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dc.contributor.authorRigo, Mauricio Menegatti
Fasoulis, Romanos
Conev, Anja
Hall-Swan, Sarah
Antunes, Dinler Amaral
Kavraki, Lydia E.
dc.date.accessioned 2022-08-09T17:09:30Z
dc.date.available 2022-08-09T17:09:30Z
dc.date.issued 2022
dc.identifier.citation Rigo, 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." Frontiers in Immunology, 13, (2022) Frontiers Media S.A.: https://doi.org/10.3389/fimmu.2022.931155.
dc.identifier.urihttps://hdl.handle.net/1911/113085
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.
dc.language.iso eng
dc.publisher Frontiers Media S.A.
dc.rights This 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.
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/
dc.title SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development
dc.type Journal article
dc.citation.journalTitle Frontiers in Immunology
dc.contributor.org Kavraki Lab
dc.citation.volumeNumber 13
dc.identifier.digital fimmu-13-931155
dc.type.dcmi Text
dc.identifier.doihttps://doi.org/10.3389/fimmu.2022.931155
dc.type.publication publisher version
dc.citation.articleNumber 931155


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