1
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Nechushtai R, Rowland L, Karmi O, Marjault HB, Nguyen TT, Mittal S, Ahmed RS, Grant D, Manrique-Acevedo C, Morcos F, Onuchic JN, Mittler R. CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance. Proc Natl Acad Sci U S A 2024; 121:e2405123121. [PMID: 38781208 DOI: 10.1073/pnas.2405123121] [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: 03/12/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria play a central role in muscle metabolism and function. A unique family of iron-sulfur proteins, termed CDGSH Iron Sulfur Domain-containing (CISD/NEET) proteins, support mitochondrial function in skeletal muscles. The abundance of these proteins declines during aging leading to muscle degeneration. Although the function of the outer mitochondrial CISD/NEET proteins, CISD1/mitoNEET and CISD2/NAF-1, has been defined in skeletal muscle cells, the role of the inner mitochondrial CISD protein, CISD3/MiNT, is currently unknown. Here, we show that CISD3 deficiency in mice results in muscle atrophy that shares proteomic features with Duchenne muscular dystrophy. We further reveal that CISD3 deficiency impairs the function and structure of skeletal muscles, as well as their mitochondria, and that CISD3 interacts with, and donates its [2Fe-2S] clusters to, complex I respiratory chain subunit NADH Ubiquinone Oxidoreductase Core Subunit V2 (NDUFV2). Using coevolutionary and structural computational tools, we model a CISD3-NDUFV2 complex with proximal coevolving residue interactions conducive of [2Fe-2S] cluster transfer reactions, placing the clusters of the two proteins 10 to 16 Å apart. Taken together, our findings reveal that CISD3/MiNT is important for supporting the biogenesis and function of complex I, essential for muscle maintenance and function. Interventions that target CISD3 could therefore impact different muscle degeneration syndromes, aging, and related conditions.
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Affiliation(s)
- Rachel Nechushtai
- Plant & Environmental Sciences, The Alexander Silberman Institute of Life Science and The Wolfson Centre for Applied Structural Biology, Faculty of Science and Mathematics, The Edmond J. Safra Campus at Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Linda Rowland
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65201
| | - Ola Karmi
- Plant & Environmental Sciences, The Alexander Silberman Institute of Life Science and The Wolfson Centre for Applied Structural Biology, Faculty of Science and Mathematics, The Edmond J. Safra Campus at Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Henri-Baptiste Marjault
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65201
| | - Thi Thao Nguyen
- Gehrke Proteomics Center, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211
| | - Shubham Mittal
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080
| | - Raheel S Ahmed
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080
| | - DeAna Grant
- Electron Microscopy Core Facility, University of Missouri, NextGen Precision Health Institute, Columbia, MO 65211
| | - Camila Manrique-Acevedo
- Division of Endocrinology and Metabolism, Department of Medicine, University of Missouri, Columbia, MO 65201
- NextGen Precision Health, University of Missouri, Columbia, MO 65201
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201
| | - Faruck Morcos
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX 75080
- Department of Physics, University of Texas at Dallas, Richardson, TX 75080
- Center for Systems Biology, University of Texas at Dallas, Richardson, TX 75080
| | - José N Onuchic
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77005
- Department of Physics and Astronomy, Rice University, Houston, TX 77005
- Department of Chemistry, Rice University, Houston, TX 77005
- Department of Biosciences, Rice University, Houston, TX 77005
| | - Ron Mittler
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65201
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2
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Vallières C, Benoit O, Guittet O, Huang ME, Lepoivre M, Golinelli-Cohen MP, Vernis L. Iron-sulfur protein odyssey: exploring their cluster functional versatility and challenging identification. Metallomics 2024; 16:mfae025. [PMID: 38744662 DOI: 10.1093/mtomcs/mfae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Iron-sulfur (Fe-S) clusters are an essential and ubiquitous class of protein-bound prosthetic centers that are involved in a broad range of biological processes (e.g. respiration, photosynthesis, DNA replication and repair and gene regulation) performing a wide range of functions including electron transfer, enzyme catalysis, and sensing. In a general manner, Fe-S clusters can gain or lose electrons through redox reactions, and are highly sensitive to oxidation, notably by small molecules such as oxygen and nitric oxide. The [2Fe-2S] and [4Fe-4S] clusters, the most common Fe-S cofactors, are typically coordinated by four amino acid side chains from the protein, usually cysteine thiolates, but other residues (e.g. histidine, aspartic acid) can also be found. While diversity in cluster coordination ensures the functional variety of the Fe-S clusters, the lack of conserved motifs makes new Fe-S protein identification challenging especially when the Fe-S cluster is also shared between two proteins as observed in several dimeric transcriptional regulators and in the mitoribosome. Thanks to the recent development of in cellulo, in vitro, and in silico approaches, new Fe-S proteins are still regularly identified, highlighting the functional diversity of this class of proteins. In this review, we will present three main functions of the Fe-S clusters and explain the difficulties encountered to identify Fe-S proteins and methods that have been employed to overcome these issues.
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Affiliation(s)
- Cindy Vallières
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Orane Benoit
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Olivier Guittet
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Meng-Er Huang
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Michel Lepoivre
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Marie-Pierre Golinelli-Cohen
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
| | - Laurence Vernis
- Université Paris-Saclay, Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Gif-sur-Yvette cedex 91198, France
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3
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Meyniel-Schicklin L, Amaudrut J, Mallinjoud P, Guillier F, Mangeot PE, Lines L, Aublin-Gex A, Scholtes C, Punginelli C, Joly S, Vasseur F, Manet E, Gruffat H, Henry T, Halitim F, Paparin JL, Machin P, Darteil R, Sampson D, Mikaelian I, Lane L, Navratil V, Golinelli-Cohen MP, Terzi F, André P, Lotteau V, Vonderscher J, Meldrum EC, de Chassey B. Viruses traverse the human proteome through peptide interfaces that can be biomimetically leveraged for drug discovery. Proc Natl Acad Sci U S A 2024; 121:e2308776121. [PMID: 38252831 PMCID: PMC10835127 DOI: 10.1073/pnas.2308776121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
We present a drug design strategy based on structural knowledge of protein-protein interfaces selected through virus-host coevolution and translated into highly potential small molecules. This approach is grounded on Vinland, the most comprehensive atlas of virus-human protein-protein interactions with annotation of interacting domains. From this inspiration, we identified small viral protein domains responsible for interaction with human proteins. These peptides form a library of new chemical entities used to screen for replication modulators of several pathogens. As a proof of concept, a peptide from a KSHV protein, identified as an inhibitor of influenza virus replication, was translated into a small molecule series with low nanomolar antiviral activity. By targeting the NEET proteins, these molecules turn out to be of therapeutic interest in a nonalcoholic steatohepatitis mouse model with kidney lesions. This study provides a biomimetic framework to design original chemistries targeting cellular proteins, with indications going far beyond infectious diseases.
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Affiliation(s)
| | | | | | | | - Philippe E. Mangeot
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | | | - Anne Aublin-Gex
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Caroline Scholtes
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Claire Punginelli
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | | | - Florence Vasseur
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département “Croissance et Signalisation”, Paris75015, France
| | - Evelyne Manet
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Henri Gruffat
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Thomas Henry
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | | | | | | | | | | | - Ivan Mikaelian
- Université de Lyon, Université Claude Bernard Lyon 1, INSERM 1052, CNRS 5286, Centre Léon Bérard, Centre de recherche en cancérologie de Lyon, Lyon69373, France
| | - Lydie Lane
- Computer and Laboratory Investigation of Proteins of Human Origin Group, Swiss Institute of Bioinformatics, Lausanne1015, Switzerland
| | - Vincent Navratil
- Pôle Rhône-Alpes de bioinformatique, Rhône-Alpes Bioinformatics Center, Université Lyon 1, Villeurbanne69622, France
- European Virus Bio-informatiques Center, Jena07743, Germany
- Institut Français de Bioinformatique, IFB-core, UMS 3601, Évry91057, France
| | - Marie-Pierre Golinelli-Cohen
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, Unité Propre de Recherche 2301, Gif-sur-Yvette91198, France
| | - Fabiola Terzi
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département “Croissance et Signalisation”, Paris75015, France
| | - Patrice André
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
| | - Vincent Lotteau
- Centre International de Recherche en Infectiologie, University Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Supérieure de Lyon, Lyon69007, France
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4
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Zuo K, Kranjc A, Capelli R, Rossetti G, Nechushtai R, Carloni P. Metadynamics simulations of ligands binding to protein surfaces: a novel tool for rational drug design. Phys Chem Chem Phys 2023; 25:13819-13824. [PMID: 37184538 DOI: 10.1039/d3cp01388j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Structure-based drug design protocols may encounter difficulties to investigate poses when the biomolecular targets do not exhibit typical binding pockets. In this study, by providing two concrete examples from our labs, we suggest that the combination of metadynamics free energy methods (validated against affinity measurements), along with experimental structural information (by X-ray crystallography and NMR), can help to identify the poses of ligands on protein surfaces. The simulation workflow proposed here was implemented in a widely used code, namely GROMACS, and it could straightforwardly be applied to various drug-design campaigns targeting ligands' binding to protein surfaces.
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Affiliation(s)
- Ke Zuo
- Computational Biomedicine, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52425, Germany.
- Department of Physics, RWTH Aachen University, Aachen 52074, Germany
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
- Department of Physics, Università degli Studi di Ferrara, Ferrara 44121, Italy
| | - Agata Kranjc
- Computational Biomedicine, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52425, Germany.
| | - Riccardo Capelli
- Department of Biosciences, Università degli Studi di Milano, Via Celoria 26, Milan 20133, Italy
| | - Giulia Rossetti
- Computational Biomedicine, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52425, Germany.
- Jülich Supercomputing Center (JSC), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
- Department of Neurology, Faculty of Medicine, RWTH Aachen University, Aachen 52074, Germany
| | - Rachel Nechushtai
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 91904, Israel
| | - Paolo Carloni
- Computational Biomedicine, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52425, Germany.
- Department of Physics, RWTH Aachen University, Aachen 52074, Germany
- JARA Institute: Molecular Neuroscience and Imaging, Institute of Neuroscience and Medicine INM-11, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
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5
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Iron metabolism and ferroptosis in type 2 diabetes mellitus and complications: mechanisms and therapeutic opportunities. Cell Death Dis 2023; 14:186. [PMID: 36882414 PMCID: PMC9992652 DOI: 10.1038/s41419-023-05708-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/18/2023] [Accepted: 02/22/2023] [Indexed: 03/09/2023]
Abstract
The maintenance of iron homeostasis is essential for proper endocrine function. A growing body of evidence suggests that iron imbalance is a key factor in the development of several endocrine diseases. Nowadays, ferroptosis, an iron-dependent form of regulated cell death, has become increasingly recognized as an important process to mediate the pathogenesis and progression of type 2 diabetes mellitus (T2DM). It has been shown that ferroptosis in pancreas β cells leads to decreased insulin secretion; and ferroptosis in the liver, fat, and muscle induces insulin resistance. Understanding the mechanisms concerning the regulation of iron metabolism and ferroptosis in T2DM may lead to improved disease management. In this review, we summarized the connection between the metabolic pathways and molecular mechanisms of iron metabolism and ferroptosis in T2DM. Additionally, we discuss the potential targets and pathways concerning ferroptosis in treating T2DM and analysis the current limitations and future directions concerning these novel T2DM treatment targets.
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6
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Grifagni D, Silva JM, Cantini F, Piccioli M, Banci L. Relaxation-based NMR assignment: Spotlights on ligand binding sites in human CISD3. J Inorg Biochem 2023; 239:112089. [PMID: 36502664 DOI: 10.1016/j.jinorgbio.2022.112089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/26/2022] [Accepted: 12/01/2022] [Indexed: 12/12/2022]
Abstract
CISD3 is a mitochondrial protein belonging to the NEET proteins family, bearing two [Fe2S2] clusters coordinated by CDGSH domains. At variance with the other proteins of the NEET family, very little is known about its structure-function relationships. NMR is the only technique to obtain information at the atomic level in solution on the residues involved in intermolecular interactions; however, in paramagnetic proteins this is limited by the broadening of signals of residues around the paramagnetic center. Tailored experiments can revive signals of the cluster surrounding; however, signals identification without specific residue assignment remains useless. Here, we show how paramagnetic relaxation can drive the signal assignment of residues in the proximity of the paramagnetic center(s). This allowed us to identify the potential key players of the biological function of the CISD3 protein.
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Affiliation(s)
- Deborah Grifagni
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - José M Silva
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Francesca Cantini
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Mario Piccioli
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Lucia Banci
- Magnetic Resonance Center and Department of Chemistry, University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy; Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
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7
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Zuo K, Capelli R, Rossetti G, Nechushtai R, Carloni P. Predictions of the Poses and Affinity of a Ligand over the Entire Surface of a NEET Protein: The Case of Human MitoNEET. J Chem Inf Model 2023; 63:643-654. [PMID: 36623826 PMCID: PMC9875805 DOI: 10.1021/acs.jcim.2c01280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Indexed: 01/11/2023]
Abstract
Human NEET proteins contain two [2Fe-2S] iron-sulfur clusters, bound to three Cys residues and one His residue. They exist in two redox states. Recently, these proteins have revealed themselves as attractive drug targets for mitochondrial dysfunction-related diseases, such as type 2 diabetes, Wolfram syndrome 2, and cancers. Unfortunately, the lack of information and mechanistic understanding of ligands binding to the whole functional, cytoplasmatic domain has limited rational drug design approaches. Here, we use an enhanced sampling technique, volume-based metadynamics, recently developed by a team involving some of us, to predict the poses and affinity of the 2-benzamido-4-(1,2,3,4-tetrahydronaphthalen-2-yl)-thiophene-3-carboxylate ligand to the entire surface of the cytoplasmatic domain of the human NEET protein mitoNEET (mNT) in an aqueous solution. The calculations, based on the recently published X-ray structure of the complex, are consistent with the measured affinity. The calculated free energy landscape revealed that the ligand can bind in multiple sites and with poses other than the one found in the X-ray. This difference is likely to be caused by crystal packing effects that allow the ligand to interact with multiple adjacent NEET protein copies. Such extra contacts are of course absent in the solution; therefore, the X-ray pose is only transient in our calculations, where the binding free energy correlates with the number of contacts. We further evaluated how the reduction and protonation of the Fe-bound histidine, as well as temperature, can affect ligand binding. Both such modifications introduce the possibility for the ligand to bind in an area of the protein other than the one observed in the X-ray, with no or little impact on affinity. Overall, our study can provide insights on the molecular recognition mechanisms of ligand binding to mNT in different oxidative conditions, possibly helping rational drug design of NEET ligands.
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Affiliation(s)
- Ke Zuo
- The
Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904 Jerusalem, Israel
- Department
of Physics, RWTH Aachen University, 52074 Aachen, Germany
- Computational
Biomedicine, Institute of Advanced Simulation IAS-5 and Institute
of Neuroscience and Medicine INM-9, Forschungszentrum
Jülich GmbH, 52425 Jülich, Germany
- Department
of Physics, Università di Ferrara, 44121 Ferrara, Italy
| | - Riccardo Capelli
- Department
of Biosciences, Università degli
Studi di Milano, Via
Celoria 26, 20133 Milan, Italy
| | - Giulia Rossetti
- Computational
Biomedicine, Institute of Advanced Simulation IAS-5 and Institute
of Neuroscience and Medicine INM-9, Forschungszentrum
Jülich GmbH, 52425 Jülich, Germany
- Jülich
Supercomputing Center (JSC), Forschungszentrum
Jülich GmbH, 52425 Jülich, Germany
- Department
of Neurology, Faculty of Medicine, RWTH
Aachen University, 52074 Aachen, Germany
| | - Rachel Nechushtai
- The
Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, 91904 Jerusalem, Israel
| | - Paolo Carloni
- Department
of Physics, RWTH Aachen University, 52074 Aachen, Germany
- Computational
Biomedicine, Institute of Advanced Simulation IAS-5 and Institute
of Neuroscience and Medicine INM-9, Forschungszentrum
Jülich GmbH, 52425 Jülich, Germany
- JARA
Institute: Molecular Neuroscience and Imaging, Institute of Neuroscience
and Medicine INM-11, Forschungszentrum Jülich
GmbH, 52425 Jülich, Germany
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8
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Liu F, Dong Y, Zhong F, Guo H, Dong P. CISD1 Is a Breast Cancer Prognostic Biomarker Associated with Diabetes Mellitus. Biomolecules 2022; 13:biom13010037. [PMID: 36671422 PMCID: PMC9855828 DOI: 10.3390/biom13010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Women with diabetes mellitus are believed to have increased risk of developing breast cancer and lower life expectancies. This study aims to depict the association between the CISD1, the co-expressed genes, and diabetes mellitus to offer potential therapeutic targets for further mechanical research. The TCGA-BRCA RNAseq data is acquired. All the data and analyzed using R packages and web-based bioinformatics tools. CISD1 gene expression was evaluated between tumor bulk and adjacent tissue. Immune cell infiltration evaluation was performed. CISD1 expressed significantly higher in tumor tissue than that of the normal tissue, indicating poor overall survival rates. High expression level of CISD1 in tumor shows less pDC and NK cells penetration. There are 138 genes shared between CISD1 co-expressed gene pool in BRCA and diabetes mellitus related genes using "diabetes" as the term for text mining. These shared genes enrich in "cell cycle" and other pathways. MCODE analysis demonstrates that p53-independent G1/S DNA damage checkpoint, p53-independent DNA damage response, and ubiquitin mediated degradation of phosphorylated cdc25A are top-ranked than other terms. CISD1 and co-expressed genes, especially shared ones with diabetes mellitus, can be the focused genes considered when addressing clinical problems in breast cancer with a diabetes mellitus background.
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Affiliation(s)
- Fangfang Liu
- Department of Breast Cancer Pathology and Research Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China
| | - Yifeng Dong
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Fuyu Zhong
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Haodan Guo
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
| | - Pengzhi Dong
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin 301617, China
- Correspondence:
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9
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Nnatubeugo C, Johnson E, Gisondi S, Roland F, Geldenhuys WJ, Menze MA, Konkle ME. The Mitochondrial Protein MitoNEET as a Probe for the Allostery of Glutamate Dehydrogenase. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238314. [PMID: 36500407 PMCID: PMC9737137 DOI: 10.3390/molecules27238314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/22/2022] [Accepted: 11/24/2022] [Indexed: 12/02/2022]
Abstract
The proteins glutamate dehydrogenase (GDH) and mitoNEET are both targets of drug development efforts to treat metabolic disorders, cancer, and neurodegenerative diseases. However, these two proteins differ starkly in the current knowledge about ligand binding sites. MitoNEET is a [2Fe-2S]-containing protein with no obvious binding site for small ligands observed in its crystal structures. In contrast, GDH is known to have a variety of ligands at multiple allosteric sites thereby leading to complex regulation in activity. In fact, while GDH can utilize either NAD(H) or NADP(H) for catalysis at the active site, only NAD(H) binds at a regulatory site to inhibit GDH activity. Previously, we found that mitoNEET forms a covalent bond with GDH in vitro and increases the catalytic activity of the enzyme. In this study we evaluated the effects of mitoNEET binding on the allosteric control of GDH conferred by inhibitors. We examined all effectors using NAD or NADP as the coenzyme to determine allosteric linkage by the NAD-binding regulatory site. We found that GDH activity, in the presence of the inhibitory palmitoyl-CoA and EGCG, can be rescued by mitoNEET, regardless of the coenzyme used. This suggests that mitoNEET rescues GDH by stabilizing the open conformation.
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Affiliation(s)
- Chimere Nnatubeugo
- Department of Chemistry, Ball State University, 2000 W. University Avenue, Muncie, IN 47306, USA
| | - Erica Johnson
- Department of Chemistry, Ball State University, 2000 W. University Avenue, Muncie, IN 47306, USA
| | - Sarah Gisondi
- Department of Chemistry, Eastern Illinois University, Charleston, IL 61920, USA
| | - Felicia Roland
- Department of Chemistry, Eastern Illinois University, Charleston, IL 61920, USA
| | - Werner J. Geldenhuys
- Pharmaceutical Sciences, School of Pharmacy, West Virginia University, Morgantown, WV 26506, USA
- Department of Neuroscience, School of Medicine, West Virginia University, Morgantown, WV 26505, USA
| | - Michael A. Menze
- Department of Biology, University of Louisville, Louisville, KY 40292, USA
| | - Mary E. Konkle
- Department of Chemistry, Ball State University, 2000 W. University Avenue, Muncie, IN 47306, USA
- Department of Chemistry, Eastern Illinois University, Charleston, IL 61920, USA
- Correspondence:
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Marjault HB, Yang-Sung S, Zuo K, Carloni P, Mittler R, Nechushtai R. Structure-Based Screening Reveals a Ligand That Stabilizes the [2Fe-2S] Clusters of Human mitoNEET and Reduces Ovarian Cancer Cell Proliferation. J Phys Chem B 2022; 126:9559-9565. [PMID: 36374279 DOI: 10.1021/acs.jpcb.2c05728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Human NEET proteins play an important role in a variety of diseases, including cancer. Using the recently published X-ray structure of the human mNT-M1 complex, we screened a commercial chemical compound library and identified a new human mitoNEET (mNT) binding ligand (NTS-01). Biochemical investigations revealed that NTS-01 specifically binds to the human mNT protein and stabilizes its [2Fe-2S] clusters under oxidative conditions in vitro. Treatment of ovarian cancer cells with NTS-01 induces ovarian cancer (SKOV-3) mitochondrial fragmentation (fission) and reduces ovarian cancer cell proliferation in a 2D single-layer cell culture, as well as in a 3D-spheroids culture. The NTS-01 molecule represents therefore a new lead compound for further drug design studies attempting to develop efficient treatment against ovarian cancer.
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Affiliation(s)
- Henri-Baptiste Marjault
- The Alexander Silberman Institute of Life Science and The Wolfson Centre for Applied Structural Biology, Faculty of Science and Mathematics, The Edmond J. Safra Campus at Givat Ram, The Hebrew University of Jerusalem, Jerusalem91904, Israel
- Department of Physics, RWTH Aachen University, 52074Aachen, Germany
| | - Sohn Yang-Sung
- The Alexander Silberman Institute of Life Science and The Wolfson Centre for Applied Structural Biology, Faculty of Science and Mathematics, The Edmond J. Safra Campus at Givat Ram, The Hebrew University of Jerusalem, Jerusalem91904, Israel
| | - Ke Zuo
- The Alexander Silberman Institute of Life Science and The Wolfson Centre for Applied Structural Biology, Faculty of Science and Mathematics, The Edmond J. Safra Campus at Givat Ram, The Hebrew University of Jerusalem, Jerusalem91904, Israel
- Department of Physics, RWTH Aachen University, 52074Aachen, Germany
| | - Paolo Carloni
- Department of Physics, RWTH Aachen University, 52074Aachen, Germany
- Computational Biomedicine Section, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52425Jülich, Germany
- Computational Biomedicine, Institute of Advanced Simulation IAS-5 and Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52425Jülich, Germany
- JARA Institute: Molecular Neuroscience and Imaging, Institute of Neuroscience and Medicine INM-11, Forschungszentrum Jülich GmbH, 52425Jülich, Germany
| | - Ron Mittler
- Department of Surgery, University of Missouri School of Medicine, and Interdisciplinary Plant Group, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, Missouri65211, United States
| | - Rachel Nechushtai
- The Alexander Silberman Institute of Life Science and The Wolfson Centre for Applied Structural Biology, Faculty of Science and Mathematics, The Edmond J. Safra Campus at Givat Ram, The Hebrew University of Jerusalem, Jerusalem91904, Israel
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