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

• Main Authors: Quartararo, Anthony James (Author), Gates, Zachary P (Author), Somsen, Bente A. (Author), Hartrampf, Nina (Author), Ye, Xiyun (Author), Shimada, Arisa (Author), Kajihara, Yasuhiro (Author), Ottmann, Christian (Author), Pentelute, Bradley L. (Author)
• Other Authors: Massachusetts Institute of Technology. Department of Chemistry (Contributor), Massachusetts Institute of Technology. Center for Environmental Health Sciences (Contributor), Koch Institute for Integrative Cancer Research at MIT (Contributor)
• Format: Article
• Language: English
• Published: Springer Science and Business Media LLC, 2020-10-27T20:18:24Z.
• Subjects: Article
• Online Access: Get fulltext

 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.