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Aziz UBA, Saoud A, Bermudez M, Mieth M, Atef A, Rudolf T, Arkona C, Trenkner T, Böttcher C, Ludwig K, Hoelzemer A, Hocke AC, Wolber G, Rademann J. Author Correction: Targeted small molecule inhibitors blocking the cytolytic effects of pneumolysin and homologous toxins. Nat Commun 2024; 15:4323. [PMID: 38773122 DOI: 10.1038/s41467-024-48642-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024] Open
Affiliation(s)
- Umer Bin Abdul Aziz
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Ali Saoud
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Marcel Bermudez
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstr. 48, 48149, Münster, Germany
| | - Maren Mieth
- Department of Infectious Diseases, Respiratory Medicine, and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Amira Atef
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assuit University, Assiut, 71526, Egypt
| | - Thomas Rudolf
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Christoph Arkona
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Timo Trenkner
- Leibniz Institute of Virology, Hamburg, 20251, Germany
| | - Christoph Böttcher
- Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy (FZEM), Freie Universität Berlin, Fabeckstraße 36A, 14195, Berlin, Germany
| | - Kai Ludwig
- Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy (FZEM), Freie Universität Berlin, Fabeckstraße 36A, 14195, Berlin, Germany
| | - Angelique Hoelzemer
- Leibniz Institute of Virology, Hamburg, 20251, Germany
- First Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), 20251, Hamburg, Germany
| | - Andreas C Hocke
- Department of Infectious Diseases, Respiratory Medicine, and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany.
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Aziz UBA, Saoud A, Bermudez M, Mieth M, Atef A, Rudolf T, Arkona C, Trenkner T, Böttcher C, Ludwig K, Hoelzemer A, Hocke AC, Wolber G, Rademann J. Targeted small molecule inhibitors blocking the cytolytic effects of pneumolysin and homologous toxins. Nat Commun 2024; 15:3537. [PMID: 38670939 PMCID: PMC11053136 DOI: 10.1038/s41467-024-47741-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Pneumolysin (PLY) is a cholesterol-dependent cytolysin (CDC) from Streptococcus pneumoniae, the main cause for bacterial pneumonia. Liberation of PLY during infection leads to compromised immune system and cytolytic cell death. Here, we report discovery, development, and validation of targeted small molecule inhibitors of PLY (pore-blockers, PB). PB-1 is a virtual screening hit inhibiting PLY-mediated hemolysis. Structural optimization provides PB-2 with improved efficacy. Cryo-electron tomography reveals that PB-2 blocks PLY-binding to cholesterol-containing membranes and subsequent pore formation. Scaffold-hopping delivers PB-3 with superior chemical stability and solubility. PB-3, formed in a protein-templated reaction, binds to Cys428 adjacent to the cholesterol recognition domain of PLY with a KD of 256 nM and a residence time of 2000 s. It acts as anti-virulence factor preventing human lung epithelial cells from PLY-mediated cytolysis and cell death during infection with Streptococcus pneumoniae and is active against the homologous Cys-containing CDC perfringolysin (PFO) as well.
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Affiliation(s)
- Umer Bin Abdul Aziz
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Ali Saoud
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Marcel Bermudez
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
- Institute for Pharmaceutical and Medicinal Chemistry, University of Münster, Corrensstr. 48, 48149, Münster, Germany
| | - Maren Mieth
- Department of Infectious Diseases, Respiratory Medicine, and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Amira Atef
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
- Department of Medicinal Chemistry, Faculty of Pharmacy, Assuit University, Assiut, 71526, Egypt
| | - Thomas Rudolf
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Christoph Arkona
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Timo Trenkner
- Leibniz Institute of Virology, Hamburg, 20251, Germany
| | - Christoph Böttcher
- Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy (FZEM), Freie Universität Berlin, Fabeckstraße 36A, 14195, Berlin, Germany
| | - Kai Ludwig
- Institute of Chemistry and Biochemistry, Research Center of Electron Microscopy (FZEM), Freie Universität Berlin, Fabeckstraße 36A, 14195, Berlin, Germany
| | - Angelique Hoelzemer
- Leibniz Institute of Virology, Hamburg, 20251, Germany
- First Department of Medicine, University Medical Center Hamburg-Eppendorf (UKE), 20251, Hamburg, Germany
| | - Andreas C Hocke
- Department of Infectious Diseases, Respiratory Medicine, and Critical Care, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Gerhard Wolber
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2+4, 14195, Berlin, Germany.
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Wamser R, Pach S, Arkona C, Baumgardt M, Aziz UBA, Hocke AC, Wolber G, Rademann J. A Critical Study on Acylating and Covalent Reversible Fragment Inhibitors of SARS-CoV-2 Main Protease Targeting the S1 Site with Pyridine. ChemMedChem 2023; 18:e202200635. [PMID: 36812048 DOI: 10.1002/cmdc.202200635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
SARS coronavirus main proteases (3CL proteases) have been validated as pharmacological targets for the treatment of coronavirus infections. Current inhibitors of SARS main protease, including the clinically admitted drug nirmatrelvir are peptidomimetics with the downsides of this class of drugs including limited oral bioavailability, cellular permeability, and rapid metabolic degradation. Here, we investigate covalent fragment inhibitors of SARS Mpro as potential alternatives to peptidomimetic inhibitors in use today. Starting from inhibitors acylating the enzyme's active site, a set of reactive fragments was synthesized, and the inhibitory potency was correlated with the chemical stability of the inhibitors and the kinetic stability of the covalent enzyme-inhibitor complex. We found that all tested acylating carboxylates, several of them published prominently, were hydrolyzed in assay buffer and the inhibitory acyl-enzyme complexes were rapidly degraded leading to the irreversible inactivation of these drugs. Acylating carbonates were found to be more stable than acylating carboxylates, however, were inactive in infected cells. Finally, reversibly covalent fragments were investigated as chemically stable SARS CoV-2 inhibitors. Best was a pyridine-aldehyde fragment with an IC50 of 1.8 μM at a molecular weight of 211 g/mol, showing that pyridine fragments indeed are able to block the active site of SARS-CoV-2 main protease.
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Affiliation(s)
- Rebekka Wamser
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str.2+4, 14195, Berlin, Germany
| | - Szymon Pach
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str.2+4, 14195, Berlin, Germany
| | - Christoph Arkona
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str.2+4, 14195, Berlin, Germany
| | - Morris Baumgardt
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Umer Bin Abdul Aziz
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str.2+4, 14195, Berlin, Germany
| | - Andreas C Hocke
- Department of Infectious Diseases, Respiratory Medicine and Critical Care, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Gerhard Wolber
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str.2+4, 14195, Berlin, Germany
| | - Jörg Rademann
- Department of Biology, Chemistry and Pharmacy, Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str.2+4, 14195, Berlin, Germany
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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] [What about the content of this article? (0)] [Affiliation(s)] [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: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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