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

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
DOI: 10.1038/s41467-020-16920-3 Publication Date: 2020-06-23T10:03:35Z
ABSTRACT
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.
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