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Alam S, Doherty E, Ortega-Prieto P, Arizanova J, Fets L. Membrane transporters in cell physiology, cancer metabolism and drug response. Dis Model Mech 2023; 16:dmm050404. [PMID: 38037877 PMCID: PMC10695176 DOI: 10.1242/dmm.050404] [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] [Indexed: 12/02/2023] Open
Abstract
By controlling the passage of small molecules across lipid bilayers, membrane transporters influence not only the uptake and efflux of nutrients, but also the metabolic state of the cell. With more than 450 members, the Solute Carriers (SLCs) are the largest transporter super-family, clustering into families with different substrate specificities and regulatory properties. Cells of different types are, therefore, able to tailor their transporter expression signatures depending on their metabolic requirements, and the physiological importance of these proteins is illustrated by their mis-regulation in a number of disease states. In cancer, transporter expression is heterogeneous, and the SLC family has been shown to facilitate the accumulation of biomass, influence redox homeostasis, and also mediate metabolic crosstalk with other cell types within the tumour microenvironment. This Review explores the roles of membrane transporters in physiological and malignant settings, and how these roles can affect drug response, through either indirect modulation of sensitivity or the direct transport of small-molecule therapeutic compounds into cells.
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Affiliation(s)
- Sara Alam
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Emily Doherty
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Paula Ortega-Prieto
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Julia Arizanova
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
| | - Louise Fets
- Drug Transport and Tumour Metabolism Lab, MRC Laboratory of Medical Sciences, Hammersmith Hospital Campus, Du Cane Road, London, W12 0NN, UK
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2
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Kremer DM, Lyssiotis CA. Targeting allosteric regulation of cancer metabolism. Nat Chem Biol 2022; 18:441-450. [PMID: 35484254 DOI: 10.1038/s41589-022-00997-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/14/2022] [Indexed: 12/13/2022]
Abstract
Metabolic reprogramming is observed across all cancer types. Indeed, the success of many classic chemotherapies stems from their targeting of cancer metabolism. Contemporary research in this area has refined our understanding of tumor-specific metabolic mechanisms and has revealed strategies for exploiting these vulnerabilities selectively. Based on this growing understanding, new small-molecule tools and drugs have been developed to study and target tumor metabolism. Here, we highlight allosteric modulation of metabolic enzymes as an attractive mechanism of action for small molecules that target metabolic enzymes. We then discuss the mechanistic insights garnered from their application in cancer studies and highlight the achievements of this approach in targeting cancer metabolism. Finally, we discuss technological advances in drug discovery for allosteric modulators of enzyme activity.
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Affiliation(s)
- Daniel M Kremer
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA.,Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA.,Department of Chemistry, the Scripps Research Institute, La Jolla, CA, USA
| | - Costas A Lyssiotis
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI, USA. .,Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI, USA. .,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
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3
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Chung CH, Lin DW, Eames A, Chandrasekaran S. Next-Generation Genome-Scale Metabolic Modeling through Integration of Regulatory Mechanisms. Metabolites 2021; 11:606. [PMID: 34564422 PMCID: PMC8470976 DOI: 10.3390/metabo11090606] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/18/2022] Open
Abstract
Genome-scale metabolic models (GEMs) are powerful tools for understanding metabolism from a systems-level perspective. However, GEMs in their most basic form fail to account for cellular regulation. A diverse set of mechanisms regulate cellular metabolism, enabling organisms to respond to a wide range of conditions. This limitation of GEMs has prompted the development of new methods to integrate regulatory mechanisms, thereby enhancing the predictive capabilities and broadening the scope of GEMs. Here, we cover integrative models encompassing six types of regulatory mechanisms: transcriptional regulatory networks (TRNs), post-translational modifications (PTMs), epigenetics, protein-protein interactions and protein stability (PPIs/PS), allostery, and signaling networks. We discuss 22 integrative GEM modeling methods and how these have been used to simulate metabolic regulation during normal and pathological conditions. While these advances have been remarkable, there remains a need for comprehensive and widespread integration of regulatory constraints into GEMs. We conclude by discussing challenges in constructing GEMs with regulation and highlight areas that need to be addressed for the successful modeling of metabolic regulation. Next-generation integrative GEMs that incorporate multiple regulatory mechanisms and their crosstalk will be invaluable for discovering cell-type and disease-specific metabolic control mechanisms.
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Affiliation(s)
- Carolina H. Chung
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (C.H.C.); (A.E.)
| | - Da-Wei Lin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Alec Eames
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (C.H.C.); (A.E.)
| | - Sriram Chandrasekaran
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; (C.H.C.); (A.E.)
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA;
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA
- Center for Bioinformatics and Computational Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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Engberg O, Bochicchio A, Brandner AF, Gupta A, Dey S, Böckmann RA, Maiti S, Huster D. Serotonin Alters the Phase Equilibrium of a Ternary Mixture of Phospholipids and Cholesterol. Front Physiol 2020; 11:578868. [PMID: 33192582 PMCID: PMC7645218 DOI: 10.3389/fphys.2020.578868] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/06/2020] [Indexed: 12/20/2022] Open
Abstract
Unsaturated and saturated phospholipids tend to laterally segregate, especially in the presence of cholesterol. Small molecules such as neurotransmitters, toxins, drugs etc. possibly modulate this lateral segregation. The small aromatic neurotransmitter serotonin (5-HT) has been found to bind to membranes. We studied the lipid structure and packing of a ternary membrane mixture consisting of palmitoyl-oleoyl-phosphatidylcholine, palmitoyl-sphingomyelin, and cholesterol at a molar ratio of 4/4/2 in the absence and in the presence of 5-HT, using a combination of solid-state 2H NMR, atomic force microscopy, and atomistic molecular dynamics (MD) simulations. Both NMR and MD report formation of a liquid ordered (L o ) and a liquid disordered (L d ) phase coexistence with small domains. Lipid exchange between the domains was fast such that single component 2H NMR spectra are detected over a wide temperature range. A drastic restructuring of the domains was induced when 5-HT is added to the membranes at a 9 mol% concentration relative to the lipids. 2H NMR spectra of all components of the mixture showed two prominent contributions indicative of molecules of the same kind residing both in the disordered and the ordered phase. Compared to the data in the absence of 5-HT, the lipid chain order in the disordered phase was further decreased in the presence of 5-HT. Likewise, addition of serotonin increased lipid chain order within the ordered phase. These characteristic lipid chain order changes were confirmed by MD simulations. The 5-HT-induced larger difference in lipid chain order results in more pronounced differences in the hydrophobic thickness of the individual membrane domains. The correspondingly enlarged hydrophobic mismatch between ordered and disordered phases is assumed to increase the line tension at the domain boundary, which drives the system into formation of larger size domains. These results not only demonstrate that small membrane binding molecules such as neurotransmitters have a profound impact on essential membrane properties. It also suggests a mechanism by which the interaction of small molecules with membranes can influence the function of membrane proteins and non-cognate receptors. Altered membrane properties may modify lateral sorting of membrane protein, membrane protein conformation, and thus influence their function as suspected for neurotransmitters, local anesthetics, and other small drug molecules.
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Affiliation(s)
- Oskar Engberg
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
| | - Anna Bochicchio
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Astrid F. Brandner
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Ankur Gupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Simli Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Rainer A. Böckmann
- Computational Biology, Department of Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Daniel Huster
- Institute for Medical Physics and Biophysics, University of Leipzig, Leipzig, Germany
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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Macpherson JA, Theisen A, Masino L, Fets L, Driscoll PC, Encheva V, Snijders AP, Martin SR, Kleinjung J, Barran PE, Fraternali F, Anastasiou D. Functional cross-talk between allosteric effects of activating and inhibiting ligands underlies PKM2 regulation. eLife 2019; 8:e45068. [PMID: 31264961 PMCID: PMC6636998 DOI: 10.7554/elife.45068] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 07/01/2019] [Indexed: 12/18/2022] Open
Abstract
Several enzymes can simultaneously interact with multiple intracellular metabolites, however, how the allosteric effects of distinct ligands are integrated to coordinately control enzymatic activity remains poorly understood. We addressed this question using, as a model system, the glycolytic enzyme pyruvate kinase M2 (PKM2). We show that the PKM2 activator fructose 1,6-bisphosphate (FBP) alone promotes tetramerisation and increases PKM2 activity, but addition of the inhibitor L-phenylalanine (Phe) prevents maximal activation of FBP-bound PKM2 tetramers. We developed a method, AlloHubMat, that uses eigenvalue decomposition of mutual information derived from molecular dynamics trajectories to identify residues that mediate FBP-induced allostery. Experimental mutagenesis of these residues identified PKM2 variants in which activation by FBP remains intact but cannot be attenuated by Phe. Our findings reveal residues involved in FBP-induced allostery that enable the integration of allosteric input from Phe and provide a paradigm for the coordinate regulation of enzymatic activity by simultaneous allosteric inputs.
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Affiliation(s)
- Jamie A Macpherson
- Cancer Metabolism LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
- Randall Centre for Cell and Molecular BiophysicsKing’s College LondonLondonUnited Kingdom
| | - Alina Theisen
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of ChemistryUniversity of ManchesterManchesterUnited Kingdom
| | - Laura Masino
- Structural Biology Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Louise Fets
- Cancer Metabolism LaboratoryThe Francis Crick InstituteLondonUnited Kingdom
| | - Paul C Driscoll
- Metabolomics Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Vesela Encheva
- Proteomics Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Ambrosius P Snijders
- Proteomics Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Stephen R Martin
- Structural Biology Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Jens Kleinjung
- Computational Biology Science Technology PlatformThe Francis Crick InstituteLondonUnited Kingdom
| | - Perdita E Barran
- Michael Barber Centre for Collaborative Mass Spectrometry, Manchester Institute of Biotechnology, School of ChemistryUniversity of ManchesterManchesterUnited Kingdom
| | - Franca Fraternali
- Randall Centre for Cell and Molecular BiophysicsKing’s College LondonLondonUnited Kingdom
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He X, Ni D, Lu S, Zhang J. Characteristics of Allosteric Proteins, Sites, and Modulators. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:107-139. [DOI: 10.1007/978-981-13-8719-7_6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Gehrig S, Macpherson JA, Driscoll PC, Symon A, Martin SR, MacRae JI, Kleinjung J, Fraternali F, Anastasiou D. An engineered photoswitchable mammalian pyruvate kinase. FEBS J 2017; 284:2955-2980. [PMID: 28715126 PMCID: PMC5637921 DOI: 10.1111/febs.14175] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/24/2017] [Accepted: 07/13/2017] [Indexed: 01/06/2023]
Abstract
Changes in allosteric regulation of glycolytic enzymes have been linked to metabolic reprogramming involved in cancer. Remarkably, allosteric mechanisms control enzyme function at significantly shorter time-scales compared to the long-term effects of metabolic reprogramming on cell proliferation. It remains unclear if and how the speed and reversibility afforded by rapid allosteric control of metabolic enzymes is important for cell proliferation. Tools that allow specific, dynamic modulation of enzymatic activities in mammalian cells would help address this question. Towards this goal, we have used molecular dynamics simulations to guide the design of mPKM2 internal light/oxygen/voltage-sensitive domain 2 (LOV2) fusion at position D24 (PiL[D24]), an engineered pyruvate kinase M2 (PKM2) variant that harbours an insertion of the light-sensing LOV2 domain from Avena Sativa within a region implicated in allosteric regulation by fructose 1,6-bisphosphate (FBP). The LOV2 photoreaction is preserved in the PiL[D24] chimera and causes secondary structure changes that are associated with a 30% decrease in the Km of the enzyme for phosphoenolpyruvate resulting in increased pyruvate kinase activity after light exposure. Importantly, this change in activity is reversible upon light withdrawal. Expression of PiL[D24] in cells leads to light-induced increase in labelling of pyruvate from glucose. PiL[D24] therefore could provide a means to modulate cellular glucose metabolism in a remote manner and paves the way for studying the importance of rapid allosteric phenomena in the regulation of metabolism and enzyme control.
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Affiliation(s)
- Stefanie Gehrig
- Cancer Metabolism LaboratoryThe Francis Crick InstituteLondonUK
| | | | - Paul C. Driscoll
- Metabolomics Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - Alastair Symon
- Instrument Prototyping Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - Stephen R. Martin
- Structural Biology Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - James I. MacRae
- Metabolomics Science Technology PlatformThe Francis Crick InstituteLondonUK
| | - Jens Kleinjung
- Computational BiologyThe Francis Crick InstituteLondonUK
| | - Franca Fraternali
- Randall Division of Cell and Molecular BiophysicsKing's CollegeLondonUK
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Rinaldi G, Rossi M, Fendt SM. Metabolic interactions in cancer: cellular metabolism at the interface between the microenvironment, the cancer cell phenotype and the epigenetic landscape. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2017; 10. [DOI: 10.1002/wsbm.1397] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Gianmarco Rinaldi
- Laboratory of Cellular Metabolism and Metabolic Regulation; VIB Center for Cancer Biology; Leuven Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology; KU Leuven and Leuven Cancer Institute (LKI); Leuven Belgium
| | - Matteo Rossi
- Laboratory of Cellular Metabolism and Metabolic Regulation; VIB Center for Cancer Biology; Leuven Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology; KU Leuven and Leuven Cancer Institute (LKI); Leuven Belgium
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation; VIB Center for Cancer Biology; Leuven Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology; KU Leuven and Leuven Cancer Institute (LKI); Leuven Belgium
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