EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes
The ongoing coronavirus 2019 (COVID-19) pandemic, triggered by the emerging SARS-CoV-2 virus, represents a global public health challenge. Therefore, the development of effective vaccines is an urgent need to prevent and control virus spread. One of the vaccine production strategies uses the in sili...
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2021-11-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/12548.pdf |
| _version_ | 1827605512815902720 |
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| author | Cristina S. Ferreira Yasmmin C. Martins Rangel Celso Souza Ana Tereza R. Vasconcelos |
| author_facet | Cristina S. Ferreira Yasmmin C. Martins Rangel Celso Souza Ana Tereza R. Vasconcelos |
| author_sort | Cristina S. Ferreira |
| collection | DOAJ |
| description | The ongoing coronavirus 2019 (COVID-19) pandemic, triggered by the emerging SARS-CoV-2 virus, represents a global public health challenge. Therefore, the development of effective vaccines is an urgent need to prevent and control virus spread. One of the vaccine production strategies uses the in silico epitope prediction from the virus genome by immunoinformatic approaches, which assist in selecting candidate epitopes for in vitro and clinical trials research. This study introduces the EpiCurator workflow to predict and prioritize epitopes from SARS-CoV-2 genomes by combining a series of computational filtering tools. To validate the workflow effectiveness, SARS-CoV-2 genomes retrieved from the GISAID database were analyzed. We identified 11 epitopes in the receptor-binding domain (RBD) of Spike glycoprotein, an important antigenic determinant, not previously described in the literature or published on the Immune Epitope Database (IEDB). Interestingly, these epitopes have a combination of important properties: recognized in sequences of the current variants of concern, present high antigenicity, conservancy, and broad population coverage. The RBD epitopes were the source for a multi-epitope design to in silico validation of their immunogenic potential. The multi-epitope overall quality was computationally validated, endorsing its efficiency to trigger an effective immune response since it has stability, high antigenicity and strong interactions with Toll-Like Receptors (TLR). Taken together, the findings in the current study demonstrated the efficacy of the workflow for epitopes discovery, providing target candidates for immunogen development. |
| first_indexed | 2024-03-09T06:21:53Z |
| format | Article |
| id | doaj.art-69230c67c5b94501a12fe1d8cc21c8b8 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:21:53Z |
| publishDate | 2021-11-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-69230c67c5b94501a12fe1d8cc21c8b82023-12-03T11:34:45ZengPeerJ Inc.PeerJ2167-83592021-11-019e1254810.7717/peerj.12548EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopesCristina S. Ferreira0Yasmmin C. Martins1Rangel Celso Souza2Ana Tereza R. Vasconcelos3Bioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, BrazilBioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, BrazilBioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, BrazilBioinformatics Laboratory, National Laboratory of Scientific Computation, Petrópolis, Rio de Janeiro, BrazilThe ongoing coronavirus 2019 (COVID-19) pandemic, triggered by the emerging SARS-CoV-2 virus, represents a global public health challenge. Therefore, the development of effective vaccines is an urgent need to prevent and control virus spread. One of the vaccine production strategies uses the in silico epitope prediction from the virus genome by immunoinformatic approaches, which assist in selecting candidate epitopes for in vitro and clinical trials research. This study introduces the EpiCurator workflow to predict and prioritize epitopes from SARS-CoV-2 genomes by combining a series of computational filtering tools. To validate the workflow effectiveness, SARS-CoV-2 genomes retrieved from the GISAID database were analyzed. We identified 11 epitopes in the receptor-binding domain (RBD) of Spike glycoprotein, an important antigenic determinant, not previously described in the literature or published on the Immune Epitope Database (IEDB). Interestingly, these epitopes have a combination of important properties: recognized in sequences of the current variants of concern, present high antigenicity, conservancy, and broad population coverage. The RBD epitopes were the source for a multi-epitope design to in silico validation of their immunogenic potential. The multi-epitope overall quality was computationally validated, endorsing its efficiency to trigger an effective immune response since it has stability, high antigenicity and strong interactions with Toll-Like Receptors (TLR). Taken together, the findings in the current study demonstrated the efficacy of the workflow for epitopes discovery, providing target candidates for immunogen development.https://peerj.com/articles/12548.pdfEpitopes predictionSARS-CoV-2HLA alleles binding affinityImmunoinformatic approachesEpiCurator |
| spellingShingle | Cristina S. Ferreira Yasmmin C. Martins Rangel Celso Souza Ana Tereza R. Vasconcelos EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes PeerJ Epitopes prediction SARS-CoV-2 HLA alleles binding affinity Immunoinformatic approaches EpiCurator |
| title | EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes |
| title_full | EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes |
| title_fullStr | EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes |
| title_full_unstemmed | EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes |
| title_short | EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes |
| title_sort | epicurator an immunoinformatic workflow to predict and prioritize sars cov 2 epitopes |
| topic | Epitopes prediction SARS-CoV-2 HLA alleles binding affinity Immunoinformatic approaches EpiCurator |
| url | https://peerj.com/articles/12548.pdf |
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