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Tavoulari S, Sichrovsky M, Kunji ERS. Fifty years of the mitochondrial pyruvate carrier: New insights into its structure, function, and inhibition. Acta Physiol (Oxf) 2023; 238:e14016. [PMID: 37366179 PMCID: PMC10909473 DOI: 10.1111/apha.14016] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023]
Abstract
The mitochondrial pyruvate carrier (MPC) resides in the mitochondrial inner membrane, where it links cytosolic and mitochondrial metabolism by transporting pyruvate produced in glycolysis into the mitochondrial matrix. Due to its central metabolic role, it has been proposed as a potential drug target for diabetes, non-alcoholic fatty liver disease, neurodegeneration, and cancers relying on mitochondrial metabolism. Little is known about the structure and mechanism of MPC, as the proteins involved were only identified a decade ago and technical difficulties concerning their purification and stability have hindered progress in functional and structural analyses. The functional unit of MPC is a hetero-dimer comprising two small homologous membrane proteins, MPC1/MPC2 in humans, with the alternative complex MPC1L/MPC2 forming in the testis, but MPC proteins are found throughout the tree of life. The predicted topology of each protomer consists of an amphipathic helix followed by three transmembrane helices. An increasing number of inhibitors are being identified, expanding MPC pharmacology and providing insights into the inhibitory mechanism. Here, we provide critical insights on the composition, structure, and function of the complex and we summarize the different classes of small molecule inhibitors and their potential in therapeutics.
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Affiliation(s)
- Sotiria Tavoulari
- Medical Research Council Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Maximilian Sichrovsky
- Medical Research Council Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
| | - Edmund R. S. Kunji
- Medical Research Council Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
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2
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Tavoulari S, Schirris TJJ, Mavridou V, Thangaratnarajah C, King MS, Jones DTD, Ding S, Fearnley IM, Kunji ERS. Key features of inhibitor binding to the human mitochondrial pyruvate carrier hetero-dimer. Mol Metab 2022; 60:101469. [PMID: 35278701 PMCID: PMC8968063 DOI: 10.1016/j.molmet.2022.101469] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE The mitochondrial pyruvate carrier (MPC) has emerged as a promising drug target for metabolic disorders, including non-alcoholic steatohepatitis and diabetes, metabolically dependent cancers and neurodegenerative diseases. A range of structurally diverse small molecule inhibitors have been proposed, but the nature of their interaction with MPC is not understood, and the composition of the functional human MPC is still debated. The goal of this study was to characterise the human MPC protein in vitro, to understand the chemical features that determine binding of structurally diverse inhibitors and to develop novel higher affinity ones. METHODS We recombinantly expressed and purified human MPC hetero-complexes and studied their composition, transport and inhibitor binding properties by establishing in vitro transport assays, high throughput thermostability shift assays and pharmacophore modeling. RESULTS We determined that the functional unit of human MPC is a hetero-dimer. We compared all different classes of MPC inhibitors to find that three closely arranged hydrogen bond acceptors followed by an aromatic ring are shared characteristics of all inhibitors and represent the minimal requirement for high potency. We also demonstrated that high affinity binding is not attributed to covalent bond formation with MPC cysteines, as previously proposed. Following the basic pharmacophore properties, we identified 14 new inhibitors of MPC, one outperforming compound UK5099 by tenfold. Two are the commonly prescribed drugs entacapone and nitrofurantoin, suggesting an off-target mechanism associated with their adverse effects. CONCLUSIONS This work defines the composition of human MPC and the essential MPC inhibitor characteristics. In combination with the functional assays we describe, this new understanding will accelerate the development of clinically relevant MPC modulators.
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Affiliation(s)
- Sotiria Tavoulari
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom.
| | - Tom J J Schirris
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Vasiliki Mavridou
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Chancievan Thangaratnarajah
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Martin S King
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Daniel T D Jones
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Shujing Ding
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Ian M Fearnley
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom.
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Wang Y, Liu Y, Yuan Y, Zhang Y, Luo Y, Han S, Yan Y, Wang Z, Liu X, Zhao L. Downregulation of mitochondrial pyruvate carrier 2 aggravates neuronal injury in the cortex following cerebral ischemia in rat. Brain Res Bull 2022; 185:193-202. [DOI: 10.1016/j.brainresbull.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/18/2022] [Accepted: 05/11/2022] [Indexed: 11/02/2022]
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Zeng Q, Si H, Lv K, Mo J, Wang X, Yan B, Zhang J. Determination and pharmacokinetics study of UK-5099 in mouse plasma by LC-MS/MS. BMC Vet Res 2022; 18:145. [PMID: 35443692 PMCID: PMC9020015 DOI: 10.1186/s12917-022-03245-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 04/12/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND UK-5099 is a potent mitochondrial acetone carrier inhibitor, that exhibits anticancer activity. Recently, the anti-Toxoplasma gondii activity of UK-5099 was proposed, and in vivo studies of its pharmacokinetics in BALB/c mice are necessary to further evaluate the clinical effect of UK-5099. METHODS AND RESULTS A simple and fast high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) analysis method was established and verified in terms of its linearity, matrix effect, accuracy, precision, recovery and stability. The analytes were separated by an Agilent ZORBAX XDB-C18 column (2.1 × 50 mm, 3.5 μm) at 30 °C. A gradient mobile phase consisting of water with 0.1% formic acid (FA) (phase A) and acetonitrile (ACN) (phase B) was delivered at a flow rate of 0.40 mL·min-1 with an injection volume of 5 μL. A good linear response was obtained in a concentration range of 5-5000 ng·mL-1 (r2 = 0.9947). The lower limit of quantification (LLOQ) was 5 ng·mL-1. The extraction recovery of UK-5099 was greater than 95%. The inter- and intra-day accuracy and precision of the method showed relative standard deviations (RSDs) of less than 15%. This method has been successfully applied to the pharmacokinetic evaluation of UK-5099 in mouse plasma. In health mice, the main pharmacokinetic parameters of UK-5099 after intraperitoneal administration were measured using a noncompartmental model, in which the AUC0-t was 42,103 ± 12,072 ng·h·mL-1 and the MRT0-t was 0.857 ± 0.143 h. The peak concentration (Cmax) was 82,500 ± 20,745 ng·h·mL-1, which occurred at a peak time (Tmax) = 0.250 ± 0.000 h. CONCLUSIONS A fast and sensitive HPLC-MS/MS method was developed, validated and successfully used for the determination of UK-5099 levels in mice after intraperitoneal administration. This study was the first report of the pharmacokinetic parameters of UK-5099 in mice, which will help to further study the administration of UK-5099 in animals and humans.
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Affiliation(s)
- Qingyuan Zeng
- Intensive Care Unit, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China.,Ningbo University School of Medicine, Ningbo University, Ningbo, China
| | - Hongfei Si
- College of Pharmacy, Jinan University, Guangzhou, China
| | - Kun Lv
- Ningbo University School of Business, Ningbo University, Ningbo, China
| | - Jiao Mo
- Ningbo University School of Medicine, Ningbo University, Ningbo, China
| | - Xinnian Wang
- Intensive Care Unit, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Biqing Yan
- Intensive Care Unit, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China
| | - Jili Zhang
- Intensive Care Unit, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, China. .,Ningbo University School of Medicine, Ningbo University, Ningbo, China. .,Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 315211, China.
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Xu L, Phelix CF, Chen LY. Structural Insights into the Human Mitochondrial Pyruvate Carrier Complexes. J Chem Inf Model 2021; 61:5614-5625. [PMID: 34664967 DOI: 10.1021/acs.jcim.1c00879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyruvate metabolism requires the mitochondrial pyruvate carrier (MPC) proteins to transport pyruvate from the intermembrane space through the inner mitochondrial membrane to the mitochondrial matrix. The lack of the atomic structures of MPC hampers the understanding of the functional states of MPC and molecular interactions with the substrate or inhibitor. Here, we develop the de novo models of human MPC complexes and characterize the conformational dynamics of the MPC heterodimer formed by MPC1 and MPC2 (MPC1/2) by computational simulations. Our results reveal that functional MPC1/2 prefers to adopt an inward-open conformation, with the carrier open to the matrix side, whereas the outward-open states are less populated. The energy barrier for pyruvate transport in MPC1/2 is low enough, and the inhibitor UK5099 blocks the pyruvate transport by stably binding to MPC1/2. Notably, consistent with experimental results, the MPC1 L79H mutation significantly alters the conformations of MPC1/2 and thus fails for substrate transport. However, the MPC1 R97W mutation seems to retain the transport activity. The present de novo models of MPC complexes provide structural insights into the conformational states of MPC complexes and mechanistic understanding of interactions between the substrate/inhibitor and MPC proteins.
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Affiliation(s)
- Liang Xu
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
| | - Clyde F Phelix
- Department of Integrative Biology, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
| | - Liao Y Chen
- Department of Physics and Astronomy, The University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, United States
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Sutanto F, Shaabani S, Neochoritis CG, Zarganes-Tzitzikas T, Patil P, Ghonchepour E, Dömling A. Multicomponent reaction-derived covalent inhibitor space. SCIENCE ADVANCES 2021; 7:eabd9307. [PMID: 33536213 PMCID: PMC7857676 DOI: 10.1126/sciadv.abd9307] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/15/2020] [Indexed: 05/16/2023]
Abstract
The area of covalent inhibitors is gaining momentum due to recently introduced clinical drugs, but libraries of these compounds are scarce. Multicomponent reaction (MCR) chemistry is well known for its easy access to a very large and diverse chemical space. Here, we show that MCRs are highly suitable to generate libraries of electrophiles based on different scaffolds and three-dimensional shapes and highly compatible with multiple functional groups. According to the building block principle of MCR, acrylamide, acrylic acid ester, sulfurylfluoride, chloroacetic acid amide, nitrile, and α,β-unsaturated sulfonamide warheads can be easily incorporated into many different scaffolds. We show examples of each electrophile on 10 different scaffolds on a preparative scale as well as in a high-throughput synthesis mode on a nanoscale to produce libraries of potential covalent binders in a resource- and time-saving manner. Our operational procedure is simple, mild, and step economical to facilitate future covalent library synthesis.
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Affiliation(s)
- Fandi Sutanto
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Shabnam Shaabani
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | | | - Tryfon Zarganes-Tzitzikas
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Pravin Patil
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Ehsan Ghonchepour
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9700 AD Groningen, The Netherlands
| | - Alexander Dömling
- Department of Drug Design, University of Groningen, A. Deusinglaan 1, 9700 AD Groningen, The Netherlands.
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Insights on the Quest for the Structure-Function Relationship of the Mitochondrial Pyruvate Carrier. BIOLOGY 2020; 9:biology9110407. [PMID: 33227948 PMCID: PMC7699257 DOI: 10.3390/biology9110407] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/14/2020] [Accepted: 11/17/2020] [Indexed: 01/19/2023]
Abstract
Simple Summary The atomic structure of a biological macromolecule determines its function. Discovering how one or more amino acid chains fold and interact to form a protein complex is critical, from understanding the most fundamental cellular processes to developing new therapies. However, this is far from a straightforward task, especially when studying a membrane protein. The functional link between the oligomeric state and complex composition of the proteins involved in the active mitochondrial transport of cytosolic pyruvate is a decades-old question but remains urgent. We present a brief historical review beginning with the identification of the so-called mitochondrial pyruvate carrier (MPC) proteins, followed by a rigorous conceptual analysis of technical approaches in more recent biochemical studies that seek to isolate and reconstitute the functional MPC complex(es) in vitro. We correlate these studies with early kinetic observations and current experimental and computational knowledge to assess their main contributions, identify gaps, resolve ambiguities, and better define the research goal. Abstract The molecular identity of the mitochondrial pyruvate carrier (MPC) was presented in 2012, forty years after the active transport of cytosolic pyruvate into the mitochondrial matrix was first demonstrated. An impressive amount of in vivo and in vitro studies has since revealed an unexpected interplay between one, two, or even three protein subunits defining different functional MPC assemblies in a metabolic-specific context. These have clear implications in cell homeostasis and disease, and on the development of future therapies. Despite intensive efforts by different research groups using state-of-the-art computational tools and experimental techniques, MPCs’ structure-based mechanism remains elusive. Here, we review the current state of knowledge concerning MPCs’ molecular structures by examining both earlier and recent studies and presenting novel data to identify the regulatory, structural, and core transport activities to each of the known MPC subunits. We also discuss the potential application of cryogenic electron microscopy (cryo-EM) studies of MPC reconstituted into nanodiscs of synthetic copolymers for solving human MPC2.
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