Ultra-large chemical libraries for the discovery of high-affinity peptide binders
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-s...
| Main Authors: | , , , , , , , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
Springer Science and Business Media LLC
2020
|
| Online Access: | https://hdl.handle.net/1721.1/128217 |
| _version_ | 1826209560953618432 |
|---|---|
| author | Quartararo, Anthony James Gates, Zachary P Somsen, Bente A. Hartrampf, Nina Ye, Xiyun Shimada, Arisa Kajihara, Yasuhiro Ottmann, Christian Pentelute, Bradley L. |
| author2 | Massachusetts Institute of Technology. Department of Chemistry |
| author_facet | Massachusetts Institute of Technology. Department of Chemistry Quartararo, Anthony James Gates, Zachary P Somsen, Bente A. Hartrampf, Nina Ye, Xiyun Shimada, Arisa Kajihara, Yasuhiro Ottmann, Christian Pentelute, Bradley L. |
| author_sort | Quartararo, Anthony James |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T14:24:35Z |
| format | Article |
| id | mit-1721.1/128217 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T14:24:35Z |
| publishDate | 2020 |
| publisher | Springer Science and Business Media LLC |
| record_format | dspace |
| spelling | mit-1721.1/1282172022-10-01T21:10:41Z Ultra-large chemical libraries for the discovery of high-affinity peptide binders Quartararo, Anthony James Gates, Zachary P Somsen, Bente A. Hartrampf, Nina Ye, Xiyun Shimada, Arisa Kajihara, Yasuhiro Ottmann, Christian Pentelute, Bradley L. Massachusetts Institute of Technology. Department of Chemistry Massachusetts Institute of Technology. Center for Environmental Health Sciences Koch Institute for Integrative Cancer Research at MIT 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. NIH/NIGMS (Grant T32-GM008334) 2020-10-27T20:18:24Z 2020-10-27T20:18:24Z 2020-06 2019-12 2020-09-21T14:56:31Z Article http://purl.org/eprint/type/JournalArticle 2041-1723 https://hdl.handle.net/1721.1/128217 Quartararo, Anthony J. et al. "Ultra-large chemical libraries for the discovery of high-affinity peptide binders." Nature Communications 11, 1 (June 2020): 3183 © 2020 The Author(s) en http://dx.doi.org/10.1038/s41467-020-16920-3 Nature Communications Creative Commons Attribution 4.0 International license https://creativecommons.org/licenses/by/4.0/ application/pdf Springer Science and Business Media LLC Nature |
| spellingShingle | Quartararo, Anthony James Gates, Zachary P Somsen, Bente A. Hartrampf, Nina Ye, Xiyun Shimada, Arisa Kajihara, Yasuhiro Ottmann, Christian Pentelute, Bradley L. Ultra-large chemical libraries for the discovery of high-affinity peptide binders |
| title | Ultra-large chemical libraries for the discovery of high-affinity peptide binders |
| title_full | Ultra-large chemical libraries for the discovery of high-affinity peptide binders |
| title_fullStr | Ultra-large chemical libraries for the discovery of high-affinity peptide binders |
| title_full_unstemmed | Ultra-large chemical libraries for the discovery of high-affinity peptide binders |
| title_short | Ultra-large chemical libraries for the discovery of high-affinity peptide binders |
| title_sort | ultra large chemical libraries for the discovery of high affinity peptide binders |
| url | https://hdl.handle.net/1721.1/128217 |
| work_keys_str_mv | AT quartararoanthonyjames ultralargechemicallibrariesforthediscoveryofhighaffinitypeptidebinders AT gateszacharyp ultralargechemicallibrariesforthediscoveryofhighaffinitypeptidebinders AT somsenbentea ultralargechemicallibrariesforthediscoveryofhighaffinitypeptidebinders AT hartrampfnina ultralargechemicallibrariesforthediscoveryofhighaffinitypeptidebinders AT yexiyun ultralargechemicallibrariesforthediscoveryofhighaffinitypeptidebinders AT shimadaarisa ultralargechemicallibrariesforthediscoveryofhighaffinitypeptidebinders AT kajiharayasuhiro ultralargechemicallibrariesforthediscoveryofhighaffinitypeptidebinders AT ottmannchristian ultralargechemicallibrariesforthediscoveryofhighaffinitypeptidebinders AT pentelutebradleyl ultralargechemicallibrariesforthediscoveryofhighaffinitypeptidebinders |