Fragment‐Based Stabilizers of Protein–Protein Interactions through Imine‐Based Tethering
Small‐molecule stabilization of protein–protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a “bottom‐up” approach is largely unanswered. We report a novel concept for identifying initial chemical matter for...
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| Published in: | Angewandte Chemie International Edition Vol. 59; no. 48; pp. 21520 - 21524 |
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| Main Authors: | , , , , , , , , , |
| Format: | Journal Article |
| Language: | English |
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23.11.2020
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| Edition: | International ed. in English |
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| ISSN: | 1433-7851, 1521-3773, 1521-3773 |
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| Abstract | Small‐molecule stabilization of protein–protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a “bottom‐up” approach is largely unanswered. We report a novel concept for identifying initial chemical matter for PPI stabilization based on imine‐forming fragments. The imine bond offers a covalent anchor for site‐directed fragment targeting, whereas its transient nature enables efficient analysis of structure–activity relationships. This bond enables fragment identification and optimisation using protein crystallography. We report novel fragments that bind specifically to a lysine at the PPI interface of the p65‐subunit‐derived peptide of NF‐κB with the adapter protein 14‐3‐3. Those fragments that subsequently establish contacts with the p65‐derived peptide, rather than with 14‐3‐3, efficiently stabilize the 14‐3‐3/p65 complex and offer novel starting points for molecular glues.
A novel concept for optimizing orthosteric protein–protein interaction (PPI) stabilization is reported. Increasing interactions with the protein partner that contributes less to the composite binding pocket of the stabilizer (NF‐κB, red surface) results in increased stabilization, whereas further enhancing the interaction with the dominant partner protein (14‐3‐3, white surface) does not contribute to the stabilizing effect. |
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| AbstractList | Small‐molecule stabilization of protein–protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a “bottom‐up” approach is largely unanswered. We report a novel concept for identifying initial chemical matter for PPI stabilization based on imine‐forming fragments. The imine bond offers a covalent anchor for site‐directed fragment targeting, whereas its transient nature enables efficient analysis of structure–activity relationships. This bond enables fragment identification and optimisation using protein crystallography. We report novel fragments that bind specifically to a lysine at the PPI interface of the p65‐subunit‐derived peptide of NF‐κB with the adapter protein 14‐3‐3. Those fragments that subsequently establish contacts with the p65‐derived peptide, rather than with 14‐3‐3, efficiently stabilize the 14‐3‐3/p65 complex and offer novel starting points for molecular glues. Small‐molecule stabilization of protein–protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a “bottom‐up” approach is largely unanswered. We report a novel concept for identifying initial chemical matter for PPI stabilization based on imine‐forming fragments. The imine bond offers a covalent anchor for site‐directed fragment targeting, whereas its transient nature enables efficient analysis of structure–activity relationships. This bond enables fragment identification and optimisation using protein crystallography. We report novel fragments that bind specifically to a lysine at the PPI interface of the p65‐subunit‐derived peptide of NF‐κB with the adapter protein 14‐3‐3. Those fragments that subsequently establish contacts with the p65‐derived peptide, rather than with 14‐3‐3, efficiently stabilize the 14‐3‐3/p65 complex and offer novel starting points for molecular glues. A novel concept for optimizing orthosteric protein–protein interaction (PPI) stabilization is reported. Increasing interactions with the protein partner that contributes less to the composite binding pocket of the stabilizer (NF‐κB, red surface) results in increased stabilization, whereas further enhancing the interaction with the dominant partner protein (14‐3‐3, white surface) does not contribute to the stabilizing effect. Small-molecule stabilization of protein-protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a "bottom-up" approach is largely unanswered. We report a novel concept for identifying initial chemical matter for PPI stabilization based on imine-forming fragments. The imine bond offers a covalent anchor for site-directed fragment targeting, whereas its transient nature enables efficient analysis of structure-activity relationships. This bond enables fragment identification and optimisation using protein crystallography. We report novel fragments that bind specifically to a lysine at the PPI interface of the p65-subunit-derived peptide of NF-kappa B with the adapter protein 14-3-3. Those fragments that subsequently establish contacts with the p65-derived peptide, rather than with 14-3-3, efficiently stabilize the 14-3-3/p65 complex and offer novel starting points for molecular glues. Small‐molecule stabilization of protein–protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a “bottom‐up” approach is largely unanswered. We report a novel concept for identifying initial chemical matter for PPI stabilization based on imine‐forming fragments. The imine bond offers a covalent anchor for site‐directed fragment targeting, whereas its transient nature enables efficient analysis of structure–activity relationships. This bond enables fragment identification and optimisation using protein crystallography. We report novel fragments that bind specifically to a lysine at the PPI interface of the p65‐subunit‐derived peptide of NF‐κB with the adapter protein 14‐3‐3. Those fragments that subsequently establish contacts with the p65‐derived peptide, rather than with 14‐3‐3, efficiently stabilize the 14‐3‐3/p65 complex and offer novel starting points for molecular glues. A novel concept for optimizing orthosteric protein–protein interaction (PPI) stabilization is reported. Increasing interactions with the protein partner that contributes less to the composite binding pocket of the stabilizer (NF‐κB, red surface) results in increased stabilization, whereas further enhancing the interaction with the dominant partner protein (14‐3‐3, white surface) does not contribute to the stabilizing effect. Small-molecule stabilization of protein-protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a "bottom-up" approach is largely unanswered. We report a novel concept for identifying initial chemical matter for PPI stabilization based on imine-forming fragments. The imine bond offers a covalent anchor for site-directed fragment targeting, whereas its transient nature enables efficient analysis of structure-activity relationships. This bond enables fragment identification and optimisation using protein crystallography. We report novel fragments that bind specifically to a lysine at the PPI interface of the p65-subunit-derived peptide of NF-κB with the adapter protein 14-3-3. Those fragments that subsequently establish contacts with the p65-derived peptide, rather than with 14-3-3, efficiently stabilize the 14-3-3/p65 complex and offer novel starting points for molecular glues.Small-molecule stabilization of protein-protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design chemical starting points in a "bottom-up" approach is largely unanswered. We report a novel concept for identifying initial chemical matter for PPI stabilization based on imine-forming fragments. The imine bond offers a covalent anchor for site-directed fragment targeting, whereas its transient nature enables efficient analysis of structure-activity relationships. This bond enables fragment identification and optimisation using protein crystallography. We report novel fragments that bind specifically to a lysine at the PPI interface of the p65-subunit-derived peptide of NF-κB with the adapter protein 14-3-3. Those fragments that subsequently establish contacts with the p65-derived peptide, rather than with 14-3-3, efficiently stabilize the 14-3-3/p65 complex and offer novel starting points for molecular glues. |
| Author | Valenti, Dario Cossar, Peter J. Levy, Laura M. Hristeva, Stanimira Hoffmann, Torsten Brunsveld, Luc Ottmann, Christian Wolter, Madita Tzalis, Dimitrios Genski, Thorsten |
| AuthorAffiliation | 2 Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany 1 Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands 3 Department of Chemistry University of Duisburg-Essen Universitätsstrasse 7 45117 Essen Germany |
| AuthorAffiliation_xml | – name: 1 Laboratory of Chemical Biology Department of Biomedical, Engineering and Institute for Complex Molecular Systems Eindhoven University of Technology P.O. Box 513 5600 MB Eindhoven The Netherlands – name: 2 Taros Chemicals GmbH & Co. KG Emil-Figge-Straße 76a 44227 Dortmund Germany – name: 3 Department of Chemistry University of Duisburg-Essen Universitätsstrasse 7 45117 Essen Germany |
| Author_xml | – sequence: 1 givenname: Madita surname: Wolter fullname: Wolter, Madita organization: Eindhoven University of Technology – sequence: 2 givenname: Dario surname: Valenti fullname: Valenti, Dario organization: Taros Chemicals GmbH & Co. KG – sequence: 3 givenname: Peter J. surname: Cossar fullname: Cossar, Peter J. organization: Eindhoven University of Technology – sequence: 4 givenname: Laura M. surname: Levy fullname: Levy, Laura M. organization: Taros Chemicals GmbH & Co. KG – sequence: 5 givenname: Stanimira surname: Hristeva fullname: Hristeva, Stanimira organization: Taros Chemicals GmbH & Co. KG – sequence: 6 givenname: Thorsten surname: Genski fullname: Genski, Thorsten organization: Taros Chemicals GmbH & Co. KG – sequence: 7 givenname: Torsten surname: Hoffmann fullname: Hoffmann, Torsten organization: Taros Chemicals GmbH & Co. KG – sequence: 8 givenname: Luc surname: Brunsveld fullname: Brunsveld, Luc organization: Eindhoven University of Technology – sequence: 9 givenname: Dimitrios surname: Tzalis fullname: Tzalis, Dimitrios email: DTzalis@taros.de organization: Taros Chemicals GmbH & Co. KG – sequence: 10 givenname: Christian orcidid: 0000-0001-7315-0315 surname: Ottmann fullname: Ottmann, Christian email: C.Ottmann@tue.nl organization: University of Duisburg-Essen |
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| Keywords | 14-3-3 proteins fragment-based drug discovery DRUG DISCOVERY TARGETS imine chemistry cooperative effects protein-protein interactions |
| Language | English |
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| Title | Fragment‐Based Stabilizers of Protein–Protein Interactions through Imine‐Based Tethering |
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