Prediction of epitopes of viral antigens recognized by cytotoxic T Lymphocytes as an immunoinformatics approach to anti-HIV/AIDS vaccine design

Vaccine design is a principal application of the recently emerged biomedical field of immunoinformatics, also known as computational immunology. Algorithms may be used to model immunological data in order to map potential B- and T-lymphocyte epitopes, or antigenic determinants, of foreign proteins which elicit specific responses from an immunized individual. Determination of antibody residues is a key factor in identifying antigen resistance mutations, designing epitope­specific probes for antibody isolation, and for developing epitope­based vaccines. Optimally, epitopes are determined at the atomic level structure of an antibody­antigen complex, although this may not in all instances be possible. Epitopes are of particular interest to both clinical and basic biomedical researchers since they hold huge potential for vaccine design, disease prevention, diagnosis and treatment. Since human immunodeficiency virus (HIV)­1 was identified in 1983, it has attracted a research impetus unrivalled in breadth and complexity, the ultimate objectives of which – a preventive vaccine and a curative treatment – remain elusive. Development of an efficacious and cost-effective vaccine is part of a strategy that is required urgently to combat acquired immunodeficiency syndrome, AIDS, the spectrum of conditions which is caused by infection with HIV-1. The challenge of predicting a viral phenotype from sequence data has considerable potential in HIV-1 vaccine design. Here, the major approaches which may be used for epitope prediction in HIV/AIDS research are discussed.