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Tiemann M, Nawrotzky E, Schmieder P, Wehrhan L, Bergemann S, Martos V, Song W, Arkona C, Keller BG, Rademann J. A Formylglycine-Peptide for the Site-Directed Identification of Phosphotyrosine-Mimetic Fragments. Chemistry 2022; 28:e202201282. [PMID: 35781901 PMCID: PMC9804470 DOI: 10.1002/chem.202201282] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Indexed: 01/05/2023]
Abstract
Discovery of protein-binding fragments for precisely defined binding sites is an unmet challenge to date. Herein, formylglycine is investigated as a molecular probe for the sensitive detection of fragments binding to a spatially defined protein site . Formylglycine peptide 3 was derived from a phosphotyrosine-containing peptide substrate of protein tyrosine phosphatase PTP1B by replacing the phosphorylated amino acid with the reactive electrophile. Fragment ligation with formylglycine occurred in situ in aqueous physiological buffer. Structures and kinetics were validated by NMR spectroscopy. Screening and hit validation revealed fluorinated and non-fluorinated hit fragments being able to replace the native phosphotyrosine residue. The formylglycine probe identified low-affinity fragments with high spatial resolution as substantiated by molecular modelling. The best fragment hit, 4-amino-phenyl-acetic acid, was converted into a cellularly active, nanomolar inhibitor of the protein tyrosine phosphatase SHP2.
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Affiliation(s)
- Markus Tiemann
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Eric Nawrotzky
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Peter Schmieder
- Leibniz Institute of Molecular Pharmacology (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Leon Wehrhan
- Department of Biology, Chemistry, PharmacyInstitute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Silke Bergemann
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Vera Martos
- Leibniz Institute of Molecular Pharmacology (FMP)Robert-Rössle-Strasse 1013125BerlinGermany
| | - Wei Song
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Christoph Arkona
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
| | - Bettina G. Keller
- Department of Biology, Chemistry, PharmacyInstitute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Jörg Rademann
- Department of Biology, Chemistry, PharmacyInstitute of PharmacyFreie Universität BerlinKönigin-Luise-Strasse 2+414195BerlinGermany
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2
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Tauber C, Wamser R, Arkona C, Tügend M, Abdul Aziz UB, Pach S, Schulz R, Jochmans D, Wolber G, Neyts J, Rademann J. Chemische Evolution antiviraler Wirkstoffe gegen Enterovirus D68 durch Proteintemplat‐gesteuerte Knoevenagelreaktionen. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Carolin Tauber
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Rebekka Wamser
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Christoph Arkona
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Marisa Tügend
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Umer Bin Abdul Aziz
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Szymon Pach
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Robert Schulz
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Dirk Jochmans
- Department of Microbiology, Immunology and Transplantation Rega Institute KU Leuven Leuven Belgien
| | - Gerhard Wolber
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
| | - Johan Neyts
- Department of Microbiology, Immunology and Transplantation Rega Institute KU Leuven Leuven Belgien
| | - Jörg Rademann
- Fachbereich Biologie, Chemie and Pharmazie Institut für Pharmazie Medizinische Chemie Freie Universität Berlin Königin-Luise-Str. 2+4 14195 Berlin Deutschland
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Tauber C, Wamser R, Arkona C, Tügend M, Abdul Aziz UB, Pach S, Schulz R, Jochmans D, Wolber G, Neyts J, Rademann J. Chemical Evolution of Antivirals Against Enterovirus D68 through Protein-Templated Knoevenagel Reactions. Angew Chem Int Ed Engl 2021; 60:13294-13301. [PMID: 33749121 PMCID: PMC8252737 DOI: 10.1002/anie.202102074] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Indexed: 02/06/2023]
Abstract
The generation of bioactive molecules from inactive precursors is a crucial step in the chemical evolution of life, however, mechanistic insights into this aspect of abiogenesis are scarce. Here, we investigate the protein-catalyzed formation of antivirals by the 3C-protease of enterovirus D68. The enzyme induces aldol condensations yielding inhibitors with antiviral activity in cells. Kinetic and thermodynamic analyses reveal that the bioactivity emerges from a dynamic reaction system including inhibitor formation, alkylation of the protein target by the inhibitors, and competitive addition of non-protein nucleophiles to the inhibitors. The most active antivirals are slowly reversible inhibitors with elongated target residence times. The study reveals first examples for the chemical evolution of bio-actives through protein-catalyzed, non-enzymatic C-C couplings. The discovered mechanism works under physiological conditions and might constitute a native process of drug development.
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Affiliation(s)
- Carolin Tauber
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Rebekka Wamser
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Christoph Arkona
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Marisa Tügend
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Umer Bin Abdul Aziz
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Szymon Pach
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Robert Schulz
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Dirk Jochmans
- Department of Microbiology, Immunology and TransplantationRega InstituteKU LeuvenLeuvenBelgium
| | - Gerhard Wolber
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
| | - Johan Neyts
- Department of Microbiology, Immunology and TransplantationRega InstituteKU LeuvenLeuvenBelgium
| | - Jörg Rademann
- Department of Biology, Chemistry and PharmacyInstitute of PharmacyMedicinal ChemistryFreie Universität BerlinKönigin-Luise-Str. 2+414195BerlinGermany
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Mancini F, Unver MY, Elgaher WAM, Jumde VR, Alhayek A, Lukat P, Herrmann J, Witte MD, Köck M, Blankenfeldt W, Müller R, Hirsch AKH. Protein-Templated Hit Identification through an Ugi Four-Component Reaction*. Chemistry 2020; 26:14585-14593. [PMID: 32428268 PMCID: PMC7756422 DOI: 10.1002/chem.202002250] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 12/21/2022]
Abstract
Kinetic target-guided synthesis represents an efficient hit-identification strategy, in which the protein assembles its own inhibitors from a pool of complementary building blocks via an irreversible reaction. Herein, we pioneered an in situ Ugi reaction for the identification of novel inhibitors of a model enzyme and binders for an important drug target, namely, the aspartic protease endothiapepsin and the bacterial β-sliding clamp DnaN, respectively. Highly sensitive mass-spectrometry methods enabled monitoring of the protein-templated reaction of four complementary reaction partners, which occurred in a background-free manner for endothiapepsin or with a clear amplification of two binders in the presence of DnaN. The Ugi products we identified show low micromolar activity on endothiapepsin or moderate affinity for the β-sliding clamp. We succeeded in expanding the portfolio of chemical reactions and biological targets and demonstrated the efficiency and sensitivity of this approach, which can find application on any drug target.
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Affiliation(s)
- Federica Mancini
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
| | - M. Yagiz Unver
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
| | - Walid A. M. Elgaher
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
| | - Varsha R. Jumde
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
| | - Alaa Alhayek
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
| | - Peer Lukat
- Department of Structure and Function of ProteinsHZI38124BraunschweigGermany
| | - Jennifer Herrmann
- Department of Microbial Natural ProductsHIPS–HZI66123SaarbrückenGermany
| | - Martin D. Witte
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
| | - Matthias Köck
- Department of Microbial Natural ProductsHIPS–HZI66123SaarbrückenGermany
| | - Wulf Blankenfeldt
- Department of Structure and Function of ProteinsHZI38124BraunschweigGermany
- Institute for Biochemistry, Biotechnology and BioinformaticsTechnische Universität BraunschweigSpielmannstr. 738106BraunschweigGermany
| | - Rolf Müller
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
- Department of Microbial Natural ProductsHIPS–HZI66123SaarbrückenGermany
| | - Anna K. H. Hirsch
- Department for Drug Design and OptimizationHelmholtz Institute for Pharmaceutical Research Saarland (HIPS)–, Helmholtz Centre for Infection Research (HZI)Campus Building E8.166123SaarbrückenGermany
- Department of PharmacySaarland UniversityCampus Building E8.166123SaarbrückenGermany
- Stratingh Institute for ChemistryUniversity of GroningenNijenborgh 79747AGGroningenThe Netherlands
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Gladysz R, Vrijdag J, Van Rompaey D, Lambeir A, Augustyns K, De Winter H, Van der Veken P. Efforts towards an On‐Target Version of the Groebke–Blackburn–Bienaymé (GBB) Reaction for Discovery of Druglike Urokinase (uPA) Inhibitors. Chemistry 2019; 25:12380-12393. [DOI: 10.1002/chem.201901917] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 06/18/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Rafaela Gladysz
- Laboratory of Medicinal Chemistry (UAMC)Department of Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - Johannes Vrijdag
- Laboratory of Medicinal Chemistry (UAMC)Department of Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
- Laboratory of Medical BiochemistryDepartment of, Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - Dries Van Rompaey
- Laboratory of Medicinal Chemistry (UAMC)Department of Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - Anne‐Marie Lambeir
- Laboratory of Medical BiochemistryDepartment of, Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry (UAMC)Department of Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - Hans De Winter
- Laboratory of Medicinal Chemistry (UAMC)Department of Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
| | - Pieter Van der Veken
- Laboratory of Medicinal Chemistry (UAMC)Department of Pharmaceutical SciencesUniversity of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium
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6
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Jaegle M, Wong EL, Tauber C, Nawrotzky E, Arkona C, Rademann J. Proteintemplat-gesteuerte Fragmentligationen - von der molekularen Erkennung zur Wirkstofffindung. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 129:7464-7485. [PMID: 32313319 PMCID: PMC7159557 DOI: 10.1002/ange.201610372] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/10/2017] [Indexed: 12/28/2022]
Abstract
AbstractProteintemplat‐gesteuerte Fragmentligationen sind ein neuartiges Konzept zur Unterstützung der Wirkstofffindung und können dazu beitragen, die Wirksamkeit von Proteinliganden zu verbessern. Es handelt sich dabei um chemische Reaktionen zwischen niedermolekularen Verbindungen (“Fragmenten”), die die Oberfläche eines Proteins als Reaktionsgefäß verwenden, um die Bildung eines Proteinliganden mit erhöhter Bindungsaffinität zu katalysieren. Die Methode nutzt die molekulare Erkennung kleiner reaktiver Fragmente durch die Proteine sowohl zur Assemblierung der Liganden als auch zur Identifizierung bioaktiver Fragmentkombinationen. Chemische Synthese und Bioassay werden dabei in einem Schritt vereint. Dieser Aufsatz diskutiert die biophysikalischen Grundlagen der reversiblen und irreversiblen Fragmentligationen und gibt einen Überblick über die Methoden, mit denen die durch das Proteintemplat gebildeten Ligationsprodukte detektiert werden können. Der chemische Reaktionsraum und aktuelle Anwendungen wie auch die Bedeutung dieses Konzeptes für die Wirkstofffindung werden erörtert.
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Affiliation(s)
- Mike Jaegle
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Ee Lin Wong
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Carolin Tauber
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Eric Nawrotzky
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Christoph Arkona
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
| | - Jörg Rademann
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Straße 2+4Berlin14195Deutschland
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Jaegle M, Wong EL, Tauber C, Nawrotzky E, Arkona C, Rademann J. Protein-Templated Fragment Ligations-From Molecular Recognition to Drug Discovery. Angew Chem Int Ed Engl 2017; 56:7358-7378. [PMID: 28117936 PMCID: PMC7159684 DOI: 10.1002/anie.201610372] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/10/2017] [Indexed: 12/14/2022]
Abstract
Protein-templated fragment ligation is a novel concept to support drug discovery and can help to improve the efficacy of protein ligands. Protein-templated fragment ligations are chemical reactions between small molecules ("fragments") utilizing a protein's surface as a reaction vessel to catalyze the formation of a protein ligand with increased binding affinity. The approach exploits the molecular recognition of reactive small-molecule fragments by proteins both for ligand assembly and for the identification of bioactive fragment combinations. In this way, chemical synthesis and bioassay are integrated in one single step. This Review discusses the biophysical basis of reversible and irreversible fragment ligations and gives an overview of the available methods to detect protein-templated ligation products. The chemical scope and recent applications as well as future potential of the concept in drug discovery are reviewed.
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Affiliation(s)
- Mike Jaegle
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Ee Lin Wong
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Carolin Tauber
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Eric Nawrotzky
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Christoph Arkona
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
| | - Jörg Rademann
- Freie Universität BerlinMedicinal ChemistryKönigin-Luise-Strasse 2+4Berlin14195Germany
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