1
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Isigkeit L, Hörmann T, Schallmayer E, Scholz K, Lillich FF, Ehrler JHM, Hufnagel B, Büchner J, Marschner JA, Pabel J, Proschak E, Merk D. Automated design of multi-target ligands by generative deep learning. Nat Commun 2024; 15:7946. [PMID: 39261471 PMCID: PMC11390726 DOI: 10.1038/s41467-024-52060-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 08/23/2024] [Indexed: 09/13/2024] Open
Abstract
Generative deep learning models enable data-driven de novo design of molecules with tailored features. Chemical language models (CLM) trained on string representations of molecules such as SMILES have been successfully employed to design new chemical entities with experimentally confirmed activity on intended targets. Here, we probe the application of CLM to generate multi-target ligands for designed polypharmacology. We capitalize on the ability of CLM to learn from small fine-tuning sets of molecules and successfully bias the model towards designing drug-like molecules with similarity to known ligands of target pairs of interest. Designs obtained from CLM after pooled fine-tuning are predicted active on both proteins of interest and comprise pharmacophore elements of ligands for both targets in one molecule. Synthesis and testing of twelve computationally favored CLM designs for six target pairs reveals modulation of at least one intended protein by all selected designs with up to double-digit nanomolar potency and confirms seven compounds as designed dual ligands. These results corroborate CLM for multi-target de novo design as source of innovation in drug discovery.
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Affiliation(s)
- Laura Isigkeit
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
| | - Tim Hörmann
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Espen Schallmayer
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
| | - Katharina Scholz
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Felix F Lillich
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596, Frankfurt, Germany
| | - Johanna H M Ehrler
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
| | - Benedikt Hufnagel
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
| | - Jasmin Büchner
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
| | - Julian A Marschner
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Jörg Pabel
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany
| | - Ewgenij Proschak
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, 60596, Frankfurt, Germany
| | - Daniel Merk
- Goethe University Frankfurt, Institute of Pharmaceutical Chemistry, 60438, Frankfurt, Germany.
- Ludwig-Maximilians-Universität München, Department of Pharmacy, 81377, Munich, Germany.
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2
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Dötsch L, Davies C, Hennes E, Schönfeld J, Kumar A, Guita CDC, Ehrler JH, Hiesinger K, Thavam S, Janning P, Sievers S, Knapp S, Proschak E, Ziegler S, Waldmann H. Discovery of the sEH Inhibitor Epoxykynin as a Potent Kynurenine Pathway Modulator. J Med Chem 2024; 67:4691-4706. [PMID: 38470246 PMCID: PMC10983002 DOI: 10.1021/acs.jmedchem.3c02245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 03/13/2024]
Abstract
Disease-related phenotypic assays enable unbiased discovery of novel bioactive small molecules and may provide novel insights into physiological systems and unprecedented molecular modes of action (MMOA). Herein, we report the identification and characterization of epoxykynin, a potent inhibitor of the soluble epoxide hydrolase (sEH). Epoxykynin was discovered by means of a cellular assay monitoring modulation of kynurenine (Kyn) levels in BxPC-3 cells upon stimulation with the cytokine interferon-γ (IFN-γ) and subsequent target identification employing affinity-based chemical proteomics. Increased Kyn levels are associated with immune suppression in the tumor microenvironment and, thus, the Kyn pathway and its key player indoleamine 2,3-dioxygenase 1 (IDO1) are appealing targets in immuno-oncology. However, targeting IDO1 directly has led to limited success in clinical investigations, demonstrating that alternative approaches to reduce Kyn levels are in high demand. We uncover a cross-talk between sEH and the Kyn pathway that may provide new opportunities to revert cancer-induced immune tolerance.
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Affiliation(s)
- Lara Dötsch
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Department
of Chemical Biology, Technical University
of Dortmund, Otto-Hahn-Strasse
6, Dortmund 44227, Germany
| | - Caitlin Davies
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Elisabeth Hennes
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Julia Schönfeld
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Adarsh Kumar
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
- Structural
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, Frankfurt 60438, Germany
| | - Celine Da Cruz
Lopes Guita
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Johanna H.M. Ehrler
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Kerstin Hiesinger
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Sasikala Thavam
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Petra Janning
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Sonja Sievers
- Compound
Management and Screening Center (COMAS), Otto-Hahn-Strasse 15, Dortmund 44227, Germany
| | - Stefan Knapp
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
- Structural
Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strasse 15, Frankfurt 60438, Germany
| | - Ewgenij Proschak
- Goethe
University Frankfurt, Institute of Pharmaceutical Chemistry, Max-von-Laue-Strasse 9, Frankfurt 60438, Germany
| | - Slava Ziegler
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
| | - Herbert Waldmann
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn-Strasse 11, Dortmund 44227, Germany
- Department
of Chemical Biology, Technical University
of Dortmund, Otto-Hahn-Strasse
6, Dortmund 44227, Germany
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3
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Lillich FF, Willems S, Ni X, Kilu W, Borkowsky C, Brodsky M, Kramer JS, Brunst S, Hernandez-Olmos V, Heering J, Schierle S, Kestner RI, Mayser FM, Helmstädter M, Göbel T, Weizel L, Namgaladze D, Kaiser A, Steinhilber D, Pfeilschifter W, Kahnt AS, Proschak A, Chaikuad A, Knapp S, Merk D, Proschak E. Structure-Based Design of Dual Partial Peroxisome Proliferator-Activated Receptor γ Agonists/Soluble Epoxide Hydrolase Inhibitors. J Med Chem 2021; 64:17259-17276. [PMID: 34818007 DOI: 10.1021/acs.jmedchem.1c01331] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Polypharmaceutical regimens often impair treatment of patients with metabolic syndrome (MetS), a complex disease cluster, including obesity, hypertension, heart disease, and type II diabetes. Simultaneous targeting of soluble epoxide hydrolase (sEH) and peroxisome proliferator-activated receptor γ (PPARγ) synergistically counteracted MetS in various in vivo models, and dual sEH inhibitors/PPARγ agonists hold great potential to reduce the problems associated with polypharmacy in the context of MetS. However, full activation of PPARγ leads to fluid retention associated with edema and weight gain, while partial PPARγ agonists do not have these drawbacks. In this study, we designed a dual partial PPARγ agonist/sEH inhibitor using a structure-guided approach. Exhaustive structure-activity relationship studies lead to the successful optimization of the designed lead. Crystal structures of one representative compound with both targets revealed potential points for optimization. The optimized compounds exhibited favorable metabolic stability, toxicity, selectivity, and desirable activity in adipocytes and macrophages.
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Affiliation(s)
- Felix F Lillich
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Sabine Willems
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Xiaomin Ni
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt, Germany
| | - Whitney Kilu
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Carmen Borkowsky
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Mirko Brodsky
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Jan S Kramer
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Steffen Brunst
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Victor Hernandez-Olmos
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany
| | - Jan Heering
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany
| | - Simone Schierle
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Roxane-I Kestner
- Department of Neurology, University Hospital Frankfurt, Goethe University, D-60590 Frankfurt am Main, Germany
| | - Franziska M Mayser
- Department of Neurology, University Hospital Frankfurt, Goethe University, D-60590 Frankfurt am Main, Germany
| | - Moritz Helmstädter
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Tamara Göbel
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Lilia Weizel
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Dmitry Namgaladze
- Institute of Biochemistry I, University Hospital Frankfurt, Goethe University, D-60590 Frankfurt am Main, Germany
| | - Astrid Kaiser
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Waltraud Pfeilschifter
- Department of Neurology, University Hospital Frankfurt, Goethe University, D-60590 Frankfurt am Main, Germany
| | - Astrid S Kahnt
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Anna Proschak
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University, Max-von-Laue-Str. 15, D-60438 Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany.,Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, D-60596 Frankfurt, Germany
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4
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Burmistrov VV, Karlov DS, Butov GM, Novakov IA. Prospects for the inhibition of the phosphatase domain of human soluble epoxide hydrolase (sEH-P). Russ Chem Bull 2021. [DOI: 10.1007/s11172-021-3185-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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5
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Hiesinger K, Kramer JS, Beyer S, Eckes T, Brunst S, Flauaus C, Wittmann SK, Weizel L, Kaiser A, Kretschmer SBM, George S, Angioni C, Heering J, Geisslinger G, Schubert-Zsilavecz M, Schmidtko A, Pogoryelov D, Pfeilschifter J, Hofmann B, Steinhilber D, Schwalm S, Proschak E. Design, Synthesis, and Structure–Activity Relationship Studies of Dual Inhibitors of Soluble Epoxide Hydrolase and 5-Lipoxygenase. J Med Chem 2020; 63:11498-11521. [DOI: 10.1021/acs.jmedchem.0c00561] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kerstin Hiesinger
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9 D-60438 Frankfurt a.M., Germany
| | - Jan S. Kramer
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9 D-60438 Frankfurt a.M., Germany
| | - Sandra Beyer
- Institute of General Pharmacology and Toxicology, Pharmazentrum Frankfurt, ZAFES, Theodor-Stern-Kai 7, D-60590 Frankfurt a.M., Germany
| | - Timon Eckes
- Institute of General Pharmacology and Toxicology, Pharmazentrum Frankfurt, ZAFES, Theodor-Stern-Kai 7, D-60590 Frankfurt a.M., Germany
| | - Steffen Brunst
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9 D-60438 Frankfurt a.M., Germany
| | - Cathrin Flauaus
- Institute of Pharmacology and Clinical Pharmacy, Goethe-University of Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt a.M., Germany
| | - Sandra K. Wittmann
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9 D-60438 Frankfurt a.M., Germany
| | - Lilia Weizel
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9 D-60438 Frankfurt a.M., Germany
| | - Astrid Kaiser
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9 D-60438 Frankfurt a.M., Germany
| | - Simon B. M. Kretschmer
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9 D-60438 Frankfurt a.M., Germany
| | - Sven George
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9 D-60438 Frankfurt a.M., Germany
| | - Carlo Angioni
- Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, ZAFES, Theodor-Stern-Kai 7, D-60590 Frankfurt a.M., Germany
| | - Jan Heering
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, D-60590 Frankfurt a.M., Germany
| | - Gerd Geisslinger
- Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, ZAFES, Theodor-Stern-Kai 7, D-60590 Frankfurt a.M., Germany
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, D-60590 Frankfurt a.M., Germany
| | - Manfred Schubert-Zsilavecz
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9 D-60438 Frankfurt a.M., Germany
| | - Achim Schmidtko
- Institute of Pharmacology and Clinical Pharmacy, Goethe-University of Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt a.M., Germany
| | - Denys Pogoryelov
- Institute of Biochemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9, D-60438 Frankfurt a.M., Germany
| | - Josef Pfeilschifter
- Institute of General Pharmacology and Toxicology, Pharmazentrum Frankfurt, ZAFES, Theodor-Stern-Kai 7, D-60590 Frankfurt a.M., Germany
| | - Bettina Hofmann
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9 D-60438 Frankfurt a.M., Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9 D-60438 Frankfurt a.M., Germany
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, D-60590 Frankfurt a.M., Germany
| | - Stephanie Schwalm
- Institute of General Pharmacology and Toxicology, Pharmazentrum Frankfurt, ZAFES, Theodor-Stern-Kai 7, D-60590 Frankfurt a.M., Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9 D-60438 Frankfurt a.M., Germany
- Branch for Translational Medicine and Pharmacology, Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Theodor-Stern-Kai 7, D-60590 Frankfurt a.M., Germany
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6
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Kramer JS, Woltersdorf S, Duflot T, Hiesinger K, Lillich FF, Knöll F, Wittmann SK, Klingler FM, Brunst S, Chaikuad A, Morisseau C, Hammock BD, Buccellati C, Sala A, Rovati GE, Leuillier M, Fraineau S, Rondeaux J, Hernandez-Olmos V, Heering J, Merk D, Pogoryelov D, Steinhilber D, Knapp S, Bellien J, Proschak E. Discovery of the First in Vivo Active Inhibitors of the Soluble Epoxide Hydrolase Phosphatase Domain. J Med Chem 2019; 62:8443-8460. [PMID: 31436984 DOI: 10.1021/acs.jmedchem.9b00445] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The emerging pharmacological target soluble epoxide hydrolase (sEH) is a bifunctional enzyme exhibiting two different catalytic activities that are located in two distinct domains. Although the physiological role of the C-terminal hydrolase domain is well-investigated, little is known about its phosphatase activity, located in the N-terminal phosphatase domain of sEH (sEH-P). Herein we report the discovery and optimization of the first inhibitor of human and rat sEH-P that is applicable in vivo. X-ray structure analysis of the sEH phosphatase domain complexed with an inhibitor provides insights in the molecular basis of small-molecule sEH-P inhibition and helps to rationalize the structure-activity relationships. 4-(4-(3,4-Dichlorophenyl)-5-phenyloxazol-2-yl)butanoic acid (22b, SWE101) has an excellent pharmacokinetic and pharmacodynamic profile in rats and enables the investigation of the physiological and pathophysiological role of sEH-P in vivo.
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Affiliation(s)
- Jan S Kramer
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany
| | - Stefano Woltersdorf
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany
| | - Thomas Duflot
- Laboratory of Pharmacokinetics, Toxicology and Pharmacogenetics , Rouen University Hospital , 76000 Rouen , France.,Normandie Université, UNIROUEN, INSERM U1096 , 1 rue de Germont , 76000 Rouen , France
| | - Kerstin Hiesinger
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany
| | - Felix F Lillich
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany
| | - Felix Knöll
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany
| | - Sandra K Wittmann
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany
| | - Franca-M Klingler
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany
| | - Steffen Brunst
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany.,Structural Genomics Consortium, Buchmann Institute for Life Sciences , Goethe-University Frankfurt , Max-von-Laue-Strasse 15 , 60438 Frankfurt am Main , Germany
| | - Christophe Morisseau
- Department of Entomology and Nematology and UC Davis Comprehensive Cancer Center , University of California Davis , Davis , California 95616 , United States
| | - Bruce D Hammock
- Department of Entomology and Nematology and UC Davis Comprehensive Cancer Center , University of California Davis , Davis , California 95616 , United States
| | - Carola Buccellati
- Department of Pharmacological and Biomolecular Sciences , University of Milan , Via Balzaretti 9 , 20133 Milan , Italy
| | - Angelo Sala
- Department of Pharmacological and Biomolecular Sciences , University of Milan , Via Balzaretti 9 , 20133 Milan , Italy
| | - G Enrico Rovati
- Department of Pharmacological and Biomolecular Sciences , University of Milan , Via Balzaretti 9 , 20133 Milan , Italy
| | - Matthieu Leuillier
- Normandie Université, UNIROUEN, INSERM U1096 , 1 rue de Germont , 76000 Rouen , France
| | - Sylvain Fraineau
- Normandie Université, UNIROUEN, INSERM U1096 , 1 rue de Germont , 76000 Rouen , France
| | - Julie Rondeaux
- Normandie Université, UNIROUEN, INSERM U1096 , 1 rue de Germont , 76000 Rouen , France
| | - Victor Hernandez-Olmos
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP , Theodor-Stern-Kai 7 , 60596 Frankfurt am Main , Germany
| | - Jan Heering
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Branch for Translational Medicine and Pharmacology TMP , Theodor-Stern-Kai 7 , 60596 Frankfurt am Main , Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany
| | - Denys Pogoryelov
- Institute of Biochemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany.,Laboratory of Pharmacokinetics, Toxicology and Pharmacogenetics , Rouen University Hospital , 76000 Rouen , France
| | - Jeremy Bellien
- Normandie Université, UNIROUEN, INSERM U1096 , 1 rue de Germont , 76000 Rouen , France.,Department of Clinical Pharmacology , Rouen University Hospital , 76000 Rouen , France
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry , Goethe-University Frankfurt , Max-von-Laue-Strasse 9 , 60438 Frankfurt am Main , Germany
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7
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Lukin A, Kramer J, Hartmann M, Weizel L, Hernandez-Olmos V, Falahati K, Burghardt I, Kalinchenkova N, Bagnyukova D, Zhurilo N, Rautio J, Forsberg M, Ihalainen J, Auriola S, Leppänen J, Konstantinov I, Pogoryelov D, Proschak E, Dar'in D, Krasavin M. Discovery of polar spirocyclic orally bioavailable urea inhibitors of soluble epoxide hydrolase. Bioorg Chem 2018; 80:655-667. [PMID: 30059891 DOI: 10.1016/j.bioorg.2018.07.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/05/2018] [Accepted: 07/12/2018] [Indexed: 10/28/2022]
Abstract
Spirocyclic 1-oxa-9-azaspiro[5.5]undecan-4-amine scaffold was explored as a basis for the design of potential inhibitors of soluble epoxide hydrolase (sEH). Synthesis and testing of the initial SAR-probing library followed by biochemical testing against sEH allowed nominating a racemic lead compound (±)-22. The latter showed remarkable (> 0.5 mM) solubility in aqueous phosphate buffer solution, unusually low (for sEH inhibitors) lipophilicity as confirmed by experimentally determined logD7.4 of 0.99, and an excellent oral bioavailability in mice (as well as other pharmacokinetic characteristics). Individual enantiomer profiling revealed that the inhibitory potency primarily resided with the dextrorotatory eutomer (+)-22 (IC50 4.99 ± 0.18 nM). For the latter, a crystal structure of its complex with a C-terminal domain of sEH was obtained and resolved. These data fully validate (+)-22 as a new non-racemic advanced lead compound for further development as a potential therapeutic agent for use in such areas as cardiovascular disease, inflammation and pain.
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Affiliation(s)
- Alexey Lukin
- Lomonosov Institute of Fine Chemical Technologies, Moscow Technological University, Moscow 117571, Russian Federation
| | - Jan Kramer
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Markus Hartmann
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Lilia Weizel
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | | | - Konstantin Falahati
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt, Germany
| | - Irene Burghardt
- Fraunhofer IME-TMP, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Natalia Kalinchenkova
- Lomonosov Institute of Fine Chemical Technologies, Moscow Technological University, Moscow 117571, Russian Federation
| | - Darya Bagnyukova
- Lomonosov Institute of Fine Chemical Technologies, Moscow Technological University, Moscow 117571, Russian Federation
| | - Nikolay Zhurilo
- Lomonosov Institute of Fine Chemical Technologies, Moscow Technological University, Moscow 117571, Russian Federation
| | - Jarkko Rautio
- School of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland
| | - Markus Forsberg
- School of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland
| | - Jouni Ihalainen
- School of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland
| | - Seppo Auriola
- School of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland
| | - Jukka Leppänen
- School of Pharmacy, University of Eastern Finland, 70211 Kuopio, Finland
| | - Igor Konstantinov
- N. D. Zelinsky Institute of Organic Chemistry, 47 Leninsky Prospect, Moscow 119991, Russian Federation
| | - Denys Pogoryelov
- Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University, Frankfurt, Max-von-Laue-Straße 9, 60438 Frankfurt, Germany
| | - Dmitry Dar'in
- Saint Petersburg State University, Saint Petersburg 199034, Russian Federation
| | - Mikhail Krasavin
- Saint Petersburg State University, Saint Petersburg 199034, Russian Federation.
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8
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Kramer J, Proschak E. Phosphatase activity of soluble epoxide hydrolase. Prostaglandins Other Lipid Mediat 2017; 133:88-92. [PMID: 28729091 DOI: 10.1016/j.prostaglandins.2017.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 06/26/2017] [Accepted: 07/11/2017] [Indexed: 11/25/2022]
Abstract
Soluble epoxide hydrolase (sEH) is a bifunctional enzyme that exhibits lipid epoxide hydrolase (sEH-H) and lipid phosphatase activity (sEH-P), with each being located in its own distinct domain. While the epoxide hydrolase activity is well-investigated, the role of the phosphatase domain remains unclear. This article briefly summarizes the evolution, structure and SNPs of the human sEH, with a special focus on the function and postulated role of the N-terminal domain of sEH. Furthermore, the article provides an overview of tools to study sEH-P.
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Affiliation(s)
- Jan Kramer
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9, D-60439, Frankfurt am Main, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe-University of Frankfurt, Max-von-Laue Str. 9, D-60439, Frankfurt am Main, Germany.
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9
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Klingler FM, Wolf M, Wittmann S, Gribbon P, Proschak E. Bacterial Expression and HTS Assessment of Soluble Epoxide Hydrolase Phosphatase. ACTA ACUST UNITED AC 2016; 21:689-94. [PMID: 27009944 DOI: 10.1177/1087057116637609] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 02/16/2016] [Indexed: 12/23/2022]
Abstract
Soluble epoxide hydrolase (sEH) is a bifunctional enzyme that possesses an epoxide hydrolase and lipid phosphatase activity (sEH-P) at two distinct catalytic domains. While the physiological role of the epoxide hydrolase domain is well understood, the consequences of the phosphatase activity remain unclear. Herein we describe the bacterial expression of the recombinant N-terminal domain of sEH-P and the development of a high-throughput screening protocol using a sensitive and commercially available substrate fluorescein diphosphate. The usability of the assay system was demonstrated and novel inhibitors of sEH-P were identified.
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Affiliation(s)
- Franca-Maria Klingler
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Markus Wolf
- Fraunhofer Institute for Molecular Biology and Environmental Ecology ScreeningPort, Hamburg, Germany
| | - Sandra Wittmann
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Molecular Biology and Environmental Ecology ScreeningPort, Hamburg, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
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10
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Role of phosphatase activity of soluble epoxide hydrolase in regulating simvastatin-activated endothelial nitric oxide synthase. Sci Rep 2015; 5:13524. [PMID: 26304753 PMCID: PMC4548251 DOI: 10.1038/srep13524] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 07/28/2015] [Indexed: 01/10/2023] Open
Abstract
Soluble epoxide hydrolase (sEH) has C-terminal epoxide hydrolase and N-terminal lipid phosphatase activity. Its hydrolase activity is associated with endothelial nitric oxide synthase (eNOS) dysfunction. However, little is known about the role of sEH phosphatase in regulating eNOS activity. Simvastatin, a clinical lipid-lowering drug, also has a pleiotropic effect on eNOS activation. However, whether sEH phosphatase is involved in simvastatin-activated eNOS activity remains elusive. We investigated the role of sEH phosphatase activity in simvastatin-mediated activation of eNOS in endothelial cells (ECs). Simvastain increased the phosphatase activity of sEH, which was diminished by pharmacological inhibitors of sEH phosphatase. In addition, pharmacological inhibition of sEH phosphatase or overexpressing the inactive phosphatase domain of sEH enhanced simvastatin-induced NO bioavailability, tube formation and phosphorylation of eNOS, Akt, and AMP-activated protein kinase (AMPK). In contrast, overexpressing the phosphatase domain of sEH limited the simvastatin-increased NO biosynthesis and eNOS phosphorylation at Ser1179. Simvastatin evoked epidermal growth factor receptor–c-Src–increased Tyr phosphorylation of sEH and formation of an sEH–Akt–AMPK–eNOS complex, which was abolished by the c-Src kinase inhibitor PP1 or c-Src dominant-negative mutant K298M. These findings suggest that sEH phosphatase activity negatively regulates simvastatin-activated eNOS by impeding the Akt–AMPK–eNOS signaling cascade.
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11
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Fleming I. The Pharmacology of the Cytochrome P450 Epoxygenase/Soluble Epoxide Hydrolase Axis in the Vasculature and Cardiovascular Disease. Pharmacol Rev 2014; 66:1106-40. [DOI: 10.1124/pr.113.007781] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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12
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Buscató E, Büttner D, Brüggerhoff A, Klingler FM, Weber J, Scholz B, Zivković A, Marschalek R, Stark H, Steinhilber D, Bode HB, Proschak E. From a multipotent stilbene to soluble epoxide hydrolase inhibitors with antiproliferative properties. ChemMedChem 2013; 8:919-23. [PMID: 23596124 DOI: 10.1002/cmdc.201300057] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Indexed: 12/19/2022]
Abstract
Inspired by nature: Natural product isopropylstilbene was identified as an inhibitor of soluble epoxide hydrolase exhibiting antiproliferative properties. Following the natural product inspired design approach, a library of (E)-styryl-1H-benzo[d]imidazoles was synthesized and evaluated with recombinant enzyme and on several cancer cell lines.
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Affiliation(s)
- Estella Buscató
- Institut für Pharmazeutische Chemie, Goethe Universität Frankfurt am Main, Frankfurt am Main, Germany
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13
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Meirer K, Rödl CB, Wisniewska JM, George S, Häfner AK, Buscató EL, Klingler FM, Hahn S, Berressem D, Wittmann SK, Steinhilber D, Hofmann B, Proschak E. Synthesis and structure-activity relationship studies of novel dual inhibitors of soluble epoxide hydrolase and 5-lipoxygenase. J Med Chem 2013; 56:1777-81. [PMID: 23356879 DOI: 10.1021/jm301617j] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Current research leads to the assumption that drugs affecting more than one target could result in a more efficient treatment of diseases and fewer safety concerns. Administration of drugs inhibiting only one branch of the arachidonic acid cascade is usually accompanied by side effects. We therefore designed and synthesized a library of hybrid molecules incorporating an imidazo[1,2-a]pyridine and an urea moiety as novel soluble epoxide hydrolase (sEH)/5-lipoxygenase (5-LO) dual inhibitors. Evaluation of the compounds was accomplished by in vitro testing using recombinant enzyme assays.
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Affiliation(s)
- Karin Meirer
- Institute of Pharmaceutical Chemistry, ZAFES/LiFF/OSF, Goethe-University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt/Main, Germany
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Morisseau C, Sahdeo S, Cortopassi G, Hammock BD. Development of an HTS assay for EPHX2 phosphatase activity and screening of nontargeted libraries. Anal Biochem 2012; 434:105-11. [PMID: 23219563 DOI: 10.1016/j.ab.2012.11.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 11/13/2012] [Accepted: 11/22/2012] [Indexed: 01/01/2023]
Abstract
The EPXH2 gene encodes soluble epoxide hydrolase (sEH), which has two distinct enzyme activities: epoxide hydrolase (Cterm-EH) and phosphatase (Nterm-phos). The Cterm-EH is involved in the metabolism of arachidonic acid epoxides that play important roles in blood pressure, cell growth, inflammation, and pain. While recent findings suggested complementary biological roles for Nterm-phos, research is limited by the lack of potent bioavailable inhibitors of this phosphatase activity. Also, a potent bioavailable inhibitor of this activity could be important in the development of therapy for cardiovascular diseases. We report herein the development of an HTS enzyme-based assay for Nterm-phos (Z'>0.9) using AttoPhos as the substrate. This assay was used to screen a wide variety of chemical entities, including a library of known drugs that have reached through clinical evaluation (Pharmakon 1600), as well as a library of pesticides and environmental toxins. We discovered that ebselen inhibits sEH phosphatase activity. Ebselen binds to the N-terminal domain of sEH (K(I)=550 nM) and chemically reacts with the enzyme to quickly and irreversibly inhibit Nterm-phos, and subsequently Cterm-EH, and thus represents a new class of sEH inhibitor.
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