Improving SH3 domain ligand selectivity using a non-natural scaffold
BACKGROUND: Src homology
3 (SH3) domains bind sequences bearing the consensus motif PxxP (where P is
proline and x is any amino acid), wherein domain specificity is mediated largely
by sequences flanking the PxxP core. This specificity is limited, however,
as most SH3 domains show high ligand cross-reactivity. We have recently shown
that diverse N-substituted residues (peptoids) can replace the prolines in
the PxxP motif, yielding a new source of ligand specificity.
RESULTS: We have tested
the effects of combining multiple peptoid substitutions with specific flanking
sequences on ligand affinity and specificity. We show that by varying these
different elements, a ligand can be selectively tuned to target a single SH3
domain in a test set. In addition, we show that by making multiple peptoid
substitutions, high-affinity ligands can be generated that completely lack
the canonical PxxP motif. The resulting ligands can potently disrupt natural
SH3-mediated interactions.
CONCLUSIONS: Peptide-peptoid
hybrid scaffolds yield SH3 ligands with markedly improved domain selectivity,
overcoming one of the principal challenges in designing inhibitors against
these domains. These compounds represent important leads in the search for
orthogonal inhibitors of SH3 domains, and can serve as tools for the dissection
of complex signaling pathways.