Combinatorial peptide library binding assay

A variation of the pharmacophore library was seen in an approach used to determine CD4+ T cell epitopes.31 In a 14-mer peptide, the researchers keep residues in positions 1, 4, and 6 constant since they functioned as anchor positions for binding receptor, and proceeded to vary the other residues in the peptide. This allowed the use of a shorter synthetic route compared to one that would be needed if all positions were to be varied. Limiting the size of the library allowed the authors to obtain better assays. By doing a partial release of the peptides, the authors were able to find the final peptide that represented the epitope of the T cell receptor. In another example, the epitope to inhibit stimulation of the thyrotropin receptor also was found via combinatorial libraries.32 Since the synthesis of a totally random hexapeptide library was deemed impractical, the authors opted to hold one position constant while the other five residues were randomized. This method was repeated for each residue in the peptide. The residues that were determined to be the most active were used as a basis for a second-generation library. The only limitation of the library was not the quantity of product synthesized, but to properly pinpoint the peptides in an assay. 

Wiesmtiller K-H, Feiertag S, Fleckenstein B, Kienle S, Stoll D. Herrmann M, Jung G (1996) Peptide and cyclopeptide libraries Automated synthesis, analysis and receptor binding assays. In Jung 0 (ed) Combinatorial Peptide and Nonpeptide Libraries - A Handbook for the Search of Lead Structures, pp 203-246, Verlag Chemie, Weinheim, Germany. 

In 1991, we first introduced the one-bead one-compound (OBOC ) combinatorial library method.1 Since then, it has been successfully applied to the identification of ligands for a large number of biological targets.2,3 Using well-established on-bead binding or functional assays, the OBOC method is highly efficient and practical. A random library of millions of beads can be rapidly screened in parallel for a specific acceptor molecule (receptor, antibody, enzyme, virus, etc.). The amount of acceptor needed is minute compared to solution phase assay in microtiter plates. The positive beads with active compounds are easily isolated and subjected to structural determination. For peptides that contain natural amino acids and have a free N-terminus, we routinely use an automatic protein sequencer with Edman chemistry, which converts each a-amino acid sequentially to its phenylthiohydantoin (PTH) derivatives, to determine the structure of peptide on the positive beads. 

Another decoration pool library L23 was reported by Nestler (49), who presented the appendage of a peptidic chain to the two hydroxylic functions of a steroid scaffold (Fig. 4.15). The library was made up of 10 x 10 x 10 x 10 = 10,000 individuals using a chemical encoding method (39) and L-a-amino acids as monomer sets (R1-R4). The assay of the library as a source of artificial two-armed receptors for enkephalin-related peptides produced positives with micromolar affinity. Much larger libraries could be obtained by simply increasing the monomer sets and the length of the two arms this could lead to a primary library of peptide-binding artificial receptors similar scaffolds have been repeatedly exploited for combinatorial purposes (50-52). 

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