Structure-based identification of SARS-derived peptides with potential to induce broad protective immunity

In 2019, a pandemic age caused by a novel strain of coronavirus (SARS-CoV-2) with a fast-growing number of confirmed cases all over the world took place. Several efforts are underway to produce a new vaccine, promoting immediate and long-term cell-mediated immunity based on T cell lymphocytes. T cell responses are particularly important for fighting viral infections because they can find and eliminate infected cells. This project will develop a computational pipeline to enable the identification of peptides that are conserved across different SARS-CoV strains, and that can potentially be used to induce broad protective cellular immunity against these viruses. The approach is based on the combined use of gold-standard sequence-based methods, and new cutting-edge methods for the structural modeling and analysis of peptides bound to different Human Leukocyte Antigen (HLA) receptors. HLAs are responsible for displaying the peptides to T-cell lymphocytes, and the proposed pipeline will enable the identification of conserved hot-spots capable of triggering T-cell responses against multiple SARS-CoV variants. In the context of this project, research will target conserved peptides from the Nucleocapsid (N) protein of SARS-CoV-2. If needed, the optimization of predicted peptides will be conducted for different prevalent HLA alleles. The proposed computational pipeline will be built using general software-engineering principles, making it also applicable to study different proteins from SARS-CoV variants, and even other pathogens.

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This work has been supported by grant NSF DBI 2033262.

Related Publications

  1. M. M. Rigo, R. Fasoulis, A. Conev, S. Hall-Swan, D. Amaral Antunes, and L. Kavraki, “SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development,” Frontiers in Immunology, vol. 13, Jul. 2022.
  2. R. F. Tarabini, M. M. Rigo, A. Faustino Fonseca, F. Rubin, R. Bellé, L. E. Kavraki, T. C. Ferreto, D. Amaral Antunes, and A. P. D. de Souza, “Large-Scale Structure-Based Screening of Potential T Cell Cross-Reactivities Involving Peptide-Targets From BCG Vaccine and SARS-CoV-2,” Frontiers in Immunology, vol. 12, Jan. 2022.
  3. S. Hall-Swan, D. Devaurs, M. M. Rigo, D. A. Antunes, L. E. Kavraki, and G. Zanatta, “DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins,” Computers in Biology and Medicine, vol. 139, p. 104943, 2021.