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Kolos JM, Pomplun S, Jung S, Rieß B, Purder PL, Voll AM, Merz S, Gnatzy M, Geiger TM, Quist-Løkken I, Jatzlau J, Knaus P, Holien T, Bracher A, Meyners C, Czodrowski P, Krewald V, Hausch F. Picomolar FKBP inhibitors enabled by a single water-displacing methyl group in bicyclic [4.3.1] aza-amides. Chem Sci 2021; 12:14758-14765. [PMID: 34820091 PMCID: PMC8597852 DOI: 10.1039/d1sc04638a] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/22/2021] [Indexed: 01/30/2023] Open
Abstract
Methyl groups can have profound effects in drug discovery but the underlying mechanisms are diverse and incompletely understood. Here we report the stereospecific effect of a single, solvent-exposed methyl group in bicyclic [4.3.1] aza-amides, robustly leading to a 2 to 10-fold increase in binding affinity for FK506-binding proteins (FKBPs). This resulted in the most potent and efficient FKBP ligands known to date. By a combination of co-crystal structures, isothermal titration calorimetry (ITC), density-functional theory (DFT), and 3D reference interaction site model (3D-RISM) calculations we elucidated the origin of the observed affinity boost, which was purely entropically driven and relied on the displacement of a water molecule at the protein-ligand-bulk solvent interface. The best compounds potently occupied FKBPs in cells and enhanced bone morphogenic protein (BMP) signaling. Our results show how subtle manipulation of the solvent network can be used to design atom-efficient ligands for difficult, solvent-exposed binding pockets.
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Affiliation(s)
- Jürgen M Kolos
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany .,Max Planck Institute of Psychiatry Kraepelinstr. 2-10 80804 München Germany
| | - Sebastian Pomplun
- Max Planck Institute of Psychiatry Kraepelinstr. 2-10 80804 München Germany
| | - Sascha Jung
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie Otto-Hahn-Straße 6 44227 Dortmund Germany
| | - Benedikt Rieß
- Max Planck Institute of Psychiatry Kraepelinstr. 2-10 80804 München Germany
| | - Patrick L Purder
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Andreas M Voll
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Stephanie Merz
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Monika Gnatzy
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Thomas M Geiger
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Ingrid Quist-Løkken
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology 7491 Trondheim Norway.,Department of Immunology and Transfusion Medicine, St. Olav's University Hospital 7030 Trondheim Norway.,Department of Hematology, St. Olav's University Hospital 7030 Trondheim Norway
| | - Jerome Jatzlau
- Institute for Chemistry and Biochemistry, Freie Universität Berlin 14195 Berlin Germany
| | - Petra Knaus
- Institute for Chemistry and Biochemistry, Freie Universität Berlin 14195 Berlin Germany
| | - Toril Holien
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology 7491 Trondheim Norway.,Department of Immunology and Transfusion Medicine, St. Olav's University Hospital 7030 Trondheim Norway.,Department of Hematology, St. Olav's University Hospital 7030 Trondheim Norway
| | - Andreas Bracher
- Research Department Cellular Biochemistry, Max Planck Institute of Biochemistry Am Klopferspitz 18, 82152 Planegg Germany
| | - Christian Meyners
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Paul Czodrowski
- Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie Otto-Hahn-Straße 6 44227 Dortmund Germany
| | - Vera Krewald
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
| | - Felix Hausch
- Department of Chemistry, Technical University of Darmstadt Alarich-Weiss-Straße 4 64293 Darmstadt Germany
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