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Ruiz-Rodríguez VM, Torres-González CA, Salas-Canedo KM, Pecina-Maza NQ, Martínez-Leija ME, Portales-Pérez DP, Estrada-Sánchez AM. Dynamical changes in the expression of GABAergic and purinergic components occur during the polarization of THP-1 monocytes to proinflammatory macrophages. Biochem Biophys Rep 2023; 36:101558. [PMID: 37881409 PMCID: PMC10594599 DOI: 10.1016/j.bbrep.2023.101558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/11/2023] [Indexed: 10/27/2023] Open
Abstract
The monocytes are key components of innate immunity, as they can differentiate into phagocytic cells or macrophages with proinflammatory or anti-inflammatory phenotypes. The gamma-aminobutyric acid (GABA) and adenosine triphosphate (ATP), two known neurotransmitters, are two environmental signals that contribute to the differentiation of monocytes into macrophages and their subsequent polarization into proinflammatory M1 and anti-inflammatory M2 macrophages. Although monocytes and macrophages express proteins related to GABA and ATP-mediated response (GABAergic and purinergic systems, respectively), it is unknown whether changes in their expression occur during monocyte activation or their differentiation and polarization into macrophages. Therefore, we evaluated the expression levels of GABAergic and purinergic signaling components in the THP-1 monocyte cell line and their changes during monocyte activation, differentiation, and polarization to M1 proinflammatory macrophages. Our results showed that activated monocytes are characterized by increased expression of two GABAergic components, the GABA transporter 2 (GAT-2) and the glutamic acid decarboxylase (GAD)-67, an enzyme involved in GABA synthesis. Also, monocytes showed a pronounced expression of the purinergic receptors P2X4 and P2X7. Interestingly, during differentiation, monocytes increased the expression of the β2 subunit of GABA A-type receptor (GABA-AR), while the purinergic receptors P2X1 and P2X1del were reduced. In contrast, proinflammatory M1 macrophages showed a reduced expression in the α4 subunit of GABA-AR and GAD67, while P2X4 and P2X7 were overexpressed. These results indicate that dynamical changes in the GABAergic and purinergic components occur during the transition from monocytes to macrophages. Since GABA and ATP are two neurotransmitters, our results suggest that monocytes and macrophages respond to neurotransmitter-induced stimulation and may represent a path of interaction between the nervous and immune systems during peripheral inflammation and neuroinflammation development.
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Affiliation(s)
- Victor Manuel Ruiz-Rodríguez
- División de Biología Molecular, Laboratorio de Neurobiología, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, San Luis Potosí, México
| | - Carlos Alberto Torres-González
- División de Biología Molecular, Laboratorio de Neurobiología, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, San Luis Potosí, México
- Translational and Molecular Medicine Laboratory, Research Center for Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí, México
| | - Karina Monserrat Salas-Canedo
- División de Biología Molecular, Laboratorio de Neurobiología, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, San Luis Potosí, México
- Translational and Molecular Medicine Laboratory, Research Center for Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí, México
| | - Nicole Quibey Pecina-Maza
- División de Biología Molecular, Laboratorio de Neurobiología, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, San Luis Potosí, México
- Translational and Molecular Medicine Laboratory, Research Center for Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí, México
| | - Miguel Ernesto Martínez-Leija
- Translational and Molecular Medicine Laboratory, Research Center for Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí, México
| | - Diana Patricia Portales-Pérez
- Translational and Molecular Medicine Laboratory, Research Center for Health Sciences and Biomedicine, Autonomous University of San Luis Potosí, San Luis Potosí, México
| | - Ana María Estrada-Sánchez
- División de Biología Molecular, Laboratorio de Neurobiología, Instituto Potosino de Investigación Científica y Tecnológica (IPICYT), San Luis Potosí, San Luis Potosí, México
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2
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GABA signaling enforces intestinal germinal center B cell differentiation. Proc Natl Acad Sci U S A 2022; 119:e2215921119. [PMID: 36279432 PMCID: PMC9636909 DOI: 10.1073/pnas.2215921119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recent compelling results indicate possible links between neurotransmitters, intestinal mucosal IgA
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B cell responses, and immunoglobulin A nephropathy (IgAN) pathogenesis. Here, we demonstrated that γ-amino butyric acid (GABA) transporter-2 (GAT-2) deficiency induces intestinal germinal center (GC) B cell differentiation and worsens the symptoms of IgAN in a mouse model. Mechanistically, GAT-2 deficiency enhances GC B cell differentiation through activation of GABA–mammalian target of rapamycin complex 1 (mTORC1) signaling. In addition, IgAN patients have lower GAT-2 expression but higher activation of mTORC1 in blood B cells, and both are correlated with kidney function in IgAN patients. Collectively, this study describes GABA signaling–mediated intestinal mucosal immunity as a previously unstudied pathogenesis mechanism of IgAN and challenges the current paradigms of IgAN.
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3
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Joseph D, Nayak SR, Penmatsa A. Structural insights into GABA transport inhibition using an engineered neurotransmitter transporter. EMBO J 2022; 41:e110735. [PMID: 35796008 PMCID: PMC9340486 DOI: 10.15252/embj.2022110735] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/08/2022] [Accepted: 06/12/2022] [Indexed: 01/14/2023] Open
Abstract
γ-aminobutyric acid (GABA) is the major inhibitory neurotransmitter, and its levels in the synaptic space are controlled by the GABA transporter isoforms (GATs). GATs are structurally related to biogenic amine transporters but display interactions with distinct inhibitors used as anti-epileptics. In this study, we engineer the binding pocket of Drosophila melanogaster dopamine transporter to resemble GAT1 and determine high-resolution X-ray structures of the modified transporter in the substrate-free state and in complex with GAT1 inhibitors NO711 and SKF89976a that are analogs of tiagabine, a medication prescribed for the treatment of partial seizures. We observe that the primary binding site undergoes substantial shifts in subsite architecture in the modified transporter to accommodate the two GAT1 inhibitors. We also observe that SKF89976a additionally interacts at an allosteric site in the extracellular vestibule, yielding an occluded conformation. Interchanging SKF89976a interacting residue in the extracellular loop 4 between GAT1 and dDAT suggests a role for this motif in the selective control of neurotransmitter uptake. Our findings, therefore, provide vital insights into the organizational principles dictating GAT1 activity and inhibition.
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Affiliation(s)
- Deepthi Joseph
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
| | | | - Aravind Penmatsa
- Molecular Biophysics UnitIndian Institute of ScienceBangaloreIndia
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4
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Lizarraga SB, Ma L, Maguire AM, van Dyck LI, Wu Q, Ouyang Q, Kavanaugh BC, Nagda D, Livi LL, Pescosolido MF, Schmidt M, Alabi S, Cowen MH, Brito-Vargas P, Hoffman-Kim D, Gamsiz Uzun ED, Schlessinger A, Jones RN, Morrow EM. Human neurons from Christianson syndrome iPSCs reveal mutation-specific responses to rescue strategies. Sci Transl Med 2021; 13:13/580/eaaw0682. [PMID: 33568516 DOI: 10.1126/scitranslmed.aaw0682] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 06/04/2020] [Accepted: 09/18/2020] [Indexed: 12/16/2022]
Abstract
Christianson syndrome (CS), an X-linked neurological disorder characterized by postnatal attenuation of brain growth (postnatal microcephaly), is caused by mutations in SLC9A6, the gene encoding endosomal Na+/H+ exchanger 6 (NHE6). To hasten treatment development, we established induced pluripotent stem cell (iPSC) lines from patients with CS representing a mutational spectrum, as well as biologically related and isogenic control lines. We demonstrated that pathogenic mutations lead to loss of protein function by a variety of mechanisms: The majority of mutations caused loss of mRNA due to nonsense-mediated mRNA decay; however, a recurrent, missense mutation (the G383D mutation) had both loss-of-function and dominant-negative activities. Regardless of mutation, all patient-derived neurons demonstrated reduced neurite growth and arborization, likely underlying diminished postnatal brain growth in patients. Phenotype rescue strategies showed mutation-specific responses: A gene transfer strategy was effective in nonsense mutations, but not in the G383D mutation, wherein residual protein appeared to interfere with rescue. In contrast, application of exogenous trophic factors (BDNF or IGF-1) rescued arborization phenotypes across all mutations. These results may guide treatment development in CS, including gene therapy strategies wherein our data suggest that response to treatment may be dictated by the class of mutation.
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Affiliation(s)
- Sofia B Lizarraga
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.,Center for Childhood Neurotherapeutics, University of South Carolina, Columbia, SC 29208, USA
| | - Li Ma
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA
| | - Abbie M Maguire
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI 02912, USA
| | - Laura I van Dyck
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Qing Wu
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA.,Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA
| | - Qing Ouyang
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA
| | - Brian C Kavanaugh
- Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI 02912, USA.,Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Emma Pendleton Bradley Hospital, East Providence, RI 02915, USA
| | - Dipal Nagda
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Liane L Livi
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA
| | - Matthew F Pescosolido
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI 02912, USA.,Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Emma Pendleton Bradley Hospital, East Providence, RI 02915, USA
| | - Michael Schmidt
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA.,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI 02912, USA.,Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Emma Pendleton Bradley Hospital, East Providence, RI 02915, USA
| | - Shanique Alabi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mara H Cowen
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.,Center for Childhood Neurotherapeutics, University of South Carolina, Columbia, SC 29208, USA
| | - Paul Brito-Vargas
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.,Center for Childhood Neurotherapeutics, University of South Carolina, Columbia, SC 29208, USA
| | - Diane Hoffman-Kim
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA.,Robert J. and Nancy D. Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA.,Center for Biomedical Engineering, Brown University, Providence, RI 02912, USA
| | - Ece D Gamsiz Uzun
- Center for Computational Molecular Biology, Brown University, Providence, RI 02912, USA.,Department of Pathology and Laboratory Medicine, Warren Alpert Medical School of Brown University, Providence, RI 02912, USA
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Richard N Jones
- Quantitative Sciences Program, Department of Psychiatry and Human Behavior and Department of Neurology, Warren Alpert Medical School of Brown University, Providence, RI 02912, USA
| | - Eric M Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA. .,Center for Translational Neuroscience, Robert J. and Nancy D. Carney Institute for Brain Science and Brown Institute for Translational Science, Brown University, Providence, RI 02912, USA.,Hassenfeld Child Health Innovation Institute, Brown University, Providence, RI 02912, USA.,Developmental Disorders Genetics Research Program, Department of Psychiatry and Human Behavior, Emma Pendleton Bradley Hospital, East Providence, RI 02915, USA
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5
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Gut-inhabiting Clostridia build human GPCR ligands by conjugating neurotransmitters with diet- and human-derived fatty acids. Nat Microbiol 2021; 6:792-805. [PMID: 33846627 DOI: 10.1038/s41564-021-00887-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/01/2021] [Indexed: 02/01/2023]
Abstract
Human physiology is regulated by endogenous signalling compounds, including fatty acid amides (FAAs), chemical mimics of which are made by bacteria. The molecules produced by human-associated microbes are difficult to identify because they may only be made in a local niche or they require a substrate sourced from the host, diet or other microbes. We identified a set of uncharacterized gene clusters in metagenomics data from the human gut microbiome. These clusters were discovered to make FAAs by fusing exogenous fatty acids with amines. Using an in vitro assay, we tested their ability to incorporate 25 fatty acids and 53 amines known to be present in the human gut, from which the production of six FAAs was deduced (oleoyl dopamine, oleoyl tyramine, lauroyl tryptamine, oleoyl aminovaleric acid, α-linolenoyl phenylethylamine and caproyl tryptamine). These molecules were screened against panels of human G-protein-coupled receptors to deduce their putative human targets. Lauroyl tryptamine is found to be an antagonist to the immunomodulatory receptor EBI2 against its native oxysterol ligand (0.98 μM half-maximal inhibitory concentration), is produced in culture by Eubacterium rectale and is present in human faecal samples. FAAs produced by Clostridia may serve as a mechanism to modulate their host by mimicking human signalling molecules.
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6
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Wątły J, Miller A, Kozłowski H, Rowińska-Żyrek M. Peptidomimetics - An infinite reservoir of metal binding motifs in metabolically stable and biologically active molecules. J Inorg Biochem 2021; 217:111386. [PMID: 33610030 DOI: 10.1016/j.jinorgbio.2021.111386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022]
Abstract
The involvement of metal ions in interactions with therapeutic peptides is inevitable. They are one of the factors able to fine-tune the biological properties of antimicrobial peptides, a promising group of drugs with one large drawback - a problematic metabolic stability. Appropriately chosen, proteolytically stable peptidomimetics seem to be a reasonable solution of the problem, and the use of D-, β-, γ-amino acids, unnatural amino acids, azapeptides, peptoids, cyclopeptides and dehydropeptides is an infinite reservoir of metal binding motifs in metabolically stable, well-designed, biologically active molecules. Below, their specific structural features, metal-chelating abilities and antimicrobial potential are discussed.
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Affiliation(s)
- Joanna Wątły
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland.
| | - Adriana Miller
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland
| | - Henryk Kozłowski
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland; Department of Health Sciences, University of Opole, Katowicka 68, Opole 45-060, Poland
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7
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Łątka K, Jończyk J, Bajda M. Structure modeling of γ-aminobutyric acid transporters - Molecular basics of ligand selectivity. Int J Biol Macromol 2020; 158:S0141-8130(20)33135-4. [PMID: 32376252 DOI: 10.1016/j.ijbiomac.2020.04.263] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 11/15/2022]
Abstract
γ-Aminobutyric acid transporters are responsible for regulating the GABA level in the synaptic cleft. In this way, they affect GABA-ergic transmission which is important for the proper functioning of the central nervous system. The exact structure of GABA transporters is still unknown, which hinders the design of new, potent and selective inhibitors. For these reasons, we decided to create models of all types of human gamma-aminobutyric acid transporters. They were built based on crystal structures of related proteins from the SLC6 family using homology modeling methods. The reliability of the received models has been confirmed by a number of tools assessing the quality of protein models. To determine the ligand binding mode and indicate the amino acids responsible for selectivity, docking studies and molecular dynamics simulations were performed. The amino acids lining the bottom of the main binding site have a major impact on the selective ligand binding. In addition, an important element is the non-helical fragment of the transmembrane domain 10, and several amino acids within the vestibule of the transporters, which affect its volume. To check whether obtained models are suitable to distinguish active compounds from inactive ones, enrichment plots were prepared. Results suggest that our models may be useful in the search for new inhibitors of GABA transporters of the desired selectivity.
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Affiliation(s)
- Kamil Łątka
- Jagiellonian University Medical College, Faculty of Pharmacy, Department of Physicochemical Drug Analysis, 30-688 Cracow, Medyczna 9, Poland
| | - Jakub Jończyk
- Jagiellonian University Medical College, Faculty of Pharmacy, Department of Physicochemical Drug Analysis, 30-688 Cracow, Medyczna 9, Poland
| | - Marek Bajda
- Jagiellonian University Medical College, Faculty of Pharmacy, Department of Physicochemical Drug Analysis, 30-688 Cracow, Medyczna 9, Poland.
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8
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Łątka K, Jończyk J, Bajda M. γ-Aminobutyric acid transporters as relevant biological target: Their function, structure, inhibitors and role in the therapy of different diseases. Int J Biol Macromol 2020; 158:S0141-8130(20)32987-1. [PMID: 32360967 DOI: 10.1016/j.ijbiomac.2020.04.126] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/17/2020] [Accepted: 04/18/2020] [Indexed: 12/13/2022]
Abstract
γ-Aminobutyric acid (GABA) is a major inhibitory neurotransmitter in the nervous system. It plays a crucial role in many physiological processes. Upon release from the presynaptic element, it is removed from the synaptic cleft by reuptake due to the action of GABA transporters (GATs). GATs belong to a large SLC6 protein family whose characteristic feature is sodium-dependent relocation of neurotransmitters through the cell membrane. GABA transporters are characterized in many contexts, but their spatial structure is not fully known. They are divided into four types, which differ in occurrence and role. Herein, the special attention was paid to these transporting proteins. This comprehensive review presents the current knowledge about GABA transporters. Their distribution in the body, physiological functions and possible utilization in the therapy of different diseases were fully discussed. The important structural features were described based on published data, including sequence analysis, mutagenesis studies, and comparison with known SLC6 transporters for leucine (LeuT), dopamine (DAT) and serotonin (SERT). Moreover, the most important inhibitors of GABA transporters of various basic scaffolds, diverse selectivity and potency were presented.
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Affiliation(s)
- Kamil Łątka
- Jagiellonian University Medical College, Faculty of Pharmacy, Department of Physicochemical Drug Analysis, 30-688 Cracow, Medyczna 9, Poland
| | - Jakub Jończyk
- Jagiellonian University Medical College, Faculty of Pharmacy, Department of Physicochemical Drug Analysis, 30-688 Cracow, Medyczna 9, Poland
| | - Marek Bajda
- Jagiellonian University Medical College, Faculty of Pharmacy, Department of Physicochemical Drug Analysis, 30-688 Cracow, Medyczna 9, Poland.
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9
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Studies of structural determinants of substrate binding in the Creatine Transporter (CreaT, SLC6A8) using molecular models. Sci Rep 2020; 10:6241. [PMID: 32277128 PMCID: PMC7148354 DOI: 10.1038/s41598-020-63189-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 03/26/2020] [Indexed: 01/17/2023] Open
Abstract
Creatine is a crucial metabolite that plays a fundamental role in ATP homeostasis in tissues with high-energy demands. The creatine transporter (CreaT, SLC6A8) belongs to the solute carrier 6 (SLC6) transporters family, and more particularly to the GABA transporters (GATs) subfamily. Understanding the molecular determinants of specificity within the SLC6 transporters in general, and the GATs in particular is very challenging due to the high similarity of these proteins. In the study presented here, our efforts focused on finding key structural features involved in binding selectivity for CreaT using structure-based computational methods. Due to the lack of three-dimensional structures of SLC6A8, our approach was based on the realization of two reliable homology models of CreaT using the structures of two templates, i.e. the human serotonin transporter (hSERT) and the prokaryotic leucine transporter (LeuT). Our models reveal that an optimal complementarity between the shape of the binding site and the size of the ligands is necessary for transport. These findings provide a framework for a deeper understanding of substrate selectivity of the SLC6 family and other LeuT fold transporters.
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Kickinger S, Hellsberg E, Frølund B, Schousboe A, Ecker GF, Wellendorph P. Structural and molecular aspects of betaine-GABA transporter 1 (BGT1) and its relation to brain function. Neuropharmacology 2019; 161:107644. [PMID: 31108110 DOI: 10.1016/j.neuropharm.2019.05.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/14/2019] [Accepted: 05/16/2019] [Indexed: 01/09/2023]
Abstract
ɣ-aminobutyric-acid (GABA) functions as the principal inhibitory neurotransmitter in the central nervous system. Imbalances in GABAergic neurotransmission are involved in the pathophysiology of various neurological diseases such as epilepsy, Alzheimer's disease and stroke. GABA transporters (GATs) facilitate the termination of GABAergic signaling by transporting GABA together with sodium and chloride from the synaptic cleft into presynaptic neurons and surrounding glial cells. Four different GATs have been identified that all belong to the solute carrier 6 (SLC6) transporter family: GAT1-3 (SLC6A1, SLC6A13, SLC6A11) and betaine/GABA transporter 1 (BGT1, SLC6A12). BGT1 has emerged as an interesting target for treating epilepsy due to animal studies that reported anticonvulsant effects for the GAT1/BGT1 selective inhibitor EF1502 and the BGT1 selective inhibitor RPC-425. However, the precise involvement of BGT1 in epilepsy remains elusive because of its controversial expression levels in the brain and the lack of highly selective and potent tool compounds. This review gathers the current structural and functional knowledge on BGT1 with emphasis on brain relevance, discusses all available compounds, and tries to shed light on the molecular determinants driving BGT1 selectivity. This article is part of the issue entitled 'Special Issue on Neurotransmitter Transporters'.
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Affiliation(s)
- Stefanie Kickinger
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090, Vienna, Austria
| | - Eva Hellsberg
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090, Vienna, Austria
| | - Bente Frølund
- University of Copenhagen, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, 2 Universitetsparken, 2100, Copenhagen, Denmark
| | - Arne Schousboe
- University of Copenhagen, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, 2 Universitetsparken, 2100, Copenhagen, Denmark
| | - Gerhard F Ecker
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090, Vienna, Austria
| | - Petrine Wellendorph
- University of Copenhagen, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, 2 Universitetsparken, 2100, Copenhagen, Denmark.
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11
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Héja L, Simon Á, Szabó Z, Kardos J. Feedback adaptation of synaptic excitability via Glu:Na + symport driven astrocytic GABA and Gln release. Neuropharmacology 2019; 161:107629. [PMID: 31103619 DOI: 10.1016/j.neuropharm.2019.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/30/2019] [Accepted: 05/07/2019] [Indexed: 02/08/2023]
Abstract
Glutamatergic transmission composed of the arriving of action potential at the axon terminal, fast vesicular Glu release, postsynaptic Glu receptor activation, astrocytic Glu clearance and Glu→Gln shuttle is an abundantly investigated phenomenon. Despite its essential role, however, much less is known about the consequences of the mechanistic connotations of Glu:Na+ symport. Due to the coupled Na+ transport, Glu uptake results in significantly elevated intracellular astrocytic [Na+] that markedly alters the driving force of other Na+-coupled astrocytic transporters. The resulting GABA and Gln release by reverse transport through the respective GAT-3 and SNAT3 transporters help to re-establish the physiological Na+ homeostasis without ATP dissipation and consequently leads to enhanced tonic inhibition and replenishment of axonal glutamate pool. Here, we place this emerging astrocytic adjustment of synaptic excitability into the centre of future perspectives. This article is part of the issue entitled 'Special Issue on Neurotransmitter Transporters'.
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Affiliation(s)
- László Héja
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Ágnes Simon
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Zsolt Szabó
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary
| | - Julianna Kardos
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, 1117, Budapest, Hungary.
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12
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Garibsingh RAA, Otte NJ, Ndaru E, Colas C, Grewer C, Holst J, Schlessinger A. Homology Modeling Informs Ligand Discovery for the Glutamine Transporter ASCT2. Front Chem 2018; 6:279. [PMID: 30137742 PMCID: PMC6066518 DOI: 10.3389/fchem.2018.00279] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 06/20/2018] [Indexed: 12/12/2022] Open
Abstract
The Alanine-Serine-Cysteine transporter (SLC1A5, ASCT2), is a neutral amino acid exchanger involved in the intracellular homeostasis of amino acids in peripheral tissues. Given its role in supplying glutamine to rapidly proliferating cancer cells in several tumor types such as triple-negative breast cancer and melanoma, ASCT2 has been identified as a key drug target. Here we use a range of computational methods, including homology modeling and ligand docking, in combination with cell-based assays, to develop hypotheses for structure-function relationships in ASCT2. We perform a phylogenetic analysis of the SLC1 family and its prokaryotic homologs to develop a useful multiple sequence alignment for this protein family. We then generate homology models of ASCT2 in two different conformations, based on the human EAAT1 structures. Using ligand enrichment calculations, the ASCT2 models are then compared to crystal structures of various homologs for their utility in discovering ASCT2 inhibitors. We use virtual screening, cellular uptake and electrophysiology experiments to identify a non-amino acid ASCT2 inhibitor that is predicted to interact with the ASCT2 substrate binding site. Our results provide insights into the structural basis of substrate specificity in the SLC1 family, as well as a framework for the design of future selective and potent ASCT2 inhibitors as cancer therapeutics.
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Affiliation(s)
- Rachel-Ann A Garibsingh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Nicholas J Otte
- Origins of Cancer Program, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Elias Ndaru
- Department of Chemistry, Binghamton University, Binghamton, NY, United States
| | - Claire Colas
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Christof Grewer
- Department of Chemistry, Binghamton University, Binghamton, NY, United States
| | - Jeff Holst
- Origins of Cancer Program, Centenary Institute, University of Sydney, Sydney, NSW, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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13
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Andley UP, Tycksen E, McGlasson-Naumann BN, Hamilton PD. Probing the changes in gene expression due to α-crystallin mutations in mouse models of hereditary human cataract. PLoS One 2018; 13:e0190817. [PMID: 29338044 PMCID: PMC5770019 DOI: 10.1371/journal.pone.0190817] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/20/2017] [Indexed: 11/30/2022] Open
Abstract
The mammalian eye lens expresses a high concentration of crystallins (α, β and γ-crystallins) to maintain the refractive index essential for lens transparency. Crystallins are long-lived proteins that do not turnover throughout life. The structural destabilization of crystallins by UV exposure, glycation, oxidative stress and mutations in crystallin genes leads to protein aggregation and development of cataracts. Several destabilizing mutations in crystallin genes are linked with human autosomal dominant hereditary cataracts. To investigate the mechanism by which the α-crystallin mutations Cryaa-R49C and Cryab-R120G lead to cataract formation, we determined whether these mutations cause an altered expression of specific transcripts in the lens at an early postnatal age by RNA-seq analysis. Using knock-in mouse models previously generated in our laboratory, in the present work, we identified genes that exhibited altered abundance in the mutant lenses, including decreased transcripts for Clic5, an intracellular water channel in Cryaa-R49C heterozygous mutant lenses, and increased transcripts for Eno1b in Cryab-R120G heterozygous mutant lenses. In addition, RNA-seq analysis revealed increased histones H2B, H2A, and H4 gene expression in Cryaa-R49C mutant lenses, suggesting that the αA-crystallin mutation regulates histone expression via a transcriptional mechanism. Additionally, these studies confirmed the increased expression of histones H2B, H2A, and H4 by proteomic analysis of Cryaa-R49C knock-in and Cryaa;Cryab gene knockout lenses reported previously. Taken together, these findings offer additional insight into the early transcriptional changes caused by Cryaa and Cryab mutations associated with autosomal dominant human cataracts, and indicate that the transcript levels of certain genes are affected by the expression of mutant α-crystallin in vivo.
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Affiliation(s)
- Usha P. Andley
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
| | - Eric Tycksen
- Genome Technology Access Center, Washington University in St. Louis, St. Louis, Missouri, United States of America
| | - Brittney N. McGlasson-Naumann
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Paul D. Hamilton
- Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, Missouri, United States of America
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14
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Jørgensen L, Al-Khawaja A, Kickinger S, Vogensen SB, Skovgaard-Petersen J, Rosenthal E, Borkar N, Löffler R, Madsen KK, Bräuner-Osborne H, Schousboe A, Ecker GF, Wellendorph P, Clausen RP. Structure–Activity Relationship, Pharmacological Characterization, and Molecular Modeling of Noncompetitive Inhibitors of the Betaine/γ-Aminobutyric Acid Transporter 1 (BGT1). J Med Chem 2017; 60:8834-8846. [DOI: 10.1021/acs.jmedchem.7b00924] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Lars Jørgensen
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Anas Al-Khawaja
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Stefanie Kickinger
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Stine B. Vogensen
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jonas Skovgaard-Petersen
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Emil Rosenthal
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Nrupa Borkar
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Rebekka Löffler
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Karsten K. Madsen
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Hans Bräuner-Osborne
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Arne Schousboe
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Gerhard F. Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Petrine Wellendorph
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Rasmus P. Clausen
- Department of Drug
Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, 2100 Copenhagen, Denmark
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15
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Khuri N, Zur AA, Wittwer MB, Lin L, Yee SW, Sali A, Giacomini KM. Computational Discovery and Experimental Validation of Inhibitors of the Human Intestinal Transporter OATP2B1. J Chem Inf Model 2017; 57:1402-1413. [PMID: 28562037 DOI: 10.1021/acs.jcim.6b00720] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Human organic anion transporters (OATPs) are vital for the uptake and efflux of drugs and endogenous compounds. Current identification of inhibitors of these transporters is based on experimental screening. Virtual screening remains a challenge due to a lack of experimental three-dimensional protein structures. Here, we describe a workflow to identify inhibitors of the OATP2B1 transporter in the DrugBank library of over 5,000 drugs and druglike molecules. OATP member 2B1 transporter is highly expressed in the intestine, where it participates in oral absorption of drugs. Predictions from a Random forest classifier, prioritized by docking against multiple comparative protein structure models of OATP2B1, indicated that 33 of the 5,000 compounds were putative inhibitors of OATP2B1. Ten predicted inhibitors that are prescription drugs were tested experimentally in cells overexpressing the OATP2B1 transporter. Three of these ten were validated as potent inhibitors of estrone-3-sulfate uptake (defined as more than 50% inhibition at 20 μM) and tested in multiple concentrations to determine exact IC50. The IC50 values of bicalutamide, ticagrelor, and meloxicam suggest that they might inhibit intestinal OATP2B1 at clinically relevant concentrations and therefore modulate the absorption of other concomitantly administered drugs.
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Affiliation(s)
- Natalia Khuri
- Bioengineering Department, Stanford University , Stanford, California 94305, United States
| | | | | | | | | | - Andrej Sali
- Department of Pharmaceutical Chemistry and California Institute of Quantitative Biosciences (QB3), University of California San Francisco , San Francisco, California 94158, United States
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16
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Chen EC, Khuri N, Liang X, Stecula A, Chien HC, Yee SW, Huang Y, Sali A, Giacomini KM. Discovery of Competitive and Noncompetitive Ligands of the Organic Cation Transporter 1 (OCT1; SLC22A1). J Med Chem 2017; 60:2685-2696. [PMID: 28230985 DOI: 10.1021/acs.jmedchem.6b01317] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Organic cation transporter 1 (OCT1) plays a critical role in the hepatocellular uptake of structurally diverse endogenous compounds and xenobiotics. Here we identified competitive and noncompetitive OCT1-interacting ligands in a library of 1780 prescription drugs by combining in silico and in vitro methods. Ligands were predicted by docking against a comparative model based on a eukaryotic homologue. In parallel, high-throughput screening (HTS) was conducted using the fluorescent probe substrate ASP+ in cells overexpressing human OCT1. Thirty competitive OCT1 ligands, defined as ligands predicted in silico as well as found by HTS, were identified. Of the 167 ligands identified by HTS, five were predicted to potentially cause clinical drug interactions. Finally, virtual screening of 29 332 metabolites predicted 146 competitive OCT1 ligands, of which an endogenous neurotoxin, 1-benzyl-1,2,3,4-tetrahydroisoquinoline, was experimentally validated. In conclusion, by combining docking and in vitro HTS, competitive and noncompetitive ligands of OCT1 can be predicted.
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Affiliation(s)
- Eugene C Chen
- Department of Bioengineering and Therapeutic Sciences, University of California , San Francisco, California 94143, United States
| | - Natalia Khuri
- Department of Bioengineering and Therapeutic Sciences, University of California , San Francisco, California 94143, United States
| | - Xiaomin Liang
- Department of Bioengineering and Therapeutic Sciences, University of California , San Francisco, California 94143, United States
| | - Adrian Stecula
- Department of Bioengineering and Therapeutic Sciences, University of California , San Francisco, California 94143, United States
| | - Huan-Chieh Chien
- Department of Bioengineering and Therapeutic Sciences, University of California , San Francisco, California 94143, United States
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, University of California , San Francisco, California 94143, United States
| | - Yong Huang
- Optivia Biotechnology , Menlo Park, California 94025, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California , San Francisco, California 94143, United States.,Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States.,California Institute of Quantitative Biosciences, University of California , San Francisco, California 94158, United States
| | - Kathleen M Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California , San Francisco, California 94143, United States.,Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States.,California Institute of Quantitative Biosciences, University of California , San Francisco, California 94158, United States.,Institute of Human Genetics, University of California , San Francisco, California 94143, United States
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17
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Wellendorph P, Jacobsen J, Skovgaard-Petersen J, Jurik A, Vogensen SB, Ecker G, Schousboe A, Krogsgaard-Larsen P, Clausen RP. γ-Aminobutyric Acid and Glycine Neurotransmitter Transporters. METHODS AND PRINCIPLES IN MEDICINAL CHEMISTRY 2017. [DOI: 10.1002/9783527679430.ch4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Petrine Wellendorph
- University of Copenhagen; Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology; Universitetsparken 2, DK-2100 Copenhagen Denmark
| | - Julie Jacobsen
- University of Copenhagen; Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology; Universitetsparken 2, DK-2100 Copenhagen Denmark
| | - Jonas Skovgaard-Petersen
- University of Copenhagen; Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology; Universitetsparken 2, DK-2100 Copenhagen Denmark
| | - Andreas Jurik
- University of Vienna; Department of Pharmaceutical Chemistry; Althanstrasse 14, A-1090 Vienna Austria
| | - Stine B. Vogensen
- University of Copenhagen; Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology; Universitetsparken 2, DK-2100 Copenhagen Denmark
| | - Gerhard Ecker
- University of Vienna; Department of Pharmaceutical Chemistry; Althanstrasse 14, A-1090 Vienna Austria
| | - Arne Schousboe
- University of Copenhagen; Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology; Universitetsparken 2, DK-2100 Copenhagen Denmark
| | - Povl Krogsgaard-Larsen
- University of Copenhagen; Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology; Universitetsparken 2, DK-2100 Copenhagen Denmark
| | - Rasmus P. Clausen
- University of Copenhagen; Faculty of Health and Medical Sciences, Department of Drug Design and Pharmacology; Universitetsparken 2, DK-2100 Copenhagen Denmark
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18
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Damgaard M, Haugaard AS, Kickinger S, Al-Khawaja A, Lie MEK, Ecker GF, Clausen RP, Frølund B. Development of Non-GAT1-Selective Inhibitors: Challenges and Achievements. ADVANCES IN NEUROBIOLOGY 2017; 16:315-332. [DOI: 10.1007/978-3-319-55769-4_16] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
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19
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Ung PMU, Song W, Cheng L, Zhao X, Hu H, Chen L, Schlessinger A. Inhibitor Discovery for the Human GLUT1 from Homology Modeling and Virtual Screening. ACS Chem Biol 2016; 11:1908-16. [PMID: 27128978 DOI: 10.1021/acschembio.6b00304] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The human Glucose Transporter 1 (hGLUT1 or SLC2A1) is a facilitative membrane transporter found in the liver, intestines, kidney, and brain, where it transports sugars such as d-glucose and d-galactose. Genetic variations in hGLUT1 are associated with a broad range of diseases and metabolic disorders. For example, hGLUT1 is upregulated in various cancer types (e.g., breast carcinoma) to support the increased anaerobic glycolysis and the Warburg effect. Thus, hGLUT1 is an emerging therapeutic target, which also transports commonly used cancer biomarkers (e.g., (18)F-DG). In this study, we use computational prediction followed by experimental testing, to characterize hGLUT1. We construct homology models of hGLUT1 in a partially occluded outward open ("occluded") conformation based on the X-ray structure of the E. coli xylose transporter, XylE. Comparison of the binding site of the occluded models to experimentally determined hGLUT structures revealed a hydrophobic pocket adjacent to the sugar-binding site, which was tested experimentally via site-directed mutagenesis. Virtual screening of various libraries of purchasable compounds against the occluded models, followed by experimental testing with cellular assays revealed seven previously unknown hGLUT1 ligands with IC50 values ranging from 0.45 μM to 59 μM. These ligands represent three unique chemotypes that are chemically different from any other known hGLUT1 ligands. The newly characterized hydrophobic pocket can potentially be utilized by the new ligands for increased affinity. Furthermore, the previously unknown hGLUT1 ligands can serve as chemical tools to further characterize hGLUT1 function or lead molecules for future drug development.
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Affiliation(s)
- Peter Man-Un Ung
- Department
of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Wenxin Song
- School
of Pharmaceutical Sciences, Tsinghua University, Beijing, China 100084
| | - Lili Cheng
- School
of Pharmaceutical Sciences, Tsinghua University, Beijing, China 100084
| | - Xinbin Zhao
- School
of Pharmaceutical Sciences, Tsinghua University, Beijing, China 100084
| | - Hailin Hu
- School
of Pharmaceutical Sciences, Tsinghua University, Beijing, China 100084
| | - Ligong Chen
- School
of Pharmaceutical Sciences, Tsinghua University, Beijing, China 100084
| | - Avner Schlessinger
- Department
of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
- Department
of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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20
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Colas C, Ung PMU, Schlessinger A. SLC Transporters: Structure, Function, and Drug Discovery. MEDCHEMCOMM 2016; 7:1069-1081. [PMID: 27672436 PMCID: PMC5034948 DOI: 10.1039/c6md00005c] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The human Solute Carrier (SLC) transporters are important targets for drug development. Structure-based drug discovery for SLC transporters requires the description of their structure, dynamics, and mechanism of interaction with small molecule ligands and ions. The recent determination of atomic structures of human SLC transporters and their homologs, combined with improved computational power and prediction methods have led to an increased applicability of structure-based drug design methods for human SLC members. In this review, we provide an overview of the SLC transporters' structures and transport mechanisms. We then describe computational techniques, such as homology modeling and virtual screening that are emerging as key tools to discover chemical probes for human SLC members. We illustrate the utility of these methods by presenting case studies in which rational integration of computation and experiment was used to characterize SLC members that transport key nutrients and metabolites, including the amino acid transporters LAT-1 and ASCT2, the SLC13 family of citric acid cycle intermediate transporters, and the glucose transporter GLUT1. We conclude with a brief discussion about future directions in structure-based drug discovery for the human SLC superfamily, one of the most structurally and functionally diverse protein families in human.
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Affiliation(s)
- Claire Colas
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Peter Man-Un Ung
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Avner Schlessinger
- Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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21
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Volkova A, Shadrina M, Kolomin T, Andreeva L, Limborska S, Myasoedov N, Slominsky P. Selank Administration Affects the Expression of Some Genes Involved in GABAergic Neurotransmission. Front Pharmacol 2016; 7:31. [PMID: 26924987 PMCID: PMC4757669 DOI: 10.3389/fphar.2016.00031] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/03/2016] [Indexed: 01/11/2023] Open
Abstract
Clinical studies have shown the similarity of the spectrum of physiological effects of Selank and classical benzodiazepines, such as diazepam and phenazepam. These data suggest that there is a similar basis of their mechanism of action. To test this hypothesis we studied the effect of Selank and GABA on the expression of genes involved in neurotransmission. We analyzed the expression of 84 genes involved in neurotransmission (e.g., major subunit of the GABA receptor, transporters, ion channels, dopamine, and serotonin receptors) in the frontal cortex of rats 1 and 3 h after the administration of Selank or GABA (300 μg/kg) using real-time PCR method. We found significant changes in the expression of 45 genes 1 h after the administration of the compounds. Three hours after Selank or GABA administration, 22 genes changed their expression. We found positive correlation between the changes in genes expression within 1 h after administration of Selank or GABA. Our results showed that Selank caused a number of alterations in the expression of genes involved in neurotransmission. The data obtained indicate that Selank is characterized by its complex effects on nerve cells, and one of its possible molecular mechanisms is associated with allosteric modulation of the GABAergic system.
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Affiliation(s)
- Anastasiya Volkova
- The Department of Molecular Basis of Human Genetics, Institute of Molecular Genetics Russian Academy of SciencesMoscow, Russia
| | - Maria Shadrina
- The Department of Molecular Basis of Human Genetics, Institute of Molecular Genetics Russian Academy of SciencesMoscow, Russia
| | - Timur Kolomin
- The Department of Molecular Basis of Human Genetics, Institute of Molecular Genetics Russian Academy of SciencesMoscow, Russia
| | - Lyudmila Andreeva
- The Department of Chemistry of Physiologically Active Compounds, Institute of Molecular Genetics Russian Academy of SciencesMoscow, Russia
| | - Svetlana Limborska
- The Department of Molecular Basis of Human Genetics, Institute of Molecular Genetics Russian Academy of SciencesMoscow, Russia
| | - Nikolay Myasoedov
- The Department of Chemistry of Physiologically Active Compounds, Institute of Molecular Genetics Russian Academy of SciencesMoscow, Russia
| | - Petr Slominsky
- The Department of Molecular Basis of Human Genetics, Institute of Molecular Genetics Russian Academy of SciencesMoscow, Russia
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22
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Li Z, Li Y, Sun L, Tang Y, Liu L, Zhu W. Artificial neural network cascade identifies multi-P450 inhibitors in natural compounds. PeerJ 2015; 3:e1524. [PMID: 26719820 PMCID: PMC4696407 DOI: 10.7717/peerj.1524] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 11/30/2015] [Indexed: 12/27/2022] Open
Abstract
Substantial evidence has shown that most exogenous substances are metabolized by multiple
cytochrome P450 (P450) enzymes instead of by merely one P450 isoform. Thus, multi-P450
inhibition leads to greater drug-drug interaction risk than specific P450 inhibition.
Herein, we innovatively established an artificial neural network cascade (NNC) model
composed of 23 cascaded networks in a ladder-like framework to identify potential
multi-P450 inhibitors among natural compounds by integrating 12 molecular descriptors into
a P450 inhibition score (PIS). Experimental data reporting in vitro
inhibition of five P450 isoforms (CYP1A2, CYP2C9, CYP2C19, CYP2D6, and CYP3A4) were
obtained for 8,148 compounds from the Cytochrome P450 Inhibitors Database (CPID). The
results indicate significant positive correlation between the PIS values and the number of
inhibited P450 isoforms (Spearman’s ρ = 0.684, p <
0.0001). Thus, a higher PIS indicates a greater possibility for a chemical to inhibit the
enzyme activity of at least three P450 isoforms. Ten-fold cross-validation of the NNC
model suggested an accuracy of 78.7% for identifying whether a compound is a multi-P450
inhibitor or not. Using our NNC model, 22.2% of the approximately 160,000 natural
compounds in TCM Database@Taiwan were identified as potential multi-P450 inhibitors.
Furthermore, chemical similarity calculations suggested that the prevailing parent
structures of natural multi-P450 inhibitors were alkaloids. Our findings show that
dissection of chemical structure contributes to confident identification of natural
multi-P450 inhibitors and provides a feasible method for virtually evaluating multi-P450
inhibition risk for a known structure.
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Affiliation(s)
- Zhangming Li
- Department of Pharmacy Administration, Harbin Medical University , Harbin , China
| | - Yan Li
- Department of Pharmacy, The Fourth Hospital of Harbin Medical University , Harbin , China
| | - Lu Sun
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai , China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , Shanghai , China
| | - Lanru Liu
- Department of Pharmacy Administration, Harbin Medical University , Harbin , China
| | - Wenliang Zhu
- Institute of Clinical Pharmacology, The Second Affiliated Hospital of Harbin Medical University , Harbin , China
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23
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Ma X, Lubin H, Ioja E, Kékesi O, Simon Á, Apáti Á, Orbán TI, Héja L, Kardos J, Markó IE. Straightforward and effective synthesis of γ-aminobutyric acid transporter subtype 2-selective acyl-substituted azaspiro[4.5]decanes. Bioorg Med Chem Lett 2015; 26:417-423. [PMID: 26706177 DOI: 10.1016/j.bmcl.2015.11.100] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 11/26/2015] [Accepted: 11/27/2015] [Indexed: 10/22/2022]
Abstract
Supply of major metabolites such as γ-aminobutyric acid (GABA), β-alanine and taurine is an essential instrument that shapes signalling, proper cell functioning and survival in the brain and peripheral organs. This background motivates the synthesis of novel classes of compounds regulating their selective transport through various fluid-organ barriers via the low-affinity γ-aminobutyric acid (GABA) transporter subtype 2 (GAT2). Natural and synthetic spirocyclic compounds or therapeutics with a range of structures and biological activity are increasingly recognised in this regard. Based on pre-validated GABA transport activity, straightforward and efficient synthesis method was developed to provide an azaspiro[4.5]decane scaffold, holding a variety of charge, substituent and 3D constrain of spirocyclic amine. Investigation of the azaspiro[4.5]decane scaffold in cell lines expressing the four GABA transporter subtypes led to the discovery of a subclass of a GAT2-selective compounds with acyl-substituted azaspiro[4.5]decane core.
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Affiliation(s)
- Xiaofeng Ma
- Organic and Medicinal Chemistry Laboratories, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Hodney Lubin
- Organic and Medicinal Chemistry Laboratories, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
| | - Enikő Ioja
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Orsolya Kékesi
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Ágnes Simon
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Ágota Apáti
- Laboratory of Molecular Cell Biology, Institute of Enzimology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Tamás I Orbán
- Biomembrane Research Group, Institute of Enzimology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - László Héja
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary
| | - Julianna Kardos
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, H-1117 Budapest, Hungary.
| | - István E Markó
- Organic and Medicinal Chemistry Laboratories, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium.
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24
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Colas C, Grewer C, Otte NJ, Gameiro A, Albers T, Singh K, Shere H, Bonomi M, Holst J, Schlessinger A. Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening. PLoS Comput Biol 2015; 11:e1004477. [PMID: 26444490 PMCID: PMC4596572 DOI: 10.1371/journal.pcbi.1004477] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/23/2015] [Indexed: 12/20/2022] Open
Abstract
The Alanine-Serine-Cysteine transporter ASCT2 (SLC1A5) is a membrane protein that transports neutral amino acids into cells in exchange for outward movement of intracellular amino acids. ASCT2 is highly expressed in peripheral tissues such as the lung and intestines where it contributes to the homeostasis of intracellular concentrations of neutral amino acids. ASCT2 also plays an important role in the development of a variety of cancers such as melanoma by transporting amino acid nutrients such as glutamine into the proliferating tumors. Therefore, ASCT2 is a key drug target with potentially great pharmacological importance. Here, we identify seven ASCT2 ligands by computational modeling and experimental testing. In particular, we construct homology models based on crystallographic structures of the aspartate transporter GltPh in two different conformations. Optimization of the models' binding sites for protein-ligand complementarity reveals new putative pockets that can be targeted via structure-based drug design. Virtual screening of drugs, metabolites, fragments-like, and lead-like molecules from the ZINC database, followed by experimental testing of 14 top hits with functional measurements using electrophysiological methods reveals seven ligands, including five activators and two inhibitors. For example, aminooxetane-3-carboxylate is a more efficient activator than any other known ASCT2 natural or unnatural substrate. Furthermore, two of the hits inhibited ASCT2 mediated glutamine uptake and proliferation of a melanoma cancer cell line. Our results improve our understanding of how substrate specificity is determined in amino acid transporters, as well as provide novel scaffolds for developing chemical tools targeting ASCT2, an emerging therapeutic target for cancer and neurological disorders.
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Affiliation(s)
- Claire Colas
- Department of Pharmacology and Systems Therapeutics, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Christof Grewer
- Department of Chemistry, Binghamton University, Binghamton, New York, United States of America
| | - Nicholas James Otte
- Origins of Cancer Laboratory Centenary Program, Camperdown, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
| | - Armanda Gameiro
- Department of Chemistry, Binghamton University, Binghamton, New York, United States of America
| | - Thomas Albers
- Department of Chemistry, Binghamton University, Binghamton, New York, United States of America
| | - Kurnvir Singh
- Department of Chemistry, Binghamton University, Binghamton, New York, United States of America
| | - Helen Shere
- Department of Pharmacology and Systems Therapeutics, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | | | - Jeff Holst
- Origins of Cancer Laboratory Centenary Program, Camperdown, Australia
- Sydney Medical School, University of Sydney, Sydney, Australia
- * E-mail: (JH); (AS)
| | - Avner Schlessinger
- Department of Pharmacology and Systems Therapeutics, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
- * E-mail: (JH); (AS)
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25
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Abstract
We delineate perspectives for the design and discovery of antiepileptic drugs (AEDs) with fewer side effects by focusing on astroglial modulation of spatiotemporal seizure dynamics. It is now recognized that the major inhibitory neurotransmitter of the brain, γ-aminobutyric acid (GABA), can be released through the reversal of astroglial GABA transporters. Synaptic spillover and subsequent glutamate (Glu) uptake in neighboring astrocytes evoke replacement of extracellular Glu for GABA, driving neurons away from the seizure threshold. Attenuation of synaptic signaling by this negative feedback through the interplay of Glu and GABA transporters of adjacent astroglia can result in shortened seizures. By contrast, long-range activation of astroglia through gap junctions may promote recurrent seizures on the model of pharmacoresistant temporal lobe epilepsy. From their first detection to our current understanding, we identify various targets that shape both short- and long-range neuro-astroglia coupling, as these are manifest in epilepsy phenomena and in the associated research promotions of AED.
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Affiliation(s)
- Julianna Kardos
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Hungary
| | - Zsolt Szabó
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Hungary
| | - László Héja
- Functional Pharmacology Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1117 Budapest, Hungary
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26
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Colas C, Pajor AM, Schlessinger A. Structure-Based Identification of Inhibitors for the SLC13 Family of Na(+)/Dicarboxylate Cotransporters. Biochemistry 2015; 54:4900-8. [PMID: 26176240 DOI: 10.1021/acs.biochem.5b00388] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In mammals, citric acid cycle intermediates play a key role in regulating various metabolic processes, such as fatty acid synthesis and glycolysis. Members of the sodium-dependent SLC13 transporter family mediate the transport of di- and tricarboxylates into cells. SLC13 family members have been implicated in lifespan extension and resistance to high-fat diets; thus, they are emerging drug targets for aging and metabolic disorders. We previously characterized key structural determinants of substrate and cation binding for the human NaDC3/SLC13A3 transporter using a homology model. Here, we combine computational modeling and virtual screening with functional and biochemical testing, to identify nine previously unknown inhibitors for multiple members of the SLC13 family from human and mouse. Our results reveal previously unknown substrate selectivity determinants for the SLC13 family, including key residues that mediate ligand binding and transport, as well as promiscuous and specific SLC13 small molecule ligands. The newly discovered ligands can serve as chemical tools for further characterization of the SLC13 family or as lead molecules for the future development of potent inhibitors for the treatment of metabolic diseases and aging. Our results improve our understanding of the structural components that are important for substrate specificity in this physiologically important family as well as in other structurally related transport systems.
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Affiliation(s)
- Claire Colas
- †Department of Pharmacology and Systems Therapeutics, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Ana M Pajor
- ‡Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California-San Diego, La Jolla, California 92130-0718, United States
| | - Avner Schlessinger
- †Department of Pharmacology and Systems Therapeutics, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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27
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Lin L, Yee SW, Kim RB, Giacomini KM. SLC transporters as therapeutic targets: emerging opportunities. Nat Rev Drug Discov 2015; 14:543-60. [PMID: 26111766 DOI: 10.1038/nrd4626] [Citation(s) in RCA: 512] [Impact Index Per Article: 56.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Solute carrier (SLC) transporters - a family of more than 300 membrane-bound proteins that facilitate the transport of a wide array of substrates across biological membranes - have important roles in physiological processes ranging from the cellular uptake of nutrients to the absorption of drugs and other xenobiotics. Several classes of marketed drugs target well-known SLC transporters, such as neurotransmitter transporters, and human genetic studies have provided powerful insight into the roles of more-recently characterized SLC transporters in both rare and common diseases, indicating a wealth of new therapeutic opportunities. This Review summarizes knowledge on the roles of SLC transporters in human disease, describes strategies to target such transporters, and highlights current and investigational drugs that modulate SLC transporters, as well as promising drug targets.
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Affiliation(s)
- Lawrence Lin
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California 94158, USA
| | - Sook Wah Yee
- Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California 94158, USA
| | - Richard B Kim
- Division of Clinical Pharmacology, Department of Medicine, University of Western Ontario, London Health Science Centre, London, Ontario N6A 5A5, Canada
| | - Kathleen M Giacomini
- 1] Department of Bioengineering and Therapeutic Sciences, Schools of Pharmacy and Medicine, University of California San Francisco, San Francisco, California 94158, USA. [2] Institute for Human Genetics, University of California San Francisco, San Francisco, California 94158, USA
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28
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Abstract
Transporters comprise the largest family of membrane proteins in human organism, including members of solute carrier transporter and ATP-binding cassette transporter families. They play pivotal roles in the absorption, distribution and excretion of xenobiotic and endogenous molecules. Transporters are widely expressed in various human tissues and are routinely evaluated during the process of drug development and approval. Over the past decade, increasing evidence shows that drug transporters are important in both normal physiology and disease. Currently, transporters are utilized as therapeutic targets to treat numerous diseases such as diabetes, major depression, hypertension and constipation. Despite the steady growth of the field of transporter biology, more than half of the members in transporter superfamily have little information available about their endogenous substrate(s) or physiological functions. This review outlines current research methods in transporter studies, and summarizes the drug-transporter interactions including drug-drug and drug-endogenous substrate interactions. In the end, we also discuss the therapeutic perspective of transporters based on their physiological and pathophysiological roles.
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Jurik A, Zdrazil B, Holy M, Stockner T, Sitte HH, Ecker GF. A binding mode hypothesis of tiagabine confirms liothyronine effect on γ-aminobutyric acid transporter 1 (GAT1). J Med Chem 2015; 58:2149-58. [PMID: 25679268 PMCID: PMC4360375 DOI: 10.1021/jm5015428] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
![]()
Elevating
GABA levels in the synaptic cleft by inhibiting its reuptake
carrier GAT1 is an established approach for the treatment of CNS disorders
like epilepsy. With the increasing availability of crystal structures
of transmembrane transporters, structure-based approaches to elucidate
the molecular basis of ligand–transporter interaction also
become feasible. Experimental data guided docking of derivatives of
the GAT1 inhibitor tiagabine into a protein homology model of GAT1
allowed derivation of a common binding mode for this class of inhibitors
that is able to account for the distinct structure–activity
relationship pattern of the data set. Translating essential binding
features into a pharmacophore model followed by in silico screening
of the DrugBank identified liothyronine as a drug potentially exerting
a similar effect on GAT1. Experimental testing further confirmed the
GAT1 inhibiting properties of this thyroid hormone.
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Affiliation(s)
- Andreas Jurik
- University of Vienna , Department of Pharmaceutical Chemistry, Division of Drug Design and Medicinal Chemistry, Althanstraße 14, 1090 Vienna, Austria
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30
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Dahlin A, Wittwer M, de la Cruz M, Woo JM, Bam R, Scharen-Guivel V, Flaherty J, Ray AS, Cihlar T, Gupta SK, Giacomini KM. A pharmacogenetic candidate gene study of tenofovir-associated Fanconi syndrome. Pharmacogenet Genomics 2015; 25:82-92. [PMID: 25485598 PMCID: PMC4331349 DOI: 10.1097/fpc.0000000000000110] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Tenofovir disoproxil fumarate (TDF) is a widely used antiretroviral agent with favorable efficacy, safety, and tolerability profiles. However, renal adverse events, including the rare Fanconi syndrome (FS), may occur in a small subset of patients treated for HIV infections. OBJECTIVES The aim of this study was to identify genetic variants that may be associated with TDF-associated FS (TDF-FS). METHODS DNA samples collected from 19 cases with TDF-FS and 36 matched controls were sequenced, and genetic association studies were conducted on eight candidate genes: ATP-binding cassette (ABC) transporters ABCC2 (MRP2) and ABCC4 (MRP4), solute carrier family members SLC22A6 (OAT1) and SLC22A8 (OAT3), adenylate kinases 2 (AK2) and 4 (AK4), chloride transporter CIC-5 CLCN5, and Lowe syndrome protein OCRL. The functional effects of a single nucleotide polymorphism (SNP) predicted to alter the transport of tenofovir were then investigated in cells expressing an identified variant of ABCC4. RESULTS The case group showed a trend toward a higher proportion of rare alleles. Six SNPs in ABCC2 (three SNPs), ABCC4 (one SNP), and OCRL (two SNPs) were associated with TDF-FS case status; however, this association did not remain significant after correction for multiple testing. Six SNPs, present in OCRL (four SNPs) and ABCC2 (two SNPs), were significantly associated with increased serum creatinine levels in the cases, and this association remained significant after multiple test correction (P < 2 × 10). One synonymous SNP in ABCC2 (rs8187707, P = 2.10 × 10, β = -73.3 ml/min/1.73 m(2)) was also significantly associated with the decreased estimated glomerular filtration rate of creatinine among cases. However, these results were driven by rare SNPs present in a small number of severely affected cases. Finally, a previously uncharacterized, nonsynonymous SNP, rs11568694, that was predicted to alter MRP4 function had no significant effect on tenofovir cellular accumulation in vitro. CONCLUSION Although no single predictive genetic marker for the development of TDF-FS was identified, the findings from our study suggest that rare variants in multiple genes involved in the renal handling of tenofovir, and/or renal cell homeostasis, may be associated with increased susceptibility to TDF-FS.
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Affiliation(s)
- Amber Dahlin
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Matthias Wittwer
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
| | - Melanie de la Cruz
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
- Genomics Core Facility, Institute for Human Genetics, San Francisco, CA 94143, United States
| | - Jonathan M. Woo
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
- Genomics Core Facility, Institute for Human Genetics, San Francisco, CA 94143, United States
| | - Rujuta Bam
- Gilead Sciences, Inc., Foster City, CA, 94404, United States
| | | | - John Flaherty
- Gilead Sciences, Inc., Foster City, CA, 94404, United States
| | - Adrian S. Ray
- Gilead Sciences, Inc., Foster City, CA, 94404, United States
| | - Tomas Cihlar
- Gilead Sciences, Inc., Foster City, CA, 94404, United States
| | - Samir K. Gupta
- Division of Infectious Diseases, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Kathleen M. Giacomini
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94158, United States
- Institute of Human Genetics, University of California, San Francisco, San Francisco, California, 94143, United States
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31
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Thomas JR, Gedeon PC, Madura JD. Structural dynamics of the monoamine transporter homolog LeuT from accelerated conformational sampling and channel analysis. Proteins 2014; 82:2289-302. [PMID: 24753369 DOI: 10.1002/prot.24588] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/29/2014] [Accepted: 04/10/2014] [Indexed: 01/28/2023]
Abstract
The bacterial leucine transporter LeuT retains significant secondary structure similarities to the human monoamine transporters (MAT) such as the dopamine and serotonin reuptake proteins. The primary method of computational study of the MATs has been through the use of the crystallized LeuT structure. Different conformations of LeuT can give insight into mechanistic details of the MAT family. A conformational sampling performed through accelerated molecular dynamics simulations testing different combinations of the leucine substrate and bound sodium ions revealed seven distinct conformational clusters. Further analysis has been performed to target salt-bridge residues R30-D404, Y108-F253, and R5-D369 and transmembrane domains on both the seven isolated structures and the total trajectories. In addition, solvent accessibility of LeuT and its substrate binding pockets has been analyzed using a program for calculating channel radii. Occupation of the Na2 site stabilizes the outward conformation and should bind to the open outward conformation before the leucine and Na1 sodium while two possible pathways were found to be available for intracellular transport.
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Affiliation(s)
- James R Thomas
- Department of Chemistry and Biochemistry and the Center for Computational Sciences, Duquesne University, Pittsburgh, Pennsylvania; Mylan School of Pharmacy, Duquesne University, Pittsburgh, Pennsylvania
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32
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Schlessinger A, Sun NN, Colas C, Pajor AM. Determinants of substrate and cation transport in the human Na+/dicarboxylate cotransporter NaDC3. J Biol Chem 2014; 289:16998-7008. [PMID: 24808185 DOI: 10.1074/jbc.m114.554790] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Metabolic intermediates, such as succinate and citrate, regulate important processes ranging from energy metabolism to fatty acid synthesis. Cytosolic concentrations of these metabolites are controlled, in part, by members of the SLC13 gene family. The molecular mechanism underlying Na(+)-coupled di- and tricarboxylate transport by this family is understood poorly. The human Na(+)/dicarboxylate cotransporter NaDC3 (SLC13A3) is found in various tissues, including the kidney, liver, and brain. In addition to citric acid cycle intermediates such as α-ketoglutarate and succinate, NaDC3 transports other compounds into cells, including N-acetyl aspartate, mercaptosuccinate, and glutathione, in keeping with its dual roles in cell nutrition and detoxification. In this study, we construct a homology structural model of NaDC3 on the basis of the structure of the Vibrio cholerae homolog vcINDY. Our computations are followed by experimental testing of the predicted NaDC3 structure and mode of interaction with various substrates. The results of this study show that the substrate and cation binding domains of NaDC3 are composed of residues in the opposing hairpin loops and unwound portions of adjacent helices. Furthermore, these results provide a possible explanation for the differential substrate specificity among dicarboxylate transporters that underpin their diverse biological roles in metabolism and detoxification. The structural model of NaDC3 provides a framework for understanding substrate selectivity and the Na(+)-coupled anion transport mechanism by the human SLC13 family and other key solute carrier transporters.
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Affiliation(s)
- Avner Schlessinger
- From the Department of Pharmacology and Systems Therapeutics, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029 and
| | - Nina N Sun
- the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92130-0718
| | - Claire Colas
- From the Department of Pharmacology and Systems Therapeutics, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029 and
| | - Ana M Pajor
- the Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92130-0718
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33
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Schlessinger A, Khuri N, Giacomini KM, Sali A. Molecular modeling and ligand docking for solute carrier (SLC) transporters. Curr Top Med Chem 2014; 13:843-56. [PMID: 23578028 DOI: 10.2174/1568026611313070007] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 01/29/2013] [Accepted: 02/01/2013] [Indexed: 12/21/2022]
Abstract
Solute Carrier (SLC) transporters are membrane proteins that transport solutes, such as ions, metabolites, peptides, and drugs, across biological membranes, using diverse energy coupling mechanisms. In human, there are 386 SLC transporters, many of which contribute to the absorption, distribution, metabolism, and excretion of drugs and/or can be targeted directly by therapeutics. Recent atomic structures of SLC transporters determined by X-ray crystallography and NMR spectroscopy have significantly expanded the applicability of structure-based prediction of SLC transporter ligands, by enabling both comparative modeling of additional SLC transporters and virtual screening of small molecules libraries against experimental structures as well as comparative models. In this review, we begin by describing computational tools, including sequence analysis, comparative modeling, and virtual screening, that are used to predict the structures and functions of membrane proteins such as SLC transporters. We then illustrate the applications of these tools to predicting ligand specificities of select SLC transporters, followed by experimental validation using uptake kinetic measurements and other assays. We conclude by discussing future directions in the discovery of the SLC transporter ligands.
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Affiliation(s)
- Avner Schlessinger
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 1700 4th Street, San Francisco, CA 94158, USA.
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34
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Webb B, Eswar N, Fan H, Khuri N, Pieper U, Dong G, Sali A. Comparative Modeling of Drug Target Proteins☆. REFERENCE MODULE IN CHEMISTRY, MOLECULAR SCIENCES AND CHEMICAL ENGINEERING 2014. [PMCID: PMC7157477 DOI: 10.1016/b978-0-12-409547-2.11133-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In this perspective, we begin by describing the comparative protein structure modeling technique and the accuracy of the corresponding models. We then discuss the significant role that comparative prediction plays in drug discovery. We focus on virtual ligand screening against comparative models and illustrate the state-of-the-art by a number of specific examples.
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35
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Coleman RG, Carchia M, Sterling T, Irwin JJ, Shoichet BK. Ligand pose and orientational sampling in molecular docking. PLoS One 2013; 8:e75992. [PMID: 24098414 PMCID: PMC3787967 DOI: 10.1371/journal.pone.0075992] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Accepted: 08/13/2013] [Indexed: 12/19/2022] Open
Abstract
Molecular docking remains an important tool for structure-based screening to find new ligands and chemical probes. As docking ambitions grow to include new scoring function terms, and to address ever more targets, the reliability and extendability of the orientation sampling, and the throughput of the method, become pressing. Here we explore sampling techniques that eliminate stochastic behavior in DOCK3.6, allowing us to optimize the method for regularly variable sampling of orientations. This also enabled a focused effort to optimize the code for efficiency, with a three-fold increase in the speed of the program. This, in turn, facilitated extensive testing of the method on the 102 targets, 22,805 ligands and 1,411,214 decoys of the Directory of Useful Decoys - Enhanced (DUD-E) benchmarking set, at multiple levels of sampling. Encouragingly, we observe that as sampling increases from 50 to 500 to 2000 to 5000 to 20000 molecular orientations in the binding site (and so from about 1×1010 to 4×1010 to 1×1011 to 2×1011 to 5×1011 mean atoms scored per target, since multiple conformations are sampled per orientation), the enrichment of ligands over decoys monotonically increases for most DUD-E targets. Meanwhile, including internal electrostatics in the evaluation ligand conformational energies, and restricting aromatic hydroxyls to low energy rotamers, further improved enrichment values. Several of the strategies used here to improve the efficiency of the code are broadly applicable in the field.
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Affiliation(s)
- Ryan G. Coleman
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Michael Carchia
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Teague Sterling
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - John J. Irwin
- Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Brian K. Shoichet
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
- Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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36
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2-Substituted 4-hydroxybutanamides as potential inhibitors of γ-aminobutyric acid transporters mGAT1–mGAT4: Synthesis and biological evaluation. Bioorg Med Chem 2013; 21:5154-67. [DOI: 10.1016/j.bmc.2013.06.038] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 06/12/2013] [Accepted: 06/16/2013] [Indexed: 11/22/2022]
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37
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Sałat K, Kulig K, Gajda J, Więckowski K, Filipek B, Malawska B. Evaluation of anxiolytic-like, anticonvulsant, antidepressant-like and antinociceptive properties of new 2-substituted 4-hydroxybutanamides with affinity for GABA transporters in mice. Pharmacol Biochem Behav 2013; 110:145-53. [PMID: 23850524 DOI: 10.1016/j.pbb.2013.06.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Revised: 06/14/2013] [Accepted: 06/28/2013] [Indexed: 01/01/2023]
Abstract
PURPOSE The inhibition of plasma membrane GABA transporters (GATs) is responsible for anxiolytic-like, anticonvulsant, antinociceptive and antidepressant-like effects in mice. It also influences animals' motor coordination and their sensitivity to ethanol. The aim of this study was to assess the pharmacological activity of two novel 2-substituted 4-hydroxybutanamides (BM 130 and BM 131) in some screening models. An attempt has been made to establish the relationship between the inhibition of GAT subtype and the observed in vivo activity. METHODS The affinity for GAT subtypes was evaluated by means of [(3)H]GABA uptake assay. It indicated that BM 130 inhibited GAT1 and GAT2, whereas BM 131 inhibited GAT1 and GAT3. In mice anxiolytic-like, antidepressant-like, anticonvulsant and antinociceptive properties of the test compounds were assessed. Their influence on motor coordination, locomotor activity and the ability to potentiate effects of subnarcotic doses of ethanol was also tested. RESULTS Both compounds administered intraperitoneally exerted a significant anxiolytic-like effect in the four plate test with ED50 values 3.4 and 7.9 mg/kg, respectively. At 30 mg/kg they reduced duration of immobility in the forced swim test for 33% and 19%, respectively. They had no effect on electroconvulsive threshold or pain reactivity in the hot plate assay but they were antinociceptive in the acetic acid-induced writhing test (ED50 values were 12.7 and 18.6 mg/kg, respectively) and in both phases of the formalin test (ED50 values in the first phase were 10.2 and 2.1 mg/kg for BM 130 and BM 131, respectively). No motor adverse effects were observed in mice pretreated with the test compounds in the rotarod or chimney tests but BM 131 caused a transient but statistically significant decrease of animals' locomotor activity. CONCLUSIONS In mice BM 130 and BM 131 have anxiolytic-like, antidepressant-like and antinociceptive properties which can be attributed to their affinity for not only mGAT1 but also mGAT2-4.
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Affiliation(s)
- Kinga Sałat
- Department of Pharmacodynamics, Jagiellonian University, Medical College, Medyczna 9, 30-688 Cracow, Poland.
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38
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Structure-based ligand discovery for the Large-neutral Amino Acid Transporter 1, LAT-1. Proc Natl Acad Sci U S A 2013; 110:5480-5. [PMID: 23509259 DOI: 10.1073/pnas.1218165110] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Large-neutral Amino Acid Transporter 1 (LAT-1)--a sodium-independent exchanger of amino acids, thyroid hormones, and prescription drugs--is highly expressed in the blood-brain barrier and various types of cancer. LAT-1 plays an important role in cancer development as well as in mediating drug and nutrient delivery across the blood-brain barrier, making it a key drug target. Here, we identify four LAT-1 ligands, including one chemically novel substrate, by comparative modeling, virtual screening, and experimental validation. These results may rationalize the enhanced brain permeability of two drugs, including the anticancer agent acivicin. Finally, two of our hits inhibited proliferation of a cancer cell line by distinct mechanisms, providing useful chemical tools to characterize the role of LAT-1 in cancer metabolism.
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