New ligands binding to the human leukocyte antigen class II molecule DRB1(*)0101 based on the activity pattern of an undecapeptide library

Major histocompatibility complex (MHC) class II molecules present peptide antigens to CD4(+)-T cells. These heterogeneous peptides are derived from internalized exogenous proteins or from endogenous membrane proteins that are processed by the antigen-presenting cell. Peptides are bound to the MHC class II molecules in an extended conformation and extend out of the binding groove. The aim of this study was to estimate the influence of every amino acid in all the possible undecapeptide amides (2.048X10(14) individuals) on the binding to human MHC-DRB1*0101 molecules (HLA-DR1) and to identify new peptide ligands. 220 undecapeptide sublibraries, O/X(10), each composed of ten degenerate positions and one defined position, were screened for binding to isolated HLA-DR1. Competition of the sublibraries with a fluorescence-labeled peptide ligand allowed definition of the amino acids favourable or unfavourable for DR1-binding at every sequence position. From the activity pattern of the undecapeptide library, 54 individual peptides were deduced (27 potential hits and 27 potential falls) and prepared by chemical synthesis. As anticipated, 27 positive and 27 negative results were obtained from the competition experiments. The 27 peptides that bind obey the rules for the HLA-DR1-binding motif. The synthetic peptide library approach proved to be valuable for the design of synthetic MHC class II ligands and thus can be considered as a basis for drug design in immunotherapy.