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López-Sánchez U, Munro LJ, Ladefoged LK, Pedersen AJ, Brun CC, Lyngby SM, Baud D, Juillan-Binard C, Pedersen MG, Lummis SCR, Bang-Andersen B, Schiøtt B, Chipot C, Schoehn G, Neyton J, Dehez F, Nury H, Kristensen AS. Structural determinants for activity of the antidepressant vortioxetine at human and rodent 5-HT 3 receptors. Nat Struct Mol Biol 2024; 31:1232-1242. [PMID: 38698207 DOI: 10.1038/s41594-024-01282-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/19/2024] [Indexed: 05/05/2024]
Abstract
Vortioxetine (VTX) is a recently approved antidepressant that targets a variety of serotonin receptors. Here, we investigate the drug's molecular mechanism of operation at the serotonin 5-HT3 receptor (5-HT3R), which features two properties: VTX acts differently on rodent and human 5-HT3R, and VTX appears to suppress any subsequent response to agonists. Using a combination of cryo-EM, electrophysiology, voltage-clamp fluorometry and molecular dynamics, we show that VTX stabilizes a resting inhibited state of the mouse 5-HT3R and an agonist-bound-like state of human 5-HT3R, in line with the functional profile of the drug. We report four human 5-HT3R structures and show that the human receptor transmembrane domain is intrinsically fragile. We also explain the lack of recovery after VTX administration via a membrane partition mechanism.
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Affiliation(s)
- Uriel López-Sánchez
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Lachlan Jake Munro
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | | | - Anders Juel Pedersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Christian Colding Brun
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Signe Meisner Lyngby
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Delphine Baud
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | | | - Sarah C R Lummis
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Christophe Chipot
- Université de Lorraine, CNRS, LPCT, Nancy, France
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Guy Schoehn
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Jacques Neyton
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Francois Dehez
- Université de Lorraine, CNRS, LPCT, Nancy, France
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France
| | - Hugues Nury
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.
| | - Anders S Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
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2
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Peverini L, Shi S, Medjebeur K, Corringer PJ. Mapping the molecular motions of 5-HT 3 serotonin-gated channel by voltage-clamp fluorometry. eLife 2024; 12:RP93174. [PMID: 38913422 PMCID: PMC11196107 DOI: 10.7554/elife.93174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024] Open
Abstract
The serotonin-gated ion channel (5-HT3R) mediates excitatory neuronal communication in the gut and the brain. It is the target for setrons, a class of competitive antagonists widely used as antiemetics, and is involved in several neurological diseases. Cryo-electron microscopy (cryo-EM) of the 5-HT3R in complex with serotonin or setrons revealed that the protein has access to a wide conformational landscape. However, assigning known high-resolution structures to actual states contributing to the physiological response remains a challenge. In the present study, we used voltage-clamp fluorometry (VCF) to measure simultaneously, for 5-HT3R expressed at a cell membrane, conformational changes by fluorescence and channel opening by electrophysiology. Four positions identified by mutational screening report motions around and outside the serotonin-binding site through incorporation of cysteine-tethered rhodamine dyes with or without a nearby quenching tryptophan. VCF recordings show that the 5-HT3R has access to four families of conformations endowed with distinct fluorescence signatures: 'resting-like' without ligand, 'inhibited-like' with setrons, 'pre-active-like' with partial agonists, and 'active-like' (open channel) with partial and strong agonists. Data are remarkably consistent with cryo-EM structures, the fluorescence partners matching respectively apo, setron-bound, 5-HT bound-closed, and 5-HT-bound-open conformations. Data show that strong agonists promote a concerted motion of all fluorescently labeled sensors during activation, while partial agonists, especially when loss-of-function mutations are engineered, stabilize both active and pre-active conformations. In conclusion, VCF, though the monitoring of electrophysiologically silent conformational changes, illuminates allosteric mechanisms contributing to signal transduction and their differential regulation by important classes of physiological and clinical effectors.
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Affiliation(s)
- Laurie Peverini
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Channel-Receptors UnitParisFrance
| | - Sophie Shi
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Channel-Receptors UnitParisFrance
| | - Karima Medjebeur
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Channel-Receptors UnitParisFrance
| | - Pierre-Jean Corringer
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Channel-Receptors UnitParisFrance
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3
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Illumination of a progressive allosteric mechanism mediating the glycine receptor activation. Nat Commun 2023; 14:795. [PMID: 36781912 PMCID: PMC9925812 DOI: 10.1038/s41467-023-36471-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 02/02/2023] [Indexed: 02/15/2023] Open
Abstract
Pentameric ligand-gated ion channel mediate signal transduction at chemical synapses by transiting between resting and open states upon neurotransmitter binding. Here, we investigate the gating mechanism of the glycine receptor fluorescently labeled at the extracellular-transmembrane interface by voltage-clamp fluorometry (VCF). Fluorescence reports a glycine-elicited conformational change that precedes pore opening. Low concentrations of glycine, partial agonists or specific mixtures of glycine and strychnine trigger the full fluorescence signal while weakly activating the channel. Molecular dynamic simulations of a partial agonist bound-closed Cryo-EM structure show a highly dynamic nature: a marked structural flexibility at both the extracellular-transmembrane interface and the orthosteric site, generating docking properties that recapitulate VCF data. This work illuminates a progressive propagating transition towards channel opening, highlighting structural plasticity within the mechanism of action of allosteric effectors.
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4
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Petroff JT, Dietzen NM, Santiago-McRae E, Deng B, Washington MS, Chen LJ, Trent Moreland K, Deng Z, Rau M, Fitzpatrick JAJ, Yuan P, Joseph TT, Hénin J, Brannigan G, Cheng WWL. Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Nat Commun 2022; 13:7017. [PMID: 36385237 PMCID: PMC9668969 DOI: 10.1038/s41467-022-34813-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 11/08/2022] [Indexed: 11/18/2022] Open
Abstract
Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are sensitive to their lipid environment. The mechanism of phospholipid modulation of any pLGIC is not well understood. We demonstrate that the model pLGIC, ELIC (Erwinia ligand-gated ion channel), is positively modulated by the anionic phospholipid, phosphatidylglycerol, from the outer leaflet of the membrane. To explore the mechanism of phosphatidylglycerol modulation, we determine a structure of ELIC in an open-channel conformation. The structure shows a bound phospholipid in an outer leaflet site, and structural changes in the phospholipid binding site unique to the open-channel. In combination with streamlined alchemical free energy perturbation calculations and functional measurements in asymmetric liposomes, the data support a mechanism by which an anionic phospholipid stabilizes the activated, open-channel state of a pLGIC by specific, state-dependent binding to this site.
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Affiliation(s)
- John T Petroff
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Noah M Dietzen
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Ezry Santiago-McRae
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
| | - Brett Deng
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Maya S Washington
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Lawrence J Chen
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - K Trent Moreland
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Zengqin Deng
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
| | - Michael Rau
- Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, USA
| | - James A J Fitzpatrick
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for Cellular Imaging, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Biomedical Engineering, Washington University School of Medicine, Saint Louis, MO, USA
| | - Peng Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO, USA
- Center for the Investigation of Membrane Excitability Diseases, Washington University School of Medicine, Saint Louis, MO, USA
| | - Thomas T Joseph
- Department of Anesthesiology and Critical Care, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jérôme Hénin
- Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Université Paris Cité, CNRS UPR 9080, Paris, France
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, USA
- Department of Physics, Rutgers University, Camden, NJ, USA
| | - Wayland W L Cheng
- Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.
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Noviello CM, Kreye J, Teng J, Prüss H, Hibbs RE. Structural mechanisms of GABA A receptor autoimmune encephalitis. Cell 2022; 185:2469-2477.e13. [PMID: 35803245 DOI: 10.1016/j.cell.2022.06.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 04/22/2022] [Accepted: 06/13/2022] [Indexed: 11/26/2022]
Abstract
Autoantibodies targeting neuronal membrane proteins can cause encephalitis, seizures, and severe behavioral abnormalities. While antibodies for several neuronal targets have been identified, structural details on how they regulate function are unknown. Here we determined cryo-electron microscopy structures of antibodies derived from an encephalitis patient bound to the γ-aminobutyric acid type A (GABAA) receptor. These antibodies induced severe encephalitis by directly inhibiting GABAA function, resulting in nervous-system hyperexcitability. The structures reveal mechanisms of GABAA inhibition and pathology. One antibody directly competes with a neurotransmitter and locks the receptor in a resting-like state. The second antibody targets the subunit interface involved in binding benzodiazepines and antagonizes diazepam potentiation. We identify key residues in these antibodies involved in specificity and affinity and confirm structure-based hypotheses for functional effects using electrophysiology. Together these studies define mechanisms of direct functional antagonism of neurotransmission underlying autoimmune encephalitis in a human patient.
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Affiliation(s)
- Colleen M Noviello
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jakob Kreye
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany; Department of Pediatric Neurology and Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Jinfeng Teng
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Harald Prüss
- German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany; Department of Neurology and Experimental Neurology, Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Ryan E Hibbs
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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