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Todosenko N, Khaziakhmatova O, Malashchenko V, Yurova K, Bograya M, Beletskaya M, Vulf M, Gazatova N, Litvinova L. Mitochondrial Dysfunction Associated with mtDNA in Metabolic Syndrome and Obesity. Int J Mol Sci 2023; 24:12012. [PMID: 37569389 PMCID: PMC10418437 DOI: 10.3390/ijms241512012] [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: 07/04/2023] [Revised: 07/22/2023] [Accepted: 07/25/2023] [Indexed: 08/13/2023] Open
Abstract
Metabolic syndrome (MetS) is a precursor to the major health diseases associated with high mortality in industrialized countries: cardiovascular disease and diabetes. An important component of the pathogenesis of the metabolic syndrome is mitochondrial dysfunction, which is associated with tissue hypoxia, disruption of mitochondrial integrity, increased production of reactive oxygen species, and a decrease in ATP, leading to a chronic inflammatory state that affects tissues and organ systems. The mitochondrial AAA + protease Lon (Lonp1) has a broad spectrum of activities. In addition to its classical function (degradation of misfolded or damaged proteins), enzymatic activity (proteolysis, chaperone activity, mitochondrial DNA (mtDNA)binding) has been demonstrated. At the same time, the spectrum of Lonp1 activity extends to the regulation of cellular processes inside mitochondria, as well as outside mitochondria (nuclear localization). This mitochondrial protease with enzymatic activity may be a promising molecular target for the development of targeted therapy for MetS and its components. The aim of this review is to elucidate the role of mtDNA in the pathogenesis of metabolic syndrome and its components as a key component of mitochondrial dysfunction and to describe the promising and little-studied AAA + LonP1 protease as a potential target in metabolic disorders.
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Affiliation(s)
- Natalia Todosenko
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Olga Khaziakhmatova
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Vladimir Malashchenko
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Kristina Yurova
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Maria Bograya
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Maria Beletskaya
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Maria Vulf
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Natalia Gazatova
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
| | - Larisa Litvinova
- Center for Immunology and Cellular Biotechnology, Immanuel Kant Baltic Federal University, 236001 Kaliningrad, Russia; (N.T.); (O.K.); (V.M.); (K.Y.); (M.B.); (M.B.); (M.V.); (N.G.)
- Laboratory of Cellular and Microfluidic Technologies, Siberian State Medical University, 634050 Tomsk, Russia
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2
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Daglish SCD, Fennell EMJ, Graves LM. Targeting Mitochondrial DNA Transcription by POLRMT Inhibition or Depletion as a Potential Strategy for Cancer Treatment. Biomedicines 2023; 11:1598. [PMID: 37371693 PMCID: PMC10295849 DOI: 10.3390/biomedicines11061598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Transcription of the mitochondrial genome is essential for the maintenance of oxidative phosphorylation (OXPHOS) and other functions directly related to this unique genome. Considerable evidence suggests that mitochondrial transcription is dysregulated in cancer and cancer metastasis and contributes significantly to cancer cell metabolism. Recently, inhibitors of the mitochondrial DNA-dependent RNA polymerase (POLRMT) were identified as potentially attractive new anti-cancer compounds. These molecules (IMT1, IMT1B) inactivate cancer cell metabolism through reduced transcription of mitochondrially-encoded OXPHOS subunits such as ND1-5 (Complex I) and COI-IV (Complex IV). Studies from our lab have discovered small molecule regulators of the mitochondrial matrix caseinolytic protease (ClpP) as probable inhibitors of mitochondrial transcription. These compounds activate ClpP proteolysis and lead to the rapid depletion of POLRMT and other matrix proteins, resulting in inhibition of mitochondrial transcription and growth arrest. Herein we present a comparison of POLRMT inhibition and ClpP activation, both conceptually and experimentally, and evaluate the results of these treatments on mitochondrial transcription, inhibition of OXPHOS, and ultimately cancer cell growth. We discuss the potential for targeting mitochondrial transcription as a cancer cell vulnerability.
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Affiliation(s)
| | | | - Lee M. Graves
- Department of Pharmacology and the Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (S.C.D.D.); (E.M.J.F.)
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3
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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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4
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Liao WT, Chu PY, Su CC, Wu CC, Li CJ. Mitochondrial AAA protease gene associated with immune infiltration is a prognostic biomarker in human ovarian cancer. Pathol Res Pract 2022; 240:154215. [DOI: 10.1016/j.prp.2022.154215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/19/2022] [Accepted: 11/08/2022] [Indexed: 11/13/2022]
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Wlodawer A, Sekula B, Gustchina A, Rotanova TV. Structure and the Mode of Activity of Lon Proteases from Diverse Organisms. J Mol Biol 2022; 434:167504. [PMID: 35183556 PMCID: PMC9013511 DOI: 10.1016/j.jmb.2022.167504] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/14/2022] [Accepted: 02/14/2022] [Indexed: 11/19/2022]
Abstract
Lon proteases, members of the AAA+ superfamily of enzymes, are key components of the protein quality control system in bacterial cells, as well as in the mitochondria and other specialized organelles of higher organisms. These enzymes have been subject of extensive biochemical and structural investigations, resulting in 72 crystal and solution structures, including structures of the individual domains, multi-domain constructs, and full-length proteins. However, interpretation of the latter structures still leaves some questions unanswered. Based on their amino acid sequence and details of their structure, Lon proteases can be divided into at least three subfamilies, designated as LonA, LonB, and LonC. Protomers of all Lons are single-chain polypeptides and contain two functional domains, ATPase and protease. The LonA enzymes additionally include a large N-terminal region, and different Lons may also include non-conserved inserts in the principal domains. These ATP-dependent proteases function as homohexamers, in which unfolded substrates are translocated to a large central chamber where they undergo proteolysis by a processive mechanism. X-ray crystal structures provided high-resolution models which verified that Lons are hydrolases with the rare Ser-Lys catalytic dyad. Full-length LonA enzymes have been investigated by cryo-electron microscopy (cryo-EM), providing description of the functional enzyme at different stages of the catalytic cycle, indicating extensive flexibility of their N-terminal domains, and revealing insights into the substrate translocation mechanism. Structural studies of Lon proteases provide an interesting case for symbiosis of X-ray crystallography and cryo-EM, currently the two principal techniques for determination of macromolecular structures.
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Affiliation(s)
- Alexander Wlodawer
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA.
| | - Bartosz Sekula
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Alla Gustchina
- Protein Structure Section, Center for Structural Biology, National Cancer Institute, Frederick, MD 21702, USA
| | - Tatyana V Rotanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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Lee J, Pandey AK, Venkatesh S, Thilagavathi J, Honda T, Singh K, Suzuki CK. Inhibition of mitochondrial LonP1 protease by allosteric blockade of ATP binding and hydrolysis via CDDO and its derivatives. J Biol Chem 2022; 298:101719. [PMID: 35151690 PMCID: PMC8921294 DOI: 10.1016/j.jbc.2022.101719] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/01/2022] Open
Abstract
The mitochondrial protein LonP1 is an ATP-dependent protease that mitigates cell stress and calibrates mitochondrial metabolism and energetics. Biallelic mutations in the LONP1 gene are known to cause a broad spectrum of diseases, and LonP1 dysregulation is also implicated in cancer and age-related disorders. Despite the importance of LonP1 in health and disease, specific inhibitors of this protease are unknown. Here, we demonstrate that 2-cyano-3,12-dioxooleana-1,9(11)-dien-28-oic acid (CDDO) and its -methyl and -imidazole derivatives reversibly inhibit LonP1 by a noncompetitive mechanism, blocking ATP-hydrolysis and thus proteolysis. By contrast, we found that CDDO-anhydride inhibits the LonP1 ATPase competitively. Docking of CDDO derivatives in the cryo-EM structure of LonP1 shows these compounds bind a hydrophobic pocket adjacent to the ATP-binding site. The binding site of CDDO derivatives was validated by amino acid substitutions that increased LonP1 inhibition and also by a pathogenic mutation that causes cerebral, ocular, dental, auricular and skeletal (CODAS) syndrome, which ablated inhibition. CDDO failed to inhibit the ATPase activity of the purified 26S proteasome, which like LonP1 belongs to the AAA+ superfamily of ATPases Associated with diverse cellular Activities, suggesting that CDDO shows selectivity within this family of ATPases. Furthermore, we show that noncytotoxic concentrations of CDDO derivatives in cultured cells inhibited LonP1, but not the 26S proteasome. Taken together, these findings provide insights for future development of LonP1-specific inhibitors with chemotherapeutic potential.
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Affiliation(s)
- Jae Lee
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers - New Jersey Medical School, Newark, New Jersey, USA
| | - Ashutosh K Pandey
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers - New Jersey Medical School, Newark, New Jersey, USA
| | - Sundararajan Venkatesh
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers - New Jersey Medical School, Newark, New Jersey, USA
| | - Jayapalraja Thilagavathi
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers - New Jersey Medical School, Newark, New Jersey, USA
| | - Tadashi Honda
- Department of Chemistry and Institution of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York, USA
| | - Kamal Singh
- Christopher Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA; Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, USA; Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Carolyn K Suzuki
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers - New Jersey Medical School, Newark, New Jersey, USA.
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Wang G, Fan Y, Cao P, Tan K. Insight into the mitochondrial unfolded protein response and cancer: opportunities and challenges. Cell Biosci 2022; 12:18. [PMID: 35180892 PMCID: PMC8857832 DOI: 10.1186/s13578-022-00747-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 01/18/2022] [Indexed: 02/08/2023] Open
Abstract
The mitochondrial unfolded protein response (UPRmt) is an evolutionarily conserved protective transcriptional response that maintains mitochondrial proteostasis by inducing the expression of mitochondrial chaperones and proteases in response to various stresses. The UPRmt-mediated transcriptional program requires the participation of various upstream signaling pathways and molecules. The factors regulating the UPRmt in Caenorhabditis elegans (C. elegans) and mammals are both similar and different. Cancer cells, as malignant cells with uncontrolled proliferation, are exposed to various challenges from endogenous and exogenous stresses. Therefore, in cancer cells, the UPRmt is hijacked and exploited for the repair of mitochondria and the promotion of tumor growth, invasion and metastasis. In this review, we systematically introduce the inducers of UPRmt, the biological processes in which UPRmt participates, the mechanisms regulating the UPRmt in C. elegans and mammals, cross-tissue signal transduction of the UPRmt and the roles of the UPRmt in promoting cancer initiation and progression. Disrupting proteostasis in cancer cells by targeting UPRmt constitutes a novel anticancer therapeutic strategy.
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Affiliation(s)
- Ge Wang
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Hebei, 050024, China.,Department of Human Anatomy, Histology and Embryology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing, 100191, China
| | - Yumei Fan
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Hebei, 050024, China
| | - Pengxiu Cao
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Hebei, 050024, China
| | - Ke Tan
- Key Laboratory of Molecular and Cellular Biology of Ministry of Education, Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Hebei, 050024, China.
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8
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Alavi MV. OMA1 High-Throughput Screen Reveals Protease Activation by Kinase Inhibitors. ACS Chem Biol 2021; 16:2202-2211. [PMID: 34672515 DOI: 10.1021/acschembio.1c00350] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mitochondrial proteases are interesting but challenging drug targets for multifactorial diseases, such as neurodegeneration and cancer. The mitochondrial inner membrane protease OMA1 is a bona fide drug target for heart failure supported by data from human linkage analysis and animal disease models, but presumably relevant for more indications. OMA1 acts at the intersection of energy metabolism and stress signaling. The protease cleaves the structural protein OPA1, which organizes the cristae, as well as the signaling peptide DELE1, which can stimulate the integrated stress response. OMA1 shows little activity under physiological conditions but hydrolyzes OPA1 in mitochondria destined for mitophagy and during apoptosis. Little is known about OMA1, its structure has not been solved, let alone its context-dependent regulation. Autocatalytic processing and the lack of OMA1 inhibitors are thereby creating the biggest roadblocks. This study introduces a scalable, cellular OMA1 protease assay suitable for high-throughput drug screening. The assay utilizes an engineered luciferase targeted to the inner membrane as artificial OMA1 substrate, whereby the reporter signal inversely correlates to OMA1 activity. Testing different screening protocols and sampling different compound collections validated the reporter and demonstrated that both OMA1 activators as well as OMA1 inhibitors can be identified with the assay. Ten kinase-targeted cancer drugs triggered OMA1 in the assays, which suggests─considering cardiotoxicity as a rather common side-effect of this class of drugs─cross-reactivity with the OMA1 pathway.
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Affiliation(s)
- Marcel V. Alavi
- 712 North Inc., QB3 Incubator at UC Berkeley, 130 Stanley Hall, #3220, Berkeley, California 94720, United States
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9
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Perrone MG, Ruggiero A, Centonze A, Carrieri A, Ferorelli S, Scilimati A. Diffuse Intrinsic Pontine Glioma (DIPG): Breakthrough and Clinical Perspective. Curr Med Chem 2021; 28:3287-3317. [PMID: 32767913 DOI: 10.2174/0929867327666200806110206] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/16/2020] [Accepted: 07/23/2020] [Indexed: 11/22/2022]
Abstract
Diffuse intrinsic pontine glioma (DIPG) mainly affects children with a median age of 6-7 years old. It accounts for 10% of all pediatric tumors. Unfortunately, DIPG has a poor prognosis, and the median survival is generally less than 16-24 months independently from the treatment received. Up to now, children with DIPG are treated with focal radiotherapy alone or in combination with antitumor agents. In the last decade, ONC201 known as dopamine receptor antagonist was uncovered, by a high throughput screening of public libraries of compounds, to be endowed with cytotoxic activity against several cancer cell lines. Efforts were made to identify the real ONC201 target, responsible for its antiproliferative effect. The hypothesized targets were the Tumor necrosis factor-Related Apoptosis-Inducing Ligand stimulation (TRAIL), two oncogenic kinases (ERK/AKT system) that target the same tumor-suppressor gene (FOXO3a), dopamine receptors (DRD2 and DRD3 subtypes) and finally the mitochondrial Caseynolitic Protease P (ClpP). ONC201 structure-activity relationship is extensively discussed in this review, together with other two classes of compounds, namely ADEPs and D9, already known for their antibiotic activity but noteworthy to be discussed and studied as potential "leads" for the development of new drugs to be used in the treatment of DIPG. In this review, a detailed and critical description of ONC201, ADEPs, and D9 pro-apoptotic activity is made, with particular attention to the specific interactions established with its targets that also are intimately described. Pubmed published patents and clinical trial reports of the last ten years were used as the bibliographic source.
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Affiliation(s)
- Maria Grazia Perrone
- Department of Pharmacy and Pharmaceutical Sciences, University of Bari, Via E. Orabona 4, 70125 Bari, Italy
| | - Antonio Ruggiero
- Pediatric Oncology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Antonella Centonze
- Department of Pharmacy and Pharmaceutical Sciences, University of Bari, Via E. Orabona 4, 70125 Bari, Italy
| | - Antonio Carrieri
- Department of Pharmacy and Pharmaceutical Sciences, University of Bari, Via E. Orabona 4, 70125 Bari, Italy
| | - Savina Ferorelli
- Department of Pharmacy and Pharmaceutical Sciences, University of Bari, Via E. Orabona 4, 70125 Bari, Italy
| | - Antonio Scilimati
- Department of Pharmacy and Pharmaceutical Sciences, University of Bari, Via E. Orabona 4, 70125 Bari, Italy
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10
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Shin M, Watson ER, Song AS, Mindrebo JT, Novick SJ, Griffin PR, Wiseman RL, Lander GC. Structures of the human LONP1 protease reveal regulatory steps involved in protease activation. Nat Commun 2021; 12:3239. [PMID: 34050165 PMCID: PMC8163871 DOI: 10.1038/s41467-021-23495-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/29/2021] [Indexed: 12/29/2022] Open
Abstract
The human mitochondrial AAA+ protein LONP1 is a critical quality control protease involved in regulating diverse aspects of mitochondrial biology including proteostasis, electron transport chain activity, and mitochondrial transcription. As such, genetic or aging-associated imbalances in LONP1 activity are implicated in pathologic mitochondrial dysfunction associated with numerous human diseases. Despite this importance, the molecular basis for LONP1-dependent proteolytic activity remains poorly defined. Here, we solved cryo-electron microscopy structures of human LONP1 to reveal the underlying molecular mechanisms governing substrate proteolysis. We show that, like bacterial Lon, human LONP1 adopts both an open and closed spiral staircase orientation dictated by the presence of substrate and nucleotide. Unlike bacterial Lon, human LONP1 contains a second spiral staircase within its ATPase domain that engages substrate as it is translocated toward the proteolytic chamber. Intriguingly, and in contrast to its bacterial ortholog, substrate binding within the central ATPase channel of LONP1 alone is insufficient to induce the activated conformation of the protease domains. To successfully induce the active protease conformation in substrate-bound LONP1, substrate binding within the protease active site is necessary, which we demonstrate by adding bortezomib, a peptidomimetic active site inhibitor of LONP1. These results suggest LONP1 can decouple ATPase and protease activities depending on whether AAA+ or both AAA+ and protease domains bind substrate. Importantly, our structures provide a molecular framework to define the critical importance of LONP1 in regulating mitochondrial proteostasis in health and disease.
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Affiliation(s)
- Mia Shin
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Edmond R Watson
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Albert S Song
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | - Jeffrey T Mindrebo
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Scott J Novick
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | - R Luke Wiseman
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA.
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA.
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11
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Kingsley LJ, He X, McNeill M, Nelson J, Nikulin V, Ma Z, Lu W, Zhou VW, Manuia M, Kreusch A, Gao MY, Witmer D, Vaillancourt MT, Lu M, Greenblatt S, Lee C, Vashisht A, Bender S, Spraggon G, Michellys PY, Jia Y, Haling JR, Lelais G. Structure-Based Design of Selective LONP1 Inhibitors for Probing In Vitro Biology. J Med Chem 2021; 64:4857-4869. [PMID: 33821636 DOI: 10.1021/acs.jmedchem.0c02152] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
LONP1 is an AAA+ protease that maintains mitochondrial homeostasis by removing damaged or misfolded proteins. Elevated activity and expression of LONP1 promotes cancer cell proliferation and resistance to apoptosis-inducing reagents. Despite the importance of LONP1 in human biology and disease, very few LONP1 inhibitors have been described in the literature. Herein, we report the development of selective boronic acid-based LONP1 inhibitors using structure-based drug design as well as the first structures of human LONP1 bound to various inhibitors. Our efforts led to several nanomolar LONP1 inhibitors with little to no activity against the 20S proteasome that serve as tool compounds to investigate LONP1 biology.
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Affiliation(s)
- Laura J Kingsley
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Xiaohui He
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Matthew McNeill
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - John Nelson
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Victor Nikulin
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Zhiwei Ma
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Wenshuo Lu
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Vicki W Zhou
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Mari Manuia
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Andreas Kreusch
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Mu-Yun Gao
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Darbi Witmer
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Mei-Ting Vaillancourt
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Min Lu
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Sarah Greenblatt
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Christian Lee
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Ajay Vashisht
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Steven Bender
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Glen Spraggon
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Pierre-Yves Michellys
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Yong Jia
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Jacob R Haling
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
| | - Gérald Lelais
- Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Dr., San Diego, California 92121, United States
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Ripstein ZA, Vahidi S, Houry WA, Rubinstein JL, Kay LE. A processive rotary mechanism couples substrate unfolding and proteolysis in the ClpXP degradation machinery. eLife 2020; 9:e52158. [PMID: 31916936 PMCID: PMC7112952 DOI: 10.7554/elife.52158] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/08/2020] [Indexed: 12/21/2022] Open
Abstract
The ClpXP degradation machine consists of a hexameric AAA+ unfoldase (ClpX) and a pair of heptameric serine protease rings (ClpP) that unfold, translocate, and subsequently degrade client proteins. ClpXP is an important target for drug development against infectious diseases. Although structures are available for isolated ClpX and ClpP rings, it remains unknown how symmetry mismatched ClpX and ClpP work in tandem for processive substrate translocation into the ClpP proteolytic chamber. Here, we present cryo-EM structures of the substrate-bound ClpXP complex from Neisseria meningitidis at 2.3 to 3.3 Å resolution. The structures allow development of a model in which the sequential hydrolysis of ATP is coupled to motions of ClpX loops that lead to directional substrate translocation and ClpX rotation relative to ClpP. Our data add to the growing body of evidence that AAA+ molecular machines generate translocating forces by a common mechanism.
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Affiliation(s)
- Zev A Ripstein
- Department of BiochemistryUniversity of TorontoTorontoCanada
- The Hospital for Sick Children Research InstituteTorontoCanada
| | - Siavash Vahidi
- Department of BiochemistryUniversity of TorontoTorontoCanada
- The Hospital for Sick Children Research InstituteTorontoCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoCanada
- Department of ChemistryUniversity of TorontoTorontoCanada
| | - Walid A Houry
- Department of BiochemistryUniversity of TorontoTorontoCanada
- Department of ChemistryUniversity of TorontoTorontoCanada
| | - John L Rubinstein
- Department of BiochemistryUniversity of TorontoTorontoCanada
- The Hospital for Sick Children Research InstituteTorontoCanada
- Department of Medical BiophysicsUniversity of TorontoTorontoCanada
| | - Lewis E Kay
- Department of BiochemistryUniversity of TorontoTorontoCanada
- The Hospital for Sick Children Research InstituteTorontoCanada
- Department of Molecular GeneticsUniversity of TorontoTorontoCanada
- Department of ChemistryUniversity of TorontoTorontoCanada
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