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Lin F, Mabanglo MF, Zhou JL, Binepal G, Barghash MM, Wong KS, Gray-Owen SD, Batey RA, Houry WA. Structure-Based Design and Development of Phosphine Oxides as a Novel Chemotype for Antibiotics that Dysregulate Bacterial ClpP Proteases. J Med Chem 2024; 67:15131-15147. [PMID: 39221504 DOI: 10.1021/acs.jmedchem.4c00773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
A series of arylsulfones and heteroarylsulfones have previously been demonstrated to dysregulate the conserved bacterial ClpP protease, causing the unspecific degradation of essential cellular housekeeping proteins and ultimately resulting in cell death. A cocrystal structure of a 2-β-sulfonylamide analog, ACP1-06, with Escherichia coli ClpP showed that its 2-pyridyl sulfonyl substituent adopts two orientations in the binding site related through a sulfone bond rotation. From this, a new bis-aryl phosphine oxide scaffold, designated as ACP6, was designed based on a "conformation merging" approach of the dual orientation of the ACP1-06 sulfone. One analog, ACP6-12, exhibited over a 10-fold increase in activity over the parent ACP1-06 compound, and a cocrystal X-ray structure with ClpP confirmed its predicted binding conformation. This allowed for a comparative analysis of how different ligand classes bind to the hydrophobic binding site. The study highlights the successful application of structure-based rational design of novel phosphine oxide-based antibiotics.
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Affiliation(s)
- Funing Lin
- 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
| | - Jin Lin Zhou
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Gursonika Binepal
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Marim M Barghash
- 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
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Robert A Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Acceleration Consortium, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Walid A Houry
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1, Canada
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2
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Illigmann A, Vielberg MT, Lakemeyer M, Wolf F, Dema T, Stange P, Kuttenlochner W, Liebhart E, Kulik A, Staudt ND, Malik I, Grond S, Sieber SA, Kaysser L, Groll M, Brötz-Oesterhelt H. Structure of Staphylococcus aureus ClpP Bound to the Covalent Active-Site Inhibitor Cystargolide A. Angew Chem Int Ed Engl 2024; 63:e202314028. [PMID: 38029352 DOI: 10.1002/anie.202314028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023]
Abstract
The caseinolytic protease is a highly conserved serine protease, crucial to prokaryotic and eukaryotic protein homeostasis, and a promising antibacterial and anticancer drug target. Herein, we describe the potent cystargolides as the first natural β-lactone inhibitors of the proteolytic core ClpP. Based on the discovery of two clpP genes next to the cystargolide biosynthetic gene cluster in Kitasatospora cystarginea, we explored ClpP as a potential cystargolide target. We show the inhibition of Staphylococcus aureus ClpP by cystargolide A and B by different biochemical methods in vitro. Synthesis of semisynthetic derivatives and probes with improved cell penetration allowed us to confirm ClpP as a specific target in S. aureus cells and to demonstrate the anti-virulence activity of this natural product class. Crystal structures show cystargolide A covalently bound to all 14 active sites of ClpP from S. aureus, Aquifex aeolicus, and Photorhabdus laumondii, and reveal the molecular mechanism of ClpP inhibition by β-lactones, the predominant class of ClpP inhibitors.
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Affiliation(s)
- Astrid Illigmann
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Marie-Theres Vielberg
- Chair of Biochemistry, Centre for Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer-Strasse 8, 85748, Garching, Germany
| | - Markus Lakemeyer
- Chair of Organic Chemistry II, Technical University Munich, School of Natural Sciences, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Straße 8/I, 85748, Garching b.München, Germany
- Current address: Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstrasse 10, 07743, Jena, Germany
| | - Felix Wolf
- Synthetic Biology of Anti-infective Agents, Pharmaceutical Institute, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Taulant Dema
- Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Patrik Stange
- Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Wolfgang Kuttenlochner
- Chair of Biochemistry, Centre for Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer-Strasse 8, 85748, Garching, Germany
| | - Elisa Liebhart
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Andreas Kulik
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Nicole D Staudt
- Synthetic Biology of Anti-infective Agents, Pharmaceutical Institute, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Imran Malik
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
| | - Stephanie Grond
- Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Stephan A Sieber
- Chair of Organic Chemistry II, Technical University Munich, School of Natural Sciences, Center for Functional Protein Assemblies (CPA), Ernst-Otto-Fischer-Straße 8/I, 85748, Garching b.München, Germany
| | - Leonard Kaysser
- Synthetic Biology of Anti-infective Agents, Pharmaceutical Institute, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
- Pharmazeutische Biologie, Institut für Wirkstoffentwicklung, Universitätsklinikum Leipzig, Eilenburger Strasse 15a, 04317, Leipzig, Germany
| | - Michael Groll
- Chair of Biochemistry, Centre for Protein Assemblies, Technical University Munich, Ernst-Otto-Fischer-Strasse 8, 85748, Garching, Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
- Cluster of Excellence Controlling Microbes to Fight Infections, University of Tübingen, Auf der Morgenstelle 28, 72076, Tübingen, Germany
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3
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Bhardwaj S, Roy KK. ClpP Peptidase as a Plausible Target for the Discovery of Novel Antibiotics. Curr Drug Targets 2024; 25:108-120. [PMID: 38151841 DOI: 10.2174/0113894501274958231220053714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/16/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023]
Abstract
Antimicrobial resistance (AMR) to currently available antibiotics/drugs is a global threat. It is desirable to develop new drugs that work through a novel target(s) to avoid drug resistance. This review discusses the potential of the caseinolytic protease P (ClpP) peptidase complex as a novel target for finding novel antibiotics, emphasising the ClpP's structure and function. ClpP contributes to the survival of bacteria via its ability to destroy misfolded or aggregated proteins. In consequence, its inhibition may lead to microbial death. Drugs inhibiting ClpP activity are currently being tested, but no drug against this target has been approved yet. It was demonstrated that Nblocked dipeptides are essential for activating ClpP's proteolytic activity. Hence, compounds mimicking these dipeptides could act as inhibitors of the formation of an active ClpP complex. Drugs, including Bortezomib, Cisplatin, Cefmetazole, and Ixazomib, inhibit ClpP activation. However, they were not approved as drugs against the target because of their high toxicity, likely due to the presence of strong electrophiles in their warheads. The modifications of these warheads could be a good strategy to reduce the toxicity of these molecules. For instance, a boronate warhead was replaced by a chloromethyl ketone, and this new molecule was shown to exhibit selectivity for prokaryotic ClpP. A better understanding of the structure and function of the ClpP complex would benefit the search for compounds mimicking N-blocked dipeptides that would inhibit ClpP complex activity and cause bacterial death.
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Affiliation(s)
- Smriti Bhardwaj
- School of Health Sciences and Technology, UPES, Dehradun - 248007, Uttarakhand, India
| | - Kuldeep K Roy
- School of Health Sciences and Technology, UPES, Dehradun - 248007, Uttarakhand, India
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4
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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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5
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Xia F, Zhang H, Yang H, Zheng M, Min W, Sun C, Yuan K, Yang P. Targeting polyketide synthase 13 for the treatment of tuberculosis. Eur J Med Chem 2023; 259:115702. [PMID: 37544185 DOI: 10.1016/j.ejmech.2023.115702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/15/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023]
Abstract
Tuberculosis (TB) is one of the most threatening diseases for humans, however, the drug treatment strategy for TB has been stagnant and inadequate, which could not meet current treatment needs. TB is caused by Mycobacterial tuberculosis, which has a unique cell wall that plays a crucial role in its growth, virulence, and drug resistance. Polyketide synthase 13 (Pks13) is an essential enzyme that catalyzes the biosynthesis of the cell wall and its critical role is only found in Mycobacteria. Therefore, Pks13 is a promising target for developing novel anti-TB drugs. In this review, we first introduced the mechanism of targeting Pks13 for TB treatment. Subsequently, we focused on summarizing the recent advance of Pks13 inhibitors, including the challenges encountered during their discovery and the rational design strategies employed to overcome these obstacles, which could be helpful for the development of novel Pks13 inhibitors in the future.
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Affiliation(s)
- Fei Xia
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Haoling Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Huanaoyu Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Mingming Zheng
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Wenjian Min
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Chengliang Sun
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Kai Yuan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China.
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6
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Ogbonna EC, Anderson HR, Beardslee PC, Bheemreddy P, Schmitz KR. Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1. Microbiol Spectr 2023; 11:e0454822. [PMID: 37341639 PMCID: PMC10433963 DOI: 10.1128/spectrum.04548-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 05/31/2023] [Indexed: 06/22/2023] Open
Abstract
The prevalence of drug-resistant Mycobacterium tuberculosis infections has prompted extensive efforts to exploit new drug targets in this globally important pathogen. ClpC1, the unfoldase component of the essential ClpC1P1P2 protease, has emerged as one particularly promising antibacterial target. However, efforts to identify and characterize compounds that impinge on ClpC1 activity are constrained by our limited knowledge of Clp protease function and regulation. To expand our understanding of ClpC1 physiology, we employed a coimmunoprecipitation and mass spectrometry workflow to identify proteins that interact with ClpC1 in Mycolicibacterium smegmatis, a surrogate for M. tuberculosis. We identify a diverse panel of interaction partners, many of which coimmunoprecipitate with both the regulatory N-terminal domain and the ATPase core of ClpC1. Notably, our interactome analysis establishes MSMEI_3879, a truncated gene product unique to M. smegmatis, as a novel proteolytic substrate. Degradation of MSMEI_3879 by ClpC1P1P2 in vitro requires exposure of its N-terminal sequence, reinforcing the idea that ClpC1 selectively recognizes disordered motifs on substrates. Fluorescent substrates incorporating MSMEI_3879 may be useful in screening for novel ClpC1-targeting antibiotics to help address the challenge of M. tuberculosis drug resistance. IMPORTANCE Drug-resistant tuberculosis infections are a major challenge to global public health. Much effort has been invested in identifying new drug targets in the causative pathogen, Mycobacterium tuberculosis. One such target is the ClpC1 unfoldase. Compounds have been identified that kill M. tuberculosis by disrupting ClpC1 activity, yet the physiological function of ClpC1 in cells has remained poorly defined. Here, we identify interaction partners of ClpC1 in a model mycobacterium. By building a broader understanding of the role of this prospective drug target, we can more effectively develop compounds that inhibit its essential cellular activities.
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Affiliation(s)
- Emmanuel C. Ogbonna
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Henry R. Anderson
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Patrick C. Beardslee
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Priyanka Bheemreddy
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Karl R. Schmitz
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
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7
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Schmitz KR, Handy EL, Compton CL, Gupta S, Bishai WR, Sauer RT, Sello JK. Acyldepsipeptide Antibiotics and a Bioactive Fragment Thereof Differentially Perturb Mycobacterium tuberculosis ClpXP1P2 Activity in Vitro. ACS Chem Biol 2023; 18:724-733. [PMID: 32083462 PMCID: PMC7842861 DOI: 10.1021/acschembio.9b00454] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Proteolytic complexes in Mycobacterium tuberculosis (Mtb), the deadliest bacterial pathogen, are major foci in tuberculosis drug development programs. The Clp proteases, which are essential for Mtb viability, are high-priority targets. These proteases function through the collaboration of ClpP1P2, a barrel-shaped heteromeric peptidase, with associated ATP-dependent chaperones like ClpX and ClpC1 that recognize and unfold specific substrates in an ATP-dependent fashion. The critical interaction of the peptidase and its unfoldase partners is blocked by the competitive binding of acyldepsipeptide antibiotics (ADEPs) to the interfaces of the ClpP2 subunits. The resulting inhibition of Clp protease activity is lethal to Mtb. Here, we report the surprising discovery that a fragment of the ADEPs retains anti-Mtb activity yet stimulates rather than inhibits the ClpXP1P2-catalyzed degradation of proteins. Our data further suggest that the fragment stabilizes the ClpXP1P2 complex and binds ClpP1P2 in a fashion distinct from that of the intact ADEPs. A structure-activity relationship study of the bioactive fragment defines the pharmacophore and points the way toward the development of new drug leads for the treatment of tuberculosis.
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Affiliation(s)
- Karl R. Schmitz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
- Department of Biological Sciences, University of Delaware, Newark, DE
| | - Emma L. Handy
- Department of Chemistry, Brown University, Providence, RI
| | | | - Shashank Gupta
- Department of Chemistry, Brown University, Providence, RI
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins University, Baltimore, MD
| | - Robert T. Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA
| | - Jason K. Sello
- Department of Chemistry, Brown University, Providence, RI
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA
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8
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Xu X, Zhang L, Yang T, Qiu Z, Bai L, Luo Y. Targeting caseinolytic protease P and its AAA1 chaperone for tuberculosis treatment. Drug Discov Today 2023; 28:103508. [PMID: 36706830 DOI: 10.1016/j.drudis.2023.103508] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
Caseinolytic protease P with its AAA1 chaperone, known as Mycobacterium tuberculosis (Mtb)ClpP1P2 proteolytic machinery, maintains protein homeostasis in Mtb cells and is essential for bacterial survival. It is regarded as an important biological target with the potential to address the increasingly serious issue of multidrug-resistant (MDR) TB. Over the past 10 years, many MtbClpP1P2-targeted modulators have been identified and characterized, some of which have shown potent anti-TB activity. In this review, we describe current understanding of the substrates, structure and function of MtbClpP1P2, classify the modulators of this important protein machine into several categories based on their binding subunits or pockets, and discuss their binding details; Such information provides insights for use in candidate drug research and development of TB treatments by targeting MtbClpP1P2 proteolytic machinery.
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Affiliation(s)
- Xin Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Laiying Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
| | - Tao Yang
- Laboratory of Human Diseases and Immunotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zhiqiang Qiu
- State Key Laboratory of Biotherapy and Cancer Center, 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
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China.
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9
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Malarney KP, Chang PV. Chemoproteomic Approaches for Unraveling Prokaryotic Biology. Isr J Chem 2023; 63:e202200076. [PMID: 37842282 PMCID: PMC10575470 DOI: 10.1002/ijch.202200076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Indexed: 03/07/2023]
Abstract
Bacteria are ubiquitous lifeforms with important roles in the environment, biotechnology, and human health. Many of the functions that bacteria perform are mediated by proteins and enzymes, which catalyze metabolic transformations of small molecules and modifications of proteins. To better understand these biological processes, chemical proteomic approaches, including activity-based protein profiling, have been developed to interrogate protein function and enzymatic activity in physiologically relevant contexts. Here, chemoproteomic strategies and technological advances for studying bacterial physiology, pathogenesis, and metabolism are discussed. The development of chemoproteomic approaches for characterizing protein function and enzymatic activity within bacteria remains an active area of research, and continued innovations are expected to provide breakthroughs in understanding bacterial biology.
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Affiliation(s)
- Kien P Malarney
- Department of Microbiology, Cornell University, Ithaca, NY 14853 (USA)
| | - Pamela V Chang
- Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Center for Immunology, Cornell University, Ithaca, NY 14853 (USA)
- Cornell Institute of Host-Microbe Interactions and Disease, Cornell University, Ithaca, NY 14853 (USA)
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10
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Xu W, Gao W, Bu Q, Li Y. Degradation Mechanism of AAA+ Proteases and Regulation of Streptomyces Metabolism. Biomolecules 2022; 12:biom12121848. [PMID: 36551276 PMCID: PMC9775585 DOI: 10.3390/biom12121848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Hundreds of proteins work together in microorganisms to coordinate and control normal activity in cells. Their degradation is not only the last step in the cell's lifespan but also the starting point for its recycling. In recent years, protein degradation has been extensively studied in both eukaryotic and prokaryotic organisms. Understanding the degradation process is essential for revealing the complex regulatory network in microorganisms, as well as further artificial reconstructions and applications. This review will discuss several studies on protein quality-control family members Lon, FtsH, ClpP, the proteasome in Streptomyces, and a few classical model organisms, mainly focusing on their structure, recognition mechanisms, and metabolic influences.
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Affiliation(s)
- Weifeng Xu
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Wenli Gao
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Qingting Bu
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
| | - Yongquan Li
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou 310058, China
- Correspondence:
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11
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Ogbonna EC, Anderson HR, Schmitz KR. Identification of Arginine Phosphorylation in Mycolicibacterium smegmatis. Microbiol Spectr 2022; 10:e0204222. [PMID: 36214676 PMCID: PMC9604228 DOI: 10.1128/spectrum.02042-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/19/2022] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis is a leading cause of worldwide infectious mortality. The prevalence of multidrug-resistant Mycobacterium tuberculosis infections drives an urgent need to exploit new drug targets. One such target is the ATP-dependent protease ClpC1P1P2, which is strictly essential for viability. However, few proteolytic substrates of mycobacterial ClpC1P1P2 have been identified to date. Recent studies in Bacillus subtilis have shown that the orthologous ClpCP protease recognizes proteolytic substrates bearing posttranslational arginine phosphorylation. While several lines of evidence suggest that ClpC1P1P2 is similarly capable of recognizing phosphoarginine-bearing proteins, the existence of phosphoarginine modifications in mycobacteria has remained in question. Here, we confirm the presence of posttranslational phosphoarginine modifications in Mycolicibacterium smegmatis, a nonpathogenic surrogate of M. tuberculosis. Using a phosphopeptide enrichment workflow coupled with shotgun phosphoproteomics, we identified arginine phosphosites on several functionally diverse targets within the M. smegmatis proteome. Interestingly, phosphoarginine modifications are not upregulated by heat stress, suggesting divergent roles in mycobacteria and Bacillus. Our findings provide new evidence supporting the existence of phosphoarginine-mediated proteolysis by ClpC1P1P2 in mycobacteria and other actinobacterial species. IMPORTANCE Mycobacteria that cause tuberculosis infections employ proteolytic pathways that modulate cellular behavior by destroying specific proteins in a highly regulated manner. Some proteolytic enzymes have emerged as novel antibacterial targets against drug-resistant tuberculosis infections. However, we have only a limited understanding of how these enzymes function in the cell and how they select proteins for destruction. Some proteolytic enzymes are capable of recognizing proteins that carry an unusual chemical modification, arginine phosphorylation. Here, we confirm the existence of arginine phosphorylation in mycobacterial proteins. Our work expands our understanding of a promising drug target in an important global pathogen.
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Affiliation(s)
- Emmanuel C. Ogbonna
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
| | - Henry R. Anderson
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Karl R. Schmitz
- Department of Biological Sciences, University of Delaware, Newark, Delaware, USA
- Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware, USA
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12
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The Development of the Bengamides as New Antibiotics against Drug-Resistant Bacteria. Mar Drugs 2022; 20:md20060373. [PMID: 35736176 PMCID: PMC9228497 DOI: 10.3390/md20060373] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 02/04/2023] Open
Abstract
The bengamides comprise an interesting family of natural products isolated from sponges belonging to the prolific Jaspidae family. Their outstanding antitumor properties, coupled with their unique mechanism of action and unprecedented molecular structures, have prompted an intense research activity directed towards their total syntheses, analogue design, and biological evaluations for their development as new anticancer agents. Together with these biological studies in cancer research, in recent years, the bengamides have been identified as potential antibiotics by their impressive biological activities against various drug-resistant bacteria such as Mycobacterium tuberculosis and Staphylococcus aureus. This review reports on the new advances in the chemistry and biology of the bengamides during the last years, paying special attention to their development as promising new antibiotics. Thus, the evolution of the bengamides from their initial exploration as antitumor agents up to their current status as antibiotics is described in detail, highlighting the manifold value of these marine natural products as valid hits in medicinal chemistry.
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13
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ClpP inhibitors are produced by a widespread family of bacterial gene clusters. Nat Microbiol 2022; 7:451-462. [PMID: 35246663 DOI: 10.1038/s41564-022-01073-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/31/2022] [Indexed: 11/08/2022]
Abstract
The caseinolytic protease (ClpP) is part of a highly conserved proteolytic complex whose disruption can lead to antibacterial activity but for which few specific inhibitors have been discovered. Specialized metabolites produced by bacteria have been shaped by evolution for specific functions, making them a potential source of selective ClpP inhibitors. Here, we describe a target-directed genome mining strategy for discovering ClpP-interacting compounds by searching for biosynthetic gene clusters that contain duplicated copies of ClpP as putative antibiotic resistance genes. We identify a widespread family of ClpP-associated clusters that are known to produce pyrrolizidine alkaloids but whose connection to ClpP has never been made. We show that previously characterized molecules do not affect ClpP function but are shunt metabolites derived from the genuine product of these gene clusters, a reactive covalent ClpP inhibitor. Focusing on one such cryptic gene cluster from Streptomyces cattleya, we identify the relevant inhibitor, which we name clipibicyclene, and show that it potently and selectively inactivates ClpP. Finally, we solve the crystal structure of clipibicyclene-modified Escherichia coli ClpP. Clipibicyclene's discovery reveals the authentic function of a family of natural products whose specificity for ClpP and abundance in nature illuminate the role of eco-evolutionary forces during bacterial competition.
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14
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Labana P, Dornan MH, Lafrenière M, Czarny TL, Brown ED, Pezacki JP, Boddy CN. Armeniaspirols inhibit the AAA+ proteases ClpXP and ClpYQ leading to cell division arrest in Gram-positive bacteria. Cell Chem Biol 2021; 28:1703-1715.e11. [PMID: 34293284 DOI: 10.1016/j.chembiol.2021.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 04/22/2021] [Accepted: 06/29/2021] [Indexed: 01/16/2023]
Abstract
Multi-drug-resistant bacteria present an urgent threat to modern medicine, creating a desperate need for antibiotics with new modes of action. As natural products remain an unsurpassed source for clinically viable antibiotic compounds, we investigate the mechanism of action of armeniaspirol. The armeniaspirols are a structurally unique class of Gram-positive antibiotic discovered from Streptomyces armeniacus for which resistance cannot be readily obtained. We show that armeniaspirol inhibits the ATP-dependent proteases ClpXP and ClpYQ in vitro and in the model Gram-positive Bacillus subtilis. This inhibition dysregulates the divisome and elongasome supported by an upregulation of key proteins FtsZ, DivIVA, and MreB inducing cell division arrest. The inhibition of ClpXP and ClpYQ to dysregulate cell division represents a unique antibiotic mechanism of action and armeniaspirol is the only known natural product inhibitor of the coveted anti-virulence target ClpP. Thus, armeniaspirol possesses a promising lead scaffold for antibiotic development with unique pharmacology.
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Affiliation(s)
- Puneet Labana
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Mark H Dornan
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Matthew Lafrenière
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Tomasz L Czarny
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Eric D Brown
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - John P Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Christopher N Boddy
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON K1N 6N5, Canada.
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15
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Brown NW, Shirley JD, Marshall AP, Carlson EE. Comparison of Bioorthogonal β-Lactone Activity-Based Probes for Selective Labeling of Penicillin-Binding Proteins. Chembiochem 2021; 22:193-202. [PMID: 32964667 PMCID: PMC7790944 DOI: 10.1002/cbic.202000556] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/21/2020] [Indexed: 01/20/2023]
Abstract
Penicillin-binding proteins (PBPs) are a family of bacterial enzymes that are key components of cell-wall biosynthesis and the target of β-lactam antibiotics. Most microbial pathogens contain multiple structurally homologous PBP isoforms, making it difficult to target individual PBPs. To study the roles and regulation of specific PBP isoforms, a panel of bioorthogonal β-lactone probes was synthesized and compared. Fluorescent labeling confirmed selectivity, and PBPs were selectively enriched from Streptococcus pneumoniae lysates. Comparisons between fluorescent labeling of probes revealed that the accessibility of bioorthogonal reporter molecules to the bound probe in the native protein environment exerts a more significant effect on labeling intensity than the bioorthogonal reaction used, observations that are likely applicable beyond this class of probes or proteins. Selective, bioorthogonal activity-based probes for PBPs will facilitate the activity-based determination of the roles and regulation of specific PBP isoforms, a key gap in knowledge that has yet to be filled.
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Affiliation(s)
- Nathaniel W Brown
- Department of Chemistry, University of Minnesota-Twin Cities 139 Smith Hall, Pleasant Street SE, Minneapolis, MN, 55455, USA
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
| | - Andrew P Marshall
- Department of Chemistry, University of Minnesota-Twin Cities 139 Smith Hall, Pleasant Street SE, Minneapolis, MN, 55455, USA
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota-Twin Cities 139 Smith Hall, Pleasant Street SE, Minneapolis, MN, 55455, USA
- Department of Medicinal Chemistry, University of Minnesota-Twin Cities, 308 Harvard Street SE, Minneapolis, MN, 55455, USA
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota-Twin Cities, 321 Church Street SE, Minneapolis, MN, 55455, USA
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16
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Harnagel A, Lopez Quezada L, Park SW, Baranowski C, Kieser K, Jiang X, Roberts J, Vaubourgeix J, Yang A, Nelson B, Fay A, Rubin E, Ehrt S, Nathan C, Lupoli TJ. Nonredundant functions of Mycobacterium tuberculosis chaperones promote survival under stress. Mol Microbiol 2020; 115:272-289. [PMID: 32996193 DOI: 10.1111/mmi.14615] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022]
Abstract
Bacterial chaperones ClpB and DnaK, homologs of the respective eukaryotic heat shock proteins Hsp104 and Hsp70, are essential in the reactivation of toxic protein aggregates that occur during translation or periods of stress. In the pathogen Mycobacterium tuberculosis (Mtb), the protective effect of chaperones extends to survival in the presence of host stresses, such as protein-damaging oxidants. However, we lack a full understanding of the interplay of Hsps and other stress response genes in mycobacteria. Here, we employ genome-wide transposon mutagenesis to identify the genes that support clpB function in Mtb. In addition to validating the role of ClpB in Mtb's response to oxidants, we show that HtpG, a homolog of Hsp90, plays a distinct role from ClpB in the proteotoxic stress response. While loss of neither clpB nor htpG is lethal to the cell, loss of both through genetic depletion or small molecule inhibition impairs recovery after exposure to host-like stresses, especially reactive nitrogen species. Moreover, defects in cells lacking clpB can be complemented by overexpression of other chaperones, demonstrating that Mtb's stress response network depends upon finely tuned chaperone expression levels. These results suggest that inhibition of multiple chaperones could work in concert with host immunity to disable Mtb.
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Affiliation(s)
- Alexa Harnagel
- Department of Chemistry, New York University, New York, NY, USA
| | - Landys Lopez Quezada
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Sae Woong Park
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Catherine Baranowski
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Karen Kieser
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xiuju Jiang
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Julia Roberts
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Amy Yang
- Department of Chemistry, New York University, New York, NY, USA
| | - Brock Nelson
- Department of Chemistry, New York University, New York, NY, USA
| | - Allison Fay
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric Rubin
- Immunology Program, Sloan Kettering Institute, New York, NY, USA
| | - Sabine Ehrt
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Carl Nathan
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
| | - Tania J Lupoli
- Department of Chemistry, New York University, New York, NY, USA.,Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY, USA
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17
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Sharifzadeh S, Brown NW, Shirley JD, Bruce KE, Winkler ME, Carlson EE. Chemical tools for selective activity profiling of bacterial penicillin-binding proteins. Methods Enzymol 2020; 638:27-55. [PMID: 32416917 DOI: 10.1016/bs.mie.2020.02.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Penicillin-binding proteins (PBPs) are membrane-associated proteins involved in the biosynthesis of peptidoglycan (PG), the main component of bacterial cell walls. These proteins were discovered and named for their affinity to bind the β-lactam antibiotic penicillin. The importance of the PBPs has long been appreciated; however, specific roles of individual family members in each bacterial strain, as well as their protein-protein interactions, are yet to be understood. The apparent functional redundancy of the 4-18 PBPs that most eubacteria possess makes determination of their individual roles difficult. Existing techniques to study PBPs are not ideal because they do not directly visualize protein activity and can suffer from artifacts and perturbations of native PBP function. Therefore, development of new methods for studying the roles of individual PBPs in cell wall synthesis is required. We recently generated a library of fluorescent chemical probes containing a β-lactone scaffold that specifically targets the PBPs, enabling the visualization of their catalytic activity. Herein, we describe a general protocol to label and detect the activity of individual PBPs in Streptococcus pneumoniae using our fluorescent β-lactone probes.
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Affiliation(s)
- Shabnam Sharifzadeh
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Nathaniel W Brown
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Joshua D Shirley
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States
| | - Kevin E Bruce
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Malcolm E Winkler
- Department of Biology, Indiana University, Bloomington, IN, United States
| | - Erin E Carlson
- Department of Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN, United States; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.
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18
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Matern WM, Jenquin RL, Bader JS, Karakousis PC. Identifying the essential genes of Mycobacterium avium subsp. hominissuis with Tn-Seq using a rank-based filter procedure. Sci Rep 2020; 10:1095. [PMID: 31974396 PMCID: PMC6978383 DOI: 10.1038/s41598-020-57845-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 01/08/2020] [Indexed: 12/31/2022] Open
Abstract
Mycobacterium avium subsp. hominissuis (MAH) is increasingly recognized as a significant cause of morbidity, particularly in elderly patients or those with immune deficiency or underlying lung impairment. Disease due to MAH is particularly difficult to treat, often requiring years of antibiotic therapy. Identification of genes essential for MAH growth may lead to novel strategies for improving curative therapy. Here we have generated saturating genome-wide transposon mutant pools in a strain of MAH (MAC109) and developed a novel computational technique for classifying annotated genomic features based on the in vitro effect of transposon mutagenesis. Our findings may help guide future genetic and biochemical studies of MAH pathogenesis and aid in the identification of new drugs to improve the treatment of these serious infections.
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Affiliation(s)
- William M Matern
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Robert L Jenquin
- High-Throughput Biology Center, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- High-Throughput Biology Center, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Petros C Karakousis
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD, USA.
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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19
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Guo C, Xiao Y, Bi F, Lin W, Wang H, Yao, H, Lin D. Recombinant expression, biophysical and functional characterization of ClpS from Mycobacterium tuberculosis. Acta Biochim Biophys Sin (Shanghai) 2019; 51:1158-1167. [PMID: 31650179 DOI: 10.1093/abbs/gmz102] [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: 06/18/2019] [Indexed: 11/13/2022] Open
Abstract
Intracellular proteolysis is attracting more and more attention for its unique and important character in Mycobacterium tuberculosis (Mt). The ClpS protein from Mt (MtClpS) plays a critical role in intracellular proteolysis by recognizing N-end rule substrates, which makes it become a potential target for antibacterial drugs. However, the molecular mechanism of MtClpS recognizing N-end rule substrates remains unclear. Preparation of highly concentrated and pure MtClpS protein is a prerequisite for further structural and functional studies. In the present work, we tried several fusion tags and various expression conditions to maximize the production of MtClpS in Escherichia coli. We established an efficient approach for preparing the MtClpS protein with a high yield of 24.7 mg/l and a high purity of 98%. After buffer screening, we obtained a stable MtClpS protein sample concentrated at 0.63 mM in the presence of glycerol, l-Arginine, and l-Glutamate. Moreover, circular dichroism characterization indicated that the secondary structure of MtClpS consists of 38% α-helix and 24% β-sheet. The 2D 1H-15N HSQC nuclear magnetic resonance spectrum showed a good dispersion of resonance peaks with uniform intensity, indicating that the purified MtClpS protein was well folded and conformationally homogeneous. Isothermal titration calorimetry experiments revealed significant interactions of MtClpS with N-end rule peptides beginning with Leu, Tyr, Trp, or Phe. Furthermore, residues D34, D35, and H66 were confirmed as key residues for MtClpS recognizing the N-end rule peptide. The successful expression and biophysical characterization of MtClpS enabled us to gain insight into the molecular mechanism of MtClpS recognizing N-end rule substrates. The obtained stable and pure recombinant MtClpS will enable future inhibitor screening experiments.
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Affiliation(s)
- Chenyun Guo
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yihang Xiao
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Fangkai Bi
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Weiliang Lin
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Huilin Wang
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Hongwei Yao,
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Donghai Lin
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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20
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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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21
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Moreno-Cinos C, Goossens K, Salado IG, Van Der Veken P, De Winter H, Augustyns K. ClpP Protease, a Promising Antimicrobial Target. Int J Mol Sci 2019; 20:ijms20092232. [PMID: 31067645 PMCID: PMC6540193 DOI: 10.3390/ijms20092232] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 01/25/2023] Open
Abstract
The caseinolytic protease proteolytic subunit (ClpP) is a serine protease playing an important role in proteostasis of eukaryotic organelles and prokaryotic cells. Alteration of ClpP function has been proved to affect the virulence and infectivity of a number of pathogens. Increased bacterial resistance to antibiotics has become a global problem and new classes of antibiotics with novel mechanisms of action are needed. In this regard, ClpP has emerged as an attractive and potentially viable option to tackle pathogen fitness without suffering cross-resistance to established antibiotic classes and, when not an essential target, without causing an evolutionary selection pressure. This opens a greater window of opportunity for the host immune system to clear the infection by itself or by co-administration with commonly prescribed antibiotics. A comprehensive overview of the function, regulation and structure of ClpP across the different organisms is given. Discussion about mechanism of action of this protease in bacterial pathogenesis and human diseases are outlined, focusing on the compounds developed in order to target the activation or inhibition of ClpP.
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Affiliation(s)
- Carlos Moreno-Cinos
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Kenneth Goossens
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Irene G Salado
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Pieter Van Der Veken
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Hans De Winter
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
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22
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Fraga H, Rodriguez B, Bardera A, Cid C, Akopian T, Kandror O, Park A, Colmenarejo G, Lelievre J, Goldberg A. Development of high throughput screening methods for inhibitors of ClpC1P1P2 from Mycobacteria tuberculosis. Anal Biochem 2018; 567:30-37. [PMID: 30543804 DOI: 10.1016/j.ab.2018.12.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 12/03/2018] [Indexed: 01/10/2023]
Abstract
Tuberculosis affects about 100 million people worldwide and causes nearly 2 million deaths annually. It has been estimated that one third of all humans is infected with latent Mycobacterium tuberculosis (Mtb). Moreover, Mtb has become increasingly resistant to available antibiotics. Consequently, it is important to identify and characterize new therapeutic targets in Mtb and to synthesize selective inhibitors. ClpP1, ClpP2 and their associated regulatory ATPases, ClpX and ClpC1 are required for the growth of Mtb and for its virulence during murine infection and are highly attractive drug targets, especially since they are not present in the cytosol of mammalian cells, and they differ markedly from the mitochondrial ClpP complex. The importance of these proteins in Mtb is emphasized by the existence of several natural antibiotics targeting this system. In order to find new inhibitors of ClpC1P1P2 system, we developed an assay based on the ATP-dependent degradation of a fluorescent protein substrate. The hits obtained were further characterized with a set of secondary assays to identify precise targets within a complex. A large library of compounds was screened and led to the identification of a ClpC1 ATPase inhibitor demonstrating that this approach can be used in future searches for anti-TB agents.
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Affiliation(s)
- Hugo Fraga
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain; Department Cell Biology, Harvard Medical School, USA; Institut de Biologie Structurale, Grenoble, France; Departamento de Bioquímica, Faculdade de Medicina da Universidade do Porto, Portugal.
| | - Beatriz Rodriguez
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain
| | - Ana Bardera
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain
| | - Concha Cid
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain
| | - Tatos Akopian
- School of Public Health, Harvard Medical School, USA
| | - Olga Kandror
- School of Public Health, Harvard Medical School, USA
| | - Annie Park
- School of Public Health, Harvard Medical School, USA
| | - Gonzalo Colmenarejo
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain; Biostatisics and Bioinformatics Unit, IMDEA Food Institute, Madrid, Spain
| | - Joel Lelievre
- Diseases of the Developing World, Global Health R&D, GlaxoSmithKline, Severo Ochoa 2, 28760, Tres Cantos, Spain
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23
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Konaklieva MI. Addressing Antimicrobial Resistance through New Medicinal and Synthetic Chemistry Strategies. SLAS DISCOVERY 2018; 24:419-439. [PMID: 30523713 DOI: 10.1177/2472555218812657] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Over the past century, a multitude of derivatives of structural scaffolds with established antimicrobial potential have been prepared and tested, and a variety of new scaffolds have emerged. The effectiveness of antibiotics, however, is in sharp decline because of the emergence of drug-resistant microorganisms. The prevalence of drug resistance, both in clinical and community settings, is a consequence of bacterial ingenuity in altering pathways and/or cell morphology, making it a persistent threat to human health. The fundamental ability of pathogens to survive in a multitude of habitats can be triggered by recognition of chemical signals that warn organisms of exposure to a potentially harmful environment. Host immune defenses, including reactive oxygen intermediates and antibacterial substances, are among the multitude of chemical signals that can subsequently trigger expression of phenotypes better adapted for survival in that hostile environment. Thus, resistance development appears to be unavoidable, which leads to the conclusion that developing an alternative perspective for treatment options is vital. This review will discuss emerging medicinal chemistry approaches for addressing the global multidrug resistance in the 21st century.
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24
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Abstract
Regulated proteolysis is a vital process that affects all living things. Bacteria use energy-dependent AAA+ proteases to power degradation of misfolded and native regulatory proteins. Given that proteolysis is an irreversible event, specificity and selectivity in degrading substrates are key. Specificity is often augmented through the use of adaptors that modify the inherent specificity of the proteolytic machinery. Regulated protein degradation is intricately linked to quality control, cell-cycle progression, and physiological transitions. In this review, we highlight recent work that has shed light on our understanding of regulated proteolysis in bacteria. We discuss the role AAA+ proteases play during balanced growth as well as how these proteases are deployed during changes in growth. We present examples of how protease selectivity can be controlled in increasingly complex ways. Finally, we describe how coupling a core recognition determinant to one or more modifying agents is a general theme for regulated protein degradation.
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Affiliation(s)
- Samar A Mahmoud
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA; ,
| | - Peter Chien
- Department of Biochemistry and Molecular Biology, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA; ,
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25
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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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26
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Lupoli TJ, Vaubourgeix J, Burns-Huang K, Gold B. Targeting the Proteostasis Network for Mycobacterial Drug Discovery. ACS Infect Dis 2018; 4:478-498. [PMID: 29465983 PMCID: PMC5902792 DOI: 10.1021/acsinfecdis.7b00231] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains one of the world's deadliest infectious diseases and urgently requires new antibiotics to treat drug-resistant strains and to decrease the duration of therapy. During infection, Mtb encounters numerous stresses associated with host immunity, including hypoxia, reactive oxygen and nitrogen species, mild acidity, nutrient starvation, and metal sequestration and intoxication. The Mtb proteostasis network, composed of chaperones, proteases, and a eukaryotic-like proteasome, provides protection from stresses and chemistries of host immunity by maintaining the integrity of the mycobacterial proteome. In this Review, we explore the proteostasis network as a noncanonical target for antibacterial drug discovery.
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Affiliation(s)
- Tania J. Lupoli
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Julien Vaubourgeix
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Kristin Burns-Huang
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
| | - Ben Gold
- Department of Microbiology and Immunology, Weill Cornell Medicine, 413 East 69th Street, New York, New York 10021, United States
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27
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Lehmann J, Cheng TY, Aggarwal A, Park AS, Zeiler E, Raju RM, Akopian T, Kandror O, Sacchettini JC, Moody DB, Rubin EJ, Sieber SA. An Antibacterial β-Lactone Kills Mycobacterium tuberculosis by Disrupting Mycolic Acid Biosynthesis. Angew Chem Int Ed Engl 2017; 57:348-353. [PMID: 29067779 DOI: 10.1002/anie.201709365] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 10/17/2017] [Indexed: 12/31/2022]
Abstract
The spread of antibiotic resistance is a major challenge for the treatment of Mycobacterium tuberculosis infections. In addition, the efficacy of drugs is often limited by the restricted permeability of the mycomembrane. Frontline antibiotics inhibit mycomembrane biosynthesis, leading to rapid cell death. Inspired by this mechanism, we exploited β-lactones as putative mycolic acid mimics to block serine hydrolases involved in their biosynthesis. Among a collection of β-lactones, we found one hit with potent anti-mycobacterial and bactericidal activity. Chemical proteomics using an alkynylated probe identified Pks13 and Ag85 serine hydrolases as major targets. Validation through enzyme assays and customized 13 C metabolite profiling showed that both targets are functionally impaired by the β-lactone. Co-administration with front-line antibiotics enhanced the potency against M. tuberculosis by more than 100-fold, thus demonstrating the therapeutic potential of targeting mycomembrane biosynthesis serine hydrolases.
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Affiliation(s)
- Johannes Lehmann
- Center for Integrated Protein Science Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany.,Division of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Tan-Yun Cheng
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anup Aggarwal
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Annie S Park
- Division of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Evelyn Zeiler
- Center for Integrated Protein Science Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany
| | - Ravikiran M Raju
- Division of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Tatos Akopian
- Division of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Olga Kandror
- Division of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - D Branch Moody
- Department of Medicine, Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric J Rubin
- Division of Immunology and Infectious Diseases, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Stephan A Sieber
- Center for Integrated Protein Science Department of Chemistry, Technische Universität München, Lichtenbergstraße 4, 85747, Garching, Germany
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28
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Lehmann J, Cheng TY, Aggarwal A, Park AS, Zeiler E, Raju RM, Akopian T, Kandror O, Sacchettini JC, Moody DB, Rubin EJ, Sieber SA. Ein antibakterielles β-Lacton bekämpft Mycobacterium tuberculosis
durch Infiltration der Mykolsäurebiosynthese. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201709365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Johannes Lehmann
- Center for Integrated Protein Science, Fakultät für Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
- Division of Immunology and Infectious Diseases; Harvard TH Chan School of Public Health; Boston MA USA
| | - Tan-Yun Cheng
- Department of Medicine; Division of Rheumatology, Immunology and Allergy; Brigham and Women's Hospital; Harvard Medical School; Boston MA USA
| | - Anup Aggarwal
- Department of Biochemistry and Biophysics; Texas A&M University; College Station TX USA
| | - Annie S. Park
- Division of Immunology and Infectious Diseases; Harvard TH Chan School of Public Health; Boston MA USA
| | - Evelyn Zeiler
- Center for Integrated Protein Science, Fakultät für Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Ravikiran M. Raju
- Division of Immunology and Infectious Diseases; Harvard TH Chan School of Public Health; Boston MA USA
| | - Tatos Akopian
- Division of Immunology and Infectious Diseases; Harvard TH Chan School of Public Health; Boston MA USA
| | - Olga Kandror
- Division of Immunology and Infectious Diseases; Harvard TH Chan School of Public Health; Boston MA USA
| | - James C. Sacchettini
- Department of Biochemistry and Biophysics; Texas A&M University; College Station TX USA
| | - D. Branch Moody
- Department of Medicine; Division of Rheumatology, Immunology and Allergy; Brigham and Women's Hospital; Harvard Medical School; Boston MA USA
| | - Eric J. Rubin
- Division of Immunology and Infectious Diseases; Harvard TH Chan School of Public Health; Boston MA USA
| | - Stephan A. Sieber
- Center for Integrated Protein Science, Fakultät für Chemie; Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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29
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Sharifzadeh S, Boersma MJ, Kocaoglu O, Shokri A, Brown CL, Shirley JD, Winkler ME, Carlson EE. Novel Electrophilic Scaffold for Imaging of Essential Penicillin-Binding Proteins in Streptococcus pneumoniae. ACS Chem Biol 2017; 12:2849-2857. [PMID: 28990753 DOI: 10.1021/acschembio.7b00614] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidoglycan (PG) is a mesh-like heteropolymer made up of glycan chains cross-linked by short peptides and is the major scaffold of eubacterial cell walls, determining cell shape, size, and chaining. This structure, which is required for growth and survival, is located outside of the cytoplasmic membrane of bacterial cells, making it highly accessible to antibiotics. Penicillin-binding proteins (PBPs) are essential for construction of PG and perform transglycosylase activities to generate the glycan strands and transpeptidation to cross-link the appended peptides. The β-lactam antibiotics, which are among the most clinically effective antibiotics for the treatment of bacterial infections, inhibit PBP transpeptidation, ultimately leading to cell lysis. Despite this importance, the discrete functions of individual PBP homologues have been difficult to determine. These major gaps in understanding of PBP activation and macromolecular interactions largely result from a lack of tools to assess the functional state of specific PBPs in bacterial cells. We have identified β-lactones as a privileged scaffold for the generation of PBP-selective probes and utilized these compounds for imaging of the essential proteins, PBP2x and PBP2b, in Streptococcus pneumoniae. We demonstrated that while PBP2b activity is restricted to a ring surrounding the division sites, PBP2x activity is present both at the septal center and at the surrounding ring. These spatially separate regions of PBP2x activity could not be detected by previous activity-based approaches, which highlights a critical strength of our PBP-selective imaging strategy.
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Affiliation(s)
- Shabnam Sharifzadeh
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Michael J. Boersma
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Ozden Kocaoglu
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Alireza Shokri
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Clayton L. Brown
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Joshua D. Shirley
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Malcolm E. Winkler
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Erin E. Carlson
- Departments
of Chemistry, ‡Medicinal Chemistry, and Biochemistry, §Molecular Biology
and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Departments of Biology, ⊥Molecular and Cellular Biochemistry,
and #Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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30
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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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31
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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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32
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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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33
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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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34
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Ni T, Ye F, Liu X, Zhang J, Liu H, Li J, Zhang Y, Sun Y, Wang M, Luo C, Jiang H, Lan L, Gan J, Zhang A, Zhou H, Yang CG. Characterization of Gain-of-Function Mutant Provides New Insights into ClpP Structure. ACS Chem Biol 2016; 11:1964-72. [PMID: 27171654 DOI: 10.1021/acschembio.6b00390] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
ATP-dependent Clp protease (ClpP), a highly conserved serine protease in vast bacteria, could be converted into a noncontrollable enzyme capable of degrading mature proteins in the presence of acyldepsipeptides (ADEPs). Here, we design such a gain-of-function mutant of Staphylococcus aureus ClpP (SaClpP) capable of triggering the same level of dysfunctional activity that occurs upon ADEPs treatment. The SaClpPY63A mutant degrades FtsZ in vivo and inhibits staphylococcal growth. The crystal structure of SaClpPY63A indicates that Asn42 would be an important domino to fall for further activation of ClpP. Indeed, the SaClpPN42AY63A mutant demonstrates promoted self-activated proteolysis, which is a result of an enlarged entrance pore as observed in cryo-electron microscopy images. In addition, the expression of the engineered clpP allele phenocopies treatment with ADEPs; inhibition of cell division occurs as does showing sterilizing with rifampicin antibiotics. Collectively, we show that the gain-of-function SaClpPN42AY63A mutant becomes a fairly nonspecific protease and kills persisters by degrading over 500 proteins, thus providing new insights into the structure of the ClpP protease.
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Affiliation(s)
- Tengfeng Ni
- Laboratory
of Chemical Biology, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Ye
- College
of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
- Drug
Design and Discovery Center, State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xing Liu
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jie Zhang
- Laboratory
of Chemical Biology, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hongchuan Liu
- Laboratory
of Chemical Biology, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, 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
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yingyi Zhang
- National
Center for Protein Science Shanghai, Institute of Biochemistry and
Cell Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yinqiang Sun
- Experiment
Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Meining Wang
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cheng Luo
- Drug
Design and Discovery Center, State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hualiang Jiang
- University of Chinese Academy of Sciences, Beijing 100049, China
- Drug
Design and Discovery Center, State Key Laboratory of Drug Research,
Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Lefu Lan
- Laboratory
of Chemical Biology, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhua Gan
- School
of Life Sciences, Fudan University, Shanghai 200433, China
| | - Ao Zhang
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS
Key Laboratory of Receptor Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hu Zhou
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS
Key Laboratory of Receptor 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
- University of Chinese Academy of Sciences, Beijing 100049, China
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35
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Goodreid JD, Janetzko J, Santa Maria JP, Wong KS, Leung E, Eger BT, Bryson S, Pai EF, Gray-Owen SD, Walker S, Houry WA, Batey RA. Development and Characterization of Potent Cyclic Acyldepsipeptide Analogues with Increased Antimicrobial Activity. J Med Chem 2016; 59:624-46. [PMID: 26818454 DOI: 10.1021/acs.jmedchem.5b01451] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The problem of antibiotic resistance has prompted the search for new antibiotics with novel mechanisms of action. Analogues of the A54556 cyclic acyldepsipeptides (ADEPs) represent an attractive class of antimicrobial agents that act through dysregulation of caseinolytic protease (ClpP). Previous studies have shown that ADEPs are active against Gram-positive bacteria (e.g., MRSA, VRE, PRSP (penicillin-resistant Streptococcus pneumoniae)); however, there are currently few studies examining Gram-negative bacteria. In this study, the synthesis and biological evaluation of 14 novel ADEPs against a variety of pathogenic Gram-negative and Gram-positive organisms is outlined. Optimization of the macrocyclic core residues and N-acyl side chain culminated in the development of 26, which shows potent activity against the Gram-negative species Neisseria meningitidis and Neisseria gonorrheae and improved activity against the Gram-positive organisms Staphylococcus aureus and Enterococcus faecalis in comparison with known analogues. In addition, the co-crystal structure of an ADEP-ClpP complex derived from N. meningitidis was solved.
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Affiliation(s)
- Jordan D Goodreid
- Davenport Research Laboratories, Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - John Janetzko
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - John P Santa Maria
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Keith S Wong
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Elisa Leung
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Bryan T Eger
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Steve Bryson
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- The Campbell Family Institute for Cancer Research, University Health Network , Toronto, Ontario M5G 1L7, Canada
| | - Emil F Pai
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
- The Campbell Family Institute for Cancer Research, University Health Network , Toronto, Ontario M5G 1L7, Canada
| | - Scott D Gray-Owen
- Department of Molecular Genetics, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Suzanne Walker
- Department of Microbiology and Immunobiology, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Walid A Houry
- Department of Biochemistry, University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Robert A Batey
- Davenport Research Laboratories, Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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36
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Olivares AO, Baker TA, Sauer RT. Mechanistic insights into bacterial AAA+ proteases and protein-remodelling machines. Nat Rev Microbiol 2015; 14:33-44. [PMID: 26639779 DOI: 10.1038/nrmicro.2015.4] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
To maintain protein homeostasis, AAA+ proteolytic machines degrade damaged and unneeded proteins in bacteria, archaea and eukaryotes. This process involves the ATP-dependent unfolding of a target protein and its subsequent translocation into a self-compartmentalized proteolytic chamber. Related AAA+ enzymes also disaggregate and remodel proteins. Recent structural and biochemical studies, in combination with direct visualization of unfolding and translocation in single-molecule experiments, have illuminated the molecular mechanisms behind these processes and suggest how remodelling of macromolecular complexes by AAA+ enzymes could occur without global denaturation. In this Review, we discuss the structural and mechanistic features of AAA+ proteases and remodelling machines, focusing on the bacterial ClpXP and ClpX as paradigms. We also consider the potential of these enzymes as antibacterial targets and outline future challenges for the field.
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Affiliation(s)
- Adrian O Olivares
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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37
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An ensemble-guided approach identifies ClpP as a major regulator of transcript levels in nitric oxide-stressed Escherichia coli. Metab Eng 2015; 31:22-34. [DOI: 10.1016/j.ymben.2015.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 03/21/2015] [Accepted: 06/15/2015] [Indexed: 11/23/2022]
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38
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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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39
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Wu G, Zhang Z, Chen H, Lin K. De novo design of caseinolytic protein proteases inhibitors based on pharmacophore and 2D molecular fingerprints. Bioorg Med Chem Lett 2015; 25:2345-52. [DOI: 10.1016/j.bmcl.2015.04.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 03/25/2015] [Accepted: 04/07/2015] [Indexed: 10/23/2022]
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40
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Target mechanism-based whole-cell screening identifies bortezomib as an inhibitor of caseinolytic protease in mycobacteria. mBio 2015; 6:e00253-15. [PMID: 25944857 PMCID: PMC4436076 DOI: 10.1128/mbio.00253-15] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
A novel type of antibacterial screening method, a target mechanism-based whole-cell screening method, was developed to combine the advantages of target mechanism- and whole-cell-based approaches. A mycobacterial reporter strain with a synthetic phenotype for caseinolytic protease (ClpP1P2) activity was engineered, allowing the detection of inhibitors of this enzyme inside intact bacilli. A high-throughput screening method identified bortezomib, a human 26S proteasome drug, as a potent inhibitor of ClpP1P2 activity and bacterial growth. A battery of secondary assays was employed to demonstrate that bortezomib indeed exerts its antimicrobial activity via inhibition of ClpP1P2: Down- or upmodulation of the intracellular protease level resulted in hyper- or hyposensitivity of the bacteria, the drug showed specific potentiation of translation error-inducing aminoglycosides, ClpP1P2-specific substrate WhiB1 accumulated upon exposure, and growth inhibition potencies of bortezomib derivatives correlated with ClpP1P2 inhibition potencies. Furthermore, molecular modeling showed that the drug can bind to the catalytic sites of ClpP1P2. This work demonstrates the feasibility of target mechanism-based whole-cell screening, provides chemical validation of ClpP1P2 as a target, and identifies a drug in clinical use as a new lead compound for tuberculosis therapy. During the last decade, antibacterial drug discovery relied on biochemical assays, rather than whole-cell approaches, to identify molecules that interact with purified target proteins derived by genomics. This approach failed to deliver antibacterial compounds with whole-cell activity, either because of cell permeability issues that medicinal chemistry cannot easily fix or because genomic data of essentiality insufficiently predicted the vulnerability of the target identified. As a consequence, the field largely moved back to a whole-cell approach whose main limitation is its black-box nature, i.e., that it requires trial-and-error chemistry because the cellular target is unknown. We developed a novel type of antibacterial screening method, target mechanism-based whole-cell screening, to combine the advantages of both approaches. We engineered a mycobacterial reporter strain with a synthetic phenotype allowing us to identify inhibitors of the caseinolytic protease (ClpP1P2) inside the cell. This approach identified bortezomib, an anticancer drug, as a specific inhibitor of ClpP1P2. We further confirmed the specific “on-target” activity of bortezomib by independent approaches including, but not limited to, genetic manipulation of the target level (over- and underexpressing strains) and by establishing a dynamic structure-activity relationship between ClpP1P2 and growth inhibition. Identifying an “on-target” compound is critical to optimize the efficacy of the compound without compromising its specificity. This work demonstrates the feasibility of target mechanism-based whole-cell screening methods, validates ClpP1P2 as a druggable target, and delivers a lead compound for tuberculosis therapy.
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41
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Leodolter J, Warweg J, Weber-Ban E. The Mycobacterium tuberculosis ClpP1P2 Protease Interacts Asymmetrically with Its ATPase Partners ClpX and ClpC1. PLoS One 2015; 10:e0125345. [PMID: 25933022 PMCID: PMC4416901 DOI: 10.1371/journal.pone.0125345] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/17/2015] [Indexed: 11/19/2022] Open
Abstract
Clp chaperone-proteases are cylindrical complexes built from ATP-dependent chaperone rings that stack onto a proteolytic ClpP double-ring core to carry out substrate protein degradation. Interaction of the ClpP particle with the chaperone is mediated by an N-terminal loop and a hydrophobic surface patch on the ClpP ring surface. In contrast to E. coli, Mycobacterium tuberculosis harbors not only one but two ClpP protease subunits, ClpP1 and ClpP2, and a homo-heptameric ring of each assembles to form the ClpP1P2 double-ring core. Consequently, this hetero double-ring presents two different potential binding surfaces for the interaction with the chaperones ClpX and ClpC1. To investigate whether ClpX or ClpC1 might preferentially interact with one or the other double-ring face, we mutated the hydrophobic chaperone-interaction patch on either ClpP1 or ClpP2, generating ClpP1P2 particles that are defective in one of the two binding patches and thereby in their ability to interact with their chaperone partners. Using chaperone-mediated degradation of ssrA-tagged model substrates, we show that both Mycobacterium tuberculosis Clp chaperones require the intact interaction face of ClpP2 to support degradation, resulting in an asymmetric complex where chaperones only bind to the ClpP2 side of the proteolytic core. This sets the Clp proteases of Mycobacterium tuberculosis, and probably other Actinobacteria, apart from the well-studied E. coli system, where chaperones bind to both sides of the protease core, and it frees the ClpP1 interaction interface for putative new binding partners.
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Affiliation(s)
- Julia Leodolter
- Institute for Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Jannis Warweg
- Institute for Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
| | - Eilika Weber-Ban
- Institute for Molecular Biology & Biophysics, ETH Zurich, Zurich, Switzerland
- * E-mail:
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42
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Mdluli K, Kaneko T, Upton A. The tuberculosis drug discovery and development pipeline and emerging drug targets. Cold Spring Harb Perspect Med 2015; 5:a021154. [PMID: 25635061 PMCID: PMC4448709 DOI: 10.1101/cshperspect.a021154] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The recent accelerated approval for use in extensively drug-resistant and multidrug-resistant-tuberculosis (MDR-TB) of two first-in-class TB drugs, bedaquiline and delamanid, has reinvigorated the TB drug discovery and development field. However, although several promising clinical development programs are ongoing to evaluate new TB drugs and regimens, the number of novel series represented is few. The global early-development pipeline is also woefully thin. To have a chance of achieving the goal of better, shorter, safer TB drug regimens with utility against drug-sensitive and drug-resistant disease, a robust and diverse global TB drug discovery pipeline is key, including innovative approaches that make use of recently acquired knowledge on the biology of TB. Fortunately, drug discovery for TB has resurged in recent years, generating compounds with varying potential for progression into developable leads. In parallel, advances have been made in understanding TB pathogenesis. It is now possible to apply the lessons learned from recent TB hit generation efforts and newly validated TB drug targets to generate the next wave of TB drug leads. Use of currently underexploited sources of chemical matter and lead-optimization strategies may also improve the efficiency of future TB drug discovery. Novel TB drug regimens with shorter treatment durations must target all subpopulations of Mycobacterium tuberculosis existing in an infection, including those responsible for the protracted TB treatment duration. This review summarizes the current TB drug development pipeline and proposes strategies for generating improved hits and leads in the discovery phase that could help achieve this goal.
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Affiliation(s)
- Khisimuzi Mdluli
- Global Alliance for TB Drug Development, New York, New York 10005
| | - Takushi Kaneko
- Global Alliance for TB Drug Development, New York, New York 10005
| | - Anna Upton
- Global Alliance for TB Drug Development, New York, New York 10005
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43
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Schmitz KR, Carney DW, Sello JK, Sauer RT. Crystal structure of Mycobacterium tuberculosis ClpP1P2 suggests a model for peptidase activation by AAA+ partner binding and substrate delivery. Proc Natl Acad Sci U S A 2014; 111:E4587-95. [PMID: 25267638 PMCID: PMC4217457 DOI: 10.1073/pnas.1417120111] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Caseinolytic peptidase P (ClpP), a double-ring peptidase with 14 subunits, collaborates with ATPases associated with diverse activities (AAA+) partners to execute ATP-dependent protein degradation. Although many ClpP enzymes self-assemble into catalytically active homo-tetradecamers able to cleave small peptides, the Mycobacterium tuberculosis enzyme consists of discrete ClpP1 and ClpP2 heptamers that require a AAA+ partner and protein-substrate delivery or a peptide agonist to stabilize assembly of the active tetradecamer. Here, we show that cyclic acyldepsipeptides (ADEPs) and agonist peptides synergistically activate ClpP1P2 by mimicking AAA+ partners and substrates, respectively, and determine the structure of the activated complex. Our studies establish the basis of heteromeric ClpP1P2 assembly and function, reveal tight coupling between the conformations of each ring, show that ADEPs bind only to one ring but appear to open the axial pores of both rings, provide a foundation for rational drug development, and suggest strategies for studying the roles of individual ClpP1 and ClpP2 rings in Clp-family proteolysis.
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Affiliation(s)
- Karl R Schmitz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and
| | - Daniel W Carney
- Department of Chemistry, Brown University, Providence, RI 02912
| | - Jason K Sello
- Department of Chemistry, Brown University, Providence, RI 02912
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139; and
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44
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Schmitz KR, Sauer RT. Substrate delivery by the AAA+ ClpX and ClpC1 unfoldases activates the mycobacterial ClpP1P2 peptidase. Mol Microbiol 2014; 93:617-28. [PMID: 24976069 DOI: 10.1111/mmi.12694] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/25/2014] [Indexed: 11/29/2022]
Abstract
Mycobacterial Clp-family proteases function via collaboration of the heteromeric ClpP1P2 peptidase with a AAA+ partner, ClpX or ClpC1. These enzymes are essential for M. tuberculosis viability and are validated antibacterial drug targets, but the requirements for assembly and regulation of functional proteolytic complexes are poorly understood. Here, we report the reconstitution of protein degradation by mycobacterial Clp proteases in vitro and describe novel features of these enzymes that distinguish them from orthologues in other bacteria. Both ClpX and ClpC1 catalyse ATP-dependent unfolding and degradation of native protein substrates in conjunction with ClpP1P2, but neither mediates protein degradation with just ClpP1 or ClpP2. ClpP1P2 alone has negligible peptidase activity, but is strongly stimulated by translocation of protein substrates into ClpP1P2 by either AAA+ partner. Interestingly, our results support a model in which both binding of a AAA+ partner and protein-substrate delivery are required to stabilize active ClpP1P2. Our model has implications for therapeutically targeting ClpP1P2 in dormant M. tuberculosis, and our reconstituted systems should facilitate identification of novel Clp protease inhibitors and activators.
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Affiliation(s)
- Karl R Schmitz
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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45
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Abstract
Current tuberculosis (TB) therapies take too long and the regimens are complex and subject to adverse effects and drug-drug interactions with concomitant medications. The emergence of drug-resistant TB strains exacerbates the situation. Drug discovery for TB has resurged in recent years, generating compounds (hits) with varying potential for progression into developable leads. In parallel, advances have been made in understanding TB pathogenesis. It is now possible to apply the lessons learned from recent TB hit generation efforts and newly validated TB drug targets to generate the next wave of TB drug leads. Use of currently underexploited sources of chemical matter and lead-optimization strategies may also improve the efficiency of future TB drug discovery. Novel TB drug regimens with shorter treatment durations must target all subpopulations of Mycobacterium tuberculosis existing in an infection, including those responsible for the protracted TB treatment duration. This review proposes strategies for generating improved hits and leads that could help achieve this goal.
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46
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Carney D, Schmitz KR, Truong J, Sauer RT, Sello JK. Restriction of the conformational dynamics of the cyclic acyldepsipeptide antibiotics improves their antibacterial activity. J Am Chem Soc 2014; 136:1922-9. [PMID: 24422534 PMCID: PMC4004210 DOI: 10.1021/ja410385c] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Indexed: 02/07/2023]
Abstract
The cyclic acyldepsipeptide (ADEP) antibiotics are a new class of antibacterial agents that kill bacteria via a mechanism that is distinct from all clinically used drugs. These molecules bind and dysregulate the activity of the ClpP peptidase. The potential of these antibiotics as antibacterial drugs has been enhanced by the elimination of pharmacological liabilities through medicinal chemistry efforts. Here, we demonstrate that the ADEP conformation observed in the ADEP-ClpP crystal structure is fortified by transannular hydrogen bonding and can be further stabilized by judicious replacement of constituent amino acids within the peptidolactone core structure with more conformationally constrained counterparts. Evidence supporting constraint of the molecule into the bioactive conformer was obtained by measurements of deuterium-exchange kinetics of hydrogens that were proposed to be engaged in transannular hydrogen bonds. We show that the rigidified ADEP analogs bind and activate ClpP at lower concentrations in vitro. Remarkably, these compounds have up to 1200-fold enhanced antibacterial activity when compared to those with the peptidolactone core structure common to two ADEP natural products. This study compellingly demonstrates how rational modulation of conformational dynamics may be used to improve the bioactivities of natural products.
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Affiliation(s)
- Daniel
W. Carney
- Department
of Chemistry, Brown University, 324 Brook Street, Providence, Rhode Island 02912, United States
| | - Karl R. Schmitz
- Department
of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jonathan
V. Truong
- Department
of Chemistry, Brown University, 324 Brook Street, Providence, Rhode Island 02912, United States
| | - Robert T. Sauer
- Department
of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Jason K. Sello
- Department
of Chemistry, Brown University, 324 Brook Street, Providence, Rhode Island 02912, United States
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