Directed discovery of bivalent peptide ligands to an SH3 domain

Abstract

The Caenorhabditis elegans SEM-5 SH3 domains recognize proline-rich peptide segments with modest affinity. We developed a bivalent peptide ligand that contains a naturally occurring proline-rich binding sequence, tethered by a glycine linker to a disulfide-closed loop segment containing six variable residues. The glycine linker allows the loop segment to explore regions of greatest diversity in sequence and structure of the SH3 domain: the RT and n-Src loops. The bivalent ligand was optimized using phage display, leading to a peptide (PP-G 4 -L) with 1000-fold increased affinity for the SEM-5 C-terminal SH3 domain over that of a natural ligand. NMR analysis of the complex confirms that the peptide loop segment is targeted to the RT and n-Src loops and parts of the ␤-sheet scaffold of this SH3 domain. This binding region is comparable to that targeted by a natural non-PXXP peptide to the p67 phox SH3 domain, a region not known to be targeted in the Grb2 SH3 domain family. PP-G 4 -L may aid in the discovery of additional binding partners of Grb2 family SH3 domains.

Molecular Determinants of TRIF Proteolysis Mediated by the Hepatitis C Virus NS3/4A Protease

“…Previous structure-based drug design studies have provided proof of concept for bivalent peptides. The "tethering" of two different peptides that bind in weak mM range at closely proximate sites on a target molecule may result in binding affinities in the submicromolar range because of the reduction in the rotational and translational entropy associated with the tethering (57). We hypothesize that the TRIF sequence thus acts as a naturally occurring bivalent ligand, wherein the polyproline sequence acts as an anchor and further enhances affinity of the substrate for the protease.…”

Potential Disease Targets for Drugs that Disrupt Protein - Protein Interactions of Grb2 and Crk Family Adaptors

“…Although it may be difficult to develop small (MW < 500) molecule SH3 domain inhibitors to systemically inhibit Grb2 interactions 'in vivo', more complex 'composite inhibitors', could eventually become an option. Encouragingly, a recent study targeting the Sem-5 SH3C domain succeeded to generate a ligand peptide with very high affinity [284] and peptoid dimers show a greatly increased binding to the Grb2 SH3 domains [285].…”

Optimizing the Amino Acid Sequences of Peptides and Improving Their Specificity of Binding to SH3 Domains of Target Proteins

“…42 And Ferguson et al used phage display for ligand optimization and obtained a peptide 1000-fold increased affinity for the SEM-5 SH3 domain. 43 Here we provided a novel clue as to increasing the specificity of binding to SH3 domain. The current results will inspire more subsequent work on optimization of amino acid sequence, so as to improve the safety of therapeutic peptides.…”