Design, synthesis and evaluation of high-affinity binders for the celiac disease associated HLA-DQ2 molecule

• Published in: Molecular immunology 2010-02, Vol.47 (5), p.1091-1097
• Main Authors: Kapoerchan, Varsha V., Wiesner, Martina, Hillaert, Ulrik, Drijfhout, Jan W., Overhand, Mark, Alard, Philippe, van der Marel, Gijs A., Overkleeft, Hermen S., Koning, Frits
• Format: Article
• Language: English
• Subjects: Alleles; Amino acids; Blockers; CD4-Positive T-Lymphocytes - immunology; Celiac disease; Celiac Disease - drug therapy; Celiac Disease - genetics; Celiac Disease - immunology; Genetic Predisposition to Disease; Gluten; Glutens - genetics; Glutens - immunology; HLA-DQ Antigens - genetics; HLA-DQ Antigens - immunology; HLA-DQ2; Humans; Peptides; Peptides - chemical synthesis; Peptides - chemistry; Peptides - genetics; Peptides - immunology
• ISSN: 0161-5890; 1872-9142
• DOI: 10.1016/j.molimm.2009.10.036

Celiac disease is caused by uncontrolled CD4 T-cell responses directed to wheat-derived gluten peptides bound to the disease predisposing HLA-DQ molecules. The only available treatment is a life-long gluten-free diet which is complicated by the widespread use of wheat-derived gluten in the food industry. As the binding of gluten-derived peptides is a prerequisite for the induction of the inflammatory T-cell response, blockers that would prevent gluten peptide binding to the HLA-DQ molecules might be used as an alternative to the gluten-free diet. In the present study we have analyzed the binding properties of a set of previously identified natural ligands for HLA-DQ2, the primary disease predisposing allele. An in silico method, Epibase, ranked these peptides and the top one, a peptide with a nine amino acid core FVAEYEPVL, was measured among these peptides as the peptide with the highest binding affinity for HLA-DQ2. In a stepwise approach we subsequently tested the impact of N-terminal extensions and systematic single amino acid substitutions within the core of this peptide which revealed that an N-terminal extension with the tripeptide sequence ADA increased binding affinity 5- to 6-fold. In addition the substitution analysis indicated which amino acids were most preferred at anchor residues in the lead peptide, generally leading to an increase of binding affinity with a factor of 2. Next we tested which combinations of such preferred amino acids yielded the best results. The combined results indicate that a peptide with sequence ADAYDYESEELFAA (core in bold) had superior binding properties. This peptide was chosen as a lead peptide for further optimization with non-natural amino acids at the p1 position, since molecular modeling indicated that none of the natural amino acids is able to optimally occupy the p1 pocket. A set of 8 non-proteinogenic amino acids was designed, synthesized and incorporated in the lead peptide (and in two control peptides) and tested for binding to HLA-DQ2. The results indicate that the effect of the incorporation of these non-proteinogenic amino acids depended on the peptide in which they were incorporated and that the maximum increase in binding affinity obtained was approximately 2-fold. Altogether lead sequences were obtained that have a binding affinity for HLA-DQ2 that is 100- to 200-fold higher compared to that of the gluten-derived peptide that has the highest affinity for HLA-DQ2. Such peptides are candidate lead pept