MOLECULAR-BASIS FOR THE BINDING OF SH3 LIGANDS WITH NONPEPTIDE ELEMENTS IDENTIFIED BY COMBINATORIAL SYNTHESIS

Background: Protein-structure-based combinatorial chemistry has recent ly been used to discover several ligands containing non-peptide bindin g elements to the Src SH3 domain. The encoded library used has the for m Cap-M1-M2-M3-PLPPLP, in which the Cap and Mi's are composed of a div erse set of organic monomers. The PLPPLP portion provided a structural bias directing the non-peptide fragment Cap-M1-M2-M3 to the SH3 speci ficity pocket. Fifteen ligands were selected from >1.1 million distinc t compounds. The structural basis for selection was unknown. Results: The solution structures of the Src SH3 domain complexed with two ligan ds containing non-peptide elements selected from the library were dete rmined by multidimensional NMR spectroscopy. The non-peptide moieties of the ligands interact with the specificity pocket of Src SH3 domain differently from peptides complexed with SH3 domains. Structural infor mation about the ligands was used to design various homologs, whose af finities for the SH3 domain were measured. The results provide a struc tural basis for understanding the selection of a few optimal ligands f rom a large library. Conclusions: The cycle of protein-structure-based combinatorial chemistry followed by structure determination of the fe w highest affinity ligands provides a powerful new tool for the field of molecular recognition.