1
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Gries R, Chhen J, van Gumpel E, Theobald SJ, Sonnenkalb L, Utpatel C, Metzen F, Koch M, Dallenga T, Djaout K, Baulard A, Dal Molin M, Rybniker J. Discovery of dual-active ethionamide boosters inhibiting the Mycobacterium tuberculosis ESX-1 secretion system. Cell Chem Biol 2024; 31:699-711.e6. [PMID: 38181799 DOI: 10.1016/j.chembiol.2023.12.007] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 08/22/2023] [Accepted: 12/08/2023] [Indexed: 01/07/2024]
Abstract
Drug-resistant Mycobacterium tuberculosis (Mtb) remains a major public health concern requiring complementary approaches to standard anti-tuberculous regimens. Anti-virulence molecules or compounds that enhance the activity of antimicrobial prodrugs are promising alternatives to conventional antibiotics. Exploiting host cell-based drug discovery, we identified an oxadiazole compound (S3) that blocks the ESX-1 secretion system, a major virulence factor of Mtb. S3-treated mycobacteria showed impaired intracellular growth and a reduced ability to lyse macrophages. RNA sequencing experiments of drug-exposed bacteria revealed strong upregulation of a distinct set of genes including ethA, encoding a monooxygenase activating the anti-tuberculous prodrug ethionamide. Accordingly, we found a strong ethionamide boosting effect in S3-treated Mtb. Extensive structure-activity relationship experiments revealed that anti-virulence and ethionamide-boosting activity can be uncoupled by chemical modification of the primary hit molecule. To conclude, this series of dual-active oxadiazole compounds targets Mtb via two distinct mechanisms of action.
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Affiliation(s)
- Raphael Gries
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany
| | - Jason Chhen
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Edeltraud van Gumpel
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Sebastian J Theobald
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Lindsay Sonnenkalb
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Christian Utpatel
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany; Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Fabian Metzen
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Manuel Koch
- Institute for Dental Research and Oral Musculoskeletal Biology, Center for Biochemistry, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Tobias Dallenga
- German Center for Infection Research (DZIF), Partner Site Hamburg-Lübeck-Borstel-Riems, 23845 Borstel, Germany; Cellular Microbiology, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany
| | - Kamel Djaout
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, 59000 Lille, France
| | - Alain Baulard
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, 59000 Lille, France
| | - Michael Dal Molin
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany
| | - Jan Rybniker
- Department I of Internal Medicine, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50937 Cologne, Germany; Center for Molecular Medicine Cologne (CMMC), University of Cologne, 50931 Cologne, Germany; German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50931 Cologne, Germany.
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2
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Karabanovich G, Fabiánová V, Vocat A, Dušek J, Valášková L, Stolaříková J, Kitson RRA, Pávek P, Vávrová K, Djaout K, Mikušová K, Baulard AR, Cole ST, Korduláková J, Roh J. Both Nitro Groups Are Essential for High Antitubercular Activity of 3,5-Dinitrobenzylsulfanyl Tetrazoles and 1,3,4-Oxadiazoles through the Deazaflavin-Dependent Nitroreductase Activation Pathway. J Med Chem 2024; 67:81-109. [PMID: 38157261 PMCID: PMC10788908 DOI: 10.1021/acs.jmedchem.3c00925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/25/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024]
Abstract
3,5-Dinitrobenzylsulfanyl tetrazoles and 1,3,4-oxadiazoles, previously identified as having high in vitro activities against both replicating and nonreplicating mycobacteria and favorable cytotoxicity and genotoxicity profiles were investigated. First we demonstrated that these compounds act in a deazaflavin-dependent nitroreduction pathway and thus require a nitro group for their activity. Second, we confirmed the necessity of both nitro groups for antimycobacterial activity through extensive structure-activity relationship studies using 32 structural types of analogues, each in a five-membered series. Only the analogues with shifted nitro groups, namely, 2,5-dinitrobenzylsulfanyl oxadiazoles and tetrazoles, maintained high antimycobacterial activity but in this case mainly as a result of DprE1 inhibition. However, these analogues also showed increased toxicity to the mammalian cell line. Thus, both nitro groups in 3,5-dinitrobenzylsulfanyl-containing antimycobacterial agents remain essential for their high efficacy, and further efforts should be directed at finding ways to address the possible toxicity and solubility issues, for example, by targeted delivery.
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Affiliation(s)
- Galina Karabanovich
- Charles
University, Faculty of Pharmacy
in Hradec Králové, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Viktória Fabiánová
- Faculty
of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, Mlynská
dolina, 842 15 Bratislava, Slovakia
| | - Anthony Vocat
- Global
Health Institute, École Polytechnique
Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jan Dušek
- Charles
University, Faculty of Pharmacy
in Hradec Králové, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Lenka Valášková
- Charles
University, Faculty of Pharmacy
in Hradec Králové, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Jiřina Stolaříková
- Regional
Institute of Public Health, Department of
Bacteriology and Mycology, Partyzánské náměstí 7, 70200 Ostrava, Czech Republic
| | - Russell R. A. Kitson
- Charles
University, Faculty of Pharmacy
in Hradec Králové, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Petr Pávek
- Charles
University, Faculty of Pharmacy
in Hradec Králové, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Kateřina Vávrová
- Charles
University, Faculty of Pharmacy
in Hradec Králové, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
| | - Kamel Djaout
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Katarína Mikušová
- Faculty
of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, Mlynská
dolina, 842 15 Bratislava, Slovakia
| | - Alain R. Baulard
- Univ.
Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and
Immunity of Lille, F-59000 Lille, France
| | - Stewart T. Cole
- Global
Health Institute, École Polytechnique
Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jana Korduláková
- Faculty
of Natural Sciences, Department of Biochemistry, Comenius University in Bratislava, Ilkovičova 6, Mlynská
dolina, 842 15 Bratislava, Slovakia
| | - Jaroslav Roh
- Charles
University, Faculty of Pharmacy
in Hradec Králové, Akademika Heyrovského 1203, 50005 Hradec Králové, Czech Republic
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3
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Pandey S, Vilchèze C, Werngren J, Bainomugisa A, Mansjö M, Groenheit R, Miotto P, Cirillo DM, Coulter C, Baulard AR, Schön T, Jacobs WR, Djaout K, Köser CU. Loss-of-function mutations in ndh do not confer delamanid, ethionamide, isoniazid, or pretomanid resistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2024; 68:e0109623. [PMID: 38038476 PMCID: PMC10777854 DOI: 10.1128/aac.01096-23] [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: 08/23/2023] [Accepted: 10/13/2023] [Indexed: 12/02/2023] Open
Abstract
Results from clinical strains and knockouts of the H37Rv and CDC1551 laboratory strains demonstrated that ndh (Rv1854c) is not a resistance-conferring gene for isoniazid, ethionamide, delamanid, or pretomanid in Mycobacterium tuberculosis. This difference in the susceptibility to NAD-adduct-forming drugs compared with other mycobacteria may be driven by differences in the absolute intrabacterial NADH concentration.
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Affiliation(s)
- Sushil Pandey
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Catherine Vilchèze
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Arnold Bainomugisa
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | | | | | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela M. Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Christopher Coulter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Alain R. Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Thomas Schön
- Department of Infectious Diseases, Linköping University Hospital, Linköping, Sweden
- Division of Infection and Inflammation, Institute of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
- Department of Infectious Diseases, Region Östergötland and Kalmar County Hospital, Linköping University, Linköping, Sweden
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Kamel Djaout
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, Lille, France
| | - Claudio U. Köser
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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4
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Flipo M, Frita R, Bourotte M, Martínez-Martínez MS, Boesche M, Boyle GW, Derimanov G, Drewes G, Gamallo P, Ghidelli-Disse S, Gresham S, Jiménez E, de Mercado J, Pérez-Herrán E, Porras-De Francisco E, Rullas J, Casado P, Leroux F, Piveteau C, Kiass M, Mathys V, Soetaert K, Megalizzi V, Tanina A, Wintjens R, Antoine R, Brodin P, Delorme V, Moune M, Djaout K, Slupek S, Kemmer C, Gitzinger M, Ballell L, Mendoza-Losana A, Lociuro S, Deprez B, Barros-Aguirre D, Remuiñán MJ, Willand N, Baulard AR. The small-molecule SMARt751 reverses Mycobacterium tuberculosis resistance to ethionamide in acute and chronic mouse models of tuberculosis. Sci Transl Med 2022; 14:eaaz6280. [PMID: 35507672 DOI: 10.1126/scitranslmed.aaz6280] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The sensitivity of Mycobacterium tuberculosis, the pathogen that causes tuberculosis (TB), to antibiotic prodrugs is dependent on the efficacy of the activation process that transforms the prodrugs into their active antibacterial moieties. Various oxidases of M. tuberculosis have the potential to activate the prodrug ethionamide. Here, we used medicinal chemistry coupled with a phenotypic assay to select the N-acylated 4-phenylpiperidine compound series. The lead compound, SMARt751, interacted with the transcriptional regulator VirS of M. tuberculosis, which regulates the mymA operon encoding a monooxygenase that activates ethionamide. SMARt751 boosted the efficacy of ethionamide in vitro and in mouse models of acute and chronic TB. SMARt751 also restored full efficacy of ethionamide in mice infected with M. tuberculosis strains carrying mutations in the ethA gene, which cause ethionamide resistance in the clinic. SMARt751 was shown to be safe in tests conducted in vitro and in vivo. A model extrapolating animal pharmacokinetic and pharmacodynamic parameters to humans predicted that as little as 25 mg of SMARt751 daily would allow a fourfold reduction in the dose of ethionamide administered while retaining the same efficacy and reducing side effects.
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Affiliation(s)
- Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Rosangela Frita
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Marilyne Bourotte
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France.,BioVersys SAS, Lille, France
| | | | - Markus Boesche
- Cellzome GmbH . A GSK Company, 69117 Heidelberg, Germany
| | - Gary W Boyle
- GSK, David Jack Centre for R&D, Park Road, Ware, Hertfordshire SG12 ODP, UK
| | - Geo Derimanov
- GSK, Clinical Pharmacology and Experimental Medicine, 1250 South Collegeville Road, Collegeville, PA 19426, USA
| | - Gerard Drewes
- Cellzome GmbH . A GSK Company, 69117 Heidelberg, Germany
| | - Pablo Gamallo
- GSK, Tres Cantos R&D, PTM, Tres Cantos, 28760 Madrid, Spain
| | | | - Stephanie Gresham
- GSK, David Jack Centre for R&D, Park Road, Ware, Hertfordshire SG12 ODP, UK
| | - Elena Jiménez
- GSK, Tres Cantos R&D, PTM, Tres Cantos, 28760 Madrid, Spain
| | | | | | | | - Joaquín Rullas
- GSK, Tres Cantos R&D, PTM, Tres Cantos, 28760 Madrid, Spain
| | | | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Mehdi Kiass
- National Reference Center for Tuberculosis and Mycobacteria, Sciensano, Brussels, Belgium
| | - Vanessa Mathys
- National Reference Center for Tuberculosis and Mycobacteria, Sciensano, Brussels, Belgium
| | - Karine Soetaert
- National Reference Center for Tuberculosis and Mycobacteria, Sciensano, Brussels, Belgium
| | - Véronique Megalizzi
- Microbiology, Bioorganic and Macromolecular Chemistry, Facult. de Pharmacie, Universit. Libre de Bruxelles, Brussels, Belgium
| | - Abdalkarim Tanina
- Microbiology, Bioorganic and Macromolecular Chemistry, Facult. de Pharmacie, Universit. Libre de Bruxelles, Brussels, Belgium
| | - René Wintjens
- Microbiology, Bioorganic and Macromolecular Chemistry, Facult. de Pharmacie, Universit. Libre de Bruxelles, Brussels, Belgium
| | - Rudy Antoine
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Priscille Brodin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | - Vincent Delorme
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Martin Moune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Kamel Djaout
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Stéphanie Slupek
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France
| | | | | | - Lluis Ballell
- GSK, Tres Cantos R&D, PTM, Tres Cantos, 28760 Madrid, Spain
| | | | | | - Benoit Deprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
| | | | | | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, F-59000 Lille, France
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR9017 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.,Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UAR 2014 - PLBS, F-59000 Lille, France
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5
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Faïon L, Djaout K, Frita R, Pintiala C, Cantrelle FX, Moune M, Vandeputte A, Bourbiaux K, Piveteau C, Herledan A, Biela A, Leroux F, Kremer L, Blaise M, Tanina A, Wintjens R, Hanoulle X, Déprez B, Willand N, Baulard AR, Flipo M. Discovery of the first Mycobacterium tuberculosis MabA (FabG1) inhibitors through a fragment-based screening. Eur J Med Chem 2020; 200:112440. [PMID: 32505086 DOI: 10.1016/j.ejmech.2020.112440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 03/04/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 12/15/2022]
Abstract
Mycobacterium tuberculosis (M.tb), the etiologic agent of tuberculosis, remains the leading cause of death from a single infectious agent worldwide. The emergence of drug-resistant M.tb strains stresses the need for drugs acting on new targets. Mycolic acids are very long chain fatty acids playing an essential role in the architecture and permeability of the mycobacterial cell wall. Their biosynthesis involves two fatty acid synthase (FAS) systems. Among the four enzymes (MabA, HadAB/BC, InhA and KasA/B) of the FAS-II cycle, MabA (FabG1) remains the only one for which specific inhibitors have not been reported yet. The development of a new LC-MS/MS based enzymatic assay allowed the screening of a 1280 fragment-library and led to the discovery of the first small molecules that inhibit MabA activity. A fragment from the anthranilic acid series was optimized into more potent inhibitors and their binding to MabA was confirmed by 19F ligand-observed NMR experiments.
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Affiliation(s)
- Léo Faïon
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Kamel Djaout
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Rosangela Frita
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Catalin Pintiala
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Francois-Xavier Cantrelle
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France; CNRS, ERL9002 - Integrative Structural Biology, F-59000, Lille, France
| | - Martin Moune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Alexandre Vandeputte
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Kevin Bourbiaux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Catherine Piveteau
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Adrien Herledan
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Alexandre Biela
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Florence Leroux
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, 34293, Montpellier, France; INSERM, Institut de Recherche en Infectiologie de Montpellier, Montpellier, France
| | - Mickael Blaise
- Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, CNRS UMR 9004, 34293, Montpellier, France
| | - Abdalkarim Tanina
- Unité Microbiologie, Chimie Bioorganique et Macromoléculaire (CP206/04), Département RD3, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - René Wintjens
- Unité Microbiologie, Chimie Bioorganique et Macromoléculaire (CP206/04), Département RD3, Faculté de Pharmacie, Université Libre de Bruxelles, B-1050, Brussels, Belgium
| | - Xavier Hanoulle
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000, Lille, France; CNRS, ERL9002 - Integrative Structural Biology, F-59000, Lille, France
| | - Benoit Déprez
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Nicolas Willand
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Center for Infection and Immunity of Lille, F-59000, Lille, France
| | - Marion Flipo
- Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000, Lille, France.
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6
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Blondiaux N, Moune M, Desroses M, Frita R, Flipo M, Mathys V, Soetaert K, Kiass M, Delorme V, Djaout K, Trebosc V, Kemmer C, Wintjens R, Wohlkönig A, Antoine R, Huot L, Hot D, Coscolla M, Feldmann J, Gagneux S, Locht C, Brodin P, Gitzinger M, Déprez B, Willand N, Baulard AR. Reversion of antibiotic resistance in Mycobacterium tuberculosis by spiroisoxazoline SMARt-420. Science 2017; 355:1206-1211. [PMID: 28302858 DOI: 10.1126/science.aag1006] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 02/20/2017] [Indexed: 11/02/2022]
Abstract
Antibiotic resistance is one of the biggest threats to human health globally. Alarmingly, multidrug-resistant and extensively drug-resistant Mycobacterium tuberculosis have now spread worldwide. Some key antituberculosis antibiotics are prodrugs, for which resistance mechanisms are mainly driven by mutations in the bacterial enzymatic pathway required for their bioactivation. We have developed drug-like molecules that activate a cryptic alternative bioactivation pathway of ethionamide in M. tuberculosis, circumventing the classic activation pathway in which resistance mutations have now been observed. The first-of-its-kind molecule, named SMARt-420 (Small Molecule Aborting Resistance), not only fully reverses ethionamide-acquired resistance and clears ethionamide-resistant infection in mice, it also increases the basal sensitivity of bacteria to ethionamide.
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Affiliation(s)
- Nicolas Blondiaux
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Martin Moune
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Matthieu Desroses
- Université Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France.,Division of Translational Medicine and Chemical Biology, Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rosangela Frita
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Marion Flipo
- Université Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France
| | - Vanessa Mathys
- National Reference Center for Tuberculosis and Mycobacteria, Bacterial Diseases Service, Operational Direction Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Karine Soetaert
- National Reference Center for Tuberculosis and Mycobacteria, Bacterial Diseases Service, Operational Direction Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Mehdi Kiass
- National Reference Center for Tuberculosis and Mycobacteria, Bacterial Diseases Service, Operational Direction Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Vincent Delorme
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France.,Tuberculosis Research Laboratory, Institut Pasteur Korea, South Korea
| | - Kamel Djaout
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Vincent Trebosc
- Bioversys AG, Hochbergerstrasse 60C, 4057 Basel, Switzerland.,Biozentrum, University of Basel, Basel, Switzerland
| | | | - René Wintjens
- Laboratoire des Biopolymères et des Nanomatériaux Supramoléculaires, Université Libre de Bruxelles, Brussels, Belgium
| | - Alexandre Wohlkönig
- VIB Center for Structural Biology, VIB, Pleinlaan 2, 1050 Brussels, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, 1050 Brussels, Belgium
| | - Rudy Antoine
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Ludovic Huot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - David Hot
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Mireia Coscolla
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Julia Feldmann
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Camille Locht
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Priscille Brodin
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France
| | - Marc Gitzinger
- Bioversys AG, Hochbergerstrasse 60C, 4057 Basel, Switzerland
| | - Benoit Déprez
- Université Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France.
| | - Nicolas Willand
- Université Lille, Inserm, Institut Pasteur de Lille, U1177-Drugs and Molecules for Living Systems, F-59000 Lille, France.
| | - Alain R Baulard
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR8204-CIIL-Center for Infection and Immunity of Lille, F-59000 Lille, France.
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7
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Becker HF, Héliou A, Djaout K, Lestini R, Regnier M, Myllykallio H. High-throughput sequencing reveals circular substrates for an archaeal RNA ligase. RNA Biol 2017; 14:1075-1085. [PMID: 28277897 DOI: 10.1080/15476286.2017.1302640] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
It is only recently that the abundant presence of circular RNAs (circRNAs) in all kingdoms of Life, including the hyperthermophilic archaeon Pyrococcus abyssi, has emerged. This led us to investigate the physiologic significance of a previously observed weak intramolecular ligation activity of Pab1020 RNA ligase. Here we demonstrate that this enzyme, despite sharing significant sequence similarity with DNA ligases, is indeed an RNA-specific polynucleotide ligase efficiently acting on physiologically significant substrates. Using a combination of RNA immunoprecipitation assays and RNA-seq, our genome-wide studies revealed 133 individual circRNA loci in P. abyssi. The large majority of these loci interacted with Pab1020 in cells and circularization of selected C/D Box and 5S rRNA transcripts was confirmed biochemically. Altogether these studies revealed that Pab1020 is required for RNA circularization. Our results further suggest the functional speciation of an ancestral NTase domain and/or DNA ligase toward RNA ligase activity and prompt for further characterization of the widespread functions of circular RNAs in prokaryotes. Detailed insight into the cellular substrates of Pab1020 may facilitate the development of new biotechnological applications e.g. in ligation of preadenylated adaptors to RNA molecules.
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Affiliation(s)
- Hubert F Becker
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France.,b Sorbonne Universités, UPMC Univ Paris 06 , 4 Place Jussieu, Paris , France
| | - Alice Héliou
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France.,c LIX, Ecole Polytechnique, CNRS, Université Paris-Saclay, INRIA , Palaiseau , France
| | - Kamel Djaout
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France
| | - Roxane Lestini
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France
| | - Mireille Regnier
- c LIX, Ecole Polytechnique, CNRS, Université Paris-Saclay, INRIA , Palaiseau , France
| | - Hannu Myllykallio
- a LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay , Palaiseau , France
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8
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Skouloubris S, Djaout K, Lamarre I, Lambry JC, Anger K, Briffotaux J, Liebl U, de Reuse H, Myllykallio H. Targeting of Helicobacter pylori thymidylate synthase ThyX by non-mitotoxic hydroxy-naphthoquinones. Open Biol 2016; 5:150015. [PMID: 26040760 PMCID: PMC4632503 DOI: 10.1098/rsob.150015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
ThyX is an essential thymidylate synthase that is mechanistically and structurally unrelated to the functionally analogous human enzyme, thus providing means for selective inhibition of bacterial growth. To identify novel compounds with anti-bacterial activity against the human pathogenic bacterium Helicobacter pylori, based on our earlier biochemical and structural analyses, we designed a series of eighteen 2-hydroxy-1,4-naphthoquinones (2-OH-1,4-NQs) that target HpThyX. Our lead-like molecules markedly inhibited the NADPH oxidation and 2′-deoxythymidine-5′-monophosphate-forming activities of HpThyX enzyme in vitro, with inhibitory constants in the low nanomolar range. The identification of non-cytotoxic and non-mitotoxic 2-OH-1,4-NQ inhibitors permitted testing their in vivo efficacy in a mouse model for H. pylori infections. Despite the widely assumed toxicity of naphthoquinones (NQs), we identified tight-binding ThyX inhibitors that were tolerated in mice and can be associated with a modest effect in reducing the number of colonizing bacteria. Our results thus provide proof-of-concept that targeting ThyX enzymes is a highly feasible strategy for the development of therapies against H. pylori and a high number of other ThyX-dependent pathogenic bacteria. We also demonstrate that chemical reactivity of NQs does not prevent their exploitation as anti-microbial compounds, particularly when mitotoxicity screening is used to prioritize these compounds for further experimentation.
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Affiliation(s)
- Stéphane Skouloubris
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France Department of Biology, Université Paris-Sud, Orsay 91405, France
| | - Kamel Djaout
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Isabelle Lamarre
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Jean-Christophe Lambry
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Karine Anger
- Department of Microbiology, Institut Pasteur, Unité Pathogenèse de Helicobacter, 28 rue du Dr. Roux, Paris 75724, France
| | - Julien Briffotaux
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Ursula Liebl
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
| | - Hilde de Reuse
- Department of Microbiology, Institut Pasteur, Unité Pathogenèse de Helicobacter, 28 rue du Dr. Roux, Paris 75724, France
| | - Hannu Myllykallio
- Laboratoire d'Optique et Biosciences, CNRS UMR7645, INSERM U1182, Ecole Polytechnique, Palaiseau 91128, France
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