1
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Wamser R, Zhang X, Kuropka B, Arkona C, Rademann J. Protein-Templated Ugi Reactions versus In-Situ Ligation Screening: Two Roads to the Identification of SARS-CoV-2 Main Protease Inhibitors. Chemistry 2024; 30:e202303940. [PMID: 38246870 DOI: 10.1002/chem.202303940] [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: 11/27/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024]
Abstract
Protein-templated fragment ligation was established as a method for the rapid identification of high affinity ligands, and multicomponent reactions (MCR) such as the Ugi four-component reaction (Ugi 4CR) have been efficient in the synthesis of drug candidates. Thus, the combination of both strategies should provide a powerful approach to drug discovery. Here, we investigate protein-templated Ugi 4CR quantitatively using a fluorescence-based enzyme assay, HPLC-QTOF mass spectrometry (MS), and native protein MS with SARS-CoV-2 main protease as template. Ugi reactions were analyzed in aqueous buffer at varying pH and fragment concentration. Potent inhibitors of the protease were formed in presence of the protein via Ugi 4CR together with Ugi three-component reaction (Ugi 3CR) products. Binding of inhibitors to the protease was confirmed by native MS and resulted in the dimerization of the protein target. Formation of Ugi products was, however, more efficient in the non-templated reaction, apparently due to interactions of the protein with the isocyanide and imine fragments. Consequently, in-situ ligation screening of Ugi 4CR products was identified as a superior approach to the discovery of SARS-CoV-2 protease inhibitors.
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Affiliation(s)
- Rebekka Wamser
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str.2+4, 14195, Berlin, Germany
| | - Xinting Zhang
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str.2+4, 14195, Berlin, Germany
| | - Benno Kuropka
- Department of Biology, Chemistry and Pharmacy, Institute of Chemistry and Biochemistry, Freie Universität Berlin, Thielallee 63, 14195, Berlin, Germany
| | - Christoph Arkona
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str.2+4, 14195, Berlin, Germany
| | - Jörg Rademann
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str.2+4, 14195, Berlin, Germany
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2
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Dong R, Yang X, Wang B, Ji X. Mutual leveraging of proximity effects and click chemistry in chemical biology. Med Res Rev 2023; 43:319-342. [PMID: 36177531 DOI: 10.1002/med.21927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 08/14/2022] [Accepted: 09/11/2022] [Indexed: 02/05/2023]
Abstract
Nature has the remarkable ability to realize reactions under physiological conditions that normally would require high temperature and other forcing conditions. In doing so, often proximity effects such as simultaneous binding of two reactants in the same pocket and/or strategic positioning of catalytic functional groups are used as ways to achieve otherwise kinetically challenging reactions. Though true biomimicry is challenging, there have been many beautiful examples of how to leverage proximity effects in realizing reactions that otherwise would not readily happen under near-physiological conditions. Along this line, click chemistry is often used to endow proximity effects, and proximity effects are also used to further leverage the facile and bioorthogonal nature of click chemistry. This review brings otherwise seemingly unrelated topics in chemical biology and drug discovery under one unifying theme of mutual leveraging of proximity effects and click chemistry and aims to critically analyze the biomimicry use of such leveraging effects as powerful approaches in chemical biology and drug discovery. We hope that this review demonstrates the power of employing mutual leveraging proximity effects and click chemistry and inspires the development of new strategies that will address unmet needs in chemistry and biology.
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Affiliation(s)
- Ru Dong
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
| | - Xiaoxiao Yang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Binghe Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia, USA
| | - Xingyue Ji
- Department of Medicinal Chemistry, College of Pharmaceutical Science, Soochow University, Suzhou, Jiangsu, China
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3
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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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4
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Rademann J, Ahsanullah A, Hassan A, Ansari FL. Integration of C-Acylation in the Solid-Phase Synthesis of Peptides and Peptidomimetics Employing Meldrum’s Acid, Phosphorus, and Sulfur Ylides. SYNTHESIS-STUTTGART 2022. [DOI: 10.1055/a-1667-3648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractThe modification of native peptides to peptidomimetics is an important goal in medicinal chemistry and requires, in many cases, the integration of C-acylation steps involving amino acids with classical peptide synthesis. Many classical C-acylation protocols involving Claisen condensations and the use of ylides are not compatible with peptide synthesis, mostly due to the requirements for strong bases leading to epimerization or deprotection of peptides. Meldrum’s acid as well as several specific phosphorus and sulfur ylides, however, are acidic enough to provide reactive C-nucleophiles under mildly basic conditions tolerated during peptide synthesis. This review provides an overview of peptide-compatible C-acylations using Meldrum’s acid and phosphorus and sulfur ylides, and their application in the medicinal chemistry of peptides.1 Introduction2 C-Acylation of Meldrum’s Acid2.1 C-Acylation of Meldrum’s Acid on Solid Phase3 Ylides as Substrates for C-Acylation3.1 C-Acylation of Phosphorus Ylides in Solution Phase3.2 C-Acylation of Solid-Supported Phosphorus Ylides3.3 C-Acylation of Sulfur Ylides3.4 C-Acylation of Solid-Supported Sulfur Ylides4 Miscellaneous Ylides as Acyl Anion Equivalents5 Summary
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Affiliation(s)
- Jörg Rademann
- Institut für Pharmazie, Medizinische Chemie, Freie Universität Berlin
| | | | - Abbas Hassan
- Department of Chemistry, Quaid-i-Azam University
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5
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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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6
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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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7
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Wagh SB, Maslivetc V, La Clair JJ, Kornienko A. A fluorescent target-guided Paal-Knorr reaction. RSC Adv 2020; 10:37035-37039. [PMID: 34262697 PMCID: PMC8276889 DOI: 10.1039/d0ra06962k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
It has become increasingly apparent that high-diversity chemical reactions play a significant role in the discovery of bioactive small molecules. Here, we describe an expanse of this paradigm, combining a 'target-guided synthesis' concept with Paal-Knorr chemistry applied to the preparation of fluorescent ligands for human prostaglandin-endoperoxide synthase (COX-2).
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Affiliation(s)
- Sachin B Wagh
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos 78666, USA
| | - Vladimir Maslivetc
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos 78666, USA
| | | | - Alexander Kornienko
- The Department of Chemistry and Biochemistry, Texas State University, San Marcos 78666, USA
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8
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Wong EL, Nawrotzky E, Arkona C, Kim BG, Beligny S, Wang X, Wagner S, Lisurek M, Carstanjen D, Rademann J. The transcription factor STAT5 catalyzes Mannich ligation reactions yielding inhibitors of leukemic cell proliferation. Nat Commun 2019; 10:66. [PMID: 30622248 PMCID: PMC6325109 DOI: 10.1038/s41467-018-07923-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 12/06/2018] [Indexed: 12/19/2022] Open
Abstract
Protein-templated fragment ligations have been established as a powerful method for the assembly and detection of optimized protein ligands. Initially developed for reversible ligations, the method has been expanded to irreversible reactions enabling the formation of super-additive fragment combinations. Here, protein-induced Mannich ligations are discovered as a biocatalytic reaction furnishing inhibitors of the transcription factor STAT5. STAT5 protein catalyzes multicomponent reactions of a phosphate mimetic, formaldehyde, and 1H-tetrazoles yielding protein ligands with greatly increased binding affinity and ligand efficiency. Reactions are induced under physiological conditions selectively by native STAT5 but not by other proteins. Formation of ligation products and (auto-)inhibition of the reaction are quantified and the mechanism is investigated. Inhibitors assembled by STAT5 block specifically the phosphorylation of this protein in a cellular model of acute myeloid leukemia (AML), DNA-binding of STAT5 dimers, expression of downstream targets of the transcription factor, and the proliferation of cancer cells in mice. The oncogene STAT5 is involved in cancer cell proliferation. Here, the authors use STAT5 protein to assemble its own small molecule inhibitors via Mannich ligation (three-component-reactions) and show that the resultant ligands can inhibit the proliferation of cancer cells in a mouse model.
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Affiliation(s)
- Ee Lin Wong
- Department of Biology, Chemistry and Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Eric Nawrotzky
- Department of Biology, Chemistry and Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Christoph Arkona
- Department of Biology, Chemistry and Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Boo Geun Kim
- Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Samuel Beligny
- Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Xinning Wang
- Department of Biology, Chemistry and Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Stefan Wagner
- Department of Biology, Chemistry and Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Michael Lisurek
- Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Dirk Carstanjen
- Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany
| | - Jörg Rademann
- Department of Biology, Chemistry and Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany. .,Department of Medicinal Chemistry, Leibniz Institut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, 13125, Berlin, Germany.
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9
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Zhong DC, Lu TB. Molecular recognition and activation by polyaza macrocyclic compounds based on host-guest interactions. Chem Commun (Camb) 2018; 52:10322-37. [PMID: 27381748 DOI: 10.1039/c6cc03660k] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design and syntheses of supramolecular hosts for the recognition and activation of molecules and anions are one of the most active research fields in supramolecular chemistry, in which polyaza macrocyclic ligands and their complexes have drawn particular attention due to their strong host-guest interactions. This review mainly focuses on the recent progress in the recognition of molecules and anions by polyaza macrocyclic compounds including polyaza macrocycles, polyaza macrobicycles and polyaza macrotricycles, as well as the activation of molecules by polyaza macrocyclic ligands and their metal complexes.
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Affiliation(s)
- Di-Chang Zhong
- Institute of New Energy Materials & Low Carbon Technology, School of Material Science & Engineering, Tianjin University of Technology, Tianjin 300384, China. and Key Laboratory of Jiangxi University for Functional Material Chemistry, College of Chemistry & Chemical Engineering, Gannan Normal University, Ganzhou 341000, P. R. China
| | - Tong-Bu Lu
- Institute of New Energy Materials & Low Carbon Technology, School of Material Science & Engineering, Tianjin University of Technology, Tianjin 300384, China. and MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, China
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10
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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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11
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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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12
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Jaegle M, Steinmetzer T, Rademann J. Protein-Templated Formation of an Inhibitor of the Blood Coagulation Factor Xa through a Background-Free Amidation Reaction. Angew Chem Int Ed Engl 2017; 56:3718-3722. [PMID: 28199769 PMCID: PMC5363247 DOI: 10.1002/anie.201611547] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Indexed: 11/16/2022]
Abstract
Protein‐templated reactions enable the target‐guided formation of protein ligands from reactive fragments, ideally with no background reaction. Herein, we investigate the templated formation of amides. A nucleophilic fragment that binds to the coagulation factor Xa was incubated with the protein and thirteen differentially activated dipeptides. The protein induced a non‐catalytic templated reaction for the phenyl and trifluoroethyl esters; the latter was shown to be a completely background‐free reaction. Starting from two fragments with millimolar affinity, a 29 nm superadditive inhibitor of factor Xa was obtained. The fragment ligation reaction was detected with high sensitivity by an enzyme activity assay and by mass spectrometry. The reaction progress and autoinhibition of the templated reaction by the formed ligation product were determined, and the structure of the protein–inhibitor complex was elucidated.
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Affiliation(s)
- Mike Jaegle
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195, Berlin, Germany
| | - Torsten Steinmetzer
- Philipps-Universität Marburg, Fachbereich Pharmazie, Institut für Pharmazeutische Chemie, Marbacher Weg 6, 35037, Marburg, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Medicinal Chemistry, Freie Universität Berlin, Königin-Luise-Strasse 2+4, 14195, Berlin, Germany
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13
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Jaegle M, Steinmetzer T, Rademann J. Proteintemplat‐gesteuerte Bildung eines Inhibitors des Koagulationsfaktors Xa durch eine Amidierung ohne Hintergrundreaktion. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611547] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mike Jaegle
- Medizinische Chemie Institut für Pharmazie Freie Universität Berlin Königin-Luise-Straße 2+4 14195 Berlin Deutschland
| | - Torsten Steinmetzer
- Philipps-Universität Marburg Fachbereich Pharmazie Institut für Pharmazeutische Chemie Marbacher Weg 6 35037 Marburg Deutschland
| | - Jörg Rademann
- Medizinische Chemie Institut für Pharmazie Freie Universität Berlin Königin-Luise-Straße 2+4 14195 Berlin Deutschland
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14
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Irreversible inhibitors of the 3C protease of Coxsackie virus through templated assembly of protein-binding fragments. Nat Commun 2016; 7:12761. [PMID: 27677239 PMCID: PMC5052702 DOI: 10.1038/ncomms12761] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 07/29/2016] [Indexed: 02/01/2023] Open
Abstract
Small-molecule fragments binding to biomacromolecules can be starting points for the development of drugs, but are often difficult to detect due to low affinities. Here we present a strategy that identifies protein-binding fragments through their potential to induce the target-guided formation of covalently bound, irreversible enzyme inhibitors. A protein-binding nucleophile reacts reversibly with a bis-electrophilic warhead, thereby positioning the second electrophile in close proximity of the active site of a viral protease, resulting in the covalent de-activation of the enzyme. The concept is implemented for Coxsackie virus B3 3C protease, a pharmacological target against enteroviral infections. Using an aldehyde-epoxide as bis-electrophile, active fragment combinations are validated through measuring the protein inactivation rate and by detecting covalent protein modification in mass spectrometry. The structure of one enzyme-inhibitor complex is determined by X-ray crystallography. The presented warhead activation assay provides potent non-peptidic, broad-spectrum inhibitors of enteroviral proteases.
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15
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Mondal M, Radeva N, Fanlo-Virgós H, Otto S, Klebe G, Hirsch AKH. Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment-Based Drug Design Facilitated by Dynamic Combinatorial Chemistry. Angew Chem Int Ed Engl 2016; 55:9422-6. [PMID: 27400756 PMCID: PMC5113778 DOI: 10.1002/anie.201603074] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 05/05/2016] [Indexed: 12/31/2022]
Abstract
Fragment-based drug design (FBDD) affords active compounds for biological targets. While there are numerous reports on FBDD by fragment growing/optimization, fragment linking has rarely been reported. Dynamic combinatorial chemistry (DCC) has become a powerful hit-identification strategy for biological targets. We report the synergistic combination of fragment linking and DCC to identify inhibitors of the aspartic protease endothiapepsin. Based on X-ray crystal structures of endothiapepsin in complex with fragments, we designed a library of bis-acylhydrazones and used DCC to identify potent inhibitors. The most potent inhibitor exhibits an IC50 value of 54 nm, which represents a 240-fold improvement in potency compared to the parent hits. Subsequent X-ray crystallography validated the predicted binding mode, thus demonstrating the efficiency of the combination of fragment linking and DCC as a hit-identification strategy. This approach could be applied to a range of biological targets, and holds the potential to facilitate hit-to-lead optimization.
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Affiliation(s)
- Milon Mondal
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands
| | - Nedyalka Radeva
- Institute of Pharmaceutical Chemistry, Marbach Weg 6, 35032, Marburg, Germany
| | - Hugo Fanlo-Virgós
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Marbach Weg 6, 35032, Marburg, Germany
| | - Anna K H Hirsch
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG, Groningen, The Netherlands.
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16
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Mondal M, Radeva N, Fanlo‐Virgós H, Otto S, Klebe G, Hirsch AKH. Fragmentverknüpfung und ‐optimierung von Hemmstoffen der Aspartylprotease Endothiapepsin: Fragmentbasiertes Wirkstoffdesign beschleunigt durch dynamische kombinatorische Chemie. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603074] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Milon Mondal
- Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh 7 9747 AG Groningen Niederlande
| | - Nedyalka Radeva
- Institute of Pharmaceutical Chemistry Marbach Weg 6 35032 Marburg Deutschland
| | - Hugo Fanlo‐Virgós
- Centre for Systems Chemistry, Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9747 AG Groningen Niederlande
| | - Sijbren Otto
- Centre for Systems Chemistry, Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh 4 9747 AG Groningen Niederlande
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry Marbach Weg 6 35032 Marburg Deutschland
| | - Anna K. H. Hirsch
- Stratingh Institute for ChemistryUniversity of Groningen Nijenborgh 7 9747 AG Groningen Niederlande
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17
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Zhang Y, Jayawardena HSN, Yan M, Ramström O. Enzyme classification using complex dynamic hemithioacetal systems. Chem Commun (Camb) 2016; 52:5053-6. [PMID: 26987550 PMCID: PMC4820758 DOI: 10.1039/c6cc01823h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A complex dynamic hemithioacetal system was used in combination with pattern recognition methodology to classify lipases into distinct groups.
A complex dynamic hemithioacetal system was generated for the evaluation of lipase reactivities in organic media. In combination with pattern recognition methodology, twelve different lipases were successfully classified into four distinct groups following their reaction selectivities and reactivities. A probe lipase was further categorized using the training matrix with predicted reactivity.
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Affiliation(s)
- Yan Zhang
- Department of Chemistry, KTH - Royal Institute of Technology, Teknikringen 30, 10044 Stockholm, Sweden.
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