1
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Li J, Zhao Z, You D, Xie Y, Feng Y, Li X, Cui Z, Fuai L. Hemiprotonic ph-ph + with two targets inhibits metastatic breast cancer and concurrent candidiasis. Biochem Pharmacol 2024; 226:116394. [PMID: 38942090 DOI: 10.1016/j.bcp.2024.116394] [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: 03/26/2024] [Revised: 05/22/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Concurrent infection in breast cancer patients is the direct cause of the high mortality rate of the disease. However, there is no available method to increase the survival rate until now. To address the problem, we propose one drug with two target strategy to treat the refractory disease. A small chemical, ph-ph+, was attempted to be used in the study to explore the feasibility of the approach in anticancer and antifungus at the same time. The results showed that ph-ph+ could prevent the proliferation and metastasis of breast cancer cells, and kill C. albicans simultaneously. The molecular mechanism was associated with the activation of an evolutionarily conserved protease CLpP in the cancer and C. albicans cells. Also, the signaling pathway mediated by PLAGL2 that highly expressed in cancer cells participated in preventing cell metastasis and inducing apoptosis of ph-ph+. The one drug with dual targets inhibited the growth and metastasis of the cancer cells, and meanwhile eliminated C. albicans in tissues in the experimental animals. The results suggested that ph-ph+ with dual targets of CLpP and PLAGL2 would be a feasible approach to prolong the survival rate in patients with metastatic breast cancer and pathogenic infection.
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Affiliation(s)
- Jingli Li
- School of Pharmaceutical Sciences, Southwest University, China
| | - Zizhen Zhao
- School of Pharmaceutical Sciences, Southwest University, China
| | - Dongmei You
- School of Pharmaceutical Sciences, Southwest University, China
| | - Yafang Xie
- School of Pharmaceutical Sciences, Southwest University, China
| | - Yixiao Feng
- School of Pharmaceutical Sciences, Southwest University, China
| | - Xiaorong Li
- School of Pharmaceutical Sciences, Southwest University, China
| | - Zhihong Cui
- School of Pharmaceutical Sciences, Southwest University, China.
| | - Ling Fuai
- School of Pharmaceutical Sciences, Southwest University, China.
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2
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El Moudaka T, Murugan P, Abdul Rahman MB, Ario Tejo B. Discovery of Mycobacterium tuberculosis CYP121 New Inhibitor via Structure-based Drug Repurposing. PERTANIKA JOURNAL OF SCIENCE AND TECHNOLOGY 2023. [DOI: 10.47836/pjst.31.3.21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Tuberculosis (TB) remains a serious threat to human health with the advent of multi-drug resistant tuberculosis (MDR-TB) and extensively drug-resistant tuberculosis (XDR-TB). The urge to find novel drugs to deal with the appearance of drug-resistant TB and its variants is highly needed. This study aims to find new CYP121 inhibitors by screening 8,773 compounds from the drug repositioning database RepoDB. The selection of CYP121 potential inhibitors was based on two criteria: the new inhibitor should bind to CYP121 with higher affinity than its original ligand and interact with catalytically important residues for the function of CYP121. The ligands were docked onto CYP121 using AutoDock Vina, and the molecular dynamics simulation of the selected ligand was conducted using YASARA Structure. We found that antrafenine, an anti-inflammatory and analgesic agent with high CYP inhibitory promiscuity, was bound to CYP121 with a binding affinity of -12.6 kcal/mol and interacted with important residues at the CYP121 binding site. Molecular dynamics analysis of CYP121 bound to the original ligand and antrafenine showed that both ligands affected the dynamics of residues located distantly from the active site. Antrafenine caused more structural changes to CYP121 than the original ligand, as indicated by a significantly higher number of affected residues and rigid body movements caused by the binding of antrafenine to CYP121.
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3
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Wedam R, Greer YE, Wisniewski DJ, Weltz S, Kundu M, Voeller D, Lipkowitz S. Targeting Mitochondria with ClpP Agonists as a Novel Therapeutic Opportunity in Breast Cancer. Cancers (Basel) 2023; 15:cancers15071936. [PMID: 37046596 PMCID: PMC10093243 DOI: 10.3390/cancers15071936] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/20/2023] [Accepted: 03/21/2023] [Indexed: 04/14/2023] Open
Abstract
Breast cancer is the most frequently diagnosed malignancy worldwide and the leading cause of cancer mortality in women. Despite the recent development of new therapeutics including targeted therapies and immunotherapy, triple-negative breast cancer remains an aggressive form of breast cancer, and thus improved treatments are needed. In recent decades, it has become increasingly clear that breast cancers harbor metabolic plasticity that is controlled by mitochondria. A myriad of studies provide evidence that mitochondria are essential to breast cancer progression. Mitochondria in breast cancers are widely reprogrammed to enhance energy production and biosynthesis of macromolecules required for tumor growth. In this review, we will discuss the current understanding of mitochondrial roles in breast cancers and elucidate why mitochondria are a rational therapeutic target. We will then outline the status of the use of mitochondria-targeting drugs in breast cancers, and highlight ClpP agonists as emerging mitochondria-targeting drugs with a unique mechanism of action. We also illustrate possible drug combination strategies and challenges in the future breast cancer clinic.
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Affiliation(s)
- Rohan Wedam
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yoshimi Endo Greer
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David J Wisniewski
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sarah Weltz
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Manjari Kundu
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Donna Voeller
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Stanley Lipkowitz
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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4
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Zhang J, Qiao W, Luo Y. Mitochondrial quality control proteases and their modulation for cancer therapy. Med Res Rev 2023; 43:399-436. [PMID: 36208112 DOI: 10.1002/med.21929] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 09/04/2022] [Accepted: 09/26/2022] [Indexed: 02/05/2023]
Abstract
Mitochondria, the main provider of energy in eukaryotic cells, contains more than 1000 different proteins and is closely related to the development of cells. However, damaged proteins impair mitochondrial function, further contributing to several human diseases. Evidence shows mitochondrial proteases are critically important for protein maintenance. Most importantly, quality control enzymes exert a crucial role in the modulation of mitochondrial functions by degrading misfolded, aged, or superfluous proteins. Interestingly, cancer cells thrive under stress conditions that damage proteins, so targeting mitochondrial quality control proteases serves as a novel regulator for cancer cells. Not only that, mitochondrial quality control proteases have been shown to affect mitochondrial dynamics by regulating the morphology of optic atrophy 1 (OPA1), which is closely related to the occurrence and progression of cancer. In this review, we introduce mitochondrial quality control proteases as promising targets and related modulators in cancer therapy with a focus on caseinolytic protease P (ClpP), Lon protease (LonP1), high-temperature requirement protein A2 (HrtA2), and OMA-1. Further, we summarize our current knowledge of the advances in clinical trials for modulators of mitochondrial quality control proteases. Overall, the content proposed above serves to suggest directions for the development of novel antitumor drugs.
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Affiliation(s)
- Jiangnan Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
| | - Wenliang Qiao
- Lung Cancer Center, Laboratory of Lung Cancer, Western China Hospital of Sichuan University, Chengdu, China
| | - Youfu Luo
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu, Sichuan, China
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5
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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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6
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Nguyen T, Gronauer TF, Nast‐Kolb T, Sieber SA, Lang K. Substrate Profiling of Mitochondrial Caseinolytic Protease P via a Site‐Specific Photocrosslinking Approach. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111085] [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)
- Tuan‐Anh Nguyen
- Department of Chemistry Group of Synthetic Biochemistry Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
| | - Thomas F. Gronauer
- Center for Protein Assemblies (CPA) Department of Chemistry Chair of Organic Chemistry II Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
| | - Timon Nast‐Kolb
- Center for Protein Assemblies (CPA) and Lehrstuhl für Biophysik (E27) Physics Department Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
| | - Stephan A. Sieber
- Center for Protein Assemblies (CPA) Department of Chemistry Chair of Organic Chemistry II Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
| | - Kathrin Lang
- Department of Chemistry Group of Synthetic Biochemistry Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
- Laboratory of Organic Chemistry Department of Chemistry and Applied Biosciences Chair of Chemical Biology ETH Zürich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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7
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Nguyen TA, Gronauer T, Nast-Kolb T, Sieber S, Lang K. Substrate profiling of mitochondrial caseinolytic protease P via a site-specific photocrosslinking approach. Angew Chem Int Ed Engl 2021; 61:e202111085. [PMID: 34847623 PMCID: PMC9306725 DOI: 10.1002/anie.202111085] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Indexed: 11/17/2022]
Abstract
Approaches for profiling protease substrates are critical for defining protease functions, but remain challenging tasks. We combine genetic code expansion, photocrosslinking and proteomics to identify substrates of the mitochondrial (mt) human caseinolytic protease P (hClpP). Site‐specific incorporation of the diazirine‐bearing amino acid DiazK into the inner proteolytic chamber of hClpP, followed by UV‐irradiation of cells, allows to covalently trap substrate proteins of hClpP and to substantiate hClpP's major involvement in maintaining overall mt homeostasis. In addition to confirming many of the previously annotated hClpP substrates, our approach adds a diverse set of new proteins to the hClpP interactome. Importantly, our workflow allows identifying substrate dynamics upon application of external cues in an unbiased manner. Identification of unique hClpP‐substrate proteins upon induction of mt oxidative stress, suggests that hClpP counteracts oxidative stress by processing of proteins that are involved in respiratory chain complex synthesis and maturation as well as in catabolic pathways.
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Affiliation(s)
- Tuan-Anh Nguyen
- Technical University of Munich: Technische Universitat Munchen, Chemistry, Lichtenbergstr. 4, 85748, Garching, GERMANY
| | - Thomas Gronauer
- Technical University of Munich: Technische Universitat Munchen, Chemistry, Lichtenbergstr. 4, 85748, Garching, GERMANY
| | - Timon Nast-Kolb
- Technische Universität München: Technische Universitat Munchen, Physics, GERMANY
| | - Stephan Sieber
- Technical University of Munich: Technische Universitat Munchen, Chemistry, Lichtenbergstr. 4, 85748, Garching, GERMANY
| | - Kathrin Lang
- ETH-Zürich LOC: Eidgenossische Technische Hochschule Zurich Laboratorium fur Organische Chemie, Chemistry and Applied Biosciences, Vladimir-Prelog-Weg. 3, 8093, Zürich, SWITZERLAND
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8
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Yang T, Zhang T, Zhou X, Wang P, Gan J, Song B, Yang S, Yang CG. Dysregulation of ClpP by Small-Molecule Activators Used Against Xanthomonas oryzae pv. oryzae Infections. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:7545-7553. [PMID: 34218658 DOI: 10.1021/acs.jafc.1c01470] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Rice bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is considered a destructive plant bacterial disease. The looming crisis of antibiotic resistance necessitates the discovery of antibiotics with new modes of action. Activated caseinolytic protease P (ClpP) can degrade bacterial FtsZ proteins that are essential for cell division; thus, we hypothesized that small-molecule-induced dysregulation of XooClpP may result in degradation of XooFtsZ to treat leaf blight diseases. In this work, we have determined the crystal structures of XooClpP, and its mutant bound with ADEP4, which revealed the action modes of XooClpP assemblies and XooFtsZ degradation by dysregulated XooClpP in the presence of small-molecule activators, such as ONC212 and ADEP4. Additionally, an antibacterial assessment demonstrated that ONC212 displays excellent activity against Xoo and prevents rice bacterial leaf blight in vivo. Thus, these unique antibacterial effects of small-molecule activators of XooClpP represent a potential strategy for the development of agricultural antibiotics by targeting bacterial ClpP.
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Affiliation(s)
- Teng Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
- The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Tao Zhang
- The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Xiang Zhou
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Pengyu Wang
- The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Jianhua Gan
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Cai-Guang Yang
- The Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, UCAS, Hangzhou 310024, China
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9
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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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10
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Feng Y, Nouri K, Schimmer AD. Mitochondrial ATP-Dependent Proteases-Biological Function and Potential Anti-Cancer Targets. Cancers (Basel) 2021; 13:2020. [PMID: 33922062 PMCID: PMC8122244 DOI: 10.3390/cancers13092020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/11/2021] [Accepted: 04/18/2021] [Indexed: 12/20/2022] Open
Abstract
Cells must eliminate excess or damaged proteins to maintain protein homeostasis. To ensure protein homeostasis in the cytoplasm, cells rely on the ubiquitin-proteasome system and autophagy. In the mitochondria, protein homeostasis is regulated by mitochondria proteases, including four core ATP-dependent proteases, m-AAA, i-AAA, LonP, and ClpXP, located in the mitochondrial membrane and matrix. This review will discuss the function of mitochondrial proteases, with a focus on ClpXP as a novel therapeutic target for the treatment of malignancy. ClpXP maintains the integrity of the mitochondrial respiratory chain and regulates metabolism by degrading damaged and misfolded mitochondrial proteins. Inhibiting ClpXP genetically or chemically impairs oxidative phosphorylation and is toxic to malignant cells with high ClpXP expression. Likewise, hyperactivating the protease leads to increased degradation of ClpXP substrates and kills cancer cells. Thus, targeting ClpXP through inhibition or hyperactivation may be novel approaches for patients with malignancy.
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Affiliation(s)
- Yue Feng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; (Y.F.); (K.N.)
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Kazem Nouri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; (Y.F.); (K.N.)
| | - Aaron D. Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; (Y.F.); (K.N.)
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
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11
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Nouri K, Feng Y, Schimmer AD. Mitochondrial ClpP serine protease-biological function and emerging target for cancer therapy. Cell Death Dis 2020; 11:841. [PMID: 33037181 PMCID: PMC7547079 DOI: 10.1038/s41419-020-03062-z] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/22/2020] [Accepted: 09/24/2020] [Indexed: 12/12/2022]
Abstract
Mitochondrial ClpP is a serine protease located in the mitochondrial matrix. This protease participates in mitochondrial protein quality control by degrading misfolded or damaged proteins, thus maintaining normal metabolic function. Mitochondrial ClpP is a stable heptamer ring with peptidase activity that forms a multimeric complex with the ATP-dependent unfoldase ClpX (ClpXP) leading to proteolytic activity. Emerging evidence demonstrates that ClpXP is over-expressed in hematologic malignancies and solid tumors and is necessary for the viability of a subset of tumors. In addition, both inhibition and hyperactivation of ClpXP leads to impaired respiratory chain activity and causes cell death in cancer cells. Therefore, targeting mitochondrial ClpXP could be a novel therapeutic strategy for the treatment of malignancy. Here, we review the structure and function of mitochondrial ClpXP as well as strategies to target this enzyme complex as a novel therapeutic approach for malignancy.
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Affiliation(s)
- Kazem Nouri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Yue Feng
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Aaron D Schimmer
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
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12
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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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13
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Eyermann B, Meixner M, Brötz‐Oesterhelt H, Antes I, Sieber SA. Acyldepsipeptide Probes Facilitate Specific Detection of Caseinolytic Protease P Independent of Its Oligomeric and Activity State. Chembiochem 2020; 21:235-240. [PMID: 31487112 PMCID: PMC7003903 DOI: 10.1002/cbic.201900477] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Indexed: 12/21/2022]
Abstract
Caseinolytic protease P (ClpP) is a tetradecameric peptidase that assembles with chaperones such as ClpX to gain proteolytic activity. Acyldepsipeptides (ADEPs) are small-molecule mimics of ClpX that bind into hydrophobic pockets on the apical site of the complex, thereby activating ClpP. Detection of ClpP has so far been facilitated with active-site-directed probes which depend on the activity and oligomeric state of the complex. To expand the scope of ClpP labeling, we took a stepwise synthetic approach toward customized ADEP photoprobes. Structure-activity relationship studies with small fragments and ADEP derivatives paired with modeling studies revealed the design principles for suitable probe molecules. The derivatives were tested for activation of ClpP and subsequently applied in labeling studies of the wild-type peptidase as well as enzymes bearing mutations at the active site and an oligomerization sensor. Satisfyingly, the ADEP photoprobes provided a labeling readout of ClpP independent of its activity and oligomeric state.
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Affiliation(s)
- Barbara Eyermann
- Department ChemieTechnische Universität MünchenLichtenbergstrasse 485748GarchingGermany
| | - Maximilian Meixner
- Department für BiowissenschaftenTechnische Universität MünchenEmil-Erlenmeyer-Forum 885354FreisingGermany
| | - Heike Brötz‐Oesterhelt
- Interfaculty Institute of Microbiology and Infection MedicineMicrobial Bioactive CompoundsUniversity of TübingenAuf der Morgenstelle 28, E-Bau, Ebene 872076TübingenGermany
| | - Iris Antes
- Department für BiowissenschaftenTechnische Universität MünchenEmil-Erlenmeyer-Forum 885354FreisingGermany
| | - Stephan A. Sieber
- Department ChemieTechnische Universität MünchenLichtenbergstrasse 485748GarchingGermany
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14
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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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15
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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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16
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Stahl M, Korotkov VS, Balogh D, Kick LM, Gersch M, Pahl A, Kielkowski P, Richter K, Schneider S, Sieber SA. Selektive Aktivierung der humanen caseinolytischen Protease P (ClpP). Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808189] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Matthias Stahl
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
- Department of Oncology-Pathology; Science for Life Laboratory; Karolinska Institutet; Tomtebodavägen 23A 171 65 Solna Schweden
| | - Vadim S. Korotkov
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Dóra Balogh
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Leonhard M. Kick
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Malte Gersch
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
- Medical Research Council Laboratory of, Molecular Biology; Francis Crick Avenue CB2 0QH Cambridge Großbritannien
| | - Axel Pahl
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
- Max-Planck-Institut für Molekulare Physiologie; Compound Management and Screening Center (COMAS); Otto-Hahn-Straße 11 44227 Dortmund Deutschland
| | - Pavel Kielkowski
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Klaus Richter
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Sabine Schneider
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
| | - Stephan A. Sieber
- Fakultät für Chemie; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Deutschland
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17
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Stahl M, Korotkov VS, Balogh D, Kick LM, Gersch M, Pahl A, Kielkowski P, Richter K, Schneider S, Sieber SA. Selective Activation of Human Caseinolytic Protease P (ClpP). Angew Chem Int Ed Engl 2018; 57:14602-14607. [DOI: 10.1002/anie.201808189] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 08/15/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Matthias Stahl
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
- Present address: Department of Oncology-Pathology; Science for Life Laboratory; Karolinska Institutet; Tomtebodavägen 23A 171 65 Solna Sweden
| | - Vadim S. Korotkov
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Dóra Balogh
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Leonhard M. Kick
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Malte Gersch
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
- Present address; Medical Research Council Laboratory of Molecular Biology; Francis Crick Avenue CB2 0QH Cambridge UK
| | - Axel Pahl
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
- Present address: Max-Planck-Institut für Molekulare Physiologie; Compound Management and Screening Center (COMAS); Otto-Hahn-Straße 11 44227 Dortmund Germany
| | - Pavel Kielkowski
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Klaus Richter
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Sabine Schneider
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
| | - Stephan A. Sieber
- Department of Chemistry; Center for Integrated Protein Science Munich (CIPS ); Technische Universität München; Lichtenbergstraße 4 85747 Garching Germany
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