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

High-diversity genetically-encoded combinatorial libraries (10 8 −10 13 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 ~ 10 6 compounds by screening. Here we show that...

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Vydáno v:	Nature communications Ročník 11; číslo 1; s. 3183 - 11
Hlavní autoři:	Quartararo, Anthony J., Gates, Zachary P., Somsen, Bente A., Hartrampf, Nina, Ye, Xiyun, Shimada, Arisa, Kajihara, Yasuhiro, Ottmann, Christian, Pentelute, Bradley L.
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	London Nature Publishing Group UK 23.06.2020 Nature Publishing Group Nature Portfolio
Témata:	14-3-3 protein 49/1 49/75 631/1647/296 639/638/45/611 639/638/92/2132/605 82/58 82/75 Affinity Amino Acid Sequence Amino Acids Antibodies, Monoclonal - chemistry Antibody Affinity Binders Binding Carrier Proteins - chemistry Chromatography, Liquid Combinatorial analysis Combinatorial libraries Crystallography, X-Ray Drug Design Drug Discovery Humanities and Social Sciences Libraries Liquid chromatography Mass spectrometry Mass spectroscopy MDM2 protein Models, Molecular Monoclonal antibodies multidisciplinary p53 Protein Peptide libraries Peptide Library Peptides Peptides - chemistry Proto-Oncogene Proteins c-mdm2 - chemistry Proto-Oncogene Proteins c-mdm2 - metabolism Randomization Science Science (multidisciplinary) Small Molecule Libraries - chemistry
ISSN:	2041-1723, 2041-1723
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Shrnutí:	High-diversity genetically-encoded combinatorial libraries (10 8 −10 13 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 ~ 10 6 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 10 8 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 10 6 –10 8 . 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. Synthetic peptide libraries can access broad chemical space, but generally examine only ~ 10 6 compounds. Here, the authors show that in-solution affinity selection, interfaced with nLC-MS/MS sequencing, can identify binders from fully randomized synthetic libraries of 10 8 members.
Bibliografie:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 14 content type line 23
ISSN:	2041-1723 2041-1723
DOI:	10.1038/s41467-020-16920-3