SARS-Arena

SARS-Arena identifies conserved peptide candidates from the nucleocapsid (N) protein of SARS-CoV-2 and related coronaviruses to support T-cell epitope discovery for vaccine design.

Key Features:

• Nucleocapsid (N) protein targeting: Focuses analysis on the N protein, which is less susceptible to selection pressure than envelope proteins such as spike.
• Sequence- and structure-based analyses: Integrates sequence-based methods and structure-based analyses for comprehensive evaluation of N protein sequences across SARS-CoV-related strains.
• Multiple Sequence Alignment (MSA): Conducts MSA on N protein sequences to identify conserved regions across viral strains.
• Candidate peptide recovery: Recovers candidate peptides of varying lengths from conserved regions as potential T-cell targets.
• 3D structural modeling in HLA context: Models three-dimensional structures of conserved peptides in the context of various Human Leukocyte Antigen (HLA) molecules to assess potential presentation.

Scientific Applications:

• T-cell epitope discovery for vaccine development: Identifies conserved N protein peptides to inform vaccine strategies aimed at eliciting T-cell–mediated immune responses against SARS-CoV-2 and related coronaviruses.
• Assessment of peptide-HLA presentation: Provides structural models to evaluate peptide binding and presentation by different HLA alleles.

Methodology:

Performs computational analysis of protein sequences from biological databases, using MSA to detect conserved regions in the N protein; recovers candidate peptides of varying lengths from conserved regions and performs 3D structural modeling of peptides in complex with HLA molecules; has identified peptides such as SPRWYFYYL recognized by CD8+ T-cells in the context of HLA-B7+.