From consensus sequence to high-affinity ligands: acquisition of signaling protein modulators

Protein kinases recognize and bind to specific amino acid sequences on their protein substrates. These sequences can be readily identified using combinatorial peptide libraries. Unfortunately, conventional peptide libraries are not designed to identify subtle structural factors that can dramatically enhance enzyme affinity since the "local" diversity associated with these libraries is limited to the 20 standard amino acids. A parallel synthesis strategy was developed that possesses 2 key attributes: moderate size ( approximately 1000 members each), yet high structural diversity (50-fold greater than that of conventional peptide libraries). Due to their small size, these libraries can be synthesized in parallel, which allows each library member to be individually evaluated, and eliminates the requirement for subsequent structural deconvolution. Furthermore, since these libraries possess a high structural diversity focused within narrow spatial windows on the target protein, small regions of the protein can be challenged with a multitude of functionality containing structural differences that vary from subtle to gross.