SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development

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dc.citation.articleNumber931155en_US
dc.citation.journalTitleFrontiers in Immunologyen_US
dc.citation.volumeNumber13en_US
dc.contributor.authorRigo, Mauricio Menegattien_US
dc.contributor.authorFasoulis, Romanosen_US
dc.contributor.authorConev, Anjaen_US
dc.contributor.authorHall-Swan, Sarahen_US
dc.contributor.authorAntunes, Dinler Amaralen_US
dc.contributor.authorKavraki, Lydia E.en_US
dc.contributor.orgKavraki Laben_US
dc.date.accessioned2022-08-09T17:09:30Zen_US
dc.date.available2022-08-09T17:09:30Zen_US
dc.date.issued2022en_US
dc.description.abstractThe pandemic caused by the SARS-CoV-2 virus, the agent responsible for the COVID-19 disease, has affected millions of people worldwide. There is constant search for new therapies to either prevent or mitigate the disease. Fortunately, we have observed the successful development of multiple vaccines. Most of them are focused on one viral envelope protein, the spike protein. However, such focused approaches may contribute for the rise of new variants, fueled by the constant selection pressure on envelope proteins, and the widespread dispersion of coronaviruses in nature. Therefore, it is important to examine other proteins, preferentially those that are less susceptible to selection pressure, such as the nucleocapsid (N) protein. Even though the N protein is less accessible to humoral response, peptides from its conserved regions can be presented by class I Human Leukocyte Antigen (HLA) molecules, eliciting an immune response mediated by T-cells. Given the increased number of protein sequences deposited in biological databases daily and the N protein conservation among viral strains, computational methods can be leveraged to discover potential new targets for SARS-CoV-2 and SARS-CoV-related viruses. Here we developed SARS-Arena, a user-friendly computational pipeline that can be used by practitioners of different levels of expertise for novel vaccine development. SARS-Arena combines sequence-based methods and structure-based analyses to (i) perform multiple sequence alignment (MSA) of SARS-CoV-related N protein sequences, (ii) recover candidate peptides of different lengths from conserved protein regions, and (iii) model the 3D structure of the conserved peptides in the context of different HLAs. We present two main Jupyter Notebook workflows that can help in the identification of new T-cell targets against SARS-CoV viruses. In fact, in a cross-reactive case study, our workflows identified a conserved N protein peptide (SPRWYFYYL) recognized by CD8+ T-cells in the context of HLA-B7+. SARS-Arena is available at https://github.com/KavrakiLab/SARS-Arena.en_US
dc.identifier.citationRigo, Mauricio Menegatti, Fasoulis, Romanos, Conev, Anja, et al.. "SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development." <i>Frontiers in Immunology,</i> 13, (2022) Frontiers Media S.A.: https://doi.org/10.3389/fimmu.2022.931155.en_US
dc.identifier.digitalfimmu-13-931155en_US
dc.identifier.doihttps://doi.org/10.3389/fimmu.2022.931155en_US
dc.identifier.urihttps://hdl.handle.net/1911/113085en_US
dc.language.isoengen_US
dc.publisherFrontiers Media S.A.en_US
dc.rightsThis is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.en_US
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en_US
dc.titleSARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Developmenten_US
dc.typeJournal articleen_US
dc.type.dcmiTexten_US
dc.type.publicationpublisher versionen_US
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