NY-ESO-1, a commonly expressed tumor antigen of the cancer-testis family, is expressed by a wide range of tumors but not found in normal adult somatic tissue, making it an ideal cancer vaccine candidate. Peptides derived from NY-ESO-1 have shown preclinical and clinical trial promise; however, biochemical features of these peptides have complicated their formulation and led to heterogeneous immune responses. We have taken a rational approach to engineer an HLA A2-restricted NY-ESO-1-derived T cell epitope with improved formulation and immunogenicity to the wild type peptide. To accomplish this, we have solved the x-ray crystallographic structures of HLA A2 complexed to NY-ESO (157-165) and two analogues of this peptide in which the C-terminal cysteine residue has been substituted to alanine or serine. Substitution of cysteine by serine maintained peptide conformation yet reduced complex stability, resulting in poor cytotoxic T lymphocyte recognition. Conversely, substitution with alanine maintained complex stability and cytotoxic T lymphocyte recognition. Based on the structures of the three HLA A2 complexes, we incorporated 2-aminoisobutyric acid, an isostereomer of cysteine, into the epitope. This analogue is impervious to oxidative damage, cysteinylation, and dimerization of the peptide epitope upon formulation that is characteristic of the wild type peptide. Therefore, this approach has yielded a potential therapeutic molecule that satiates the hydrophobic F pocket of HLA A2 and exhibited superior immunogenicity relative to the wild type peptide.Class I major histocompatibility complex (MHC) 1 molecules play a crucial role in immune surveillance by selectively binding to intracellular peptide antigens (Ag) and presenting them at the cell surface to CD8 ϩ T lymphocytes (T CD8 ), including cytotoxic T lymphocytes (CTL). Eradication of tumors is associated with a robust cytotoxic T cell response to antigens expressed by the tumor (tumor-associated antigens (TAA)). Because many TAA are self-proteins or closely related to selfproteins, they tend to be poorly immunogenic (1-5). Moreover, many TAA-derived peptides are not strong binders to class I molecules, making strategies that revolve around tumor Ag delivery poor inducers of CD8 T cell immunity (6). Synthetic peptide-based vaccines offer a flexible, relatively simple and cost-effective way to treat a variety of human diseases, including the immunotherapy of cancer. Moreover, synthetic peptides are easily engineered to improve the efficacy of the immunogen. Such engineering may include optimizing target MHC class I binding by substituting key residues with more appropriate anchor residues. In addition, peptide-based therapeutics can be engineered to improve formulation and storage properties, and strategies exist to protect labile peptide bonds by incorporating nonpeptidic structures (7-11). Several studies have incorporated nonnatural amino acids in peptidic structures to improve compound stability and maintain T cell cross-reactivity. For example, some studie...