The epitope is the portion of a foreign protein or antigen that is capable of stimulating an immune response. The epitope is recognized as part of the antigen by antibodies, B cells or T cells. The epitope binds to the antigen receptor on the surface of a B cell if their structures are complementary and activates production of antibodies by B cells. The epitope is also the region of the antigen that antibodies recognize to remove the antigen from the body.
T-cell receptors (TCR) on the surface of T cells recognize epitopes bound to major histocompatibility complex (MHC) molecules that are displayed on the surface of antigen-presenting cells (APCs). APCs include dendritic cells, macrophages, Langerhans cells and B cells. T cell epitopes are peptides derived from antigens and presented by class I and class II MHC molecules. When CD8 T cells and CD4 T cells recognize an epitope they become cytotoxic T lymphocytes and helper T cells respectively.
In any vaccination a particular antigen is introduced into the immune system in order to produce a targeted immune reaction. Vaccines may be composed of live or fixed whole pathogens, native protein antigens purified from the pathogen or DNA or RNA capable of expressing the sequences of pathogen protein antigens. In epitope vaccine development, short amino acid sequences of a protein are used to induce a direct immune response and the epitope is recognized by the immune system as part of the antigen. Immunoinformatic tools are used to search for potential epitopes.
Previously prophylactic vaccines directed against viral infections mainly focused on induction of neutralizing antibodies by B cells but more recently vaccines seek to elicit a T cell response as well. Stimulation of an immune response depends on epitopes being presented to circulating T-cells via the human leukocyte antigens (HLA) complex. Part of the epitope choice is based on HLA-binding prediction tools such as HLA ligandome analysis which use machine learning. HLA is the human version of the major histocompatibility complex (MHC) found in many species. T cell epitope immunogenicity is also dependent on antigen processing and recognition by the TCR.
Epitopes.world is an AI-powered platform that uses an algorithm called CAMAP that predicts which parts of the virus will most likely form epitopes and be exposed at the surface of infected cells. The platform was developed by Tariq Daouda and researchers at Harvard and Université de Montréal with the aim of speeding up vaccine development for COVID-19. CAMAP was originally developed for cancer immunotherapy. Epitopes.world is available on GitHub and a public API is available.
