TY - JOUR
T1 - Binary combinatorial scanning reveals potent poly-alanine-substituted inhibitors of protein-protein interactions
AU - Ye, Xiyun
AU - Lee, Yen Chun
AU - Gates, Zachary P.
AU - Ling, Yingjie
AU - Mortensen, Jennifer C.
AU - Yang, Fan Shen
AU - Lin, Yu Shan
AU - Pentelute, Bradley L.
N1 - Publisher Copyright:
© 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - Establishing structure–activity relationships is crucial to understand and optimize the activity of peptide-based inhibitors of protein–protein interactions. Single alanine substitutions provide limited information on the residues that tolerate simultaneous modifications with retention of biological activity. To guide optimization of peptide binders, we use combinatorial peptide libraries of over 4,000 variants—in which each position is varied with either the wild-type residue or alanine—with a label-free affinity selection platform to study protein–ligand interactions. Applying this platform to a peptide binder to the oncogenic protein MDM2, several multi-alanine-substituted analogs with picomolar binding affinity were discovered. We reveal a non-additive substitution pattern in the selected sequences. The alanine substitution tolerances for peptide ligands of the 12ca5 antibody and 14-3-3 regulatory protein are also characterized, demonstrating the general applicability of this new platform. We envision that binary combinatorial alanine scanning will be a powerful tool for investigating structure–activity relationships.
AB - Establishing structure–activity relationships is crucial to understand and optimize the activity of peptide-based inhibitors of protein–protein interactions. Single alanine substitutions provide limited information on the residues that tolerate simultaneous modifications with retention of biological activity. To guide optimization of peptide binders, we use combinatorial peptide libraries of over 4,000 variants—in which each position is varied with either the wild-type residue or alanine—with a label-free affinity selection platform to study protein–ligand interactions. Applying this platform to a peptide binder to the oncogenic protein MDM2, several multi-alanine-substituted analogs with picomolar binding affinity were discovered. We reveal a non-additive substitution pattern in the selected sequences. The alanine substitution tolerances for peptide ligands of the 12ca5 antibody and 14-3-3 regulatory protein are also characterized, demonstrating the general applicability of this new platform. We envision that binary combinatorial alanine scanning will be a powerful tool for investigating structure–activity relationships.
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U2 - 10.1038/s42004-022-00737-w
DO - 10.1038/s42004-022-00737-w
M3 - Article
AN - SCOPUS:85140982055
SN - 2399-3669
VL - 5
JO - Communications Chemistry
JF - Communications Chemistry
IS - 1
M1 - 128
ER -