Design of gliadin peptide analogues with low affinity for the celiac disease associated HLA-DQ2 protein

The HLA-DQ2.5 receptors bind gluten-derived peptides and present them to the T cells in the intestinal mucosa thus inducing the development of immune responses typical of the celiac disease. On the basis of the X-ray structure of the domain of HLA-DQ2.5 bound to the DQ2.5-glia-α1a epitope, fifteen peptides were designed with the aim of lowering the epitope binding affinity, thus reducing the autoimmune response. Hydroxylation of Pro residues was proposed as a suitable functionalization given that both enzymatic and chemical synthetic methods are available. Then, a computational study on the effects of Pro hydroxylation on HLA-DQ2.5 binding was performed by molecular docking. A docking protocol able to reproduce the binding geometry of the known crystallographic complex was set up and applied to the designed DQ2.5-glia-α1a analogues. Among them, the one including four di-hydroxylated Pro residues was predicted to lower the binding affinity to the greatest extent. Therefore, the same functionalization was also computationally tested for other celiac disease relevant epitopes, DQ2.5-glia-α1b and DQ2.5-glia-α2, and their ability for inhibiting the binding to HLA-DQ2.5 was confirmed. On this basis, these hydroxylated peptides are expected to significantly affect the gluten activity involved in celiac disease and, after experimental validation, a synthetic method will be developed for introducing this gluten modification directly in flour. The proposed approach is a promising tool to study the binding of other gliadin and glutenin derived T-cell epitopes as well as their variants.