Ultra-large chemical libraries for the discovery of high-affinity peptide binders

Anthony J. Quartararo, Zachary P. Gates, Bente A. Somsen, Nina Hartrampf, Xiyun Ye, Arisa Shimada, Yasuhiro Kajihara, Christian Ottmann, Bradley L. Pentelute (Corresponding author)

Research output: Contribution to journalArticleAcademicpeer-review

62 Citations (Scopus)


High-diversity genetically-encoded combinatorial libraries (108−1013 members) are a rich source of peptide-based binding molecules, identified by affinity selection. Synthetic libraries can access broader chemical space, but typically examine only ~ 106 compounds by screening. Here we show that in-solution affinity selection can be interfaced with nano-liquid chromatography-tandem mass spectrometry peptide sequencing to identify binders from fully randomized synthetic libraries of 108 members—a 100-fold gain in diversity over standard practice. To validate this approach, we show that binders to a monoclonal antibody are identified in proportion to library diversity, as diversity is increased from 106–108. These results are then applied to the discovery of p53-like binders to MDM2, and to a family of 3–19 nM-affinity, α/β-peptide-based binders to 14-3-3. An X-ray structure of one of these binders in complex with 14-3-3σ is determined, illustrating the role of β-amino acids in facilitating a key binding contact.

Original languageEnglish
Article number3183
Number of pages11
JournalNature Communications
Issue number1
Publication statusPublished - 23 Jun 2020


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