Quantitative structure-activity relations by the MTD-method for binding of nonapeptides to the HLA-A2.1 molecule

Binding of large series of nonapeptides to the HLA-A2.1 molecule was studied by a group of Sette in order to predict strongly binding peptides with possible therapeutic interest. Here we establish QSAR-s for these series. The MTD-method was used for steric requirements concerning amino acidic side chains as well as side chain hydrophobicities. Binding of these peptides to the HLA-A2.1 molecule is favored by a lipophylic character of side chains for the anchor position 2 and 9 and for positions 1,3 and 6 and by steric features that allow predictions for some modified amino acidic residues in these positions that should increase the peptide-HLA-molecule affinity.