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Luo G, Ming T, Yang L, He L, Tao T, Wang Y. Modulators targeting protein-protein interactions in Mycobacterium tuberculosis. Microbiol Res 2024; 284:127675. [PMID: 38636239 DOI: 10.1016/j.micres.2024.127675] [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: 09/27/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/20/2024]
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (M. tuberculosis), mainly transmitted through droplets to infect the lungs, and seriously affecting patients' health and quality of life. Clinically, anti-TB drugs often entail side effects and lack efficacy against resistant strains. Thus, the exploration and development of novel targeted anti-TB medications are imperative. Currently, protein-protein interactions (PPIs) offer novel avenues for anti-TB drug development, and the study of targeted modulators of PPIs in M. tuberculosis has become a prominent research focus. Furthermore, a comprehensive PPI network has been constructed using computational methods and bioinformatics tools. This network allows for a more in-depth analysis of the structural biology of PPIs and furnishes essential insights for the development of targeted small-molecule modulators. Furthermore, this article provides a detailed overview of the research progress and regulatory mechanisms of PPI modulators in M. tuberculosis, the causative agent of TB. Additionally, it summarizes potential targets for anti-TB drugs and discusses the prospects of existing PPI modulators.
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Affiliation(s)
- Guofeng Luo
- School of Medical and Life Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Tianqi Ming
- State Key Laboratory of Southwestern Chinese Medicine Resources, Department of Pharmacology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Luchuan Yang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Lei He
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Tao Tao
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China
| | - Yanmei Wang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu 610031, China.
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2
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Kumari S, Ali A, Kumar M. Nucleotide-induced ClpC oligomerization and its non-preferential association with ClpP isoforms of pathogenic Leptospira. Int J Biol Macromol 2024; 266:131371. [PMID: 38580013 DOI: 10.1016/j.ijbiomac.2024.131371] [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: 12/27/2023] [Revised: 03/15/2024] [Accepted: 04/02/2024] [Indexed: 04/07/2024]
Abstract
Bacterial caseinolytic protease-chaperone complexes participate in the elimination of misfolded and aggregated protein substrates. The spirochete Leptospira interrogans possess a set of Clp-chaperones (ClpX, ClpA, and ClpC), which may associate functionally with two different isoforms of LinClpP (ClpP1 and ClpP2). The L. interrogans ClpC (LinClpC) belongs to class-I chaperone with two active ATPase domains separated by a middle domain. Using the size exclusion chromatography, ANS dye binding, and dynamic light scattering analysis, the LinClpC is suggested to undergo nucleotide-induced oligomerization. LinClpC associates with either pure LinClpP1 or LinClpP2 isoforms non-preferentially and with equal affinity. Regardless, pure LinClpP isoforms cannot constitute an active protease complex with LinClpC. Interestingly, the heterocomplex LinClpP1P2 in association with LinClpC forms a functional proteolytic machinery and degrade β-casein or FITC-casein in an energy-independent manner. Adding either ATP or ATPγS further fosters the LinClpCP1P2 complex protease activity by nurturing the functional oligomerization of LinClpC. The antibiotic, acyldepsipeptides (ADEP1) display a higher activatory role on LinClpP1P2 protease activity than LinClpC. Altogether, this work illustrates an in-depth study of hetero-tetradecamer LinClpP1P2 association with its cognate ATPase and unveils a new insight into the structural reorganization of LinClpP1P2 in the presence of chaperone, LinClpC to gain protease activity.
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Affiliation(s)
- Surbhi Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Arfan Ali
- Department of Veterinary Microbiology, College of Veterinary Science, Assam Agricultural University, Khanapara, Assam 781022, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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3
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Alves França B, Falke S, Rohde H, Betzel C. Molecular insights into the dynamic modulation of bacterial ClpP function and oligomerization by peptidomimetic boronate compounds. Sci Rep 2024; 14:2572. [PMID: 38296985 PMCID: PMC10830462 DOI: 10.1038/s41598-024-51787-0] [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: 10/26/2023] [Accepted: 01/09/2024] [Indexed: 02/02/2024] Open
Abstract
Bacterial caseinolytic protease P subunit (ClpP) is important and vital for cell survival and infectivity. Recent publications describe and discuss the complex structure-function relationship of ClpP and its processive activity mediated by 14 catalytic sites. Even so, there are several aspects yet to be further elucidated, such as the paradoxical allosteric modulation of ClpP by peptidomimetic boronates. These compounds bind to all catalytic sites, and in specific conditions, they stimulate a dysregulated degradation of peptides and globular proteins, instead of inhibiting the enzymatic activity, as expected for serine proteases in general. Aiming to explore and explain this paradoxical effect, we solved and refined the crystal structure of native ClpP from Staphylococcus epidermidis (Se), an opportunistic pathogen involved in nosocomial infections, as well as ClpP in complex with ixazomib at 1.90 Å and 2.33 Å resolution, respectively. The interpretation of the crystal structures, in combination with complementary biochemical and biophysical data, shed light on how ixazomib affects the ClpP conformational state and activity. Moreover, SEC-SAXS and DLS measurements show, for the first time, that a peptidomimetic boronate compound also induces the assembly of the tetradecameric structure from isolated homomeric heptameric rings of a gram-positive organism.
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Affiliation(s)
- Bruno Alves França
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Build. 22a, Notkestraße 85, 22607, Hamburg, Germany
| | - Sven Falke
- Center for Free-Electron Laser Science CFEL, DESY, Notkestraße 85, 22607, Hamburg, Germany
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany
| | - Christian Betzel
- Institute of Biochemistry and Molecular Biology, Laboratory for Structural Biology of Infection and Inflammation, University of Hamburg, c/o DESY, Build. 22a, Notkestraße 85, 22607, Hamburg, Germany.
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4
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Kumari S, Dhara A, Kumar M. Leptospira ClpP mutant variants in association with the ClpX, acyldepsipeptide, and the trigger factor displays unprecedented gain-of-function. Int J Biol Macromol 2024; 254:127753. [PMID: 38287595 DOI: 10.1016/j.ijbiomac.2023.127753] [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: 04/19/2023] [Revised: 10/05/2023] [Accepted: 10/27/2023] [Indexed: 01/31/2024]
Abstract
The functionally active ClpP (LinClpP) of Leptospira interrogans is composed of two different isoforms (LinClpP1 and LinClpP2). In this study, five mutants of LinClpP (LinClpP1E170D, LinClpP1N172D, LinClpP2IG_del, LinClpP2S40AK41N, LinClpP2Y62A) targeting its critical hotspot residues were generated. The functional activity of pure LinClpP mutant variants or its heterocomplex and its effect when associated with a chaperone (LinClpX)/antibiotic acyldepsipeptide (ADEP1)/trigger factor (LinTF) was examined. The two mutants (LinClpP2S40AK41N and LinClpP2Y62A) displayed gain-of-function (GOF) in peptidase activity. The ADEP1-bound heterocomplex (LinClpP1P2S40AK41N and LinClpP1P2Y62A) measured 1.7 and 1.5-fold higher protease activity than ADEP-bound LinClpP1P2. The dynamic light scattering analysis of ADEP1-bound GOF mutants displayed increased hydrodynamic diameter. In the presence of LinTF, the heterocomplex (LinClpP1P2S40AK41N and LinClpP1P2Y62A) exhibited a 3-fold surge in peptidase activity. The deletion mutant (LinClpP2IG_del) or its heterocomplex (LinClpP1P2IG_del) displayed no activity. Similarly, the pure LinClpP1E170D and LinClpP1N172D could not cleave a model dipeptide. However, its heterocomplex (LinClpP1E170DP2 and LinClpP1N172DP2) showed 0.5-fold lower peptidase activity than the LinClpP1P2. Collectively, two mutants (LinClpP2S40AK41N and LinClpP2Y62A) have GOF and can degrade model dipeptide substrate without the aid of LinClpP1 isoform and thus provide new insights into unprecedented LinClpP activation.
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Affiliation(s)
- Surbhi Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Anusua Dhara
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Manish Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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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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6
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Petkov R, Camp AH, Isaacson RL, Torpey JH. Targeting bacterial degradation machinery as an antibacterial strategy. Biochem J 2023; 480:1719-1731. [PMID: 37916895 PMCID: PMC10657178 DOI: 10.1042/bcj20230191] [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: 05/16/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 11/03/2023]
Abstract
The exploitation of a cell's natural degradation machinery for therapeutic purposes is an exciting research area in its infancy with respect to bacteria. Here, we review current strategies targeting the ClpCP system, which is a proteolytic degradation complex essential in the biology of many bacterial species of scientific interest. Strategies include using natural product antibiotics or acyldepsipeptides to initiate the up- or down-regulation of ClpCP activity. We also examine exciting recent forays into BacPROTACs to trigger the degradation of specific proteins of interest through the hijacking of the ClpCP machinery. These strategies represent an important emerging avenue for combatting antimicrobial resistance.
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Affiliation(s)
- Radoslav Petkov
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - Amy H. Camp
- Department of Biological Sciences, Mount Holyoke College, 50 College Street, South Hadley, Massachusetts 01075, U.S.A
| | - Rivka L. Isaacson
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
| | - James H. Torpey
- Department of Chemistry, King's College London, Britannia House, 7 Trinity Street, London SE1 1DB, U.K
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7
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [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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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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9
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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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10
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Antibiotic Acyldepsipeptides Stimulate the Streptomyces Clp-ATPase/ClpP Complex for Accelerated Proteolysis. mBio 2022; 13:e0141322. [PMID: 36286522 PMCID: PMC9765437 DOI: 10.1128/mbio.01413-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Clp proteases consist of a proteolytic, tetradecameric ClpP core and AAA+ Clp-ATPases. Streptomycetes, producers of a plethora of secondary metabolites, encode up to five different ClpP homologs, and the composition of their unusually complex Clp protease machinery has remained unsolved. Here, we report on the composition of the housekeeping Clp protease in Streptomyces, consisting of a heterotetradecameric core built of ClpP1, ClpP2, and the cognate Clp-ATPases ClpX, ClpC1, or ClpC2, all interacting with ClpP2 only. Antibiotic acyldepsipeptides (ADEP) dysregulate the Clp protease for unregulated proteolysis. We observed that ADEP binds Streptomyces ClpP1, but not ClpP2, thereby not only triggering the degradation of nonnative protein substrates but also accelerating Clp-ATPase-dependent proteolysis. The explanation is the concomitant binding of ADEP and Clp-ATPases to opposite sides of the ClpP1P2 barrel, hence revealing a third, so far unknown mechanism of ADEP action, i.e., the accelerated proteolysis of native protein substrates by the Clp protease. IMPORTANCE Clp proteases are antibiotic and anticancer drug targets. Composed of the proteolytic core ClpP and a regulatory Clp-ATPase, the protease machinery is important for protein homeostasis and regulatory proteolysis. The acyldepsipeptide antibiotic ADEP targets ClpP and has shown promise for treating multiresistant and persistent bacterial infections. The molecular mechanism of ADEP is multilayered. Here, we present a new way how ADEP can deregulate the Clp protease system. Clp-ATPases and ADEP bind to opposite sides of Streptomyces ClpP, accelerating the degradation of natural Clp protease substrates. We also demonstrate the composition of the major Streptomyces Clp protease complex, a heteromeric ClpP1P2 core with the Clp-ATPases ClpX, ClpC1, or ClpC2 exclusively bound to ClpP2, and the killing mechanism of ADEP in Streptomyces.
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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: 1] [Impact Index Per Article: 0.5] [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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Acyldepsipeptide Analogues: A Future Generation Antibiotics for Tuberculosis Treatment. Pharmaceutics 2022; 14:pharmaceutics14091956. [PMID: 36145704 PMCID: PMC9502522 DOI: 10.3390/pharmaceutics14091956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/09/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022] Open
Abstract
Acyldepsipeptides (ADEPs) are a new class of emerging antimicrobial peptides (AMPs), which are currently explored for treatment of pathogenic infections, including tuberculosis (TB). These cyclic hydrophobic peptides have a unique bacterial target to the conventional anti-TB drugs, and present a therapeutic window to overcome Mycobacterium Tuberculosis (M. tb) drug resistance. ADEPs exerts their antibacterial activity on M. tb strains through activation of the protein homeostatic regulatory protease, the caseinolytic protease (ClpP1P2). ClpP1P2 is normally regulated and activated by the ClpP-ATPases to degrade misfolded and toxic peptides and/or short proteins. ADEPs bind and dysregulate all the homeostatic capabilities of ClpP1P2 while inducing non-selective proteolysis. The uncontrolled proteolysis leads to M. tb cell death within the host. ADEPs analogues that have been tested possess cytotoxicity and poor pharmacokinetic and pharmacodynamic properties. However, these can be improved by drug design techniques. Moreover, the use of nanomaterial in conjunction with ADEPs would yield effective synergistic effect. This new mode of action has potential to combat and eradicate the extensive multi-drug resistance (MDR) problem that is currently faced by the public health pertaining bacterial infections, especially TB.
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13
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ESKAPE Pathogens: Looking at Clp ATPases as Potential Drug Targets. Antibiotics (Basel) 2022; 11:antibiotics11091218. [PMID: 36139999 PMCID: PMC9495089 DOI: 10.3390/antibiotics11091218] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/05/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
Bacterial antibiotic resistance is rapidly growing globally and poses a severe health threat as the number of multidrug resistant (MDR) and extensively drug-resistant (XDR) bacteria increases. The observed resistance is partially due to natural evolution and to a large extent is attributed to antibiotic misuse and overuse. As the rate of antibiotic resistance increases, it is crucial to develop new drugs to address the emergence of MDR and XDR pathogens. A variety of strategies are employed to address issues pertaining to bacterial antibiotic resistance and these strategies include: (1) the anti-virulence approach, which ultimately targets virulence factors instead of killing the bacterium, (2) employing antimicrobial peptides that target key proteins for bacterial survival and, (3) phage therapy, which uses bacteriophages to treat infectious diseases. In this review, we take a renewed look at a group of ESKAPE pathogens which are known to cause nosocomial infections and are able to escape the bactericidal actions of antibiotics by reducing the efficacy of several known antibiotics. We discuss previously observed escape mechanisms and new possible therapeutic measures to combat these pathogens and further suggest caseinolytic proteins (Clp) as possible therapeutic targets to combat ESKAPE pathogens. These proteins have displayed unmatched significance in bacterial growth, viability and virulence upon chronic infection and under stressful conditions. Furthermore, several studies have showed promising results with targeting Clp proteins in bacterial species, such as Mycobacterium tuberculosis, Staphylococcus aureus and Bacillus subtilis.
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14
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d’Andrea FB, Poulton NC, Froom R, Tam K, Campbell EA, Rock JM. The essential M. tuberculosis Clp protease is functionally asymmetric in vivo. SCIENCE ADVANCES 2022; 8:eabn7943. [PMID: 35507665 PMCID: PMC9067928 DOI: 10.1126/sciadv.abn7943] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
The Clp protease system is a promising, noncanonical drug target against Mycobacterium tuberculosis (Mtb). Unlike in Escherichia coli, the Mtb Clp protease consists of two distinct proteolytic subunits, ClpP1 and ClpP2, which hydrolyze substrates delivered by the chaperones ClpX and ClpC1. While biochemical approaches uncovered unique aspects of Mtb Clp enzymology, its essentiality complicates in vivo studies. To address this gap, we leveraged new genetic tools to mechanistically interrogate the in vivo essentiality of the Mtb Clp protease. While validating some aspects of the biochemical model, we unexpectedly found that only the proteolytic activity of ClpP1, but not of ClpP2, is essential for substrate degradation and Mtb growth and infection. Our observations not only support a revised model of Mtb Clp biology, where ClpP2 scaffolds chaperone binding while ClpP1 provides the essential proteolytic activity of the complex; they also have important implications for the ongoing development of inhibitors toward this emerging therapeutic target.
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Affiliation(s)
- Felipe B. d’Andrea
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, Weill Cornell Medicine, New York, NY, USA
| | - Nicholas C. Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | - Ruby Froom
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA
| | - Kayan Tam
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
| | | | - Jeremy M. Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY, USA
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15
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Sauer RT, Fei X, Bell TA, Baker TA. Structure and function of ClpXP, a AAA+ proteolytic machine powered by probabilistic ATP hydrolysis. Crit Rev Biochem Mol Biol 2022; 57:188-204. [PMID: 34923891 PMCID: PMC9871882 DOI: 10.1080/10409238.2021.1979461] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
ClpXP is an archetypical AAA+ protease, consisting of ClpX and ClpP. ClpX is an ATP-dependent protein unfoldase and polypeptide translocase, whereas ClpP is a self-compartmentalized peptidase. ClpXP is currently the only AAA+ protease for which high-resolution structures exist, the molecular basis of recognition for a protein substrate is understood, extensive biochemical and genetic analysis have been performed, and single-molecule optical trapping has allowed direct visualization of the kinetics of substrate unfolding and translocation. In this review, we discuss our current understanding of ClpXP structure and function, evaluate competing sequential and probabilistic mechanisms of ATP hydrolysis, and highlight open questions for future exploration.
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Affiliation(s)
- Robert T. Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Xue Fei
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tristan A. Bell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tania A. Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
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16
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Mabanglo MF, Houry WA. Recent structural insights into the mechanism of ClpP protease regulation by AAA+ chaperones and small molecules. J Biol Chem 2022; 298:101781. [PMID: 35245501 PMCID: PMC9035409 DOI: 10.1016/j.jbc.2022.101781] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 11/19/2022] Open
Abstract
ClpP is a highly conserved serine protease that is a critical enzyme in maintaining protein homeostasis and is an important drug target in pathogenic bacteria and various cancers. In its functional form, ClpP is a self-compartmentalizing protease composed of two stacked heptameric rings that allow protein degradation to occur within the catalytic chamber. ATPase chaperones such as ClpX and ClpA are hexameric ATPases that form larger complexes with ClpP and are responsible for the selection and unfolding of protein substrates prior to their degradation by ClpP. Although individual structures of ClpP and ATPase chaperones have offered mechanistic insights into their function and regulation, their structures together as a complex have only been recently determined to high resolution. Here, we discuss the cryoelectron microscopy structures of ClpP-ATPase complexes and describe findings previously inaccessible from individual Clp structures, including how a hexameric ATPase and a tetradecameric ClpP protease work together in a functional complex. We then discuss the consensus mechanism for substrate unfolding and translocation derived from these structures, consider alternative mechanisms, and present their strengths and limitations. Finally, new insights into the allosteric control of ClpP gained from studies using small molecules and gain or loss-of-function mutations are explored. Overall, this review aims to underscore the multilayered regulation of ClpP that may present novel ideas for structure-based drug design.
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Affiliation(s)
- Mark F Mabanglo
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Walid A Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada; Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
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17
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Illigmann A, Thoma Y, Pan S, Reinhardt L, Brötz-Oesterhelt H. Contribution of the Clp Protease to Bacterial Survival and Mitochondrial Homoeostasis. Microb Physiol 2021; 31:260-279. [PMID: 34438398 DOI: 10.1159/000517718] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/07/2021] [Indexed: 11/19/2022]
Abstract
Fast adaptation to environmental changes ensures bacterial survival, and proteolysis represents a key cellular process in adaptation. The Clp protease system is a multi-component machinery responsible for protein homoeostasis, protein quality control, and targeted proteolysis of transcriptional regulators in prokaryotic cells and prokaryote-derived organelles of eukaryotic cells. A functional Clp protease complex consists of the tetradecameric proteolytic core ClpP and a hexameric ATP-consuming Clp-ATPase, several of which can associate with the same proteolytic core. Clp-ATPases confer substrate specificity by recognising specific degradation tags, and further selectivity is conferred by adaptor proteins, together allowing for a fine-tuned degradation process embedded in elaborate regulatory networks. This review focuses on the contribution of the Clp protease system to prokaryotic survival and summarises the current state of knowledge for exemplary bacteria in an increasing degree of interaction with eukaryotic cells. Starting from free-living bacteria as exemplified by a non-pathogenic and a pathogenic member of the Firmicutes, i.e., Bacillus subtilis and Staphylococcus aureus, respectively, we turn our attention to facultative and obligate intracellular bacterial pathogens, i.e., Mycobacterium tuberculosis, Listeria monocytogenes, and Chlamydia trachomatis, and conclude with mitochondria. Under stress conditions, the Clp protease system exerts its pivotal role in the degradation of damaged proteins and controls the timing and extent of the heat-shock response by regulatory proteolysis. Key regulators of developmental programmes like natural competence, motility, and sporulation are also under Clp proteolytic control. In many pathogenic species, the Clp system is required for the expression of virulence factors and essential for colonising the host. In accordance with its evolutionary origin, the human mitochondrial Clp protease strongly resembles its bacterial counterparts, taking a central role in protein quality control and homoeostasis, energy metabolism, and apoptosis in eukaryotic cells, and several cancer cell types depend on it for proliferation.
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Affiliation(s)
- Astrid Illigmann
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Yvonne Thoma
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Stefan Pan
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Laura Reinhardt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.,Cluster of Excellence Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
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18
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Li Y, Sharma MR, Koripella RK, Banavali NK, Agrawal RK, Ojha AK. Ribosome hibernation: a new molecular framework for targeting nonreplicating persisters of mycobacteria. MICROBIOLOGY-SGM 2021; 167. [PMID: 33555244 DOI: 10.1099/mic.0.001035] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Treatment of tuberculosis requires a multi-drug regimen administered for at least 6 months. The long-term chemotherapy is attributed in part to a minor subpopulation of nonreplicating Mycobacterium tuberculosis cells that exhibit phenotypic tolerance to antibiotics. The origins of these cells in infected hosts remain unclear. Here we discuss some recent evidence supporting the hypothesis that hibernation of ribosomes in M. tuberculosis, induced by zinc starvation, could be one of the primary mechanisms driving the development of nonreplicating persisters in hosts. We further analyse inconsistencies in previously reported studies to clarify the molecular principles underlying mycobacterial ribosome hibernation.
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Affiliation(s)
- Yunlong Li
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Manjuli R Sharma
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Ravi K Koripella
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Nilesh K Banavali
- Department of Biomedical Sciences, University at Albany, Albany, NY, USA.,Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA
| | - Rajendra K Agrawal
- Division of Translational Medicine, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY, USA
| | - Anil K Ojha
- Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY, USA
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19
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Cazzaniga G, Mori M, Chiarelli LR, Gelain A, Meneghetti F, Villa S. Natural products against key Mycobacterium tuberculosis enzymatic targets: Emerging opportunities for drug discovery. Eur J Med Chem 2021; 224:113732. [PMID: 34399099 DOI: 10.1016/j.ejmech.2021.113732] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/15/2021] [Accepted: 07/28/2021] [Indexed: 11/16/2022]
Abstract
For centuries, natural products (NPs) have served as powerful therapeutics against a variety of human ailments. Nowadays, they still represent invaluable resources for the treatment of many diseases, including bacterial infections. After nearly three decades since the World Health Organization's (WHO) declaration of tuberculosis (TB) as a global health emergency, Mycobacterium tuberculosis (Mtb) continues to claim millions of lives, remaining among the leading causes of death worldwide. In the last years, several efforts have been devoted to shortening and improving treatment outcomes, and to overcoming the increasing resistance phenomenon. Nature has always provided a virtually unlimited source of bioactive molecules, which have inspired the development of new drugs. NPs are characterized by an exceptional chemical and structural diversity, the result of millennia of evolutionary responses to various stimuli. Thanks to their favorable structural features and their enzymatic origin, they are naturally prone to bind proteins and exhibit bioactivities. Furthermore, their worldwide distribution and ease of accessibility has contributed to promote investigations on their activity. Overall, these characteristics make NPs excellent models for the design of novel therapeutics. This review offers a critical and comprehensive overview of the most promising NPs, isolated from plants, fungi, marine species, and bacteria, endowed with inhibitory properties against traditional and emerging mycobacterial enzymatic targets. A selection of 86 compounds is here discussed, with a special emphasis on their biological activity, structure-activity relationships, and mechanism of action. Our study corroborates the antimycobacterial potential of NPs, substantiating their relevance in future drug discovery and development efforts.
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Affiliation(s)
- Giulia Cazzaniga
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
| | - Matteo Mori
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
| | - Laurent Roberto Chiarelli
- Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, via A. Ferrata 9, 27100, Pavia, Italy
| | - Arianna Gelain
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
| | - Fiorella Meneghetti
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy.
| | - Stefania Villa
- Department of Pharmaceutical Sciences, University of Milan, via L. Mangiagalli 25, 20133, Milano, Italy
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20
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Brötz-Oesterhelt H, Vorbach A. Reprogramming of the Caseinolytic Protease by ADEP Antibiotics: Molecular Mechanism, Cellular Consequences, Therapeutic Potential. Front Mol Biosci 2021; 8:690902. [PMID: 34109219 PMCID: PMC8182300 DOI: 10.3389/fmolb.2021.690902] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 04/28/2021] [Indexed: 12/14/2022] Open
Abstract
Rising antibiotic resistance urgently calls for the discovery and evaluation of novel antibiotic classes and unique antibiotic targets. The caseinolytic protease Clp emerged as an unprecedented target for antibiotic therapy 15 years ago when it was observed that natural product-derived acyldepsipeptide antibiotics (ADEP) dysregulated its proteolytic core ClpP towards destructive proteolysis in bacterial cells. A substantial database has accumulated since on the interaction of ADEP with ClpP, which is comprehensively compiled in this review. On the molecular level, we describe the conformational control that ADEP exerts over ClpP, the nature of the protein substrates degraded, and the emerging structure-activity-relationship of the ADEP compound class. On the physiological level, we review the multi-faceted antibacterial mechanism, species-dependent killing modes, the activity against carcinogenic cells, and the therapeutic potential of the compound class.
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Affiliation(s)
- Heike Brötz-Oesterhelt
- Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tübingen, Germany.,Cluster of Excellence: Controlling Microbes to Fight Infection, Tübingen, Germany
| | - Andreas Vorbach
- Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tübingen, Germany
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21
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Kahne SC, Darwin KH. Structural determinants of regulated proteolysis in pathogenic bacteria by ClpP and the proteasome. Curr Opin Struct Biol 2021; 67:120-126. [PMID: 33221704 PMCID: PMC8096641 DOI: 10.1016/j.sbi.2020.09.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 01/05/2023]
Abstract
Bacteria use gated proteolytic machines for routine protein quality control and regulated responses to environmental conditions. This review discusses recent advances in understanding the structure and regulation of ClpP proteases, nanomachines widely distributed across bacteria, and the bacterial proteasome, a protease found in relatively few species. For both machines, activators confer substrate specificity. We highlight new data from organisms encoding two ClpP isoforms and the central role of activators as platforms for integrating regulatory signals. Because proteolytic systems contribute to survival and virulence of many bacterial pathogens, understanding their forms and functions enables new approaches to design targeted therapeutics.
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Affiliation(s)
- Shoshanna C Kahne
- New York University Robert Grossman School of Medicine, Department of Microbiology, 430 E. 29th Street, Room 312, New York, NY 10016, USA
| | - K Heran Darwin
- New York University Robert Grossman School of Medicine, Department of Microbiology, 430 E. 29th Street, Room 312, New York, NY 10016, USA.
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22
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Baptista R, Bhowmick S, Shen J, Mur LAJ. Molecular Docking Suggests the Targets of Anti-Mycobacterial Natural Products. Molecules 2021; 26:475. [PMID: 33477495 PMCID: PMC7831053 DOI: 10.3390/molecules26020475] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/06/2021] [Accepted: 01/11/2021] [Indexed: 11/16/2022] Open
Abstract
Tuberculosis (TB) is a major global threat, mostly due to the development of antibiotic-resistant forms of Mycobacterium tuberculosis, the causal agent of the disease. Driven by the pressing need for new anti-mycobacterial agents several natural products (NPs) have been shown to have in vitro activities against M. tuberculosis. The utility of any NP as a drug lead is augmented when the anti-mycobacterial target(s) is unknown. To suggest these, we used a molecular reverse docking approach to predict the interactions of 53 selected anti-mycobacterial NPs against known "druggable" mycobacterial targets ClpP1P2, DprE1, InhA, KasA, PanK, PknB and Pks13. The docking scores/binding free energies were predicted and calculated using AutoDock Vina along with physicochemical and structural properties of the NPs, using PaDEL descriptors. These were compared to the established inhibitor (control) drugs for each mycobacterial target. The specific interactions of the bisbenzylisoquinoline alkaloids 2-nortiliacorinine, tiliacorine and 13'-bromotiliacorinine against the targets PknB and DprE1 (-11.4, -10.9 and -9.8 kcal·mol-1; -12.7, -10.9 and -10.3 kcal·mol-1, respectively) and the lignan α-cubebin and Pks13 (-11.0 kcal·mol-1) had significantly superior docking scores compared to controls. Our approach can be used to suggest predicted targets for the NP to be validated experimentally, but these in silico steps are likely to facilitate drug optimization.
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Affiliation(s)
- Rafael Baptista
- Institute of Biological, Environmental and Rural Sciences, Penglais Campus, Aberystwyth University, Aberystwyth, Wales SY23 2DA, UK; (R.B.); (S.B.)
| | - Sumana Bhowmick
- Institute of Biological, Environmental and Rural Sciences, Penglais Campus, Aberystwyth University, Aberystwyth, Wales SY23 2DA, UK; (R.B.); (S.B.)
| | - Jianying Shen
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Luis A. J. Mur
- Institute of Biological, Environmental and Rural Sciences, Penglais Campus, Aberystwyth University, Aberystwyth, Wales SY23 2DA, UK; (R.B.); (S.B.)
- Artemisinin Research Center, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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23
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Acyldepsipeptide activated ClpP1P2 macromolecule of Leptospira, an ideal Achilles' heel to hamper the cell survival and deregulate ClpP proteolytic activity. Res Microbiol 2021; 172:103797. [PMID: 33460738 DOI: 10.1016/j.resmic.2021.103797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/30/2020] [Accepted: 01/07/2021] [Indexed: 11/22/2022]
Abstract
Antibiotic acyldepsipeptide (ADEP) targets the bacterial ClpP serine protease and can inhibit the growth of numerous bacterial species by activating/dysregulating the protease activity within the cell. The spirochete Leptospira interrogans harbors two ClpP isoforms (LepClpP1 and LepClpP2). Supplementation of ADEP in the Leptospira growth medium resulted in the inhibition of bacterial growth. The ADEP mediated activation of the LepClpP mixture was dependent on the time allowed for the self-assembly of LepClpP1 and LepClpP2. The dynamic light scattering of the LepClpP mixture in the presence of the ADEP indicated a conformational transformation of the LepClpP machinery. Serine 98, a catalytic triad residue of the LepClpP1 in the LepClpP1P2 heterocomplex, was critical for the ADEP mediated activation. The computational prototype of the LepClpP1P2 structure suggested that the hydrophobic pockets wherein the ADEPs or the physiological chaperone ClpX predominantly dock are exclusively present in the LepClpP2 heptamer. Using the ADEP as a tool, this investigation provides an insight into the molecular function of the LepClpP1P2 in a coalition with its ATPase chaperone LepClpX. The shreds of the evidence illustrated in this investigation verify that ADEP1 possesses the ability to control the LepClpP system in an unconventional approach than the other organisms.
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24
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Texier P, Bordes P, Nagpal J, Sala AJ, Mansour M, Cirinesi AM, Xu X, Dougan DA, Genevaux P. ClpXP-mediated Degradation of the TAC Antitoxin is Neutralized by the SecB-like Chaperone in Mycobacterium tuberculosis. J Mol Biol 2021; 433:166815. [PMID: 33450247 DOI: 10.1016/j.jmb.2021.166815] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 12/27/2020] [Accepted: 01/05/2021] [Indexed: 01/31/2023]
Abstract
Bacterial toxin-antitoxin (TA) systems are composed of a deleterious toxin and its antagonistic antitoxin. They are widespread in bacterial genomes and mobile genetic elements, and their functions remain largely unknown. Some TA systems, known as TAC modules, include a cognate SecB-like chaperone that assists the antitoxin in toxin inhibition. Here, we have investigated the involvement of proteases in the activation cycle of the TAC system of the human pathogen Mycobacterium tuberculosis. We show that the deletion of endogenous AAA+ proteases significantly bypasses the need for a dedicated chaperone and identify the mycobacterial ClpXP1P2 complex as the main protease involved in TAC antitoxin degradation. In addition, we show that the ClpXP1P2 degron is located at the extreme C-terminal end of the chaperone addiction (ChAD) region of the antitoxin, demonstrating that ChAD functions as a hub for both chaperone binding and recognition by proteases.
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Affiliation(s)
- Pauline Texier
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Patricia Bordes
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France.
| | - Jyotsna Nagpal
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Ambre Julie Sala
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Moise Mansour
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Anne-Marie Cirinesi
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Xibing Xu
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - David Andrew Dougan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia.
| | - Pierre Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse, France.
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25
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Progression from remodeling to hibernation of ribosomes in zinc-starved mycobacteria. Proc Natl Acad Sci U S A 2020; 117:19528-19537. [PMID: 32723821 PMCID: PMC7431043 DOI: 10.1073/pnas.2013409117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We previously reported that hibernation of 70S ribosomes in mycobacteria is induced as a response to zinc starvation. Because zinc limitation also induces ribosome remodeling, our findings raise questions about the conditions for ribosome remodeling and hibernation. Here, we show that the two processes are induced at different concentrations of zinc and that the caseinolytic protease system plays a crucial role in zinc-dependent inhibition of hibernation during remodeling. The findings offer insights into the molecular pathway underlying the transition from remodeling of ribosomes to hibernation in response to progressive zinc depletion in mycobacteria. This study is also a demonstration of reactivation of hibernating ribosomes by zinc. Finally, this study correlates ribosome hibernation with streptomycin tolerance in Mycobacterium tuberculosis during infection. Zinc starvation in mycobacteria leads to remodeling of ribosomes, in which multiple ribosomal (r-) proteins containing the zinc-binding CXXC motif are replaced by their motif-free paralogues, collectively called C− r-proteins. We previously reported that the 70S C− ribosome is exclusively targeted for hibernation by mycobacterial-specific protein Y (Mpy), which binds to the decoding center and stabilizes the ribosome in an inactive and drug-resistant state. In this study, we delineate the conditions for ribosome remodeling and hibernation and provide further insight into how zinc depletion induces Mpy recruitment to C− ribosomes. Specifically, we show that ribosome hibernation in a batch culture is induced at an approximately two-fold lower cellular zinc concentration than remodeling. We further identify a growth phase in which the C− ribosome remains active, while its hibernation is inhibited by the caseinolytic protease (Clp) system in a zinc-dependent manner. The Clp protease system destabilizes a zinc-bound form of Mpy recruitment factor (Mrf), which is stabilized upon further depletion of zinc, presumably in a zinc-free form. Stabilized Mrf binds to the 30S subunit and recruits Mpy to the ribosome. Replenishment of zinc to cells harboring hibernating ribosomes restores Mrf instability and dissociates Mpy from the ribosome. Finally, we demonstrate zinc-responsive binding of Mpy to ribosomes in Mycobacterium tuberculosis (Mtb) and show Mpy-dependent antibiotic tolerance of Mtb in mouse lungs. Together, we propose that ribosome hibernation is a specific and conserved response to zinc depletion in both environmental and pathogenic mycobacteria.
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Malik IT, Pereira R, Vielberg M, Mayer C, Straetener J, Thomy D, Famulla K, Castro H, Sass P, Groll M, Brötz‐Oesterhelt H. Functional Characterisation of ClpP Mutations Conferring Resistance to Acyldepsipeptide Antibiotics in Firmicutes. Chembiochem 2020; 21:1997-2012. [PMID: 32181548 PMCID: PMC7496096 DOI: 10.1002/cbic.201900787] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Indexed: 12/18/2022]
Abstract
Acyldepsipeptide (ADEP) is an exploratory antibiotic with a novel mechanism of action. ClpP, the proteolytic core of the caseinolytic protease, is deregulated towards unrestrained proteolysis. Here, we report on the mechanism of ADEP resistance in Firmicutes. This bacterial phylum contains important pathogens that are relevant for potential ADEP therapy. For Staphylococcus aureus, Bacillus subtilis, enterococci and streptococci, spontaneous ADEP-resistant mutants were selected in vitro at a rate of 10-6 . All isolates carried mutations in clpP. All mutated S. aureus ClpP proteins characterised in this study were functionally impaired; this increased our understanding of the mode of operation of ClpP. For molecular insights, crystal structures of S. aureus ClpP bound to ADEP4 were determined. Well-resolved N-terminal domains in the apo structure allow the pore-gating mechanism to be followed. The compilation of mutations presented here indicates residues relevant for ClpP function and suggests that ADEP resistance will occur at a lower rate during the infection process.
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Affiliation(s)
- Imran T. Malik
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Rebeca Pereira
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
- Laboratory of AntibioticsBiochemistryEducation and Molecular modelingDepartment of Molecular and Cell BiologyFederal Fluminense UniversityOuteiro São João Batista, CentroNiterói24210130Rio de JaneiroBrazil
| | - Marie‐Theres Vielberg
- Center for Integrated Protein Science at the Department of ChemistryTechnical University MunichLichtenbergstrasse 485748GarchingGermany
| | - Christian Mayer
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Jan Straetener
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Dhana Thomy
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Kirsten Famulla
- Institute for Pharmaceutical Biology and BiotechnologyUniversity of DüsseldorfUniversitätsstrasse 1, Building 26.23.40225DüsseldorfGermany
| | - Helena Castro
- Laboratory of AntibioticsBiochemistryEducation and Molecular modelingDepartment of Molecular and Cell BiologyFederal Fluminense UniversityOuteiro São João Batista, CentroNiterói24210130Rio de JaneiroBrazil
| | - Peter Sass
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
| | - Michael Groll
- Center for Integrated Protein Science at the Department of ChemistryTechnical University MunichLichtenbergstrasse 485748GarchingGermany
| | - Heike Brötz‐Oesterhelt
- Interfaculty Institute of Microbiology and Infection MedicineDept. of Microbial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 2872076TuebingenGermany
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Cell Division Protein FtsZ Is Unfolded for N-Terminal Degradation by Antibiotic-Activated ClpP. mBio 2020; 11:mBio.01006-20. [PMID: 32605984 PMCID: PMC7327170 DOI: 10.1128/mbio.01006-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Acyldepsipeptide (ADEP) antibiotics effectively kill multidrug-resistant Gram-positive pathogens, including vancomycin-resistant enterococcus, penicillin-resistant Streptococcus pneumoniae (PRSP), and methicillin-resistant Staphylococcus aureus (MRSA). The antibacterial activity of ADEP depends on a new mechanism of action, i.e., the deregulation of bacterial protease ClpP that leads to bacterial self-digestion. Our data allow new insights into the mode of ADEP action by providing a molecular explanation for the distinct bacterial phenotypes observed at low versus high ADEP concentrations. In addition, we show that ClpP alone, in the absence of any unfoldase or energy-consuming system, and only activated by the small molecule antibiotic ADEP, leads to the unfolding of the cell division protein FtsZ. Antibiotic acyldepsipeptides (ADEPs) deregulate ClpP, the proteolytic core of the bacterial Clp protease, thereby inhibiting its native functions and concomitantly activating it for uncontrolled proteolysis of nonnative substrates. Importantly, although ADEP-activated ClpP is assumed to target multiple polypeptide and protein substrates in the bacterial cell, not all proteins seem equally susceptible. In Bacillus subtilis, the cell division protein FtsZ emerged to be particularly sensitive to degradation by ADEP-activated ClpP at low inhibitory ADEP concentrations. In fact, FtsZ is the only bacterial protein that has been confirmed to be degraded in vitro as well as within bacterial cells so far. However, the molecular reason for this preferred degradation remained elusive. Here, we report the unexpected finding that ADEP-activated ClpP alone, in the absence of any Clp-ATPase, leads to an unfolding and subsequent degradation of the N-terminal domain of FtsZ, which can be prevented by the stabilization of the FtsZ fold via nucleotide binding. At elevated antibiotic concentrations, importantly, the C terminus of FtsZ is notably targeted for degradation in addition to the N terminus. Our results show that different target structures are more or less accessible to ClpP, depending on the ADEP level present. Moreover, our data assign a Clp-ATPase-independent protein unfolding capability to the ClpP core of the bacterial Clp protease and suggest that the protein fold of FtsZ may be more flexible than previously anticipated.
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28
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Ziemski M, Leodolter J, Taylor G, Kerschenmeyer A, Weber-Ban E. Genome-wide interaction screen for Mycobacterium tuberculosis ClpCP protease reveals toxin-antitoxin systems as a major substrate class. FEBS J 2020; 288:111-126. [PMID: 32301575 DOI: 10.1111/febs.15335] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/12/2020] [Accepted: 04/14/2020] [Indexed: 12/30/2022]
Abstract
In Mycobacterium tuberculosis (Mtb), the Clp protease degradation pathway, mediated by the modular ClpCP and ClpXP protease complexes, is essential for growth and presents an attractive drug target. Employing a bacterial adenylate cyclase two-hybrid (BACTH) screening approach that we adapted to screen the proteome of an Mtb ORF library, we identify protein interaction partners of the ClpC1 chaperone on a genome-wide level. Our results demonstrate that bipartite type II toxin-antitoxin (TA) systems represent a major substrate class. Out of the 67 type II TA systems known in Mtb, 25 appear as ClpC1 interaction partners in the BACTH screen, including members of the VapBC, MazEF, and ParDE families, as well as a RelBE member that was identified biochemically. We show that antitoxins of the Vap and Rel families are degraded by ClpCP in vitro. We also demonstrate that ClpCP is responsible for mediating the N-end rule pathway, since the adaptor protein ClpS supports ClpC-dependent degradation of an N-end rule model substrate in vitro.
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Affiliation(s)
- Michal Ziemski
- Institute of Molecular Biology & Biophysics, ETH Zurich, Switzerland
| | - Julia Leodolter
- Institute of Molecular Biology & Biophysics, ETH Zurich, Switzerland
| | - Gabrielle Taylor
- Institute of Molecular Biology & Biophysics, ETH Zurich, Switzerland
| | | | - Eilika Weber-Ban
- Institute of Molecular Biology & Biophysics, ETH Zurich, Switzerland
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29
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An allosteric switch regulates Mycobacterium tuberculosis ClpP1P2 protease function as established by cryo-EM and methyl-TROSY NMR. Proc Natl Acad Sci U S A 2020; 117:5895-5906. [PMID: 32123115 PMCID: PMC7084164 DOI: 10.1073/pnas.1921630117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The 300-kDa ClpP1P2 protease from Mycobacterium tuberculosis collaborates with the AAA+ (ATPases associated with a variety of cellular activities) unfoldases, ClpC1 and ClpX, to degrade substrate proteins. Unlike in other bacteria, all of the components of the Clp system are essential for growth and virulence of mycobacteria, and their inhibitors show promise as antibiotics. MtClpP1P2 is unique in that it contains a pair of distinct ClpP1 and ClpP2 rings and also requires the presence of activator peptides, such as benzoyl-leucyl-leucine (Bz-LL), for function. Understanding the structural basis for this requirement has been elusive but is critical for the rational design and improvement of antituberculosis (anti-TB) therapeutics that target the Clp system. Here, we present a combined biophysical and biochemical study to explore the structure-dynamics-function relationship in MtClpP1P2. Electron cryomicroscopy (cryo-EM) structures of apo and acyldepsipeptide-bound MtClpP1P2 explain their lack of activity by showing loss of a key β-sheet in a sequence known as the handle region that is critical for the proper formation of the catalytic triad. Methyl transverse relaxation-optimized spectroscopy (TROSY)-based NMR, cryo-EM, and biochemical assays show that, on binding Bz-LL or covalent inhibitors, MtClpP1P2 undergoes a conformational change from an inactive compact state to an active extended structure that can be explained by a modified Monod-Wyman-Changeux model. Our study establishes a critical role for the handle region as an on/off switch for function and shows extensive allosteric interactions involving both intra- and interring communication that regulate MtClpP1P2 activity and that can potentially be exploited by small molecules to target M. tuberculosis.
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30
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Fei X, Bell TA, Jenni S, Stinson BM, Baker TA, Harrison SC, Sauer RT. Structures of the ATP-fueled ClpXP proteolytic machine bound to protein substrate. eLife 2020; 9:52774. [PMID: 32108573 PMCID: PMC7112951 DOI: 10.7554/elife.52774] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/27/2020] [Indexed: 01/11/2023] Open
Abstract
ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the E. coli enzyme that show how asymmetric hexameric rings of ClpX bind symmetric heptameric rings of ClpP and interact with protein substrates. Subunits in the ClpX hexamer assume a spiral conformation and interact with two-residue segments of substrate in the axial channel, as observed for other AAA+ proteases and protein-remodeling machines. Strictly sequential models of ATP hydrolysis and a power stroke that moves two residues of the substrate per translocation step have been inferred from these structural features for other AAA+ unfoldases, but biochemical and single-molecule biophysical studies indicate that ClpXP operates by a probabilistic mechanism in which five to eight residues are translocated for each ATP hydrolyzed. We propose structure-based models that could account for the functional results.
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Affiliation(s)
- Xue Fei
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Tristan A Bell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Simon Jenni
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States
| | - Benjamin M Stinson
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
| | - Tania A Baker
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - Stephen C Harrison
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States.,Howard Hughes Medical Institute, Chevy Chase, United States
| | - Robert T Sauer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
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31
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Nagpal J, Paxman JJ, Zammit JE, Thomas AA, Truscott KN, Heras B, Dougan DA. Molecular and structural insights into an asymmetric proteolytic complex (ClpP1P2) from Mycobacterium smegmatis. Sci Rep 2019; 9:18019. [PMID: 31792243 PMCID: PMC6889138 DOI: 10.1038/s41598-019-53736-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/25/2019] [Indexed: 11/09/2022] Open
Abstract
The ClpP protease is found in all kingdoms of life, from bacteria to humans. In general, this protease forms a homo-oligomeric complex composed of 14 identical subunits, which associates with its cognate ATPase in a symmetrical manner. Here we show that, in contrast to this general architecture, the Clp protease from Mycobacterium smegmatis (Msm) forms an asymmetric hetero-oligomeric complex ClpP1P2, which only associates with its cognate ATPase through the ClpP2 ring. Our structural and functional characterisation of this complex demonstrates that asymmetric docking of the ATPase component is controlled by both the composition of the ClpP1 hydrophobic pocket (Hp) and the presence of a unique C-terminal extension in ClpP1 that guards this Hp. Our structural analysis of MsmClpP1 also revealed openings in the side-walls of the inactive tetradecamer, which may represent sites for product egress.
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Affiliation(s)
- Jyotsna Nagpal
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Australia
| | - Jason J Paxman
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Australia
| | - Jessica E Zammit
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Australia
| | - Adam A. Thomas
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Australia
| | - Kaye N Truscott
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Australia
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Australia.
| | - David A Dougan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, 3086, Australia.
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32
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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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33
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Griffith EC, Zhao Y, Singh AP, Conlon BP, Tangallapally R, Shadrick WR, Liu J, Wallace MJ, Yang L, Elmore JM, Li Y, Zheng Z, Miller DJ, Cheramie MN, Lee RB, LaFleur MD, Lewis K, Lee RE. Ureadepsipeptides as ClpP Activators. ACS Infect Dis 2019; 5:1915-1925. [PMID: 31588734 DOI: 10.1021/acsinfecdis.9b00245] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Acyldepsipeptides are a unique class of antibiotics that act via allosterically dysregulated activation of the bacterial caseinolytic protease (ClpP). The ability of ClpP activators to kill nongrowing bacteria represents a new opportunity to combat deep-seated biofilm infections. However, the acyldepsipeptide scaffold is subject to rapid metabolism. Herein, we explore alteration of the potentially metabolically reactive α,β unsaturated acyl chain. Through targeted synthesis, a new class of phenyl urea substituted depsipeptide ClpP activators with improved metabolic stability is described. The ureadepsipeptides are potent activators of Staphylococcus aureus ClpP and show activity against Gram-positive bacteria, including S. aureus biofilms. These studies demonstrate that a phenyl urea motif can successfully mimic the double bond, maintaining potency equivalent to acyldepsipeptides but with decreased metabolic liability. Although removal of the double bond from acyldepsipeptides generally has a significant negative impact on potency, structural studies revealed that the phenyl ureadepsipeptides can retain potency through the formation of a third hydrogen bond between the urea and the key Tyr63 residue in the ClpP activation domain. Ureadepsipeptides represent a new class of ClpP activators with improved drug-like properties, potent antibacterial activity, and the tractability to be further optimized.
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Affiliation(s)
- Elizabeth C. Griffith
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Ying Zhao
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Aman P. Singh
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Brian P. Conlon
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Rajendra Tangallapally
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - William R. Shadrick
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Jiuyu Liu
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Miranda J. Wallace
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - John M. Elmore
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Yong Li
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhong Zheng
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Darcie J. Miller
- Department of Structure Biology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Martin N. Cheramie
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Robin B. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Michael D. LaFleur
- Arietis Pharma, 650 Albany Street, Suite 114, Boston, Massachusetts 02118, United States
| | - Kim Lewis
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
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34
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Gatsogiannis C, Balogh D, Merino F, Sieber SA, Raunser S. Cryo-EM structure of the ClpXP protein degradation machinery. Nat Struct Mol Biol 2019; 26:946-954. [PMID: 31582852 PMCID: PMC6783313 DOI: 10.1038/s41594-019-0304-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/19/2019] [Indexed: 12/23/2022]
Abstract
The ClpXP machinery is a two component protease complex performing
targeted protein degradation in bacteria and mitochondria. The complex consists
of the AAA+ chaperone ClpX and the peptidase ClpP. The hexameric ClpX utilizes
the energy of ATP binding and hydrolysis to engage, unfold and translocate
substrates into the catalytic chamber of tetradecameric ClpP where they are
degraded. Formation of the complex involves a symmetry mismatch, since hexameric
AAA+ rings bind axially to the opposing stacked heptameric rings of the
tetradecameric ClpP. Here we present the cryo-EM structure of ClpXP from
Listeria monocytogenes. We unravel the heptamer-hexamer
binding interface and provide novel insights into the ClpX-ClpP crosstalk and
activation mechanism. The comparison with available crystal structures of ClpP
and ClpX in different states allows us to understand important aspects of
ClpXP’s complex mode of action and provides a structural framework for
future pharmacological applications.
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Affiliation(s)
- Christos Gatsogiannis
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Dora Balogh
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany
| | - Felipe Merino
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Stephan A Sieber
- Department of Chemistry, Chair of Organic Chemistry II, Center for Integrated Protein Science (CIPSM), Technische Universität München, Garching, Germany.
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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Felix J, Weinhäupl K, Chipot C, Dehez F, Hessel A, Gauto DF, Morlot C, Abian O, Gutsche I, Velazquez-Campoy A, Schanda P, Fraga H. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. SCIENCE ADVANCES 2019; 5:eaaw3818. [PMID: 31517045 PMCID: PMC6726451 DOI: 10.1126/sciadv.aaw3818] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 08/02/2019] [Indexed: 05/14/2023]
Abstract
Coordinated conformational transitions in oligomeric enzymatic complexes modulate function in response to substrates and play a crucial role in enzyme inhibition and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which has emerged as a drug target against multiple pathogenic bacteria. Activation of different ClpPs by inhibitors has been independently reported from drug development efforts, but no rationale for inhibitor-induced activation has been hitherto proposed. Using an integrated approach that includes x-ray crystallography, solid- and solution-state nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP active-site serine, mimicking a peptide substrate, and induces a concerted allosteric activation of the complex. The bortezomib-activated conformation also exhibits a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric mechanism, where substrate binding to a single subunit locks ClpP into an active conformation optimized for chaperone association and protein processive degradation.
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Affiliation(s)
- Jan Felix
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, F-38044 Grenoble, France
| | - Katharina Weinhäupl
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, F-38044 Grenoble, France
| | - Christophe Chipot
- LPCT, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
- Department of Physics, University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL 61801, USA
| | - François Dehez
- LPCT, UMR 7019 Université de Lorraine CNRS, Vandoeuvre-les-Nancy F-54500, France
- Laboratoire International Associé CNRS and University of Illinois at Urbana−Champaign, Vandoeuvre-les-Nancy F-54506, France
| | - Audrey Hessel
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, F-38044 Grenoble, France
| | - Diego F. Gauto
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, F-38044 Grenoble, France
| | - Cecile Morlot
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, F-38044 Grenoble, France
| | - Olga Abian
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, and Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), 50009 Zaragoza, Spain
- Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), Madrid, Spain
- Aragon Health Sciences Institute (IACS), 50009 Zaragoza, Spain
| | - Irina Gutsche
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, F-38044 Grenoble, France
| | - Adrian Velazquez-Campoy
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Units IQFR-CSIC-BIFI and GBsC-CSIC-BIFI, and Department of Biochemistry and Molecular and Cell Biology, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Aragon Institute for Health Research (IIS Aragon), 50009 Zaragoza, Spain
- Biomedical Research Networking Centre for Liver and Digestive Diseases (CIBERehd), Madrid, Spain
- Fundacion ARAID, Government of Aragon, 50018 Zaragoza, Spain
| | - Paul Schanda
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, F-38044 Grenoble, France
- Corresponding author. (H.F.); (P.S.)
| | - Hugo Fraga
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, IBS, 71 Avenue des Martyrs, F-38044 Grenoble, France
- Departamento de Biomedicina, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- Corresponding author. (H.F.); (P.S.)
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Korman M, Schlussel S, Vishkautzan M, Gur E. Multiple layers of regulation determine the cellular levels of the Pup ligase PafA inMycobacterium smegmatis. Mol Microbiol 2019; 112:620-631. [DOI: 10.1111/mmi.14278] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Maayan Korman
- Department of Life Sciences Ben‐Gurion University of the Negev Beer‐Sheva 84105Israel
| | - Shai Schlussel
- Department of Life Sciences Ben‐Gurion University of the Negev Beer‐Sheva 84105Israel
| | - Marina Vishkautzan
- Department of Life Sciences Ben‐Gurion University of the Negev Beer‐Sheva 84105Israel
- The National Institute for Biotechnology in the Negev Ben‐Gurion University of the Negev Beer‐Sheva84105Israel
| | - Eyal Gur
- Department of Life Sciences Ben‐Gurion University of the Negev Beer‐Sheva 84105Israel
- The National Institute for Biotechnology in the Negev Ben‐Gurion University of the Negev Beer‐Sheva84105Israel
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Lakemeyer M, Bertosin E, Möller F, Balogh D, Strasser R, Dietz H, Sieber SA. Tailored Peptide Phenyl Esters Block ClpXP Proteolysis by an Unusual Breakdown into a Heptamer–Hexamer Assembly. Angew Chem Int Ed Engl 2019; 58:7127-7132. [DOI: 10.1002/anie.201901056] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Markus Lakemeyer
- Center for Integrated Protein Science (CIPSM) at theDepartment of ChemistryTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
| | - Eva Bertosin
- Physics Department and Institute for Advanced StudyTechnische Universität München Am Coulombwall 4a 85748 Garching Germany
| | | | - Dóra Balogh
- Center for Integrated Protein Science (CIPSM) at theDepartment of ChemistryTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
| | - Ralf Strasser
- Dynamic Biosensors GmbH Lochhamerstr. 15 82152 Planegg Germany
| | - Hendrik Dietz
- Physics Department and Institute for Advanced StudyTechnische Universität München Am Coulombwall 4a 85748 Garching Germany
| | - Stephan A. Sieber
- Center for Integrated Protein Science (CIPSM) at theDepartment of ChemistryTechnische Universität München Lichtenbergstr. 4 85747 Garching Germany
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Lakemeyer M, Bertosin E, Möller F, Balogh D, Strasser R, Dietz H, Sieber SA. Blockade der ClpXP‐vermittelten Proteolyse mit maßgeschneiderten Peptid‐Phenylestern durch den ungewöhnlichen Zerfall in eine Heptamer‐Hexamer‐Anordnung. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Markus Lakemeyer
- Center for Integrated Protein Science (CIPSM) amDepartment ChemieTechnische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Eva Bertosin
- Physik Department und Institute for Advanced StudyTechnische Universität München Am Coulombwall 4a 85748 Garching Deutschland
| | - Friederike Möller
- Dynamic Biosensors GmbH Lochhamerstraße 15 82152 Planegg Deutschland
| | - Dóra Balogh
- Center for Integrated Protein Science (CIPSM) amDepartment ChemieTechnische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
| | - Ralf Strasser
- Dynamic Biosensors GmbH Lochhamerstraße 15 82152 Planegg Deutschland
| | - Hendrik Dietz
- Physik Department und Institute for Advanced StudyTechnische Universität München Am Coulombwall 4a 85748 Garching Deutschland
| | - Stephan A. Sieber
- Center for Integrated Protein Science (CIPSM) amDepartment ChemieTechnische Universität München Lichtenbergstraße 4 85747 Garching Deutschland
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Lavey NP, Shadid T, Ballard JD, Duerfeldt AS. Clostridium difficile ClpP Homologues are Capable of Uncoupled Activity and Exhibit Different Levels of Susceptibility to Acyldepsipeptide Modulation. ACS Infect Dis 2019; 5:79-89. [PMID: 30411608 DOI: 10.1021/acsinfecdis.8b00199] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Caseinolytic protease P (ClpP) has emerged as a promising new target for antibacterial development. While ClpPs from single isoform expressing bacteria have been studied in detail, the function and regulation of systems with more than one ClpP homologue are still poorly understood. Herein, we present fundamental studies toward understanding the ClpP system in C. difficile, an anaerobic spore-forming pathogen that contains two chromosomally distant isoforms of ClpP. Examination of proteomic and genomic data suggest that ClpP1 is the primary isoform responsible for normal growth and virulence, but little is known about the function of ClpP2 or the context required for the formation of functional proteases. For the first time in a pathogenic bacterium, we demonstrate that both isoforms are capable of forming operative proteases. Interestingly, ClpP1 is the only homologue that possesses characteristic response to small molecule acyldepsipeptide activation. On the contrary, both ClpP1 and ClpP2 respond to cochaperone activation to degrade an ssrA-tagged substrate. These observations indicate that ClpP2 is less susceptible to acyldepsipeptide activation but retains the ability to interact with a known cochaperone. Homology models reveal no obvious characteristics that would allow one to predict less efficient acyldepsipeptide binding. The reported findings establish the uniqueness of the ClpP system in C. difficile, open new avenues of inquiry, and highlight the importance of more detailed structural, genetic, and biological characterization of the ClpP system in C. difficile.
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Affiliation(s)
- Nathan P. Lavey
- Institute for Natural Products Applications and Research Technologies and Department of Chemistry & Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
| | - Tyler Shadid
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, Oklahoma City, Oklahoma 73014, United States
| | - Jimmy D. Ballard
- Department of Microbiology & Immunology, University of Oklahoma Health Sciences Center, 940 Stanton L. Young Boulevard, Oklahoma City, Oklahoma 73014, United States
| | - Adam S. Duerfeldt
- Institute for Natural Products Applications and Research Technologies and Department of Chemistry & Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Stephenson Life Sciences Research Center, Norman, Oklahoma 73019, United States
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Initial Characterization of the Two ClpP Paralogs of Chlamydia trachomatis Suggests Unique Functionality for Each. J Bacteriol 2018; 201:JB.00635-18. [PMID: 30396899 DOI: 10.1128/jb.00635-18] [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: 10/16/2018] [Accepted: 10/24/2018] [Indexed: 12/28/2022] Open
Abstract
Members of Chlamydia are obligate intracellular bacteria that differentiate between two distinct functional and morphological forms during their developmental cycle, elementary bodies (EBs) and reticulate bodies (RBs). EBs are nondividing small electron-dense forms that infect host cells. RBs are larger noninfectious replicative forms that develop within a membrane-bound vesicle, termed an inclusion. Given the unique properties of each developmental form of this bacterium, we hypothesized that the Clp protease system plays an integral role in proteomic turnover by degrading specific proteins from one developmental form or the other. Chlamydia spp. have five uncharacterized clp genes, clpX, clpC, two clpP paralogs, and clpB In other bacteria, ClpC and ClpX are ATPases that unfold and feed proteins into the ClpP protease to be degraded, and ClpB is a deaggregase. Here, we focused on characterizing the ClpP paralogs. Transcriptional analyses and immunoblotting determined that these genes are expressed midcycle. Bioinformatic analyses of these proteins identified key residues important for activity. Overexpression of inactive clpP mutants in Chlamydia spp. suggested independent function of each ClpP paralog. To further probe these differences, we determined interactions between the ClpP proteins using bacterial two-hybrid assays and native gel analysis of recombinant proteins. Homotypic interactions of the ClpP proteins, but not heterotypic interactions between the ClpP paralogs, were detected. Interestingly, protease activity of ClpP2, but not ClpP1, was detected in vitro This activity was stimulated by antibiotics known to activate ClpP, which also blocked chlamydial growth. Our data suggest the chlamydial ClpP paralogs likely serve distinct and critical roles in this important pathogen.IMPORTANCE Chlamydia trachomatis is the leading cause of preventable infectious blindness and of bacterial sexually transmitted infections worldwide. Chlamydiae are developmentally regulated obligate intracellular pathogens that alternate between two functional and morphologic forms, with distinct repertoires of proteins. We hypothesize that protein degradation is a critical aspect to the developmental cycle. A key system involved in protein turnover in bacteria is the Clp protease system. Here, we characterized the two chlamydial ClpP paralogs by examining their expression in Chlamydia spp., their ability to oligomerize, and their proteolytic activity. This work will help understand the evolutionarily diverse Clp proteases in the context of intracellular organisms, which may aid in the study of other clinically relevant intracellular bacteria.
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Wong KS, Mabanglo MF, Seraphim TV, Mollica A, Mao YQ, Rizzolo K, Leung E, Moutaoufik MT, Hoell L, Phanse S, Goodreid J, Barbosa LR, Ramos CH, Babu M, Mennella V, Batey RA, Schimmer AD, Houry WA. Acyldepsipeptide Analogs Dysregulate Human Mitochondrial ClpP Protease Activity and Cause Apoptotic Cell Death. Cell Chem Biol 2018; 25:1017-1030.e9. [DOI: 10.1016/j.chembiol.2018.05.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 04/14/2018] [Accepted: 05/18/2018] [Indexed: 12/17/2022]
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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: 87] [Impact Index Per Article: 14.5] [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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Liu P, Yang Y, Ju Y, Tang Y, Sang Z, Chen L, Yang T, An Q, Zhang T, Luo Y. Design, synthesis and biological evaluation of novel pyrrole derivatives as potential ClpP1P2 inhibitor against Mycobacterium tuberculosis. Bioorg Chem 2018; 80:422-432. [PMID: 30005200 DOI: 10.1016/j.bioorg.2018.06.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 05/21/2018] [Accepted: 06/03/2018] [Indexed: 02/05/2023]
Abstract
In an effort to discover novel inhibitors of M. tuberculosis Caseinolytic proteases (ClpP1P2), a combination strategy of virtual high-throughput screening and in vitro assay was employed and a new pyrrole compound, 1-(2-chloro-6-fluorobenzyl)-2, 5-dimethyl-4-((phenethylamino)methyl)-1H-pyrrole-3-carboxylate was found to display inhibitory effects against H37Ra with an MIC value of 77 µM. In order for discovery of more potent anti-tubercular agents that inhibit ClpP1P2 peptidase in M. tuberculosis, a series of pyrrole derivatives were designed and synthesized based on this hit compound. The synthesized compounds were evaluated forin vitrostudies against ClpP1P2 peptidase and anti-tubercular activities were also evaluated. The most promising compounds 2-(4-bromophenyl)-N-((1-(2-chloro-6-fluorophenyl)-2, 5-dimethyl-1H- pyrrolyl)methyl)ethan-1-aminehydrochloride 7d, ethyl 4-(((4-bromophenethyl) amino) methyl)-2,5-dimethyl-1-phenyl-1H-pyrrole-3-carboxylate hydrochloride 13i, ethyl 1-(4-chlorophenyl)-4-(((2-fluorophenethyl)amino)methyl)-2-methyl-5-phenyl-1H-pyrrole-3-carboxylate hydrochloride 13n exhibited favorable anti-mycobacterial activity with MIC value at 5 µM against Mtb H37Ra, respectively.
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Affiliation(s)
- Pingxian Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yang Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yuan Ju
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Yunxiang Tang
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China; Institute of Physical Science and Information Technology, Anhui University, Hefei 230601, China
| | - Zitai Sang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Lijuan Chen
- Guangdong Zhongsheng Pharmaceutical Co., Ltd, Dongguan, Guangdong 523325, China
| | - Tao Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
| | - Qi An
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Regenerative Medicine and Health Guangdong Laboratory (GRMH-GDL), Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou 510530, China.
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
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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: 41] [Impact Index Per Article: 5.9] [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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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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Abstract
The Mycobacterium tuberculosis (Mtb) serine protease Hip1 (hydrolase important for pathogenesis; Rv2224c) promotes tuberculosis (TB) pathogenesis by impairing host immune responses through proteolysis of a protein substrate, Mtb GroEL2. The cell surface localization of Hip1 and its immunomodulatory functions make Hip1 a good drug target for new adjunctive immune therapies for TB. Here, we report the crystal structure of Hip1 to a resolution of 2.6 Å and the kinetic studies of the enzyme against model substrates and the protein GroEL2. The structure shows a two-domain protein, one of which contains the catalytic residues that are the signature of a serine protease. Surprisingly, a threonine is located within the active site close enough to hydrogen bond with the catalytic residues Asp463 and His490. Mutation of this residue, Thr466, to alanine established its importance for function. Our studies provide insights into the structure of a member of a novel family of proteases. Knowledge of the Hip1 structure will aid in designing inhibitors that could block Hip1 activity.
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Moreira W, Santhanakrishnan S, Dymock BW, Dick T. Bortezomib Warhead-Switch Confers Dual Activity against Mycobacterial Caseinolytic Protease and Proteasome and Selectivity against Human Proteasome. Front Microbiol 2017; 8:746. [PMID: 28496439 PMCID: PMC5406460 DOI: 10.3389/fmicb.2017.00746] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 04/11/2017] [Indexed: 11/13/2022] Open
Abstract
Mycobacteria harbor two main degradative proteolytic machineries, the caseinolytic protease ClpP1P2 and a proteasome. We recently showed that Bortezomib inhibits ClpP1P2 and exhibits whole cell activity against Mycobacterium tuberculosis. Bortezomib, a dipeptide with a boronic acid warhead, is a human proteasome inhibitor approved for cancer therapy. The boronic acid warhead of the compound has been shown to drive potency against both the human proteasome and ClpP1P2 protease. Selectivity for the bacterial ClpP1P2 protease over the human proteasome is lacking but needs to be achieved to move this new anti-tuberculosis lead forward. In this study we explored whether an alternative warhead could influence Bortezomib's selectivity. We synthesized an analog containing a chloromethyl ketone instead of the boronic acid warhead and determined potencies against the bacterial and human enzymes. Surprisingly, the analog retained activity against mycobacterial ClpP1P2 and was active against the mycobacterial proteasome, but was devoid of activity against the human proteasome. Interrogation of a set of chloromethyl ketone peptides identified three additional compounds similarly inhibiting both ClpP1P2 and the proteasome in the bacteria while leaving the human proteasome untouched. Finally, we showed that these compounds display bactericidal activity against M. tuberculosis with cytotoxicity ranging from acceptable to undetectable. These results suggest that selectivity over the human proteasome is achievable. Selectivity, together with dual-targeting of mycobacterial ClpP1P2 and proteasome makes this new scaffold an attractive starting point for optimization.
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Affiliation(s)
- Wilfried Moreira
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of SingaporeSingapore, Singapore
| | | | - Brian W Dymock
- Department of Pharmacy, National University of SingaporeSingapore, Singapore
| | - Thomas Dick
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of SingaporeSingapore, Singapore.,Public Health Research Institute, New Jersey Medical School, Rutgers, The State University of New JerseyNewark, NJ, USA
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Towards Selective Mycobacterial ClpP1P2 Inhibitors with Reduced Activity against the Human Proteasome. Antimicrob Agents Chemother 2017; 61:AAC.02307-16. [PMID: 28193668 PMCID: PMC5404560 DOI: 10.1128/aac.02307-16] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/28/2017] [Indexed: 12/02/2022] Open
Abstract
Mycobacterium tuberculosis is responsible for the greatest number of deaths worldwide due to a bacterial agent. We recently identified bortezomib (Velcade; compound 1) as a promising antituberculosis (anti-TB) compound. We showed that compound 1 inhibits the mycobacterial caseinolytic proteases P1 and P2 (ClpP1P2) and exhibits bactericidal activity, and we established compound 1 and ClpP1P2 as an attractive lead/target couple. However, compound 1 is a human-proteasome inhibitor currently approved for cancer therapy and, as such, exhibits significant toxicity. Selective inhibition of the bacterial protease over the human proteasome is desirable in order to maintain antibacterial activity while reducing toxicity. We made use of structural data in order to design a series of dipeptidyl-boronate derivatives of compound 1. We tested these derivatives for whole-cell ClpP1P2 and human-proteasome inhibition as well as bacterial-growth inhibition and identified compounds that were up to 100-fold-less active against the human proteasome but that retained ClpP1P2 and mycobacterial-growth inhibition as well as bactericidal potency. The lead compound, compound 58, had low micromolar ClpP1P2 and anti-M. tuberculosis activity, good aqueous solubility, no cytochrome P450 liabilities, moderate plasma protein binding, and low toxicity in two human liver cell lines, and despite high clearance in microsomes, this compound was only moderately cleared when administered intravenously or orally to mice. Higher-dose oral pharmacokinetics indicated good dose linearity. Furthermore, compound 58 was inhibitory to only 11% of a panel of 62 proteases. Our work suggests that selectivity over the human proteasome can be achieved with a drug-like template while retaining potency against ClpP1P2 and, crucially, anti-M. tuberculosis activity.
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Two Isoforms of Clp Peptidase in Pseudomonas aeruginosa Control Distinct Aspects of Cellular Physiology. J Bacteriol 2017; 199:JB.00568-16. [PMID: 27849175 DOI: 10.1128/jb.00568-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/20/2016] [Indexed: 02/07/2023] Open
Abstract
Caseinolytic peptidases (ClpPs) regulate diverse aspects of cellular physiology in bacteria. Some species have multiple ClpPs, including the opportunistic pathogen Pseudomonas aeruginosa, in which there is an archetypical isoform, ClpP1, and a second isoform, ClpP2, about which little is known. Here, we use phenotypic assays to investigate the biological roles of ClpP1 and ClpP2 and biochemical assays to characterize purified ClpP1, ClpP2, ClpX, and ClpA. Interestingly, ClpP1 and ClpP2 have distinct intracellular roles for motility, pigment production, iron scavenging, and biofilm formation. Of particular interest, ClpP2, but not ClpP1, is required for microcolony organization, where multicellular organized structures first form on the pathway to biofilm production. We found that purified ClpP1 with ClpX or ClpA was enzymatically active, yet to our surprise, ClpP2 was inactive and not fully assembled in vitro; attempts to assist ClpP2 assembly and activation by mixing with the other Clp components failed to turn on ClpP2, as did solution conditions that have helped activate other ClpPs in vitro We postulate that the active form of ClpP2 has yet to be discovered, and we present several potential models to explain its activation as well as the unique role ClpP2 plays in the development of the clinically important biofilms in P. aeruginosaIMPORTANCEPseudomonas aeruginosa is responsible for severe infections of immunocompromised patients. Our work demonstrates that two different isoforms of the Clp peptidase, ClpP1 and ClpP2, control distinct aspects of cellular physiology for this organism. In particular, we identify ClpP2 as being necessary for microcolony organization. Pure active forms of ClpP1 and either ClpX or ClpA were characterized as assembled and active, and ClpP2 was incompletely assembled and inactive. By establishing both the unique biological roles of ClpP1 and ClpP2 and their initial biochemical assemblies, we have set the stage for important future work on the structure, function, and biological targets of Clp proteolytic enzymes in this important opportunistic pathogen.
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Malik IT, Brötz-Oesterhelt H. Conformational control of the bacterial Clp protease by natural product antibiotics. Nat Prod Rep 2017; 34:815-831. [DOI: 10.1039/c6np00125d] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Natural products targeting the bacterial Clp protease unravel key interfaces for protein–protein–interaction and long-distance conformational control.
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Affiliation(s)
- I. T. Malik
- Department of Microbial Bioactive Compounds
- Interfaculty Institute of Microbiology and Infection Medicine
- University of Tuebingen
- Germany
| | - H. Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds
- Interfaculty Institute of Microbiology and Infection Medicine
- University of Tuebingen
- Germany
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