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Yang Y, Zhao N, Xu X, Zhou Y, Luo B, Zhang J, Sui J, Huang J, Qiu Z, Zhang X, Zeng J, Bai L, Bao R, Luo Y. Discovery and Mechanistic Study of Novel Mycobacterium tuberculosis ClpP1P2 Inhibitors. J Med Chem 2023; 66:16597-16614. [PMID: 38088921 DOI: 10.1021/acs.jmedchem.3c01054] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Caseinolytic protease P (ClpP) responsible for the proteolysis of damaged or misfolded proteins plays a critical role in proteome homeostasis. MtbClpP1P2, a ClpP enzyme complex, is required for survival in Mycobacterium tuberculosis, and it is therefore considered as a promising target for the development of antituberculosis drugs. Here, we discovered that cediranib and some of its derivatives are potent MtbClpP1P2 inhibitors and suppress M. tuberculosis growth. Protein pull-down and loss-of-function assays validated the in situ targeting of MtbClpP1P2 by cediranib and its active derivatives. Structural and mutational studies revealed that cediranib binds to MtbClpP1P2 by binding to an allosteric pocket at the equatorial handle domain of the MtbClpP1 subunit, which represents a unique binding mode compared to other known ClpP modulators. These findings provide us insights for rational drug design of antituberculosis therapies and implications for our understanding of the biological activity of MtbClpP1P2.
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Affiliation(s)
- Yang Yang
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
- Capital Institute of Pediatrics, Beijing 100020, PR China
| | - Ninglin Zhao
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Xin Xu
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Yuanzheng Zhou
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Baozhu Luo
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Jiangnan Zhang
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Jing Sui
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Jiasheng Huang
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Zhiqiang Qiu
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Xuelian Zhang
- School of Life Science, Fudan University, Shanghai 200438, PR China
| | - Jumei Zeng
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Lang Bai
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Rui Bao
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
| | - Youfu Luo
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, PR China
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2
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Cacace E, Kim V, Varik V, Knopp M, Tietgen M, Brauer-Nikonow A, Inecik K, Mateus A, Milanese A, Mårli MT, Mitosch K, Selkrig J, Brochado AR, Kuipers OP, Kjos M, Zeller G, Savitski MM, Göttig S, Huber W, Typas A. Systematic analysis of drug combinations against Gram-positive bacteria. Nat Microbiol 2023; 8:2196-2212. [PMID: 37770760 PMCID: PMC10627819 DOI: 10.1038/s41564-023-01486-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 08/30/2023] [Indexed: 09/30/2023]
Abstract
Drug combinations can expand options for antibacterial therapies but have not been systematically tested in Gram-positive species. We profiled ~8,000 combinations of 65 antibacterial drugs against the model species Bacillus subtilis and two prominent pathogens, Staphylococcus aureus and Streptococcus pneumoniae. Thereby, we recapitulated previously known drug interactions, but also identified ten times more novel interactions in the pathogen S. aureus, including 150 synergies. We showed that two synergies were equally effective against multidrug-resistant S. aureus clinical isolates in vitro and in vivo. Interactions were largely species-specific and synergies were distinct from those of Gram-negative species, owing to cell surface and drug uptake differences. We also tested 2,728 combinations of 44 commonly prescribed non-antibiotic drugs with 62 drugs with antibacterial activity against S. aureus and identified numerous antagonisms that might compromise the efficacy of antimicrobial therapies. We identified even more synergies and showed that the anti-aggregant ticagrelor synergized with cationic antibiotics by modifying the surface charge of S. aureus. All data can be browsed in an interactive interface ( https://apps.embl.de/combact/ ).
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Affiliation(s)
- Elisabetta Cacace
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Vladislav Kim
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Vallo Varik
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Michael Knopp
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Manuela Tietgen
- Goethe University Frankfurt, University Hospital, Institute for Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | | | - Kemal Inecik
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Alessio Milanese
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
- Department of Biology, Institute of Microbiology, and Swiss Institute of Bioinformatics, ETH Zurich, Zurich, Switzerland
| | - Marita Torrissen Mårli
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Karin Mitosch
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Joel Selkrig
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Institute of Medical Microbiology, University Hospital of RWTH, Aachen, Germany
| | - Ana Rita Brochado
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Molecular Biology and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Georg Zeller
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Stephan Göttig
- Goethe University Frankfurt, University Hospital, Institute for Medical Microbiology and Infection Control, Frankfurt am Main, Germany
| | - Wolfgang Huber
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | - Athanasios Typas
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany.
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany.
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3
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Illigmann A, Thoma Y, Pan S, Reinhardt L, Brötz-Oesterhelt H. Contribution of the Clp Protease to Bacterial Survival and Mitochondrial Homoeostasis. Microb Physiol 2021; 31:260-279. [PMID: 34438398 DOI: 10.1159/000517718] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/07/2021] [Indexed: 11/19/2022]
Abstract
Fast adaptation to environmental changes ensures bacterial survival, and proteolysis represents a key cellular process in adaptation. The Clp protease system is a multi-component machinery responsible for protein homoeostasis, protein quality control, and targeted proteolysis of transcriptional regulators in prokaryotic cells and prokaryote-derived organelles of eukaryotic cells. A functional Clp protease complex consists of the tetradecameric proteolytic core ClpP and a hexameric ATP-consuming Clp-ATPase, several of which can associate with the same proteolytic core. Clp-ATPases confer substrate specificity by recognising specific degradation tags, and further selectivity is conferred by adaptor proteins, together allowing for a fine-tuned degradation process embedded in elaborate regulatory networks. This review focuses on the contribution of the Clp protease system to prokaryotic survival and summarises the current state of knowledge for exemplary bacteria in an increasing degree of interaction with eukaryotic cells. Starting from free-living bacteria as exemplified by a non-pathogenic and a pathogenic member of the Firmicutes, i.e., Bacillus subtilis and Staphylococcus aureus, respectively, we turn our attention to facultative and obligate intracellular bacterial pathogens, i.e., Mycobacterium tuberculosis, Listeria monocytogenes, and Chlamydia trachomatis, and conclude with mitochondria. Under stress conditions, the Clp protease system exerts its pivotal role in the degradation of damaged proteins and controls the timing and extent of the heat-shock response by regulatory proteolysis. Key regulators of developmental programmes like natural competence, motility, and sporulation are also under Clp proteolytic control. In many pathogenic species, the Clp system is required for the expression of virulence factors and essential for colonising the host. In accordance with its evolutionary origin, the human mitochondrial Clp protease strongly resembles its bacterial counterparts, taking a central role in protein quality control and homoeostasis, energy metabolism, and apoptosis in eukaryotic cells, and several cancer cell types depend on it for proliferation.
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Affiliation(s)
- Astrid Illigmann
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Yvonne Thoma
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Stefan Pan
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Laura Reinhardt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.,Cluster of Excellence Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
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4
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Ju Y, An Q, Zhang Y, Sun K, Bai L, Luo Y. Recent advances in Clp protease modulation to address virulence, resistance and persistence of MRSA infection. Drug Discov Today 2021; 26:2190-2197. [PMID: 34048895 DOI: 10.1016/j.drudis.2021.05.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/17/2021] [Accepted: 05/20/2021] [Indexed: 02/05/2023]
Abstract
The Clp protease is an AAA+ protease that executes abnormally folded or malfunctioning proteins, and has an important role in producing virulence factors, forming biofilms or persisters and developing methicillin-resistant Staphylococcus aureus (MRSA). Recent studies showed that Clp protease controls virulence via agr signaling and degrades antitoxins of the toxin-antitoxin system to modulate the formation of persisters and biofilms. In this review, we focus on recent developments concerning the virulence and persistence regulatory pathways and resistance-related mechanism of Clp protease in S. aureus, with an overview of the Clp modulators developed to treat MRSA infection.
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Affiliation(s)
- Yuan Ju
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China; Sichuan University Library, Sichuan University, Chengdu 610041, China
| | - Qi An
- Public Health Clinical Center of Chengdu, Chengdu 610041, China
| | - Yiwen Zhang
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Ke Sun
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Lang Bai
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
| | - Youfu Luo
- Center of Infectious Diseases and State Key Laboratory of Biotherapy, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
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5
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Dighe SN, van Akker SR, Mathew M, Perera M, Collet TA. Discovery of a Novel Antimicrobial Agent by the Virtual Screening of a Library of Small Molecules. Mol Inform 2021; 40:e2100035. [PMID: 33891375 DOI: 10.1002/minf.202100035] [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: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/12/2022]
Abstract
A virtual screening approach based upon a combination of docking and pharmacophore methods was utilized on a library of 1.4 million molecules to identify novel antimicrobial agents, which may potentially act via inhibition of the caseinolytic protease. Using this method, compound 6 was found to be bactericidal against three staphylococcal species (minimum inhibitory concentration (MIC)=4-16 μg/mL). Further, subsequent structural optimization of 6 led to the identification of compound 24, which was shown to be the most potent analog within the series (MIC=4 μg/mL) and outperforming the antibiotic controls for two of the staphylococcal species. The newly discovered antimicrobial agent (24) demonstrated excellent in silico ADME properties and was non-toxic when tested on two human skin cell lines. As such, compound 24 has the potential for use as a lead molecule in the development of a novel class of antimicrobial agents.
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Affiliation(s)
- Satish N Dighe
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
| | - Suzannah R van Akker
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
| | - Marina Mathew
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
| | - Madusha Perera
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
| | - Trudi A Collet
- Queensland University of Technology, Institute of Health & Biomedical Innovation, 60 Musk Avenue, Kelvin Grove, Brisbane, QLD, Australia, 4059
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6
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Malik IT, Pereira R, Vielberg M, Mayer C, Straetener J, Thomy D, Famulla K, Castro H, Sass P, Groll M, Brötz‐Oesterhelt H. Functional Characterisation of ClpP Mutations Conferring Resistance to Acyldepsipeptide Antibiotics in Firmicutes. Chembiochem 2020; 21:1997-2012. [PMID: 32181548 PMCID: PMC7496096 DOI: 10.1002/cbic.201900787] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Indexed: 12/18/2022]
Abstract
Acyldepsipeptide (ADEP) is an exploratory antibiotic with a novel mechanism of action. ClpP, the proteolytic core of the caseinolytic protease, is deregulated towards unrestrained proteolysis. Here, we report on the mechanism of ADEP resistance in Firmicutes. This bacterial phylum contains important pathogens that are relevant for potential ADEP therapy. For Staphylococcus aureus, Bacillus subtilis, enterococci and streptococci, spontaneous ADEP-resistant mutants were selected in vitro at a rate of 10-6 . All isolates carried mutations in clpP. All mutated S. aureus ClpP proteins characterised in this study were functionally impaired; this increased our understanding of the mode of operation of ClpP. For molecular insights, crystal structures of S. aureus ClpP bound to ADEP4 were determined. Well-resolved N-terminal domains in the apo structure allow the pore-gating mechanism to be followed. The compilation of mutations presented here indicates residues relevant for ClpP function and suggests that ADEP resistance will occur at a lower rate during the infection process.
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Affiliation(s)
- Imran T. Malik
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Rebeca Pereira
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
- Laboratory of AntibioticsBiochemistryEducation and Molecular modelingDepartment of Molecular and Cell BiologyFederal Fluminense UniversityOuteiro São João Batista, CentroNiterói24210130Rio de JaneiroBrazil
| | - Marie‐Theres Vielberg
- Center for Integrated Protein Science at the Department of ChemistryTechnical University MunichLichtenbergstrasse 485748GarchingGermany
| | - Christian Mayer
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Jan Straetener
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Dhana Thomy
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Kirsten Famulla
- Institute for Pharmaceutical Biology and BiotechnologyUniversity of DüsseldorfUniversitätsstrasse 1, Building 26.23.40225DüsseldorfGermany
| | - Helena Castro
- Laboratory of AntibioticsBiochemistryEducation and Molecular modelingDepartment of Molecular and Cell BiologyFederal Fluminense UniversityOuteiro São João Batista, CentroNiterói24210130Rio de JaneiroBrazil
| | - Peter Sass
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Michael Groll
- Center for Integrated Protein Science at the Department of ChemistryTechnical University MunichLichtenbergstrasse 485748GarchingGermany
| | - Heike Brötz‐Oesterhelt
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
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7
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Ju Y, He L, Zhou Y, Yang T, Sun K, Song R, Yang Y, Li C, Sang Z, Bao R, Luo Y. Discovery of Novel Peptidomimetic Boronate ClpP Inhibitors with Noncanonical Enzyme Mechanism as Potent Virulence Blockers in Vitro and in Vivo. J Med Chem 2020; 63:3104-3119. [PMID: 32031798 DOI: 10.1021/acs.jmedchem.9b01746] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Caseinolytic protease P (ClpP) is considered as a promising target for the treatment of Staphylococcus aureus infections. In an unbiased screen of 2632 molecules, a peptidomimetic boronate, MLN9708, was found to be a potent suppressor of SaClpP function. A time-saving and cost-efficient strategy integrating in silico position scanning, multistep miniaturized synthesis, and bioactivity testing was deployed for optimization of this hit compound and led to fast exploration of structure-activity relationships. Five of 150 compounds from the miniaturized synthesis exhibited improved inhibitory activity. Compound 43Hf was the most active inhibitor and showed reversible covalent binding to SaClpP while did not destabilize the tetradecameric structure of SaClpP. The crystal structure of 43Hf-SaClpP complex provided mechanistic insight into the covalent binding mode of peptidomimetic boronate and SaClpP. Furthermore, 43Hf could bind endogenous ClpP in S. aureus cells and exhibited significant efficacy in attenuating S. aureus virulence in vitro and in vivo.
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Affiliation(s)
- Yuan Ju
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lihui He
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yuanzheng Zhou
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.,Laboratory of Human Disease and Immunotherapies, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ke Sun
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Rao Song
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Chengwei Li
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China.,Suzhou Zelgen Biopharmaceuticals Co., Ltd., Kunshan, Jiangsu 215301, China
| | - Zitai Sang
- Institute of Life Science, Luoyang Normal University, Luoyang, Henan 471934, China
| | - Rui Bao
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center/Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
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8
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Mabanglo MF, Leung E, Vahidi S, Seraphim TV, Eger BT, Bryson S, Bhandari V, Zhou JL, Mao YQ, Rizzolo K, Barghash MM, Goodreid JD, Phanse S, Babu M, Barbosa LRS, Ramos CHI, Batey RA, Kay LE, Pai EF, Houry WA. ClpP protease activation results from the reorganization of the electrostatic interaction networks at the entrance pores. Commun Biol 2019; 2:410. [PMID: 31754640 PMCID: PMC6853987 DOI: 10.1038/s42003-019-0656-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 10/17/2019] [Indexed: 01/07/2023] Open
Abstract
Bacterial ClpP is a highly conserved, cylindrical, self-compartmentalizing serine protease required for maintaining cellular proteostasis. Small molecule acyldepsipeptides (ADEPs) and activators of self-compartmentalized proteases 1 (ACP1s) cause dysregulation and activation of ClpP, leading to bacterial cell death, highlighting their potential use as novel antibiotics. Structural changes in Neisseria meningitidis and Escherichia coli ClpP upon binding to novel ACP1 and ADEP analogs were probed by X-ray crystallography, methyl-TROSY NMR, and small angle X-ray scattering. ACP1 and ADEP induce distinct conformational changes in the ClpP structure. However, reorganization of electrostatic interaction networks at the ClpP entrance pores is necessary and sufficient for activation. Further activation is achieved by formation of ordered N-terminal axial loops and reduction in the structural heterogeneity of the ClpP cylinder. Activating mutations recapitulate the structural effects of small molecule activator binding. Our data, together with previous findings, provide a structural basis for a unified mechanism of compound-based ClpP activation.
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Affiliation(s)
- Mark F. Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Elisa Leung
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Siavash Vahidi
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4 Canada
| | - Thiago V. Seraphim
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2 Canada
| | - Bryan T. Eger
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Steve Bryson
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Ontario Cancer Institute/Princess Margaret Hospital, Campbell Family Institute for Cancer Research, Toronto, Ontario M5G 1L7 Canada
| | - Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Jin Lin Zhou
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
| | - Yu-Qian Mao
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Kamran Rizzolo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Marim M. Barghash
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
| | - Jordan D. Goodreid
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
| | - Sadhna Phanse
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2 Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2 Canada
| | | | - Carlos H. I. Ramos
- Institute of Chemistry, University of Campinas UNICAMP, Campinas SP, 13083-970 Brazil
| | - Robert A. Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
| | - Lewis E. Kay
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, Ontario M5G 0A4 Canada
| | - Emil F. Pai
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
- Ontario Cancer Institute/Princess Margaret Hospital, Campbell Family Institute for Cancer Research, Toronto, Ontario M5G 1L7 Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5S 1A8 Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 Canada
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9
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The functional ClpXP protease of Chlamydia trachomatis requires distinct clpP genes from separate genetic loci. Sci Rep 2019; 9:14129. [PMID: 31575885 PMCID: PMC6773864 DOI: 10.1038/s41598-019-50505-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/13/2019] [Indexed: 12/15/2022] Open
Abstract
Clp proteases play a central role in bacterial physiology and, for some bacterial species, are even essential for survival. Also due to their conservation among bacteria including important human pathogens, Clp proteases have recently attracted considerable attention as antibiotic targets. Here, we functionally reconstituted and characterized the ClpXP protease of Chlamydia trachomatis (ctClpXP), an obligate intracellular pathogen and the causative agent of widespread sexually transmitted diseases in humans. Our in vitro data show that ctClpXP is formed by a hetero-tetradecameric proteolytic core, composed of two distinct homologs of ClpP (ctClpP1 and ctClpP2), that associates with the unfoldase ctClpX via ctClpP2 for regulated protein degradation. Antibiotics of the ADEP class interfere with protease functions by both preventing the interaction of ctClpX with ctClpP1P2 and activating the otherwise dormant proteolytic core for unregulated proteolysis. Thus, our results reveal molecular insight into ctClpXP function, validating this protease as an antibacterial target.
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10
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Santucci P, Dedaki C, Athanasoulis A, Gallorini L, Munoz A, Canaan S, Cavalier J, Magrioti V. Synthesis of Long‐Chain β‐Lactones and Their Antibacterial Activities against Pathogenic Mycobacteria. ChemMedChem 2019; 14:349-358. [DOI: 10.1002/cmdc.201800720] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Pierre Santucci
- Aix-Marseille UniversitéCNRS, LISM, IMM FR3479 Marseille France
| | - Christina Dedaki
- Department of ChemistryNational and Kapodistrian University of Athens, Panepistimiopolis Athens 15771 Greece
| | - Alexandros Athanasoulis
- Department of ChemistryNational and Kapodistrian University of Athens, Panepistimiopolis Athens 15771 Greece
| | - Laura Gallorini
- Aix-Marseille UniversitéCNRS, LISM, IMM FR3479 Marseille France
| | - Anaïs Munoz
- Aix-Marseille UniversitéCNRS, LISM, IMM FR3479 Marseille France
| | - Stéphane Canaan
- Aix-Marseille UniversitéCNRS, LISM, IMM FR3479 Marseille France
| | | | - Victoria Magrioti
- Department of ChemistryNational and Kapodistrian University of Athens, Panepistimiopolis Athens 15771 Greece
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11
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Thinking Outside the Box-Novel Antibacterials To Tackle the Resistance Crisis. Angew Chem Int Ed Engl 2018; 57:14440-14475. [PMID: 29939462 DOI: 10.1002/anie.201804971] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Indexed: 12/13/2022]
Abstract
The public view on antibiotics as reliable medicines changed when reports about "resistant superbugs" appeared in the news. While reasons for this resistance development are easily spotted, solutions for re-establishing effective antibiotics are still in their infancy. This Review encompasses several aspects of the antibiotic development pipeline from very early strategies to mature drugs. An interdisciplinary overview is given of methods suitable for mining novel antibiotics and strategies discussed to unravel their modes of action. Select examples of antibiotics recently identified by using these platforms not only illustrate the efficiency of these measures, but also highlight promising clinical candidates with therapeutic potential. Furthermore, the concept of molecules that disarm pathogens by addressing gatekeepers of virulence will be covered. The Review concludes with an evaluation of antibacterials currently in clinical development. Overall, this Review aims to connect select innovative antimicrobial approaches to stimulate interdisciplinary partnerships between chemists from academia and industry.
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Affiliation(s)
- Markus Lakemeyer
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Weining Zhao
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Franziska A Mandl
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases, Sanofi-Aventis (Deutschland) GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
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12
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Lakemeyer M, Zhao W, Mandl FA, Hammann P, Sieber SA. Über bisherige Denkweisen hinaus - neue Wirkstoffe zur Überwindung der Antibiotika-Krise. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201804971] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Markus Lakemeyer
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Weining Zhao
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Franziska A. Mandl
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Peter Hammann
- R&D Therapeutic Area Infectious Diseases; Sanofi-Aventis (Deutschland) GmbH; Industriepark Höchst 65926 Frankfurt am Main Deutschland
| | - Stephan A. Sieber
- Fakultät für Chemie; Lehrstuhl für Organische Chemie II, Center for Integrated Protein Science (CIPSM); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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13
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Gronauer TF, Mandl MM, Lakemeyer M, Hackl MW, Meßner M, Korotkov VS, Pachmayr J, Sieber SA. Design and synthesis of tailored human caseinolytic protease P inhibitors. Chem Commun (Camb) 2018; 54:9833-9836. [PMID: 30109319 DOI: 10.1039/c8cc05265d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human caseinolytic protease P (hClpP) is important for degradation of misfolded proteins in the mitochondrial unfolded protein response. We here introduce tailored hClpP inhibitors that utilize a steric discrimination in their core naphthofuran scaffold to selectively address the human enzyme. This novel inhibitor generation exhibited superior activity compared to previously introduced beta-lactones, optimized for bacterial ClpP. Further insights into the bioactivity and binding to cellular targets were obtained via chemical proteomics as well as proliferation- and migration studies in cancer cells.
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Affiliation(s)
- Thomas F Gronauer
- Center for Integrated Protein Science Munich, Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85748 Garching, Germany.
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Ding B, Li Q, Guo M, Dong K, Zhang Y, Guo X, Liu Q, Li L, Cui Z. Prevention of Dermal Abscess Formation Caused by Staphylococcus aureus Using Phage JD007 in Nude Mice. Front Microbiol 2018; 9:1553. [PMID: 30083139 PMCID: PMC6064926 DOI: 10.3389/fmicb.2018.01553] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 06/22/2018] [Indexed: 12/31/2022] Open
Abstract
Aim: In this study, Staphylococcus phage JD007 bactericidal activity and induced immune responses during treatment were assessed in a dermal abscess model. Materials and Methods: Dermal abscesses in nude mice were established by injecting a clinical isolate of S. aureus SA325 isolated from the back under-dermal abscess of an in-patient. Results: Phage JD007 was able to inhibit the growth of S. aureus SA325 at MOI = 1 or 10, significantly preventing the formation of dermal abscesses. Moderate immune responses were observed in the prevention group through detection of cytokines. Conclusion: Phage JD007 inhibits the formation of dermal abscesses caused by a clinical S. aureus strain in nude mice without robust immune responses.
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Affiliation(s)
- Bingyu Ding
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingtian Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mingquan Guo
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ke Dong
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Zhang
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaokui Guo
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingzhong Liu
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Li Li
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zelin Cui
- Department of Laboratory Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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15
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Bhandari V, Wong KS, Zhou JL, Mabanglo MF, Batey RA, Houry WA. The Role of ClpP Protease in Bacterial Pathogenesis and Human Diseases. ACS Chem Biol 2018; 13:1413-1425. [PMID: 29775273 DOI: 10.1021/acschembio.8b00124] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In prokaryotic cells and eukaryotic organelles, the ClpP protease plays an important role in proteostasis. The disruption of the ClpP function has been shown to influence the infectivity and virulence of a number of bacterial pathogens. More recently, ClpP has been found to be involved in various forms of carcinomas and in Perrault syndrome, which is an inherited condition characterized by hearing loss in males and females and by ovarian abnormalities in females. Hence, targeting ClpP is a potentially viable, attractive option for the treatment of different ailments. Herein, the biochemical and cellular activities of ClpP are discussed along with the mechanisms by which ClpP affects bacterial pathogenesis and various human diseases. In addition, a comprehensive overview is given of the new classes of compounds in development that target ClpP. Many of these compounds are currently primarily aimed at treating bacterial infections. Some of these compounds inhibit ClpP activity, while others activate the protease and lead to its dysregulation. The ClpP activators are remarkable examples of small molecules that inhibit protein-protein interactions but also result in a gain of function.
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Affiliation(s)
- Vaibhav Bhandari
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Keith S. Wong
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Jin Lin Zhou
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Mark F. Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
| | - Robert A. Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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16
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Sharifzadeh S, Shirley JD, Carlson EE. Activity-Based Protein Profiling Methods to Study Bacteria: The Power of Small-Molecule Electrophiles. Curr Top Microbiol Immunol 2018; 420:23-48. [PMID: 30232601 DOI: 10.1007/82_2018_135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
ABPP methods have been utilized for the last two decades as a means to investigate complex proteomes in all three domains of life. Extensive use in eukaryotes has provided a more fundamental understanding of the biological processes involved in numerous diseases and has driven drug discovery and treatment campaigns. However, the use of ABPP in prokaryotes has been less common, although it has gained more attention over the last decade. The urgent need for understanding bacteriophysiology and bacterial pathogenicity at a foundational level has never been more apparent, as the rise in antibiotic resistance has resulted in the inadequate and ineffective treatment of infections. This is not only a result of resistance to clinically used antibiotics, but also a lack of new drugs and equally as important, new drug targets. ABPP provides a means for which new, clinically relevant drug targets may be identified through gaining insight into biological processes. In this chapter, we place particular focus on the discussion of ABPP strategies that have been applied to study different classes of bacterial enzymes.
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Affiliation(s)
- Shabnam Sharifzadeh
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA. .,Department of Medicinal Chemistry, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA. .,Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, Minneapolis, MN, 55455, USA.
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17
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Vermote A, Van Calenbergh S. Small-Molecule Potentiators for Conventional Antibiotics against Staphylococcus aureus. ACS Infect Dis 2017; 3:780-796. [PMID: 28889735 DOI: 10.1021/acsinfecdis.7b00084] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Antimicrobial resistance constitutes a global health problem, while the discovery and development of novel antibiotics is stagnating. Methicillin-resistant Staphylococcus aureus, responsible for the establishment of recalcitrant, biofilm-related infections, is a well-known and notorious example of a highly resistant micro-organism. Since resistance development is unavoidable with conventional antibiotics that target bacterial viability, it is vital to develop alternative treatment options on top. Strategies aimed at more subtle manipulation of bacterial behavior have recently attracted attention. Here, we provide a literature overview of several small-molecule potentiators for antibiotics, identified for the treatment of Staphylococcus aureus infection. Typically, these potentiators are not bactericidal by themselves and function by reversing resistance mechanisms, by attenuating Staphylococcus aureus virulence, and/or by interfering with quorum sensing.
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Affiliation(s)
- Arno Vermote
- Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
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18
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Fetzer C, Korotkov VS, Thänert R, Lee KM, Neuenschwander M, von Kries JP, Medina E, Sieber SA. Verringerung der Virulenz von multiresistentem Staphylococcus aureus
mithilfe eines chemischen Disruptors des ClpX-Chaperon-Komplexes. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708454] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Christian Fetzer
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Vadim S. Korotkov
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Robert Thänert
- Infektionsimmunologie, Helmholtz-Zentrum für Infektionsforschung; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Kyu Myung Lee
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Martin Neuenschwander
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Straße 10 13125 Berlin Deutschland
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Straße 10 13125 Berlin Deutschland
| | - Eva Medina
- Infektionsimmunologie, Helmholtz-Zentrum für Infektionsforschung; Inhoffenstraße 7 38124 Braunschweig Deutschland
| | - Stephan A. Sieber
- Center for Integrated Protein Science am Department Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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19
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Fetzer C, Korotkov VS, Thänert R, Lee KM, Neuenschwander M, von Kries JP, Medina E, Sieber SA. A Chemical Disruptor of the ClpX Chaperone Complex Attenuates the Virulence of Multidrug-Resistant Staphylococcus aureus. Angew Chem Int Ed Engl 2017; 56:15746-15750. [DOI: 10.1002/anie.201708454] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/08/2017] [Indexed: 12/27/2022]
Affiliation(s)
- Christian Fetzer
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
| | - Vadim S. Korotkov
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
| | - Robert Thänert
- Infection Immunology Research Group; Helmholtz Centre for Infection Research; Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Kyu Myung Lee
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
| | - Martin Neuenschwander
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Jens Peter von Kries
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Eva Medina
- Infection Immunology Research Group; Helmholtz Centre for Infection Research; Inhoffenstrasse 7 38124 Braunschweig Germany
| | - Stephan A. Sieber
- Center for Integrated Protein Science at the Department of Chemistry; Technische Universität München; Lichtenbergstrasse 4 85747 Garching Germany
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20
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Malapit CA, Luvaga IK, Caldwell DR, Schipper NK, Howell AR. Rh-Catalyzed Conjugate Addition of Aryl and Alkenyl Boronic Acids to α-Methylene-β-lactones: Stereoselective Synthesis of trans-3,4-Disubstituted β-Lactones. Org Lett 2017; 19:4460-4463. [PMID: 28809569 DOI: 10.1021/acs.orglett.7b01994] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A one-step preparation of 3,4-disubstituted β-lactones through Rh-catalyzed conjugate addition of aryl or alkenyl boronic acids to α-methylene-β-lactones is described. The operationally simple, stereoselective transformation provides a broad range of β-lactones from individual α-methylene-β-lactone templates. This methodology allowed for a direct, final-step C-3 diversification of nocardiolactone, an antimicrobial natural product.
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Affiliation(s)
- Christian A Malapit
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269-3060 United States
| | - Irungu K Luvaga
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269-3060 United States
| | - Donald R Caldwell
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269-3060 United States
| | - Nicholas K Schipper
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269-3060 United States
| | - Amy R Howell
- Department of Chemistry, University of Connecticut , Storrs, Connecticut 06269-3060 United States
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21
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Ye F, Li J, Yang CG. The development of small-molecule modulators for ClpP protease activity. MOLECULAR BIOSYSTEMS 2017; 13:23-31. [PMID: 27831584 DOI: 10.1039/c6mb00644b] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The global spread of antibiotic resistance among important human pathogens emphasizes the need to find new antibacterial drugs with a novel mode of action. The ClpP protease has been shown to demonstrate its pivotal importance to both the survival and the virulence of pathogenic bacteria during host infection. Deregulating ClpP activity either through overactivation or inhibition could lead to antibacterial activity, declaiming the dual molecular mechanism for small-molecule modulation. Recently, natural products acyldepsipeptides (ADEPs) have been identified as a new class of antibiotics that activate ClpP to a dysfunctional state in the absence of cognate ATPases. ADEPs in combination with rifampicin eradicate deep-seated mouse biofilm infections. In addition, several non-ADEP compounds have been identified as activators of the ClpP proteolytic core without the involvement of ATPases. These findings indicate a general principle for killing dormant cells, the activation and corruption of the ClpP protease, rather than through conventional inhibition. Deletion of the clpP gene reduced the virulence of Staphylococcus aureus, thus making it an ideal antivirulence target. Multiple inhibitors have been developed in order to attenuate the production of extracellular virulence factors of bacteria through covalent modifications on serine in the active site or disruption of oligomerization of ClpP. Interestingly, due to the unusual composition and activation mechanism of ClpP in Mycobacterium tuberculosis, mycobacteria are killed by ADEPs through inhibition of ClpP activity rather than overactivation. In this short review, we will summarize recent progress in the development of small molecules modulating ClpP protease activity for both antibiotics and antivirulence.
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Affiliation(s)
- Fei Ye
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jiahui Li
- Laboratory of Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Cai-Guang Yang
- Laboratory of Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
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22
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Alhuwaider AAH, Dougan DA. AAA+ Machines of Protein Destruction in Mycobacteria. Front Mol Biosci 2017; 4:49. [PMID: 28770209 PMCID: PMC5515868 DOI: 10.3389/fmolb.2017.00049] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 06/27/2017] [Indexed: 01/05/2023] Open
Abstract
The bacterial cytosol is a complex mixture of macromolecules (proteins, DNA, and RNA), which collectively are responsible for an enormous array of cellular tasks. Proteins are central to most, if not all, of these tasks and as such their maintenance (commonly referred to as protein homeostasis or proteostasis) is vital for cell survival during normal and stressful conditions. The two key aspects of protein homeostasis are, (i) the correct folding and assembly of proteins (coupled with their delivery to the correct cellular location) and (ii) the timely removal of unwanted or damaged proteins from the cell, which are performed by molecular chaperones and proteases, respectively. A major class of proteins that contribute to both of these tasks are the AAA+ (ATPases associated with a variety of cellular activities) protein superfamily. Although much is known about the structure of these machines and how they function in the model Gram-negative bacterium Escherichia coli, we are only just beginning to discover the molecular details of these machines and how they function in mycobacteria. Here we review the different AAA+ machines, that contribute to proteostasis in mycobacteria. Primarily we will focus on the recent advances in the structure and function of AAA+ proteases, the substrates they recognize and the cellular pathways they control. Finally, we will discuss the recent developments related to these machines as novel drug targets.
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Affiliation(s)
- Adnan Ali H Alhuwaider
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe UniversityMelbourne, VIC, Australia
| | - David A Dougan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe UniversityMelbourne, VIC, Australia
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23
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Krysiak J, Stahl M, Vomacka J, Fetzer C, Lakemeyer M, Fux A, Sieber SA. Quantitative Map of β-Lactone-Induced Virulence Regulation. J Proteome Res 2017; 16:1180-1192. [DOI: 10.1021/acs.jproteome.6b00705] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Joanna Krysiak
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Matthias Stahl
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Jan Vomacka
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Christian Fetzer
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Markus Lakemeyer
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Anja Fux
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
| | - Stephan A. Sieber
- Department of Chemistry, Chair
of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Lichtenbergstrasse 4, D-85747 Garching, Germany
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24
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Malik IT, Brötz-Oesterhelt H. Conformational control of the bacterial Clp protease by natural product antibiotics. Nat Prod Rep 2017; 34:815-831. [DOI: 10.1039/c6np00125d] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Natural products targeting the bacterial Clp protease unravel key interfaces for protein–protein–interaction and long-distance conformational control.
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Affiliation(s)
- I. T. Malik
- Department of Microbial Bioactive Compounds
- Interfaculty Institute of Microbiology and Infection Medicine
- University of Tuebingen
- Germany
| | - H. Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds
- Interfaculty Institute of Microbiology and Infection Medicine
- University of Tuebingen
- Germany
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25
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Culp E, Wright GD. Bacterial proteases, untapped antimicrobial drug targets. J Antibiot (Tokyo) 2016; 70:366-377. [PMID: 27899793 DOI: 10.1038/ja.2016.138] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/29/2016] [Accepted: 10/06/2016] [Indexed: 01/05/2023]
Abstract
Bacterial proteases are an extensive collection of enzymes that have vital roles in cell viability, stress response and pathogenicity. Although their perturbation clearly offers the potential for antimicrobial drug development, both as traditional antibiotics and anti-virulence drugs, they are not yet the target of any clinically used therapeutics. Here we describe the potential for and recent progress in the development of compounds targeting bacterial proteases with a focus on AAA+ family proteolytic complexes and signal peptidases (SPs). Caseinolytic protease (ClpP) belongs to the AAA+ family of proteases, a group of multimeric barrel-shaped complexes whose activity is tightly regulated by associated AAA+ ATPases. The opportunity for chemical perturbation of these complexes is demonstrated by compounds targeting ClpP for inhibition, activation or perturbation of its associated ATPase. Meanwhile, SPs are also a proven antibiotic target. Responsible for the cleavage of targeting peptides during protein secretion, both type I and type II SPs have been successfully targeted by chemical inhibitors. As the threat of pan-antibiotic resistance continues to grow, these and other bacterial proteases offer an arsenal of novel antibiotic targets ripe for development.
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Affiliation(s)
- Elizabeth Culp
- Michael G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Gerard D Wright
- Michael G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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26
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Vomacka J, Korotkov VS, Bauer B, Weinandy F, Kunzmann MH, Krysiak J, Baron O, Böttcher T, Lorenz-Baath K, Sieber SA. An Aromatic Hydroxyamide Attenuates MultiresistantStaphylococcus aureusToxin Expression. Chemistry 2016; 22:1622-30. [DOI: 10.1002/chem.201503981] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 02/02/2023]
Affiliation(s)
- Jan Vomacka
- Department of Chemistry; AVIRU, GO-Bio-project of the Federal Ministry of Education and Research, FKZ: 031A131; Technische Universität München (TUM); Lichtenbergstrasse 4 85747 Garching Germany
| | - Vadim S. Korotkov
- Department of Chemistry; AVIRU, GO-Bio-project of the Federal Ministry of Education and Research, FKZ: 031A131; Technische Universität München (TUM); Lichtenbergstrasse 4 85747 Garching Germany
| | - Bianca Bauer
- Department of Chemistry; AVIRU, GO-Bio-project of the Federal Ministry of Education and Research, FKZ: 031A131; Technische Universität München (TUM); Lichtenbergstrasse 4 85747 Garching Germany
| | - Franziska Weinandy
- Department of Chemistry; AVIRU, GO-Bio-project of the Federal Ministry of Education and Research, FKZ: 031A131; Technische Universität München (TUM); Lichtenbergstrasse 4 85747 Garching Germany
| | - Martin H. Kunzmann
- Department of Chemistry; Chair of Organic Chemistry II; Center for Integrated Protein Science (CIPSM); Institute of Advanced Studies (IAS); Technische Universität München (TUM); Lichtenbergstrasse 4 85747 Garching Germany
| | - Joanna Krysiak
- Department of Chemistry; Chair of Organic Chemistry II; Center for Integrated Protein Science (CIPSM); Institute of Advanced Studies (IAS); Technische Universität München (TUM); Lichtenbergstrasse 4 85747 Garching Germany
| | - Oliver Baron
- Department of Chemistry; Center for Integrated Protein Science (CIPSM); Ludwig-Maximilians-Universität München (LMU); Butenandtstrasse 5-13 81377 Munich Germany
| | - Thomas Böttcher
- Department of Chemistry; Universität Konstanz; Universitätsstrasse 10 78457 Konstanz Germany
| | - Katrin Lorenz-Baath
- Department of Chemistry; AVIRU, GO-Bio-project of the Federal Ministry of Education and Research, FKZ: 031A131; Technische Universität München (TUM); Lichtenbergstrasse 4 85747 Garching Germany
| | - Stephan A. Sieber
- Department of Chemistry; Chair of Organic Chemistry II; Center for Integrated Protein Science (CIPSM); Institute of Advanced Studies (IAS); Technische Universität München (TUM); Lichtenbergstrasse 4 85747 Garching Germany
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27
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Pahl A, Lakemeyer M, Vielberg M, Hackl MW, Vomacka J, Korotkov VS, Stein ML, Fetzer C, Lorenz‐Baath K, Richter K, Waldmann H, Groll M, Sieber SA. Reversible Inhibitors Arrest ClpP in a Defined Conformational State that Can Be Revoked by ClpX Association. Angew Chem Int Ed Engl 2015; 54:15892-6. [DOI: 10.1002/anie.201507266] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 09/15/2015] [Indexed: 01/29/2023]
Affiliation(s)
- Axel Pahl
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Markus Lakemeyer
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Marie‐Theres Vielberg
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Mathias W. Hackl
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Jan Vomacka
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Vadim S. Korotkov
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Martin L. Stein
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Christian Fetzer
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Katrin Lorenz‐Baath
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Klaus Richter
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Herbert Waldmann
- Department of Chemistry and Chemical Biology, Technische Universität Dortmund, Otto‐Hahn‐Strasse 6, 44221 Dortmund (Germany)
| | - Michael Groll
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
| | - Stephan A. Sieber
- Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching (Germany)
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28
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Pahl A, Lakemeyer M, Vielberg M, Hackl MW, Vomacka J, Korotkov VS, Stein ML, Fetzer C, Lorenz‐Baath K, Richter K, Waldmann H, Groll M, Sieber SA. Reversible Inhibitoren arretieren ClpP in einer definierten Konformation, die durch Bindung von ClpX aufgehoben wird. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507266] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Axel Pahl
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Markus Lakemeyer
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Marie‐Theres Vielberg
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Mathias W. Hackl
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Jan Vomacka
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Vadim S. Korotkov
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Martin L. Stein
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Christian Fetzer
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Katrin Lorenz‐Baath
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Klaus Richter
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Herbert Waldmann
- Department für Chemie und Chemische Biologie, Technische Universität Dortmund, Otto‐Hahn‐Straße 6, 44221 Dortmund (Deutschland)
| | - Michael Groll
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
| | - Stephan A. Sieber
- Center for Integrated Protein Science am Department Chemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching (Deutschland)
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29
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Hackl MW, Lakemeyer M, Dahmen M, Glaser M, Pahl A, Lorenz-Baath K, Menzel T, Sievers S, Böttcher T, Antes I, Waldmann H, Sieber SA. Phenyl Esters Are Potent Inhibitors of Caseinolytic Protease P and Reveal a Stereogenic Switch for Deoligomerization. J Am Chem Soc 2015; 137:8475-83. [PMID: 26083639 DOI: 10.1021/jacs.5b03084] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Caseinolytic protease P (ClpP) represents a central bacterial degradation machinery that is involved in cell homeostasis and pathogenicity. The functional role of ClpP has been studied by genetic knockouts and through the use of beta-lactones, which remain the only specific inhibitors of ClpP discovered to date. Beta-lactones have served as chemical tools to manipulate ClpP in several organisms; however, their potency, selectivity and stability is limited. Despite detailed structural insights into the composition and conformational flexibility of the ClpP active site, no rational efforts to design specific non-beta-lactone inhibitors have been reported to date. In this work, an unbiased screen of more than 137 000 compounds was used to identify five phenyl ester compounds as highly potent ClpP inhibitors that were selective for bacterial, but not human ClpP. The potency of phenyl esters largely exceeded that of beta-lactones in ClpP peptidase and protease inhibition assays and displayed unique target selectivity in living S. aureus cells. Analytical studies revealed that while phenyl esters are cleaved like native peptide substrates, they remain covalently trapped as acyl-enzyme intermediates in the active site. The synthesis of 36 derivatives and subsequent structure-activity relationship (SAR) studies provided insights into conserved structural elements that are important for inhibition potency and acylation reactivity. Moreover, the stereochemistry of a methyl-substituent at the alpha position to the ester, resembling amino acid side chains in peptide substrates, impacted ClpP complex stability, causing either dissociation into heptamers or retention of the tetradecameric state. Mechanistic insights into this intriguing stereo switch and the phenyl ester binding mode were obtained by molecular docking experiments.
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Affiliation(s)
- Mathias W Hackl
- †Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747, Germany
| | - Markus Lakemeyer
- †Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747, Germany
| | - Maria Dahmen
- †Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747, Germany
| | - Manuel Glaser
- ‡Center for Integrated Protein Science at the Department of Life Sciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany
| | - Axel Pahl
- †Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747, Germany
| | - Katrin Lorenz-Baath
- †Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747, Germany
| | - Thomas Menzel
- †Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747, Germany
| | - Sonja Sievers
- §Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
| | - Thomas Böttcher
- ⊥Department of Chemistry, Universität Konstanz, Universitätsstrasse 10, D-78457 Konstanz, Germany
| | - Iris Antes
- ‡Center for Integrated Protein Science at the Department of Life Sciences, Technische Universität München, Emil-Erlenmeyer-Forum 8, D-85354 Freising, Germany
| | - Herbert Waldmann
- §Max-Planck-Institut für Molekulare Physiologie, Abteilung Chemische Biologie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.,∥Technische Universität Dortmund, Fakultät für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44221 Dortmund, Germany
| | - Stephan A Sieber
- †Center for Integrated Protein Science at the Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, Garching, D-85747, Germany
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30
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Camara K, Kamat SS, Lasota CC, Cravatt BF, Howell AR. Combining cross-metathesis and activity-based protein profiling: new β-lactone motifs for targeting serine hydrolases. Bioorg Med Chem Lett 2015; 25:317-21. [PMID: 25541002 PMCID: PMC4279111 DOI: 10.1016/j.bmcl.2014.11.038] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 11/11/2014] [Accepted: 11/13/2014] [Indexed: 11/27/2022]
Abstract
β-Lactones are a privileged structural motif as enzyme inhibitors and chemical probes, particularly for the inhibition of enzymes from the serine hydrolase class. Herein, we demonstrate that cross-metathesis (CM) of α-methylene-β-lactones offers rapid access to structurally diverse, previously unexplored β-lactones. Combining this approach with competitive activity-based protein profiling (ABPP) identified lead β-lactone inhibitors/probes for several serine hydrolases, including disease-associated enzymes and enzymes of uncharacterized function. The structural diversity afforded by the α-methylene-β-lactone scaffold thus expands the landscape of serine hydrolases that can be targeted by small-molecule inhibitors and should further the functional characterization of enzymes from this class through the optimization of target-selective probes.
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Affiliation(s)
- Kaddy Camara
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3060, United States
| | - Siddhesh S Kamat
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92307, United States
| | - Celina C Lasota
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3060, United States
| | - Benjamin F Cravatt
- Department of Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92307, United States.
| | - Amy R Howell
- Department of Chemistry, University of Connecticut, Storrs, CT 06269-3060, United States.
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31
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Koch G, Yepes A, Förstner KU, Wermser C, Stengel ST, Modamio J, Ohlsen K, Foster KR, Lopez D. Evolution of resistance to a last-resort antibiotic in Staphylococcus aureus via bacterial competition. Cell 2014; 158:1060-1071. [PMID: 25171407 PMCID: PMC4163622 DOI: 10.1016/j.cell.2014.06.046] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 04/28/2014] [Accepted: 06/23/2014] [Indexed: 01/02/2023]
Abstract
Antibiotic resistance is a key medical concern, with antibiotic use likely being an important cause. However, here we describe an alternative route to clinically relevant antibiotic resistance that occurs solely due to competitive interactions among bacterial cells. We consistently observe that isolates of Methicillin-resistant Staphylococcus aureus diversify spontaneously into two distinct, sequentially arising strains. The first evolved strain outgrows the parent strain via secretion of surfactants and a toxic bacteriocin. The second is resistant to the bacteriocin. Importantly, this second strain is also resistant to intermediate levels of vancomycin. This so-called VISA (vancomycin-intermediate S. aureus) phenotype is seen in many hard-to-treat clinical isolates. This strain diversification also occurs during in vivo infection in a mouse model, which is consistent with the fact that both coevolved phenotypes resemble strains commonly found in clinic. Our study shows how competition between coevolving bacterial strains can generate antibiotic resistance and recapitulate key clinical phenotypes.
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Affiliation(s)
- Gudrun Koch
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Ana Yepes
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Konrad U Förstner
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Charlotte Wermser
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Stephanie T Stengel
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Jennifer Modamio
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany
| | - Knut Ohlsen
- Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany
| | - Kevin R Foster
- Department of Zoology, University of Oxford, Oxford OX1 3QU, UK; Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3QU, UK
| | - Daniel Lopez
- Research Centre for Infectious Diseases (ZINF), University of Würzburg, Würzburg 97080, Germany; Institute for Molecular Infection Biology (IMIB), University of Würzburg, Würzburg 97080, Germany.
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