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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Veröffentlicht in:	Angewandte Chemie International Edition Jg. 59; H. 48; S. 21520 - 21524
Hauptverfasser:	Wolter, Madita, Valenti, Dario, Cossar, Peter J., Levy, Laura M., Hristeva, Stanimira, Genski, Thorsten, Hoffmann, Torsten, Brunsveld, Luc, Tzalis, Dimitrios, Ottmann, Christian
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	WEINHEIM Wiley 23.11.2020 Wiley Subscription Services, Inc John Wiley and Sons Inc
Ausgabe:	International ed. in English
Schlagworte:	14-3-3 proteins 14-3-3 Proteins - chemistry Adapter proteins Adapters Adhesives Chemistry Chemistry, Multidisciplinary Communication Communications cooperative effects Crystallography Drug development fragment-based drug discovery Fragments Glues imine chemistry Imines - chemistry Lysine Molecular Structure Optimization Peptides Physical Sciences Protein Binding Protein interaction Protein Stability Proteins protein–protein interactions Science & Technology Small Molecule Libraries - chemistry Stabilization Structure-Activity Relationship Tethering Transcription Factor RelA - chemistry 14-3-3 proteins fragment-based drug discovery DRUG DISCOVERY TARGETS imine chemistry cooperative effects protein-protein interactions
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.
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
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BackLink	https://www.ncbi.nlm.nih.gov/pubmed/32816380$$D View this record in MEDLINE/PubMed
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Keywords	14-3-3 proteins fragment-based drug discovery DRUG DISCOVERY TARGETS imine chemistry cooperative effects protein-protein interactions
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Snippet	Small‐molecule stabilization of protein–protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design... Small-molecule stabilization of protein-protein interactions (PPIs) is a promising concept in drug discovery, however the question how to identify or design...
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SubjectTerms	14-3-3 proteins 14-3-3 Proteins - chemistry Adapter proteins Adapters Adhesives Chemistry Chemistry, Multidisciplinary Communication Communications cooperative effects Crystallography Drug development fragment-based drug discovery Fragments Glues imine chemistry Imines - chemistry Lysine Molecular Structure Optimization Peptides Physical Sciences Protein Binding Protein interaction Protein Stability Proteins protein–protein interactions Science & Technology Small Molecule Libraries - chemistry Stabilization Structure-Activity Relationship Tethering Transcription Factor RelA - chemistry
Title	Fragment‐Based Stabilizers of Protein–Protein Interactions through Imine‐Based Tethering
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