1
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Ishikawa F, Homma M, Tanabe G, Uchihashi T. Protein degradation by a component of the chaperonin-linked protease ClpP. Genes Cells 2024. [PMID: 38965067 DOI: 10.1111/gtc.13141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/03/2024] [Accepted: 06/19/2024] [Indexed: 07/06/2024]
Abstract
In cells, proteins are synthesized, function, and degraded (dead). Protein synthesis (spring) is important for the life of proteins. However, how proteins die is equally important for organisms. Proteases are secreted from cells and used as nutrients to break down external proteins. Proteases degrade unwanted and harmful cellular proteins. In eukaryotes, a large enzyme complex called the proteasome is primarily responsible for cellular protein degradation. Prokaryotes, such as bacteria, have similar protein degradation systems. In this review, we describe the structure and function of the ClpXP complex in the degradation system, which is an ATP-dependent protease in bacterial cells, with a particular focus on ClpP.
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Affiliation(s)
| | - Michio Homma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, Osaka, Japan
| | - Takayuki Uchihashi
- Division of Material Science, Graduate School of Science, Nagoya University, Nagoya, Japan
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2
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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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3
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Won HI, Zinga S, Kandror O, Akopian T, Wolf ID, Schweber JTP, Schmid EW, Chao MC, Waldor M, Rubin EJ, Zhu J. Targeted protein degradation in mycobacteria uncovers antibacterial effects and potentiates antibiotic efficacy. Nat Commun 2024; 15:4065. [PMID: 38744895 PMCID: PMC11094019 DOI: 10.1038/s41467-024-48506-8] [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: 02/14/2023] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) represent a new therapeutic modality involving selectively directing disease-causing proteins for degradation through proteolytic systems. Our ability to exploit targeted protein degradation (TPD) for antibiotic development remains nascent due to our limited understanding of which bacterial proteins are amenable to a TPD strategy. Here, we use a genetic system to model chemically-induced proximity and degradation to screen essential proteins in Mycobacterium smegmatis (Msm), a model for the human pathogen M. tuberculosis (Mtb). By integrating experimental screening of 72 protein candidates and machine learning, we find that drug-induced proximity to the bacterial ClpC1P1P2 proteolytic complex leads to the degradation of many endogenous proteins, especially those with disordered termini. Additionally, TPD of essential Msm proteins inhibits bacterial growth and potentiates the effects of existing antimicrobial compounds. Together, our results provide biological principles to select and evaluate attractive targets for future Mtb PROTAC development, as both standalone antibiotics and potentiators of existing antibiotic efficacy.
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Affiliation(s)
- Harim I Won
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Samuel Zinga
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Olga Kandror
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Tatos Akopian
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ian D Wolf
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Jessica T P Schweber
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ernst W Schmid
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Blavatnik Institute, Boston, MA, 02115, USA
| | - Michael C Chao
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Maya Waldor
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
| | - Junhao Zhu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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4
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Ishikawa F, Homma M, Tanabe G, Uchihashi T. [Protein degradation in bacteria: focus on the ClpP protease]. Nihon Saikingaku Zasshi 2024; 79:1-13. [PMID: 38382970 DOI: 10.3412/jsb.79.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Proteins in the cells are born (synthesized), work, and die (decomposed). In the life of a protein, its birth is obviously important, but how it dies is equally important in living organisms. Proteases secreted into the outside of cells are used to decompose the external proteins and the degradation products are taken as the nutrients. On the other hand, there are also proteases that decompose unnecessary or harmful proteins which are generated in the cells. In eukaryotes, a large enzyme complex called the proteasome is primarily responsible for degradation of such proteins. Bacteria, which are prokaryotes, have a similar system as the proteasome. We would like to explain the bacterial degradation system of proteins or the death of proteins, which is performed by ATP-dependent protease Clp, with a particular focus on the ClpXP complex, and with an aspect as a target for antibiotics against bacteria.
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Affiliation(s)
| | - Michio Homma
- Division of Physics, Graduate School of Science, Nagoya University
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5
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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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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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7
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Hong J, Duc NM, Jeong BC, Cho S, Shetye G, Cao J, Lee H, Jeong C, Lee H, Suh JW. Identification of the inhibitory mechanism of ecumicin and rufomycin 4-7 on the proteolytic activity of Mycobacterium tuberculosis ClpC1/ClpP1/ClpP2 complex. Tuberculosis (Edinb) 2023; 138:102298. [PMID: 36580851 PMCID: PMC9892302 DOI: 10.1016/j.tube.2022.102298] [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: 08/29/2022] [Revised: 12/15/2022] [Accepted: 12/18/2022] [Indexed: 12/25/2022]
Abstract
Ecumicin and rufomycin 4-7 disrupt protein homeostasis in Mycobacterium tuberculosis by inhibiting the proteolytic activity of the ClpC1/ClpP1/ClpP2 complex. Although these compounds target ClpC1, their effects on the ATPase activity of ClpC1 and proteolytic activity of ClpC1/ClpP1/ClpP2 vary. Herein, we explored the ClpC1 molecular dynamics with these compounds through fluorescence correlation spectroscopy. The effect of these compounds on the ATPase activity of ClpC1-cys, the recombinant protein for fluorescence labeling, and proteolytic activity of ClpC1-cys/ClpP1/ClpP2 were identical to those of native ClpC1, whereas the intermolecular dynamics of fluorescence-labelled ClpC1 were different. Treatment with up to 1 nM ecumicin increased the population of slower diffused ClpC1 components compared with ClpC1 without ecumicin. However, this population was considerably reduced when treated with 10 nM ecumicin. Rufomycin 4-7 treatment resulted in a slower diffused component of ClpC1, and the portion of this component increased in a concentration-dependent manner. Ecumicin can generate an abnormal ClpC1 component, which cannot form normal ClpC1/ClpP1/ClpP2, via two different modes. Rufomycin 4-7 only generates slower diffused ClpC1 component that is inadequate to form normal ClpC1/ClpP1/ClpP2. Overall, we demonstrate that ecumicin and rufomycin 4-7 use different action mechanisms to generate abnormal ClpC1 components that cannot couple with ClpP1/ClpP2.
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Affiliation(s)
- Jeongpyo Hong
- Interdisciplinary Program of Biomodulation, Graduate School, Myongji University, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Nguyen Minh Duc
- Interdisciplinary Program of Biomodulation, Graduate School, Myongji University, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Byeong-Chul Jeong
- Division of Biosciences and Bioinformatics, College of Natural Science, Myongji University, Yongin, Gyeonggi-do, 17058, Republic of Korea
| | - Sanghyun Cho
- Institute for Tuberculosis Research, Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, United States
| | - Gauri Shetye
- Institute for Tuberculosis Research, Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, United States
| | - Jin Cao
- Institute for Tuberculosis Research, Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, 60612, United States
| | - Hyun Lee
- Biophysics Core at Resource Center, University of Illinois at Chicago, Chicago, IL, 60612, United States
| | - Cherlhyun Jeong
- Chemical & Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, 02792, Republic of Korea; KHU-KIST Department of Converging Science and Technology, Kyunghee University, Seoul, 02447, Republic of Korea.
| | - Hanki Lee
- Interdisciplinary Program of Biomodulation, Graduate School, Myongji University, Yongin, Gyeonggi-do, 17058, Republic of Korea.
| | - Joo-Won Suh
- MJ Bioefficacy Research Center, Myongji University, Yongin, Gyeonggi-do, 17058, Republic of Korea.
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8
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Structure of the drug target ClpC1 unfoldase in action provides insights on antibiotic mechanism of action. J Biol Chem 2022; 298:102553. [PMID: 36208775 PMCID: PMC9661721 DOI: 10.1016/j.jbc.2022.102553] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/23/2022] [Accepted: 09/25/2022] [Indexed: 11/13/2022] Open
Abstract
The unfoldase ClpC1 is one of the most exciting drug targets against tuberculosis. This AAA+ unfoldase works in cooperation with the ClpP1P2 protease and is the target of at least four natural product antibiotics: cyclomarin, ecumicin, lassomycin, and rufomycin. Although these molecules are promising starting points for drug development, their mechanisms of action remain largely unknown. Taking advantage of a middle domain mutant, we determined the first structure of Mycobacterium tuberculosis ClpC1 in its apo, cyclomarin-, and ecumicin-bound states via cryo-EM. The obtained structure displays features observed in other members of the AAA+ family and provides a map for further drug development. While the apo and cyclomarin-bound structures are indistinguishable and have N-terminal domains that are invisible in their respective EM maps, around half of the ecumicin-bound ClpC1 particles display three of their six N-terminal domains in an extended conformation. Our structural observations suggest a mechanism where ecumicin functions by mimicking substrate binding, leading to ATPase activation and changes in protein degradation profile.
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9
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Fanti RC, Vasconcelos SNS, Catta-Preta CMC, Sullivan JR, Riboldi GP, Dos Reis CV, Ramos PZ, Edwards AM, Behr MA, Couñago RM. A Target Engagement Assay to Assess Uptake, Potency, and Retention of Antibiotics in Living Bacteria. ACS Infect Dis 2022; 8:1449-1467. [PMID: 35815896 DOI: 10.1021/acsinfecdis.2c00073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New antibiotics are urgently needed to counter the emergence of antimicrobial-resistant pathogenic bacteria. A major challenge in antibiotic drug discovery is to turn potent biochemical inhibitors of essential bacterial components into effective antimicrobials. This difficulty is underpinned by a lack of methods to investigate the physicochemical properties needed for candidate antibiotics to permeate the bacterial cell envelope and avoid clearance by the action of bacterial efflux pumps. To address these issues, here we used a target engagement assay to measure the equilibrium and kinetic binding parameters of antibiotics targeting dihydrofolate reductase (DHFR) in live bacteria. We also used this assay to identify novel DHFR ligands having antimicrobial activity. We validated this approach using the Gram-negative bacteria Escherichia coli and the emerging human pathogen Mycobacterium abscessus. We expect the use of target engagement assays in bacteria to expedite the discovery and progression of novel, cell-permeable antibiotics with on-target activity.
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Affiliation(s)
- Rebeka C Fanti
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil.,Post-Graduate Program in Genetics and Molecular Biology (PGBM), UNICAMP, Campinas 13083-970, Brazil
| | - Stanley N S Vasconcelos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Carolina M C Catta-Preta
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Jaryd R Sullivan
- Department of Microbiology & Immunology, McGill University, Montréal H3A 2B4, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal H4A 3J1, Canada.,McGill International TB Centre, Montréal H4A 3S5, Canada
| | - Gustavo P Riboldi
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Caio V Dos Reis
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Priscila Z Ramos
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil
| | - Aled M Edwards
- Structural Genomics Consortium, 101 College Street, Toronto M5G 1L7, Canada
| | - Marcel A Behr
- Department of Microbiology & Immunology, McGill University, Montréal H3A 2B4, Canada.,Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal H4A 3J1, Canada.,McGill International TB Centre, Montréal H4A 3S5, Canada.,Department of Medicine, McGill University Health Centre, Montréal H4A 3J1, Canada
| | - Rafael M Couñago
- Centro de Química Medicinal (CQMED), Centro de Biologia Molecular e Engenharia Genética (CBMEG), Universidade Estadual de Campinas (UNICAMP), Campinas 13083-886, Brazil.,Post-Graduate Program in Genetics and Molecular Biology (PGBM), UNICAMP, Campinas 13083-970, Brazil
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10
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Addison W, Frederickson M, Coyne AG, Abell C. Potential therapeutic targets from Mycobacterium abscessus (Mab): Recently reported efforts towards the discovery of novel antibacterial agents to treat Mab infections. RSC Med Chem 2022; 13:392-404. [PMID: 35647542 PMCID: PMC9020770 DOI: 10.1039/d1md00359c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/09/2022] [Indexed: 11/21/2022] Open
Abstract
Mycobacterium abscessus (Mab) are rapidly growing mycobacteria that cause severe and persistent infections in both skin and lung tissues. Treatment regimens involve the extended usage of complex combinations of drugs, often leading to severe adverse side effects, particularly in immunocompromised patients. Current macrolide therapies are gradually proving to be less effective, largely due to emergence of antibiotic resistance; there is therefore an increasing need for the discovery of new antibacterials that are active against Mab. This review highlights recent research centred upon a number of potential therapeutic targets from Mab (Ag85C, ClpC1, GyrB, MmpL3 and TrmD), and discusses the various approaches used to discover small molecule inhibitors, in the search for future antibiotics for the treatment of Mab infections. Recently reported inhibitors developed against targets from Mycobacterium absecessus (Mab).![]()
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Affiliation(s)
- William Addison
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Martyn Frederickson
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Anthony G Coyne
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Chris Abell
- Yusuf Hamied Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
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11
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Bordes P, Genevaux P. Control of Toxin-Antitoxin Systems by Proteases in Mycobacterium Tuberculosis. Front Mol Biosci 2021; 8:691399. [PMID: 34079824 PMCID: PMC8165232 DOI: 10.3389/fmolb.2021.691399] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/06/2021] [Indexed: 12/30/2022] Open
Abstract
Toxin-antitoxin (TA) systems are small genetic elements composed of a noxious toxin and a counteracting cognate antitoxin. Although they are widespread in bacterial chromosomes and in mobile genetic elements, their cellular functions and activation mechanisms remain largely unknown. It has been proposed that toxin activation or expression of the TA operon could rely on the degradation of generally less stable antitoxins by cellular proteases. The resulting active toxin would then target essential cellular processes and inhibit bacterial growth. Although interplay between proteases and TA systems has been observed, evidences for such activation cycle are very limited. Herein, we present an overview of the current knowledge on TA recognition by proteases with a main focus on the major human pathogen Mycobacterium tuberculosis, which harbours multiple TA systems (over 80), the essential AAA + stress proteases, ClpC1P1P2 and ClpXP1P2, and the Pup-proteasome system.
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Affiliation(s)
- Patricia Bordes
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre Genevaux
- Laboratoire de Microbiologie et de Génétique Moléculaires, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, Toulouse, France
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12
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Su C, Tuan NQ, Lee MJ, Zhang XY, Cheng JH, Jin YY, Zhao XQ, Suh JW. Enhanced Production of Active Ecumicin Component with Higher Antituberculosis Activity by the Rare Actinomycete Nonomuraea sp. MJM5123 Using a Novel Promoter-Engineering Strategy. ACS Synth Biol 2020; 9:3019-3029. [PMID: 32916055 DOI: 10.1021/acssynbio.0c00248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Ecumicins are potent antituberculosis natural compounds produced by the rare actinomycete Nonomuraea sp. MJM5123. Here, we report an efficient genetic manipulation platform of this rare actinomycete. CRISPR/Cas9-based genome editing was achieved based on successful sporulation. Two genes in the ecumicin gene cluster were further investigated, ecuN and ecuE, which potentially encode a pretailoring cytochrome P450 hydroxylase and the core peptide synthase, respectively. Deletion of ecuN led to an enhanced ratio of the ecumicin compound EcuH16 relative to that of EcuH14, indicating that EcuN is indeed a P450 hydroxylase, and there is catalyzed hydroxylation at the C-3 position in unit12 phenylalanine to transform EcuH16 to the compound EcuH14. Furthermore, promoter engineering of ecuE by employing the strong promoter kasO*P was performed and optimized. We found that integrating the endogenous ribosome-binding site (RBS) of ecuE together with the RBS from kasO*P led to improved ecumicin production and resulted in a remarkably high EcuH16/EcuH14 ratio. Importantly, production of the more active component EcuH16 was considerably increased in the double RBSs engineered strain EPR1 compared to that in the wild-type strain, reaching 310 mg/L. At the same time, this production level was 2.3 times higher than that of the control strain EPA1 with only one RBS from kasO*P. To the best of our knowledge, this is the first report of genome editing and promoter engineering on the rare actinomycete Nonomuraea.
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Affiliation(s)
- Chun Su
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
| | - Nguyen-Quang Tuan
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
| | - Mi-Jin Lee
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
| | - Xia-Ying Zhang
- National Engineering Laboratory for Resource Developing of Endangered Chinese Crude Drugs in Northwest China, College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China
| | - Jin-Hua Cheng
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
| | - Ying-Yu Jin
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
- R&D Center, MANBANGBIO CO., LTD, Cheoingu, Yongin, Gyeonggi-Do 17058, Republic of Korea
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Joo-Won Suh
- Center for Nutraceutical and Pharmaceutical Materials, Myongji University, Yongin, Gyeonggi, 17058, Republic of Korea
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Dittmar D, Reder A, Schlüter R, Riedel K, Hecker M, Gerth U. Complementation studies with human ClpP in Bacillus subtilis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118744. [PMID: 32442436 DOI: 10.1016/j.bbamcr.2020.118744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 11/29/2022]
Abstract
ATP-dependent intracellular proteolysis is essential for all living organisms. ClpP, the proteolytic subunit of the ATP-dependent Clp proteases, shares 56% protein identity between B. subtilis and man. The aim of this study was to verify, whether human ClpP (HClpP) is able to substitute the bacterial pendant, BClpP, irrespectively of the huge evolutionary distance. For this reason hclpP was expressed from the natural B. subtilis promoters at the original chromosomal site. Growth at 37 °C as well as sporulation in the presence of hclpP depict an intermediate phenotype between wild type and clpP mutant suggesting a partial functional substitution of BClpP by HClpP. Northern as well as Western blot analyses show a similar induction pattern of both, bclpP and hclpP during heat stress on the mRNA as well as on the protein levels. Co-immunoprecipitation experiments imply specific interaction of HClpP with bacterial ClpC, ClpX and ClpE during control as well as heat stress conditions. Radioactive pulse-chase labeling and immunoprecipitation revealed that a ClpXP substrate, the short-living regulatory protein MgsR, is degraded by HClpP, although with an extremely slower rate in comparison to BClpP. The occurrence of an exceptional thickened cell wall of a clpP mutant can be almost fully reversed by the complementation with HClpP. The utilization of the HClpP expressing strain as a test system for new biological or synthetic active substances targeting BClpP is discussed.
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Affiliation(s)
- Denise Dittmar
- Institute of Microbiology of the Department of Biology, University of Greifswald, Germany; Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Alexander Reder
- Institute of Microbiology of the Department of Biology, University of Greifswald, Germany; Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Rabea Schlüter
- Imaging Center of the Department of Biology, University of Greifswald, Germany
| | - Katharina Riedel
- Institute of Microbiology of the Department of Biology, University of Greifswald, Germany
| | - Michael Hecker
- Institute of Microbiology of the Department of Biology, University of Greifswald, Germany
| | - Ulf Gerth
- Institute of Microbiology of the Department of Biology, University of Greifswald, Germany.
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14
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Huang M, Zhao Y, Feng L, Zhu L, Zhan L, Chen X. Role of the ClpX from Corynebacterium crenatum involved in stress responses and energy metabolism. Appl Microbiol Biotechnol 2020; 104:5505-5517. [PMID: 32300856 DOI: 10.1007/s00253-020-10597-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/24/2020] [Accepted: 03/31/2020] [Indexed: 02/04/2023]
Abstract
ClpX and ClpP are involved in many important functions, including stress responses and energy metabolism, in microorganisms. However, the ClpX and ClpP of microbes used in industrial scale have rarely been studied. Industrial bacterial fermentation experiences a variety of stresses, and energy metabolism is extremely important for industrial bacteria. Thus, the role played by the ClpX and ClpP of industrial bacteria in fermentation should be investigated. Most microorganisms have a single clpP gene, while Corynebacterium crenatum AS 1.542 possesses two clpPs. Herein, the clpX, clpP1, and clpP2 of C. crenatum were cloned, and its fusion protein was expressed and characterized. We also constructed clpX deletion mutant and complementation strain. Results indicate that ClpX serves an important function in thermal, pH, and ethanol stresses. It is also involved in NADPH synthesis and glucose consumption during fermentation.
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Affiliation(s)
- Mingzhu Huang
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China.,School of Life Science, Key Laboratory of Functional Small Organic Molecule of Ministry of Education, Jiangxi Normal University, 99 Ziyang Road, Nanchang, 330096, People's Republic of China
| | - Yue Zhao
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Lin Feng
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Lingfeng Zhu
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Li Zhan
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China
| | - Xuelan Chen
- Department of Life Science, Jiangxi Normal University, Nanchang, 330096, People's Republic of China. .,School of Life Science, Key Laboratory of Functional Small Organic Molecule of Ministry of Education, Jiangxi Normal University, 99 Ziyang Road, Nanchang, 330096, People's Republic of China.
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15
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Moreno-Cinos C, Goossens K, Salado IG, Van Der Veken P, De Winter H, Augustyns K. ClpP Protease, a Promising Antimicrobial Target. Int J Mol Sci 2019; 20:ijms20092232. [PMID: 31067645 PMCID: PMC6540193 DOI: 10.3390/ijms20092232] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/18/2019] [Accepted: 04/29/2019] [Indexed: 01/25/2023] Open
Abstract
The caseinolytic protease proteolytic subunit (ClpP) is a serine protease playing an important role in proteostasis of eukaryotic organelles and prokaryotic cells. Alteration of ClpP function has been proved to affect the virulence and infectivity of a number of pathogens. Increased bacterial resistance to antibiotics has become a global problem and new classes of antibiotics with novel mechanisms of action are needed. In this regard, ClpP has emerged as an attractive and potentially viable option to tackle pathogen fitness without suffering cross-resistance to established antibiotic classes and, when not an essential target, without causing an evolutionary selection pressure. This opens a greater window of opportunity for the host immune system to clear the infection by itself or by co-administration with commonly prescribed antibiotics. A comprehensive overview of the function, regulation and structure of ClpP across the different organisms is given. Discussion about mechanism of action of this protease in bacterial pathogenesis and human diseases are outlined, focusing on the compounds developed in order to target the activation or inhibition of ClpP.
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Affiliation(s)
- Carlos Moreno-Cinos
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Kenneth Goossens
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Irene G Salado
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Pieter Van Der Veken
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Hans De Winter
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium.
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