1
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Hovah ME, Holzgrabe U. Bivalent and bitopic ligands of the opioid receptors: The prospects of a dual approach. Med Res Rev 2024; 44:2545-2599. [PMID: 38751227 DOI: 10.1002/med.22050] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 04/09/2024] [Accepted: 05/05/2024] [Indexed: 10/05/2024]
Abstract
Opioid receptors belonging to the class A G-protein coupled receptors (GPCRs) are the targets of choice in the treatment of acute and chronic pain. However, their on-target side effects such as respiratory depression, tolerance and addiction have led to the advent of the 'opioid crisis'. In the search for safer analgesics, bivalent and more recently, bitopic ligands have emerged as valuable tool compounds to probe these receptors. The activity of bivalent and bitopic ligands rely greatly on the allosteric nature of the GPCRs. Bivalent ligands consist of two pharmacophores, each binding to the individual orthosteric binding site (OBS) of the monomers within a dimer. Bitopic or dualsteric ligands bridge the gap between the OBS and the spatially distinct, less conserved allosteric binding site (ABS) through the simultaneous occupation of these two sites. Bivalent and bitopic ligands stabilize distinct conformations of the receptors which ultimately translates into unique signalling and pharmacological profiles. Some of the interesting properties shown by these ligands include improved affinity and/or efficacy, subtype and/or functional selectivity and reduced side effects. This review aims at providing an overview of some of the bivalent and bitopic ligands of the opioid receptors and, their pharmacology in the hope of inspiring the design and discovery of the next generation of opioid analgesics.
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Affiliation(s)
- Marie Emilie Hovah
- Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, Wuerzburg, Germany
| | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, Wuerzburg, Germany
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2
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Wu Z, Sun X, Su J, Zhang X, Hu J, Li C. Revealing the graded activation mechanism of neurotensin receptor 1. Int J Biol Macromol 2024; 278:134488. [PMID: 39111461 DOI: 10.1016/j.ijbiomac.2024.134488] [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: 04/17/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 08/16/2024]
Abstract
Graded activation contributes to the precise regulation of GPCR activity, presenting new opportunities for drug design. In this work, a total of 10 μs enhanced-sampling simulations are performed to provide molecular insights into the binding dynamics differences of the neurotensin receptor 1 (NTSR1) to the full agonist SRI-9829, partial agonist RTI-3a and inverse agonist SR48692. The possible graded activation mechanism of NTSR1 is revealed by an integrated analysis utilizing the reweighted potential of mean force (PMF), deep learning (DL) and transfer entropy (TE). Specifically, the orthosteric pocket is observed to undergo expansion and contraction, with the G-protein-binding site experiencing interconversions among the inactive, intermediate and active-like states. Detailed structural comparisons capture subtle conformational differences arising from ligand binding in allosteric signaling, which can well explain the graded activation. Critical microswitches that contribute to graded activation are efficiently identified with the DL model. TE calculations enable the visualization of allosteric communication networks within the receptor, elucidating the driver-responder relationships associated with signal transduction. Fortunately, the dissociation of the full agonist from the orthosteric pocket is observed. The current findings systematically reveal the mechanism of NTSR1 graded activation, and also provide implications for structure-based drug design.
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Affiliation(s)
- Zhixiang Wu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Xiaohan Sun
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Jingjie Su
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Xinyu Zhang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China.
| | - Chunhua Li
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China.
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3
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Ertl F, Kopanchuk S, Dijon NC, Veikšina S, Tahk MJ, Laasfeld T, Schettler F, Gattor AO, Hübner H, Archipowa N, Köckenberger J, Heinrich MR, Gmeiner P, Kutta RJ, Holliday ND, Rinken A, Keller M. Dually Labeled Neurotensin NTS 1R Ligands for Probing Radiochemical and Fluorescence-Based Binding Assays. J Med Chem 2024; 67:16664-16691. [PMID: 39261089 PMCID: PMC11440508 DOI: 10.1021/acs.jmedchem.4c01470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/21/2024] [Accepted: 09/02/2024] [Indexed: 09/13/2024]
Abstract
The determination of ligand-receptor binding affinities plays a key role in the development process of pharmaceuticals. While the classical radiochemical binding assay uses radioligands, fluorescence-based binding assays require fluorescent probes. Usually, radio- and fluorescence-labeled ligands are dissimilar in terms of structure and bioactivity, and can be used in either radiochemical or fluorescence-based assays. Aiming for a close comparison of both assay types, we synthesized tritiated fluorescent neurotensin receptor ligands ([3H]13, [3H]18) and their nontritiated analogues (13, 18). The labeled probes were studied in radiochemical and fluorescence-based (high-content imaging, flow cytometry, fluorescence anisotropy) binding assays. Equilibrium saturation binding yielded well-comparable ligand-receptor affinities, indicating that all these setups can be used for the screening of new drugs. In contrast, discrepancies were found in the kinetic behavior of the probes, which can be attributed to technical differences of the methods and require further studies with respect to the elucidation of the underlying mechanisms.
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Affiliation(s)
- Fabian
J. Ertl
- Institute
of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
| | - Sergei Kopanchuk
- Institute
of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Nicola C. Dijon
- School
of Life Sciences, University of Nottingham,
Queen’s Medical Centre, Nottingham NG7 2UH, U.K.
| | - Santa Veikšina
- Institute
of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Maris-Johanna Tahk
- Institute
of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Tõnis Laasfeld
- Institute
of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Franziska Schettler
- Institute
of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
| | - Albert O. Gattor
- Institute
of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
| | - Harald Hübner
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University, Nikolaus-Fiebiger-Straβe 10, D-91058 Erlangen, Germany
| | - Nataliya Archipowa
- Institute
of Biophysics and Physical Biochemistry, Faculty of Biology and Preclinical
Medicine, University of Regensburg, Universitätsstraβe
31, D-93053 Regensburg, Germany
| | - Johannes Köckenberger
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University, Nikolaus-Fiebiger-Straβe 10, D-91058 Erlangen, Germany
| | - Markus R. Heinrich
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University, Nikolaus-Fiebiger-Straβe 10, D-91058 Erlangen, Germany
| | - Peter Gmeiner
- Department
of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich Alexander University, Nikolaus-Fiebiger-Straβe 10, D-91058 Erlangen, Germany
| | - Roger J. Kutta
- Institute
of Physical and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
| | - Nicholas D. Holliday
- School
of Life Sciences, University of Nottingham,
Queen’s Medical Centre, Nottingham NG7 2UH, U.K.
| | - Ago Rinken
- Institute
of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Max Keller
- Institute
of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraβe 31, D-93053 Regensburg, Germany
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4
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Burger WAC, Draper-Joyce CJ, Valant C, Christopoulos A, Thal DM. Positive allosteric modulation of a GPCR ternary complex. SCIENCE ADVANCES 2024; 10:eadp7040. [PMID: 39259792 PMCID: PMC11389776 DOI: 10.1126/sciadv.adp7040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 08/06/2024] [Indexed: 09/13/2024]
Abstract
The activation of a G protein-coupled receptor (GPCR) leads to the formation of a ternary complex between agonist, receptor, and G protein that is characterized by high-affinity binding. Allosteric modulators bind to a distinct binding site from the orthosteric agonist and can modulate both the affinity and the efficacy of orthosteric agonists. The influence allosteric modulators have on the high-affinity active state of the GPCR-G protein ternary complex is unknown due to limitations on attempting to characterize this interaction in recombinant whole cell or membrane-based assays. Here, we use the purified M2 muscarinic acetylcholine receptor reconstituted into nanodiscs to show that, once the agonist-bound high-affinity state is promoted by the G protein, positive allosteric modulators stabilize the ternary complex that, in the presence of nucleotides, leads to an enhanced initial rate of signaling. Our results enhance our understanding of how allosteric modulators influence orthosteric ligand signaling and will aid the design of allosteric therapeutics.
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Affiliation(s)
- Wessel A C Burger
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- Australian Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Christopher J Draper-Joyce
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Celine Valant
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- Australian Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- Australian Research Council Centre for Cryo-Electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
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5
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Morales P, Scharf MM, Bermudez M, Egyed A, Franco R, Hansen OK, Jagerovic N, Jakubík J, Keserű GM, Kiss DJ, Kozielewicz P, Larsen O, Majellaro M, Mallo-Abreu A, Navarro G, Prieto-Díaz R, Rosenkilde MM, Sotelo E, Stark H, Werner T, Wingler LM. Progress on the development of Class A GPCR-biased ligands. Br J Pharmacol 2024. [PMID: 39261899 DOI: 10.1111/bph.17301] [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: 12/11/2023] [Revised: 05/06/2024] [Accepted: 05/18/2024] [Indexed: 09/13/2024] Open
Abstract
Class A G protein-coupled receptors (GPCRs) continue to garner interest for their essential roles in cell signalling and their importance as drug targets. Although numerous drugs in the clinic target these receptors, over 60% GPCRs remain unexploited. Moreover, the adverse effects triggered by the available unbiased GPCR modulators, limit their use and therapeutic value. In this context, the elucidation of biased signalling has opened up new pharmacological avenues holding promise for safer therapeutics. Functionally selective ligands favour receptor conformations facilitating the recruitment of specific effectors and the modulation of the associated pathways. This review surveys the current drug discovery landscape of GPCR-biased modulators with a focus on recent advances. Understanding the biological effects of this preferential coupling is at different stages depending on the Class A GPCR family. Therefore, with a focus on individual GPCR families, we present a compilation of the functionally selective modulators reported over the past few years. In doing so, we dissect their therapeutic relevance, molecular determinants and potential clinical applications.
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Affiliation(s)
- Paula Morales
- Instituto de Química Médica, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Magdalena M Scharf
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Marcel Bermudez
- Institute for Pharmaceutical and Medicinal Chemistry, University of Münster, Münster, Germany
| | - Attila Egyed
- Medicinal Chemistry Research Group and National Drug Discovery and Development Laboratory, Research Centre for Natural Sciences, Budapest, Hungary
| | - Rafael Franco
- Molecular Neurobiology Laboratory, Department of Biochemistry and Molecular Biology, Universitat de Barcelona, Barcelona, Spain
- CiberNed. Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, Madrid, Spain
- School of Chemistry, Universitat de Barcelona, Barcelona, Spain
| | - Olivia K Hansen
- Laboratory of Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nadine Jagerovic
- Instituto de Química Médica, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Jan Jakubík
- Institute of Physiology Czech Academy of Sciences, Prague, Czech Republic
| | - György M Keserű
- Medicinal Chemistry Research Group and National Drug Discovery and Development Laboratory, Research Centre for Natural Sciences, Budapest, Hungary
| | - Dóra Judit Kiss
- Medicinal Chemistry Research Group and National Drug Discovery and Development Laboratory, Research Centre for Natural Sciences, Budapest, Hungary
| | - Pawel Kozielewicz
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Olav Larsen
- Laboratory of Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Ana Mallo-Abreu
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, Santiago de Compostela, Spain
- Laboratory of Medicinal Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Institute of Biomedicine (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Gemma Navarro
- CiberNed. Network Center for Neurodegenerative Diseases, National Spanish Health Institute Carlos III, Madrid, Spain
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Science, Universitat de Barcelona, Barcelona, Spain
| | - Rubén Prieto-Díaz
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Mette M Rosenkilde
- Laboratory of Molecular Pharmacology, Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Eddy Sotelo
- Center for Research in Biological Chemistry and Molecular Materials (CIQUS), University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Holger Stark
- Heinrich Heine University Düsseldorf, Institut fuer Pharmazeutische und Medizinische Chemie, Duesseldorf, Germany
| | - Tobias Werner
- Heinrich Heine University Düsseldorf, Institut fuer Pharmazeutische und Medizinische Chemie, Duesseldorf, Germany
| | - Laura M Wingler
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina, USA
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6
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Zhang MY, Ao JY, Liu N, Chen T, Lu SY. Exploring the constitutive activation mechanism of the class A orphan GPR20. Acta Pharmacol Sin 2024:10.1038/s41401-024-01385-7. [PMID: 39256608 DOI: 10.1038/s41401-024-01385-7] [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: 07/11/2024] [Accepted: 08/22/2024] [Indexed: 09/12/2024] Open
Abstract
GPR20, an orphan G protein-coupled receptor (GPCR), shows significant expression in intestinal tissue and represents a potential therapeutic target to treat gastrointestinal stromal tumors. GPR20 performs high constitutive activity when coupling with Gi. Despite the pharmacological importance of GPCR constitutive activation, determining the mechanism has long remained unclear. In this study, we explored the constitutive activation mechanism of GPR20 through large-scale unbiased molecular dynamics simulations. Our results unveil the allosteric nature of constitutively activated GPCR signal transduction involving extracellular and intracellular domains. Moreover, the constitutively active state of the GPR20 requires both the N-terminal cap and Gi protein. The N-terminal cap of GPR20 functions like an agonist and mediates long-range activated conformational shift. Together with the previous study, this study enhances our knowledge of the self-activation mechanism of the orphan receptor, facilitates the drug discovery efforts that target GPR20.
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Affiliation(s)
- Ming-Yang Zhang
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jian-Yang Ao
- Department of Hepatobiliary and Pancreatic Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200120, China
- Institute of Hepatobiliary and Pancreatic Surgery, Tongji University School of Medicine, Shanghai, 200120, China
| | - Ning Liu
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China
| | - Ting Chen
- Department of Cardiology, Changzheng Hospital, Affiliated to Naval Medical University, Shanghai, 200003, China.
| | - Shao-Yong Lu
- Key Laboratory of Protection, Development and Utilization of Medicinal Resources in Liupanshan Area, Ministry of Education, Peptide & Protein Drug Research Center, School of Pharmacy, Ningxia Medical University, Yinchuan, 750004, China.
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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7
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Gusach A, Lee Y, Khoshgrudi AN, Mukhaleva E, Ma N, Koers EJ, Chen Q, Edwards PC, Huang F, Kim J, Mancia F, Veprintsev DB, Vaidehi N, Weyand SN, Tate CG. Molecular recognition of an odorant by the murine trace amine-associated receptor TAAR7f. Nat Commun 2024; 15:7555. [PMID: 39215004 PMCID: PMC11364543 DOI: 10.1038/s41467-024-51793-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/15/2024] [Indexed: 09/04/2024] Open
Abstract
There are two main families of G protein-coupled receptors that detect odours in humans, the odorant receptors (ORs) and the trace amine-associated receptors (TAARs). Their amino acid sequences are distinct, with the TAARs being most similar to the aminergic receptors such as those activated by adrenaline, serotonin, dopamine and histamine. To elucidate the structural determinants of ligand recognition by TAARs, we have determined the cryo-EM structure of a murine receptor, mTAAR7f, coupled to the heterotrimeric G protein Gs and bound to the odorant N,N-dimethylcyclohexylamine (DMCHA) to an overall resolution of 2.9 Å. DMCHA is bound in a hydrophobic orthosteric binding site primarily through van der Waals interactions and a strong charge-charge interaction between the tertiary amine of the ligand and an aspartic acid residue. This site is distinct and non-overlapping with the binding site for the odorant propionate in the odorant receptor OR51E2. The structure, in combination with mutagenesis data and molecular dynamics simulations suggests that the activation of the receptor follows a similar pathway to that of the β-adrenoceptors, with the significant difference that DMCHA interacts directly with one of the main activation microswitch residues, Trp6.48.
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Affiliation(s)
- Anastasiia Gusach
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Yang Lee
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Armin Nikpour Khoshgrudi
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, NG7 2RD, UK
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Elizaveta Mukhaleva
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, CA, 91016, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, CA, 91016, USA
| | - Eline J Koers
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, NG7 2RD, UK
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Qingchao Chen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Patricia C Edwards
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Fanglu Huang
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK
| | - Jonathan Kim
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Dmitry B Veprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, NG7 2RD, UK
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1218 S 5th Ave, Monrovia, CA, 91016, USA
| | - Simone N Weyand
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, UK.
- Department of Medicine, University of Cambridge, Victor Phillip Dahdaleh Building, Heart & Lung Research Institute, Papworth Road, Cambridge Biomedical Campus, Cambridge, CB2 0BB, UK.
- Cambridge Institute for Medical Research, Keith Peters Building, Biomedical Campus, Hills Rd, Cambridge, CB2 0XY, UK.
- EMBL's European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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8
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Kogut-Günthel MM, Zara Z, Nicoli A, Steuer A, Lopez-Balastegui M, Selent J, Karanth S, Koehler M, Ciancetta A, Abiko LA, Hagn F, Di Pizio A. The path to the G protein-coupled receptor structural landscape: Major milestones and future directions. Br J Pharmacol 2024. [PMID: 39209310 DOI: 10.1111/bph.17314] [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: 12/20/2023] [Revised: 06/14/2024] [Accepted: 06/28/2024] [Indexed: 09/04/2024] Open
Abstract
G protein-coupled receptors (GPCRs) play a crucial role in cell function by transducing signals from the extracellular environment to the inside of the cell. They mediate the effects of various stimuli, including hormones, neurotransmitters, ions, photons, food tastants and odorants, and are renowned drug targets. Advancements in structural biology techniques, including X-ray crystallography and cryo-electron microscopy (cryo-EM), have driven the elucidation of an increasing number of GPCR structures. These structures reveal novel features that shed light on receptor activation, dimerization and oligomerization, dichotomy between orthosteric and allosteric modulation, and the intricate interactions underlying signal transduction, providing insights into diverse ligand-binding modes and signalling pathways. However, a substantial portion of the GPCR repertoire and their activation states remain structurally unexplored. Future efforts should prioritize capturing the full structural diversity of GPCRs across multiple dimensions. To do so, the integration of structural biology with biophysical and computational techniques will be essential. We describe in this review the progress of nuclear magnetic resonance (NMR) to examine GPCR plasticity and conformational dynamics, of atomic force microscopy (AFM) to explore the spatial-temporal dynamics and kinetic aspects of GPCRs, and the recent breakthroughs in artificial intelligence for protein structure prediction to characterize the structures of the entire GPCRome. In summary, the journey through GPCR structural biology provided in this review illustrates how far we have come in decoding these essential proteins architecture and function. Looking ahead, integrating cutting-edge biophysics and computational tools offers a path to navigating the GPCR structural landscape, ultimately advancing GPCR-based applications.
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Affiliation(s)
| | - Zeenat Zara
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Faculty of Science, University of South Bohemia in Ceske Budejovice, České Budějovice, Czech Republic
| | - Alessandro Nicoli
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Professorship for Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
| | - Alexandra Steuer
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Professorship for Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
| | - Marta Lopez-Balastegui
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute & Pompeu Fabra University, Barcelona, Spain
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute & Pompeu Fabra University, Barcelona, Spain
| | - Sanjai Karanth
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Melanie Koehler
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- TUM Junior Fellow at the Chair of Nutritional Systems Biology, Technical University of Munich, Freising, Germany
| | - Antonella Ciancetta
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, Ferrara, Italy
| | - Layara Akemi Abiko
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, Basel, Switzerland
| | - Franz Hagn
- Structural Membrane Biochemistry, Bavarian NMR Center, Dept. Bioscience, School of Natural Sciences, Technical University of Munich, Munich, Germany
- Institute of Structural Biology (STB), Helmholtz Munich, Neuherberg, Germany
| | - Antonella Di Pizio
- Leibniz Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
- Professorship for Chemoinformatics and Protein Modelling, Department of Molecular Life Science, School of Life Science, Technical University of Munich, Freising, Germany
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9
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Wu Z, Chen G, Qiu C, Yan X, Xu L, Jiang S, Xu J, Han R, Shi T, Liu Y, Gao W, Wang Q, Li J, Ye F, Pan X, Zhang Z, Ning P, Zhang B, Chen J, Du Y. Structural basis for the ligand recognition and G protein subtype selectivity of kisspeptin receptor. SCIENCE ADVANCES 2024; 10:eadn7771. [PMID: 39151001 PMCID: PMC11328905 DOI: 10.1126/sciadv.adn7771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 07/11/2024] [Indexed: 08/18/2024]
Abstract
Kisspeptin receptor (KISS1R), belonging to the class A peptide-GPCR family, plays a key role in the regulation of reproductive physiology after stimulation by kisspeptin and is regarded as an attractive drug target for reproductive diseases. Here, we demonstrated that KISS1R can couple to the Gi/o pathway besides the well-known Gq/11 pathway. We further resolved the cryo-electron microscopy (cryo-EM) structure of KISS1R-Gq and KISS1R-Gi complexes bound to the synthetic agonist TAK448 and structure of KISS1R-Gq complex bound to the endogenous agonist KP54. The high-resolution structures provided clear insights into mechanism of KISS1R recognition by its ligand and can facilitate the design of targeted drugs with high affinity to improve treatment effects. Moreover, the structural and functional analyses indicated that conformational differences in the extracellular loops (ECLs), intracellular loops (ICLs) of the receptor, and the "wavy hook" of the Gα subunit may account for the specificity of G protein coupling for KISS1R signaling.
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Affiliation(s)
- Zhangsong Wu
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Geng Chen
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Chen Qiu
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Xiaoyi Yan
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Lezhi Xu
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Shirui Jiang
- The Huanan Affiliated Hospital of Shenzhen University, Shenzhen University, 518000 Shenzhen, Guangdong, China
| | - Jun Xu
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA, USA
| | - Runyuan Han
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Tingyi Shi
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Yiming Liu
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Wei Gao
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Qian Wang
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
- The Huanan Affiliated Hospital of Shenzhen University, Shenzhen University, 518000 Shenzhen, Guangdong, China
| | - Jiancheng Li
- Instrumental Analysis Center, Shenzhen University, Shenzhen 518055, Guangdong, China
| | - Fang Ye
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Xin Pan
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Zhiyi Zhang
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Peiruo Ning
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Binghao Zhang
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
| | - Jing Chen
- Neurobiology Institute, Jining Medical University, 272067 Jining, Shandong, China
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Yang Du
- Kobilka Institute of Innovative Drug Discovery, Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong, 518172 Shenzhen, Guangdong, China
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10
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Eberle SA, Gustavsson M. Bilayer lipids modulate ligand binding to atypical chemokine receptor 3. Structure 2024; 32:1174-1183.e5. [PMID: 38776922 DOI: 10.1016/j.str.2024.04.018] [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: 10/18/2023] [Revised: 02/28/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024]
Abstract
Chemokine receptors belong to the large class of G protein-coupled receptors (GPCRs) and are involved in a number of (patho)physiological processes. Previous studies highlighted the importance of membrane lipids for modulating GPCR structure and function. However, the underlying mechanisms of how lipids regulate GPCRs are often poorly understood. Here, we report that anionic lipid bilayers increase the binding affinity of the chemokine CXCL12 for the atypical chemokine receptor 3 (ACKR3) by modulating the CXCL12 binding kinetics. Notably, the anionic bilayer favors CXCL12 over the more positively charged chemokine CXCL11, which we explained by bilayer interactions orienting CXCL12 but not CXCL11 for productive ACKR3 binding. Furthermore, our data suggest a stabilization of active ACKR3 conformations in anionic bilayers. Taken together, the described regulation of chemokine selectivity of ACKR3 by the lipid bilayer proposes an extended version of the classical model of chemokine binding including the lipid environment of the receptor.
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Affiliation(s)
- Stefanie Alexandra Eberle
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Martin Gustavsson
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
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11
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Knight KM, Krumm BE, Kapolka NJ, Ludlam WG, Cui M, Mani S, Prytkova I, Obarow EG, Lefevre TJ, Wei W, Ma N, Huang XP, Fay JF, Vaidehi N, Smrcka AV, Slesinger PA, Logothetis DE, Martemyanov KA, Roth BL, Dohlman HG. A neurodevelopmental disorder mutation locks G proteins in the transitory pre-activated state. Nat Commun 2024; 15:6643. [PMID: 39103320 DOI: 10.1038/s41467-024-50964-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 07/25/2024] [Indexed: 08/07/2024] Open
Abstract
Many neurotransmitter receptors activate G proteins through exchange of GDP for GTP. The intermediate nucleotide-free state has eluded characterization, due largely to its inherent instability. Here we characterize a G protein variant associated with a rare neurological disorder in humans. GαoK46E has a charge reversal that clashes with the phosphate groups of GDP and GTP. As anticipated, the purified protein binds poorly to guanine nucleotides yet retains wild-type affinity for G protein βγ subunits. In cells with physiological concentrations of nucleotide, GαoK46E forms a stable complex with receptors and Gβγ, impeding effector activation. Further, we demonstrate that the mutant can be easily purified in complex with dopamine-bound D2 receptors, and use cryo-electron microscopy to determine the structure, including both domains of Gαo, without nucleotide or stabilizing nanobodies. These findings reveal the molecular basis for the first committed step of G protein activation, establish a mechanistic basis for a neurological disorder, provide a simplified strategy to determine receptor-G protein structures, and a method to detect high affinity agonist binding in cells.
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Affiliation(s)
- Kevin M Knight
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Brian E Krumm
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nicholas J Kapolka
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - W Grant Ludlam
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Meng Cui
- Department of Pharmaceutical Sciences Northeastern University, Boston, MA, USA
| | - Sepehr Mani
- Department of Pharmaceutical Sciences Northeastern University, Boston, MA, USA
| | - Iya Prytkova
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Elizabeth G Obarow
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tyler J Lefevre
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | - Wenyuan Wei
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jonathan F Fay
- Department of Biochemistry and Molecular Biology, School of Medicine, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Alan V Smrcka
- Department of Pharmacology, University of Michigan, Ann Arbor, MI, USA
| | - Paul A Slesinger
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Kirill A Martemyanov
- Department of Neuroscience, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, University of Florida, Jupiter, FL, USA
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Henrik G Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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12
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Yang X, Zhou P, Shen S, Hu Q, Tian C, Xia A, Wang Y, Yang Z, Nan J, Zhou Y, Chen S, Tian X, Wu C, Lin G, Zhang L, Wang K, Zheng T, Zou J, Yan W, Shao Z, Yang S. Entropy drives the ligand recognition in G-protein-coupled receptor subtypes. Proc Natl Acad Sci U S A 2024; 121:e2401091121. [PMID: 39024109 PMCID: PMC11287286 DOI: 10.1073/pnas.2401091121] [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: 01/17/2024] [Accepted: 05/22/2024] [Indexed: 07/20/2024] Open
Abstract
Achieving ligand subtype selectivity within highly homologous subtypes of G-protein-coupled receptor (GPCR) is critical yet challenging for GPCR drug discovery, primarily due to the unclear mechanism underlying ligand subtype selectivity, which hampers the rational design of subtype-selective ligands. Herein, we disclose an unusual molecular mechanism of entropy-driven ligand recognition in cannabinoid (CB) receptor subtypes, revealed through atomic-level molecular dynamics simulations, cryoelectron microscopy structure, and mutagenesis experiments. This mechanism is attributed to the distinct conformational dynamics of the receptor's orthosteric pocket, leading to variations in ligand binding entropy and consequently, differential binding affinities, which culminate in specific ligand recognition. We experimentally validated this mechanism and leveraged it to design ligands with enhanced or ablated subtype selectivity. One such ligand demonstrated favorable pharmacokinetic properties and significant efficacy in rodent inflammatory analgesic models. More importantly, it is precisely due to the high subtype selectivity obtained based on this mechanism that this ligand does not show addictive properties in animal models. Our findings elucidate the unconventional role of entropy in CB receptor subtype selectivity and suggest a strategy for rational design of ligands to achieve entropy-driven subtype selectivity for many pharmaceutically important GPCRs.
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Affiliation(s)
- Xin Yang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Pei Zhou
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Siyuan Shen
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Qian Hu
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Chenyu Tian
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Anjie Xia
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- Department of Ophthalmology and Research Laboratory of Macular Disease, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Yifei Wang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Zhiqian Yang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Jinshan Nan
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Yangli Zhou
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Shasha Chen
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Xiaowen Tian
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Chao Wu
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Guifeng Lin
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Liting Zhang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Kexin Wang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Tao Zheng
- Engineering Research Center of Medical Information Technology, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Jun Zou
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Wei Yan
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
| | - Zhenhua Shao
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- Division of Nephrology and Kidney Research Institute, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- Frontier Medical Center, Tianfu Jincheng Laboratory, Chengdu, Sichuan610212, China
| | - Shengyong Yang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- New Cornerstone Science Laboratory, West China Hospital, Sichuan University, Chengdu, Sichuan610041, China
- Frontier Medical Center, Tianfu Jincheng Laboratory, Chengdu, Sichuan610212, China
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13
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Llinas Del Torrent C, Raïch I, Gonzalez A, Lillo J, Casajuana-Martin N, Franco R, Pardo L, Navarro G. Allosterism in the adenosine A 2A and cannabinoid CB 2 heteromer. Br J Pharmacol 2024. [PMID: 39044481 DOI: 10.1111/bph.16502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 01/24/2024] [Accepted: 03/18/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND AND PURPOSE Allosterism is a regulatory mechanism for GPCRs that can be attained by ligand-binding or protein-protein interactions with another GPCR. We have studied the influence of the dimer interface on the allosteric properties of the A2A receptor and CB2 receptor heteromer. EXPERIMENTAL APPROACH We have evaluated cAMP production, phosphorylation of signal-regulated kinases (pERK1/2), label-free dynamic mass redistribution, β-arrestin 2 recruitment and bimolecular fluorescence complementation assays in the absence and presence of synthetic peptides that disrupt the formation of the heteromer. Molecular dynamic simulations provided converging evidence that the heteromeric interface influences the allosteric properties of the A2AR-CB2R heteromer. KEY RESULTS Apo A2AR blocks agonist-induced signalling of CB2R. The disruptive peptides, with the amino acid sequence of transmembrane (TM) 6 of A2AR or CB2R, facilitate CB2R activation, suggesting that A2AR allosterically prevents the outward movement of TM 6 of CB2R for G protein binding. Significantly, binding of the selective antagonist SCH 58261 to A2AR also facilitated agonist-induced activation of CB2R. CONCLUSIONS AND IMPLICATIONS It is proposed that the A2AR-CB2R heteromer contains distinct dimerization interfaces that govern its functional properties. The molecular interface between protomers of the A2AR-CB2R heteromer interconverted from TM 6 for apo or agonist-bound A2AR, blocking CB2R activation, to mainly the TM 1/7 interface for antagonist-bound A2AR, facilitating the independent opening of intracellular cavities for G protein binding. These novel results shed light on a different type of allosteric mechanism and extend the repertoire of GPCR heteromer signalling.
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Affiliation(s)
- Claudia Llinas Del Torrent
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Iu Raïch
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Institute of Neuroscience, University of Barcelona (NeuroUB), Barcelona, Spain
| | - Angel Gonzalez
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Jaume Lillo
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Nil Casajuana-Martin
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Rafael Franco
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Leonardo Pardo
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
| | - Gemma Navarro
- Department of Biochemistry and Physiology, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Institute of Neuroscience, University of Barcelona (NeuroUB), Barcelona, Spain
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14
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Rodríguez-Frade JM, González-Granado LI, Santiago CA, Mellado M. The complex nature of CXCR4 mutations in WHIM syndrome. Front Immunol 2024; 15:1406532. [PMID: 39035006 PMCID: PMC11257845 DOI: 10.3389/fimmu.2024.1406532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/20/2024] [Indexed: 07/23/2024] Open
Abstract
Heterozygous autosomal dominant mutations in the CXCR4 gene cause WHIM syndrome, a severe combined immunodeficiency disorder. The mutations primarily affect the C-terminal region of the CXCR4 chemokine receptor, specifically several potential phosphorylation sites critical for agonist (CXCL12)-mediated receptor internalization and desensitization. Mutant receptors have a prolonged residence time on the cell surface, leading to hyperactive signaling that is responsible for some of the symptoms of WHIM syndrome. Recent studies have shown that the situation is more complex than originally thought, as mutant WHIM receptors and CXCR4 exhibit different dynamics at the cell membrane, which also influences their respective cellular functions. This review examines the functional mechanisms of CXCR4 and the impact of WHIM mutations in both physiological and pathological conditions.
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Affiliation(s)
- José Miguel Rodríguez-Frade
- Department of Immunology and Oncology, Chemokine Signaling Group, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
| | - Luis Ignacio González-Granado
- Department of Pediatrics, 12 de Octubre Health Research Institute (imas12), Madrid, Spain
- Department of Public Health School of Medicine, School of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - César A. Santiago
- X-ray Crystallography Unit, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Mario Mellado
- Department of Immunology and Oncology, Chemokine Signaling Group, Centro Nacional de Biotecnología/CSIC, Madrid, Spain
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15
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Mukhaleva E, Yang T, Sadler F, Sivaramakrishnan S, Ma N, Vaidehi N. Cellular lipids regulate the conformational ensembles of the disordered intracellular loop 3 in β2-adrenergic receptor. iScience 2024; 27:110086. [PMID: 38947516 PMCID: PMC11214514 DOI: 10.1016/j.isci.2024.110086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 03/19/2024] [Accepted: 05/20/2024] [Indexed: 07/02/2024] Open
Abstract
The intracellular loops of G protein-coupled receptors (GPCRs) have been shown to play a key role in G protein coupling and selectivity. We recently showed that the intrinsically disordered third intracellular loop (ICL3) of β2-adrenergic receptor is dynamic and equilibrates between open and closed conformations to regulate the G protein coupling. In this study, using the extensive molecular dynamics simulations in multi-lipid bilayer models, we show that the lipid phosphatidylinositol 4,5-bisphosphate (PIP2) stabilizes the active state of β2-adrenergic receptor by keeping ICL3 in an open conformation. This stabilization results in a tilt of the receptor within the membrane. Additionally, the ganglioside lipid, GM3 interacts with extracellular loops, impacting the ligand binding site allosterically. This demonstrates the active role of the chemistry of lipids in stabilizing specific GPCR conformations.
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Affiliation(s)
- Elizaveta Mukhaleva
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Tianyi Yang
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Fredrik Sadler
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Sivaraj Sivaramakrishnan
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ning Ma
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Nagarajan Vaidehi
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
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16
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Onishi Y, Yamamura Y, Hosogi M, Higashi H, Ogita K, Kinjo T, Uno K, Yoneda Y, Kuramoto N. Long-lasting increases in GABA B receptor subunit levels in hippocampal dentate gyrus of mice with a single systemic injection of trimethyltin. Heliyon 2024; 10:e29713. [PMID: 38720739 PMCID: PMC11076641 DOI: 10.1016/j.heliyon.2024.e29713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/13/2024] [Accepted: 04/14/2024] [Indexed: 05/12/2024] Open
Abstract
We have recently shown delayed increases in GABAB receptor (GABABR) subunit protein levels in the hippocampal dentate gyrus (DG), but not in the pyramidal CA1 and CA3 regions, at 15-30 days after the systemic single administration of trimethyltin (TMT) in mice. An attempt was thus made to determine whether the delayed increases return to the control levels found in naive mice afterward. In the DG on hippocampal slices obtained at 90 days after the administration, however, marked increases were still seen in protein levels of both GABABR1 and GABABR2 subunits without significant changes in calbindin and glial fibrillary acidic protein (GFAP) levels on immunoblotting analysis. Fluoro-Jade B staining clearly revealed the absence of degenerated neurons from the DG at 90 days after the administration. Although co-localization was invariably detected between GABABR2 subunit and GFAP in the DG at 30 days on immunohistochemical analysis, GABABR2-positive cells did not merge well with GFAP-positive cells in the DG at 90 days. These results suggest that both GABABR1 and GABABR2 subunits would be tardily and sustainably up-regulated by cells other than neurons and astrocytes in the murine DG at 90 days after a systemic single injection of TMT.
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Affiliation(s)
- Yuki Onishi
- Laboratory of Molecular Pharmacology,Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka, 573-0101, Japan
- The Institute of Prophylactic Pharmacology, Kita-Shinagawa, Shinagawa, 140-0001, Tokyo, Japan
| | - Yusuke Yamamura
- Laboratory of Pharmacology, Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka, 573-0101, Japan
| | - Misa Hosogi
- Laboratory of Molecular Pharmacology,Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka, 573-0101, Japan
| | - Hiroshi Higashi
- Laboratory of Molecular Pharmacology,Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka, 573-0101, Japan
| | - Kiyokazu Ogita
- Laboratory of Pharmacology, Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka, 573-0101, Japan
- The Institute of Prophylactic Pharmacology, Kita-Shinagawa, Shinagawa, 140-0001, Tokyo, Japan
| | - Toshihiko Kinjo
- Laboratory of Molecular Pharmacology,Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka, 573-0101, Japan
- The Institute of Prophylactic Pharmacology, Kita-Shinagawa, Shinagawa, 140-0001, Tokyo, Japan
| | - Kyosuke Uno
- Laboratory of Molecular Pharmacology,Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka, 573-0101, Japan
- The Institute of Prophylactic Pharmacology, Kita-Shinagawa, Shinagawa, 140-0001, Tokyo, Japan
| | - Yukio Yoneda
- The Institute of Prophylactic Pharmacology, Kita-Shinagawa, Shinagawa, 140-0001, Tokyo, Japan
| | - Nobuyuki Kuramoto
- Laboratory of Molecular Pharmacology,Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka, 573-0101, Japan
- Laboratory of Pharmacology, Faculty of Pharmaceutical Sciences, Setsunan University, Hirakata, Osaka, 573-0101, Japan
- The Institute of Prophylactic Pharmacology, Kita-Shinagawa, Shinagawa, 140-0001, Tokyo, Japan
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17
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Tauber M, Ben-Chaim Y. Voltage Sensors Embedded in G Protein-Coupled Receptors. Int J Mol Sci 2024; 25:5295. [PMID: 38791333 PMCID: PMC11120775 DOI: 10.3390/ijms25105295] [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: 04/18/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Some signaling processes mediated by G protein-coupled receptors (GPCRs) are modulated by membrane potential. In recent years, increasing evidence that GPCRs are intrinsically voltage-dependent has accumulated. A recent publication challenged the view that voltage sensors are embedded in muscarinic receptors. Herein, we briefly discuss the evidence that supports the notion that GPCRs themselves are voltage-sensitive proteins and an alternative mechanism that suggests that voltage-gated sodium channels are the voltage-sensing molecules involved in such processes.
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Affiliation(s)
| | - Yair Ben-Chaim
- Department of Natural Sciences, The Open University of Israel, Ra’anana 4353701, Israel
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18
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Papasergi-Scott MM, Pérez-Hernández G, Batebi H, Gao Y, Eskici G, Seven AB, Panova O, Hilger D, Casiraghi M, He F, Maul L, Gmeiner P, Kobilka BK, Hildebrand PW, Skiniotis G. Time-resolved cryo-EM of G-protein activation by a GPCR. Nature 2024; 629:1182-1191. [PMID: 38480881 DOI: 10.1038/s41586-024-07153-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 02/02/2024] [Indexed: 03/26/2024]
Abstract
G-protein-coupled receptors (GPCRs) activate heterotrimeric G proteins by stimulating guanine nucleotide exchange in the Gα subunit1. To visualize this mechanism, we developed a time-resolved cryo-EM approach that examines the progression of ensembles of pre-steady-state intermediates of a GPCR-G-protein complex. By monitoring the transitions of the stimulatory Gs protein in complex with the β2-adrenergic receptor at short sequential time points after GTP addition, we identified the conformational trajectory underlying G-protein activation and functional dissociation from the receptor. Twenty structures generated from sequential overlapping particle subsets along this trajectory, compared to control structures, provide a high-resolution description of the order of main events driving G-protein activation in response to GTP binding. Structural changes propagate from the nucleotide-binding pocket and extend through the GTPase domain, enacting alterations to Gα switch regions and the α5 helix that weaken the G-protein-receptor interface. Molecular dynamics simulations with late structures in the cryo-EM trajectory support that enhanced ordering of GTP on closure of the α-helical domain against the nucleotide-bound Ras-homology domain correlates with α5 helix destabilization and eventual dissociation of the G protein from the GPCR. These findings also highlight the potential of time-resolved cryo-EM as a tool for mechanistic dissection of GPCR signalling events.
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MESH Headings
- Humans
- Binding Sites
- Cryoelectron Microscopy
- GTP-Binding Protein alpha Subunits, Gs/chemistry
- GTP-Binding Protein alpha Subunits, Gs/drug effects
- GTP-Binding Protein alpha Subunits, Gs/metabolism
- GTP-Binding Protein alpha Subunits, Gs/ultrastructure
- Guanosine Triphosphate/metabolism
- Guanosine Triphosphate/pharmacology
- Models, Molecular
- Molecular Dynamics Simulation
- Protein Binding
- Receptors, Adrenergic, beta-2/metabolism
- Receptors, Adrenergic, beta-2/chemistry
- Receptors, Adrenergic, beta-2/ultrastructure
- Time Factors
- Enzyme Activation/drug effects
- Protein Domains
- Protein Structure, Secondary
- Signal Transduction/drug effects
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Affiliation(s)
- Makaía M Papasergi-Scott
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Guillermo Pérez-Hernández
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
| | - Hossein Batebi
- Institute of Medical Physics and Biophysics, Faculty of Medicine, Leipzig University, Leipzig, Germany
| | - Yang Gao
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Gözde Eskici
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Alpay B Seven
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ouliana Panova
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel Hilger
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Institute of Pharmaceutical Chemistry, Philipps-University of Marburg, Marburg, Germany
| | - Marina Casiraghi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Feng He
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Luis Maul
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Peter W Hildebrand
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Berlin, Germany
- Institute of Medical Physics and Biophysics, Faculty of Medicine, Leipzig University, Leipzig, Germany
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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19
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Gleixner J, Kopanchuk S, Grätz L, Tahk MJ, Laasfeld T, Veikšina S, Höring C, Gattor AO, Humphrys LJ, Müller C, Archipowa N, Köckenberger J, Heinrich MR, Kutta RJ, Rinken A, Keller M. Illuminating Neuropeptide Y Y 4 Receptor Binding: Fluorescent Cyclic Peptides with Subnanomolar Binding Affinity as Novel Molecular Tools. ACS Pharmacol Transl Sci 2024; 7:1142-1168. [PMID: 38633582 PMCID: PMC11019746 DOI: 10.1021/acsptsci.4c00013] [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: 01/12/2024] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 04/19/2024]
Abstract
The neuropeptide Y (NPY) Y4 receptor (Y4R), a member of the family of NPY receptors, is physiologically activated by the linear 36-amino acid peptide pancreatic polypeptide (PP). The Y4R is involved in the regulation of various biological processes, most importantly pancreatic secretion, gastrointestinal motility, and regulation of food intake. So far, Y4R binding affinities have been mostly studied in radiochemical binding assays. Except for a few fluorescently labeled PP derivatives, fluorescence-tagged Y4R ligands with high affinity have not been reported. Here, we introduce differently fluorescence-labeled (Sulfo-Cy5, Cy3B, Py-1, Py-5) Y4R ligands derived from recently reported cyclic hexapeptides showing picomolar Y4R binding affinity. With pKi values of 9.22-9.71 (radioligand competition binding assay), all fluorescent ligands (16-19) showed excellent Y4R affinity. Y4R saturation binding, binding kinetics, and competition binding with reference ligands were studied using different fluorescence-based methods: flow cytometry (Sulfo-Cy5, Cy3B, and Py-1 label), fluorescence anisotropy (Cy3B label), and NanoBRET (Cy3B label) binding assays. These experiments confirmed the high binding affinity to Y4R (equilibrium pKd: 9.02-9.9) and proved the applicability of the probes for fluorescence-based Y4R competition binding studies and imaging techniques such as single-receptor molecule tracking.
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Affiliation(s)
- Jakob Gleixner
- Institute
of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Sergei Kopanchuk
- Institute
of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Lukas Grätz
- Institute
of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Maris-Johanna Tahk
- Institute
of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Tõnis Laasfeld
- Institute
of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Santa Veikšina
- Institute
of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Carina Höring
- Institute
of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Albert O. Gattor
- Institute
of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Laura J. Humphrys
- Institute
of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Christoph Müller
- Institute
of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Nataliya Archipowa
- Institute
of Biophysics and Physical Biochemistry, Faculty of Biology and Preclinical
Medicine, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
| | - Johannes Köckenberger
- Department
of Chemistry and Pharmacy, Molecular and Clinical Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany
| | - Markus R. Heinrich
- Department
of Chemistry and Pharmacy, Molecular and Clinical Pharmacy, Friedrich-Alexander-University Erlangen-Nürnberg, Nikolaus-Fiebiger-Straße 10, D-91058 Erlangen, Germany
| | - Roger Jan Kutta
- Institute
of Physical and Theoretical Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93053 Regensburg, Germany
| | - Ago Rinken
- Institute
of Chemistry, University of Tartu, Ravila 14a, 50411 Tartu, Estonia
| | - Max Keller
- Institute
of Pharmacy, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, D-93040 Regensburg, Germany
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20
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Lee KH, Shi L. Unraveling Activation-Related Rearrangements and Intrinsic Divergence from Ligand-Specific Conformational Changes of the Dopamine D3 and D2 Receptors. J Chem Inf Model 2024; 64:1778-1793. [PMID: 38454785 DOI: 10.1021/acs.jcim.3c01956] [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: 03/09/2024]
Abstract
Effective rational drug discovery hinges on understanding the functional states of the target protein and distinguishing it from homologues. However, for the G protein coupled receptors, both activation-related conformational changes (ACCs) and intrinsic divergence among receptors can be misled or obscured by ligand-specific conformational changes (LCCs). Here, we unraveled ACCs and intrinsic divergence from LCCs of the dopamine D3 and D2 receptors (D3R and D2R), by analyzing their experimentally determined structures and the molecular dynamics (MD) simulation results of the receptors bound with various ligands. In addition to the ACCs common to other aminergic receptors, we revealed unique ACCs for these two receptors, including the extracellular portion of TM5 (TM5e) and TM6e shifting away from TM2e and TM3e, with a subtle rotation of TM5e. In identifying intrinsic divergence, we found more outward tilting of TM6e in the D2R compared to the D3R in both the experimental structures and simulations bound with ligands in different scaffolds. However, this difference was drastically reduced in the simulations bound with nonselective agonist quinpirole, suggesting a misleading effect of LCCs. Further, in the quinpirole-bound simulations, TM1 showed a greater disparity between these receptors, indicating that LCCs may also obscure intrinsic divergence. Importantly, our MD simulations revealed divergence in the dynamics of these receptors. Specifically, the D2R exhibited heightened flexibility compared to the D3R in the extracellular loops and TMs 5e, 6e, and 7e, associated with its greater ligand binding site plasticity. Our results lay the groundwork for crafting ligands specifically targeting the D2R and D3R with more precise pharmacological profiles.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
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21
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Watts SW, Townsend RR, Neubig RR. How New Developments in Pharmacology Receptor Theory Are Changing (Our Understanding of) Hypertension Therapy. Am J Hypertens 2024; 37:248-260. [PMID: 38150382 PMCID: PMC10941088 DOI: 10.1093/ajh/hpad121] [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: 10/24/2023] [Accepted: 12/21/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND Many hypertension therapeutics were developed prior to major advances in drug receptor theory. Moreover, newer drugs may take advantage of some of the newly understood modalities of receptor function. GOAL The goal of this review is to provide an up-to-date summary of drug receptor theory. This is followed by a discussion of the drug classes recognized for treating hypertension to which new concepts in receptor theory apply. RESULTS We raise ideas for mechanisms of potential new antihypertensive drugs and whether they may take advantage of new theories in drug-receptor interaction.
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Affiliation(s)
- Stephanie W Watts
- Department of Pharmacology and Toxicology, College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan 48824-131, USA
| | - Raymond R Townsend
- Department of Nephrology and Hypertension, University of Pennsylvania Medical Center, Philadelphia, Pennsylvania 19104, USA
| | - Richard R Neubig
- Department of Pharmacology and Toxicology, College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan 48824-131, USA
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22
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Madhu MK, Shewani K, Murarka RK. Biased Signaling in Mutated Variants of β 2-Adrenergic Receptor: Insights from Molecular Dynamics Simulations. J Chem Inf Model 2024; 64:449-469. [PMID: 38194225 DOI: 10.1021/acs.jcim.3c01481] [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: 01/10/2024]
Abstract
The molecular basis of receptor bias in G protein-coupled receptors (GPCRs) caused by mutations that preferentially activate specific intracellular transducers over others remains poorly understood. Two experimentally identified biased variants of β2-adrenergic receptors (β2AR), a prototypical GPCR, are a triple mutant (T68F, Y132A, and Y219A) and a single mutant (Y219A); the former bias the receptor toward the β-arrestin pathway by disfavoring G protein engagement, while the latter induces G protein signaling explicitly due to selection against GPCR kinases (GRKs) that phosphorylate the receptor as a prerequisite of β-arrestin binding. Though rigorous characterizations have revealed functional implications of these mutations, the atomistic origin of the observed transducer selectivity is not clear. In this study, we investigated the allosteric mechanism of receptor bias in β2AR using microseconds of all-atom Gaussian accelerated molecular dynamics (GaMD) simulations. Our observations reveal distinct rearrangements in transmembrane helices, intracellular loop 3, and critical residues R1313.50 and Y3267.53 in the conserved motifs D(E)RY and NPxxY for the mutant receptors, leading to their specific transducer interactions. Moreover, partial dissociation of G protein from the receptor core is observed in the simulations of the triple mutant in contrast to the single mutant and wild-type receptor. The reorganization of allosteric communications from the extracellular agonist BI-167107 to the intracellular receptor-transducer interfaces drives the conformational rearrangements responsible for receptor bias in the single and triple mutants. The molecular insights into receptor bias of β2AR presented here could improve the understanding of biased signaling in GPCRs, potentially opening new avenues for designing novel therapeutics with fewer side-effects and superior efficacy.
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Affiliation(s)
- Midhun K Madhu
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal, Madhya Pradesh 462066, India
| | - Kunal Shewani
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal, Madhya Pradesh 462066, India
| | - Rajesh K Murarka
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhopal, Madhya Pradesh 462066, India
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23
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Hamed O, Jayasinghe V, Giembycz MA. The β-Blocker Carvedilol and Related Aryloxypropanolamines Promote ERK1/2 Phosphorylation in HEK293 Cells with K A Values Distinct From Their Equilibrium Dissociation Constants as β 2-Adrenoceptor Antagonists: Evidence for Functional Affinity. J Pharmacol Exp Ther 2024; 388:688-700. [PMID: 38129128 DOI: 10.1124/jpet.123.001920] [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: 09/06/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
The determination of affinity by using functional assays is important in drug discovery because it provides a more relevant estimate of the strength of interaction of a ligand to its cognate receptor than radioligand binding. However, empirical evidence for so-called, "functional affinity" is limited. Herein, we determined whether the affinity of carvedilol, a β-adrenoceptor antagonist used to treat heart failure that also promotes extracellular signal-regulated kinases 1 and 2 (ERK1/2) phosphorylation, differed between these two pharmacological activities. Four structurally related β-adrenoceptor antagonists (alprenolol, carazolol, pindolol, propranolol) that also activated ERK1/2 were included as comparators to enhance our understanding of how these drugs work in the clinical setting. In HEK293 cells stably expressing the human β 2-adrenoceptor carvedilol and related aryloxypropanolamines were partial agonists of ERK1/2 phosphorylation with potencies ([A]50s) that were lower than their equilibrium dissociation constants (K Bs) as β 2-adrenoceptor antagonists. As the [A]50 of a partial agonist is a good approximation of its K B, then these data indicated that the affinities of carvedilol and related ligands for these two activities were distinct. Moreover, there was a significant negative rank order correlation between the [A]50 of each ligand to activate ERK1/2 and their intrinsic activities (i.e., as intrinsic activity for ERK1/2 phosphorylation increased, so did affinity). Genome editing revealed that the transducer that coupled the β 2-adrenoceptor to ERK1/2 phosphorylation in response to carvedilol and other β 2-adrenoceptor antagonists was Gαs. Collectively, these data support the concept of "functional affinity" and indicate that the ability of the β 2-adrenoceptor to recruit Gαs may influence the affinity of the activating ligand. SIGNIFICANCE STATEMENT: In HEK293 cells overexpressing the human β2-adrenoceptor carvedilol and four related aryloxypropanolamines behaved as β2-adrenoceptor antagonists and partial agonists of ERK1/2 phosphorylation with rank orders of affinity that were distinct. These data imply that carvedilol and other β-blockers can stabilize the β2-adrenoceptor in different affinity conformations that are revealed when functionally distinct responses are measured. This is the basis for the pharmacological concept of "functional affinity."
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Affiliation(s)
- Omar Hamed
- Lung Health Research Group, Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Varuna Jayasinghe
- Lung Health Research Group, Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Mark A Giembycz
- Lung Health Research Group, Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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24
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Helfinger L, Tate CG. Structures of Adrenoceptors. Handb Exp Pharmacol 2024; 285:13-26. [PMID: 37460660 DOI: 10.1007/164_2023_674] [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] [Indexed: 09/05/2024]
Abstract
The first structure of an adrenoceptor (AR), the human β2-adrenoceptor (hβ2AR) was published in 2007 and since then a total of 78 structures (up to June 2022) have been determined by X-ray crystallography and electron cryo-microscopy (cryo-EM) of all three βARs (β1, β2 and β3) and four out of six αARs (α1B, α2A, α2B, α2C). The structures are in a number of different conformational states, including the inactive state bound to an antagonist, an intermediate state bound to agonist and active states bound to agonist and an intracellular transducer (G protein or arrestin) or transducer mimetic (nanobody). The structures identify molecular details of how ligands bind in the orthosteric binding pocket (OBP; 19 antagonists, 18 agonists) and also how three different small molecule allosteric modulators bind. The structures have been used to define the molecular details of receptor activation and also the molecular determinants for transducer coupling. This chapter will give a brief overview of the structures, receptor activation, a comparison across the different subfamilies and commonalities of ligand-receptor interactions.
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25
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Rodriguez FD, Covenas R. Association of Neurokinin-1 Receptor Signaling Pathways with Cancer. Curr Med Chem 2024; 31:6460-6486. [PMID: 37594106 DOI: 10.2174/0929867331666230818110812] [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: 02/03/2023] [Revised: 06/14/2023] [Accepted: 07/01/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Numerous biochemical reactions leading to altered cell proliferation cause tumorigenesis and cancer treatment resistance. The mechanisms implicated include genetic and epigenetic changes, modified intracellular signaling, and failure of control mechanisms caused by intrinsic and extrinsic factors alone or combined. No unique biochemical events are responsible; entangled molecular reactions conduct the resident cells in a tissue to display uncontrolled growth and abnormal migration. Copious experimental research supports the etiological responsibility of NK-1R (neurokinin-1 receptor) activation, alone or cooperating with other mechanisms, in cancer appearance in different tissues. Consequently, a profound study of this receptor system in the context of malignant processes is essential to design new treatments targeting NK-1R-deviated activity. METHODS This study reviews and discusses recent literature that analyzes the main signaling pathways influenced by the activation of neurokinin 1 full and truncated receptor variants. Also, the involvement of NK-1R in cancer development is discussed. CONCLUSION NK-1R can signal through numerous pathways and cross-talk with other receptor systems. The participation of override or malfunctioning NK-1R in malignant processes needs a more precise definition in different types of cancers to apply satisfactory and effective treatments. A long way has already been traveled: the current disposal of selective and effective NK-1R antagonists and the capacity to develop new drugs with biased agonistic properties based on the receptor's structural states with functional significance opens immediate research action and clinical application.
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Affiliation(s)
- Francisco David Rodriguez
- Department of Biochemistry and Molecular Biology, Faculty of Chemical Sciences, University of Salamanca, 37007 Salamanca, Spain
- Group GIR USAL: BMD (Bases Moleculares del Desarrollo), University of Salamanca, Salamanca, Spain
| | - Rafael Covenas
- Group GIR USAL: BMD (Bases Moleculares del Desarrollo), University of Salamanca, Salamanca, Spain
- Laboratory of Neuroanatomy of the Peptidergic Systems, Institute of Neurosciences of Castilla y León (INCYL), University of Salamanca, 37007 Salamanca, Spain
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26
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Knight KM, Obarow EG, Wei W, Mani S, Esteller MI, Cui M, Ma N, Martin SA, Brinson E, Hewitt N, Soden GM, Logothetis DE, Vaidehi N, Dohlman HG. Molecular annotation of G protein variants in a neurological disorder. Cell Rep 2023; 42:113462. [PMID: 37980565 PMCID: PMC10872635 DOI: 10.1016/j.celrep.2023.113462] [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: 07/19/2023] [Revised: 10/04/2023] [Accepted: 11/02/2023] [Indexed: 11/21/2023] Open
Abstract
Heterotrimeric G proteins transduce extracellular chemical messages to generate appropriate intracellular responses. Point mutations in GNAO1, encoding the G protein αo subunit, have been implicated in a pathogenic condition characterized by seizures, movement disorders, intellectual disability, and developmental delay (GNAO1 disorder). However, the effects of these mutations on G protein structure and function are unclear. Here, we report the effects of 55 mutations on Gαo conformation, thermostability, nucleotide binding, and hydrolysis, as well as interaction with Gβγ subunits, receptors, and effectors. Our effort reveals four functionally distinct groups of mutants, including one group that sequesters receptors and another that sequesters Gβγ, both acting in a genetically dominant manner. These findings provide a more comprehensive understanding of disease-relevant mutations and reveal that GNAO1 disorder is likely composed of multiple mechanistically distinct disorders that will likely require multiple therapeutic strategies.
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Affiliation(s)
- Kevin M Knight
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Elizabeth G Obarow
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Wenyuan Wei
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Sepehr Mani
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Maria I Esteller
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Meng Cui
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
| | - Sarah A Martin
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emily Brinson
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Natalie Hewitt
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Gaby M Soden
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Diomedes E Logothetis
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA.
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA.
| | - Henrik G Dohlman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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27
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Asadollahi K, Rajput S, de Zhang LA, Ang CS, Nie S, Williamson NA, Griffin MDW, Bathgate RAD, Scott DJ, Weikl TR, Jameson GNL, Gooley PR. Unravelling the mechanism of neurotensin recognition by neurotensin receptor 1. Nat Commun 2023; 14:8155. [PMID: 38071229 PMCID: PMC10710507 DOI: 10.1038/s41467-023-44010-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
The conformational ensembles of G protein-coupled receptors (GPCRs) include inactive and active states. Spectroscopy techniques, including NMR, show that agonists, antagonists and other ligands shift the ensemble toward specific states depending on the pharmacological efficacy of the ligand. How receptors recognize ligands and the kinetic mechanism underlying this population shift is poorly understood. Here, we investigate the kinetic mechanism of neurotensin recognition by neurotensin receptor 1 (NTS1) using 19F-NMR, hydrogen-deuterium exchange mass spectrometry and stopped-flow fluorescence spectroscopy. Our results indicate slow-exchanging conformational heterogeneity on the extracellular surface of ligand-bound NTS1. Numerical analysis of the kinetic data of neurotensin binding to NTS1 shows that ligand recognition follows an induced-fit mechanism, in which conformational changes occur after neurotensin binding. This approach is applicable to other GPCRs to provide insight into the kinetic regulation of ligand recognition by GPCRs.
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Affiliation(s)
- Kazem Asadollahi
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sunnia Rajput
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Lazarus Andrew de Zhang
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Ching-Seng Ang
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Shuai Nie
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Nicholas A Williamson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ross A D Bathgate
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daniel J Scott
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Thomas R Weikl
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Guy N L Jameson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
- School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia.
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
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28
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Zhang M, Lan X, Li X, Lu S. Pharmacologically targeting intracellular allosteric sites of GPCRs for drug discovery. Drug Discov Today 2023; 28:103803. [PMID: 37852356 DOI: 10.1016/j.drudis.2023.103803] [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: 09/12/2023] [Revised: 10/07/2023] [Accepted: 10/12/2023] [Indexed: 10/20/2023]
Abstract
G-protein-coupled receptors (GPCRs) are a family of cell surface proteins that can sense a variety of extracellular stimuli and mediate multiple signaling transduction pathways involved in human physiology. Recent advances in GPCR structural biology have revealed a relatively conserved intracellular allosteric site in multiple GPCRs, which can be utilized to modulate receptors from the inside. This novel intracellular site partially overlaps with the G-protein and β-arrestin coupling sites, providing a novel avenue for biological intervention. Here, we review evidence available for GPCR structures complexed with intracellular small-molecule allosteric modulators, elucidating drug-target interactions and allosteric mechanisms. Moreover, we highlight the potential of intracellular allosteric modulators in achieving biased signaling, which provides insights into biased allosteric mechanisms.
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Affiliation(s)
- Mingyang Zhang
- School of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaobing Lan
- School of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China
| | - Xiaolong Li
- Department of Orthopedics, Changhai Hospital, The First Affiliated Hospital of Naval Medical University, Shanghai 200433, China.
| | - Shaoyong Lu
- School of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia Hui Autonomous Region 750004, China; Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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29
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Mukhaleva E, Yang T, Sadler F, Sivaramakrishnan S, Ma N, Vaidehi N. Cellular Lipids Regulate the Conformational Ensembles of the Disordered Intracellular Loop 3 in β2 Adrenergic Receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.569080. [PMID: 38077083 PMCID: PMC10705491 DOI: 10.1101/2023.11.28.569080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
The structurally disordered intracellular loops (ICLs) of G protein-coupled receptors (GPCRs) play a critical role in G protein coupling. In our previous work, we used a combination of FRET-based and computational methodologies to show that the third intracellular loop (ICL3) modulates the activity and G protein coupling selectivity in GPCRs. In the current study, we have uncovered the role of several lipid components in modulating the conformational ensemble of ICL3 of the β2-adrenergic receptor (β2AR). Our findings indicate that phosphatidylinositol 4,5-bisphosphate (PIP2) in the inner leaflet of the membrane bilayer acts as a stabilizing anchor for ICL3, opening the intracellular cavity to facilitate G protein coupling. This interaction between PIP2 and ICL3 causes tilting of β2AR within the cellular membrane. Notably, this tilting of the receptor is supported by ganglioside GM3 stabilizing the extracellular loops on the outer leaflet of the bilayer, thereby exerting an allosteric effect on the orthosteric ligand binding pocket. Our results underscore the significance of lipids in modulating GPCR activity, proposing an allosteric mechanism that occurs through the receptor's orientation within the membrane.
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Affiliation(s)
- Elizaveta Mukhaleva
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Tianyi Yang
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Fredrik Sadler
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Sivaraj Sivaramakrishnan
- Biochemistry, Molecular Biology and Biophysics Graduate Program, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Ning Ma
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Nagarajan Vaidehi
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, CA, USA
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
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30
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Lee KH, Shi L. Unraveling activation-related rearrangements and intrinsic divergence from ligand-induced conformational changes of the dopamine D3 and D2 receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566699. [PMID: 38014309 PMCID: PMC10680602 DOI: 10.1101/2023.11.11.566699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Effective rational drug discovery targeting a specific protein hinges on understanding their functional states and distinguishing it from homologs. However, for the G protein coupled receptors, both the activation-related conformational changes (ACCs) and the intrinsic divergence among receptors can be misled or obscured by ligand-induced conformational changes (LCCs). Here, we unraveled ACCs and intrinsic divergence from LCCs of the dopamine D3 and D2 receptors (D3R and D2R), by analyzing their experimentally determined structures and the molecular dynamics simulation results of the receptors bound with different ligands. In addition to the ACCs common to other aminergic receptors, we revealed unique ACCs for these two receptors including TM5e and TM6e shifting away from TM2e and TM3e, with a subtle rotation of TM5e. In identifying intrinsic divergence, we found pronounced outward tilting of TM6e in the D2R compared to the D3R in both experimental structures and simulations with ligands in different scaffolds. This tilting was drastically reduced in the simulations of the receptors bound with nonselective full agonist quinpirole, suggesting a misleading impact of LCCs. Further, in the quinpirole-bound simulations, TM1 showed a greater disparity between these receptors, indicating that LCCs may obscure intrinsic divergence. In addition, our analysis showed that the impact of the nonconserved TM1 propagated to conserved Trp7.40 and Glu2.65, both are ligand binding residues. We also found that the D2R exhibited heightened flexibility compared to the D3R in the extracellular portions of TMs 5, 6, and 7, potentially associated with its greater ligand binding site plasticity. Our results lay the groundwork for crafting ligands specifically targeting D2R or D3R with more precise pharmacological profiles.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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31
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Munro TA. Reanalysis of a μ opioid receptor crystal structure reveals a covalent adduct with BU72. BMC Biol 2023; 21:213. [PMID: 37817141 PMCID: PMC10566028 DOI: 10.1186/s12915-023-01689-w] [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: 12/12/2022] [Accepted: 08/25/2023] [Indexed: 10/12/2023] Open
Abstract
BACKGROUND The first crystal structure of the active μ opioid receptor (μOR) exhibited several unexplained features. The ligand BU72 exhibited many extreme deviations from ideal geometry, along with unexplained electron density. I previously showed that inverting the benzylic configuration resolved these problems, establishing revised stereochemistry of BU72 and its analog BU74. However, another problem remains unresolved: additional unexplained electron density contacts both BU72 and a histidine residue in the N-terminus, revealing the presence of an as-yet unidentified atom. RESULTS These short contacts and uninterrupted density are inconsistent with non-covalent interactions. Therefore, BU72 and μOR form a covalent adduct, rather than representing two separate entities as in the original model. A subsequently proposed magnesium complex is inconsistent with multiple lines of evidence. However, oxygen fits the unexplained density well. While the structure I propose is tentative, similar adducts have been reported previously in the presence of reactive oxygen species. Moreover, known sources of reactive oxygen species were present: HEPES buffer, nickel ions, and a sequence motif that forms redox-active nickel complexes. This motif contacts the unexplained density. The adduct exhibits severe strain, and the tethered N-terminus forms contacts with adjacent residues. These forces, along with the nanobody used as a G protein substitute, would be expected to influence the receptor conformation. Consistent with this, the intracellular end of the structure differs markedly from subsequent structures of active μOR bound to Gi protein. CONCLUSIONS Later Gi-bound structures are likely to be more accurate templates for ligand docking and modelling of active G protein-bound μOR. The possibility of reactions like this should be considered in the choice of protein truncation sites and purification conditions, and in the interpretation of excess or unexplained density.
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Affiliation(s)
- Thomas A Munro
- School of Life and Environmental Sciences, Deakin University, Burwood, VIC, 3125, Australia.
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32
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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: 5] [Impact Index Per Article: 5.0] [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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33
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Tauber M, Ben-Chaim Y. Functional consequences of a rare human serotonergic 5-HT 1A receptor variant. Front Pharmacol 2023; 14:1270726. [PMID: 37795037 PMCID: PMC10547147 DOI: 10.3389/fphar.2023.1270726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023] Open
Abstract
Serotonin (5-HT) plays a central role in various brain functions via the activation of a family of receptors, most of them G protein coupled receptors (GPCRs). 5-HT1A receptor, the most abundant 5-HT receptors, was implicated in many brain dysfunctions and is a major target for drug discovery. Several genetic polymorphisms within the 5-HT1A receptor gene were identified and linked to different conditions, including anxiety and depression. Here, we used Xenopus oocytes to examine the effects of one of the functional polymorphism, Arg220Leu, on the function of the receptor. We found that the mutated receptor shows normal activation of G protein and normal 5-HT binding. On the other hand, the mutated receptor shows impaired desensitization, probably due to impairment in activation of β arrestin-dependent pathway. Furthermore, while the 5-HT1A receptor was shown to exhibit voltage dependent activation by serotonin and by buspirone, the mutated receptor was voltage-independent. Our results suggest a pronounced effect of the mutation on the function of the 5-HT1A receptor and add to our understanding of the molecular mechanism of its voltage dependence. Moreover, the findings of this study may suggest a functional explanation for the possible link between this variant and brain pathologies.
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Affiliation(s)
| | - Yair Ben-Chaim
- Department of Natural Sciences, The Open University of Israel, Ra’anana, Israel
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34
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Lee KH, Manning JJ, Javitch J, Shi L. A Novel "Activation Switch" Motif Common to All Aminergic Receptors. J Chem Inf Model 2023; 63:5001-5017. [PMID: 37540602 PMCID: PMC10695015 DOI: 10.1021/acs.jcim.3c00732] [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: 08/06/2023]
Abstract
Aminergic receptors are G protein-coupled receptors (GPCRs) that transduce signals from small endogenous biogenic amines to regulate intracellular signaling pathways. Agonist binding in the ligand binding pocket on the extracellular side opens and prepares a cavity on the intracellular face of the receptors to interact with and activate G proteins and β-arrestins. Here, by reviewing and analyzing all available aminergic receptor structures, we seek to identify activation-related conformational changes that are independent of the specific scaffold of the bound agonist, which we define as "activation conformational changes" (ACCs). While some common intracellular ACCs have been well-documented, identifying common extracellular ACCs, including those in the ligand binding pocket, is complicated by local adjustments to different ligand scaffolds. Our analysis shows no common ACCs at the extracellular ends of the transmembrane helices. Furthermore, the restricted access to the ligand binding pocket identified previously in some receptors is not universal. Notably, the Trp6.48 toggle switch and the Pro5.50-Ile3.40-Phe6.44 (PIF) motif at the bottom of the ligand binding pocket have previously been proposed to mediate the conformational consequences of ligand binding to the intracellular side of the receptors. Our analysis shows that common ACCs in the ligand binding pocket are associated with the PIF motif and nearby residues, including Trp6.48, but fails to support a shared rotamer toggle associated with activation. However, we identify two common rearrangements between the extracellular and middle subsegments, and propose a novel "activation switch" motif common to all aminergic receptors. This motif includes the middle subsegments of transmembrane helices 3, 5, and 6 and integrates both the PIF motif and Trp6.48.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jamie J. Manning
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Jonathan Javitch
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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35
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Cao Y, van der Velden WJC, Namkung Y, Nivedha AK, Cho A, Sedki D, Holleran B, Lee N, Leduc R, Muk S, Le K, Bhattacharya S, Vaidehi N, Laporte SA. Unraveling allostery within the angiotensin II type 1 receptor for Gα q and β-arrestin coupling. Sci Signal 2023; 16:eadf2173. [PMID: 37552769 PMCID: PMC10640921 DOI: 10.1126/scisignal.adf2173] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 07/20/2023] [Indexed: 08/10/2023]
Abstract
G protein-coupled receptors engage both G proteins and β-arrestins, and their coupling can be biased by ligands and mutations. Here, to resolve structural elements and mechanisms underlying effector coupling to the angiotensin II (AngII) type 1 receptor (AT1R), we combined alanine scanning mutagenesis of the entire sequence of the receptor with pharmacological profiling of Gαq and β-arrestin engagement to mutant receptors and molecular dynamics simulations. We showed that Gαq coupling to AT1R involved a large number of residues spread across the receptor, whereas fewer structural regions of the receptor contributed to β-arrestin coupling regulation. Residue stretches in transmembrane domain 4 conferred β-arrestin bias and represented an important structural element in AT1R for functional selectivity. Furthermore, we identified allosteric small-molecule binding sites that were enclosed by communities of residues that produced biased signaling when mutated. Last, we showed that allosteric communication within AT1R emanating from the Gαq coupling site spread beyond the orthosteric AngII-binding site and across different regions of the receptor, including currently unresolved structural regions. Our findings reveal structural elements and mechanisms within AT1R that bias Gαq and β-arrestin coupling and that could be harnessed to design biased receptors for research purposes and to develop allosteric modulators.
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Affiliation(s)
- Yubo Cao
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Wijnand J. C. van der Velden
- Department of Computational & Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Yoon Namkung
- Department of Medicine, McGill University Health Center, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Anita K. Nivedha
- Department of Computational & Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Aaron Cho
- Department of Medicine, McGill University Health Center, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Dana Sedki
- Department of Medicine, McGill University Health Center, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Brian Holleran
- Department of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Nicholas Lee
- Department of Medicine, McGill University Health Center, McGill University, Montréal, Québec H4A 3J1, Canada
| | - Richard Leduc
- Department of Pharmacology-Physiology, Université de Sherbrooke, Sherbrooke, Québec, J1H 5N4, Canada
| | - Sanychen Muk
- Department of Computational & Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Keith Le
- Department of Computational & Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Supriyo Bhattacharya
- Department of Computational & Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Nagarajan Vaidehi
- Department of Computational & Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
| | - Stéphane A. Laporte
- Department of Pharmacology and Therapeutics, McGill University, Montréal, Québec H3G 1Y6, Canada
- Department of Medicine, McGill University Health Center, McGill University, Montréal, Québec H4A 3J1, Canada
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36
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Chen K, Zhang C, Lin S, Yan X, Cai H, Yi C, Ma L, Chu X, Liu Y, Zhu Y, Han S, Zhao Q, Wu B. Tail engagement of arrestin at the glucagon receptor. Nature 2023; 620:904-910. [PMID: 37558880 PMCID: PMC10447241 DOI: 10.1038/s41586-023-06420-x] [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] [Received: 04/03/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023]
Abstract
Arrestins have pivotal roles in regulating G protein-coupled receptor (GPCR) signalling by desensitizing G protein activation and mediating receptor internalization1,2. It has been proposed that the arrestin binds to the receptor in two different conformations, 'tail' and 'core', which were suggested to govern distinct processes of receptor signalling and trafficking3,4. However, little structural information is available for the tail engagement of the arrestins. Here we report two structures of the glucagon receptor (GCGR) bound to β-arrestin 1 (βarr1) in glucagon-bound and ligand-free states. These structures reveal a receptor tail-engaged binding mode of βarr1 with many unique features, to our knowledge, not previously observed. Helix VIII, instead of the receptor core, has a major role in accommodating βarr1 by forming extensive interactions with the central crest of βarr1. The tail-binding pose is further defined by a close proximity between the βarr1 C-edge and the receptor helical bundle, and stabilized by a phosphoinositide derivative that bridges βarr1 with helices I and VIII of GCGR. Lacking any contact with the arrestin, the receptor core is in an inactive state and loosely binds to glucagon. Further functional studies suggest that the tail conformation of GCGR-βarr governs βarr recruitment at the plasma membrane and endocytosis of GCGR, and provides a molecular basis for the receptor forming a super-complex simultaneously with G protein and βarr to promote sustained signalling within endosomes. These findings extend our knowledge about the arrestin-mediated modulation of GPCR functionalities.
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Affiliation(s)
- Kun Chen
- State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chenhui Zhang
- State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shuling Lin
- State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xinyu Yan
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Heng Cai
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Cuiying Yi
- State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Limin Ma
- State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xiaojing Chu
- State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yuchen Liu
- State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ya Zhu
- Lingang Laboratory, Shanghai, China
| | - Shuo Han
- State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
| | - Qiang Zhao
- State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, China.
| | - Beili Wu
- State Key Laboratory of Drug Research, State Key Laboratory of Chemical Biology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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37
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Huang SM, Xiong MY, Liu L, Mu J, Wang MW, Jia YL, Cai K, Tie L, Zhang C, Cao S, Wen X, Wang JL, Guo SC, Li Y, Qu CX, He QT, Cai BY, Xue C, Gan S, Xie Y, Cong X, Yang Z, Kong W, Li S, Li Z, Xiao P, Yang F, Yu X, Guan YF, Zhang X, Liu Z, Yang BX, Du Y, Sun JP. Single hormone or synthetic agonist induces G s/G i coupling selectivity of EP receptors via distinct binding modes and propagating paths. Proc Natl Acad Sci U S A 2023; 120:e2216329120. [PMID: 37478163 PMCID: PMC10372679 DOI: 10.1073/pnas.2216329120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 05/18/2023] [Indexed: 07/23/2023] Open
Abstract
To accomplish concerted physiological reactions, nature has diversified functions of a single hormone at at least two primary levels: 1) Different receptors recognize the same hormone, and 2) different cellular effectors couple to the same hormone-receptor pair [R.P. Xiao, Sci STKE 2001, re15 (2001); L. Hein, J. D. Altman, B.K. Kobilka, Nature 402, 181-184 (1999); Y. Daaka, L. M. Luttrell, R. J. Lefkowitz, Nature 390, 88-91 (1997)]. Not only these questions lie in the heart of hormone actions and receptor signaling but also dissecting mechanisms underlying these questions could offer therapeutic routes for refractory diseases, such as kidney injury (KI) or X-linked nephrogenic diabetes insipidus (NDI). Here, we identified that Gs-biased signaling, but not Gi activation downstream of EP4, showed beneficial effects for both KI and NDI treatments. Notably, by solving Cryo-electron microscope (cryo-EM) structures of EP3-Gi, EP4-Gs, and EP4-Gi in complex with endogenous prostaglandin E2 (PGE2)or two synthetic agonists and comparing with PGE2-EP2-Gs structures, we found that unique primary sequences of prostaglandin E2 receptor (EP) receptors and distinct conformational states of the EP4 ligand pocket govern the Gs/Gi transducer coupling selectivity through different structural propagation paths, especially via TM6 and TM7, to generate selective cytoplasmic structural features. In particular, the orientation of the PGE2 ω-chain and two distinct pockets encompassing agonist L902688 of EP4 were differentiated by their Gs/Gi coupling ability. Further, we identified common and distinct features of cytoplasmic side of EP receptors for Gs/Gi coupling and provide a structural basis for selective and biased agonist design of EP4 with therapeutic potential.
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Affiliation(s)
- Shen-Ming Huang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
| | - Meng-Yao Xiong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
| | - Lei Liu
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Jianqiang Mu
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong518055, China
| | - Ming-Wei Wang
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Ying-Li Jia
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
| | - Kui Cai
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
| | - Lu Tie
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
| | - Chao Zhang
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Sheng Cao
- School of Medicine, Kobilka Institute of Innovative Drug Discovery, Chinese University of Hong Kong, Shenzhen, Guangdong518172, China
| | - Xin Wen
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Jia-Le Wang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
| | - Sheng-Chao Guo
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Physiology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong250012, China
| | - Yu Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
| | - Chang-Xiu Qu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
| | - Qing-Tao He
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Physiology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong250012, China
| | - Bo-Yang Cai
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
| | - Chenyang Xue
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong518055, China
| | - Shiyi Gan
- School of Medicine, Kobilka Institute of Innovative Drug Discovery, Chinese University of Hong Kong, Shenzhen, Guangdong518172, China
| | - Yihe Xie
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
| | - Xin Cong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
| | - Zhao Yang
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Wei Kong
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
| | - Shuo Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
| | - Zijian Li
- Department of Cardiology, Institute of Vascular Medicine, Peking University Third Hospital, Research, Beijing100191, China
- Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing100191, P. R. China
| | - Peng Xiao
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Fan Yang
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Physiology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong250012, China
- Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
| | - Xiao Yu
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Physiology, School of Basic Medical Sciences, Shandong University, Jinan, Shandong250012, China
| | - You-Fei Guan
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian116044, China
| | - Xiaoyan Zhang
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian116044, China
| | - Zhongmin Liu
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong518055, China
| | - Bao-Xue Yang
- Department of Pharmacology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
| | - Yang Du
- School of Medicine, Kobilka Institute of Innovative Drug Discovery, Chinese University of Hong Kong, Shenzhen, Guangdong518172, China
| | - Jin-Peng Sun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University, Beijing100191, China
- Key Laboratory Experimental Teratology of the Ministry of Education, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
- Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing100191, P. R. China
- Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, Shandong250012, China
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38
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Gusach A, Lee Y, Khoshgrudi AN, Mukhaleva E, Ma N, Koers EJ, Chen Q, Edwards PC, Huang F, Kim J, Mancia F, Verprintsev DB, Vaidehi N, Weyand SN, Tate CG. Molecular recognition of an aversive odorant by the murine trace amine-associated receptor TAAR7f. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.07.547762. [PMID: 37461561 PMCID: PMC10350033 DOI: 10.1101/2023.07.07.547762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
There are two main families of G protein-coupled receptors that detect odours in humans, the odorant receptors (ORs) and the trace amine-associated receptors (TAARs). Their amino acid sequences are distinct, with the TAARs being most similar to the aminergic receptors such as those activated by adrenaline, serotonin and histamine. To elucidate the structural determinants of ligand recognition by TAARs, we have determined the cryo-EM structure of a murine receptor, mTAAR7f, coupled to the heterotrimeric G protein Gs and bound to the odorant N,N-dimethylcyclohexylamine (DMCH) to an overall resolution of 2.9 Å. DMCH is bound in a hydrophobic orthosteric binding site primarily through van der Waals interactions and a strong charge-charge interaction between the tertiary amine of the ligand and an aspartic acid residue. This site is distinct and non-overlapping with the binding site for the odorant propionate in the odorant receptor OR51E2. The structure, in combination with mutagenesis data and molecular dynamics simulations suggests that the activation of the receptor follows a similar pathway to that of the β-adrenoceptors, with the significant difference that DMCH interacts directly with one of the main activation microswitch residues.
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Affiliation(s)
- Anastasiia Gusach
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge CB2 0QH, UK
| | - Yang Lee
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge CB2 0QH, UK
| | - Armin Nikpour Khoshgrudi
- Centre of Membrane Proteins and Receptors (COMPARE), University
of Birmingham and University of Nottingham, Midlands, NG7 2RD, UK
- Division of Physiology, Pharmacology & Neuroscience, School
of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Elizaveta Mukhaleva
- Department of Computational and Quantitative Medicine, Beckman
Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, CA-91006, USA
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman
Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, CA-91006, USA
| | - Eline J. Koers
- Centre of Membrane Proteins and Receptors (COMPARE), University
of Birmingham and University of Nottingham, Midlands, NG7 2RD, UK
- Division of Physiology, Pharmacology & Neuroscience, School
of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Qingchao Chen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge CB2 0QH, UK
| | - Patricia C. Edwards
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge CB2 0QH, UK
| | - Fanglu Huang
- Department of Biochemistry, University of Cambridge, Tennis Court
Road, Cambridge, UK
| | - Jonathan Kim
- Department of Physiology and Cellular Biophysics, Columbia
University, Irving Medical Center, New York, NY 10032, USA
| | - Filippo Mancia
- Department of Physiology and Cellular Biophysics, Columbia
University, Irving Medical Center, New York, NY 10032, USA
| | - Dmitry B. Verprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University
of Birmingham and University of Nottingham, Midlands, NG7 2RD, UK
- Division of Physiology, Pharmacology & Neuroscience, School
of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman
Research Institute of the City of Hope, 1500 E Duarte Road, Duarte, CA-91006, USA
| | - Simone N. Weyand
- Department of Biochemistry, University of Cambridge, Tennis Court
Road, Cambridge, UK
- Department of Medicine, University of Cambridge, Victor Phillip
Dahdaleh Building, Heart & Lung Research Institute, Papworth Road, Cambridge Biomedical
Campus, Cambridge, CB2 0BB, UK
- Cambridge Institute for Medical Research, Keith Peters Building,
Biomedical Campus, Hills Rd, Cambridge CB2 0XY, UK
- EMBL’s European Bioinformatics Institute (EMBL-EBI),
Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue,
Cambridge CB2 0QH, UK
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39
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Vuckovic Z, Wang J, Pham V, Mobbs JI, Belousoff MJ, Bhattarai A, Burger WAC, Thompson G, Yeasmin M, Nawaratne V, Leach K, van der Westhuizen ET, Khajehali E, Liang YL, Glukhova A, Wootten D, Lindsley CW, Tobin A, Sexton P, Danev R, Valant C, Miao Y, Christopoulos A, Thal DM. Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics. eLife 2023; 12:83477. [PMID: 37248726 DOI: 10.7554/elife.83477] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/12/2023] [Indexed: 05/31/2023] Open
Abstract
Allosteric modulation of G protein-coupled receptors (GPCRs) is a major paradigm in drug discovery. Despite decades of research, a molecular-level understanding of the general principles that govern the myriad pharmacological effects exerted by GPCR allosteric modulators remains limited. The M4 muscarinic acetylcholine receptor (M4 mAChR) is a validated and clinically relevant allosteric drug target for several major psychiatric and cognitive disorders. In this study, we rigorously quantified the affinity, efficacy, and magnitude of modulation of two different positive allosteric modulators, LY2033298 (LY298) and VU0467154 (VU154), combined with the endogenous agonist acetylcholine (ACh) or the high-affinity agonist iperoxo (Ipx), at the human M4 mAChR. By determining the cryo-electron microscopy structures of the M4 mAChR, bound to a cognate Gi1 protein and in complex with ACh, Ipx, LY298-Ipx, and VU154-Ipx, and applying molecular dynamics simulations, we determine key molecular mechanisms underlying allosteric pharmacology. In addition to delineating the contribution of spatially distinct binding sites on observed pharmacology, our findings also revealed a vital role for orthosteric and allosteric ligand-receptor-transducer complex stability, mediated by conformational dynamics between these sites, in the ultimate determination of affinity, efficacy, cooperativity, probe dependence, and species variability. There results provide a holistic framework for further GPCR mechanistic studies and can aid in the discovery and design of future allosteric drugs.
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Affiliation(s)
- Ziva Vuckovic
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Vi Pham
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Jesse I Mobbs
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Matthew J Belousoff
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Wessel A C Burger
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Geoff Thompson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Mahmuda Yeasmin
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Vindhya Nawaratne
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Katie Leach
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Emma T van der Westhuizen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Elham Khajehali
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Yi-Lynn Liang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Alisa Glukhova
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Denise Wootten
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Craig W Lindsley
- Department of Pharmacology, Warren Center for Neuroscience Drug Discovery and Department of Chemistry, Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, United States
| | - Andrew Tobin
- The Centre for Translational Pharmacology, Advanced Research Centre (ARC), College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Patrick Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Celine Valant
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- Neuromedicines Discovery Centre, Monash University, Parkville, Australia
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
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40
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Cai B, El Daibani A, Bai Y, Che T, Krusemark CJ. Direct Selection of DNA-Encoded Libraries for Biased Agonists of GPCRs on Live Cells. JACS AU 2023; 3:1076-1088. [PMID: 37124302 PMCID: PMC10131204 DOI: 10.1021/jacsau.2c00674] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 05/03/2023]
Abstract
G protein-coupled receptors (GPCRs) are the largest superfamily of human membrane target proteins for approved drugs. GPCR ligands can have a complex array of pharmacological activities. Among these activities, biased agonists have potential to serve as both chemical probes to understand specific aspects of receptor signaling and therapeutic leads with more specific, desired activity. Challenges exist, however, in the development of new biased activators due, in part, to the low throughput of traditional screening approaches. DNA-encoded chemical libraries (DELs) dramatically improve the throughput of drug discovery by allowing a collective selection, rather than discrete screening, of large compound libraries. The use of DELs has been largely limited to affinity-based selections against purified protein targets, which identify binders only. Herein, we report a split protein complementation approach that allows direct identification of DNA-linked molecules that induce the dimerization of two proteins. We used this selection with a DEL against opioid receptor GPCRs on living cells for the identification of small molecules that possess the specific function of activation of either β-arrestin or G protein signaling pathways. This approach was applied to δ-, μ-, and κ-opioid receptors and enabled the discovery of compound [66,66], a selective, G-protein-biased agonist of the κ-opioid receptor (EC50 = 100 nM, E max = 82%, Gi bias factor = 6.6). This approach should be generally applicable for the direct selection of chemical inducers of dimerization from DELs and expand the utility of DELs to enrich molecules with a specific and desired biochemical function.
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Affiliation(s)
- Bo Cai
- Department
of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for
Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Amal El Daibani
- Center
for Clinical Pharmacology, Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Yuntian Bai
- Department
of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for
Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Tao Che
- Center
for Clinical Pharmacology, Department of Anesthesiology, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Casey J. Krusemark
- Department
of Medicinal Chemistry and Molecular Pharmacology, Purdue Center for
Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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41
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Xu X, Shonberg J, Kaindl J, Clark MJ, Stößel A, Maul L, Mayer D, Hübner H, Hirata K, Venkatakrishnan AJ, Dror RO, Kobilka BK, Sunahara RK, Liu X, Gmeiner P. Constrained catecholamines gain β 2AR selectivity through allosteric effects on pocket dynamics. Nat Commun 2023; 14:2138. [PMID: 37059717 PMCID: PMC10104803 DOI: 10.1038/s41467-023-37808-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 03/30/2023] [Indexed: 04/16/2023] Open
Abstract
G protein-coupled receptors (GPCRs) within the same subfamily often share high homology in their orthosteric pocket and therefore pose challenges to drug development. The amino acids that form the orthosteric binding pocket for epinephrine and norepinephrine in the β1 and β2 adrenergic receptors (β1AR and β2AR) are identical. Here, to examine the effect of conformational restriction on ligand binding kinetics, we synthesized a constrained form of epinephrine. Surprisingly, the constrained epinephrine exhibits over 100-fold selectivity for the β2AR over the β1AR. We provide evidence that the selectivity may be due to reduced ligand flexibility that enhances the association rate for the β2AR, as well as a less stable binding pocket for constrained epinephrine in the β1AR. The differences in the amino acid sequence of the extracellular vestibule of the β1AR allosterically alter the shape and stability of the binding pocket, resulting in a marked difference in affinity compared to the β2AR. These studies suggest that for receptors containing identical binding pocket residues, the binding selectivity may be influenced in an allosteric manner by surrounding residues, like those of the extracellular loops (ECLs) that form the vestibule. Exploiting these allosteric influences may facilitate the development of more subtype-selective ligands for GPCRs.
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Affiliation(s)
- Xinyu Xu
- State Key laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China
| | - Jeremy Shonberg
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nurnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Jonas Kaindl
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nurnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Mary J Clark
- Department of Pharmacology, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Anne Stößel
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nurnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Luis Maul
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nurnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Daniel Mayer
- Department of Pharmacology, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California, 92093, USA
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nurnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany
| | - Kunio Hirata
- Advanced Photon Technology Division, Research Infrastructure Group, SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1 Kouto Sayo-cho Sayo-gun, Hyogo, 679-5148, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - A J Venkatakrishnan
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Roger K Sunahara
- Department of Pharmacology, University of California San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California, 92093, USA.
| | - Xiangyu Liu
- State Key laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Pharmaceutical Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China.
- Beijing Key Laboratory of Cardiovascular Receptors Research, Peking University, Beijing, China.
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University Erlangen-Nurnberg, Nikolaus-Fiebiger-Straße 10, 91058, Erlangen, Germany.
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Klenk C, Scrivens M, Niederer A, Shi S, Mueller L, Gersz E, Zauderer M, Smith ES, Strohner R, Plückthun A. A Vaccinia-based system for directed evolution of GPCRs in mammalian cells. Nat Commun 2023; 14:1770. [PMID: 36997531 PMCID: PMC10063554 DOI: 10.1038/s41467-023-37191-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/06/2023] [Indexed: 04/03/2023] Open
Abstract
Directed evolution in bacterial or yeast display systems has been successfully used to improve stability and expression of G protein-coupled receptors for structural and biophysical studies. Yet, several receptors cannot be tackled in microbial systems due to their complex molecular composition or unfavorable ligand properties. Here, we report an approach to evolve G protein-coupled receptors in mammalian cells. To achieve clonality and uniform expression, we develop a viral transduction system based on Vaccinia virus. By rational design of synthetic DNA libraries, we first evolve neurotensin receptor 1 for high stability and expression. Second, we demonstrate that receptors with complex molecular architectures and large ligands, such as the parathyroid hormone 1 receptor, can be readily evolved. Importantly, functional receptor properties can now be evolved in the presence of the mammalian signaling environment, resulting in receptor variants exhibiting increased allosteric coupling between the ligand binding site and the G protein interface. Our approach thus provides insights into the intricate molecular interplay required for GPCR activation.
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Affiliation(s)
- Christoph Klenk
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Maria Scrivens
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Anina Niederer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Shuying Shi
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Loretta Mueller
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Elaine Gersz
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Maurice Zauderer
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Ernest S Smith
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Ralf Strohner
- MorphoSys AG, Semmelweisstr. 7, 82152, Planegg, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
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43
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Shpakov AO. Allosteric Regulation of G-Protein-Coupled Receptors: From Diversity of Molecular Mechanisms to Multiple Allosteric Sites and Their Ligands. Int J Mol Sci 2023; 24:6187. [PMID: 37047169 PMCID: PMC10094638 DOI: 10.3390/ijms24076187] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Allosteric regulation is critical for the functioning of G protein-coupled receptors (GPCRs) and their signaling pathways. Endogenous allosteric regulators of GPCRs are simple ions, various biomolecules, and protein components of GPCR signaling (G proteins and β-arrestins). The stability and functional activity of GPCR complexes is also due to multicenter allosteric interactions between protomers. The complexity of allosteric effects caused by numerous regulators differing in structure, availability, and mechanisms of action predetermines the multiplicity and different topology of allosteric sites in GPCRs. These sites can be localized in extracellular loops; inside the transmembrane tunnel and in its upper and lower vestibules; in cytoplasmic loops; and on the outer, membrane-contacting surface of the transmembrane domain. They are involved in the regulation of basal and orthosteric agonist-stimulated receptor activity, biased agonism, GPCR-complex formation, and endocytosis. They are targets for a large number of synthetic allosteric regulators and modulators, including those constructed using molecular docking. The review is devoted to the principles and mechanisms of GPCRs allosteric regulation, the multiplicity of allosteric sites and their topology, and the endogenous and synthetic allosteric regulators, including autoantibodies and pepducins. The allosteric regulation of chemokine receptors, proteinase-activated receptors, thyroid-stimulating and luteinizing hormone receptors, and beta-adrenergic receptors are described in more detail.
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Affiliation(s)
- Alexander O Shpakov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, 194223 St. Petersburg, Russia
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Borges JI, Suster MS, Lymperopoulos A. Cardiac RGS Proteins in Human Heart Failure and Atrial Fibrillation: Focus on RGS4. Int J Mol Sci 2023; 24:ijms24076136. [PMID: 37047106 PMCID: PMC10147095 DOI: 10.3390/ijms24076136] [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: 02/28/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/14/2023] Open
Abstract
The regulator of G protein signaling (RGS) proteins are crucial for the termination of G protein signals elicited by G protein-coupled receptors (GPCRs). This superfamily of cell membrane receptors, by far the largest and most versatile in mammals, including humans, play pivotal roles in the regulation of cardiac function and homeostasis. Perturbations in both the activation and termination of their G protein-mediated signaling underlie numerous heart pathologies, including heart failure (HF) and atrial fibrillation (AFib). Therefore, RGS proteins play important roles in the pathophysiology of these two devasting cardiac diseases, and several of them could be targeted therapeutically. Although close to 40 human RGS proteins have been identified, each RGS protein seems to interact only with a specific set of G protein subunits and GPCR types/subtypes in any given tissue or cell type. Numerous in vitro and in vivo studies in animal models, and also in diseased human heart tissue obtained from transplantations or tissue banks, have provided substantial evidence of the roles various cardiomyocyte RGS proteins play in cardiac normal homeostasis as well as pathophysiology. One RGS protein in particular, RGS4, has been reported in what are now decades-old studies to be selectively upregulated in human HF. It has also been implicated in protection against AFib via knockout mice studies. This review summarizes the current understanding of the functional roles of cardiac RGS proteins and their implications for the treatment of HF and AFib, with a specific focus on RGS4 for the aforementioned reasons but also because it can be targeted successfully with small organic molecule inhibitors.
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Affiliation(s)
- Jordana I Borges
- Laboratory for the Study of Neurohormonal Control of the Circulation, Department of Pharmaceutical Sciences, Barry and Judy Silverrman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33328-2018, USA
| | - Malka S Suster
- Laboratory for the Study of Neurohormonal Control of the Circulation, Department of Pharmaceutical Sciences, Barry and Judy Silverrman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33328-2018, USA
| | - Anastasios Lymperopoulos
- Laboratory for the Study of Neurohormonal Control of the Circulation, Department of Pharmaceutical Sciences, Barry and Judy Silverrman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, FL 33328-2018, USA
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45
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Papasergi-Scott MM, Pérez-Hernández G, Batebi H, Gao Y, Eskici G, Seven AB, Panova O, Hilger D, Casiraghi M, He F, Maul L, Gmeiner P, Kobilka BK, Hildebrand PW, Skiniotis G. Time-resolved cryo-EM of G protein activation by a GPCR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533387. [PMID: 36993214 PMCID: PMC10055275 DOI: 10.1101/2023.03.20.533387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
G protein-coupled receptors (GPCRs) activate heterotrimeric G proteins by stimulating the exchange of guanine nucleotide in the Gα subunit. To visualize this mechanism, we developed a time-resolved cryo-EM approach that examines the progression of ensembles of pre-steady-state intermediates of a GPCR-G protein complex. Using variability analysis to monitor the transitions of the stimulatory Gs protein in complex with the β 2 -adrenergic receptor (β 2 AR) at short sequential time points after GTP addition, we identified the conformational trajectory underlying G protein activation and functional dissociation from the receptor. Twenty transition structures generated from sequential overlapping particle subsets along this trajectory, compared to control structures, provide a high-resolution description of the order of events driving G protein activation upon GTP binding. Structural changes propagate from the nucleotide-binding pocket and extend through the GTPase domain, enacting alterations to Gα Switch regions and the α5 helix that weaken the G protein-receptor interface. Molecular dynamics (MD) simulations with late structures in the cryo-EM trajectory support that enhanced ordering of GTP upon closure of the alpha-helical domain (AHD) against the nucleotide-bound Ras-homology domain (RHD) correlates with irreversible α5 helix destabilization and eventual dissociation of the G protein from the GPCR. These findings also highlight the potential of time-resolved cryo-EM as a tool for mechanistic dissection of GPCR signaling events.
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46
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The Mechanisms of GPR55 Receptor Functional Selectivity during Apoptosis and Proliferation Regulation in Cancer Cells. Int J Mol Sci 2023; 24:ijms24065524. [PMID: 36982628 PMCID: PMC10054013 DOI: 10.3390/ijms24065524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/15/2023] Open
Abstract
GPR55 is a non-canonical cannabinoid receptor, important for cancer proliferation. Depending on the ligand, it induces either cell proliferation or death. The objective of the study was to establish the mechanisms of this multidirectional signaling. Using the CRISPR-Cas9 system, the GPR55, CB1, CB2, and GPR18 receptor knockouts of the MDA-MB-231 line were obtained. After the CB2 receptor knockout, the pro-apoptotic activity of the pro-apoptotic ligand docosahexaenoyl dopamine (DHA-DA) slightly increased, while the pro-proliferative activity of the most active synthetic ligand of the GPR55 receptor (ML-184) completely disappeared. On the original cell line, the stimulatory effect of ML-184 was removed by the CB2 receptor blocker and by GPR55 receptor knockout. Thus, it can be confidently assumed that when proliferation is stimulated with the participation of the GPR55 receptor, a signal is transmitted from the CB2 receptor to the GPR55 receptor due to the formation of a heterodimer. GPR18 was additionally involved in the implementation of the pro-apoptotic effect of DHA-DA, while the CB1 receptor is not involved. In the implementation of the pro-apoptotic action of DHA-DA, the elimination of Gα13 led to a decrease in cytotoxicity. The obtained data provide novel details to the mechanism of the pro-proliferative action of GPR55.
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47
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Kossoń P, Dyniewicz J, Lipiński PFJ, Matalińska J, Misicka A, Bojarski AJ, Mordalski S. Gα i-derived peptide binds the µ-opioid receptor. Pharmacol Rep 2023; 75:465-473. [PMID: 36840824 DOI: 10.1007/s43440-023-00457-5] [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: 08/16/2022] [Revised: 01/24/2023] [Accepted: 01/30/2023] [Indexed: 02/26/2023]
Abstract
BACKGROUND G protein-coupled receptors (GPCRs) transduce external stimuli into the cell by G proteins via an allosteric mechanism. Agonist binding to the receptor stimulates GDP/GTP exchange within the heterotrimeric G protein complex, whereas recent structures of GPCR-G protein complexes revealed that the H5, S1 and S2 domains of Gα are involved in binding the active receptor, earlier studies showed that a short peptide analog derived from the C-terminus (H5) of the G protein transducin (Gt) is sufficient to stabilize rhodopsin in an active form. METHODS We have used Molecular Dynamics simulations along with biological evaluation by means of radio-ligand binding assay to study the interactions between Gαi-derived peptide (G-peptide) and the µ-opioid receptor (µOR). RESULTS Here, we show that a Gαi-derived peptide of 12 amino acids binds the µ-opioid receptor and acts as an allosteric modulator. The Gαi-derived peptide increases µOR affinity for its agonist morphine in a dose-dependent way. CONCLUSIONS These results indicate that the GPCR-Gα peptide interaction observed so far for only rhodopsin can be extrapolated to µOR. In addition, we show that the C-terminal peptide of the Gαi subunit is sufficient to stabilize the active conformation of the receptor. Our approach opens the possibility to investigate the GPCR-G protein interface with peptide modification.
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Affiliation(s)
- Piotr Kossoń
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland
| | - Jolanta Dyniewicz
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland
| | - Joanna Matalińska
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland
| | - Aleksandra Misicka
- Department of Neuropeptides, Mossakowski Medical Research Centre Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry, Maj Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 313-343, Kraków, Poland
| | - Stefan Mordalski
- Department of Medicinal Chemistry, Maj Institute of Pharmacology Polish Academy of Sciences, Smetna 12, 313-343, Kraków, Poland.
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48
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Kurihara Y, Ekimoto T, Gordon CT, Uchijima Y, Sugiyama R, Kitazawa T, Iwase A, Kotani R, Asai R, Pingault V, Ikeguchi M, Amiel J, Kurihara H. Mandibulofacial dysostosis with alopecia results from ETAR gain-of-function mutations via allosteric effects on ligand binding. J Clin Invest 2023; 133:151536. [PMID: 36637912 PMCID: PMC9927936 DOI: 10.1172/jci151536] [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: 05/19/2021] [Accepted: 12/16/2022] [Indexed: 01/14/2023] Open
Abstract
Mutations of G protein-coupled receptors (GPCRs) cause various human diseases, but the mechanistic details are limited. Here, we establish p.E303K in the gene encoding the endothelin receptor type A (ETAR/EDNRA) as a recurrent mutation causing mandibulofacial dysostosis with alopecia (MFDA), with craniofacial changes similar to those caused by p.Y129F. Mouse models carrying either of these missense mutations exhibited a partial maxillary-to-mandibular transformation, which was rescued by deleting the ligand endothelin 3 (ET3/EDN3). Pharmacological experiments confirmed the causative ETAR mutations as gain of function, dependent on ET3. To elucidate how an amino acid substitution far from the ligand binding site can increase ligand affinity, we used molecular dynamics (MD) simulations. E303 is located at the intracellular end of transmembrane domain 6, and its replacement by a lysine increased flexibility of this portion of the helix, thus favoring G protein binding and leading to G protein-mediated enhancement of agonist affinity. The Y129F mutation located under the ligand binding pocket reduced the sodium-water network, thereby affecting the extracellular portion of helices in favor of ET3 binding. These findings provide insight into the pathogenesis of MFDA and into allosteric mechanisms regulating GPCR function, which may provide the basis for drug design targeting GPCRs.
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Affiliation(s)
- Yukiko Kurihara
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | | | - Yasunobu Uchijima
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryo Sugiyama
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Taro Kitazawa
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akiyasu Iwase
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Risa Kotani
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Medical Science, Graduate School of Medicine, University of Hiroshima, Hiroshima, Japan
| | - Rieko Asai
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Véronique Pingault
- Department of Genomic Medicine for Rare Diseases, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan.,Center for Computational Science, RIKEN, Yokohama, Japan
| | - Jeanne Amiel
- INSERM UMR 1163, Institut Imagine and Université Paris-Cité, Paris, France.,Department of Genomic Medicine for Rare Diseases, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Hiroki Kurihara
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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49
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Molecular basis for the selective G protein signaling of somatostatin receptors. Nat Chem Biol 2023; 19:133-140. [PMID: 36138141 DOI: 10.1038/s41589-022-01130-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/01/2022] [Indexed: 02/04/2023]
Abstract
G protein-coupled receptors (GPCRs) modulate every aspect of physiological functions mainly through activating heterotrimeric G proteins. A majority of GPCRs promiscuously couple to multiple G protein subtypes. Here we validate that in addition to the well-known Gi/o pathway, somatostatin receptor 2 and 5 (SSTR2 and SSTR5) couple to the Gq/11 pathway and show that smaller ligands preferentially activate the Gi/o pathway. We further determined cryo-electron microscopy structures of the SSTR2‒Go and SSTR2‒Gq complexes bound to octreotide and SST-14. Structural and functional analysis revealed that G protein selectivity of SSTRs is not only determined by structural elements in the receptor-G protein interface, but also by the conformation of the agonist-binding pocket. Accordingly, smaller ligands fail to stabilize a broader agonist-binding pocket of SSTRs that is required for efficient Gq/11 coupling but not Gi/o coupling. Our studies facilitate the design of drugs with selective G protein signaling to improve therapeutic efficacy.
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50
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Xu J, Wang Q, Hübner H, Hu Y, Niu X, Wang H, Maeda S, Inoue A, Tao Y, Gmeiner P, Du Y, Jin C, Kobilka BK. Structural and dynamic insights into supra-physiological activation and allosteric modulation of a muscarinic acetylcholine receptor. Nat Commun 2023; 14:376. [PMID: 36690613 PMCID: PMC9870890 DOI: 10.1038/s41467-022-35726-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 12/21/2022] [Indexed: 01/25/2023] Open
Abstract
The M2 muscarinic receptor (M2R) is a prototypical G-protein-coupled receptor (GPCR) that serves as a model system for understanding GPCR regulation by both orthosteric and allosteric ligands. Here, we investigate the mechanisms governing M2R signaling versatility using cryo-electron microscopy (cryo-EM) and NMR spectroscopy, focusing on the physiological agonist acetylcholine and a supra-physiological agonist iperoxo, as well as a positive allosteric modulator LY2119620. These studies reveal that acetylcholine stabilizes a more heterogeneous M2R-G-protein complex than iperoxo, where two conformers with distinctive G-protein orientations were determined. We find that LY2119620 increases the affinity for both agonists, but differentially modulates agonists efficacy in G-protein and β-arrestin pathways. Structural and spectroscopic analysis suggest that LY211620 stabilizes distinct intracellular conformational ensembles from agonist-bound M2R, which may enhance β-arrestin recruitment while impairing G-protein activation. These results highlight the role of conformational dynamics in the complex signaling behavior of GPCRs, and could facilitate design of better drugs.
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Affiliation(s)
- Jun Xu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Beijing Advanced Innovation Center for Structural Biology, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Qinggong Wang
- Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, Chinese University of Hong Kong, 518172, Shenzhen, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, 230027, Hefei, P. R. China
| | - Harald Hübner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University, 91058, Erlangen, Germany
| | - Yunfei Hu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, 100084, Beijing, China
- Innovation Academy for Precision Measurement Science and Technology, CAS, 430071, Wuhan, China
| | - Xiaogang Niu
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, 100084, Beijing, China
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shoji Maeda
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pharmacology, Medical School, University of Michigan 1150 Medical Center Dr., 1315 Medical Science Research Bldg III, Ann Arbor, MI, 48109, USA
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, 980-8578, Japan
| | - Yuyong Tao
- Division of Life Sciences and Medicine, University of Science and Technology of China, 230027, Hefei, P. R. China
| | - Peter Gmeiner
- Department of Chemistry and Pharmacy, Medicinal Chemistry, Friedrich-Alexander University, 91058, Erlangen, Germany
| | - Yang Du
- Kobilka Institute of Innovative Drug Discovery, School of Life and Health Sciences, Chinese University of Hong Kong, 518172, Shenzhen, China.
| | - Changwen Jin
- Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, Peking University, 100084, Beijing, China.
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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