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

• DOI: 10.1038/s41467-020-16920-3
• Publication Date: 2020-06-23T10:03:35Z
• Authors: Anthony J. Quarta...; Zachary P. Gates; Bente A. Somsen; Nina Hartrampf; Xiyun Ye; Arisa Shimada; Yasuhiro Kajihara; Christian Ottmann; Bradley L. Pentelute
• Keywords: Models, Molecular; 0301 basic medicine; Science; Q; Antibody Affinity; Antibodies, Monoclonal; Proto-Oncogene Proteins c-mdm2; Crystallography, X-Ray; Article; 3. Good health; Small Molecule Libraries; 03 medical and health sciences; Peptide Library; Drug Design; Drug Discovery; Amino Acid Sequence; Amino Acids; Carrier Proteins; Peptides; Chromatography, Liquid

AbstractHigh-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.