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Birgül Iyison N, Abboud C, Abboud D, Abdulrahman AO, Bondar AN, Dam J, Georgoussi Z, Giraldo J, Horvat A, Karoussiotis C, Paz-Castro A, Scarpa M, Schihada H, Scholz N, Güvenc Tuna B, Vardjan N. ERNEST COST action overview on the (patho)physiology of GPCRs and orphan GPCRs in the nervous system. Br J Pharmacol 2024. [PMID: 38825750 DOI: 10.1111/bph.16389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/09/2024] [Accepted: 02/24/2024] [Indexed: 06/04/2024] Open
Abstract
G protein-coupled receptors (GPCRs) are a large family of cell surface receptors that play a critical role in nervous system function by transmitting signals between cells and their environment. They are involved in many, if not all, nervous system processes, and their dysfunction has been linked to various neurological disorders representing important drug targets. This overview emphasises the GPCRs of the nervous system, which are the research focus of the members of ERNEST COST action (CA18133) working group 'Biological roles of signal transduction'. First, the (patho)physiological role of the nervous system GPCRs in the modulation of synapse function is discussed. We then debate the (patho)physiology and pharmacology of opioid, acetylcholine, chemokine, melatonin and adhesion GPCRs in the nervous system. Finally, we address the orphan GPCRs, their implication in the nervous system function and disease, and the challenges that need to be addressed to deorphanize them.
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Affiliation(s)
- Necla Birgül Iyison
- Department of Molecular Biology and Genetics, University of Bogazici, Istanbul, Turkey
| | - Clauda Abboud
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liege, Liege, Belgium
| | - Dayana Abboud
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liege, Liege, Belgium
| | | | - Ana-Nicoleta Bondar
- Faculty of Physics, University of Bucharest, Magurele, Romania
- Forschungszentrum Jülich, Institute for Computational Biomedicine (IAS-5/INM-9), Jülich, Germany
| | - Julie Dam
- Institut Cochin, CNRS, INSERM, Université Paris Cité, Paris, France
| | - Zafiroula Georgoussi
- Laboratory of Cellular Signalling and Molecular Pharmacology, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Jesús Giraldo
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, Bellaterra, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Salud Mental, CIBERSAM, Madrid, Spain
- Unitat de Neurociència Traslacional, Parc Taulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí (I3PT), Institut de Neurociències, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Anemari Horvat
- Laboratory of Neuroendocrinology - Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Laboratory of Cell Engineering, Celica Biomedical, Ljubljana, Slovenia
| | - Christos Karoussiotis
- Laboratory of Cellular Signalling and Molecular Pharmacology, Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", Athens, Greece
| | - Alba Paz-Castro
- Molecular Pharmacology of GPCRs research group, Center for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidade de Santiago de Compostela, Santiago, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain
| | - Miriam Scarpa
- Division of Clinical Geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Hannes Schihada
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Nicole Scholz
- Rudolf Schönheimer Institute of Biochemistry, Division of General Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Bilge Güvenc Tuna
- Department of Biophysics, School of Medicine, Yeditepe University, Istanbul, Turkey
| | - Nina Vardjan
- Laboratory of Neuroendocrinology - Molecular Cell Physiology, Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
- Laboratory of Cell Engineering, Celica Biomedical, Ljubljana, Slovenia
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Qiu Y, Hou Y, Gohel D, Zhou Y, Xu J, Bykova M, Yang Y, Leverenz JB, Pieper AA, Nussinov R, Caldwell JZK, Brown JM, Cheng F. Systematic characterization of multi-omics landscape between gut microbial metabolites and GPCRome in Alzheimer's disease. Cell Rep 2024; 43:114128. [PMID: 38652661 DOI: 10.1016/j.celrep.2024.114128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/06/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Shifts in the magnitude and nature of gut microbial metabolites have been implicated in Alzheimer's disease (AD), but the host receptors that sense and respond to these metabolites are largely unknown. Here, we develop a systems biology framework that integrates machine learning and multi-omics to identify molecular relationships of gut microbial metabolites with non-olfactory G-protein-coupled receptors (termed the "GPCRome"). We evaluate 1.09 million metabolite-protein pairs connecting 408 human GPCRs and 335 gut microbial metabolites. Using genetics-derived Mendelian randomization and integrative analyses of human brain transcriptomic and proteomic profiles, we identify orphan GPCRs (i.e., GPR84) as potential drug targets in AD and that triacanthine experimentally activates GPR84. We demonstrate that phenethylamine and agmatine significantly reduce tau hyperphosphorylation (p-tau181 and p-tau205) in AD patient induced pluripotent stem cell-derived neurons. This study demonstrates a systems biology framework to uncover the GPCR targets of human gut microbiota in AD and other complex diseases if broadly applied.
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Affiliation(s)
- Yunguang Qiu
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yuan Hou
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Dhruv Gohel
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yadi Zhou
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jielin Xu
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Marina Bykova
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Yuxin Yang
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - James B Leverenz
- Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| | - Andrew A Pieper
- Brain Health Medicines Center, Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA; Department of Psychiatry, Case Western Reserve University, Cleveland, OH 44106, USA; Geriatric Psychiatry, GRECC, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106, USA; Institute for Transformative Molecular Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; Department of Neurosciences, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA; Department of Pathology, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA
| | - Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Jessica Z K Caldwell
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Lou Ruvo Center for Brain Health, Neurological Institute, Cleveland Clinic, Las Vegas, NV 89106, USA
| | - J Mark Brown
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Department of Cancer Biology, Lerner Research Institute Cleveland Clinic, Cleveland, OH 44195, USA; Center for Microbiome and Human Health, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Feixiong Cheng
- Cleveland Clinic Genome Center, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA; Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA; Case Comprehensive Cancer Center, Case Western Reserve University, School of Medicine, Cleveland, OH 44106, USA.
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De Smet V, Gürbüz E, Eysackers N, Dewyse L, Smout A, Kazemzadeh Dastjerd M, Lefesvre P, Messaoudi N, Reynaert H, Verhulst S, Mannaerts I, van Grunsven LA. Orphan receptor GPR176 in hepatic stellate cells exerts a profibrotic role in chronic liver disease. JHEP Rep 2024; 6:101036. [PMID: 38694958 PMCID: PMC11061336 DOI: 10.1016/j.jhepr.2024.101036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 05/04/2024] Open
Abstract
Background & Aims Chronic liver disease (CLD) remains a global health issue associated with a significant disease burden. Liver fibrosis, a hallmark of CLD, is characterised by the activation of hepatic stellate cells (HSCs) that gain profibrotic characteristics including increased production of extracellular matrix protein. Currently, no antifibrotic therapies are available clinically, in part because of the lack of HSC-specific drug targets. Here, we aimed to identify HSC-specific membrane proteins that can serve as targets for antifibrotic drug development. Methods Small interfering RNA-mediated knockdown of GPR176 was used to assess the in vitro function of GPR176 in HSCs and in precision cut liver slices (PCLS). The in vivo role of GPR176 was assessed using the carbon tetrachloride (CCl4) and common bile duct ligation (BDL) models in wild-type and GPR176 knockout mice. GPR176 in human CLD was assessed by immunohistochemistry of diseased human livers and RNA expression analysis in human primary HSCs and transcriptomic data sets. Results We identified Gpr176, an orphan G-protein coupled receptor, as an HSC-enriched activation associated gene. In vitro, Gpr176 is strongly induced upon culture-induced and hepatocyte-damage-induced activation of primary HSCs. Knockdown of GPR176 in primary mouse HSCs or PCLS cultures resulted in reduced fibrogenic characteristics. Absence of GPR176 did not influence liver homeostasis, but Gpr176-/- mice developed less severe fibrosis in CCl4 and BDL fibrosis models. In humans, GPR176 expression was correlated with in vitro HSC activation and with fibrosis stage in patients with CLD. Conclusions GPR176 is a functional protein during liver fibrosis and reducing its activity attenuates fibrogenesis. These results highlight the potential of GPR176 as an HSC-specific antifibrotic candidate to treat CLD. Impact and implications The lack of effective antifibrotic drugs is partly attributed to the insufficient knowledge about the mechanisms involved in the development of liver fibrosis. We demonstrate that the G-protein coupled receptor GPR176 contributes to fibrosis development. Since GPR176 is specifically expressed on the membrane of activated hepatic stellate cells and is linked with fibrosis progression in humans, it opens new avenues for the development of targeted interventions.
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Affiliation(s)
- Vincent De Smet
- Liver Cell Biology Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Department of Gastro-Enterology and Hepatology, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Elif Gürbüz
- Liver Cell Biology Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Nathalie Eysackers
- Liver Cell Biology Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Liza Dewyse
- Liver Cell Biology Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Ayla Smout
- Liver Cell Biology Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | | | - Pierre Lefesvre
- Department of Pathology, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Nouredin Messaoudi
- Department of Hepatobiliary Surgery, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel) and Europe Hospitals, Brussels, Belgium
| | - Hendrik Reynaert
- Liver Cell Biology Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Department of Gastro-Enterology and Hepatology, Universitair Ziekenhuis Brussel, Brussels, Belgium
| | - Stefaan Verhulst
- Liver Cell Biology Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Inge Mannaerts
- Liver Cell Biology Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Leo A. van Grunsven
- Liver Cell Biology Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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Jobe A, Vijayan R. Orphan G protein-coupled receptors: the ongoing search for a home. Front Pharmacol 2024; 15:1349097. [PMID: 38495099 PMCID: PMC10941346 DOI: 10.3389/fphar.2024.1349097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/15/2024] [Indexed: 03/19/2024] Open
Abstract
G protein-coupled receptors (GPCRs) make up the largest receptor superfamily, accounting for 4% of protein-coding genes. Despite the prevalence of such transmembrane receptors, a significant number remain orphans, lacking identified endogenous ligands. Since their conception, the reverse pharmacology approach has been used to characterize such receptors. However, the multifaceted and nuanced nature of GPCR signaling poses a great challenge to their pharmacological elucidation. Considering their therapeutic relevance, the search for native orphan GPCR ligands continues. Despite limited structural input in terms of 3D crystallized structures, with advances in machine-learning approaches, there has been great progress with respect to accurate ligand prediction. Though such an approach proves valuable given that ligand scarcity is the greatest hurdle to orphan GPCR deorphanization, the future pairings of the remaining orphan GPCRs may not necessarily take a one-size-fits-all approach but should be more comprehensive in accounting for numerous nuanced possibilities to cover the full spectrum of GPCR signaling.
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Affiliation(s)
- Amie Jobe
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
- The Big Data Analytics Center, United Arab Emirates University, Al Ain, United Arab Emirates
- Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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Abboud D, Abboud C, Inoue A, Twizere JC, Hanson J. Basal interaction of the orphan receptor GPR101 with arrestins leads to constitutive internalization. Biochem Pharmacol 2024; 220:116013. [PMID: 38151077 DOI: 10.1016/j.bcp.2023.116013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 12/22/2023] [Accepted: 12/23/2023] [Indexed: 12/29/2023]
Abstract
GPR101 is an orphan G protein-coupled receptor that promotes growth hormone secretion in the pituitary. The microduplication of the GPR101 gene has been linked with the X-linked acrogigantism, or X-LAG, syndrome. This disease is characterized by excessive growth hormone secretion and abnormal rapid growth beginning early in life. Mechanistically, GPR101 induces growth hormone secretion through constitutive activation of multiple heterotrimeric G proteins. However, the full scope of GPR101 signaling remains largely elusive. Herein, we investigated the association of GPR101 to multiple transducers and uncovered an important basal interaction with Arrestin 2 (β-arrestin 1) and Arrestin 3 (β-arrestin 2). By using a GPR101 mutant lacking the C-terminus and cell lines with an Arrestin 2/3 null background, we show that the arrestin association leads to constitutive clathrin- and dynamin-mediated GPR101 internalization. To further highlight GPR101 intracellular fate, we assessed the colocalization of GPR101 with Rab protein markers. Internalized GPR101 was mainly colocalized with the early endosome markers, Rab5 and EEA-1, and to a lesser degree with the late endosome marker Rab7. However, GPR101 was not colocalized with the recycling endosome marker Rab11. These findings show that the basal arrestin recruitment by GPR101 C-terminal tail drives the receptor constitutive clathrin-mediated internalization. Intracellularly, GPR101 concentrates in the endosomal compartment and is degraded through the lysosomal pathway. In conclusion, we uncovered a constitutive intracellular trafficking of GPR101 that potentially represents an important layer of regulation of its signaling and function.
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Affiliation(s)
- Dayana Abboud
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liege, Liege, Belgium
| | - Clauda Abboud
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liege, Liege, Belgium
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Jean-Claude Twizere
- Laboratory of Viral Interactomes, GIGA-Molecular Biology of Diseases, University of Liege, Liege, Belgium
| | - Julien Hanson
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liege, Liege, Belgium; Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines (CIRM), University of Liege, Liege, Belgium.
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Kalinovic R, Pascariu A, Vlad G, Nitusca D, Sălcudean A, Sirbu IO, Marian C, Enatescu VR. Involvement of the Expression of G Protein-Coupled Receptors in Schizophrenia. Pharmaceuticals (Basel) 2024; 17:85. [PMID: 38256919 PMCID: PMC10818502 DOI: 10.3390/ph17010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 12/13/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
The expression of GPCRs has been associated with schizophrenia, and their expression may induce morphological changes in brain regions responsible for schizophrenia and disease-specific behavioral changes. The articles included in this review were selected using keywords and databases of scientific research websites. The expressions of GPRs have different involvements in schizophrenia, some increase the risk while others provide protection, and they may also be potential targets for new treatments. Proper evaluation of these factors is essential to have a better therapeutic response with a lower rate of chronicity and thus improve the long-term prognosis.
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Affiliation(s)
- Raluka Kalinovic
- Doctoral School, University of Medicine and Pharmacy Victor Babes Timisoara, 300041 Timisoara, Romania
- Eduard Pamfil Psychiatric Clinic, Timisoara County Emergency Clinical Hospital, 300425 Timisoara, Romania; (A.P.); (G.V.); (V.R.E.)
| | - Andrei Pascariu
- Eduard Pamfil Psychiatric Clinic, Timisoara County Emergency Clinical Hospital, 300425 Timisoara, Romania; (A.P.); (G.V.); (V.R.E.)
| | - Gabriela Vlad
- Eduard Pamfil Psychiatric Clinic, Timisoara County Emergency Clinical Hospital, 300425 Timisoara, Romania; (A.P.); (G.V.); (V.R.E.)
| | - Diana Nitusca
- Department of Biochemistry, University of Medicine and Pharmacy Victor Babes Timisoara, 300041 Timisoara, Romania; (D.N.); (I.O.S.); (C.M.)
- Center for Complex Networks Science, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
| | - Andreea Sălcudean
- Discipline of Sociobiology, Department of Ethics and Social Sciences, George Emil Palade University of Medicine, Pharmacy, Science and Technology of Târgu Mureș, 540136 Targu Mures, Romania;
| | - Ioan Ovidiu Sirbu
- Department of Biochemistry, University of Medicine and Pharmacy Victor Babes Timisoara, 300041 Timisoara, Romania; (D.N.); (I.O.S.); (C.M.)
- Center for Complex Networks Science, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
| | - Catalin Marian
- Department of Biochemistry, University of Medicine and Pharmacy Victor Babes Timisoara, 300041 Timisoara, Romania; (D.N.); (I.O.S.); (C.M.)
- Center for Complex Networks Science, Victor Babes University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timisoara, Romania
| | - Virgil Radu Enatescu
- Eduard Pamfil Psychiatric Clinic, Timisoara County Emergency Clinical Hospital, 300425 Timisoara, Romania; (A.P.); (G.V.); (V.R.E.)
- Discipline of Psychiatry, Department of Neurosciences, University of Medicine and Pharmacy Victor Babes Timisoara, 300041 Timisoara, Romania
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Pillaiyar T, Wozniak M, Abboud D, Rasch A, Liebing AD, Poso A, Kronenberger T, Stäubert C, Laufer SA, Hanson J. Development of Ligands for the Super Conserved Orphan G Protein-Coupled Receptor GPR27 with Improved Efficacy and Potency. J Med Chem 2023; 66:17118-17137. [PMID: 38060818 DOI: 10.1021/acs.jmedchem.3c02030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
The orphan G protein-coupled receptor GPR27 appears to play a role in insulin production, secretion, lipid metabolism, neuronal plasticity, and l-lactate homeostasis. However, investigations on the function of GPR27 are impaired by the lack of potent and efficacious agonists. We describe herein the development of di- and trisubstituted benzamide derivatives 4a-e, 7a-z, and 7aa-ai, which display GPR27-specific activity in a β-arrestin 2 recruitment-based assay. Highlighted compounds are PT-91 (7p: pEC50 6.15; Emax 100%) and 7ab (pEC50 6.56; Emax 99%). A putative binding mode was revealed by the docking studies of 7p and 7ab with a GPR27 homology model. The novel active compounds exhibited no GPR27-mediated activation of G proteins, indicating that the receptor may possess an atypical profile. Compound 7p displays high metabolic stability and brain exposure in mice. Thus, 7p represents a novel tool to investigate the elusive pharmacology of GPR27 and assess its potential as a drug target.
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Affiliation(s)
- Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Monika Wozniak
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, B-4000 Liège, Belgium
| | - Dayana Abboud
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, B-4000 Liège, Belgium
| | - Alexander Rasch
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
| | - Aenne-Dorothea Liebing
- Rudolf Schönheimer Institute of Biochemistry, Faculty of Medicine, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Claudia Stäubert
- Rudolf Schönheimer Institute of Biochemistry, Faculty of Medicine, Leipzig University, Johannisallee 30, 04103 Leipzig, Germany
| | - Stefan A Laufer
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided & Functionally Instructed Tumor Therapies", University of Tübingen, 72076 Tübingen, Germany
| | - Julien Hanson
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, B-4000 Liège, Belgium
- Laboratory of Medicinal Chemistry, Centre for Interdisciplinary Research on Medicines (CIRM), University of Liège, B-4000 Liège, Belgium
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8
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Tomiyasu N, Takahashi M, Toyonaga K, Yamasaki S, Bamba T, Izumi Y. Efficient lipidomic approach for the discovery of lipid ligands for immune receptors by combining LC-HRMS/MS analysis with fractionation and reporter cell assay. Anal Bioanal Chem 2023:10.1007/s00216-023-05111-w. [PMID: 38135762 DOI: 10.1007/s00216-023-05111-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/09/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023]
Abstract
C-type lectin receptors (CLRs), which are pattern recognition receptors responsible for triggering innate immune responses, recognize damaged self-components and immunostimulatory lipids from pathogenic bacteria; however, several of their ligands remain unknown. Here, we propose a new analytical platform combining liquid chromatography-high-resolution tandem mass spectrometry with microfractionation capability (LC-FRC-HRMS/MS) and a reporter cell assay for sensitive activity measurements to develop an efficient methodology for searching for lipid ligands of CLR from microbial trace samples (crude cell extracts of approximately 5 mg dry cell/mL). We also developed an in-house lipidomic library containing accurate mass and fragmentation patterns of more than 10,000 lipid molecules predicted in silico for 90 lipid subclasses and 35 acyl side chain fatty acids. Using the developed LC-FRC-HRMS/MS system, the lipid extracts of Helicobacter pylori were separated and fractionated, and HRMS and HRMS/MS spectra were obtained simultaneously. The fractionated lipid extract samples in 96-well plates were thereafter subjected to reporter cell assays using nuclear factor of activated T cells (NFAT)-green fluorescent protein (GFP) reporter cells expressing mouse or human macrophage-inducible C-type lectin (Mincle). A total of 102 lipid molecules from all fractions were annotated using an in-house lipidomic library. Furthermore, a fraction that exhibited significant activity in the NFAT-GFP reporter cell assay contained α-cholesteryl glucoside, a type of glycolipid, which was successfully identified as a lipid ligand molecule for Mincle. Our analytical platform has the potential to be a useful tool for efficient discovery of lipid ligands for immunoreceptors.
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Affiliation(s)
- Noriyuki Tomiyasu
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
| | - Masatomo Takahashi
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kenji Toyonaga
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Section of Infection Biology, Department of Functional Bioscience, Fukuoka Dental College, Fukuoka, Japan
| | - Sho Yamasaki
- Department of Molecular Immunology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
- Laboratory of Molecular Immunology, Immunology Frontier Research Center (IFReC), Osaka University, Osaka, Japan
| | - Takeshi Bamba
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yoshihiro Izumi
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Fukuoka, Japan.
- Division of Metabolomics/Mass Spectrometry Center, Medical Research Center for High Depth Omics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
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9
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Kaafarani A, Darche-Gabinaud R, Bisteau X, Imbault V, Wittamer V, Parmentier M, Pirson I. Proximity Interactome Analysis of Super Conserved Receptors Expressed in the Brain Identifies EPB41L2, SLC3A2, and LRBA as Main Partners. Cells 2023; 12:2625. [PMID: 37998360 PMCID: PMC10670248 DOI: 10.3390/cells12222625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/31/2023] [Accepted: 11/08/2023] [Indexed: 11/25/2023] Open
Abstract
The Super-Conserved Receptors Expressed in the Brain (SREBs) form a subfamily of orphan G protein-coupled receptors, highly conserved in evolution and characterized by a predominant expression in the brain. The signaling pathways activated by these receptors (if any) are presently unclear. Given the strong conservation of their intracellular loops, we used a BioID2 proximity-labeling assay to identify protein partners of SREBs that would interact with these conserved domains. Using streptavidin pull-down followed by mass spectrometry analysis, we identified the amino acid transporter SLC3A2, the AKAP protein LRBA, and the 4.1 protein EPB41L2 as potential interactors of these GPCRs. Using co-immunoprecipitation experiments, we confirmed the physical association of these proteins with the receptors. We then studied the functional relevance of the interaction between EPB41L2 and SREB1. Immunofluorescence microscopy revealed that SREB1 and EPB41L2 co-localize at the plasma membrane and that SREB1 is enriched in the β-catenin-positive cell membranes. siRNA knockdown experiments revealed that EPB41L2 promotes the localization of SREB1 at the plasma membrane and increases the solubilization of SREB1 when using detergents, suggesting a modification of its membrane microenvironment. Altogether, these data suggest that EPB41L2 could regulate the subcellular compartmentalization of SREBs and, as proposed for other GPCRs, could affect their stability or activation.
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Affiliation(s)
- Abeer Kaafarani
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium; (R.D.-G.); (X.B.); (V.I.); (V.W.); (M.P.)
| | | | | | | | | | | | - Isabelle Pirson
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium; (R.D.-G.); (X.B.); (V.I.); (V.W.); (M.P.)
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10
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Breton TS, Fike S, Francis M, Patnaude M, Murray CA, DiMaggio MA. Characterizing the SREB G protein-coupled receptor family in fish: Brain gene expression and genomic differences in upstream transcription factor binding sites. Comp Biochem Physiol A Mol Integr Physiol 2023; 285:111507. [PMID: 37611891 PMCID: PMC10529039 DOI: 10.1016/j.cbpa.2023.111507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/12/2023] [Accepted: 08/20/2023] [Indexed: 08/25/2023]
Abstract
The SREB (Super-conserved Receptors Expressed in Brain) family of orphan G protein-coupled receptors is highly conserved in vertebrates and consists of three members: SREB1 (orphan designation GPR27), SREB2 (GPR85), and SREB3 (GPR173). SREBs are associated with processes ranging from neuronal plasticity to reproductive control. Relatively little is known about similarities across the entire family, or how mammalian gene expression patterns compare to non-mammalian vertebrates. In fish, this system may be particularly complex, as some species have gained a fourth member (SREB3B) while others have lost genes. To better understand the system, the present study aimed to: 1) use qPCR to characterize sreb and related gene expression patterns in the brains of three fish species with different systems, and 2) identify possible differences in transcriptional regulation among the receptors, using upstream transcription factor binding sites across 70 ray-finned fish genomes. Overall, regional patterns of sreb expression were abundant in forebrain-related areas. However, some species-specific patterns were detected, such as abundant expression of receptors in zebrafish (Danio rerio) hypothalamic-containing sections, and divergence between sreb3a and sreb3b in pufferfish (Dichotomyctere nigroviridis). In addition, a gene possibly related to the system (dkk3a) was spatially correlated with the receptors in all three species. Genomic regions upstream of sreb2 and sreb3b, but largely not sreb1 or sreb3a, contained many highly conserved transcription factor binding sites. These results provide novel information about expression differences and transcriptional regulation across fish that may inform future research to better understand these receptors.
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Affiliation(s)
- Timothy S Breton
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938, USA.
| | - Samantha Fike
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938, USA
| | - Mullein Francis
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938, USA
| | - Michael Patnaude
- Division of Natural Sciences, University of Maine at Farmington, Farmington, ME 04938, USA
| | - Casey A Murray
- Tropical Aquaculture Laboratory, Program in Fisheries and Aquatic Sciences, School of Forest, Fisheries, and Geomatics Sciences, Institute of Food and Agricultural Sciences, University of Florida, Ruskin, FL 33570, USA
| | - Matthew A DiMaggio
- Tropical Aquaculture Laboratory, Program in Fisheries and Aquatic Sciences, School of Forest, Fisheries, and Geomatics Sciences, Institute of Food and Agricultural Sciences, University of Florida, Ruskin, FL 33570, USA
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11
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Vasudevan S, Samuels IS, Park PSH. Gpr75 knockout mice display age-dependent cone photoreceptor cell loss. J Neurochem 2023; 167:538-555. [PMID: 37840219 PMCID: PMC10777681 DOI: 10.1111/jnc.15979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023]
Abstract
GPR75 is an orphan G protein-coupled receptor for which there is currently limited information and its function in physiology and disease is only recently beginning to emerge. This orphan receptor is expressed in the retina but its function in the eye is unknown. The earliest studies on GPR75 were conducted in the retina, where the receptor was first identified and cloned and mutations in the receptor were identified as a possible contributor to retinal degenerative disease. Despite these sporadic reports, the function of GPR75 in the retina and in retinal disease has yet to be explored. To assess whether GPR75 has a functional role in the retina, the retina of Gpr75 knockout mice was characterized. Knockout mice displayed a mild progressive retinal degeneration, which was accompanied by oxidative stress. The degeneration was because of the loss of both M-cone and S-cone photoreceptor cells. Housing mice under constant dark conditions reduced oxidative stress but did not prevent cone photoreceptor cell loss, indicating that oxidative stress is not a primary cause of the observed retinal degeneration. Studies here demonstrate an important role for GPR75 in maintaining the health of cone photoreceptor cells and that Gpr75 knockout mice can be used as a model to study cone photoreceptor cell loss.
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Affiliation(s)
- Sreelakshmi Vasudevan
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, Ohio, USA
| | - Ivy S. Samuels
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio, USA
| | - Paul S.-H. Park
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, Ohio, USA
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12
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Zhao X, Stein KR, Chen V, Griffin ME, Lairson LL, Hang HC. Chemoproteomics reveals microbiota-derived aromatic monoamine agonists for GPRC5A. Nat Chem Biol 2023; 19:1205-1214. [PMID: 37248411 DOI: 10.1038/s41589-023-01328-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 04/06/2023] [Indexed: 05/31/2023]
Abstract
The microbiota generates diverse metabolites to modulate host physiology and disease, but their protein targets and mechanisms of action have not been fully elucidated. To address this challenge, we explored microbiota-derived indole metabolites and developed photoaffinity chemical reporters for proteomic studies. We identified many potential indole metabolite-interacting proteins, including metabolic enzymes, transporters, immune sensors and G protein-coupled receptors. Notably, we discovered that aromatic monoamines can bind the orphan receptor GPRC5A and stimulate β-arrestin recruitment. Metabolomic and functional profiling also revealed specific amino acid decarboxylase-expressing microbiota species that produce aromatic monoamine agonists for GPRC5A-β-arrestin recruitment. Our analysis of synthetic aromatic monoamine derivatives identified 7-fluorotryptamine as a more potent agonist of GPRC5A. These results highlight the utility of chemoproteomics to identify microbiota metabolite-interacting proteins and the development of small-molecule agonists for orphan receptors.
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Affiliation(s)
- Xiaohui Zhao
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kathryn R Stein
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Victor Chen
- Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York City, NY, USA
| | - Matthew E Griffin
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Luke L Lairson
- Department of Chemistry, Scripps Research, La Jolla, CA, USA
| | - Howard C Hang
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
- Department of Chemistry, Scripps Research, La Jolla, CA, USA.
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13
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Aleti G, Troyer EA, Hong S. G protein-coupled receptors: A target for microbial metabolites and a mechanistic link to microbiome-immune-brain interactions. Brain Behav Immun Health 2023; 32:100671. [PMID: 37560037 PMCID: PMC10407893 DOI: 10.1016/j.bbih.2023.100671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 07/30/2023] [Indexed: 08/11/2023] Open
Abstract
Human-microorganism interactions play a key role in human health. However, the underlying molecular mechanisms remain poorly understood. Small-molecules that offer a functional readout of microbe-microbe-human relationship are of great interest for deeper understanding of the inter-kingdom crosstalk at the molecular level. Recent studies have demonstrated that small-molecules from gut microbiota act as ligands for specific human G protein-coupled receptors (GPCRs) and modulate a range of human physiological functions, offering a mechanistic insight into the microbe-human interaction. To this end, we focused on analysis of bacterial metabolites that are currently recognized to bind to GPCRs and are found to activate the known downstream signaling pathways. We further mapped the distribution of these molecules across the public mass spectrometry-based metabolomics data, to identify the presence of these molecules across body sites and their association with health status. By combining this with RNA-Seq expression and spatial localization of GPCRs from a public human protein atlas database, we inferred the most predominant GPCR-mediated microbial metabolite-human cell interactions regulating gut-immune-brain axis. Furthermore, by evaluating the intestinal absorption properties and blood-brain barrier permeability of the small-molecules we elucidated their molecular interactions with specific human cell receptors, particularly expressed on human intestinal epithelial cells, immune cells and the nervous system that are shown to hold much promise for clinical translational potential. Furthermore, we provide an overview of an open-source resource for simultaneous interrogation of bioactive molecules across the druggable human GPCRome, a useful framework for integration of microbiome and metabolite cataloging with mechanistic studies for an improved understanding of gut microbiota-immune-brain molecular interactions and their potential therapeutic use.
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Affiliation(s)
- Gajender Aleti
- Department of Food and Animal Sciences, Tennessee State University, Nashville, TN, 37209, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Emily A. Troyer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Suzi Hong
- Department of Psychiatry, University of California San Diego, La Jolla, CA, 92093, USA
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, 92093, USA
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14
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Nie Y, Qiu Z, Chen S, Chen Z, Song X, Ma Y, Huang N, Cyster JG, Zheng S. Specific binding of GPR174 by endogenous lysophosphatidylserine leads to high constitutive G s signaling. Nat Commun 2023; 14:5901. [PMID: 37737235 PMCID: PMC10516915 DOI: 10.1038/s41467-023-41654-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
Many orphan G protein-coupled receptors (GPCRs) remain understudied because their endogenous ligands are unknown. Here, we show that a group of class A/rhodopsin-like orphan GPCRs including GPR61, GPR161 and GPR174 increase the cAMP level similarly to fully activated D1 dopamine receptor (D1R). We report cryo-electron microscopy structures of the GPR61‒Gs, GPR161‒Gs and GPR174‒Gs complexes without any exogenous ligands. The GPR174 structure reveals that endogenous lysophosphatidylserine (lysoPS) is copurified. While GPR174 fails to respond to exogenous lysoPS, likely owing to its maximal activation by the endogenous ligand, GPR174 mutants with lower ligand binding affinities can be specifically activated by lysoPS but not other lipids, in a dose-dependent manner. Moreover, GPR174 adopts a non-canonical Gs coupling mode. The structures of GPR161 and GPR61 reveal that the second extracellular loop (ECL2) penetrates into the orthosteric pocket, possibly contributing to constitutive activity. Our work definitively confirms lysoPS as an endogenous GPR174 ligand and suggests that high constitutive activity of some orphan GPCRs could be accounted for by their having naturally abundant ligands.
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Affiliation(s)
- Yingying Nie
- College of Life Sciences, Beijing Normal University, 100875, Beijing, China
- National Institute of Biological Sciences, 102206, Beijing, China
| | - Zeming Qiu
- National Institute of Biological Sciences, 102206, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China
| | - Sijia Chen
- National Institute of Biological Sciences, 102206, Beijing, China
| | - Zhao Chen
- National Institute of Biological Sciences, 102206, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China
| | - Xiaocui Song
- National Institute of Biological Sciences, 102206, Beijing, China
| | - Yan Ma
- National Institute of Biological Sciences, 102206, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China
| | - Niu Huang
- National Institute of Biological Sciences, 102206, Beijing, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China
| | - Jason G Cyster
- HHMI, University of California, San Francisco, CA, 94143, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, 94143, USA
| | - Sanduo Zheng
- College of Life Sciences, Beijing Normal University, 100875, Beijing, China.
- National Institute of Biological Sciences, 102206, Beijing, China.
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, 100084, Beijing, China.
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15
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Koch TL, Torres JP, Baskin RP, Salcedo PF, Chase K, Olivera BM, Safavi-Hemami H. A toxin-based approach to neuropeptide and peptide hormone discovery. Front Mol Neurosci 2023; 16:1176662. [PMID: 37720554 PMCID: PMC10501145 DOI: 10.3389/fnmol.2023.1176662] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
Peptide hormones and neuropeptides form a diverse class of bioactive secreted molecules that control essential processes in animals. Despite breakthroughs in peptide discovery, many signaling peptides remain undiscovered. Recently, we demonstrated the use of somatostatin-mimicking toxins from cone snails to identify the invertebrate ortholog of somatostatin. Here, we show that this toxin-based approach can be systematically applied to discover other unknown secretory peptides that are likely to have signaling function. Using large sequencing datasets, we searched for homologies between cone snail toxins and secreted proteins from the snails' prey. We identified and confirmed expression of five toxin families that share strong similarities with unknown secretory peptides from mollusks and annelids and in one case also from ecdysozoans. Based on several lines of evidence we propose that these peptides likely act as signaling peptides that serve important physiological functions. Indeed, we confirmed that one of the identified peptides belongs to the family of crustacean hyperglycemic hormone, a peptide not previously observed in Spiralia. We propose that this discovery pipeline can be broadly applied to other systems in which one organism has evolved molecules to manipulate the physiology of another.
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Affiliation(s)
- Thomas Lund Koch
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Biochemistry, University of Utah, Salt Lake City, UT, United States
| | - Joshua P. Torres
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Robert P. Baskin
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
- The Ohio State University College of Medicine, Columbus, OH, United States
| | - Paula Flórez Salcedo
- Department of Neurobiology, University of Utah, Salt Lake City, UT, United States
| | - Kevin Chase
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
| | - Baldomero M. Olivera
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
| | - Helena Safavi-Hemami
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Biochemistry, University of Utah, Salt Lake City, UT, United States
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
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16
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Laboute T, Zucca S, Holcomb M, Patil DN, Garza C, Wheatley BA, Roy RN, Forli S, Martemyanov KA. Orphan receptor GPR158 serves as a metabotropic glycine receptor: mGlyR. Science 2023; 379:1352-1358. [PMID: 36996198 PMCID: PMC10751545 DOI: 10.1126/science.add7150] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 03/03/2023] [Indexed: 04/01/2023]
Abstract
Glycine is a major neurotransmitter involved in several fundamental neuronal processes. The identity of the metabotropic receptor mediating slow neuromodulatory effects of glycine is unknown. We identified an orphan G protein-coupled receptor, GPR158, as a metabotropic glycine receptor (mGlyR). Glycine and a related modulator, taurine, directly bind to a Cache domain of GPR158, and this event inhibits the activity of the intracellular signaling complex regulator of G protein signaling 7-G protein β5 (RGS7-Gβ5), which is associated with the receptor. Glycine signals through mGlyR to inhibit production of the second messenger adenosine 3',5'-monophosphate. We further show that glycine, but not taurine, acts through mGlyR to regulate neuronal excitability in cortical neurons. These results identify a major neuromodulatory system involved in mediating metabotropic effects of glycine, with implications for understanding cognition and affective states.
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Affiliation(s)
- Thibaut Laboute
- Department of Neuroscience, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Stefano Zucca
- Department of Neuroscience, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Matthew Holcomb
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Dipak N. Patil
- Department of Neuroscience, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Christina Garza
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Brittany A. Wheatley
- Department of Integrative Structural and Computational Biology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Raktim N. Roy
- Department of Integrative Structural and Computational Biology, UF Scripps Biomedical Research, Jupiter, FL 33458, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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17
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Satake H. Kobayashi Award 2021: Neuropeptides, receptors, and follicle development in the ascidian, Ciona intestinalis Type A: New clues to the evolution of chordate neuropeptidergic systems from biological niches. Gen Comp Endocrinol 2023; 337:114262. [PMID: 36925021 DOI: 10.1016/j.ygcen.2023.114262] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 03/09/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023]
Abstract
Ciona intestinalis Type A (Ciona robusta) is a cosmopolitan species belonging to the phylum Urochordata, invertebrate chordates that are phylogenetically the most closely related to the vertebrates. Therefore, this species is of interest for investigation of the evolution and comparative physiology of endocrine, neuroendocrine, and nervous systems in chordates. Our group has identified>30 Ciona neuropeptides (80% of all identified ascidian neuropeptides) primarily using peptidomic approaches combined with reference to genome sequences. These neuropeptides are classified into two groups: homologs or prototypes of vertebrate neuropeptides and novel (Ciona-specific) neuropeptides. We have also identified the cognate receptors for these peptides. In particular, we elucidated multiple receptors for Ciona-specific neuropeptides by a combination of a novel machine learning system and experimental validation of the specific interaction of the predicted neuropeptide-receptor pairs, and verified unprecedented phylogenies of receptors for neuropeptides. Moreover, several neuropeptides were found to play major roles in the regulation of ovarian follicle development. Ciona tachykinin facilitates the growth of vitellogenic follicles via up-regulation of the enzymatic activities of proteases. Ciona vasopressin stimulates oocyte maturation and ovulation via up-regulation of maturation-promoting factor- and matrix metalloproteinase-directed collagen degradation, respectively. Ciona cholecystokinin also triggers ovulation via up-regulation of receptor tyrosine kinase signaling and the subsequent activation of matrix metalloproteinase. These studies revealed that the neuropeptidergic system plays major roles in ovarian follicle growth, maturation, and ovulation in Ciona, thus paving the way for investigation of the biological roles for neuropeptides in the endocrine, neuroendocrine, nervous systems of Ciona, and studies of the evolutionary processes of various neuropeptidergic systems in chordates.
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Affiliation(s)
- Honoo Satake
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan.
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18
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Szwabowski GL, Cole JA, Baker DL, Parrill AL. Structure-based pharmacophore modeling 1. Automated random pharmacophore model generation. J Mol Graph Model 2023; 121:108429. [PMID: 36804368 DOI: 10.1016/j.jmgm.2023.108429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/18/2023] [Accepted: 02/06/2023] [Indexed: 02/13/2023]
Abstract
Pharmacophores are three-dimensional arrangements of molecular features required for biological activity that are often used in virtual screening efforts to prioritize ligands for experimental testing. G protein-coupled receptors (GPCR) are integral membrane proteins of considerable interest as targets for ligand discovery and drug development. Ligand-based pharmacophore models can be constructed to identify structural commonalities between known bioactive ligands for targets including GPCR. However, structure-based pharmacophores (which only require an experimentally determined or modeled structure for a protein target) have gained more attention to aid in virtual screening efforts as the number of publicly available experimentally determined GPCR structures have increased (140 unique GPCR represented as of October 24, 2022). Thus, the goal of this study was to develop a method of structure-based pharmacophore model generation applicable to ligand discovery for GPCR that have few known ligands. Pharmacophore models were generated within the active sites of 8 class A GPCR crystal structures via automated annotation of 5 randomly selected functional group fragments to sample diverse combinations of pharmacophore features. Each of the 5000 generated pharmacophores was then used to search a database containing active and decoy/inactive compounds for 30 class A GPCR and scored using enrichment factor and goodness-of-hit metrics to assess performance. Application of this method to the set of 8 class A GPCR produced pharmacophore models possessing the theoretical maximum enrichment factor value in both resolved structures (8 of 8 cases) and homology models (7 of 8 cases), indicating that generated pharmacophore models can prove useful in the context of virtual screening.
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Affiliation(s)
| | - Judith A Cole
- Department of Biological Sciences, The University of Memphis, Memphis, TN, 38152, USA
| | - Daniel L Baker
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Abby L Parrill
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
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19
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Urban N, Leonhardt M, Schaefer M. Multiplex G Protein-Coupled Receptor Screen Reveals Reliably Acting Agonists and a Gq-Phospholipase C Coupling Mode of GPR30/GPER1. Mol Pharmacol 2023; 103:48-62. [PMID: 36400433 DOI: 10.1124/molpharm.122.000580] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 11/21/2022] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the most versatile family of pharmacological target proteins. For some "orphan" GPCRs, no ligand or drug-like modulator is known. In this study, we have established and applied a parallelized assay to coscreen 29 different human GPCRs. Three compounds, chlorhexidine, Lys-05, and 9-aminoacridine, triggered transient Ca2+ signals linked to the expression of GPR30. GPR30, also named G protein-coupled estrogen receptor 1 (GPER1), was reported to elicit increases in cAMP in response to 17β-estradiol, 4-hydroxytamoxifen, or G-1. These findings could, however, not be reproduced by other groups, and the deorphanization of GPR30 is, therefore, intensely disputed. The unbiased screen and following experiments in transiently or stably GPR30-overexpressing HEK293 cells did not show responses to 17β-estradiol, 4-hydroxytamoxifen, or G-1. A thorough analysis of the activated signaling cascade revealed a canonical Gq-coupled pathway, including phospholipase C, protein kinase C and ERK activation, receptor internalization, and sensitivity to the Gq inhibitor YM-254890. When expressed in different cell lines, the localization of a fluorescent GPR30 fusion protein appeared variable. An efficient integration into the plasma membrane and stronger functional responses were found in HEK293 and in MCF-7 cells, whereas GPR30 appeared mostly retained in endomembrane compartments in Cos-7 or HeLa cells. Thus, conflicting findings may result from the use of different cell lines. The newly identified agonists and the finding that GPR30 couples to Gq are expected to serve as a starting point for identifying physiologic responses that are controlled by this GPCR. SIGNIFICANCE STATEMENT: This study has identified and thoroughly characterized novel and reliably acting agonists of the G protein-coupled receptor GPER1/GPR30. Applying these agonists, this study demonstrates that GPR30 couples to the canonical Gq-phospholipase C pathway and is rapidly internalized upon continuous exposure to the agonists.
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Affiliation(s)
- Nicole Urban
- Medical Faculty, Rudolf-Boehm-Institute of Pharmacology and Toxicology, Leipzig University, Leipzig, Germany
| | - Marion Leonhardt
- Medical Faculty, Rudolf-Boehm-Institute of Pharmacology and Toxicology, Leipzig University, Leipzig, Germany
| | - Michael Schaefer
- Medical Faculty, Rudolf-Boehm-Institute of Pharmacology and Toxicology, Leipzig University, Leipzig, Germany
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20
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Satake H, Osugi T, Shiraishi A. Impact of Machine Learning-Associated Research Strategies on the Identification of Peptide-Receptor Interactions in the Post-Omics Era. Neuroendocrinology 2023; 113:251-261. [PMID: 34348315 DOI: 10.1159/000518572] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/19/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUNDS Elucidation of peptide-receptor pairs is a prerequisite for many studies in the neuroendocrine, endocrine, and neuroscience fields. Recent omics analyses have provided vast amounts of peptide and G protein-coupled receptor (GPCR) sequence data. GPCRs for homologous peptides are easily characterized based on homology searching, and the relevant peptide-GPCR interactions are also detected by typical signaling assays. In contrast, conventional evaluation or prediction methods, including high-throughput reverse-pharmacological assays and tertiary structure-based computational analyses, are not useful for identifying interactions between novel and omics-derived peptides and GPCRs. SUMMARY Recently, an approach combining machine learning-based prediction of novel peptide-GPCR pairs and experimental validation of the predicted pairs have been shown to breakthrough this bottleneck. A machine learning method, logistic regression for human class A GPCRs and the multiple subsequent signaling assays led to the deorphanization of human class A orphan GPCRs, namely, the identification of 18 peptide-GPCR pairs. Furthermore, using another machine learning algorithm, the support vector machine (SVM), the peptide descriptor-incorporated SVM was originally developed and employed to predict GPCRs for novel peptides characterized from the closest relative of vertebrates, Ciona intestinalis Type A (Ciona robusta). Experimental validation of the predicted pairs eventually led to the identification of 11 novel peptide-GPCR pairs. Of particular interest is that these newly identified GPCRs displayed neither significant sequence similarity nor molecular phylogenetic relatedness to known GPCRs for peptides. KEY MESSAGES These recent studies highlight the usefulness and versatility of machine learning for enabling the efficient, reliable, and systematic identification of novel peptide-GPCR interactions.
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Affiliation(s)
- Honoo Satake
- Division of Integrative Biomolecular Function, Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Tomohiro Osugi
- Division of Integrative Biomolecular Function, Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
| | - Akira Shiraishi
- Division of Integrative Biomolecular Function, Bioorganic Research Institute, Suntory Foundation for Life Sciences, Kyoto, Japan
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21
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Gómez-Cañas M, Rodríguez-Cueto C, Satta V, Hernández-Fisac I, Navarro E, Fernández-Ruiz J. Endocannabinoid-Binding Receptors as Drug Targets. Methods Mol Biol 2023; 2576:67-94. [PMID: 36152178 DOI: 10.1007/978-1-0716-2728-0_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cannabis plant has been used from ancient times with therapeutic purposes for treating human pathologies, but the identification of the cellular and molecular mechanisms underlying the therapeutic properties of the phytocannabinoids, the active compounds in this plant, occurred in the last years of the past century. In the late 1980s and early 1990s, seminal studies demonstrated the existence of cannabinoid receptors and other elements of the so-called endocannabinoid system. These G protein-coupled receptors (GPCRs) are a key element in the functions assigned to endocannabinoids and appear to serve as promising pharmacological targets. They include CB1, CB2, and GPR55, but also non-GPCRs can be activated by endocannabinoids, like ionotropic receptor TRPV1 and even nuclear receptors of the PPAR family. Their activation, inhibition, or simply modulation have been associated with numerous physiological effects at both central and peripheral levels, which may have therapeutic value in different human pathologies, then providing a solid experimental explanation for both the ancient medicinal uses of Cannabis plant and the recent advances in the development of cannabinoid-based specific therapies. This chapter will review the scientific knowledge generated in the last years around the research on the different endocannabinoid-binding receptors and their signaling mechanisms. Our intention is that this knowledge may help readers to understand the relevance of these receptors in health and disease conditions, as well as it may serve as the theoretical basis for the different experimental protocols to investigate these receptors and their signaling mechanisms that will be described in the following chapters.
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Affiliation(s)
- María Gómez-Cañas
- Instituto Universitario de Investigación en Neuroquímica, Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Complutense, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Carmen Rodríguez-Cueto
- Instituto Universitario de Investigación en Neuroquímica, Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Complutense, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Valentina Satta
- Instituto Universitario de Investigación en Neuroquímica, Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Complutense, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Inés Hernández-Fisac
- Instituto Universitario de Investigación en Neuroquímica, Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Complutense, Madrid, Spain
| | - Elisa Navarro
- Instituto Universitario de Investigación en Neuroquímica, Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Complutense, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Javier Fernández-Ruiz
- Instituto Universitario de Investigación en Neuroquímica, Departamento de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Complutense, Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain.
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22
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Stäubert C, Wozniak M, Dupuis N, Laschet C, Pillaiyar T, Hanson J. Superconserved receptors expressed in the brain: Expression, function, motifs and evolution of an orphan receptor family. Pharmacol Ther 2022; 240:108217. [PMID: 35644261 DOI: 10.1016/j.pharmthera.2022.108217] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/20/2022] [Accepted: 05/23/2022] [Indexed: 12/14/2022]
Abstract
GPR27, GPR85 and GPR173 constitute a small family of G protein-coupled receptors (GPCR) that share the distinctive characteristics of being highly conserved throughout vertebrate evolution and predominantly expressed in the brain. Accordingly, they have been coined as "Superconserved Receptors Expressed in the Brain" (SREB), although their expression profile is more complex than what was originally thought. SREBs have no known validated endogenous ligands and are thus labeled as "orphan" receptors. The investigation of this particular category of uncharacterized receptors holds great promise both in terms of physiology and drug development. In the largest GPCR family, the Rhodopsin-like or Class A, around 100 receptors are considered orphans. Because GPCRs are the most successful source of drug targets, the discovery of a novel function or ligand most likely will lead to significant breakthroughs for the discovery of innovative therapies. The high level of conservation is one of the characteristic features of the SREBs. We propose herein a detailed analysis of the putative evolutionary origin of this family. We highlight the properties that distinguish SREBs from other rhodopsin-like GPCRs. We present the current evidence for these receptors downstream signaling pathways and functions. We discuss the pharmacological challenge for the identification of natural or synthetic ligands of orphan receptors like SREBs. The different SREB-related scientific questions are presented with a highlight on what should be addressed in the near future, including the confirmation of published evidence and their validation as drug targets. In particular, we discuss in which pathological conditions these receptors may be of great relevance to solve unmet medical needs.
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Affiliation(s)
- Claudia Stäubert
- Rudolf Schönheimer Institute of Biochemistry, Faculty of Medicine, Leipzig University, Leipzig, Germany.
| | - Monika Wozniak
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium
| | - Nadine Dupuis
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium
| | - Céline Laschet
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium
| | - Thanigaimalai Pillaiyar
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tuebingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Julien Hanson
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium; Laboratory of Medicinal Chemistry, Center for Interdisciplinary Research on Medicines, University of Liège, Liège, Belgium.
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23
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Super-conserved receptors expressed in the brain: biology and medicinal chemistry efforts. Future Med Chem 2022; 14:899-913. [PMID: 35535715 DOI: 10.4155/fmc-2022-0006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The super-conserved receptors expressed in the brain (SREB) constitute a family of orphan G protein-coupled receptors that include GPR27 (SREB1), GPR85 (SREB2) and GPR173 (SREB3). Their sequences are highly conserved in vertebrates, and they are almost exclusively expressed in the central nervous system. This family of receptors has attracted much attention due to their putative physiological functions and their potential as novel drug targets. The SREB family has been postulated to play important roles in a wide range of different diseases, including pancreatic β-cell insulin secretion and regulation, schizophrenia, autism and atherosclerosis. This review intends to provide a comprehensive overview of the SREB family and its recent advances in biology and medicinal chemistry.
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24
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Hanson J. [G proteins: privileged transducers of 7-transmembrane spanning receptors]. Biol Aujourdhui 2022; 215:95-106. [PMID: 35275054 DOI: 10.1051/jbio/2021011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Indexed: 06/14/2023]
Abstract
G protein-coupled receptors or GPCR are the most abundant membrane receptors in our genome with around 800 members. They play an essential role in most physiological and pathophysiological phenomena. In addition, they constitute 30% of the targets of currently marketed drugs and remain an important reservoir for new innovative therapies. Their main effectors are heterotrimeric G proteins. These are composed of 3 subunits, α, β and γ, which, upon coupling with a GPCR, dissociate into Gα and Gβγ to activate numerous signaling pathways. This article describes some of the recent advances in understanding the function and role of heterotrimeric G proteins. After a short introduction to GPCRs, the history of the discovery of G proteins is briefly described. Then, the fundamental mechanisms of activation, signaling and regulation of G proteins are reviewed. New paradigms concerning intracellular signaling, specific recognition of G proteins by GPCRs as well as biased signaling are also discussed.
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Affiliation(s)
- Julien Hanson
- Laboratoire de Pharmacologie Moléculaire, GIGA-Molecular Biology of Diseases, Université de Liège, CHU, B34, Tour GIGA (+4), Avenue de l'Hôpital 11, B-4000 Liège, Belgique
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25
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Schebb NH, Kühn H, Kahnt AS, Rund KM, O’Donnell VB, Flamand N, Peters-Golden M, Jakobsson PJ, Weylandt KH, Rohwer N, Murphy RC, Geisslinger G, FitzGerald GA, Hanson J, Dahlgren C, Alnouri MW, Offermanns S, Steinhilber D. Formation, Signaling and Occurrence of Specialized Pro-Resolving Lipid Mediators-What is the Evidence so far? Front Pharmacol 2022; 13:838782. [PMID: 35308198 PMCID: PMC8924552 DOI: 10.3389/fphar.2022.838782] [Citation(s) in RCA: 67] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 02/02/2022] [Indexed: 12/14/2022] Open
Abstract
Formation of specialized pro-resolving lipid mediators (SPMs) such as lipoxins or resolvins usually involves arachidonic acid 5-lipoxygenase (5-LO, ALOX5) and different types of arachidonic acid 12- and 15-lipoxygenating paralogues (15-LO1, ALOX15; 15-LO2, ALOX15B; 12-LO, ALOX12). Typically, SPMs are thought to be formed via consecutive steps of oxidation of polyenoic fatty acids such as arachidonic acid, eicosapentaenoic acid or docosahexaenoic acid. One hallmark of SPM formation is that reported levels of these lipid mediators are much lower than typical pro-inflammatory mediators including the monohydroxylated fatty acid derivatives (e.g., 5-HETE), leukotrienes or certain cyclooxygenase-derived prostaglandins. Thus, reliable detection and quantification of these metabolites is challenging. This paper is aimed at critically evaluating i) the proposed biosynthetic pathways of SPM formation, ii) the current knowledge on SPM receptors and their signaling cascades and iii) the analytical methods used to quantify these pro-resolving mediators in the context of their instability and their low concentrations. Based on current literature it can be concluded that i) there is at most, a low biosynthetic capacity for SPMs in human leukocytes. ii) The identity and the signaling of the proposed G-protein-coupled SPM receptors have not been supported by studies in knock-out mice and remain to be validated. iii) In humans, SPM levels were neither related to dietary supplementation with their ω-3 polyunsaturated fatty acid precursors nor were they formed during the resolution phase of an evoked inflammatory response. iv) The reported low SPM levels cannot be reliably quantified by means of the most commonly reported methodology. Overall, these questions regarding formation, signaling and occurrence of SPMs challenge their role as endogenous mediators of the resolution of inflammation.
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Affiliation(s)
- Nils Helge Schebb
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Wuppertal, Germany,*Correspondence: Nils Helge Schebb, ; Dieter Steinhilber,
| | - Hartmut Kühn
- Department of Biochemistry, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Astrid S. Kahnt
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
| | - Katharina M. Rund
- Chair of Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Wuppertal, Germany
| | - Valerie B. O’Donnell
- School of Medicine, Systems Immunity Research Institute, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Nicolas Flamand
- Département de Médecine, Faculté de Médecine, Centre de Recherche de l’Institut Universitaire de Cardiologie et de Pneumologie de Québec, Canada Excellence Research Chair on the Microbiome-Endocannabinoidome Axis in Metabolic Health (CERC-MEND), Université Laval, Québec, QC, Canada
| | - Marc Peters-Golden
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Per-Johan Jakobsson
- Rheumatology Unit, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Karsten H. Weylandt
- Division of Medicine, Department of Gastroenterology, Metabolism and Oncology, Ruppin General Hospital, Brandenburg Medical School, Neuruppin, Germany
| | - Nadine Rohwer
- Division of Medicine, Department of Gastroenterology, Metabolism and Oncology, Ruppin General Hospital, Brandenburg Medical School, Neuruppin, Germany,Department of Molecular Toxicology, German Institute of Human Nutrition Potsdam-Rehbruecke, Nuthetal, Germany
| | - Robert C. Murphy
- Department of Pharmacology, University of Colorado-Denver, Aurora, CO, United States
| | - Gerd Geisslinger
- Institute of Clinical Pharmacology, Pharmazentrum Frankfurt, University Hospital of Goethe-University, Frankfurt, Germany,Fraunhofer Institute for Translational Medicine and Pharmacology, ITMP and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, CIMD, Frankfurt, Germany
| | - Garret A. FitzGerald
- Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Julien Hanson
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium,Laboratory of Medicinal Chemistry, Centre for Interdisciplinary Research on Medicines (CIRM), University of Liège, Liège, Belgium
| | - Claes Dahlgren
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Mohamad Wessam Alnouri
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Stefan Offermanns
- Department of Pharmacology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany,Center for Molecular Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany,Fraunhofer Institute for Translational Medicine and Pharmacology, ITMP and Fraunhofer Cluster of Excellence for Immune Mediated Diseases, CIMD, Frankfurt, Germany,*Correspondence: Nils Helge Schebb, ; Dieter Steinhilber,
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26
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The role of orphan receptor GPR139 in neuropsychiatric behavior. Neuropsychopharmacology 2022; 47:902-913. [PMID: 33479510 PMCID: PMC8882194 DOI: 10.1038/s41386-021-00962-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/01/2021] [Accepted: 01/05/2021] [Indexed: 01/30/2023]
Abstract
Orphan G protein Coupled Receptors (GPCRs) present attractive targets both for understanding neuropsychiatric diseases and for development of novel therapeutics. GPR139 is an orphan GPCR expressed in select brain circuits involved in controlling movement, motivation and reward. It has been linked to the opioid and dopamine neuromodulatory systems; however, its role in animal behavior and neuropsychiatric processes is poorly understood. Here we present a comprehensive behavioral characterization of a mouse model with a GPR139 null mutation. We show that loss of GPR139 in mice results in delayed onset hyperactivity and prominent neuropsychiatric manifestations including elevated stereotypy, increased anxiety-related traits, delayed acquisition of operant responsiveness, disruption of cued fear conditioning and social interaction deficits. Furthermore, mice lacking GPR139 exhibited complete loss of pre-pulse inhibition and developed spontaneous 'hallucinogenic' head-twitches, altogether suggesting schizophrenia-like symptomatology. Remarkably, a number of these behavioral deficits could be rescued by the administration of μ-opioid and D2 dopamine receptor (D2R) antagonists: naltrexone and haloperidol, respectively, suggesting that loss of neuropsychiatric manifestations in mice lacking GPR139 are driven by opioidergic and dopaminergic hyper-functionality. The inhibitory influence of GPR139 on D2R signaling was confirmed in cell-based functional assays. These observations define the role of GPR139 in controlling behavior and implicate in vivo actions of this receptor in the neuropsychiatric process with schizophrenia-like pathology.
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27
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Kawada T, Osugi T, Matsubara S, Sakai T, Shiraishi A, Yamamoto T, Satake H. Omics Studies for the Identification of Ascidian Peptides, Cognate Receptors, and Their Relevant Roles in Ovarian Follicular Development. Front Endocrinol (Lausanne) 2022; 13:858885. [PMID: 35321341 PMCID: PMC8936170 DOI: 10.3389/fendo.2022.858885] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/10/2022] [Indexed: 11/16/2022] Open
Abstract
Omics studies contribute to the elucidation of genomes and profiles of gene expression. In the ascidian Ciona intestinalis Type A (Ciona robusta), mass spectrometry (MS)-based peptidomic studies have detected numerous Ciona-specific (nonhomologous) neuropeptides as well as Ciona homologs of typical vertebrate neuropeptides and hypothalamic peptide hormones. Candidates for cognate G protein-coupled receptors (GPCRs) for these peptides have been found in the Ciona transcriptome by two ways. First, Ciona homologous GPCRs of vertebrate counterparts have been detected by sequence homology searches of cognate transcriptomes. Second, the transcriptome-derived GPCR candidates have been used for machine learning-based systematic prediction of interactions not only between Ciona homologous peptides and GPCRs but also between novel Ciona peptides and GPCRs. These data have ultimately led to experimental evidence for various Ciona peptide-GPCR interactions. Comparative transcriptomics between the wildtype and Ciona vasopressin (CiVP) gene-edited Ciona provide clues to the biological functions of CiVP in ovarian follicular development and whole body growth. Furthermore, the transcriptomes of follicles treated with peptides, such as Ciona tachykinin and cionin (a Ciona cholecystokinin homolog), have revealed key regulatory genes for Ciona follicle growth, maturation, and ovulation, eventually leading to the verification of essential and novel molecular mechanisms underlying these biological events. These findings indicate that omics studies, combined with artificial intelligence and single-cell technologies, pave the way for investigating in greater details the nervous, neuroendocrine, and endocrine systems of ascidians and the molecular and functional evolution and diversity of peptidergic regulatory networks throughout chordates.
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28
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Pillaiyar T, Rosato F, Wozniak M, Blavier J, Charles M, Laschet C, Kronenberger T, Müller CE, Hanson J. Structure-activity relationships of agonists for the orphan G protein-coupled receptor GPR27. Eur J Med Chem 2021; 225:113777. [PMID: 34454125 DOI: 10.1016/j.ejmech.2021.113777] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/12/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022]
Abstract
GPR27 belongs, with GPR85 and GPR173, to a small subfamily of three receptors called "Super-Conserved Receptors Expressed in the Brain" (SREB). It has been postulated to participate in key physiological processes such as neuronal plasticity, energy metabolism, and pancreatic β-cell insulin secretion and regulation. Recently, we reported the first selective GPR27 agonist, 2,4-dichloro-N-(4-(N-phenylsulfamoyl)phenyl)benzamide (I, pEC50 6.34, Emax 100%). Here, we describe the synthesis and structure-activity relationships of a series of new derivatives and analogs of I. All products were evaluated for their ability to activate GPR27 in an arrestin recruitment assay. As a result, agonists were identified with a broad range of efficacies including partial and full agonists, showing higher efficacies than the lead compound I. The most potent agonist was 4-chloro-2,5-difluoro-N-(4-(N-phenylsulfamoyl)phenyl)benzamide (7y, pEC50 6.85, Emax 37%), and the agonists with higher efficacies were 4-chloro-2-methyl-N-(4-(N-phenylsulfamoyl)phenyl)benzamide (7p, pEC50 6.04, Emax 123%), and 2-bromo-4-chloro-N-(4-(N-phenylsulfamoyl)phenyl)benzamide (7r, pEC50 5.99, Emax 123%). Docking studies predicted the putative binding site and interactions of agonist 7p with GPR27. Selected potent agonists were found to be soluble and devoid of cellular toxicity within the range of their pharmacological activity. Therefore, they represent important new tools to further characterize the (patho)physiological roles of GPR27.
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Affiliation(s)
- Thanigaimalai Pillaiyar
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany; Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.
| | - Francesca Rosato
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Monika Wozniak
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium; Institute of Nuclear Physics, Polish Academy of Sciences, Kraków, Poland
| | - Jeremy Blavier
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium
| | - Maëlle Charles
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium
| | - Céline Laschet
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany; Department of Internal Medicine VIII, University Hospital Tübingen, Otfried-Müller-Str. 14, Tübingen, 72076, Germany
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Julien Hanson
- Laboratory of Molecular Pharmacology, GIGA-Molecular Biology of Diseases, University of Liège, Liège, Belgium; Laboratory of Medicinal Chemistry, Centre for Interdisciplinary Research on Medicines (CIRM), University of Liège, Liège, Belgium
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Allosteric receptor modulation uncovers an FFA2R antagonist as a positive orthosteric modulator/agonist in disguise. Cell Signal 2021; 90:110208. [PMID: 34856356 DOI: 10.1016/j.cellsig.2021.110208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/22/2022]
Abstract
A novel receptor crosstalk activation mechanism, through which signals generated by the agonist-occupied P2Y2R (the neutrophil receptor for ATP) activate allosterically modulated free fatty acid 2 receptor (FFA2R) without the involvement of any FFA2R agonist, was used to determine the inhibitor profiles of two earlier-described, FFA2R-specific antagonists, CATPB and GLPG0974. These antagonists have been shown to have somewhat different receptor-interaction characteristics at the molecular/functional level, although both are recognized by the orthosteric site in FFA2R. The antagonists inhibited neutrophil activation induced by ATP, an activation occurred only in the presence of either of the two positive allosteric FFA2R modulators (PAMs) AZ1729 and Cmp58. No neutrophil activation was induced by either AZ1729 or Cmp58 alone, whereas together they acted as co-agonistic PAMs and activated the superoxide-generating NADPH-oxidase in neutrophils. This response was inhibited by CATPB but not by GLPG0974. In contrast, GLPG0974 acted as a positive modulator, increasing the potency, albeit not the efficacy, of the co-agonistic PAMs. GLPG0974 also altered signaling downstream of FFA2R when activated by the co-agonistic PAMs. In the presence of GLPG0974, the response of neutrophils induced by the co-agonistic PAMs included an increase in the cytosolic concentration of free calcium ions (Ca2+), and this effect was reciprocal in that GLPG0974 triggered an increase in intracellular Ca2+, demonstrating that GLPG0974 acted as an FFA2R agonist. In summary, by studying the effects of the FFA2R ligand GLPG0974 on neutrophil activation induced by the co-agonists AZ1729 + Cmp58, we show that GLPG0974 is not only an FFA2R antagonist, but also displays agonistic and positive FFA2R-modulating functions that affect NADPH-oxidase activity and alter the receptor-downstream signaling induced by the co-agonistic PAMs.
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30
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Lind S, Holdfeldt A, Mårtensson J, Granberg KL, Forsman H, Dahlgren C. Multiple ligand recognition sites in free fatty acid receptor 2 (FFA2R) direct distinct neutrophil activation patterns. Biochem Pharmacol 2021; 193:114762. [PMID: 34499871 DOI: 10.1016/j.bcp.2021.114762] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 12/13/2022]
Abstract
The allosteric modulating free fatty acid receptor 2 ligands Cmp58 and AZ1729, increased the activity induced by orthosteric receptor agonists mediating a rise in intracellular calcium ions and activation of the neutrophil NADPH-oxidase. Together, the two modulators triggered an orthosteric-agonist-independent activation of the oxidase without any rise in the concentration of intracellular calcium ions. In this study, structurally diverse compounds presumed to be ligands for free fatty acid receptor 2 were used to gain additional insights into receptor-modulation/signaling. We identified two molecules that activate neutrophils on their own and we classified one as allosteric agonist and the other as orthosteric agonist. Ten compounds were classified as allosteric FFA2R modulators. Of these, one activated neutrophils when combined with AZ1729; the nine remaining compounds activated neutrophils solely when combined with Cmp58. The activation signals were primarily biased when stimulated by two allosteric modulators interacting with different binding sites, such that two complementary modulators together triggered an activation of the NADPH-oxidase but no increase in the intracellular concentration of calcium ions. No neutrophil activation was induced when allosteric receptor modulators suggested to be recognized by the same binding site were combined, results in agreement with our proposed model for activation, in which the receptor has two different sites that selectively bind allosteric modulators. The down-stream signaling mediated by cross-sensitizing allosteric receptor modulators, occurring independent of any orthosteric agonist, represent a new mechanism for activation of the neutrophil NADPH oxidase.
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Affiliation(s)
- Simon Lind
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - André Holdfeldt
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Jonas Mårtensson
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Sweden; Unit of Rheumatology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Kenneth L Granberg
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Huamei Forsman
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Claes Dahlgren
- Department of Rheumatology and Inflammation Research, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Sweden.
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31
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Sharma S, Checco JW. Evaluating functional ligand-GPCR interactions in cell-based assays. Methods Cell Biol 2021; 166:15-42. [PMID: 34752330 DOI: 10.1016/bs.mcb.2021.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
G protein-coupled receptors (GPCRs) are a family of transmembrane proteins that act as major mediators of cellular signaling, and are the primary targets for a large portion of clinical therapeutics. Despite their critical role in biology and medicine, a large number of GPCRs are poorly understood, lacking validated ligands or potent synthetic modulators. Ligand-induced GPCR activation can be measured in cell-based assays to test hypotheses about ligand-receptor interactions or to evaluate efficacy of synthetic agonists or antagonists. However, the techniques necessary to develop and implement a cell-based assay to study a given receptor of interest are not commonplace in all laboratories. This chapter outlines methods to develop a cell-based assay to evaluate agonist-induced activation for a GPCR of interest, which can be useful to evaluate the effectiveness of predicted ligands. Examples of sample preparation protocols and data analysis are provided to help researchers from interdisciplinary fields, especially those in fields with relatively little molecular biology or cell culture experience.
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Affiliation(s)
- Sheryl Sharma
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States
| | - James W Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, United States; The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, United States.
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32
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Cai T, Lim H, Abbu KA, Qiu Y, Nussinov R, Xie L. MSA-Regularized Protein Sequence Transformer toward Predicting Genome-Wide Chemical-Protein Interactions: Application to GPCRome Deorphanization. J Chem Inf Model 2021; 61:1570-1582. [PMID: 33757283 PMCID: PMC8154251 DOI: 10.1021/acs.jcim.0c01285] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Indexed: 01/14/2023]
Abstract
Small molecules play a critical role in modulating biological systems. Knowledge of chemical-protein interactions helps address fundamental and practical questions in biology and medicine. However, with the rapid emergence of newly sequenced genes, the endogenous or surrogate ligands of a vast number of proteins remain unknown. Homology modeling and machine learning are two major methods for assigning new ligands to a protein but mostly fail when sequence homology between an unannotated protein and those with known functions or structures is low. In this study, we develop a new deep learning framework to predict chemical binding to evolutionary divergent unannotated proteins, whose ligand cannot be reliably predicted by existing methods. By incorporating evolutionary information into self-supervised learning of unlabeled protein sequences, we develop a novel method, distilled sequence alignment embedding (DISAE), for the protein sequence representation. DISAE can utilize all protein sequences and their multiple sequence alignment (MSA) to capture functional relationships between proteins without the knowledge of their structure and function. Followed by the DISAE pretraining, we devise a module-based fine-tuning strategy for the supervised learning of chemical-protein interactions. In the benchmark studies, DISAE significantly improves the generalizability of machine learning models and outperforms the state-of-the-art methods by a large margin. Comprehensive ablation studies suggest that the use of MSA, sequence distillation, and triplet pretraining critically contributes to the success of DISAE. The interpretability analysis of DISAE suggests that it learns biologically meaningful information. We further use DISAE to assign ligands to human orphan G-protein coupled receptors (GPCRs) and to cluster the human GPCRome by integrating their phylogenetic and ligand relationships. The promising results of DISAE open an avenue for exploring the chemical landscape of entire sequenced genomes.
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Affiliation(s)
- Tian Cai
- Ph.D.
Program in Computer Science, The Graduate Center, The City University of New York, New York, New York 10016, United States
| | - Hansaim Lim
- Ph.D.
Program in Biochemistry, The Graduate Center, The City University of New York, New York, New York 10016, United States
| | - Kyra Alyssa Abbu
- Department
of Computer Science, Hunter College, The
City University of New York, New York, New York 10065, United States
| | - Yue Qiu
- Ph.D.
Program in Biology, The Graduate Center, The City University of New York, New York, New York 10016, United States
| | - Ruth Nussinov
- Computational
Structural Biology Section, Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21702, United States
- Department
of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Lei Xie
- Ph.D.
Program in Computer Science, The Graduate Center, The City University of New York, New York, New York 10016, United States
- Ph.D.
Program in Biochemistry, The Graduate Center, The City University of New York, New York, New York 10016, United States
- Department
of Computer Science, Hunter College, The
City University of New York, New York, New York 10065, United States
- Ph.D.
Program in Biology, The Graduate Center, The City University of New York, New York, New York 10016, United States
- Helen
and Robert Appel Alzheimer’s Disease Research Institute, Feil
Family Brain & Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, New York 10021, United States
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33
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GPR182 is an endothelium-specific atypical chemokine receptor that maintains hematopoietic stem cell homeostasis. Proc Natl Acad Sci U S A 2021; 118:2021596118. [PMID: 33875597 PMCID: PMC8092405 DOI: 10.1073/pnas.2021596118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
G protein–coupled receptors (GPCRs) are important regulators of cellular and biological functions and are primary targets of therapeutic drugs. About 100 mammalian GPCRs are still considered orphan receptors because they lack a known endogenous ligand. We report the deorphanization of GPR182, which is expressed in endothelial cells of the microvasculature. We show that GPR182 is an atypical chemokine receptor, which binds CXCL10, 12, and 13. However, binding does not induce downstream signaling. Consistent with a scavenging function of GPR182, mice lacking GPR182 have increased plasma levels of chemokines. In line with the crucial role of CXCL12 in hematopoietic stem cell homeostasis, we found that loss of GPR182 results in increased egress of hematopoietic stem cells from the bone marrow. G protein–coupled receptor 182 (GPR182) has been shown to be expressed in endothelial cells; however, its ligand and physiological role has remained elusive. We found GPR182 to be expressed in microvascular and lymphatic endothelial cells of most organs and to bind with nanomolar affinity the chemokines CXCL10, CXCL12, and CXCL13. In contrast to conventional chemokine receptors, binding of chemokines to GPR182 did not induce typical downstream signaling processes, including Gq- and Gi-mediated signaling or β-arrestin recruitment. GPR182 showed relatively high constitutive activity in regard to β-arrestin recruitment and rapidly internalized in a ligand-independent manner. In constitutive GPR182-deficient mice, as well as after induced endothelium-specific loss of GPR182, we found significant increases in the plasma levels of CXCL10, CXCL12, and CXCL13. Global and induced endothelium-specific GPR182-deficient mice showed a significant decrease in hematopoietic stem cells in the bone marrow as well as increased colony-forming units of hematopoietic progenitors in the blood and the spleen. Our data show that GPR182 is a new atypical chemokine receptor for CXCL10, CXCL12, and CXCL13, which is involved in the regulation of hematopoietic stem cell homeostasis.
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34
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Nakagawa Y, Matsui T, Konno R, Kawashima Y, Sato T, Itakura M, Kodera Y. A highly efficient method for extracting peptides from a single mouse hypothalamus. Biochem Biophys Res Commun 2021; 548:155-160. [PMID: 33640609 DOI: 10.1016/j.bbrc.2021.02.041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 02/09/2021] [Indexed: 01/13/2023]
Abstract
Living organisms contain a variety of endogenous peptides that function as significant regulators of many biological processes. Endogenous peptides are typically analyzed using liquid chromatography-mass spectrometry (LC-MS). However, due to the low efficiency of peptide extraction and low abundance of peptides in a single animal, LC-MS-based peptidomics studies have not facilitated an understanding of the individual differences and tissue specificity of peptide abundance. In this study, we developed a peptide extraction method followed by nano-flow LC-MS/MS analysis. This method enabled highly efficient and reproducible peptide extraction from sub-milligram quantities of hypothalamus dissected from a single animal. Diverse bioactive and authentic peptides were detected from a sample volume equivalent to 135 μg of hypothalamus. This method may be useful for elucidating individual differences and tissue specificity, as well as for facilitating the discovery of novel bioactive peptides and biomarkers and developing peptide therapeutics.
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Affiliation(s)
- Yuzuru Nakagawa
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Takashi Matsui
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan; Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Ryo Konno
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, 2-5-23 Kazusa-kamatari, Kisarazu, Chiba, 292-0818, Japan
| | - Toshiya Sato
- Department of Laboratory Animal Science, School of Medicine, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan; Center for Genetic Studies of Integrated Biological Functions, School of Medicine, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Makoto Itakura
- Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan; Department of Biochemistry, School of Medicine, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Yoshio Kodera
- Department of Physics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan; Center for Disease Proteomics, School of Science, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan.
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35
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Abid MSR, Mousavi S, Checco JW. Identifying Receptors for Neuropeptides and Peptide Hormones: Challenges and Recent Progress. ACS Chem Biol 2021; 16:251-263. [PMID: 33539706 DOI: 10.1021/acschembio.0c00950] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intercellular signaling events mediated by neuropeptides and peptide hormones represent important targets for both basic science and drug discovery. For many bioactive peptides, the protein receptors that transmit information across the receiving cell membrane are not known, severely limiting these signaling pathways as potential therapeutic targets. Identifying the receptor(s) for a given peptide of interest is complicated by several factors. Most notably, cell-cell signaling peptides are generated through dynamic biosynthetic pathways, can act on many different families of receptor proteins, and can participate in complex ligand-receptor interactions that extend beyond a simple one-to-one archetype. Here, we discuss recent methodological advances to identify signaling partners for bioactive peptides. Recent efforts have centered on methods to identify candidate receptors via transcript expression, methods to match peptide-receptor pairs through high throughput screening, and methods to capture direct ligand-receptor interactions using chemical probes. Future applications of the receptor identification approaches discussed here, as well as technical advancements to address their limitations, promise to lead to a greater understanding of how cells communicate to deliver complex physiologies. Importantly, such advancements will likely provide novel targets for the treatment of human diseases within the central nervous and endocrine systems.
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Affiliation(s)
- Md Shadman Ridwan Abid
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Somayeh Mousavi
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - James W. Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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36
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Calebiro D, Koszegi Z, Lanoiselée Y, Miljus T, O'Brien S. G protein-coupled receptor-G protein interactions: a single-molecule perspective. Physiol Rev 2020; 101:857-906. [PMID: 33331229 DOI: 10.1152/physrev.00021.2020] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) regulate many cellular and physiological processes, responding to a diverse range of extracellular stimuli including hormones, neurotransmitters, odorants, and light. Decades of biochemical and pharmacological studies have provided fundamental insights into the mechanisms of GPCR signaling. Thanks to recent advances in structural biology, we now possess an atomistic understanding of receptor activation and G protein coupling. However, how GPCRs and G proteins interact in living cells to confer signaling efficiency and specificity remains insufficiently understood. The development of advanced optical methods, including single-molecule microscopy, has provided the means to study receptors and G proteins in living cells with unprecedented spatio-temporal resolution. The results of these studies reveal an unexpected level of complexity, whereby GPCRs undergo transient interactions among themselves as well as with G proteins and structural elements of the plasma membrane to form short-lived signaling nanodomains that likely confer both rapidity and specificity to GPCR signaling. These findings may provide new strategies to pharmaceutically modulate GPCR function, which might eventually pave the way to innovative drugs for common diseases such as diabetes or heart failure.
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Affiliation(s)
- Davide Calebiro
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Zsombor Koszegi
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Yann Lanoiselée
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Tamara Miljus
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Shannon O'Brien
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
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37
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Zhang L, Song J, Zang Z, Tang H, Li W, Lai S, Deng C. Adaptive evolution of GPR39 in diverse directions in vertebrates. Gen Comp Endocrinol 2020; 299:113610. [PMID: 32916170 DOI: 10.1016/j.ygcen.2020.113610] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/27/2020] [Accepted: 08/30/2020] [Indexed: 02/08/2023]
Abstract
G protein-coupled receptors (GPCRs) play an important role in physiology and disease and represent productive drug targets. Orphan GPCRs, which have unknown endogenous ligands, are considered drug targets and consequently have attracted great interest in identifying their endogenous cognate ligands for deorphanization. However, additional studies have shown that GPCRs, including many orphan GPCRs, can constitutively activate G protein signaling in a ligand-independent manner. GPR39 is such an orphan GPCR with constitutive activity. Here, we performed a phylogenetic and selection analysis of GPR39 in vertebrates, and we found that GPR39 underwent positive selection in different branches of vertebrates. Using luciferase reporter assays, we demonstrated that human, frog and chicken GPR39 can constitutively activate Gq and G12 signaling pathways in a ligand-independent manner. Zebrafish GPR39 can constitutively activate Gs, Gq and G12 signaling pathways in a ligand-independent manner. We further found that the zebrafish-H2967.35 site is crucial for the activity of the Gs signaling pathway. In addition, our mutagenesis studies indicated that the positive selection sites of GPR39 from different species had important effects on the constitutive activity of the receptor. Our results revealed the adaptive evolution of GPR39 in diverse directions, which led to differences in constitutive activity.
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Affiliation(s)
- Lina Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jingjing Song
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Zhuqing Zang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Huihao Tang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Wei Li
- Department of Dermatovenereology, Rare Disease Center, West China Hospital, Sichuan University, No. 37 Guo Xue Xiang Street, Chengdu, Sichuan 610041, China
| | - Shanshan Lai
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - Cheng Deng
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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38
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Dragano NR, Monfort-Pires M, Velloso LA. Mechanisms Mediating the Actions of Fatty Acids in the Hypothalamus. Neuroscience 2020; 447:15-27. [DOI: 10.1016/j.neuroscience.2019.10.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 10/02/2019] [Accepted: 10/03/2019] [Indexed: 12/12/2022]
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39
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Nielsen CDT, Dhasmana D, Floresta G, Wohland T, Cilibrizzi A. Illuminating the Path to Target GPCR Structures and Functions. Biochemistry 2020; 59:3783-3795. [PMID: 32956586 DOI: 10.1021/acs.biochem.0c00606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
G-Protein-coupled receptors (GPCRs) are ubiquitous within eukaryotes, responsible for a wide array of physiological and pathological processes. Indeed, the fact that they are the most drugged target in the human genome is indicative of their importance. Despite the clear interest in GPCRs, most information regarding their activity has been so far obtained by analyzing the response from a "bulk medium". As such, this Perspective summarizes some of the common methods for this indirect observation. Nonetheless, by inspecting approaches applying super-resolution imaging, we argue that imaging is perfectly situated to obtain more detailed structural and spatial information, assisting in the development of new GPCR-targeted drugs and clinical strategies. The benefits of direct optical visualization of GPCRs are analyzed in the context of potential future directions in the field.
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Affiliation(s)
- Christian D-T Nielsen
- Imperial College London, White City Campus, Molecular Sciences Research Hub, 80 Wood Lane, London W12 0BZ, U.K
| | - Divya Dhasmana
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543
| | - Giuseppe Floresta
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
| | - Thorsten Wohland
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543.,Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Agostino Cilibrizzi
- Institute of Pharmaceutical Science, King's College London, London SE1 9NH, U.K
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40
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Mair GR, Halton DW, Maule AG. The neuromuscular system of the sheep tapeworm Moniezia expansa. INVERTEBRATE NEUROSCIENCE 2020; 20:17. [PMID: 32978688 DOI: 10.1007/s10158-020-00246-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/05/2020] [Indexed: 01/06/2023]
Abstract
Cestodes are common gastrointestinal parasites of humans and livestock. They attach to the host gut and, without a mouth or intestinal system, absorb nutrients through their epidermis. Here we show that despite this simplified anatomy and sessile lifestyle, they maintain a complex neuromuscular system. We used fluorescently labelled phalloidin as a specific probe for filamentous actin to define the overall organisation of several distinct muscle systems in the cyclophyllidean Moniezia expansa. Like all flatworms, the body wall musculature below the neodermis of this intestinal parasite of sheep is characterised by outer circular and inner longitudinal muscle fibres. Diagonal fibres, typically found in free-living and trematode platyhelminths, on the other hand, are notably absent. Prominent longitudinal sheaths dominate the parenchyma and provide retractor muscles to the four acetabula in the scolex; they attach at the bottom of each cup-shaped holdfast. Within sexually mature proglottids, circular fibres dominate the duct walls of the male and female reproductive systems. Nerve cells and fibres that express serotonin or neuropeptide F supply well-developed innervation to several of the described muscle systems: emanating from the central nervous system, fibres in the periphery develop pervasive nerve nets that anastomose within body wall musculature as well as the parenchymal longitudinal and oblique muscle fibres, and innervate the sexual organs and gonopore in mature proglottids. Using homology searches, we provide evidence for 20 neuropeptide precursors together with four prepropeptide processing enzymes as well as several 5-HT signalling components to be represented in the Moniezia transcriptome.
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Affiliation(s)
- Gunnar R Mair
- Biomedical Sciences, Iowa State University, 1800 Christensen Drive, 2008 Vet Med, Ames, IA, 50011-1134, USA.
| | - David W Halton
- School of Biological Sciences, Queen's University of Belfast, Belfast, BT9 5DL, UK
| | - Aaron G Maule
- School of Biological Sciences, Queen's University of Belfast, Belfast, BT9 5DL, UK
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41
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GPR101 drives growth hormone hypersecretion and gigantism in mice via constitutive activation of G s and G q/11. Nat Commun 2020; 11:4752. [PMID: 32958754 PMCID: PMC7506554 DOI: 10.1038/s41467-020-18500-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 08/25/2020] [Indexed: 12/16/2022] Open
Abstract
Growth hormone (GH) is a key modulator of growth and GH over-secretion can lead to gigantism. One form is X-linked acrogigantism (X-LAG), in which infants develop GH-secreting pituitary tumors over-expressing the orphan G-protein coupled receptor, GPR101. The role of GPR101 in GH secretion remains obscure. We studied GPR101 signaling pathways and their effects in HEK293 and rat pituitary GH3 cell lines, human tumors and in transgenic mice with elevated somatotrope Gpr101 expression driven by the rat Ghrhr promoter (GhrhrGpr101). Here, we report that Gpr101 causes elevated GH/prolactin secretion in transgenic GhrhrGpr101 mice but without hyperplasia/tumorigenesis. We show that GPR101 constitutively activates not only Gs, but also Gq/11 and G12/13, which leads to GH secretion but not proliferation. These signatures of GPR101 signaling, notably PKC activation, are also present in human pituitary tumors with high GPR101 expression. These results underline a role for GPR101 in the regulation of somatotrope axis function.
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42
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Steinbrenner AD. The evolving landscape of cell surface pattern recognition across plant immune networks. CURRENT OPINION IN PLANT BIOLOGY 2020; 56:135-146. [PMID: 32615401 DOI: 10.1016/j.pbi.2020.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 06/11/2023]
Abstract
To recognize diverse threats, plants monitor extracellular molecular patterns and transduce intracellular immune signaling through receptor complexes at the plasma membrane. Pattern recognition occurs through a prototypical network of interacting proteins, comprising A) receptors that recognize inputs associated with a growing number of pest and pathogen classes (bacteria, fungi, oomycetes, caterpillars), B) co-receptor kinases that participate in binding and signaling, and C) cytoplasmic kinases that mediate first stages of immune output. While this framework has been elucidated in reference accessions of model organisms, network components are part of gene families with widespread variation, potentially tuning immunocompetence for specific contexts. Most dramatically, variation in receptor repertoires determines the range of ligands acting as immunogenic inputs for a given plant. Diversification of receptor kinase (RK) and related receptor-like protein (RLP) repertoires may tune responses even within a species. Comparative genomics at pangenome scale will reveal patterns and features of immune network variation.
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Affiliation(s)
- Adam D Steinbrenner
- Department of Biology, University of Washington, Seattle WA 98195, USA; Washington Research Foundation, Seattle, WA 98102, USA.
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43
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Advances in G protein-coupled receptor high-throughput screening. Curr Opin Biotechnol 2020; 64:210-217. [PMID: 32653805 DOI: 10.1016/j.copbio.2020.06.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 02/08/2023]
Abstract
G protein-coupled receptors (GPCRs) detect compounds on the cell surface and are the starting point of a number of medically relevant signaling cascades. Indeed, over 30% of FDA approved drugs target GPCRs, making them a primary target for drug discovery. Computational and experimental high-throughput screening (HTS) approaches of clinically relevant GPCRs are a first-line drug discovery effort in biomedical research. In this opinion, we review recent advances in GPCR HTS. We focus primarily on cell-based assays, and highlight recent advances in in vitro assays using purified receptors, and computational approaches for GPCR HTS. To date, GPCR HTS has led to the identification of new and repurposing of existing drugs, and the deorphanization of GPCRs with unknown ligands. As automation equipment becomes more common, GPCR HTS will move beyond a drug discovery tool to a key technology to probe basic biological processes that will have an outsized impact on personalized medicine.
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Meyrath M, Reynders N, Uchański T, Chevigné A, Szpakowska M. Systematic reassessment of chemokine-receptor pairings confirms CCL20 but not CXCL13 and extends the spectrum of ACKR4 agonists to CCL22. J Leukoc Biol 2020; 109:373-376. [PMID: 32480426 DOI: 10.1002/jlb.2ab0520-275r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/08/2020] [Accepted: 05/10/2020] [Indexed: 12/16/2022] Open
Abstract
Atypical chemokine receptors (ACKRs) have emerged as important regulators or scavengers of homeostatic and inflammatory chemokines. Among these atypical receptors, ACKR4 is reported to bind the homeostatic chemokines CCL19, CCL21, CCL25 and CXCL13. In a recent study by Matti et al., the authors show that ACKR4 is also a receptor for CCL20, previously established to bind to CCR6 only. They provide convincing evidence that, just as for its other chemokine ligands, ACKR4 rapidly internalizes CCL20 both in vitro and in vivo. Independently of this discovery, we undertook a screening program aiming at reassessing the activity of the 43 human chemokines toward ACKR4 using a highly sensitive β-arrestin recruitment assay. This systematic analysis confirmed CCL20 as a new agonist ligand for ACKR4 in addition to CCL19, CCL21, and CCL25. Furthermore, CCL22, which plays an important role in both homeostasis and inflammatory responses, and is known as a ligand for CCR4 and ACKR2 was found to also act as a potent partial agonist of ACKR4. In contrast, agonist activity of CXCL13 toward ACKR4 was disproved. This independent wide-range systematic study confirms the pairing of CCL20 with ACKR4 newly discovered by Matti and co-authors, and further refines the spectrum of chemokines activating ACKR4.
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Affiliation(s)
- Max Meyrath
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), Esch-sur-Alzette, Luxembourg
| | - Nathan Reynders
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), Esch-sur-Alzette, Luxembourg.,Faculty of Science, Technology and Communication, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Tomasz Uchański
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), Esch-sur-Alzette, Luxembourg
| | - Andy Chevigné
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), Esch-sur-Alzette, Luxembourg
| | - Martyna Szpakowska
- Immuno-Pharmacology and Interactomics, Department of Infection and Immunity, Luxembourg Institute of Health (LIH), Esch-sur-Alzette, Luxembourg
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Foster SR, Hauser AS, Vedel L, Strachan RT, Huang XP, Gavin AC, Shah SD, Nayak AP, Haugaard-Kedström LM, Penn RB, Roth BL, Bräuner-Osborne H, Gloriam DE. Discovery of Human Signaling Systems: Pairing Peptides to G Protein-Coupled Receptors. Cell 2020; 179:895-908.e21. [PMID: 31675498 PMCID: PMC6838683 DOI: 10.1016/j.cell.2019.10.010] [Citation(s) in RCA: 124] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 08/18/2019] [Accepted: 10/08/2019] [Indexed: 01/18/2023]
Abstract
The peptidergic system is the most abundant network of ligand-receptor-mediated signaling in humans. However, the physiological roles remain elusive for numerous peptides and more than 100 G protein-coupled receptors (GPCRs). Here we report the pairing of cognate peptides and receptors. Integrating comparative genomics across 313 species and bioinformatics on all protein sequences and structures of human class A GPCRs, we identify universal characteristics that uncover additional potential peptidergic signaling systems. Using three orthogonal biochemical assays, we pair 17 proposed endogenous ligands with five orphan GPCRs that are associated with diseases, including genetic, neoplastic, nervous and reproductive system disorders. We also identify additional peptides for nine receptors with recognized ligands and pathophysiological roles. This integrated computational and multifaceted experimental approach expands the peptide-GPCR network and opens the way for studies to elucidate the roles of these signaling systems in human physiology and disease. Video Abstract
Universal characteristics enabled prediction of peptide ligands and receptors Multifaceted screening enabled detection of pathway- and assay-dependent responses Peptide ligands discovered for BB3, GPR1, GPR15, GPR55, and GPR68 Each signaling system is a link to human physiology and is associated with disease
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Affiliation(s)
- Simon R Foster
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.
| | - Alexander S Hauser
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.
| | - Line Vedel
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Ryan T Strachan
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Xi-Ping Huang
- Department of Pharmacology, School of Medicine, and the Division of Medicinal Chemistry and Chemical Biology, Eshelman School of Pharmacy, and the NIMH Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ariana C Gavin
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Sushrut D Shah
- Department of Medicine, Center for Translational Medicine and Division of Pulmonary, Allergy and Critical Care Medicine; Jane and Leonard Korman Respiratory Institute, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ajay P Nayak
- Department of Medicine, Center for Translational Medicine and Division of Pulmonary, Allergy and Critical Care Medicine; Jane and Leonard Korman Respiratory Institute, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Linda M Haugaard-Kedström
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Raymond B Penn
- Department of Medicine, Center for Translational Medicine and Division of Pulmonary, Allergy and Critical Care Medicine; Jane and Leonard Korman Respiratory Institute, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Pharmacology, School of Medicine, and the Division of Medicinal Chemistry and Chemical Biology, Eshelman School of Pharmacy, and the NIMH Psychoactive Drug Screening Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hans Bräuner-Osborne
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark.
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Gault J, Liko I, Landreh M, Shutin D, Bolla JR, Jefferies D, Agasid M, Yen HY, Ladds MJGW, Lane DP, Khalid S, Mullen C, Remes PM, Huguet R, McAlister G, Goodwin M, Viner R, Syka JEP, Robinson CV. Combining native and 'omics' mass spectrometry to identify endogenous ligands bound to membrane proteins. Nat Methods 2020; 17:505-508. [PMID: 32371966 PMCID: PMC7332344 DOI: 10.1038/s41592-020-0821-0] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 03/25/2020] [Indexed: 02/08/2023]
Abstract
Ligands bound to protein assemblies provide critical information for function, yet are often difficult to capture and define. Here we develop a top-down method, 'nativeomics', unifying 'omics' (lipidomics, proteomics, metabolomics) analysis with native mass spectrometry to identify ligands bound to membrane protein assemblies. By maintaining the link between proteins and ligands, we define the lipidome/metabolome in contact with membrane porins and a mitochondrial translocator to discover potential regulators of protein function.
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Affiliation(s)
- Joseph Gault
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Idlir Liko
- Department of Chemistry, University of Oxford, Oxford, UK
- OMass Therapeutics, Oxford, UK
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Denis Shutin
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | | | - Mark Agasid
- Department of Chemistry, University of Oxford, Oxford, UK
| | | | - Marcus J G W Ladds
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Syma Khalid
- School of Chemistry, University of Southampton, Southampton, UK
| | | | | | | | | | | | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA, USA
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Ye L, Cao Z, Wang W, Zhou N. New Insights in Cannabinoid Receptor Structure and Signaling. Curr Mol Pharmacol 2020; 12:239-248. [PMID: 30767756 DOI: 10.2174/1874467212666190215112036] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Cannabinoid has long been used for medicinal purposes. Cannabinoid signaling has been considered the therapeutic target for treating pain, addiction, obesity, inflammation, and other diseases. Recent studies have suggested that in addition to CB1 and CB2, there are non-CB1 and non-CB2 cannabinoid-related orphan GPCRs including GPR18, GPR55, and GPR119. In addition, CB1 and CB2 display allosteric binding and biased signaling, revealing correlations between biased signaling and functional outcomes. Interestingly, new investigations have indicated that CB1 is functionally present within the mitochondria of striated and heart muscles directly regulating intramitochondrial signaling and respiration. CONCLUSION In this review, we summarize the recent progress in cannabinoid-related orphan GPCRs, CB1/CB2 structure, Gi/Gs coupling, allosteric ligands and biased signaling, and mitochondria-localized CB1, and discuss the future promise of this research.
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Affiliation(s)
- Lingyan Ye
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, Zhejiang University, Zijingang Campus, Hangzhou, Zhejiang, China
| | - Zheng Cao
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, Zhejiang University, Zijingang Campus, Hangzhou, Zhejiang, China
| | - Weiwei Wang
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, Zhejiang University, Zijingang Campus, Hangzhou, Zhejiang, China
| | - Naiming Zhou
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, Zhejiang University, Zijingang Campus, Hangzhou, Zhejiang, China
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Dong L, Zhang B, Wu L, Shang Z, Liu S, Jiang X, Wang H, Fan L, Zhang Y, Xiao H. Proteomics Analysis of Cellular BRS3 Receptor Activation Reveals Potential Mechanism for Signal Transduction and Cell Proliferation. J Proteome Res 2020; 19:1513-1521. [PMID: 32091899 DOI: 10.1021/acs.jproteome.9b00760] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Bombesin-like receptor 3 (BRS3), an orphan G protein-coupled receptor (GPCR), plays important roles in our biological system while the exact mechanisms behind it are less known. To get insights of the biological effects upon BRS3 activation, we utilized quantitative proteomics approach to explore the dynamic protein profiling during the stimulation by its ligand. At different time points after stimulation with BRS3 surrogate agonist, the protein profiling in BRS3 overexpressed HEK 293 cells BRS3 (HEK 293-BRS3) was analyzed by nano-LC-MS/MS. In total, 1593 cellular proteins were confidently identified and quantified, including 146 proteins dysregulated at multiple time points and 319 proteins only altered at one time point. Data analysis indicated that BRS3 activation could regulate cell death, survival, and protein synthesis, particularly mRNA translation. Key signaling pathways were revealed for BRS3 signal transduction. In particular, 21 of our identified proteins are involved in the rapamycin (mTOR) signaling pathway. The promotion of mTOR was further confirmed through monitoring its indicative targets upon BRS3 activation. Upon the inhibition of mTOR by rapamycin, cell proliferation was dramatically reversed. Our proteomics data collectively demonstrate that BRS3 activation will lead to cascades of signal transduction and promote cell proliferation. The developed strategy might be utilized to discover the roles of other GPCRs and improve our understanding of their unknown functions.
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Affiliation(s)
- Lijie Dong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Baohui Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lehao Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhi Shang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sha Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiaoteng Jiang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liuyin Fan
- Student Innovation Center, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Hauser AS, Gloriam DE, Bräuner‐Osborne H, Foster SR. Novel approaches leading towards peptide GPCR de-orphanisation. Br J Pharmacol 2020; 177:961-968. [PMID: 31863461 PMCID: PMC7042120 DOI: 10.1111/bph.14950] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 11/12/2019] [Accepted: 11/19/2019] [Indexed: 12/12/2022] Open
Abstract
The discovery of novel ligands for orphan GPCRs has profoundly affected our understanding of human biology, opening new opportunities for research, and ultimately for therapeutic development. Accordingly, much effort has been directed towards the remaining orphan receptors, yet the rate of GPCR de-orphanisation has slowed in recent years. Here, we briefly review contemporary methodologies of de-orphanisation and then highlight our recent integrated computational and experimental approach for discovery of novel peptide ligands for orphan GPCRs. We identified putative endogenous peptide ligands and found peptide receptor sequence and structural characteristics present in selected orphan receptors. With comprehensive pharmacological screening using three complementary assays, we discovered novel pairings of 17 peptides with five different orphan GPCRs and revealed potential additional ligands for nine peptide GPCRs. These promising findings lay the foundation for future studies on these peptides and receptors to characterise their roles in human physiology and disease.
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Affiliation(s)
- Alexander S. Hauser
- Department of Drug Design and PharmacologyUniversity of CopenhagenCopenhagenDenmark
| | - David E. Gloriam
- Department of Drug Design and PharmacologyUniversity of CopenhagenCopenhagenDenmark
| | - Hans Bräuner‐Osborne
- Department of Drug Design and PharmacologyUniversity of CopenhagenCopenhagenDenmark
| | - Simon R. Foster
- Department of Drug Design and PharmacologyUniversity of CopenhagenCopenhagenDenmark
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery InstituteMonash UniversityClaytonVICAustralia
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Azam S, Haque ME, Jakaria M, Jo SH, Kim IS, Choi DK. G-Protein-Coupled Receptors in CNS: A Potential Therapeutic Target for Intervention in Neurodegenerative Disorders and Associated Cognitive Deficits. Cells 2020; 9:cells9020506. [PMID: 32102186 PMCID: PMC7072884 DOI: 10.3390/cells9020506] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 12/17/2022] Open
Abstract
Neurodegenerative diseases are a large group of neurological disorders with diverse etiological and pathological phenomena. However, current therapeutics rely mostly on symptomatic relief while failing to target the underlying disease pathobiology. G-protein-coupled receptors (GPCRs) are one of the most frequently targeted receptors for developing novel therapeutics for central nervous system (CNS) disorders. Many currently available antipsychotic therapeutics also act as either antagonists or agonists of different GPCRs. Therefore, GPCR-based drug development is spreading widely to regulate neurodegeneration and associated cognitive deficits through the modulation of canonical and noncanonical signals. Here, GPCRs’ role in the pathophysiology of different neurodegenerative disease progressions and cognitive deficits has been highlighted, and an emphasis has been placed on the current pharmacological developments with GPCRs to provide an insight into a potential therapeutic target in the treatment of neurodegeneration.
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Affiliation(s)
- Shofiul Azam
- Department of Applied Life Science & Integrated Bioscience, Graduate School, Konkuk University, Chungju 27478, Korea; (S.A.); (M.E.H.); (M.J.); (S.-H.J.)
| | - Md. Ezazul Haque
- Department of Applied Life Science & Integrated Bioscience, Graduate School, Konkuk University, Chungju 27478, Korea; (S.A.); (M.E.H.); (M.J.); (S.-H.J.)
| | - Md. Jakaria
- Department of Applied Life Science & Integrated Bioscience, Graduate School, Konkuk University, Chungju 27478, Korea; (S.A.); (M.E.H.); (M.J.); (S.-H.J.)
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Song-Hee Jo
- Department of Applied Life Science & Integrated Bioscience, Graduate School, Konkuk University, Chungju 27478, Korea; (S.A.); (M.E.H.); (M.J.); (S.-H.J.)
| | - In-Su Kim
- Department of Integrated Bioscience & Biotechnology, College of Biomedical and Health Science, and Research Institute of Inflammatory Disease (RID), Konkuk University, Chungju 27478, Korea
- Correspondence: (I.-S.K.); (D.-K.C.); Tel.: +82-010-3876-4773 (I.-S.K.); +82-43-840-3610 (D.-K.C.); Fax: +82-43-840-3872 (D.-K.C.)
| | - Dong-Kug Choi
- Department of Applied Life Science & Integrated Bioscience, Graduate School, Konkuk University, Chungju 27478, Korea; (S.A.); (M.E.H.); (M.J.); (S.-H.J.)
- Department of Integrated Bioscience & Biotechnology, College of Biomedical and Health Science, and Research Institute of Inflammatory Disease (RID), Konkuk University, Chungju 27478, Korea
- Correspondence: (I.-S.K.); (D.-K.C.); Tel.: +82-010-3876-4773 (I.-S.K.); +82-43-840-3610 (D.-K.C.); Fax: +82-43-840-3872 (D.-K.C.)
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