and serine (CS) residues in between epitopes. Conclusion: The antigenicity, non-allergen, non-toxin, homology modelling, discontinuous and linear epitopes of the designed polytope authenticate to explore the envelope protein for prophylactic measures. The epitopes of polytope were found to restrict to MHC I alleles occurring frequently among South Indian Asians.Krupanidhi SreeramaOpen Exploration Publishing Inc.articlesevere acute respiratory syndrome novel coronavirus 2envelope proteinpolytopevaccine designsouth indian asiansImmunologic diseases. AllergyRC581-607ENExploration of Immunology, Vol 1, Iss 3, Pp 155-165 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	severe acute respiratory syndrome novel coronavirus 2 envelope protein polytope vaccine design south indian asians Immunologic diseases. Allergy RC581-607
spellingShingle	severe acute respiratory syndrome novel coronavirus 2 envelope protein polytope vaccine design south indian asians Immunologic diseases. Allergy RC581-607 Krupanidhi Sreerama Conserved envelope protein of nCoV2 as the possible target to design polytope vaccine
description	Aim: The envelope protein of novel coronavirus 2 (nCoV2) was reported to be highly conserved compared to its spike (S) protein which was shown to undergo several alterations in their amino acid sequences in the span of one year (2020–2021). Therefore, it is aimed to consider highly conserved structural protein of nCov2 namely envelope (E) protein to design the polytope for the formulation of the vaccine against coronavirus disease 2019 (Covid-19). Methods: Online in silico tools were employed to decipher the conservancy and antigenicity of E-protein of nCoV2. They are: to evaluate the molecular affinities among the chosen representatives of alpha and beta coronaviruses, the Molecular Evolutionary Genetics Analysis (MEGA) X 10.1.1 was used. Immune Epitope Database (IEDB)-NetMHCpan (ver. 4.1) tool was used to predict the epitopes of E protein binding to the frequently distributed major histocompatibility complex (MHC) I alleles. ProtParam, VaxJen, ToxinPred and AllerTop online tools were used to assess the physicochemical features, antigenicity, non-toxin and non-allergen aspects of constructed polytope. Secondary structure analysis and homology modelling validation of polytope were done using Phyre2 online tool. Discontinuous and linear epitopes of the designed polytope were predicted through IEDB Ellipro tool. Population coverage of epitopes of the polytope was performed using IEDB online tool with the frequent distribution of human leukocyte antigen (HLA) I alleles in the South Indian Asian population. Results: The phylogeny of envelope proteins of chosen representatives of Coronaviridae confirmed its conservancy and possible origin of nCoV2 from alpha coronaviruses through vampire CoV2. The designed polytope of E-protein was with 53 amino acid residues. The same was developed by linking with cysteine and serine (CS) residues in between epitopes. Conclusion: The antigenicity, non-allergen, non-toxin, homology modelling, discontinuous and linear epitopes of the designed polytope authenticate to explore the envelope protein for prophylactic measures. The epitopes of polytope were found to restrict to MHC I alleles occurring frequently among South Indian Asians.
format	article
author	Krupanidhi Sreerama
author_facet	Krupanidhi Sreerama
author_sort	Krupanidhi Sreerama
title	Conserved envelope protein of nCoV2 as the possible target to design polytope vaccine
title_short	Conserved envelope protein of nCoV2 as the possible target to design polytope vaccine
title_full	Conserved envelope protein of nCoV2 as the possible target to design polytope vaccine
title_fullStr	Conserved envelope protein of nCoV2 as the possible target to design polytope vaccine
title_full_unstemmed	Conserved envelope protein of nCoV2 as the possible target to design polytope vaccine
title_sort	conserved envelope protein of ncov2 as the possible target to design polytope vaccine
publisher	Open Exploration Publishing Inc.
publishDate	2021
url	https://doaj.org/article/b8d65bfdff09433d8607aafa13480af4
work_keys_str_mv	AT krupanidhisreerama conservedenvelopeproteinofncov2asthepossibletargettodesignpolytopevaccine
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Conserved envelope protein of nCoV2 as the possible target to design polytope vaccine

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