1
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Verkerke ARP, Shi X, Li M, Higuchi Y, Yamamuro T, Katoh D, Nishida H, Auger C, Abe I, Gerszten RE, Kajimura S. SLC25A48 controls mitochondrial choline import and metabolism. Cell Metab 2024; 36:2156-2166.e9. [PMID: 39111307 DOI: 10.1016/j.cmet.2024.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 05/05/2024] [Accepted: 07/09/2024] [Indexed: 09/06/2024]
Abstract
Choline is an essential nutrient for the biosynthesis of phospholipids, neurotransmitters, and one-carbon metabolism with a critical step being its import into mitochondria. However, the underlying mechanisms and biological significance remain poorly understood. Here, we report that SLC25A48, a previously uncharacterized mitochondrial inner-membrane carrier protein, controls mitochondrial choline transport and the synthesis of choline-derived methyl donors. We found that SLC25A48 was required for brown fat thermogenesis, mitochondrial respiration, and mitochondrial membrane integrity. Choline uptake into the mitochondrial matrix via SLC25A48 facilitated the synthesis of betaine and purine nucleotides, whereas loss of SLC25A48 resulted in increased production of mitochondrial reactive oxygen species and imbalanced mitochondrial lipids. Notably, human cells carrying a single nucleotide polymorphism on the SLC25A48 gene and cancer cells lacking SLC25A48 exhibited decreased mitochondrial choline import, increased oxidative stress, and impaired cell proliferation. Together, this study demonstrates that SLC25A48 regulates mitochondrial choline catabolism, bioenergetics, and cell survival.
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Affiliation(s)
- Anthony R P Verkerke
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Xu Shi
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Mark Li
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Yusuke Higuchi
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Tadashi Yamamuro
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Daisuke Katoh
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Hiroshi Nishida
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Christopher Auger
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA
| | - Ichitaro Abe
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA; Department of Cardiology and Clinical Examination, Oita University, Faculty of Medicine, Oita, Japan
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA, USA
| | - Shingo Kajimura
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center and Harvard Medical School, and Howard Hughes Medical Institute, Boston, MA, USA.
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2
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Alves LDF, Moore JB, Kell DB. The Biology and Biochemistry of Kynurenic Acid, a Potential Nutraceutical with Multiple Biological Effects. Int J Mol Sci 2024; 25:9082. [PMID: 39201768 PMCID: PMC11354673 DOI: 10.3390/ijms25169082] [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: 07/19/2024] [Revised: 08/16/2024] [Accepted: 08/19/2024] [Indexed: 09/03/2024] Open
Abstract
Kynurenic acid (KYNA) is an antioxidant degradation product of tryptophan that has been shown to have a variety of cytoprotective, neuroprotective and neuronal signalling properties. However, mammalian transporters and receptors display micromolar binding constants; these are consistent with its typically micromolar tissue concentrations but far above its serum/plasma concentration (normally tens of nanomolar), suggesting large gaps in our knowledge of its transport and mechanisms of action, in that the main influx transporters characterized to date are equilibrative, not concentrative. In addition, it is a substrate of a known anion efflux pump (ABCC4), whose in vivo activity is largely unknown. Exogeneous addition of L-tryptophan or L-kynurenine leads to the production of KYNA but also to that of many other co-metabolites (including some such as 3-hydroxy-L-kynurenine and quinolinic acid that may be toxic). With the exception of chestnut honey, KYNA exists at relatively low levels in natural foodstuffs. However, its bioavailability is reasonable, and as the terminal element of an irreversible reaction of most tryptophan degradation pathways, it might be added exogenously without disturbing upstream metabolism significantly. Many examples, which we review, show that it has valuable bioactivity. Given the above, we review its potential utility as a nutraceutical, finding it significantly worthy of further study and development.
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Affiliation(s)
- Luana de Fátima Alves
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Søltofts Plads, 2800 Kongens Lyngby, Denmark
| | - J. Bernadette Moore
- School of Food Science & Nutrition, University of Leeds, Leeds LS2 9JT, UK;
- Department of Biochemistry, Cell & Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
| | - Douglas B. Kell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Building 220, Søltofts Plads, 2800 Kongens Lyngby, Denmark
- Department of Biochemistry, Cell & Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St., Liverpool L69 7ZB, UK
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3
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Gelová Z, Ingles-Prieto A, Bohstedt T, Frommelt F, Chi G, Chang YN, Garcia J, Wolf G, Azzollini L, Tremolada S, Scacioc A, Hansen JS, Serrano I, Droce A, Bernal JC, Burgess-Brown NA, Carpenter EP, Dürr KL, Kristensen P, Geertsma ER, Štefanić S, Scarabottolo L, Wiedmer T, Puetter V, Sauer DB, Superti-Furga G. Protein Binder Toolbox for Studies of Solute Carrier Transporters. J Mol Biol 2024; 436:168665. [PMID: 38878854 DOI: 10.1016/j.jmb.2024.168665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 07/01/2024]
Abstract
Transporters of the solute carrier superfamily (SLCs) are responsible for the transmembrane traffic of the majority of chemical substances in cells and tissues and are therefore of fundamental biological importance. As is often the case with membrane proteins that can be heavily glycosylated, a lack of reliable high-affinity binders hinders their functional analysis. Purifying and reconstituting transmembrane proteins in their lipidic environments remains challenging and standard approaches to generate binders for multi-transmembrane proteins, such as SLCs, channels or G protein-coupled receptors (GPCRs) are lacking. While generating protein binders to 27 SLCs, we produced full length protein or cell lines as input material for binder generation by selected binder generation platforms. As a result, we obtained 525 binders for 22 SLCs. We validated the binders with a cell-based validation workflow using immunofluorescent and immunoprecipitation methods to process all obtained binders. Finally, we demonstrated the potential applications of the binders that passed our validation pipeline in structural, biochemical, and biological applications using the exemplary protein SLC12A6, an ion transporter relevant in human disease. With this work, we were able to generate easily renewable and highly specific binders against SLCs, which will greatly facilitate the study of this neglected protein family. We hope that the process will serve as blueprint for the generation of binders against the entire superfamily of SLC transporters.
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Affiliation(s)
- Zuzana Gelová
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tina Bohstedt
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gamma Chi
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Julio Garcia
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gernot Wolf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | | | - Andreea Scacioc
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jesper S Hansen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Iciar Serrano
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Aida Droce
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | | | - Nicola A Burgess-Brown
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Elisabeth P Carpenter
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Katharina L Dürr
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Peter Kristensen
- Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Eric R Geertsma
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Saša Štefanić
- Nanobody Service Facility, University of Zurich, AgroVet-Strickhof, Eschikon, Switzerland
| | | | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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4
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Redeker KEM, Brockmöller J. Several orphan solute carriers functionally identified as organic cation transporters: Substrates specificity compared with known cation transporters. J Biol Chem 2024; 300:107629. [PMID: 39098524 DOI: 10.1016/j.jbc.2024.107629] [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: 05/29/2024] [Revised: 07/10/2024] [Accepted: 07/25/2024] [Indexed: 08/06/2024] Open
Abstract
Organic cations comprise a significant part of medically relevant drugs and endogenous substances. Such substances need organic cation transporters for efficient transfer via cell membranes. However, the membrane transporters of most natural or synthetic organic cations are still unknown. To identify these transporters, genes of 10 known OCTs and 18 orphan solute carriers (SLC) were overexpressed in HEK293 cells and characterized concerning their transport activities with a broad spectrum of low molecular weight substances emphasizing organic cations. Several SLC35 transporters and SLC38A10 significantly enhanced the transport of numerous relatively hydrophobic organic cations. Significant organic cation transport activities have been found in gene families classified as transporters of other substance classes. For instance, SLC35G3 and SLC38A10 significantly accelerated the uptake of several cations, such as clonidine, 3,4-methylenedioxymethamphetamine, and nicotine, which are known as substrates of a thus far genetically unidentified proton/organic cation antiporter. The transporters SLC35G4 and SLC35F5 stood out by their significantly increased choline uptake, and several other SLC transported choline together with a broader spectrum of organic cations. Overall, there are many more polyspecific organic cation transporters than previously estimated. Several transporters had one predominant substrate but accepted some other cationic substrates, and others showed no particular preference for one substrate but transported several organic cations. The role of these transporters in biology and drug therapy remains to be elucidated.
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Affiliation(s)
- Kyra-Elisa Maria Redeker
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Georg-August-University Göttingen, Göttingen, Germany.
| | - Jürgen Brockmöller
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Georg-August-University Göttingen, Göttingen, Germany
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5
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Sha Z, Benkovic SJ. Purinosomes spatially co-localize with mitochondrial transporters. J Biol Chem 2024; 300:107620. [PMID: 39098527 DOI: 10.1016/j.jbc.2024.107620] [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: 02/22/2024] [Revised: 06/26/2024] [Accepted: 07/20/2024] [Indexed: 08/06/2024] Open
Abstract
In this study, we advance our understanding of the spatial relationship between the purinosome, a liquid condensate consisting of six enzymes involved in de novo purine biosynthesis, and mitochondria. Previous research has shown that purinosomes move along tubulin toward mitochondria, suggesting a direct uptake of glycine from mitochondria. Here, we propose that the purinosome is located proximally to the mitochondrial transporters SLC25A13 and SLC25A38, facilitating the uptake of glycine, aspartate, and glutamate, essential factors for purine synthesis. We utilized the proximity ligation assay and APEX proximity labeling to investigate the association between purinosome proteins and mitochondrial transporters. Our results indicate that purinosome assembly occurs close to the mitochondrial membrane under purine-deficient conditions, with the transporters migrating to be adjacent to the purinosome. Furthermore, both targeted and non-targeted analyses suggest that the SLC25A13-APEX2-V5 probe accurately reflects endogenous cellular status. These findings provide insights into the spatial organization of purine biosynthesis and lay the groundwork for further investigations into additional proteins involved in this pathway.
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Affiliation(s)
- Zhou Sha
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Stephen J Benkovic
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA.
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6
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Wang Y, Yang JS, Zhao M, Chen JQ, Xie HX, Yu HY, Liu NH, Yi ZJ, Liang HL, Xing L, Jiang HL. Mitochondrial endogenous substance transport-inspired nanomaterials for mitochondria-targeted gene delivery. Adv Drug Deliv Rev 2024; 211:115355. [PMID: 38849004 DOI: 10.1016/j.addr.2024.115355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/16/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
Mitochondrial genome (mtDNA) independent of nuclear gene is a set of double-stranded circular DNA that encodes 13 proteins, 2 ribosomal RNAs and 22 mitochondrial transfer RNAs, all of which play vital roles in functions as well as behaviors of mitochondria. Mutations in mtDNA result in various mitochondrial disorders without available cures. However, the manipulation of mtDNA via the mitochondria-targeted gene delivery faces formidable barriers, particularly owing to the mitochondrial double membrane. Given the fact that there are various transport channels on the mitochondrial membrane used to transfer a variety of endogenous substances to maintain the normal functions of mitochondria, mitochondrial endogenous substance transport-inspired nanomaterials have been proposed for mitochondria-targeted gene delivery. In this review, we summarize mitochondria-targeted gene delivery systems based on different mitochondrial endogenous substance transport pathways. These are categorized into mitochondrial steroid hormones import pathways-inspired nanomaterials, protein import pathways-inspired nanomaterials and other mitochondria-targeted gene delivery nanomaterials. We also review the applications and challenges involved in current mitochondrial gene editing systems. This review delves into the approaches of mitochondria-targeted gene delivery, providing details on the design of mitochondria-targeted delivery systems and the limitations regarding the various technologies. Despite the progress in this field is currently slow, the ongoing exploration of mitochondrial endogenous substance transport and mitochondrial biological phenomena may act as a crucial breakthrough in the targeted delivery of gene into mitochondria and even the manipulation of mtDNA.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Jing-Song Yang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Min Zhao
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Jia-Qi Chen
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hai-Xin Xie
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hao-Yuan Yu
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Na-Hui Liu
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Zi-Juan Yi
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hui-Lin Liang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Xing
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hu-Lin Jiang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China; College of Pharmacy, Yanbian University, Yanji 133002, China.
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7
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Theron CW, Salcedo-Sora JE, Grixti JM, Møller-Hansen I, Borodina I, Kell DB. Evidence for the Role of the Mitochondrial ABC Transporter MDL1 in the Uptake of Clozapine and Related Molecules into the Yeast Saccharomyces cerevisiae. Pharmaceuticals (Basel) 2024; 17:938. [PMID: 39065789 PMCID: PMC11279418 DOI: 10.3390/ph17070938] [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: 03/21/2024] [Revised: 05/25/2024] [Accepted: 07/08/2024] [Indexed: 07/28/2024] Open
Abstract
Clozapine is an antipsychotic drug whose accumulation in white cells can sometimes prove toxic; understanding the transporters and alleles responsible is thus highly desirable. We used a strategy in which a yeast (Saccharomyces cerevisiae) CRISPR-Cas9 knock-out library was exposed to cytotoxic concentrations of clozapine to determine those transporters whose absence made it more resistant; we also recognised the structural similarity of the fluorescent dye safranin O (also known as safranin T) to clozapine, allowing it to be used as a surrogate marker. Strains lacking the mitochondrial ABC transporter MDL1 (encoded by YLR188W) showed substantial resistance to clozapine. MDL1 overexpression also conferred extra sensitivity to clozapine and admitted a massive increase in the cellular and mitochondrial uptake of safranin O, as determined using flow cytometry and microscopically. Yeast lacking mitochondria showed no such unusual accumulation. Mitochondrial MDL1 is thus the main means of accumulation of clozapine in S. cerevisiae. The closest human homologue of S. cerevisiae MDL1 is ABCB10.
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Affiliation(s)
- Chrispian W. Theron
- GeneMill Biofoundry, Liverpool Shared Research Facilities, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK;
| | - J. Enrique Salcedo-Sora
- GeneMill Biofoundry, Liverpool Shared Research Facilities, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK;
| | - Justine M. Grixti
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrated Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Iben Møller-Hansen
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Søltofts Plads 220, 2800 Kongens Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Søltofts Plads 220, 2800 Kongens Lyngby, Denmark
| | - Douglas B. Kell
- GeneMill Biofoundry, Liverpool Shared Research Facilities, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK;
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrated Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Søltofts Plads 220, 2800 Kongens Lyngby, Denmark
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8
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Digles D, Ingles-Prieto A, Dvorak V, Mocking TAM, Goldmann U, Garofoli A, Homan EJ, Di Silvio A, Azzollini L, Sassone F, Fogazza M, Bärenz F, Pommereau A, Zuschlag Y, Ooms JF, Tranberg-Jensen J, Hansen JS, Stanka J, Sijben HJ, Batoulis H, Bender E, Martini R, IJzerman AP, Sauer DB, Heitman LH, Manolova V, Reinhardt J, Ehrmann A, Leippe P, Ecker GF, Huber KVM, Licher T, Scarabottolo L, Wiedmer T, Superti-Furga G. Advancing drug discovery through assay development: a survey of tool compounds within the human solute carrier superfamily. Front Pharmacol 2024; 15:1401599. [PMID: 39050757 PMCID: PMC11267547 DOI: 10.3389/fphar.2024.1401599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/31/2024] [Indexed: 07/27/2024] Open
Abstract
With over 450 genes, solute carriers (SLCs) constitute the largest transporter superfamily responsible for the uptake and efflux of nutrients, metabolites, and xenobiotics in human cells. SLCs are associated with a wide variety of human diseases, including cancer, diabetes, and metabolic and neurological disorders. They represent an important therapeutic target class that remains only partly exploited as therapeutics that target SLCs are scarce. Additionally, many small molecules reported in the literature to target SLCs are poorly characterized. Both features may be due to the difficulty of developing SLC transport assays that fulfill the quality criteria for high-throughput screening. Here, we report one of the main limitations hampering assay development within the RESOLUTE consortium: the lack of a resource providing high-quality information on SLC tool compounds. To address this, we provide a systematic annotation of tool compounds targeting SLCs. We first provide an overview on RESOLUTE assays. Next, we present a list of SLC-targeting compounds collected from the literature and public databases; we found that most data sources lacked specificity data. Finally, we report on experimental tests of 19 selected compounds against a panel of 13 SLCs from seven different families. Except for a few inhibitors, which were active on unrelated SLCs, the tested inhibitors demonstrated high selectivity for their reported targets. To make this knowledge easily accessible to the scientific community, we created an interactive dashboard displaying the collected data in the RESOLUTE web portal (https://re-solute.eu). We anticipate that our open-access resources on assays and compounds will support the development of future drug discovery campaigns for SLCs.
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Affiliation(s)
- Daniela Digles
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tamara A. M. Mocking
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Ulrich Goldmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andrea Garofoli
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Evert J. Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | | | - Felix Bärenz
- Sanofi, Integrated Drug Discovery, Industriepark Hoechst, Frankfurt am Main, Hessen, Germany
| | - Antje Pommereau
- Sanofi, Integrated Drug Discovery, Industriepark Hoechst, Frankfurt am Main, Hessen, Germany
| | - Yasmin Zuschlag
- Sanofi, Integrated Drug Discovery, Industriepark Hoechst, Frankfurt am Main, Hessen, Germany
| | - Jasper F. Ooms
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Jeppe Tranberg-Jensen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jesper S. Hansen
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Josefina Stanka
- Lead Identification and Characterization, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Hubert J. Sijben
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Helena Batoulis
- Lead Identification and Characterization, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Eckhard Bender
- Lead Identification and Characterization, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Riccardo Martini
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Adriaan P. IJzerman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - David B. Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Laura H. Heitman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | | | | | - Alexander Ehrmann
- Lead Identification and Characterization, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Philipp Leippe
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Gerhard F. Ecker
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Kilian V. M. Huber
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Thomas Licher
- Sanofi, Integrated Drug Discovery, Industriepark Hoechst, Frankfurt am Main, Hessen, Germany
| | | | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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9
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Polesel M, Wildschut MHE, Doucerain C, Kuhn M, Flace A, Sá Zanetti L, Steck AL, Wilhelm M, Ingles-Prieto A, Wiedmer T, Superti-Furga G, Manolova V, Dürrenberger F. Image-based quantification of mitochondrial iron uptake via Mitoferrin-2. Mitochondrion 2024; 78:101889. [PMID: 38692382 DOI: 10.1016/j.mito.2024.101889] [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: 10/26/2023] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/03/2024]
Abstract
Iron is a trace element that is critical for most living organisms and plays a key role in a wide variety of metabolic processes. In the mitochondrion, iron is involved in producing iron-sulfur clusters and synthesis of heme and kept within physiological ranges by concerted activity of multiple molecules. Mitochondrial iron uptake is mediated by the solute carrier transporters Mitoferrin-1 (SLC25A37) and Mitoferrin-2 (SLC25A28). While Mitoferrin-1 is mainly involved in erythropoiesis, the cellular function of the ubiquitously expressed Mitoferrin-2 remains less well defined. Furthermore, Mitoferrin-2 is associated with several human diseases, including cancer, cardiovascular and metabolic diseases, hence representing a potential therapeutic target. Here, we developed a robust approach to quantify mitochondrial iron uptake mediated by Mitoferrin-2 in living cells. We utilize HEK293 cells with inducible expression of Mitoferrin-2 and measure iron-induced quenching of rhodamine B[(1,10-phenanthroline-5-yl)-aminocarbonyl]benzyl ester (RPA) fluorescence and validate this assay for medium-throughput screening. This assay may allow identification and characterization of Mitoferrin-2 modulators and could enable drug discovery for this target.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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10
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Huang J, Osthushenrich T, MacNamara A, Mälarstig A, Brocchetti S, Bradberry S, Scarabottolo L, Ferrada E, Sosnin S, Digles D, Superti-Furga G, Ecker GF. ProteoMutaMetrics: machine learning approaches for solute carrier family 6 mutation pathogenicity prediction. RSC Adv 2024; 14:13083-13094. [PMID: 38655474 PMCID: PMC11034476 DOI: 10.1039/d4ra00748d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
The solute carrier transporter family 6 (SLC6) is of key interest for their critical role in the transport of small amino acids or amino acid-like molecules. Their dysfunction is strongly associated with human diseases such as including schizophrenia, depression, and Parkinson's disease. Linking single point mutations to disease may support insights into the structure-function relationship of these transporters. This work aimed to develop a computational model for predicting the potential pathogenic effect of single point mutations in the SLC6 family. Missense mutation data was retrieved from UniProt, LitVar, and ClinVar, covering multiple protein-coding transcripts. As encoding approach, amino acid descriptors were used to calculate the average sequence properties for both original and mutated sequences. In addition to the full-sequence calculation, the sequences were cut into twelve domains. The domains are defined according to the transmembrane domains of the SLC6 transporters to analyse the regions' contributions to the pathogenicity prediction. Subsequently, several classification models, namely Support Vector Machine (SVM), Logistic Regression (LR), Random Forest (RF), and Extreme Gradient Boosting (XGBoost) with the hyperparameters optimized through grid search were built. For estimation of model performance, repeated stratified k-fold cross-validation was used. The accuracy values of the generated models are in the range of 0.72 to 0.80. Analysis of feature importance indicates that mutations in distinct regions of SLC6 transporters are associated with an increased risk for pathogenicity. When applying the model on an independent validation set, the performance in accuracy dropped to averagely 0.6 with high precision but low sensitivity scores.
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Affiliation(s)
- Jiahui Huang
- University of Vienna, Department of Pharmaceutical Sciences Vienna Austria
| | - Tanja Osthushenrich
- Bayer AG, Division Pharmaceuticals, Biomedical Data Science II Wuppertal Germany
| | - Aidan MacNamara
- Bayer AG, Division Pharmaceuticals, Biomedical Data Science II Wuppertal Germany
| | - Anders Mälarstig
- Emerging Science & Innovation, Pfizer Worldwide Research, Development and Medical Cambridge MA USA
| | | | | | | | - Evandro Ferrada
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria
| | - Sergey Sosnin
- University of Vienna, Department of Pharmaceutical Sciences Vienna Austria
| | - Daniela Digles
- University of Vienna, Department of Pharmaceutical Sciences Vienna Austria
| | - Giulio Superti-Furga
- CeMM, Research Center for Molecular Medicine of the Austrian Academy of Sciences Vienna Austria
| | - Gerhard F Ecker
- University of Vienna, Department of Pharmaceutical Sciences Vienna Austria
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11
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Thomas JR, Shelton C, Murphy J, Brittain S, Bray MA, Aspesi P, Concannon J, King FJ, Ihry RJ, Ho DJ, Henault M, Hadjikyriacou A, Neri M, Sigoillot FD, Pham HT, Shum M, Barys L, Jones MD, Martin EJ, Blechschmidt A, Rieffel S, Troxler TJ, Mapa FA, Jenkins JL, Jain RK, Kutchukian PS, Schirle M, Renner S. Enhancing the Small-Scale Screenable Biological Space beyond Known Chemogenomics Libraries with Gray Chemical Matter─Compounds with Novel Mechanisms from High-Throughput Screening Profiles. ACS Chem Biol 2024; 19:938-952. [PMID: 38565185 PMCID: PMC11040606 DOI: 10.1021/acschembio.3c00737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 04/04/2024]
Abstract
Phenotypic assays have become an established approach to drug discovery. Greater disease relevance is often achieved through cellular models with increased complexity and more detailed readouts, such as gene expression or advanced imaging. However, the intricate nature and cost of these assays impose limitations on their screening capacity, often restricting screens to well-characterized small compound sets such as chemogenomics libraries. Here, we outline a cheminformatics approach to identify a small set of compounds with likely novel mechanisms of action (MoAs), expanding the MoA search space for throughput limited phenotypic assays. Our approach is based on mining existing large-scale, phenotypic high-throughput screening (HTS) data. It enables the identification of chemotypes that exhibit selectivity across multiple cell-based assays, which are characterized by persistent and broad structure activity relationships (SAR). We validate the effectiveness of our approach in broad cellular profiling assays (Cell Painting, DRUG-seq, and Promotor Signature Profiling) and chemical proteomics experiments. These experiments revealed that the compounds behave similarly to known chemogenetic libraries, but with a notable bias toward novel protein targets. To foster collaboration and advance research in this area, we have curated a public set of such compounds based on the PubChem BioAssay dataset and made it available for use by the scientific community.
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Affiliation(s)
- Jason R. Thomas
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Claude Shelton
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jason Murphy
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Scott Brittain
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Mark-Anthony Bray
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Peter Aspesi
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - John Concannon
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Frederick J. King
- Novartis
Biomedical Research, San Diego, California 92121, United States
| | - Robert J. Ihry
- Novartis
Biomedical Research, San Diego, California 92121, United States
| | - Daniel J. Ho
- Novartis
Biomedical Research, San Diego, California 92121, United States
| | - Martin Henault
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | | | - Marilisa Neri
- Novartis
Biomedical Research, Basel 4056, Switzerland
| | | | - Helen T. Pham
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Matthew Shum
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Louise Barys
- Novartis
Biomedical Research, Basel 4056, Switzerland
| | - Michael D. Jones
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Eric J. Martin
- Novartis
Biomedical Research, Emeryville, California 94608, United States
| | | | | | | | - Felipa A. Mapa
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Jeremy L. Jenkins
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | - Rishi K. Jain
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
| | | | - Markus Schirle
- Novartis
Biomedical Research, Cambridge, Massachusetts 02139, United States
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12
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Møller-Hansen I, Sáez-Sáez J, van der Hoek SA, Dyekjær JD, Christensen HB, Wright Muelas M, O’Hagan S, Kell DB, Borodina I. Deorphanizing solute carriers in Saccharomyces cerevisiae for secondary uptake of xenobiotic compounds. Front Microbiol 2024; 15:1376653. [PMID: 38680917 PMCID: PMC11045925 DOI: 10.3389/fmicb.2024.1376653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/25/2024] [Indexed: 05/01/2024] Open
Abstract
The exchange of small molecules between the cell and the environment happens through transporter proteins. Besides nutrients and native metabolic products, xenobiotic molecules are also transported, however it is not well understood which transporters are involved. In this study, by combining exo-metabolome screening in yeast with transporter characterization in Xenopus oocytes, we mapped the activity of 30 yeast transporters toward six small non-toxic substrates. Firstly, using LC-MS, we determined 385 compounds from a chemical library that were imported and exported by S. cerevisiae. Of the 385 compounds transported by yeast, we selected six compounds (viz. sn-glycero-3-phosphocholine, 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, acrylic acid, 2-benzoxazolol) for characterization against 30 S. cerevisiae xenobiotic transport proteins expressed in Xenopus oocytes. The compounds were selected to represent a diverse set of chemicals with a broad interest in applied microbiology. Twenty transporters showed activity toward one or more of the compounds. The tested transporter proteins were mostly promiscuous in equilibrative transport (i.e., facilitated diffusion). The compounds 2,5-furandicarboxylic acid, 2-methylpyrazine, cefadroxil, and sn-glycero-3-phosphocholine were transported equilibratively by transporters that could transport up to three of the compounds. In contrast, the compounds acrylic acid and 2-benzoxazolol, were strictly transported by dedicated transporters. The prevalence of promiscuous equilibrative transporters of non-native substrates has significant implications for strain development in biotechnology and offers an explanation as to why transporter engineering has been a challenge in metabolic engineering. The method described here can be generally applied to study the transport of other small non-toxic molecules. The yeast transporter library is available at AddGene (ID 79999).
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Affiliation(s)
- Iben Møller-Hansen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Javier Sáez-Sáez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Steven A. van der Hoek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Jane D. Dyekjær
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Hanne B. Christensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
| | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Steve O’Hagan
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Douglas B. Kell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark
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13
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Tu G, Fu T, Zheng G, Xu B, Gou R, Luo D, Wang P, Xue W. Computational Chemistry in Structure-Based Solute Carrier Transporter Drug Design: Recent Advances and Future Perspectives. J Chem Inf Model 2024; 64:1433-1455. [PMID: 38294194 DOI: 10.1021/acs.jcim.3c01736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Solute carrier transporters (SLCs) are a class of important transmembrane proteins that are involved in the transportation of diverse solute ions and small molecules into cells. There are approximately 450 SLCs within the human body, and more than a quarter of them are emerging as attractive therapeutic targets for multiple complex diseases, e.g., depression, cancer, and diabetes. However, only 44 unique transporters (∼9.8% of the SLC superfamily) with 3D structures and specific binding sites have been reported. To design innovative and effective drugs targeting diverse SLCs, there are a number of obstacles that need to be overcome. However, computational chemistry, including physics-based molecular modeling and machine learning- and deep learning-based artificial intelligence (AI), provides an alternative and complementary way to the classical drug discovery approach. Here, we present a comprehensive overview on recent advances and existing challenges of the computational techniques in structure-based drug design of SLCs from three main aspects: (i) characterizing multiple conformations of the proteins during the functional process of transportation, (ii) identifying druggability sites especially the cryptic allosteric ones on the transporters for substrates and drugs binding, and (iii) discovering diverse small molecules or synthetic protein binders targeting the binding sites. This work is expected to provide guidelines for a deep understanding of the structure and function of the SLC superfamily to facilitate rational design of novel modulators of the transporters with the aid of state-of-the-art computational chemistry technologies including artificial intelligence.
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Affiliation(s)
- Gao Tu
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Tingting Fu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | | | - Binbin Xu
- Chengdu Sintanovo Biotechnology Co., Ltd., Chengdu 610200, China
| | - Rongpei Gou
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Ding Luo
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
| | - Panpan Wang
- College of Chemistry and Pharmaceutical Engineering, Huanghuai University, Zhumadian 463000, China
| | - Weiwei Xue
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China
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14
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Ferrada E, Wiedmer T, Wang WA, Frommelt F, Steurer B, Klimek C, Lindinger S, Osthushenrich T, Garofoli A, Brocchetti S, Bradberry S, Huang J, MacNamara A, Scarabottolo L, Ecker GF, Malarstig A, Superti-Furga G. Experimental and Computational Analysis of Newly Identified Pathogenic Mutations in the Creatine Transporter SLC6A8. J Mol Biol 2024; 436:168383. [PMID: 38070861 DOI: 10.1016/j.jmb.2023.168383] [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: 08/22/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023]
Abstract
Creatine is an essential metabolite for the storage and rapid supply of energy in muscle and nerve cells. In humans, impaired metabolism, transport, and distribution of creatine throughout tissues can cause varying forms of mental disability, also known as creatine deficiency syndrome (CDS). So far, 80 mutations in the creatine transporter (SLC6A8) have been associated to CDS. To better understand the effect of human genetic variants on the physiology of SLC6A8 and their possible impact on CDS, we studied 30 missense variants including 15 variants of unknown significance, two of which are reported here for the first time. We expressed these variants in HEK293 cells and explored their subcellular localization and transport activity. We also applied computational methods to predict variant effect and estimate site-specific changes in thermodynamic stability. To explore variants that might have a differential effect on the transporter's conformers along the transport cycle, we constructed homology models of the inward facing, and outward facing conformations. In addition, we used mass-spectrometry to study proteins that interact with wild type SLC6A8 and five selected variants in HEK293 cells. In silico models of the protein complexes revealed how two variants impact the interaction interface of SLC6A8 with other proteins and how pathogenic variants lead to an enrichment of ER protein partners. Overall, our integrated analysis disambiguates the pathogenicity of 15 variants of unknown significance revealing diverse mechanisms of pathogenicity, including two previously unreported variants obtained from patients suffering from the creatine deficiency syndrome.
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Affiliation(s)
- Evandro Ferrada
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Wen-An Wang
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Barbara Steurer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Christoph Klimek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Sabrina Lindinger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Andrea Garofoli
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | | | - Jiahui Huang
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | | | | | - Gerhard F Ecker
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Anders Malarstig
- Pfizer Worldwide Research, Development and Medical, Stockholm, Sweden
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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15
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Grandits M, Ecker GF. Ligand- and Structure-based Approaches for Transmembrane Transporter Modeling. Curr Drug Res Rev 2024; 16:81-93. [PMID: 37157206 PMCID: PMC11340286 DOI: 10.2174/2589977515666230508123041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/15/2023] [Accepted: 03/28/2023] [Indexed: 05/10/2023]
Abstract
The study of transporter proteins is key to understanding the mechanism behind multidrug resistance and drug-drug interactions causing severe side effects. While ATP-binding transporters are well-studied, solute carriers illustrate an understudied family with a high number of orphan proteins. To study these transporters, in silico methods can be used to shed light on the basic molecular machinery by studying protein-ligand interactions. Nowadays, computational methods are an integral part of the drug discovery and development process. In this short review, computational approaches, such as machine learning, are discussed, which try to tackle interactions between transport proteins and certain compounds to locate target proteins. Furthermore, a few cases of selected members of the ATP binding transporter and solute carrier family are covered, which are of high interest in clinical drug interaction studies, especially for regulatory agencies. The strengths and limitations of ligand-based and structure-based methods are discussed to highlight their applicability for different studies. Furthermore, the combination of multiple approaches can improve the information obtained to find crucial amino acids that explain important interactions of protein-ligand complexes in more detail. This allows the design of drug candidates with increased activity towards a target protein, which further helps to support future synthetic efforts.
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Affiliation(s)
- Melanie Grandits
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Gerhard F. Ecker
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
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16
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Sugiura A, Beier KL, Chi C, Heintzman DR, Ye X, Wolf MM, Patterson AR, Cephus JY, Hong HS, Lyssiotis CA, Newcomb DC, Rathmell JC. Tissue-Specific Dependence of Th1 Cells on the Amino Acid Transporter SLC38A1 in Inflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.13.557496. [PMID: 37745344 PMCID: PMC10515961 DOI: 10.1101/2023.09.13.557496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Amino acid (AA) uptake is essential for T cell metabolism and function, but how tissue sites and inflammation affect CD4+ T cell subset requirements for specific AA remains uncertain. Here we tested CD4+ T cell AA demands with in vitro and multiple in vivo CRISPR screens and identify subset- and tissue-specific dependencies on the AA transporter SLC38A1 (SNAT1). While dispensable for T cell persistence and expansion over time in vitro and in vivo lung inflammation, SLC38A1 was critical for Th1 but not Th17 cell-driven Experimental Autoimmune Encephalomyelitis (EAE) and contributed to Th1 cell-driven inflammatory bowel disease. SLC38A1 deficiency reduced mTORC1 signaling and glycolytic activity in Th1 cells, in part by reducing intracellular glutamine and disrupting hexosamine biosynthesis and redox regulation. Similarly, pharmacological inhibition of SLC38 transporters delayed EAE but did not affect lung inflammation. Subset- and tissue-specific dependencies of CD4+ T cells on AA transporters may guide selective immunotherapies.
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Affiliation(s)
- Ayaka Sugiura
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Katherine L. Beier
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Channing Chi
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Darren R. Heintzman
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Xiang Ye
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Melissa M. Wolf
- Department of Medicine, Division of Hematology and Oncology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Andrew R. Patterson
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jacqueline-Yvonne Cephus
- Department of Medicine, Division of Pulmonary and Critical Care, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Hanna S. Hong
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Costas A. Lyssiotis
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Dawn C. Newcomb
- Department of Medicine, Division of Pulmonary and Critical Care, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeffrey C. Rathmell
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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17
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Dvorak V, Casiraghi A, Colas C, Koren A, Tomek T, Offensperger F, Rukavina A, Tin G, Hahn E, Dobner S, Frommelt F, Boeszoermenyi A, Bernada V, Hannich JT, Ecker GF, Winter GE, Kubicek S, Superti-Furga G. Paralog-dependent isogenic cell assay cascade generates highly selective SLC16A3 inhibitors. Cell Chem Biol 2023; 30:953-964.e9. [PMID: 37516113 PMCID: PMC10437005 DOI: 10.1016/j.chembiol.2023.06.029] [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: 01/27/2023] [Revised: 05/02/2023] [Accepted: 06/30/2023] [Indexed: 07/31/2023]
Abstract
Despite being considered druggable and attractive therapeutic targets, most of the solute carrier (SLC) membrane transporters remain pharmacologically underexploited. One of the reasons for this is a lack of reliable chemical screening assays, made difficult by functional redundancies among SLCs. In this study we leveraged synthetic lethality between the lactate transporters SLC16A1 and SLC16A3 in a screening strategy that we call paralog-dependent isogenic cell assay (PARADISO). The system involves five isogenic cell lines, each dependent on various paralog genes for survival/fitness, arranged in a screening cascade tuned for the identification of SLC16A3 inhibitors. We screened a diversity-oriented library of ∼90,000 compounds and further developed our hits into slCeMM1, a paralog-selective and potent SLC16A3 inhibitor. By implementing chemoproteomics, we showed that slCeMM1 is selective also at the proteome-wide level, thus fulfilling an important criterion for chemical probes. This study represents a framework for the development of specific cell-based drug discovery assays.
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Affiliation(s)
- Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andrea Casiraghi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Claire Colas
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Anna Koren
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Tatjana Tomek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Fabian Offensperger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andrea Rukavina
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gary Tin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Elisa Hahn
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Sarah Dobner
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Fabian Frommelt
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Andras Boeszoermenyi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Viktoriia Bernada
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - J Thomas Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria.
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18
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Alborzinia H, Chen Z, Yildiz U, Freitas FP, Vogel FCE, Varga JP, Batani J, Bartenhagen C, Schmitz W, Büchel G, Michalke B, Zheng J, Meierjohann S, Girardi E, Espinet E, Flórez AF, dos Santos AF, Aroua N, Cheytan T, Haenlin J, Schlicker L, Xavier da Silva TN, Przybylla A, Zeisberger P, Superti‐Furga G, Eilers M, Conrad M, Fabiano M, Schweizer U, Fischer M, Schulze A, Trumpp A, Friedmann Angeli JP. LRP8-mediated selenocysteine uptake is a targetable vulnerability in MYCN-amplified neuroblastoma. EMBO Mol Med 2023; 15:e18014. [PMID: 37435859 PMCID: PMC10405063 DOI: 10.15252/emmm.202318014] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/23/2023] [Accepted: 06/23/2023] [Indexed: 07/13/2023] Open
Abstract
Ferroptosis has emerged as an attractive strategy in cancer therapy. Understanding the operational networks regulating ferroptosis may unravel vulnerabilities that could be harnessed for therapeutic benefit. Using CRISPR-activation screens in ferroptosis hypersensitive cells, we identify the selenoprotein P (SELENOP) receptor, LRP8, as a key determinant protecting MYCN-amplified neuroblastoma cells from ferroptosis. Genetic deletion of LRP8 leads to ferroptosis as a result of an insufficient supply of selenocysteine, which is required for the translation of the antiferroptotic selenoprotein GPX4. This dependency is caused by low expression of alternative selenium uptake pathways such as system Xc- . The identification of LRP8 as a specific vulnerability of MYCN-amplified neuroblastoma cells was confirmed in constitutive and inducible LRP8 knockout orthotopic xenografts. These findings disclose a yet-unaccounted mechanism of selective ferroptosis induction that might be explored as a therapeutic strategy for high-risk neuroblastoma and potentially other MYCN-amplified entities.
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Affiliation(s)
- Hamed Alborzinia
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI‐STEM GmbH)HeidelbergGermany
- Division of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Zhiyi Chen
- Rudolf Virchow Zentrum (RVZ), Center for Integrative and Translational BioimagingUniversity of WürzburgWürzburgGermany
| | - Umut Yildiz
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI‐STEM GmbH)HeidelbergGermany
- Division of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
- European Molecular Biology Laboratory, Genome Biology UnitHeidelbergGermany
| | - Florencio Porto Freitas
- Rudolf Virchow Zentrum (RVZ), Center for Integrative and Translational BioimagingUniversity of WürzburgWürzburgGermany
| | - Felix C E Vogel
- Division of Tumor Metabolism and MicroenvironmentGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Julianna Patricia Varga
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI‐STEM GmbH)HeidelbergGermany
- Division of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
- European Molecular Biology OrganizationHeidelbergGermany
| | - Jasmin Batani
- Rudolf Virchow Zentrum (RVZ), Center for Integrative and Translational BioimagingUniversity of WürzburgWürzburgGermany
| | - Christoph Bartenhagen
- Center for Molecular Medicine Cologne (CMMC) and Department of Experimental Pediatric Oncology, University Children's Hospital, Medical FacultyUniversity of CologneCologneGermany
| | - Werner Schmitz
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, BiocenterUniversity of WürzburgWürzburgGermany
| | - Gabriele Büchel
- Mildred Scheel Early Career CenterUniversity Hospital WürzburgWürzburgGermany
| | - Bernhard Michalke
- Research Unit Analytical BioGeoChemistryHelmholtz Center München (HMGU)NeuherbergGermany
| | - Jashuo Zheng
- Institute of Metabolism and Cell DeathHelmholtz Zentrum München (HMGU)NeuherbergGermany
| | | | - Enrico Girardi
- CeMM‐Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Solgate GmbHKlosterneuburgAustria
| | - Elisa Espinet
- Anatomy Unit, Department of Pathology and Experimental Therapy, School of MedicineUniversity of Barcelona (UB), L'Hospitalet de LlobregatBarcelonaSpain
- Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell)Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de LlobregatBarcelonaSpain
| | - Andrés F Flórez
- Department of Molecular and Cellular BiologyHarvard UniversityCambridgeMAUSA
| | - Ancely Ferreira dos Santos
- Rudolf Virchow Zentrum (RVZ), Center for Integrative and Translational BioimagingUniversity of WürzburgWürzburgGermany
| | - Nesrine Aroua
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI‐STEM GmbH)HeidelbergGermany
- Division of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Tasneem Cheytan
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI‐STEM GmbH)HeidelbergGermany
- Division of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Julie Haenlin
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI‐STEM GmbH)HeidelbergGermany
- Division of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Lisa Schlicker
- Division of Tumor Metabolism and MicroenvironmentGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Thamara N Xavier da Silva
- Division of Tumor Metabolism and MicroenvironmentGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Adriana Przybylla
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI‐STEM GmbH)HeidelbergGermany
- Division of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Petra Zeisberger
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI‐STEM GmbH)HeidelbergGermany
- Division of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Giulio Superti‐Furga
- CeMM‐Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
- Center for Physiology and PharmacologyMedical University of ViennaViennaAustria
| | - Martin Eilers
- Department of Biochemistry and Molecular Biology, Theodor Boveri Institute, BiocenterUniversity of WürzburgWürzburgGermany
| | - Marcus Conrad
- Institute of Metabolism and Cell DeathHelmholtz Zentrum München (HMGU)NeuherbergGermany
| | - Marietta Fabiano
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich‐Wilhelms‐Universität BonnBonnGermany
| | - Ulrich Schweizer
- Institut für Biochemie und Molekularbiologie, Rheinische Friedrich‐Wilhelms‐Universität BonnBonnGermany
| | - Matthias Fischer
- Center for Molecular Medicine Cologne (CMMC) and Department of Experimental Pediatric Oncology, University Children's Hospital, Medical FacultyUniversity of CologneCologneGermany
| | - Almut Schulze
- Division of Tumor Metabolism and MicroenvironmentGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - Andreas Trumpp
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI‐STEM GmbH)HeidelbergGermany
- Division of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
| | - José Pedro Friedmann Angeli
- Rudolf Virchow Zentrum (RVZ), Center for Integrative and Translational BioimagingUniversity of WürzburgWürzburgGermany
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19
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Tardito S, MacKay C. Rethinking our approach to cancer metabolism to deliver patient benefit. Br J Cancer 2023; 129:406-415. [PMID: 37340094 PMCID: PMC10403540 DOI: 10.1038/s41416-023-02324-9] [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: 02/28/2023] [Revised: 05/25/2023] [Accepted: 06/12/2023] [Indexed: 06/22/2023] Open
Abstract
Altered cellular metabolism is a major mechanism by which tumours support nutrient consumption associated with increased cellular proliferation. Selective dependency on specific metabolic pathways provides a therapeutic vulnerability that can be targeted in cancer therapy. Anti-metabolites have been used clinically since the 1940s and several agents targeting nucleotide metabolism are now well established as standard of care treatment in a range of indications. However, despite great progress in our understanding of the metabolic requirements of cancer and non-cancer cells within the tumour microenvironment, there has been limited clinical success for novel agents targeting pathways outside of nucleotide metabolism. We believe that there is significant therapeutic potential in targeting metabolic processes within cancer that is yet to be fully realised. However, current approaches to identify novel targets, test novel therapies and select patient populations most likely to benefit are sub-optimal. We highlight recent advances in technologies and understanding that will support the identification and validation of novel targets, re-evaluation of existing targets and design of optimal clinical positioning strategies to deliver patient benefit.
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Affiliation(s)
- Saverio Tardito
- The Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Craig MacKay
- Cancer Research Horizons, The Cancer Research UK Beatson Institute, Glasgow, UK.
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20
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Bongers BJ, Sijben HJ, Hartog PBR, Tarnovskiy A, IJzerman AP, Heitman LH, van Westen GJP. Proteochemometric Modeling Identifies Chemically Diverse Norepinephrine Transporter Inhibitors. J Chem Inf Model 2023; 63:1745-1755. [PMID: 36926886 PMCID: PMC10052348 DOI: 10.1021/acs.jcim.2c01645] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Solute carriers (SLCs) are relatively underexplored compared to other prominent protein families such as kinases and G protein-coupled receptors. However, proteins from the SLC family play an essential role in various diseases. One such SLC is the high-affinity norepinephrine transporter (NET/SLC6A2). In contrast to most other SLCs, the NET has been relatively well studied. However, the chemical space of known ligands has a low chemical diversity, making it challenging to identify chemically novel ligands. Here, a computational screening pipeline was developed to find new NET inhibitors. The approach increases the chemical space to model for NETs using the chemical space of related proteins that were selected utilizing similarity networks. Prior proteochemometric models added data from related proteins, but here we use a data-driven approach to select the optimal proteins to add to the modeled data set. After optimizing the data set, the proteochemometric model was optimized using stepwise feature selection. The final model was created using a two-step approach combining several proteochemometric machine learning models through stacking. This model was applied to the extensive virtual compound database of Enamine, from which the top predicted 22,000 of the 600 million virtual compounds were clustered to end up with 46 chemically diverse candidates. A subselection of 32 candidates was synthesized and subsequently tested using an impedance-based assay. There were five hit compounds identified (hit rate 16%) with sub-micromolar inhibitory potencies toward NET, which are promising for follow-up experimental research. This study demonstrates a data-driven approach to diversify known chemical space to identify novel ligands and is to our knowledge the first to select this set based on the sequence similarity of related targets.
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Affiliation(s)
- Brandon J Bongers
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Huub J Sijben
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Peter B R Hartog
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | | | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands.,Oncode Institute, Jaarbeursplein 6, Utrecht 3521 AL, The Netherlands
| | - Gerard J P van Westen
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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21
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Yan C, Hu X, Liu X, Zhao J, Le Z, Feng J, Zhou M, Ma X, Zheng Q, Sun J. Upregulation of SLC12A3 and SLC12A9 Mediated by the HCP5/miR-140-5p Axis Confers Aggressiveness and Unfavorable Prognosis in Uveal Melanoma. J Transl Med 2023; 103:100022. [PMID: 36925204 DOI: 10.1016/j.labinv.2022.100022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/09/2022] [Accepted: 10/21/2022] [Indexed: 01/11/2023] Open
Abstract
Perturbation of solute carriers (SLCs) has been implicated in metabolic disorders and cancer, highlighting the potential for drug discovery and therapeutic opportunities. However, there is relatively little exploration of the clinical relevance and potential molecular mechanisms underlying the role of the SLC12 family in uveal melanoma (UVM). Here, we performed an integrative multiomics analysis of the SLC12 family in multicenter UVM datasets and found that high expression of SLC12A3 and SLC12A9 was associated with unfavorable prognosis. Moreover, SLC12A3 and SLC12A9 were highly expressed in UVM in vivo. We experimentally characterized the roles of these proteins in tumorigenesis in vitro and explored their association with the prognosis of UVM. Lastly, we identified the HCP5-miR-140-5p axis as a potential noncoding RNA pathway upstream of SLC12A3 and SLC12A9, which was associated with immunomodulation and may represent a novel predictor for clinical prognosis and responsiveness to checkpoint blockade immunotherapy. These findings may facilitate a better understanding of the SLCome and guide future rationalized development of SLC-targeted therapy and drug discovery for UVM.
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Affiliation(s)
- Congcong Yan
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Xiaojuan Hu
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Xiaoyan Liu
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Jingting Zhao
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Zhenmin Le
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China
| | - Jiayao Feng
- The Affiliated Ningbo Eye Hospital of Wenzhou Medical University, Ningbo, China
| | - Meng Zhou
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China; Institute of PSI Genomics, Wenzhou, China
| | - Xiaoyin Ma
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China.
| | - Qingxiang Zheng
- The Affiliated Ningbo Eye Hospital of Wenzhou Medical University, Ningbo, China.
| | - Jie Sun
- School of Ophthalmology & Optometry and Eye Hospital, School of Biomedical Engineering, Wenzhou Medical University, Wenzhou, China.
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22
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Sugar transporter Slc37a2 regulates bone metabolism in mice via a tubular lysosomal network in osteoclasts. Nat Commun 2023; 14:906. [PMID: 36810735 PMCID: PMC9945426 DOI: 10.1038/s41467-023-36484-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 02/01/2023] [Indexed: 02/23/2023] Open
Abstract
Osteoclasts are giant bone-digesting cells that harbor specialized lysosome-related organelles termed secretory lysosomes (SLs). SLs store cathepsin K and serve as a membrane precursor to the ruffled border, the osteoclast's 'resorptive apparatus'. Yet, the molecular composition and spatiotemporal organization of SLs remains incompletely understood. Here, using organelle-resolution proteomics, we identify member a2 of the solute carrier 37 family (Slc37a2) as a SL sugar transporter. We demonstrate in mice that Slc37a2 localizes to the SL limiting membrane and that these organelles adopt a hitherto unnoticed but dynamic tubular network in living osteoclasts that is required for bone digestion. Accordingly, mice lacking Slc37a2 accrue high bone mass owing to uncoupled bone metabolism and disturbances in SL export of monosaccharide sugars, a prerequisite for SL delivery to the bone-lining osteoclast plasma membrane. Thus, Slc37a2 is a physiological component of the osteoclast's unique secretory organelle and a potential therapeutic target for metabolic bone diseases.
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23
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Hydrogen-deuterium exchange coupled to mass spectrometry: A multifaceted tool to decipher the molecular mechanism of transporters. Biochimie 2023; 205:95-101. [PMID: 36037883 DOI: 10.1016/j.biochi.2022.08.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/17/2022] [Accepted: 08/19/2022] [Indexed: 11/22/2022]
Abstract
Transporters regulate trafficking through the biological membrane of living cells and organelles. Therefore, these proteins play an important role in key cellular processes. Obtaining a molecular-level description of the mechanism of transporters is highly desirable to understand and modulate such processes. Different challenges currently complicate this effort, mostly due to transporters' intrinsic properties. They are dynamic and often averse to in vitro characterization. The crossing of the membrane via a transporter depends on both global and local structural changes that will enable substrate binding from one side of the membrane and release on the other. Dedicated approaches are required to monitor these dynamic changes, ideally within the complex membrane environment. Hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) has recently emerged as a powerful biophysical tool to understand transporters' mechanism. This mini-review aims to offer to the reader an overview of the field of HDX-MS applied to transporters. It first summarizes the current workflow for HDX-MS measurements on transporters. It then provides illustrative examples on the molecular insights that are accessible thanks to the technique; following conformational transitions between different states, observing structural changes upon ligand binding and finally understanding the role of lipid-protein interactions.
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24
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Huttunen J, Kronenberger T, Montaser AB, Králová A, Terasaki T, Poso A, Huttunen KM. Sodium-Dependent Neutral Amino Acid Transporter 2 Can Serve as a Tertiary Carrier for l-Type Amino Acid Transporter 1-Utilizing Prodrugs. Mol Pharm 2023; 20:1331-1346. [PMID: 36688491 PMCID: PMC9906736 DOI: 10.1021/acs.molpharmaceut.2c00948] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Membrane transporters are the key determinants of the homeostasis of endogenous compounds in the cells and their exposure to drugs. However, the substrate specificities of distinct transporters can overlap. In the present study, the interactions of l-type amino acid transporter 1 (LAT1)-utilizing prodrugs with sodium-coupled neutral amino acid transporter 2 (SNAT2) were explored. The results showed that the cellular uptake of LAT1-utilizing prodrugs into a human breast cancer cell line, MCF-7 cells, was mediated via SNATs as the uptake was increased at higher pH (8.5), decreased in the absence of sodium, and inhibited in the presence of unselective SNAT-inhibitor, (α-(methylamino)isobutyric acid, MeAIB). Moreover, docking the compounds to a SNAT2 homology model (inward-open conformation) and further molecular dynamics simulations and the subsequent trajectory and principal component analyses confirmed the chemical features supporting the interactions of the studied compounds with SNAT2, which was found to be the main SNAT expressed in MCF-7 cells.
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Affiliation(s)
- Johanna Huttunen
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland
| | - Thales Kronenberger
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland,Department
of Internal Medicine VIII, University Hospital
Tübingen, Otfried-Müller-Strasse
14, DE 72076 Tübingen, Germany,Department
of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard-Karls-Universität,
Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany,Cluster
of Excellence iFIT (EXC 2180) “Image-Guided and Functionally
Instructed Tumor Therapies”, University
of Tübingen, 72076 Tübingen, Germany,Tübingen
Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany
| | - Ahmed B. Montaser
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland
| | - Adéla Králová
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland
| | - Tetsuya Terasaki
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland
| | - Antti Poso
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland,Department
of Internal Medicine VIII, University Hospital
Tübingen, Otfried-Müller-Strasse
14, DE 72076 Tübingen, Germany,Department
of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard-Karls-Universität,
Tübingen, Auf
der Morgenstelle 8, 72076 Tübingen, Germany,Cluster
of Excellence iFIT (EXC 2180) “Image-Guided and Functionally
Instructed Tumor Therapies”, University
of Tübingen, 72076 Tübingen, Germany,Tübingen
Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tübingen, Germany
| | - Kristiina M. Huttunen
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O.
Box 1627, FI-70211 Kuopio, Finland,
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25
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Ackloo S, Antolin AA, Bartolome JM, Beck H, Bullock A, Betz UAK, Böttcher J, Brown PJ, Chaturvedi M, Crisp A, Daniels D, Dreher J, Edfeldt K, Edwards AM, Egner U, Elkins J, Fischer C, Glendorf T, Goldberg S, Hartung IV, Hillisch A, Homan E, Knapp S, Köster M, Krämer O, Llaveria J, Lessel U, Lindemann S, Linderoth L, Matsui H, Michel M, Montel F, Mueller-Fahrnow A, Müller S, Owen DR, Saikatendu KS, Santhakumar V, Sanderson W, Scholten C, Schapira M, Sharma S, Shireman B, Sundström M, Todd MH, Tredup C, Venable J, Willson TM, Arrowsmith CH. Target 2035 – an update on private sector contributions. RSC Med Chem 2023. [DOI: 10.1039/d2md00441k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Target 2035, an international federation of biomedical scientists from the public and private sectors, is leveraging ‘open’ principles to develop a pharmacological tool for every human protein.
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Affiliation(s)
- Suzanne Ackloo
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Albert A. Antolin
- ProCURE, Catalan Institute of Oncology, Oncobell, Bellvitge Institute for Biomedical Research (IDIBELL), L'Hospitalet del Llobregat, Barcelona, Catalonia, Spain
| | | | - Hartmut Beck
- Research and Development, Bayer AG, Pharmaceuticals, 42103 Wuppertal, Germany
| | - Alex Bullock
- Center for Medicines Discovery, Old Road Campus, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | | | - Jark Böttcher
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Peter J. Brown
- Structural Genomics Consortium, University of North Carolina at Chapel Hill, USA
| | - Menorca Chaturvedi
- Boehringer Ingelheim International, Binger Str. 173, D-55216 Ingelheim, Germany
| | - Alisa Crisp
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Danette Daniels
- Foghorn Therapeutics, 500 Technology Square, Suite 700, Cambridge, MA 02139, USA
| | - Jan Dreher
- Research and Development, Bayer AG, Pharmaceuticals, 42103 Wuppertal, Germany
| | - Kristina Edfeldt
- Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Aled M. Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
| | - Ursula Egner
- Nuvisan Innovation Campus Berlin GmbH, Müllerstraße 178, 13353, Berlin, Germany
| | - Jon Elkins
- Center for Medicines Discovery, Old Road Campus, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK
| | - Christian Fischer
- Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, USA
| | - Tine Glendorf
- Research & Early Development, Novo Nordisk A/S, Måløv, Denmark
| | - Steven Goldberg
- Janssen Research and Development LLC, San Diego, California, USA
| | - Ingo V. Hartung
- Medicinal Chemistry, Global R&D, Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Alexander Hillisch
- Research and Development, Bayer AG, Pharmaceuticals, 42103 Wuppertal, Germany
| | - Evert Homan
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Markus Köster
- Boehringer Ingelheim International, Binger Str. 173, D-55216 Ingelheim, Germany
| | - Oliver Krämer
- Boehringer Ingelheim International, Binger Str. 173, D-55216 Ingelheim, Germany
| | - Josep Llaveria
- A Division of Janssen-Cilag S.A., Janssen Research and Development, Toledo, Spain
| | - Uta Lessel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, D-88397 Biberach an der Riss, Germany
| | | | - Lars Linderoth
- Research & Early Development, Novo Nordisk A/S, Måløv, Denmark
| | - Hisanori Matsui
- Neuroscience Drug Discovery Unit, Research, Takeda Pharmaceutical Company Limited, Fujisawa, Kanagawa, Japan
| | - Maurice Michel
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Florian Montel
- Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorfer Str. 65, D-88397 Biberach an der Riss, Germany
| | | | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Dafydd R. Owen
- Discovery Network Group, Pfizer Medicine Design, Cambridge, MA 02139, USA
| | - Kumar Singh Saikatendu
- Global Research Externalization, Takeda California, Inc., 9625 Towne Center Drive, San Diego, CA 92121, USA
| | | | - Wendy Sanderson
- Janssen Research & Development, Janssen Pharmaceutica N. V, Beerse, Belgium
| | - Cora Scholten
- Research and Development, Bayer AG, Pharmaceuticals, 13353 Berlin, Germany
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
- Department of Pharmacology & Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Sujata Sharma
- Janssen Research and Development LLC, San Diego, California, USA
| | - Brock Shireman
- Janssen Research and Development LLC, San Diego, California, USA
| | - Michael Sundström
- Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Matthew H. Todd
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Claudia Tredup
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Jennifer Venable
- Janssen Research and Development LLC, San Diego, California, USA
| | - Timothy M. Willson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada
- Princess Margaret Cancer Centre, Toronto, Ontario, M5G 1L7, Canada
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26
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Licciardello MP, Workman P. The era of high-quality chemical probes. RSC Med Chem 2022; 13:1446-1459. [PMID: 36545432 PMCID: PMC9749956 DOI: 10.1039/d2md00291d] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/11/2022] [Indexed: 11/29/2022] Open
Abstract
Small-molecule chemical probes are among the most important tools to study the function of proteins in cells and organisms. Regrettably, the use of weak and non-selective small molecules has generated an abundance of erroneous conclusions in the scientific literature. More recently, minimal criteria have been outlined for investigational compounds, encouraging the selection and use of high-quality chemical probes. Here, we briefly recall the milestones and key initiatives that have paved the way to this new era, illustrate examples of recent high-quality chemical probes and provide our perspective on future challenges and developments.
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Affiliation(s)
- Marco P. Licciardello
- Centre for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer ResearchLondonUK
| | - Paul Workman
- Centre for Cancer Drug Discovery, Division of Cancer Therapeutics, The Institute of Cancer ResearchLondonUK,The Chemical Probes PortalUK
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27
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Young RJ, Flitsch SL, Grigalunas M, Leeson PD, Quinn RJ, Turner NJ, Waldmann H. The Time and Place for Nature in Drug Discovery. JACS AU 2022; 2:2400-2416. [PMID: 36465532 PMCID: PMC9709949 DOI: 10.1021/jacsau.2c00415] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 05/31/2023]
Abstract
The case for a renewed focus on Nature in drug discovery is reviewed; not in terms of natural product screening, but how and why biomimetic molecules, especially those produced by natural processes, should deliver in the age of artificial intelligence and screening of vast collections both in vitro and in silico. The declining natural product-likeness of licensed drugs and the consequent physicochemical implications of this trend in the context of current practices are noted. To arrest these trends, the logic of seeking new bioactive agents with enhanced natural mimicry is considered; notably that molecules constructed by proteins (enzymes) are more likely to interact with other proteins (e.g., targets and transporters), a notion validated by natural products. Nature's finite number of building blocks and their interactions necessarily reduce potential numbers of structures, yet these enable expansion of chemical space with their inherent diversity of physical characteristics, pertinent to property-based design. The feasible variations on natural motifs are considered and expanded to encompass pseudo-natural products, leading to the further logical step of harnessing bioprocessing routes to access them. Together, these offer opportunities for enhancing natural mimicry, thereby bringing innovation to drug synthesis exploiting the characteristics of natural recognition processes. The potential for computational guidance to help identifying binding commonalities in the route map is a logical opportunity to enable the design of tailored molecules, with a focus on "organic/biological" rather than purely "synthetic" structures. The design and synthesis of prototype structures should pay dividends in the disposition and efficacy of the molecules, while inherently enabling greener and more sustainable manufacturing techniques.
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Affiliation(s)
| | - Sabine L. Flitsch
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Michael Grigalunas
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
| | - Paul D. Leeson
- Paul
Leeson Consulting Limited, The Malt House, Main Street, Congerstone, Nuneaton, Warwickshire CV13 6LZ, U.K.
| | - Ronald J. Quinn
- Griffith
Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Nicholas J. Turner
- Department
of Chemistry, University of Manchester,
Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute
of Molecular Physiology, Otto-Hahn Strasse 11, 44227 Dortmund, Germany
- Faculty of
Chemistry and Chemical Biology, Technical
University of Dortmund, Otto-Hahn-Strasse 6, 44227 Dortmund, Germany
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28
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Rebsamen M, Girardi E, Sedlyarov V, Scorzoni S, Papakostas K, Vollert M, Konecka J, Guertl B, Klavins K, Wiedmer T, Superti-Furga G. Gain-of-function genetic screens in human cells identify SLC transporters overcoming environmental nutrient restrictions. Life Sci Alliance 2022; 5:e202201404. [PMID: 36114003 PMCID: PMC9481932 DOI: 10.26508/lsa.202201404] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022] Open
Abstract
Solute carrier (SLC) transporters control fluxes of nutrients and metabolites across membranes and thereby represent a critical interface between the microenvironment and cellular and subcellular metabolism. Because of substantial functional overlap, the interplay and relative contributions of SLCs in response to environmental stresses remain poorly elucidated. To infer functional relationships between SLCs and metabolites, we developed a strategy to identify SLCs able to sustain cell viability and proliferation under growth-limiting concentrations of essential nutrients. One-by-one depletion of 13 amino acids required for cell proliferation enabled gain-of-function genetic screens using a SLC-focused CRISPR/Cas9-based transcriptional activation approach to uncover transporters relieving cells from growth-limiting metabolic bottlenecks. Among the transporters identified, we characterized the cationic amino acid transporter SLC7A3 as a gene that, when up-regulated, overcame low availability of arginine and lysine by increasing their uptake, whereas SLC7A5 was able to sustain cellular fitness upon deprivation of several neutral amino acids. Moreover, we identified metabolic compensation mediated by the glutamate/aspartate transporters SLC1A2 and SLC1A3 under glutamine-limiting conditions. Overall, this gain-of-function approach using human cells uncovered functional transporter-nutrient relationships and revealed that transport activity up-regulation may be sufficient to overcome environmental metabolic restrictions.
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Affiliation(s)
- Manuele Rebsamen
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Enrico Girardi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Vitaly Sedlyarov
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefania Scorzoni
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Konstantinos Papakostas
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Manuela Vollert
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Justyna Konecka
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Bettina Guertl
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kristaps Klavins
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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29
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Bhatt M, Di Iacovo A, Romanazzi T, Roseti C, Cinquetti R, Bossi E. The "www" of Xenopus laevis Oocytes: The Why, When, What of Xenopus laevis Oocytes in Membrane Transporters Research. MEMBRANES 2022; 12:membranes12100927. [PMID: 36295686 PMCID: PMC9610376 DOI: 10.3390/membranes12100927] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 05/16/2023]
Abstract
After 50 years, the heterologous expression of proteins in Xenopus laevis oocytes is still essential in many research fields. New approaches and revised protocols, but also classical methods, such as the two-electrode voltage clamp, are applied in studying membrane transporters. New and old methods for investigating the activity and the expression of Solute Carriers (SLC) are reviewed, and the kinds of experiment that are still useful to perform with this kind of cell are reported. Xenopus laevis oocytes at the full-grown stage have a highly efficient biosynthetic apparatus that correctly targets functional proteins at the defined compartment. This small protein factory can produce, fold, and localize almost any kind of wild-type or recombinant protein; some tricks are required to obtain high expression and to verify the functionality. The methodologies examined here are mainly related to research in the field of membrane transporters. This work is certainly not exhaustive; it has been carried out to be helpful to researchers who want to quickly find suggestions and detailed indications when investigating the functionality and expression of the different members of the solute carrier families.
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Affiliation(s)
- Manan Bhatt
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant 3, 21100 Varese, Italy
- Experimental and Translational Medicine, University of Insubria, Via Ottorino Rossi 9, 21100 Varese, Italy
| | - Angela Di Iacovo
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant 3, 21100 Varese, Italy
- Experimental and Translational Medicine, University of Insubria, Via Ottorino Rossi 9, 21100 Varese, Italy
| | - Tiziana Romanazzi
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant 3, 21100 Varese, Italy
- Experimental and Translational Medicine, University of Insubria, Via Ottorino Rossi 9, 21100 Varese, Italy
| | - Cristina Roseti
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant 3, 21100 Varese, Italy
- Centre for Neuroscience—Via Manara 7, University of Insubria, 21052 Busto Arsizio, Italy
| | - Raffaella Cinquetti
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant 3, 21100 Varese, Italy
| | - Elena Bossi
- Laboratory of Cellular and Molecular Physiology, Department of Biotechnology and Life Sciences, University of Insubria, Via Dunant 3, 21100 Varese, Italy
- Centre for Neuroscience—Via Manara 7, University of Insubria, 21052 Busto Arsizio, Italy
- Correspondence:
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30
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Giacomini KM, Yee SW, Koleske ML, Zou L, Matsson P, Chen EC, Kroetz DL, Miller MA, Gozalpour E, Chu X. New and Emerging Research on Solute Carrier and ATP Binding Cassette Transporters in Drug Discovery and Development: Outlook From the International Transporter Consortium. Clin Pharmacol Ther 2022; 112:540-561. [PMID: 35488474 PMCID: PMC9398938 DOI: 10.1002/cpt.2627] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/16/2022] [Indexed: 02/06/2023]
Abstract
Enabled by a plethora of new technologies, research in membrane transporters has exploded in the past decade. The goal of this state-of-the-art article is to describe recent advances in research on membrane transporters that are particularly relevant to drug discovery and development. This review covers advances in basic, translational, and clinical research that has led to an increased understanding of membrane transporters at all levels. At the basic level, we describe the available crystal structures of membrane transporters in both the solute carrier (SLC) and ATP binding cassette superfamilies, which has been enabled by the development of cryogenic electron microscopy methods. Next, we describe new research on lysosomal and mitochondrial transporters as well as recently deorphaned transporters in the SLC superfamily. The translational section includes a summary of proteomic research, which has led to a quantitative understanding of transporter levels in various cell types and tissues and new methods to modulate transporter function, such as allosteric modulators and targeted protein degraders of transporters. The section ends with a review of the effect of the gut microbiome on modulation of transporter function followed by a presentation of 3D cell cultures, which may enable in vivo predictions of transporter function. In the clinical section, we describe new genomic and pharmacogenomic research, highlighting important polymorphisms in transporters that are clinically relevant to many drugs. Finally, we describe new clinical tools, which are becoming increasingly available to enable precision medicine, with the application of tissue-derived small extracellular vesicles and real-world biomarkers.
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Affiliation(s)
- Kathleen M. Giacomini
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Sook W. Yee
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Megan L. Koleske
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Ling Zou
- Pharmacokinetics and Drug MetabolismAmgen Inc.South San FranciscoCaliforniaUSA
| | - Pär Matsson
- Department of PharmacologySahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Eugene C. Chen
- Department of Drug Metabolism and PharmacokineticsGenentech, Inc.South San FranciscoCaliforniaUSA
| | - Deanna L. Kroetz
- Department of Bioengineering and Therapeutic SciencesUniversity of California, San FranciscoSan FranciscoCaliforniaUSA
| | - Miles A. Miller
- Center for Systems BiologyMassachusetts General HospitalBostonMassachusettsUSA
| | - Elnaz Gozalpour
- Drug Safety and MetabolismIMED Biotech UnitSafety and ADME Translational Sciences DepartmentAstraZeneca R&DCambridgeUK
| | - Xiaoyan Chu
- Department of ADME and Discovery ToxicologyMerck & Co. IncKenilworthNew JerseyUSA
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31
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Wiedmer T, Ingles-Prieto A, Goldmann U, Steppan CM, Superti-Furga G. Accelerating SLC Transporter Research: Streamlining Knowledge and Validated Tools. Clin Pharmacol Ther 2022; 112:439-442. [PMID: 35938294 PMCID: PMC9540488 DOI: 10.1002/cpt.2639] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/06/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Ulrich Goldmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Claire M Steppan
- Pfizer Worldwide Research, Development & Medical, Groton, Connecticut, USA
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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32
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Huttunen J, Adla SK, Markowicz-Piasecka M, Huttunen KM. Increased/Targeted Brain (Pro)Drug Delivery via Utilization of Solute Carriers (SLCs). Pharmaceutics 2022; 14:pharmaceutics14061234. [PMID: 35745806 PMCID: PMC9228667 DOI: 10.3390/pharmaceutics14061234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/06/2022] [Accepted: 06/07/2022] [Indexed: 02/04/2023] Open
Abstract
Membrane transporters have a crucial role in compounds’ brain drug delivery. They allow not only the penetration of a wide variety of different compounds to cross the endothelial cells of the blood–brain barrier (BBB), but also the accumulation of them into the brain parenchymal cells. Solute carriers (SLCs), with nearly 500 family members, are the largest group of membrane transporters. Unfortunately, not all SLCs are fully characterized and used in rational drug design. However, if the structural features for transporter interactions (binding and translocation) are known, a prodrug approach can be utilized to temporarily change the pharmacokinetics and brain delivery properties of almost any compound. In this review, main transporter subtypes that are participating in brain drug disposition or have been used to improve brain drug delivery across the BBB via the prodrug approach, are introduced. Moreover, the ability of selected transporters to be utilized in intrabrain drug delivery is discussed. Thus, this comprehensive review will give insights into the methods, such as computational drug design, that should be utilized more effectively to understand the detailed transport mechanisms. Moreover, factors, such as transporter expression modulation pathways in diseases that should be taken into account in rational (pro)drug development, are considered to achieve successful clinical applications in the future.
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Affiliation(s)
- Johanna Huttunen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland; (J.H.); (S.K.A.)
| | - Santosh Kumar Adla
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland; (J.H.); (S.K.A.)
- Institute of Organic Chemistry and Biochemistry (IOCB), Czech Academy of Sciences, Flemingovo Namesti 542/2, 160 00 Prague, Czech Republic
| | - Magdalena Markowicz-Piasecka
- Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University of Lodz, ul. Muszyńskiego 1, 90-151 Lodz, Poland;
| | - Kristiina M. Huttunen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, FI-70211 Kuopio, Finland; (J.H.); (S.K.A.)
- Correspondence:
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33
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Sijben HJ, Dall’ Acqua L, Liu R, Jarret A, Christodoulaki E, Onstein S, Wolf G, Verburgt SJ, Le Dévédec SE, Wiedmer T, Superti-Furga G, IJzerman AP, Heitman LH. Impedance-Based Phenotypic Readout of Transporter Function: A Case for Glutamate Transporters. Front Pharmacol 2022; 13:872335. [PMID: 35677430 PMCID: PMC9169222 DOI: 10.3389/fphar.2022.872335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/29/2022] [Indexed: 11/18/2022] Open
Abstract
Excitatory amino acid transporters (EAAT/SLC1) mediate Na+-dependent uptake of extracellular glutamate and are potential drug targets for neurological disorders. Conventional methods to assess glutamate transport in vitro are based on radiolabels, fluorescent dyes or electrophysiology, which potentially compromise the cell’s physiology and are generally less suited for primary drug screens. Here, we describe a novel label-free method to assess human EAAT function in living cells, i.e., without the use of chemical modifications to the substrate or cellular environment. In adherent HEK293 cells overexpressing EAAT1, stimulation with glutamate or aspartate induced cell spreading, which was detected in real-time using an impedance-based biosensor. This change in cell morphology was prevented in the presence of the Na+/K+-ATPase inhibitor ouabain and EAAT inhibitors, which suggests the substrate-induced response was ion-dependent and transporter-specific. A mechanistic explanation for the phenotypic response was substantiated by actin cytoskeleton remodeling and changes in the intracellular levels of the osmolyte taurine, which suggests that the response involves cell swelling. In addition, substrate-induced cellular responses were observed for cells expressing other EAAT subtypes, as well as in a breast cancer cell line (MDA-MB-468) with endogenous EAAT1 expression. These findings allowed the development of a label-free high-throughput screening assay, which could be beneficial in early drug discovery for EAATs and holds potential for the study of other transport proteins that modulate cell shape.
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Affiliation(s)
- Hubert J. Sijben
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Laura Dall’ Acqua
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Rongfang Liu
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Abigail Jarret
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Eirini Christodoulaki
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Svenja Onstein
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Gernot Wolf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Simone J. Verburgt
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Sylvia E. Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Medical University of Vienna, Vienna, Austria
| | - Adriaan P. IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Laura H. Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
- Oncode Institute, Leiden, Netherlands
- *Correspondence: Laura H. Heitman,
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Markowicz-Piasecka M, Markiewicz A, Darłak P, Sikora J, Adla SK, Bagina S, Huttunen KM. Current Chemical, Biological, and Physiological Views in the Development of Successful Brain-Targeted Pharmaceutics. Neurotherapeutics 2022; 19:942-976. [PMID: 35391662 PMCID: PMC9294128 DOI: 10.1007/s13311-022-01228-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2022] [Indexed: 12/13/2022] Open
Abstract
One of the greatest challenges with successful pharmaceutical treatments of central nervous system (CNS) diseases is the delivery of drugs into their target sites with appropriate concentrations. For example, the physically tight blood-brain barrier (BBB) effectively blocks compounds from penetrating into the brain, also by the action of metabolizing enzymes and efflux transport mechanisms. However, many endogenous compounds, including both smaller compounds and macromolecules, like amino acids, sugars, vitamins, nucleosides, hormones, steroids, and electrolytes, have their peculiar internalization routes across the BBB. These delivery mechanisms, namely carrier-mediated transport and receptor-mediated transcytosis have been utilized to some extent in brain-targeted drug development. The incomplete knowledge of the BBB and the smaller than a desirable number of chemical tools have hindered the development of successful brain-targeted pharmaceutics. This review discusses the recent advancements achieved in the field from the point of medicinal chemistry view and discusses how brain drug delivery can be improved in the future.
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Affiliation(s)
- Magdalena Markowicz-Piasecka
- Laboratory of Bioanalysis, Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University of Lodz, ul. Muszyńskiego1, 90-151 Lodz, Poland
| | - Agata Markiewicz
- Students Research Group, Laboratory of Bioanalysis, Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University of Lodz, ul. Muszyńskiego 1, 90-151 Lodz, Poland
| | - Patrycja Darłak
- Students Research Group, Laboratory of Bioanalysis, Department of Pharmaceutical Chemistry, Drug Analysis and Radiopharmacy, Medical University of Lodz, ul. Muszyńskiego 1, 90-151 Lodz, Poland
| | - Joanna Sikora
- Department of Bioinorganic Chemistry, Medical University of Lodz, Medical University of Lodz, ul. Muszyńskiego1, 90-151 Lodz, Poland
| | - Santosh Kumar Adla
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1C, POB 1627, 70211 Kuopio, Finland
- Institute of Organic Chemistry and Biochemistry (IOCB), Czech Academy of Sciences, Flemingovo Namesti 542/2, 160 00 Prague, Czech Republic
| | - Sreelatha Bagina
- Charles River Discovery Research Services Finland Oy, Neulaniementie 4, 70210 Kuopio, Finland
| | - Kristiina M. Huttunen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Yliopistonranta 1C, POB 1627, 70211 Kuopio, Finland
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35
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Sijben HJ, Superti-Furga G, IJzerman AP, Heitman LH. Targeting solute carriers to modulate receptor–ligand interactions. Trends Pharmacol Sci 2022; 43:358-361. [DOI: 10.1016/j.tips.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 10/19/2022]
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Smirnova M, Goracci L, Cruciani G, Federici L, Declèves X, Chapy H, Cisternino S. Pharmacophore-Based Discovery of Substrates of a Novel Drug/Proton-Antiporter in the Human Brain Endothelial hCMEC/D3 Cell Line. Pharmaceutics 2022; 14:pharmaceutics14020255. [PMID: 35213988 PMCID: PMC8875908 DOI: 10.3390/pharmaceutics14020255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 11/16/2022] Open
Abstract
A drug/proton-antiporter, whose the molecular structure is still unknown, was previously evidenced at the blood-brain barrier (BBB) by functional experiments. The computational method could help in the identification of substrates of this solute carrier (SLC) transporter. Two pharmacophore models for substrates of this transporter using the FLAPpharm approach were developed. The trans-stimulation potency of 40 selected compounds for already known specific substrates ([3H]-clonidine) were determined and compared in the human brain endothelial cell line hCMEC/D3. Results. The two pharmacophore models obtained were used as templates to screen xenobiotic and endogenous compounds from four databases (e.g., Specs), and 45 hypothetical new candidates were tested to determine their substrate capacity. Psychoactive drugs such as antidepressants (e.g., imipramine, desipramine), antipsychotics/neuroleptics such as phenothiazine derivatives (chlorpromazine), sedatives anti-histamine-H1 drugs (promazine, promethazine, triprolidine, pheniramine), opiates/opioids (e.g., hydrocodone), trihexyphenidyl and sibutramine were correctly predicted as proton-antiporter substrates. The best performing pharmacophore model for the proton-antiporter substrates appeared as a good predictor of known substrates and allowed the identification of new substrate compounds. This model marks a new step in the characterization of this drug/proton-antiporter and will be of great use in uncovering its substrates and designing chemical entities with an improved influx capability to cross the BBB.
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Affiliation(s)
- Maria Smirnova
- Université de Paris, INSERM UMR_S1144, Optimisation Thérapeutique en Neuropsychopharmacologie, 75006 Paris, France; (M.S.); (L.F.); (X.D.); (H.C.)
| | - Laura Goracci
- Biology and Biotechnology, Department of Chemistry, University of Perugia, 06123 Perugia, Italy; (L.G.); (G.C.)
| | - Gabriele Cruciani
- Biology and Biotechnology, Department of Chemistry, University of Perugia, 06123 Perugia, Italy; (L.G.); (G.C.)
| | - Laetitia Federici
- Université de Paris, INSERM UMR_S1144, Optimisation Thérapeutique en Neuropsychopharmacologie, 75006 Paris, France; (M.S.); (L.F.); (X.D.); (H.C.)
| | - Xavier Declèves
- Université de Paris, INSERM UMR_S1144, Optimisation Thérapeutique en Neuropsychopharmacologie, 75006 Paris, France; (M.S.); (L.F.); (X.D.); (H.C.)
- Biologie du Médicament et Toxicologie, AP-HP, Hôpital Cochin, 75014 Paris, France
| | - Hélène Chapy
- Université de Paris, INSERM UMR_S1144, Optimisation Thérapeutique en Neuropsychopharmacologie, 75006 Paris, France; (M.S.); (L.F.); (X.D.); (H.C.)
| | - Salvatore Cisternino
- Université de Paris, INSERM UMR_S1144, Optimisation Thérapeutique en Neuropsychopharmacologie, 75006 Paris, France; (M.S.); (L.F.); (X.D.); (H.C.)
- Service Pharmacie, AP-HP, Hôpital Necker-Enfants Malades, 75015 Paris, France
- Correspondence: ; Tel.: +33-1-44-495-191
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37
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Yeast Double Transporter Gene Deletion Library for Identification of Xenobiotic Carriers in Low or High Throughput. mBio 2021; 12:e0322121. [PMID: 34903049 PMCID: PMC8669479 DOI: 10.1128/mbio.03221-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The routes of uptake and efflux should be considered when developing new drugs so that they can effectively address their intracellular targets. As a general rule, drugs appear to enter cells via protein carriers that normally carry nutrients or metabolites. A previously developed pipeline that searched for drug transporters using Saccharomyces cerevisiae mutants carrying single-gene deletions identified import routes for most compounds tested. However, due to the redundancy of transporter functions, we propose that this methodology can be improved by utilizing double mutant strains in both low- and high-throughput screens. We constructed a library of over 14,000 strains harboring double deletions of genes encoding 122 nonessential plasma membrane transporters and performed low- and high-throughput screens identifying possible drug import routes for 23 compounds. In addition, the high-throughput assay enabled the identification of putative efflux routes for 21 compounds. Focusing on azole antifungals, we were able to identify the involvement of the myo-inositol transporter, Itr1p, in the uptake of these molecules and to confirm the role of Pdr5p in their export.
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Chatzikyriakidou Y, Ahn DH, Nji E, Drew D. The GFP thermal shift assay for screening ligand and lipid interactions to solute carrier transporters. Nat Protoc 2021; 16:5357-5376. [PMID: 34707255 DOI: 10.1038/s41596-021-00619-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/19/2021] [Indexed: 02/03/2023]
Abstract
Solute carrier (SLC) transporters represent the second-largest fraction of the membrane proteome after G-protein-coupled receptors, but have been underutilized as drug targets and the function of many members of this family is still unknown. They are technically challenging to work with as they are difficult to express and highly dynamic, making them unstable in detergent solution. Many SLCs lack known inhibitors that could be utilized for stabilization. Furthermore, as they bind their physiological substrates with high micromolar to low millimolar affinities, binding and transport assays have proven to be particularly challenging to implement. Previously, we reported a GFP-based method for the overexpression and purification of membrane proteins in Saccharomyces cerevisiae. Here, we extend this expression platform with the GFP thermal shift (GFP-TS) assay, which is a simplified version of fluorescence-detection size-exclusion chromatography that combines the sample versatility of fluorescence-detection size-exclusion chromatography with the high-throughput capability of dye-based thermal shift assays. We demonstrate how GFP-TS can be used for detecting specific ligand interactions of SLC transporter fusions and measuring their affinities in crude detergent-solubilized membranes. We further show how GFP-TS can be employed on purified SLC transporter fusions to screen for specific lipid-protein interactions, which is an important complement to native mass spectrometry approaches that cannot cope easily with crude lipid-mixture preparations. This protocol is simple to perform and can be followed by researchers with a basic background in protein chemistry. Starting with an SLC transporter construct that can be expressed and purified from S. cerevisiae in a well-folded state, this protocol extension can be completed in ~4-5 d.
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Affiliation(s)
| | - Do-Hwan Ahn
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Emmanuel Nji
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - David Drew
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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Portioli C, Ruiz Munevar MJ, De Vivo M, Cancedda L. Cation-coupled chloride cotransporters: chemical insights and disease implications. TRENDS IN CHEMISTRY 2021; 3:832-849. [PMID: 34604727 PMCID: PMC8461084 DOI: 10.1016/j.trechm.2021.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cation-coupled chloride cotransporters (CCCs) modulate the transport of sodium and/or potassium cations coupled with chloride anions across the cell membrane. CCCs thus help regulate intracellular ionic concentration and consequent cell volume homeostasis. This has been largely exploited in the past to develop diuretic drugs that act on CCCs expressed in the kidney. However, a growing wealth of evidence has demonstrated that CCCs are also critically involved in a great variety of other pathologies, motivating most recent drug discovery programs targeting CCCs. Here, we examine the structure–function relationship of CCCs. By linking recent high-resolution cryogenic electron microscopy (cryo-EM) data with older biochemical/functional studies on CCCs, we discuss the mechanistic insights and opportunities to design selective CCC modulators to treat diverse pathologies. The structural topology and function of all cation-coupled chloride cotransporters (CCCs) have been continuously investigated over the past 40 years, with great progress also thanks to the recent cryogenic electron microscopy (cryo-EM) resolution of the structures of five CCCs. In particular, such studies have clarified the structure–function relationship for the Na-K-Cl cotransporter NKCC1 and K-Cl cotransporters KCC1–4. The constantly growing evidence of the crucial involvement of CCCs in physiological and various pathological conditions, as well as the evidence of their wide expression in diverse body tissues, has promoted CCCs as targets for the discovery and development of new, safer, and more selective/effective drugs for a plethora of pathologies. Post-translational modification anchor points on the structure of CCCs may offer alternative strategies for small molecule drug discovery.
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Affiliation(s)
- Corinne Portioli
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163 Genoa, Italy.,Laboratory of Molecular Modeling and Drug Discovery, IIT, Via Morego, 30 16163 Genoa, Italy
| | | | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, IIT, Via Morego, 30 16163 Genoa, Italy
| | - Laura Cancedda
- Brain Development and Disease Laboratory, Istituto Italiano di Tecnologia (IIT), Via Morego 30, 16163 Genoa, Italy.,Dulbecco Telethon Institute, Via Varese 16b, 00185 Rome, Italy
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Kell DB. The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes. Molecules 2021; 26:5629. [PMID: 34577099 PMCID: PMC8470029 DOI: 10.3390/molecules26185629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Biotechnology Ltd., IC1, Liverpool Science Park, Mount Pleasant, Liverpool L3 5TF, UK
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41
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Sachkova A, Doetsch DA, Jensen O, Brockmöller J, Ansari S. How do psychostimulants enter the human brain? Analysis of the role of the proton-organic cation antiporter. Biochem Pharmacol 2021; 192:114751. [PMID: 34464621 DOI: 10.1016/j.bcp.2021.114751] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/26/2021] [Accepted: 08/26/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND Although psychostimulants apparently do cross the BBB, it is poorly understood how these hydrophilic and positively charged molecules can pass the blood-brain barrier (BBB). That may be mediated by a genetically still uncharacterized H+/OC antiporter with high activity at the BBB. METHODS We studied the uptake of 16 psychostimulants and hallucinogens with hCMEC/D3 cells using the prototypic inhibitor imipramine (cis-inhibition), exchange transport with diphenhydramine and clonidine (trans-stimulation), proton dependency of the uptake, and we characterized the concentration-dependent uptake. RESULTS Cell uptake of methylenedioxyamphetamines, amphetamines and dimethyltryptamine (DMT) were strongly inhibited (to about 10% of the controls) by imipramine and diphenhydramine, whereas uptake of cathine was only weakly inhibited and mescaline not significantly. Amphetamine, methylamphetamine, para-Methoxy-N-methylamphetamine (PMMA), Methylenedioxymethamphetamine (MDMA), phentermine and DMT exhibited the highest exchange after preloading with diphenhydramine with only 5.5%, 5.2%, 7.8%, 6%, 1.9%, 7.6% remaining in the cells. Less and no exchange were seen with cathine and mescaline, respectively. Dependence on intracellular pH was most pronounced with the methylendioxyamphetamines while uptake of cathine, DOI and cocaine were only moderately affected and mescaline not at all. CONCLUSION Except for mescaline, all psychostimulants studied here were substrates of the H+/OC antiporter, implicating a strong need for a better characterization of this transport protein.
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Affiliation(s)
- Alexandra Sachkova
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Georg-August University, D-37075 Göttingen, Germany; Department of Anesthesiology and Intensive Care Medicine, University Medical Center Göttingen, Germany.
| | - David Alexander Doetsch
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Georg-August University, D-37075 Göttingen, Germany
| | - Ole Jensen
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Georg-August University, D-37075 Göttingen, Germany
| | - Jürgen Brockmöller
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Georg-August University, D-37075 Göttingen, Germany
| | - Salim Ansari
- Institute of Clinical Pharmacology, University Medical Center Göttingen, Georg-August University, D-37075 Göttingen, Germany
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Dvorak V, Wiedmer T, Ingles-Prieto A, Altermatt P, Batoulis H, Bärenz F, Bender E, Digles D, Dürrenberger F, Heitman LH, IJzerman AP, Kell DB, Kickinger S, Körzö D, Leippe P, Licher T, Manolova V, Rizzetto R, Sassone F, Scarabottolo L, Schlessinger A, Schneider V, Sijben HJ, Steck AL, Sundström H, Tremolada S, Wilhelm M, Wright Muelas M, Zindel D, Steppan CM, Superti-Furga G. An Overview of Cell-Based Assay Platforms for the Solute Carrier Family of Transporters. Front Pharmacol 2021; 12:722889. [PMID: 34447313 PMCID: PMC8383457 DOI: 10.3389/fphar.2021.722889] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/19/2021] [Indexed: 12/12/2022] Open
Abstract
The solute carrier (SLC) superfamily represents the biggest family of transporters with important roles in health and disease. Despite being attractive and druggable targets, the majority of SLCs remains understudied. One major hurdle in research on SLCs is the lack of tools, such as cell-based assays to investigate their biological role and for drug discovery. Another challenge is the disperse and anecdotal information on assay strategies that are suitable for SLCs. This review provides a comprehensive overview of state-of-the-art cellular assay technologies for SLC research and discusses relevant SLC characteristics enabling the choice of an optimal assay technology. The Innovative Medicines Initiative consortium RESOLUTE intends to accelerate research on SLCs by providing the scientific community with high-quality reagents, assay technologies and data sets, and to ultimately unlock SLCs for drug discovery.
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Affiliation(s)
- Vojtech Dvorak
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tabea Wiedmer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Alvaro Ingles-Prieto
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | | | - Helena Batoulis
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Felix Bärenz
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | - Eckhard Bender
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Daniela Digles
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | | | - Laura H. Heitman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Adriaan P. IJzerman
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | - Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stefanie Kickinger
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Daniel Körzö
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Philipp Leippe
- Department of Chemical Biology, Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Thomas Licher
- Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany
| | | | | | | | | | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Vanessa Schneider
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Hubert J. Sijben
- Division of Drug Discovery and Safety, LACDR, Leiden University, Leiden, Netherlands
| | | | | | | | | | - Marina Wright Muelas
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Diana Zindel
- Drug Discovery Sciences–Lead Discovery, Bayer Pharmaceuticals, Wuppertal, Germany
| | - Claire M. Steppan
- Pfizer Worldwide Research, Development and Medical, Groton, MA, United States
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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Smagin DA, Babenko VN, Redina OE, Kovalenko IL, Galyamina AG, Kudryavtseva NN. Reduced Expression of Slc Genes in the VTA and NAcc of Male Mice with Positive Fighting Experience. Genes (Basel) 2021; 12:genes12071099. [PMID: 34356115 PMCID: PMC8306410 DOI: 10.3390/genes12071099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/27/2021] [Accepted: 07/16/2021] [Indexed: 12/28/2022] Open
Abstract
A range of several psychiatric medications targeting the activity of solute carrier (SLC) transporters have proved effective for treatment. Therefore, further research is needed to elucidate the expression profiles of the Slc genes, which may serve as markers of altered brain metabolic processes and neurotransmitter activities in psychoneurological disorders. We studied the Slc differentially expressed genes (DEGs) using transcriptomic profiles in the ventral tegmental area (VTA), nucleus accumbens (NAcc), and prefrontal cortex (PFC) of control and aggressive male mice with psychosis-like behavior induced by repeated experience of aggression accompanied with wins in daily agonistic interactions. The majority of the Slc DEGs were shown to have brain region-specific expression profiles. Most of these genes in the VTA and NAcc (12 of 17 and 25 of 26, respectively) were downregulated, which was not the case in the PFC (6 and 5, up- and downregulated, respectively). In the VTA and NAcc, altered expression was observed for the genes encoding the transporters of neurotransmitters as well as inorganic and organic ions, amino acids, metals, glucose, etc. This indicates an alteration in transport functions for many substrates, which can lead to the downregulation or even disruption of cellular and neurotransmitter processes in the VTA and NAcc, which are attributable to chronic stimulation of the reward systems induced by positive fighting experience. There is not a single Slc DEG common to all three brain regions. Our findings show that in male mice with repeated experience of aggression, altered activity of neurotransmitter systems leads to a restructuring of metabolic and neurotransmitter processes in a way specific for each brain region. We assume that the scoring of Slc DEGs by the largest instances of significant expression co-variation with other genes may outline a candidate for new prognostic drug targets. Thus, we propose that the Slc genes set may be treated as a sensitive genes marker scaffold in brain RNA-Seq studies.
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Affiliation(s)
- Dmitry A. Smagin
- Neuropathology Modeling Laboratory, The FRC Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (D.A.S.); (V.N.B.); (O.E.R.); (I.L.K.); (A.G.G.)
- Neurogenetics of Social Behavior Sector, The FRC Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Vladimir N. Babenko
- Neuropathology Modeling Laboratory, The FRC Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (D.A.S.); (V.N.B.); (O.E.R.); (I.L.K.); (A.G.G.)
| | - Olga E. Redina
- Neuropathology Modeling Laboratory, The FRC Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (D.A.S.); (V.N.B.); (O.E.R.); (I.L.K.); (A.G.G.)
| | - Irina L. Kovalenko
- Neuropathology Modeling Laboratory, The FRC Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (D.A.S.); (V.N.B.); (O.E.R.); (I.L.K.); (A.G.G.)
- Neurogenetics of Social Behavior Sector, The FRC Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Anna G. Galyamina
- Neuropathology Modeling Laboratory, The FRC Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (D.A.S.); (V.N.B.); (O.E.R.); (I.L.K.); (A.G.G.)
- Neurogenetics of Social Behavior Sector, The FRC Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
| | - Natalia N. Kudryavtseva
- Neuropathology Modeling Laboratory, The FRC Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (D.A.S.); (V.N.B.); (O.E.R.); (I.L.K.); (A.G.G.)
- Neurogenetics of Social Behavior Sector, The FRC Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia
- Correspondence:
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Wang YT, Lin MR, Chen WC, Wu WH, Wang FS. Optimization of a modeling platform to predict oncogenes from genome-scale metabolic networks of non-small-cell lung cancers. FEBS Open Bio 2021. [PMID: 34137202 PMCID: PMC8329960 DOI: 10.1002/2211-5463.13231] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/19/2021] [Accepted: 06/16/2021] [Indexed: 12/25/2022] Open
Abstract
Cancer cell dysregulations result in the abnormal regulation of cellular metabolic pathways. By simulating this metabolic reprogramming using constraint-based modeling approaches, oncogenes can be predicted, and this knowledge can be used in prognosis and treatment. We introduced a trilevel optimization problem describing metabolic reprogramming for inferring oncogenes. First, this study used RNA-Seq expression data of lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) samples and their healthy counterparts to reconstruct tissue-specific genome-scale metabolic models and subsequently build the flux distribution pattern that provided a measure for the oncogene inference optimization problem for determining tumorigenesis. The platform detected 45 genes for LUAD and 84 genes for LUSC that lead to tumorigenesis. A high level of differentially expressed genes was not an essential factor for determining tumorigenesis. The platform indicated that pyruvate kinase (PKM), a well-known oncogene with a low level of differential gene expression in LUAD and LUSC, had the highest fitness among the predicted oncogenes based on computation. By contrast, pyruvate kinase L/R (PKLR), an isozyme of PKM, had a high level of differential gene expression in both cancers. Phosphatidylserine synthase 1 (PTDSS1), an oncogene in LUAD, was inferred to have a low level of differential gene expression, and overexpression could significantly reduce survival probability. According to the factor analysis, PTDSS1 characteristics were close to those of the template, but they were unobvious in LUSC. Angiotensin-converting enzyme 2 (ACE2) has recently garnered widespread interest as the SARS-CoV-2 virus receptor. Moreover, we determined that ACE2 is an oncogene of LUSC but not of LUAD. The platform developed in this study can identify oncogenes with low levels of differential expression and be used to identify potential therapeutic targets for cancer treatment.
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Affiliation(s)
- You-Tyun Wang
- Department of Chemical Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Min-Ru Lin
- Department of Chemical Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Wei-Chen Chen
- Department of Chemical Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Wu-Hsiung Wu
- Department of Chemical Engineering, National Chung Cheng University, Chiayi, Taiwan
| | - Feng-Sheng Wang
- Department of Chemical Engineering, National Chung Cheng University, Chiayi, Taiwan
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Kell DB. A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation. Adv Microb Physiol 2021; 78:1-177. [PMID: 34147184 DOI: 10.1016/bs.ampbs.2021.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative, Biology, University of Liverpool, Liverpool, United Kingdom; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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Chang ED, Owen SF, Hogstrand C, Bury NR. Developing in vitro models to assess fish gill excretion of emerging contaminants. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:1470-1478. [PMID: 33683222 DOI: 10.1039/d0ay02282a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Advances in analytical methods have enabled the detection of emerging contaminants at ever lower concentrations in freshwaters. However, such measurements need to be linked to effect-based assays to identify risks. The bioconcentration factor (BCF) forms part of a chemical's environmental risk assessment (ERA), and current regulatory testing guidelines to calculate fish BCFs use hundreds of fish per chemical. Due to ethical concerns a reduction in the numbers of animals used is desired, and there is a need to identify in vitro or in silico alternatives which meet regulatory acceptance. This study describes the successful demonstration of a FIsh Gill Cell culture System (FIGCS) to assess an often overlooked parameter in pharmacokinetics: the excretion of drugs across the gill. The FIGCS tolerates the application of natural waters on its apical surface, mimicking the situation of the live fish, and thus in combination with advanced analytical methods, offers an opportunity to take lab-based testing used for ERA, such as compound uptake, biotransformation or excretion directly into field for validation with natural waters. Here we used the basic drug propranolol and the acidic ibuprofen as a demonstration of the FIGCS utility in three separate experiments. Excretion across the apical membrane showed saturation kinetics, suggesting the involvement of carrier-mediated processes. Both propranolol and ibuprofen were excreted across the epithelium from the media (internal blood equivalent) to the water, with ibuprofen excretion being considerably slower than propranolol excretion. Further studies indicate that ibuprofen may be complexing with fetal bovine serum (FBS) reducing bioavailability; in contrast propranolol efflux rate was unaffected, indicating that drugs behave differently in the presence of FBS and other plasma proteins. A key issue in future ERA is to better understand the effects of mixtures of different pollutant classes found in environmental samples, and this model offers an ethical path to do this.
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Affiliation(s)
- Elisabeth Dohmann Chang
- King's College London, Division of Diabetes and Nutritional Sciences, Franklin Wilkins Building, 150 Stamford Street, London, SE1 9NH, UK.
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Recent developments in ligands and chemical probes targeting solute carrier transporters. Curr Opin Chem Biol 2021; 62:53-63. [PMID: 33689964 DOI: 10.1016/j.cbpa.2021.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/12/2021] [Accepted: 01/31/2021] [Indexed: 12/30/2022]
Abstract
Solute carrier (SLC) membrane transporters remain a largely unexploited target class, despite their central roles in cell identity and metabolism. This gap is reflected in the lack of high-quality chemical ligands or probes and in the small number of compounds that have progressed toward clinical development. In this review, we discuss recent advancements in SLC ligand discovery as well as new candidates that have been added to the investigational toolkit, with a particular focus on first-in-class ligands and the cognate discovery strategies. The availability of new probes expands the opportunity to elucidate the functions of SLCs and their relevance in physiology and explores any future potential of SLC druggability.
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48
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Foley TL, Burchett W, Chen Q, Flanagan ME, Kapinos B, Li X, Montgomery JI, Ratnayake AS, Zhu H, Peakman MC. Selecting Approaches for Hit Identification and Increasing Options by Building the Efficient Discovery of Actionable Chemical Matter from DNA-Encoded Libraries. SLAS DISCOVERY 2021; 26:263-280. [PMID: 33412987 DOI: 10.1177/2472555220979589] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past 20 years, the toolbox for discovering small-molecule therapeutic starting points has expanded considerably. Pharmaceutical researchers can now choose from technologies that, in addition to traditional high-throughput knowledge-based and diversity screening, now include the screening of fragment and fragment-like libraries, affinity selection mass spectrometry, and selection against DNA-encoded libraries (DELs). Each of these techniques has its own unique combination of advantages and limitations that makes them more, or less, suitable for different target classes or discovery objectives, such as desired mechanism of action. Layered on top of this are the constraints of the drug-hunters themselves, including budgets, timelines, and available platform capacity; each of these can play a part in dictating the hit identification strategy for a discovery program. In this article, we discuss some of the factors that we use to govern our building of a hit identification roadmap for a program and describe the increasing role that DELs are playing in our discovery strategy. Furthermore, we share our learning during our initial exploration of DEL and highlight the approaches we have evolved to maximize the value returned from DEL selections. Topics addressed include the optimization of library design and production, reagent validation, data analysis, and hit confirmation. We describe how our thinking in these areas has led us to build a DEL platform that has begun to deliver tractable matter to our global discovery portfolio.
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Affiliation(s)
| | | | - Qiuxia Chen
- Lead Generation Unit, HitGen Inc., Chengdu, Shuangliu District, China
| | | | | | - Xianyang Li
- Lead Generation Unit, HitGen Inc., Chengdu, Shuangliu District, China
| | | | | | - Hongyao Zhu
- Simulation and Modelling Sciences, Pfizer Inc., Groton, CT, USA
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Exploiting the metabolic dependencies of the broad amino acid transporter SLC6A14. Oncotarget 2020; 11:4490-4503. [PMID: 33400734 PMCID: PMC7721610 DOI: 10.18632/oncotarget.27758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 09/10/2020] [Indexed: 02/06/2023] Open
Abstract
Tumor cells typically enhance their metabolic capacity to sustain their higher rate of growth and proliferation. One way to elevate the nutrient intake into cancer cells is to increase the expression of genes encoding amino acid transporters, which may represent targetable vulnerabilities. Here, we study the regulation and function of the broad amino acid transporter SLC6A14 in combination with metabolic stress, providing insights into an uncharacterized aspect of the transporter activity. We analyze the pattern of transcriptional changes in a panel of breast cancer cell lines upon metabolic stress and found that SLC6A14 expression levels are increased in the absence of methionine. Methionine deprivation, which can be achieved via modulation of dietary methionine intake in tumor cells, in turn leads to a heightened activation of the AMP-activated kinase (AMPK) in SLC6A14-deficient cells. While SLC6A14 genetic deficiency does not have a major impact on cell proliferation, combined depletion of AMPK and SLC6A14 leads to an increase in apoptosis upon methionine starvation, suggesting that combined targeting of SLC6A14 and AMPK can be exploited as a therapeutic approach to starve tumor cells.
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van der Hoek SA, Borodina I. Transporter engineering in microbial cell factories: the ins, the outs, and the in-betweens. Curr Opin Biotechnol 2020; 66:186-194. [PMID: 32927362 PMCID: PMC7758712 DOI: 10.1016/j.copbio.2020.08.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/03/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022]
Abstract
Engineering the transport of small molecules is an effective approach to improve the performance of microbial cell factories. Transporter engineering can improve the utilization of low-cost alternative substrates, reduce the loss of pathway intermediates, and increase the titer and production rate of the target product. However, transporters are not commonly engineered in strain development programs because the functions of most of the transport proteins are not known. In the recent years, a variety of methods have been developed for identification of transporters for specific substrates and for characterizing transport mechanisms. This review presents recent examples of successful transport engineering for cell factories and discusses the methods for transporter identification and characterization.
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Affiliation(s)
- Steven A van der Hoek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
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