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.
Nguyen
J T
JT
Program in Biophysics, University of California, San Francisco 94143-0450, USA.
Porter
M
M
Amoui
M
M
Miller
W T
WT
Zuckermann
R N
RN
Lim
W A
WA
D020816:Amino Acid Motifs / Q000502:physiology*; D019943:Amino Acid Substitution; D001665:Binding Sites / Q000502:physiology; D002460:Cell Line; D015195:Drug Design; D006801:Humans; D008024:Ligands; D015394:Molecular Structure; D019151:Peptide Library; D010455:Peptides / Q000737:chemistry / Q000378:metabolism*; D034444:Peptoids; D011485:Protein Binding; D020539:Sequence Analysis, Protein; D015398:Signal Transduction / Q000502:physiology; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D018909:src Homology Domains / Q000502:physiology*; D019061:src-Family Kinases / Q000737:chemistry
D008024:Ligands; D019151:Peptide Library; D010455:Peptides; D034444:Peptoids; D019061:src-Family Kinases