1
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Qiu X, Chao K, Song S, Wang YQ, Chen YA, Rouse SL, Yen HY, Robinson CV. Coupling and Activation of the β1 Adrenergic Receptor - The Role of the Third Intracellular Loop. J Am Chem Soc 2024. [PMID: 39359104 DOI: 10.1021/jacs.4c11250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
G protein-coupled receptors (GPCRs) belong to the most diverse group of membrane receptors with a conserved structure of seven transmembrane (TM) α-helices connected by intracellular and extracellular loops. Intracellular loop 3 (ICL3) connects TM5 and TM6, the two helices shown to play significant roles in receptor activation. Herein, we investigate the activation and signaling of the β1 adrenergic receptor (β1AR) using mass spectrometry (MS) with a particular focus on the ICL3 loop. First, using native MS, we measure the extent of receptor coupling to an engineered Gαs subunit (mini Gs) and show preferential coupling to β1AR with an intact ICL3 (β1AR_ICL3) compared to the truncated β1AR. Next, using hydrogen-deuterium exchange (HDX)-MS, we show how helix 5 of mini Gs reports on the extent of receptor activation in the presence of a range of agonists. Then, exploring a range of solution conditions and using comparative HDX, we note additional HDX protection when ICL3 is present, implying that mini Gs helix 5 presents a different binding conformation to the surface of β1AR_ICL3, a conclusion supported by MD simulation. Considering when this conformatonal change occurs we used time-resolved HDX and employed two functional assays to measure GDP release and cAMP production, with and without ICL3. We found that ICL3 exerts its effect on Gs through enhanced cAMP production but does not affect GDP release. Together, our study uncovers potential roles of ICL3 in fine-tuning GPCR activation through subtle changes in the binding pose of helix 5, only after nucleotide release from Gs.
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Affiliation(s)
- Xingyu Qiu
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, OX1 3QU, U.K
| | - Kin Chao
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - Siyuan Song
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, OX1 3QU, U.K
| | - Yi-Quan Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115024, Taiwan
| | - Yi-An Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115024, Taiwan
| | - Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, U.K
| | - Hsin-Yung Yen
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115024, Taiwan
| | - Carol V Robinson
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3QZ, U.K
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford, OX1 3QU, U.K
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2
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Belousov A, Maslov I, Orekhov P, Khorn P, Kuzmichev P, Baleeva N, Motov V, Bogorodskiy A, Krasnova S, Mineev K, Zinchenko D, Zernii E, Ivanovich V, Permyakov S, Hofkens J, Hendrix J, Cherezov V, Gensch T, Mishin A, Baranov M, Mishin A, Borshchevskiy V. Monitoring GPCR conformation with GFP-inspired dyes. iScience 2024; 27:110466. [PMID: 39156645 PMCID: PMC11326922 DOI: 10.1016/j.isci.2024.110466] [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: 02/12/2024] [Revised: 05/15/2024] [Accepted: 07/02/2024] [Indexed: 08/20/2024] Open
Abstract
Solvatochromic compounds have emerged as valuable environment-sensitive probes for biological research. Here we used thiol-reactive solvatochromic analogs of the green fluorescent protein (GFP) chromophore to track conformational changes in two proteins, recoverin and the A2A adenosine receptor (A2AAR). Two dyes showed Ca2+-induced fluorescence changes when attached to recoverin. Our best-performing dye, DyeC, exhibited agonist-induced changes in both intensity and shape of its fluorescence spectrum when attached to A2AAR; none of these effects were observed with other common environment-sensitive dyes. Molecular dynamics simulations showed that activation of the A2AAR led to a more confined and hydrophilic environment for DyeC. Additionally, an allosteric modulator of A2AAR induced distinct fluorescence changes in the DyeC spectrum, indicating a unique receptor conformation. Our study demonstrated that GFP-inspired dyes are effective for detecting structural changes in G protein-coupled receptors (GPCRs), offering advantages such as intensity-based and ratiometric tracking, redshifted fluorescence spectra, and sensitivity to allosteric modulation.
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Affiliation(s)
- Anatoliy Belousov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan Maslov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, 3590 Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
| | - Philipp Orekhov
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Sechenov University, Moscow 119146, Russia
| | - Polina Khorn
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Pavel Kuzmichev
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Nadezhda Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Vladislav Motov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | | | - Svetlana Krasnova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- National Research University Higher School of Economics, Moscow 101000, Russia
| | - Konstantin Mineev
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Dmitry Zinchenko
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Evgeni Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | | | - Sergei Permyakov
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino 142292, Russia
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
- Max Plank Institute for Polymer Research, Mainz, Germany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, 3590 Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
| | - Vadim Cherezov
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Thomas Gensch
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
| | - Alexander Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Mikhail Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Alexey Mishin
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin Borshchevskiy
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Joint Institute for Nuclear Research, Dubna 141980, Russian Federation
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3
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Anazia K, Koenekoop L, Ferré G, Petracco E, Gutiérrez-de-Terán H, Eddy MT. Interaction networks within disease-associated Gα S variants characterized by an integrative biophysical approach. J Biol Chem 2024; 300:107497. [PMID: 38925329 PMCID: PMC11325797 DOI: 10.1016/j.jbc.2024.107497] [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: 01/31/2024] [Revised: 06/09/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Activation of G proteins through nucleotide exchange initiates intracellular signaling cascades essential for life processes. Under normal conditions, nucleotide exchange is regulated by the formation of G protein-G protein-coupled receptor complexes. Single point mutations in the Gα subunit of G proteins bypass this interaction, leading to loss of function or constitutive gain of function, which is closely linked with the onset of multiple diseases. Despite the recognized significance of Gα mutations in disease pathology, structural information for most variants is lacking, potentially due to inherent protein dynamics that pose challenges for crystallography. To address this, we leveraged an integrative spectroscopic and computational approach to structurally characterize seven of the most frequently observed and clinically relevant mutations in the stimulatory Gα subunit, GαS. A previously proposed allosteric model of Gα activation linked structural changes in the nucleotide-binding pocket with functionally important changes in interactions between switch regions. We investigated this allosteric connection in GαS by integrating data from variable temperature CD spectroscopy, which measured changes in global protein structure and stability, and molecular dynamics simulations, which observed changes in interaction networks between GαS switch regions. Additionally, saturation-transfer difference NMR spectroscopy was applied to observe changes in nucleotide interactions with residues within the nucleotide binding site. These data have enabled testing of predictions regarding how mutations in GαS result in loss or gain of function and evaluation of proposed structural mechanisms. The integration of experimental and computational data allowed us to propose a more nuanced classification of mechanisms underlying GαS gain-of-function and loss-of-function mutations.
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Affiliation(s)
- Kara Anazia
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Lucien Koenekoop
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Guillaume Ferré
- Department of Chemistry, University of Florida, Gainesville, Florida, USA
| | - Enzo Petracco
- Department of Chemistry, University of Florida, Gainesville, Florida, USA; URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech, Pomacle, France
| | | | - Matthew T Eddy
- Department of Chemistry, University of Florida, Gainesville, Florida, USA.
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4
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Picard LP, Orazietti A, Tran DP, Tucs A, Hagimoto S, Qi Z, Huang SK, Tsuda K, Kitao A, Sljoka A, Prosser RS. Balancing G protein selectivity and efficacy in the adenosine A 2A receptor. Nat Chem Biol 2024:10.1038/s41589-024-01682-6. [PMID: 39085516 DOI: 10.1038/s41589-024-01682-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 06/23/2024] [Indexed: 08/02/2024]
Abstract
The adenosine A2A receptor (A2AR) engages several G proteins, notably Go and its cognate Gs protein. This coupling promiscuity is facilitated by a dynamic ensemble, revealed by 19F nuclear magnetic resonance imaging of A2AR and G protein. Two transmembrane helix 6 (TM6) activation states, formerly associated with partial and full agonism, accommodate the differing volumes of Gs and Go. While nucleotide depletion biases TM7 toward a fully active state in A2AR-Gs, A2AR-Go is characterized by a dynamic inactive/intermediate fraction. Molecular dynamics simulations reveal that the NPxxY motif, a highly conserved switch, establishes a unique configuration in the A2AR-Go complex, failing to stabilize the helix-8 interface with Gs, and adoption of the active state. The resulting TM7 dynamics hamper G protein coupling, suggesting kinetic gating may be responsible for reduced efficacy in the noncognate G protein complex. Thus, dual TM6 activation states enable greater diversity of coupling partners while TM7 dynamics dictate coupling efficacy.
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Affiliation(s)
- Louis-Philippe Picard
- Department of Chemical and Physical Sciences, University of Toronto Mississauga (UTM), Mississauga, Ontario, Canada.
| | | | - Duy Phuoc Tran
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Andrejs Tucs
- Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
- Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan
| | - Sari Hagimoto
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Zhenzhou Qi
- Department of Chemical and Physical Sciences, University of Toronto Mississauga (UTM), Mississauga, Ontario, Canada
| | - Shuya Kate Huang
- Department of Chemical and Physical Sciences, University of Toronto Mississauga (UTM), Mississauga, Ontario, Canada
| | - Koji Tsuda
- Graduate School of Frontier Sciences, University of Tokyo, Chiba, Japan
- Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan
| | - Akio Kitao
- School of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan
| | - Adnan Sljoka
- Center for Advanced Intelligence Project, RIKEN, Tokyo, Japan.
- Department of Chemistry, York University, Toronto, Ontario, Canada.
| | - R Scott Prosser
- Department of Chemical and Physical Sciences, University of Toronto Mississauga (UTM), Mississauga, Ontario, Canada.
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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5
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Liu H, Yan P, Zhang Z, Han H, Zhou Q, Zheng J, Zhang J, Xu F, Shui W. Structural Mass Spectrometry Captures Residue-Resolved Comprehensive Conformational Rearrangements of a G Protein-Coupled Receptor. J Am Chem Soc 2024; 146:20045-20058. [PMID: 39001877 DOI: 10.1021/jacs.4c03922] [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: 07/15/2024]
Abstract
G protein-coupled receptor (GPCR) structural studies with in-solution spectroscopic approaches have offered distinctive insights into GPCR activation and signaling that highly complement those yielded from structural snapshots by crystallography or cryo-EM. While most current spectroscopic approaches allow for probing structural changes at selected residues or loop regions, they are not suitable for capturing a holistic view of GPCR conformational rearrangements across multiple domains. Herein, we develop an approach based on limited proteolysis mass spectrometry (LiP-MS) to simultaneously monitor conformational alterations of a large number of residues spanning both flexible loops and structured transmembrane domains for a given GPCR. To benchmark LiP-MS for GPCR conformational profiling, we studied the adenosine 2A receptor (A2AR) in response to different ligand binding (agonist/antagonist/allosteric modulators) and G protein coupling. Systematic and residue-resolved profiling of A2AR conformational rearrangements by LiP-MS precisely captures structural mechanisms in multiple domains underlying ligand engagement, receptor activation, and allostery, and may also reflect local conformational flexibility. Furthermore, these residue-resolution structural fingerprints of the A2AR protein allow us to readily classify ligands of different pharmacology and distinguish the G protein-coupled state. Thus, our study provides a new structural MS approach that would be generalizable to characterizing conformational transition and plasticity for challenging integral membrane proteins.
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Affiliation(s)
- Hongyue Liu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Pengfei Yan
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoyu Zhang
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongbo Han
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qingtong Zhou
- Department of Pharmacology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jie Zheng
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jian Zhang
- Medicinal Chemistry and Bioinformatics Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Fei Xu
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Wenqing Shui
- iHuman Institute, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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6
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Aguilar-Pineda J, González-Melchor M. Influence of the Water Model on the Structure and Interactions of the GPR40 Protein with the Lipid Membrane and the Solvent: Rigid versus Flexible Water Models. J Chem Theory Comput 2024; 20:6369-6387. [PMID: 38991114 PMCID: PMC11270832 DOI: 10.1021/acs.jctc.4c00571] [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: 04/28/2024] [Revised: 06/07/2024] [Accepted: 06/21/2024] [Indexed: 07/13/2024]
Abstract
G protein-coupled receptors (GPCR) are responsible for modulating various physiological functions and are thus related to the pathophysiology of different diseases. Being potential therapeutic targets, multiple computational methodologies have been developed to analyze their behavior and interactions with other species. The solvent, on the other hand, has received much less attention. In this work, we analyzed the effect of four explicit water models on the structure and interactions of the GPR40 receptor in its apo form. We employed the rigid SPC/E and TIP4P models, and their flexible versions, the FBA/ϵ and TIP4P/ϵflex. We explored the structural changes and their correlation with some bulk dynamic properties of water. Our results showed an adverse effect on the conservation of the secondary structure of the receptor with all the models due to the breaking of the intramolecular hydrogen bond network, being more evident for the TIP4P models. Notably, all four models brought the receptor to states similar to the active one, modifying the intracellular part of the TM5 and TM6 domains in a "hinge" type movement, allowing the opening of the structure. Regarding the dynamic properties, the rigid models showed results comparable to those obtained in other studies on membrane systems. However, flexible models exhibit disparities in the molecular representation of systems. Surprisingly, the FBA/ϵ model improves the molecular picture of several properties, even though their agreement with bulk diffusion is poorer. These findings reinforce our idea that exploring other water models or improving the current ones, to better represent the membrane interface, can lead to a positive impact on the description of the signal transduction mechanisms and the search of new drugs by targeting these receptors.
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Affiliation(s)
- Jorge
Alberto Aguilar-Pineda
- Instituto de Física
“Luis Rivera Terrazas”, Benemérita Universidad
Autónoma de Puebla, Av San Claudio, Cd Universitaria, Apdo. Postal
J-48, Puebla 72570, México
| | - Minerva González-Melchor
- Instituto de Física
“Luis Rivera Terrazas”, Benemérita Universidad
Autónoma de Puebla, Av San Claudio, Cd Universitaria, Apdo. Postal
J-48, Puebla 72570, México
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7
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Manchanda Y, ElEid L, Oqua AI, Ramchunder Z, Choi J, Shchepinova MM, Rutter GA, Inoue A, Tate EW, Jones B, Tomas A. Engineered mini-G proteins block the internalization of cognate GPCRs and disrupt downstream intracellular signaling. Sci Signal 2024; 17:eabq7038. [PMID: 38954638 DOI: 10.1126/scisignal.abq7038] [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: 04/25/2022] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
Mini-G proteins are engineered, thermostable variants of Gα subunits designed to stabilize G protein-coupled receptors (GPCRs) in their active conformations. Because of their small size and ease of use, they are popular tools for assessing GPCR behaviors in cells, both as reporters of receptor coupling to Gα subtypes and for cellular assays to quantify compartmentalized signaling at various subcellular locations. Here, we report that overexpression of mini-G proteins with their cognate GPCRs disrupted GPCR endocytic trafficking and associated intracellular signaling. In cells expressing the Gαs-coupled GPCR glucagon-like peptide 1 receptor (GLP-1R), coexpression of mini-Gs, a mini-G protein derived from Gαs, blocked β-arrestin 2 recruitment and receptor internalization and disrupted endosomal GLP-1R signaling. These effects did not involve changes in receptor phosphorylation or lipid nanodomain segregation. Moreover, we found that mini-G proteins derived from Gαi and Gαq also inhibited the internalization of GPCRs that couple to them. Finally, we developed an alternative intracellular signaling assay for GLP-1R using a nanobody specific for active Gαs:GPCR complexes (Nb37) that did not affect GLP-1R internalization. Our results have important implications for designing methods to assess intracellular GPCR signaling.
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Affiliation(s)
- Yusman Manchanda
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | - Liliane ElEid
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | - Affiong I Oqua
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | - Zenouska Ramchunder
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | - Jiyoon Choi
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | - Maria M Shchepinova
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
- CR-CHUM, Université de Montréal, Montréal, QC, Canada
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
| | - Ben Jones
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | - Alejandra Tomas
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
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8
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Shihoya W, Iwama A, Sano FK, Nureki O. Cryo-EM advances in GPCR structure determination. J Biochem 2024; 176:1-10. [PMID: 38498911 DOI: 10.1093/jb/mvae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 03/20/2024] Open
Abstract
G-protein-coupled receptors (GPCRs) constitute a prominent superfamily in humans and are categorized into six classes (A-F) that play indispensable roles in cellular communication and therapeutics. Nonetheless, their structural comprehension has been limited by challenges in high-resolution data acquisition. This review highlights the transformative impact of cryogenic electron microscopy (cryo-EM) on the structural determinations of GPCR-G-protein complexes. Specific technologies, such as nanobodies and mini-G-proteins, stabilize complexes and facilitate structural determination. We discuss the structural alterations upon receptor activation in different GPCR classes, revealing their diverse mechanisms. This review highlights the robust foundation for comprehending GPCR function and pave the way for future breakthroughs in drug discovery and therapeutic targeting.
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Affiliation(s)
- Wataru Shihoya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Aika Iwama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Fumiya K Sano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-Ku, Tokyo 113-0033, Japan
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9
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Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, Correia BE. Computational design of soluble and functional membrane protein analogues. Nature 2024; 631:449-458. [PMID: 38898281 PMCID: PMC11236705 DOI: 10.1038/s41586-024-07601-y] [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: 05/09/2023] [Accepted: 05/23/2024] [Indexed: 06/21/2024]
Abstract
De novo design of complex protein folds using solely computational means remains a substantial challenge1. Here we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, such as those from G-protein-coupled receptors2, are not found in the soluble proteome, and we demonstrate that their structural features can be recapitulated in solution. Biophysical analyses demonstrate the high thermal stability of the designs, and experimental structures show remarkable design accuracy. The soluble analogues were functionalized with native structural motifs, as a proof of concept for bringing membrane protein functions to the soluble proteome, potentially enabling new approaches in drug discovery. In summary, we have designed complex protein topologies and enriched them with functionalities from membrane proteins, with high experimental success rates, leading to a de facto expansion of the functional soluble fold space.
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Affiliation(s)
- Casper A Goverde
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Pacesa
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Nicolas Goldbach
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Lars J Dornfeld
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Petra E M Balbi
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sandrine Georgeon
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Stéphane Rosset
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Srajan Kapoor
- Department of Structural Biology, University at Buffalo, Buffalo, NY, USA
| | - Jagrity Choudhury
- Department of Structural Biology, University at Buffalo, Buffalo, NY, USA
| | - Justas Dauparas
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Christian Schellhaas
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Simon Kozlov
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Sergey Ovchinnikov
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alex J Vecchio
- Department of Structural Biology, University at Buffalo, Buffalo, NY, USA
| | - Bruno E Correia
- Laboratory of Protein Design and Immunoengineering, École Polytechnique Fédérale de Lausanne and Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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10
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Parikh A, Krogman W, Walker J. The impact of volatile anesthetics and propofol on phosphatidylinositol 4,5-bisphosphate signaling. Arch Biochem Biophys 2024; 757:110045. [PMID: 38801966 DOI: 10.1016/j.abb.2024.110045] [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: 02/14/2024] [Revised: 04/29/2024] [Accepted: 05/24/2024] [Indexed: 05/29/2024]
Abstract
Phosphatidylinositol 4,5-bisphosphate (PIP2), as well as other anionic phospholipids, play a pivotal role in various cellular processes, including ion channel regulation, receptor trafficking, and intracellular signaling pathways. The binding of volatile anesthetics and propofol to PIP2 leads to alterations in PIP2-mediated signaling causing modulation of ion channels such as ɣ-aminobutyric acid type A (GABAA) receptors, voltage-gated calcium channels, and potassium channels through various mechanisms. Additionally, the interaction between anionic phospholipids and G protein-coupled receptors plays a critical role in various anesthetic pathways, with these anesthetic-induced changes impacting PIP2 levels which cause cascading effects on receptor trafficking, including GABAA receptor internalization. This comprehensive review of various mechanisms of interaction provides insights into the intricate interplay between PIP2 signaling and anesthetic-induced changes, shedding light on the molecular mechanisms underlying anesthesia.
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Affiliation(s)
- Ayaan Parikh
- Wichita Collegiate School, Wichita, KS. 9115 E 13th St N, Wichita, KS, 67206, USA.
| | - William Krogman
- University of Kansas School of Medicine-Wichita, Wichita, KS, USA; Department of Anesthesiology, 929 N St Francis, Room 8079, Wichita, KS, 67214, USA
| | - James Walker
- University of Kansas School of Medicine-Wichita, Wichita, KS, USA; Department of Anesthesiology, 929 N St Francis, Room 8079, Wichita, KS, 67214, USA
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11
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Szwabowski GL, Griffing M, Mugabe EJ, O’Malley D, Baker LN, Baker DL, Parrill AL. G Protein-Coupled Receptor-Ligand Pose and Functional Class Prediction. Int J Mol Sci 2024; 25:6876. [PMID: 38999982 PMCID: PMC11241240 DOI: 10.3390/ijms25136876] [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: 05/24/2024] [Revised: 06/13/2024] [Accepted: 06/19/2024] [Indexed: 07/14/2024] Open
Abstract
G protein-coupled receptor (GPCR) transmembrane protein family members play essential roles in physiology. Numerous pharmaceuticals target GPCRs, and many drug discovery programs utilize virtual screening (VS) against GPCR targets. Improvements in the accuracy of predicting new molecules that bind to and either activate or inhibit GPCR function would accelerate such drug discovery programs. This work addresses two significant research questions. First, do ligand interaction fingerprints provide a substantial advantage over automated methods of binding site selection for classical docking? Second, can the functional status of prospective screening candidates be predicted from ligand interaction fingerprints using a random forest classifier? Ligand interaction fingerprints were found to offer modest advantages in sampling accurate poses, but no substantial advantage in the final set of top-ranked poses after scoring, and, thus, were not used in the generation of the ligand-receptor complexes used to train and test the random forest classifier. A binary classifier which treated agonists, antagonists, and inverse agonists as active and all other ligands as inactive proved highly effective in ligand function prediction in an external test set of GPR31 and TAAR2 candidate ligands with a hit rate of 82.6% actual actives within the set of predicted actives.
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Affiliation(s)
| | | | | | | | | | - Daniel L. Baker
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA; (G.L.S.); (M.G.); (E.J.M.); (D.O.); (L.N.B.)
| | - Abby L. Parrill
- Department of Chemistry, University of Memphis, Memphis, TN 38152, USA; (G.L.S.); (M.G.); (E.J.M.); (D.O.); (L.N.B.)
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12
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Smith JS, Hilibrand AS, Skiba MA, Dates AN, Calvillo-Miranda VG, Kruse AC. The M3 Muscarinic Acetylcholine Receptor Can Signal through Multiple G Protein Families. Mol Pharmacol 2024; 105:386-394. [PMID: 38641412 PMCID: PMC11114115 DOI: 10.1124/molpharm.123.000818] [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: 10/23/2023] [Revised: 04/01/2024] [Accepted: 04/08/2024] [Indexed: 04/21/2024] Open
Abstract
The M3 muscarinic acetylcholine receptor (M3R) is a G protein-coupled receptor (GPCR) that regulates important physiologic processes, including vascular tone, bronchoconstriction, and insulin secretion. It is expressed on a wide variety of cell types, including pancreatic beta, smooth muscle, neuronal, and immune cells. Agonist binding to the M3R is thought to initiate intracellular signaling events primarily through the heterotrimeric G protein Gq. However, reports differ on the ability of M3R to couple to other G proteins beyond Gq. Using members from the four primary G protein families (Gq, Gi, Gs, and G13) in radioligand binding, GTP turnover experiments, and cellular signaling assays, including live cell G protein dissociation and second messenger assessment of cAMP and inositol trisphosphate, we show that other G protein families, particularly Gi and Gs, can also interact with the human M3R. We further show that these interactions are productive as assessed by amplification of classic second messenger signaling events. Our findings demonstrate that the M3R is more promiscuous with respect to G protein interactions than previously appreciated. SIGNIFICANCE STATEMENT: The study reveals that the human M3 muscarinic acetylcholine receptor (M3R), known for its pivotal roles in diverse physiological processes, not only activates intracellular signaling via Gq as previously known but also functionally interacts with other G protein families such as Gi and Gs, expanding our understanding of its versatility in mediating cellular responses. These findings signify a broader and more complex regulatory network governed by M3R and have implications for therapeutic targeting.
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Affiliation(s)
- Jeffrey S Smith
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts (J.S.S., A.S.H., M.A.S., A.N.D., V.G.C.-M., A.C.K.) and Brigham and Women's Hospital, Boston, Massachusetts (J.S.S.)
| | - Ari S Hilibrand
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts (J.S.S., A.S.H., M.A.S., A.N.D., V.G.C.-M., A.C.K.) and Brigham and Women's Hospital, Boston, Massachusetts (J.S.S.)
| | - Meredith A Skiba
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts (J.S.S., A.S.H., M.A.S., A.N.D., V.G.C.-M., A.C.K.) and Brigham and Women's Hospital, Boston, Massachusetts (J.S.S.)
| | - Andrew N Dates
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts (J.S.S., A.S.H., M.A.S., A.N.D., V.G.C.-M., A.C.K.) and Brigham and Women's Hospital, Boston, Massachusetts (J.S.S.)
| | - Victor G Calvillo-Miranda
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts (J.S.S., A.S.H., M.A.S., A.N.D., V.G.C.-M., A.C.K.) and Brigham and Women's Hospital, Boston, Massachusetts (J.S.S.)
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts (J.S.S., A.S.H., M.A.S., A.N.D., V.G.C.-M., A.C.K.) and Brigham and Women's Hospital, Boston, Massachusetts (J.S.S.)
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13
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Claff T, Mahardhika AB, Vaaßen VJ, Schlegel J, Vielmuth C, Weiße RH, Sträter N, Müller CE. Structural Insights into Partial Activation of the Prototypic G Protein-Coupled Adenosine A 2A Receptor. ACS Pharmacol Transl Sci 2024; 7:1415-1425. [PMID: 38751633 PMCID: PMC11091970 DOI: 10.1021/acsptsci.4c00051] [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: 01/31/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 05/18/2024]
Abstract
The adenosine A2A receptor (A2AAR) belongs to the rhodopsin-like G protein-coupled receptor (GPCR) family, which constitutes the largest class of GPCRs. Partial agonists show reduced efficacy as compared to physiological agonists and can even act as antagonists in the presence of a full agonist. Here, we determined an X-ray crystal structure of the partial A2AAR agonist 2-amino-6-[(1H-imidazol-2-ylmethyl)sulfanyl]-4-p-hydroxyphenyl-3,5-pyridinedicarbonitrile (LUF5834) in complex with the A2AAR construct A2A-PSB2-bRIL, stabilized in its inactive conformation and being devoid of any mutations in the ligand binding pocket. The determined high-resolution structure (2.43 Å) resolved water networks and crucial binding pocket interactions. A direct hydrogen bond of the p-hydroxy group of LUF5834 with T883.36 was observed, an amino acid that was mutated to alanine in the most frequently used A2AAR crystallization constructs thus preventing the discovery of its interactions in most of the previous A2AAR co-crystal structures. G protein dissociation studies confirmed partial agonistic activity of LUF5834 as compared to that of the full agonist N-ethylcarboxamidoadenosine (NECA). In contrast to NECA, the partial agonist was still able to bind to the receptor construct locked in its inactive conformation by an S913.39K mutation, although with an affinity lower than that at the native receptor. This could explain the compound's partial agonistic activity: while full A2AAR agonists bind exclusively to the active conformation, likely following conformational selection, partial agonists bind to active as well as inactive conformations, showing higher affinity for the active conformation. This might be a general mechanism of partial agonism also applicable to other GPCRs.
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Affiliation(s)
- Tobias Claff
- PharmaCenter
Bonn & Pharmaceutical Institute, Department of Pharmaceutical
& Medicinal Chemistry, University of
Bonn, Bonn 53113, Germany
| | - Andhika B. Mahardhika
- PharmaCenter
Bonn & Pharmaceutical Institute, Department of Pharmaceutical
& Medicinal Chemistry, University of
Bonn, Bonn 53113, Germany
- Research
Training Group 2873, University of Bonn, Bonn 53121, Germany
| | - Victoria J. Vaaßen
- PharmaCenter
Bonn & Pharmaceutical Institute, Department of Pharmaceutical
& Medicinal Chemistry, University of
Bonn, Bonn 53113, Germany
| | - Jonathan
G. Schlegel
- PharmaCenter
Bonn & Pharmaceutical Institute, Department of Pharmaceutical
& Medicinal Chemistry, University of
Bonn, Bonn 53113, Germany
| | - Christin Vielmuth
- PharmaCenter
Bonn & Pharmaceutical Institute, Department of Pharmaceutical
& Medicinal Chemistry, University of
Bonn, Bonn 53113, Germany
| | - Renato H. Weiße
- Institute
of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Leipzig 04103, Germany
| | - Norbert Sträter
- Institute
of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, Leipzig University, Leipzig 04103, Germany
| | - Christa E. Müller
- PharmaCenter
Bonn & Pharmaceutical Institute, Department of Pharmaceutical
& Medicinal Chemistry, University of
Bonn, Bonn 53113, Germany
- Research
Training Group 2873, University of Bonn, Bonn 53121, Germany
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14
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Thakur N, Ray AP, Jin B, Afsharian NP, Lyman E, Gao ZG, Jacobson KA, Eddy MT. Membrane mimetic-dependence of GPCR energy landscapes. Structure 2024; 32:523-535.e5. [PMID: 38401537 PMCID: PMC11069452 DOI: 10.1016/j.str.2024.01.013] [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: 10/16/2023] [Revised: 01/03/2024] [Accepted: 01/30/2024] [Indexed: 02/26/2024]
Abstract
We leveraged variable-temperature 19F-NMR spectroscopy to compare the conformational equilibria of the human A2A adenosine receptor (A2AAR), a class A G protein-coupled receptor (GPCR), across a range of temperatures ranging from lower temperatures typically employed in 19F-NMR experiments to physiological temperature. A2AAR complexes with partial agonists and full agonists showed large increases in the population of a fully active conformation with increasing temperature. NMR data measured at physiological temperature were more in line with functional data. This was pronounced for complexes with partial agonists, where the population of active A2AAR was nearly undetectable at lower temperature but became evident at physiological temperature. Temperature-dependent behavior of complexes with either full or partial agonists exhibited a pronounced sensitivity to the specific membrane mimetic employed. Cellular signaling experiments correlated with the temperature-dependent conformational equilibria of A2AAR in lipid nanodiscs but not in some detergents, underscoring the importance of the membrane environment in studies of GPCR function.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka Prabha Ray
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Beining Jin
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | | | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, DE, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew T Eddy
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA.
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15
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Tutkus M, Lundgaard CV, Veshaguri S, Tønnesen A, Hatzakis N, Rasmussen SGF, Stamou D. Probing Activation and Conformational Dynamics of the Vesicle-Reconstituted β 2 Adrenergic Receptor at the Single-Molecule Level. J Phys Chem B 2024; 128:2124-2133. [PMID: 38391238 PMCID: PMC10926102 DOI: 10.1021/acs.jpcb.3c08349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
G-protein-coupled receptors (GPCRs) are structurally flexible membrane proteins that mediate a host of physiological responses to extracellular ligands like hormones and neurotransmitters. Fine features of their dynamic structural behavior are hypothesized to encode the functional plasticity seen in GPCR activity, where ligands with different efficacies can direct the same receptor toward different signaling phenotypes. Although the number of GPCR crystal structures is increasing, the receptors are characterized by complex and poorly understood conformational landscapes. Therefore, we employed a fluorescence microscopy assay to monitor conformational dynamics of single β2 adrenergic receptors (β2ARs). To increase the biological relevance of our findings, we decided not to reconstitute the receptor in detergent micelles but rather lipid membranes as proteoliposomes. The conformational dynamics were monitored by changes in the intensity of an environmentally sensitive boron-dipyrromethene (BODIPY 493/503) fluorophore conjugated to an endogenous cysteine (located at the cytoplasmic end of the sixth transmembrane helix of the receptor). Using total internal reflection fluorescence microscopy (TIRFM) and a single small unilamellar liposome assay that we previously developed, we followed the real-time dynamic properties of hundreds of single β2ARs reconstituted in a native-like environment─lipid membranes. Our results showed that β2AR-BODIPY fluctuates between several states of different intensity on a time scale of seconds, compared to BODIPY-lipid conjugates that show almost entirely stable fluorescence emission in the absence and presence of the full agonist BI-167107. Agonist stimulation changes the β2AR dynamics, increasing the population of states with higher intensities and prolonging their durations, consistent with bulk experiments. The transition density plot demonstrates that β2AR-BODIPY, in the absence of the full agonist, interconverts between states of low and moderate intensity, while the full agonist renders transitions between moderate and high-intensity states more probable. This redistribution is consistent with a mechanism of conformational selection and is a promising first step toward characterizing the conformational dynamics of GPCRs embedded in a lipid bilayer.
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Affiliation(s)
- Marijonas Tutkus
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Saulėtekio Ave. 7, LT-10257 Vilnius, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Saulėtekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Christian V Lundgaard
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Salome Veshaguri
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Asger Tønnesen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Nikos Hatzakis
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
- Department of Chemistry and Nanoscience Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
| | - Søren G F Rasmussen
- Department of Neuroscience and Pharmacology, Panum, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Dimitrios Stamou
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark
- Center for Geometrically Engineered Cellular Systems, Universitetsparken 5, DK-2100 Copenhagen, Denmark
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16
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Goverde CA, Pacesa M, Goldbach N, Dornfeld LJ, Balbi PEM, Georgeon S, Rosset S, Kapoor S, Choudhury J, Dauparas J, Schellhaas C, Kozlov S, Baker D, Ovchinnikov S, Vecchio AJ, Correia BE. Computational design of soluble functional analogues of integral membrane proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.09.540044. [PMID: 38496615 PMCID: PMC10942269 DOI: 10.1101/2023.05.09.540044] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
De novo design of complex protein folds using solely computational means remains a significant challenge. Here, we use a robust deep learning pipeline to design complex folds and soluble analogues of integral membrane proteins. Unique membrane topologies, such as those from GPCRs, are not found in the soluble proteome and we demonstrate that their structural features can be recapitulated in solution. Biophysical analyses reveal high thermal stability of the designs and experimental structures show remarkable design accuracy. The soluble analogues were functionalized with native structural motifs, standing as a proof-of-concept for bringing membrane protein functions to the soluble proteome, potentially enabling new approaches in drug discovery. In summary, we designed complex protein topologies and enriched them with functionalities from membrane proteins, with high experimental success rates, leading to a de facto expansion of the functional soluble fold space.
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17
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Rohner VL, Lamothe-Molina PJ, Patriarchi T. Engineering, applications, and future perspectives of GPCR-based genetically encoded fluorescent indicators for neuromodulators. J Neurochem 2024; 168:163-184. [PMID: 38288673 DOI: 10.1111/jnc.16045] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 02/23/2024]
Abstract
This review explores the evolving landscape of G-protein-coupled receptor (GPCR)-based genetically encoded fluorescent indicators (GEFIs), with a focus on their development, structural components, engineering strategies, and applications. We highlight the unique features of this indicator class, emphasizing the importance of both the sensing domain (GPCR structure and activation mechanism) and the reporting domain (circularly permuted fluorescent protein (cpFP) structure and fluorescence modulation). Further, we discuss indicator engineering approaches, including the selection of suitable cpFPs and expression systems. Additionally, we showcase the diversity and flexibility of their application by presenting a summary of studies where such indicators were used. Along with all the advantages, we also focus on the current limitations as well as common misconceptions that arise when using these indicators. Finally, we discuss future directions in indicator engineering, including strategies for screening with increased throughput, optimization of the ligand-binding properties, structural insights, and spectral diversity.
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Affiliation(s)
- Valentin Lu Rohner
- Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | | | - Tommaso Patriarchi
- Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
- Neuroscience Center Zurich, University and ETH Zurich, Zurich, Switzerland
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18
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Jayakody T, Inoue A, Kannan S, Nakamura G, Kawakami K, Mendis K, Nguyen TB, Li J, Herr DR, Verma CS, Dawe GS. Mechanisms of biased agonism by Gα i/o-biased stapled peptide agonists of the relaxin-3 receptor. Sci Signal 2024; 17:eabl5880. [PMID: 38349968 DOI: 10.1126/scisignal.abl5880] [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: 07/22/2021] [Accepted: 01/26/2024] [Indexed: 02/15/2024]
Abstract
The neuropeptide relaxin-3 is composed of an A chain and a B chain held together by disulfide bonds, and it modulates functions such as anxiety and food intake by binding to and activating its cognate receptor RXFP3, mainly through the B chain. Biased ligands of RXFP3 would help to determine the molecular mechanisms underlying the activation of G proteins and β-arrestins downstream of RXFP3 that lead to such diverse functions. We showed that the i, i+4 stapled relaxin-3 B chains, 14s18 and d(1-7)14s18, were Gαi/o-biased agonists of RXFP3. These peptides did not induce recruitment of β-arrestin1/2 to RXFP3 by GPCR kinases (GRKs), in contrast to relaxin-3, which enabled the GRK2/3-mediated recruitment of β-arrestin1/2 to RXFP3. Relaxin-3 and the previously reported peptide 4 (an i, i+4 stapled relaxin-3 B chain) did not exhibit biased signaling. The staple linker of peptide 4 and parts of both the A chain and B chain of relaxin-3 interacted with extracellular loop 3 (ECL3) of RXFP3, moving it away from the binding pocket, suggesting that unbiased ligands promote a more open conformation of RXFP3. These findings highlight roles for the A chain and the N-terminal residues of the B chain of relaxin-3 in inducing conformational changes in RXFP3, which will help in designing selective biased ligands with improved therapeutic efficacy.
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Affiliation(s)
- Tharindunee Jayakody
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Neurobiology Programme, Life Sciences Institute, National University of Singapore, Singapore
- Department of Chemistry, University of Colombo, P.O. Box 1490, Colombo 00300, Sri Lanka
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | | | - Gaku Nakamura
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Krishan Mendis
- Department of Chemistry, University of Colombo, P.O. Box 1490, Colombo 00300, Sri Lanka
| | - Thanh-Binh Nguyen
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Jianguo Li
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671
| | - Deron R Herr
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chandra S Verma
- Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671
- Department of Biological Sciences, National University of Singapore, 6 Science Drive 4, Singapore 117558
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr., Singapore 637551
| | - Gavin S Dawe
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Neurobiology Programme, Life Sciences Institute, National University of Singapore, Singapore
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Precision Medicine Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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19
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Araya T, Matsuba Y, Suzuki H, Doura T, Nuemket N, Nango E, Yamamoto M, Im D, Asada H, Kiyonaka S, Iwata S. Crystal structure reveals the binding mode and selectivity of a photoswitchable ligand for the adenosine A 2A receptor. Biochem Biophys Res Commun 2024; 695:149393. [PMID: 38171234 DOI: 10.1016/j.bbrc.2023.149393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024]
Abstract
Rational synthetic expansion of photoresponsive ligands is important for photopharmacological studies. Adenosine A2A receptor (A2AR) is stimulated by adenosine and related in Parkinson's disease and other diseases. Here, we report the crystal structure of the A2AR in complex with the novel photoresponsive ligand photoNECA (blue) at 3.34 Å resolution. PhotoNECA (blue) was designed for this structural study and the cell-based assay showed a photoresponsive and receptor selective characteristics of photoNECA (blue) for A2AR. The crystal structure explains the binding mode, photoresponsive mechanism and receptor selectivity of photoNECA (blue). Our study would promote not only the rational design of photoresponsive ligands but also dynamic structural studies of A2AR.
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Affiliation(s)
- Tsuyoshi Araya
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Yuya Matsuba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Harufumi Suzuki
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Tomohiro Doura
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan
| | - Nipawan Nuemket
- RIKEN SPring-8 Center, Hyogo, 679-5148, Japan; JASRI, Hyogo, 679-5148, Japan
| | - Eriko Nango
- RIKEN SPring-8 Center, Hyogo, 679-5148, Japan; Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Miyagi, 980-8577, Japan
| | | | - Dohyun Im
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Hidetsugu Asada
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
| | - Shigeki Kiyonaka
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Nagoya, 464-8603, Japan; Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Nagoya, 464-8603, Japan.
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan; RIKEN SPring-8 Center, Hyogo, 679-5148, Japan.
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20
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Anazia K, Koenekoop L, Ferré G, Petracco E, Gutiérrez-de-Teran H, Eddy MT. Visualizing the impact of disease-associated mutations on G protein-nucleotide interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.578006. [PMID: 38352316 PMCID: PMC10862895 DOI: 10.1101/2024.01.30.578006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Activation of G proteins stimulates ubiquitous intracellular signaling cascades essential for life processes. Under normal physiological conditions, nucleotide exchange is initiated upon the formation of complexes between a G protein and G protein-coupled receptor (GPCR), which facilitates exchange of bound GDP for GTP, subsequently dissociating the trimeric G protein into its Gα and Gβγ subunits. However, single point mutations in Gα circumvent nucleotide exchange regulated by GPCR-G protein interactions, leading to either loss-of-function or constitutive gain-of-function. Mutations in several Gα subtypes are closely linked to the development of multiple diseases, including several intractable cancers. We leveraged an integrative spectroscopic and computational approach to investigate the mechanisms by which seven of the most frequently observed clinically-relevant mutations in the α subunit of the stimulatory G protein result in functional changes. Variable temperature circular dichroism (CD) spectroscopy showed a bimodal distribution of thermal melting temperatures across all GαS variants. Modeling from molecular dynamics (MD) simulations established a correlation between observed thermal melting temperatures and structural changes caused by the mutations. Concurrently, saturation-transfer difference NMR (STD-NMR) highlighted variations in the interactions of GαS variants with bound nucleotides. MD simulations indicated that changes in local interactions within the nucleotide-binding pocket did not consistently align with global structural changes. This collective evidence suggests a multifaceted energy landscape, wherein each mutation may introduce distinct perturbations to the nucleotide-binding site and protein-protein interaction sites. Consequently, it underscores the importance of tailoring therapeutic strategies to address the unique challenges posed by individual mutations.
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Affiliation(s)
- Kara Anazia
- Department of Chemistry; University of Florida; Gainesville, FL, 32611; USA
| | - Lucien Koenekoop
- Department of Cell and Molecular Biology, Uppsala University; Uppsala, 75105; Sweden
| | - Guillaume Ferré
- Department of Chemistry; University of Florida; Gainesville, FL, 32611; USA
- Present address: Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UT3), Toulouse, France
| | - Enzo Petracco
- Department of Chemistry; University of Florida; Gainesville, FL, 32611; USA
- URD Agro-Biotechnologies Industrielles (ABI), CEBB, AgroParisTech, Pomacle, France
| | | | - Matthew T. Eddy
- Department of Chemistry; University of Florida; Gainesville, FL, 32611; USA
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21
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Stampelou M, Ladds G, Kolocouris A. Computational Workflow for Refining AlphaFold Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive Human Adenosine A 3 Receptor. J Phys Chem B 2024; 128:914-936. [PMID: 38236582 DOI: 10.1021/acs.jpcb.3c05986] [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: 01/19/2024]
Abstract
A structure-based drug design pipeline that considers both thermodynamic and kinetic binding data of ligands against a receptor will enable the computational design of improved drug molecules. For unresolved GPCR-ligand complexes, a workflow that can apply both thermodynamic and kinetic binding data in combination with alpha-fold (AF)-derived or other homology models and experimentally resolved binding modes of relevant ligands in GPCR-homologs needs to be tested. Here, as test case, we studied a congeneric set of ligands that bind to a structurally unresolved G protein-coupled receptor (GPCR), the inactive human adenosine A3 receptor (hA3R). We tested three available homology models from which two have been generated from experimental structures of hA1R or hA2AR and one model was a multistate alphafold 2 (AF2)-derived model. We applied alchemical calculations with thermodynamic integration coupled with molecular dynamics (TI/MD) simulations to calculate the experimental relative binding free energies and residence time (τ)-random accelerated MD (τ-RAMD) simulations to calculate the relative residence times (RTs) for antagonists. While the TI/MD calculations produced, for the three homology models, good Pearson correlation coefficients, correspondingly, r = 0.74, 0.62, and 0.67 and mean unsigned error (mue) values of 0.94, 1.31, and 0.81 kcal mol-1, the τ-RAMD method showed r = 0.92 and 0.52 for the first two models but failed to produce accurate results for the multistate AF2-derived model. With subsequent optimization of the AF2-derived model by reorientation of the side chain of R1735.34 located in the extracellular loop 2 (EL2) that blocked ligand's unbinding, the computational model showed r = 0.84 for kinetic data and improved performance for thermodynamic data (r = 0.81, mue = 0.56 kcal mol-1). Overall, after refining the multistate AF2 model with physics-based tools, we were able to show a strong correlation between predicted and experimental ligand relative residence times and affinities, achieving a level of accuracy comparable to an experimental structure. The computational workflow used can be applied to other receptors, helping to rank candidate drugs in a congeneric series and enabling the prioritization of leads with stronger binding affinities and longer residence times.
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Affiliation(s)
- Margarita Stampelou
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771 Athens, Greece
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22
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McIntire WE, Purdy MD, Leonhardt SA, Kucharska I, Hanson MA, Poulos S, Garrison JC, Linden J, Yeager M. G protein β 4 as a structural determinant of enhanced nucleotide exchange in the A 2AAR-Gs complex. RESEARCH SQUARE 2024:rs.3.rs-3814988. [PMID: 38343806 PMCID: PMC10854301 DOI: 10.21203/rs.3.rs-3814988/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Adenosine A2A receptors (A2AAR) evoke pleiotropic intracellular signaling events via activation of the stimulatory heterotrimeric G protein, Gs. Here, we used cryoEM to solve the agonist-bound structure of A2AAR in a complex with full-length Gs α and Gβ4γ2 (A2AAR-Gs α:β4γ2). The orthosteric binding site of A2AAR-Gs α:β4γ2 was similar to other structures of agonist-bound A2AAR, with or without Gs. Unexpectedly, the solvent accessible surface area within the interior of the complex was substantially larger for the complex with Gβ4 versus the closest analog, A2AAR-miniGs α:β1γ2. Consequently, there are fewer interactions between the switch II in Gs α and the Gβ4 torus. In reconstitution experiments Gβ4γ2 displayed a ten-fold higher efficiency over Gβ1γ2 in catalyzing A2AAR dependent GTPγS binding to Gs α. We propose that the less constrained switch II in A2AAR-Gs α:β4γ2 accounts for this increased efficiency. These results suggest that Gβ4 functions as a positive allosteric enhancer versus Gβ1.
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Affiliation(s)
- William E. McIntire
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, Florida 33146
| | - Michael D. Purdy
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908 USA
- Molecular Electron Microscopy Core, University of Virginia School of Medicine, Charlottesville, Virginia 22908, USA
| | - Susan A. Leonhardt
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, Florida 33146
| | - Iga Kucharska
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, Florida 33146
| | - Michael A. Hanson
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, Florida 33146
| | - Sandra Poulos
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908 USA
| | - James C. Garrison
- Department of Pharmacology, University of Virginia Health System, Charlottesville, VA 22903 Virginia 22908, USA
| | - Joel Linden
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908 USA
| | - Mark Yeager
- The Phillip and Patricia Frost Institute for Chemistry and Molecular Science, University of Miami, Coral Gables, Florida 33146
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23
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Zhang Z, Lin X, Wei L, Wu Y, Xu L, Wu L, Wei X, Zhao S, Zhu X, Xu F. A framework for Frizzled-G protein coupling and implications to the PCP signaling pathways. Cell Discov 2024; 10:3. [PMID: 38182578 PMCID: PMC10770037 DOI: 10.1038/s41421-023-00627-y] [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: 08/03/2023] [Accepted: 11/19/2023] [Indexed: 01/07/2024] Open
Abstract
The ten Frizzled receptors (FZDs) are essential in Wnt signaling and play important roles in embryonic development and tumorigenesis. Among these, FZD6 is closely associated with lens development. Understanding FZD activation mechanism is key to unlock these emerging targets. Here we present the cryo-EM structures of FZD6 and FZD3 which are known to relay non-canonical planar cell polarity (PCP) signaling pathways as well as FZD1 in their G protein-coupled states and in the apo inactive states, respectively. Comparison of the three inactive/active pairs unveiled a shared activation framework among all ten FZDs. Mutagenesis along with imaging and functional analysis on the human lens epithelial tissues suggested potential crosstalk between the G-protein coupling of FZD6 and the PCP signaling pathways. Together, this study provides an integrated understanding of FZD structure and function, and lays the foundation for developing therapeutic modulators to activate or inhibit FZD signaling for a range of disorders including cancers and cataracts.
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Affiliation(s)
- Zhibin Zhang
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xi Lin
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Ling Wei
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Lu Xu
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Lijie Wu
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Xiaohu Wei
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xiangjia Zhu
- Eye Institute and Department of Ophthalmology, Eye & ENT Hospital, Fudan University, Shanghai, China.
| | - Fei Xu
- iHuman Institute, ShanghaiTech University, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
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24
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Bloxham CJ, Hulme KD, Fierro F, Fercher C, Pegg CL, O'Brien SL, Foster SR, Short KR, Furness SGB, Reichelt ME, Niv MY, Thomas WG. Cardiac human bitter taste receptors contain naturally occurring variants that alter function. Biochem Pharmacol 2024; 219:115932. [PMID: 37989413 DOI: 10.1016/j.bcp.2023.115932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/23/2023]
Abstract
Bitter taste receptors (T2R) are a subfamily of G protein-coupled receptors that enable humans to detect aversive and toxic substances. The ability to discern bitter compounds varies between individuals and is attributed mainly to naturally occurring T2R polymorphisms. T2Rs are also expressed in numerous non-gustatory tissues, including the heart, indicating potential contributions to cardiovascular physiology. In this study. T2Rs that have previously been identified in human cardiac tissues (T2Rs - 10, 14, 30, 31, 46 and 50) and their naturally occurring polymorphisms were functionally characterised. The ligand-dependent signaling responses of some T2R variants were completely abolished (T2R30 Leu252 and T2R46 Met228), whereas other receptor variants had moderate changes in their maximal response, but not potency, relative to wild type. Using a cAMP fluorescent biosensor, we reveal the productive coupling of T2R14, but not the T2R14 Phe201 variant, to endogenous Gαi. Modeling revealed that these variants resulted in altered interactions that generally affected ligand binding (T2R30 Leu252) or Gα protein interactions (T2R46 Met228 and T2R14 Phe201), rather than receptor structural stability. Interestingly, this study is the first to show a difference in signaling for T2R50 Tyr203 (rs1376251) which has been associated with cardiovascular disease. The observation of naturally occurring functional variation in the T2Rs with the greatest expression in the heart is important, as their discovery should prove useful in deciphering the role of T2Rs within the cardiovascular system.
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Affiliation(s)
- Conor J Bloxham
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, QLD, Australia; Regenerative Medicine in Cardiovascular Diseases, First Department of Medicine, Klinikum rechts der Isar, Technical University of Munich, Germany
| | - Katina D Hulme
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, QLD, Australia; Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Fabrizio Fierro
- Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Israel
| | - Christian Fercher
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, QLD, Australia
| | - Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, QLD, Australia
| | - Shannon L O'Brien
- Institute of Metabolism and Systems Research, University of Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Simon R Foster
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, QLD, Australia; QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Kirsty R Short
- School of Chemistry and Molecular Biosciences, Faculty of Science, University of Queensland, QLD, Australia
| | - Sebastian G B Furness
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, QLD, Australia; Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Melissa E Reichelt
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, QLD, Australia
| | - Masha Y Niv
- Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Israel
| | - Walter G Thomas
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, QLD, Australia.
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25
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Jing N, Zhang K, Chen X, Liu K, Wang J, Xiao L, Zhang W, Ma P, Xu P, Cheng C, Wang D, Zhao H, He Y, Ji Z, Xin Z, Sun Y, Zhang Y, Bao W, Gong Y, Fan L, Ji Y, Zhuang G, Wang Q, Dong B, Zhang P, Xue W, Gao WQ, Zhu HH. ADORA2A-driven proline synthesis triggers epigenetic reprogramming in neuroendocrine prostate and lung cancers. J Clin Invest 2023; 133:e168670. [PMID: 38099497 PMCID: PMC10721152 DOI: 10.1172/jci168670] [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: 01/10/2023] [Accepted: 10/10/2023] [Indexed: 12/18/2023] Open
Abstract
Cell lineage plasticity is one of the major causes for the failure of targeted therapies in various cancers. However, the driver and actionable drug targets in promoting cancer cell lineage plasticity are scarcely identified. Here, we found that a G protein-coupled receptor, ADORA2A, is specifically upregulated during neuroendocrine differentiation, a common form of lineage plasticity in prostate cancer and lung cancer following targeted therapies. Activation of the ADORA2A signaling rewires the proline metabolism via an ERK/MYC/PYCR cascade. Increased proline synthesis promotes deacetylases SIRT6/7-mediated deacetylation of histone H3 at lysine 27 (H3K27), and thereby biases a global transcriptional output toward a neuroendocrine lineage profile. Ablation of Adora2a in genetically engineered mouse models inhibits the development and progression of neuroendocrine prostate and lung cancers, and, intriguingly, prevents the adenocarcinoma-to-neuroendocrine phenotypic transition. Importantly, pharmacological blockade of ADORA2A profoundly represses neuroendocrine prostate and lung cancer growth in vivo. Therefore, we believe that ADORA2A can be used as a promising therapeutic target to govern the epigenetic reprogramming in neuroendocrine malignancies.
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Affiliation(s)
- Na Jing
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
- Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Kai Zhang
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Xinyu Chen
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Kaiyuan Liu
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Jinming Wang
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Lingling Xiao
- Emergency Intensive Care Unit, Shanghai Seventh People’s Hospital of Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wentian Zhang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Pengfei Ma
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Penghui Xu
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
- Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Chaping Cheng
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Deng Wang
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
- Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Huifang Zhao
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Yuman He
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Zhongzhong Ji
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Zhixiang Xin
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Yujiao Sun
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Yingchao Zhang
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Wei Bao
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Yiming Gong
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Liancheng Fan
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Yiyi Ji
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Guanglei Zhuang
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
- Department of Obstetrics and Gynecology, Shanghai Cancer Institute, Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi Wang
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Baijun Dong
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Pengcheng Zhang
- School of Biomedical Engineering, ShanghaiTech University, Shanghai, China
| | - Wei Xue
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
| | - Wei-Qiang Gao
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
- Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, China
| | - Helen He Zhu
- State Key Laboratory of Systems Medicine for Cancer, Renji-Med-X Stem Cell Research Center, Department of Urology, Ren Ji Hospital, Shanghai Cancer Institute, School of Medicine and School of Biomedical Engineering, and
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26
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Xu Z, Guo L, Yu J, Shen S, Wu C, Zhang W, Zhao C, Deng Y, Tian X, Feng Y, Hou H, Su L, Wang H, Guo S, Wang H, Wang K, Chen P, Zhao J, Zhang X, Yong X, Cheng L, Liu L, Yang S, Yang F, Wang X, Yu X, Xu Y, Sun JP, Yan W, Shao Z. Ligand recognition and G-protein coupling of trace amine receptor TAAR1. Nature 2023; 624:672-681. [PMID: 37935376 DOI: 10.1038/s41586-023-06804-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 10/31/2023] [Indexed: 11/09/2023]
Abstract
Trace-amine-associated receptors (TAARs), a group of biogenic amine receptors, have essential roles in neurological and metabolic homeostasis1. They recognize diverse endogenous trace amines and subsequently activate a range of G-protein-subtype signalling pathways2,3. Notably, TAAR1 has emerged as a promising therapeutic target for treating psychiatric disorders4,5. However, the molecular mechanisms underlying its ability to recognize different ligands remain largely unclear. Here we present nine cryo-electron microscopy structures, with eight showing human and mouse TAAR1 in a complex with an array of ligands, including the endogenous 3-iodothyronamine, two antipsychotic agents, the psychoactive drug amphetamine and two identified catecholamine agonists, and one showing 5-HT1AR in a complex with an antipsychotic agent. These structures reveal a rigid consensus binding motif in TAAR1 that binds to endogenous trace amine stimuli and two extended binding pockets that accommodate diverse chemotypes. Combined with mutational analysis, functional assays and molecular dynamic simulations, we elucidate the structural basis of drug polypharmacology and identify the species-specific differences between human and mouse TAAR1. Our study provides insights into the mechanism of ligand recognition and G-protein selectivity by TAAR1, which may help in the discovery of ligands or therapeutic strategies for neurological and metabolic disorders.
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Affiliation(s)
- Zheng Xu
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, China
| | - Lulu Guo
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jingjing Yu
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Siyuan Shen
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Chao Wu
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Weifeng Zhang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Chang Zhao
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yue Deng
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaowen Tian
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yuying Feng
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hanlin Hou
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Lantian Su
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hongshuang Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Shuo Guo
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Heli Wang
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Kexin Wang
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Peipei Chen
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Jie Zhao
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, China
| | - Xiaoyu Zhang
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xihao Yong
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Lin Cheng
- Department of Otolaryngology Head and Neck Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Lunxu Liu
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Shengyong Yang
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Fan Yang
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Xiaohui Wang
- Laboratory of Chemical Biology, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, China
- Beijing National Laboratory for Molecular Sciences, Beijing, China
| | - Xiao Yu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Shandong University, Jinan, China.
| | - Yunfei Xu
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, China.
| | - Jin-Peng Sun
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, China.
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.
| | - Wei Yan
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.
| | - Zhenhua Shao
- Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China.
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu, China.
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27
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Liu H, Zheng Y, Wang Y, Wang Y, He X, Xu P, Huang S, Yuan Q, Zhang X, Wang L, Jiang K, Chen H, Li Z, Liu W, Wang S, Xu HE, Xu F. Recognition of methamphetamine and other amines by trace amine receptor TAAR1. Nature 2023; 624:663-671. [PMID: 37935377 DOI: 10.1038/s41586-023-06775-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/20/2023] [Indexed: 11/09/2023]
Abstract
Trace amine-associated receptor 1 (TAAR1), the founding member of a nine-member family of trace amine receptors, is responsible for recognizing a range of biogenic amines in the brain, including the endogenous β-phenylethylamine (β-PEA)1 as well as methamphetamine2, an abused substance that has posed a severe threat to human health and society3. Given its unique physiological role in the brain, TAAR1 is also an emerging target for a range of neurological disorders including schizophrenia, depression and drug addiction2,4,5. Here we report structures of human TAAR1-G-protein complexes bound to methamphetamine and β-PEA as well as complexes bound to RO5256390, a TAAR1-selective agonist, and SEP-363856, a clinical-stage dual agonist for TAAR1 and serotonin receptor 5-HT1AR (refs. 6,7). Together with systematic mutagenesis and functional studies, the structures reveal the molecular basis of methamphetamine recognition and underlying mechanisms of ligand selectivity and polypharmacology between TAAR1 and other monoamine receptors. We identify a lid-like extracellular loop 2 helix/loop structure and a hydrogen-bonding network in the ligand-binding pockets, which may contribute to the ligand recognition in TAAR1. These findings shed light on the ligand recognition mode and activation mechanism for TAAR1 and should guide the development of next-generation therapeutics for drug addiction and various neurological disorders.
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Affiliation(s)
- Heng Liu
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - You Zheng
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yue Wang
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yumeng Wang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecule Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - Xinheng He
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peiyu Xu
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sijie Huang
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qingning Yuan
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- The Shanghai Advanced Electron Microscope Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xinyue Zhang
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Ling Wang
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Kexin Jiang
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Hong Chen
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China
- Shanghai Yuansi Standard Science and Technology Co., Ltd, Shanghai, China
| | - Zhen Li
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wenbin Liu
- Shanghai Key Laboratory of Crime Scene Evidence, Shanghai Research Institute of Criminal Science and Technology, Shanghai, China.
- Shanghai Yuansi Standard Science and Technology Co., Ltd, Shanghai, China.
| | - Sheng Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecule Cell Science, Chinese Academy of Sciences, Shanghai, China.
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.
| | - H Eric Xu
- The State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Fei Xu
- iHuman Institute, School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Shanghai Clinical Research and Trial Center, Shanghai, China.
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28
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Perfilova VN, Muzyko EA, Taran AS, Shevchenko AA, Naumenko LV. Problems and prospects for finding new pharmacological agents among adenosine receptor agonists, antagonists, or their allosteric modulators for the treatment of cardiovascular diseases. BIOMEDITSINSKAIA KHIMIIA 2023; 69:353-370. [PMID: 38153051 DOI: 10.18097/pbmc20236906353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
A1-adenosine receptors (A1AR) are widely distributed in the human body and mediate many different effects. They are abundantly present in the cardiovascular system, where they control angiogenesis, vascular tone, heart rate, and conduction. This makes the cardiovascular system A1AR an attractive target for the treatment of cardiovascular diseases (CVD). The review summarizes the literature data on the structure and functioning of A1AR, and analyzes their involvement in the formation of myocardial hypertrophy, ischemia-reperfusion damage, various types of heart rhythm disorders, chronic heart failure, and arterial hypertension. Special attention is paid to the role of some allosteric regulators of A1AR as potential agents for the CVD treatment.
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Affiliation(s)
- V N Perfilova
- Volgograd State Medical University, Volgograd, Russia; Volgograd Medical Research Center, Volgograd, Russia
| | - E A Muzyko
- Volgograd State Medical University, Volgograd, Russia
| | - A S Taran
- Volgograd State Medical University, Volgograd, Russia
| | | | - L V Naumenko
- Volgograd State Medical University, Volgograd, Russia
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29
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Wei S, Pour NG, Tiruvadi-Krishnan S, Ray AP, Thakur N, Eddy MT, Lamichhane R. Single-molecule visualization of human A 2A adenosine receptor activation by a G protein and constitutively activating mutations. Commun Biol 2023; 6:1218. [PMID: 38036689 PMCID: PMC10689853 DOI: 10.1038/s42003-023-05603-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023] Open
Abstract
Mutations that constitutively activate G protein-coupled receptors (GPCRs), known as constitutively activating mutations (CAMs), modify cell signaling and interfere with drugs, resulting in diseases with limited treatment options. We utilize fluorescence imaging at the single-molecule level to visualize the dynamic process of CAM-mediated activation of the human A2A adenosine receptor (A2AAR) in real time. We observe an active-state population for all CAMs without agonist stimulation. Importantly, activating mutations significantly increase the population of an intermediate state crucial for receptor activation, notably distinct from the addition of a partner G protein. Activation kinetics show that while CAMs increase the frequency of transitions to the intermediate state, mutations altering sodium sensitivity increase transitions away from it. These findings indicate changes in GPCR function caused by mutations may be predicted based on whether they favor or disfavor formation of an intermediate state, providing a framework for designing receptors with altered functions or therapies that target intermediate states.
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Affiliation(s)
- Shushu Wei
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA
| | - Niloofar Gopal Pour
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Sriram Tiruvadi-Krishnan
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA
| | - Arka Prabha Ray
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Naveen Thakur
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA
| | - Matthew T Eddy
- Department of Chemistry, College of Liberal Arts and Sciences, University of Florida, Gainesville, FL, USA.
| | - Rajan Lamichhane
- Department of Biochemistry & Cellular and Molecular Biology, College of Arts and Sciences, University of Tennessee, Knoxville, TN, USA.
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30
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Im D, Kishikawa JI, Shiimura Y, Hisano H, Ito A, Fujita-Fujiharu Y, Sugita Y, Noda T, Kato T, Asada H, Iwata S. Structural insights into the agonists binding and receptor selectivity of human histamine H 4 receptor. Nat Commun 2023; 14:6538. [PMID: 37863901 PMCID: PMC10589313 DOI: 10.1038/s41467-023-42260-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/04/2023] [Indexed: 10/22/2023] Open
Abstract
Histamine is a biogenic amine that participates in allergic and inflammatory processes by stimulating histamine receptors. The histamine H4 receptor (H4R) is a potential therapeutic target for chronic inflammatory diseases such as asthma and atopic dermatitis. Here, we show the cryo-electron microscopy structures of the H4R-Gq complex bound with an endogenous agonist histamine or the selective agonist imetit bound in the orthosteric binding pocket. The structures demonstrate binding mode of histamine agonists and that the subtype-selective agonist binding causes conformational changes in Phe3447.39, which, in turn, form the "aromatic slot". The results provide insights into the molecular underpinnings of the agonism of H4R and subtype selectivity of histamine receptors, and show that the H4R structures may be valuable in rational drug design of drugs targeting the H4R.
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Affiliation(s)
- Dohyun Im
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Jun-Ichi Kishikawa
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuki Shiimura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
- Institute of Life Science, Kurume University, Kurume, Fukuoka, 830-0011, Japan
| | - Hiromi Hisano
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Akane Ito
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Yoko Fujita-Fujiharu
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Yukihiko Sugita
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, 606-8501, Japan
| | - Takeshi Noda
- Laboratory of Ultrastructural Virology, Institute for Life and Medical Sciences, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- Laboratory of Ultrastructural Virology, Graduate School of Biostudies, Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto, 606-8507, Japan
- CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Takayuki Kato
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Hidetsugu Asada
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan.
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, 606-8501, Japan.
- RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo, 679-5148, Japan.
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31
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Thakur N, Ray AP, Lyman E, Gao ZG, Jacobson KA, Eddy MT. Membrane Mimetic-Dependence of GPCR Energy Landscapes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562552. [PMID: 37905159 PMCID: PMC10614885 DOI: 10.1101/2023.10.16.562552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Protein function strongly depends on temperature, which is related to temperature-dependent changes in the equilibria of protein conformational states. We leveraged variable-temperature 19F-NMR spectroscopy to interrogate the temperature dependence of the conformational landscape of the human A2A adenosine receptor (A2AAR), a class A GPCR. Temperature-induced changes in the conformational equilibria of A2AAR in lipid nanodiscs were markedly dependent on the efficacy of bound drugs. While antagonist complexes displayed only modest changes as the temperature rose, both full and partial agonist complexes exhibited substantial increases in the active state population. Importantly, the temperature-dependent response of complexes with both full and partial agonists exhibited a pronounced sensitivity to the specific membrane mimetic employed. In striking contrast to observations within lipid nanodiscs, in detergent micelles the active state population exhibited different behavior for A2AAR complexes with both full and partial agonists. This underscores the importance of the protein environment in understanding the thermodynamics of GPCR activation.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Arka Prabha Ray
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew T Eddy
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
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32
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Miller RM, Sescil J, Sarcinella MC, Bailey RC, Wang W. Accessible and Generalizable in Vitro Luminescence Assay for Detecting GPCR Activation. ACS MEASUREMENT SCIENCE AU 2023; 3:337-343. [PMID: 37868356 PMCID: PMC10588934 DOI: 10.1021/acsmeasuresciau.3c00021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/11/2023] [Accepted: 06/20/2023] [Indexed: 10/24/2023]
Abstract
G protein-coupled receptors (GPCRs) serve critical physiological roles as the most abundant family of receptors. Here, we describe the design of a generalizable and cell lysate-based method that leverages the interaction between an agonist-activated GPCR and a conformation-specific binder to reconstitute split nanoluciferase (NanoLuc) in vitro. This tool, In vitro GPCR split NanoLuc ligand Triggered Reporter (IGNiTR), has broad applications. We have demonstrated IGNiTR's use with three Gs-coupled GPCRs, two Gi-coupled GPCRs and three classes of conformation-specific binders: nanobodies, miniG proteins, and G protein peptidomimetics. As an in vitro method, IGNiTR enables the use of synthetic G protein peptidomimetics and provides easily scalable and portable reagents for characterizing GPCRs and ligands. We tested three diverse applications of IGNiTR: (1) proof-of-concept GPCR ligand screening using dopamine receptor D1 IGNiTR; (2) detection of opioids for point-of-care testing; and (3) characterizing GPCR functionality during Nanodisc-based reconstitution processes. Due to IGNiTR's unique advantages and the convenience of its cell lysate-based format, this tool will find extensive applications in GPCR ligand detection, screening, and GPCR characterization.
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Affiliation(s)
- Ruby M. Miller
- Life Sciences
Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Jennifer Sescil
- Life Sciences
Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Marina C. Sarcinella
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Ryan C. Bailey
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Wenjing Wang
- Life Sciences
Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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33
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Di Marino D, Conflitti P, Motta S, Limongelli V. Structural basis of dimerization of chemokine receptors CCR5 and CXCR4. Nat Commun 2023; 14:6439. [PMID: 37833254 PMCID: PMC10575954 DOI: 10.1038/s41467-023-42082-z] [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: 10/10/2021] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are prominent drug targets responsible for extracellular-to-intracellular signal transduction. GPCRs can form functional dimers that have been poorly characterized so far. Here, we show the dimerization mechanism of the chemokine receptors CCR5 and CXCR4 by means of an advanced free-energy technique named coarse-grained metadynamics. Our results reproduce binding events between the GPCRs occurring in the minute timescale, revealing a symmetric and an asymmetric dimeric structure for each of the three investigated systems, CCR5/CCR5, CXCR4/CXCR4, and CCR5/CXCR4. The transmembrane helices TM4-TM5 and TM6-TM7 are the preferred binding interfaces for CCR5 and CXCR4, respectively. The identified dimeric states differ in the access to the binding sites of the ligand and G protein, indicating that dimerization may represent a fine allosteric mechanism to regulate receptor activity. Our study offers structural basis for the design of ligands able to modulate the formation of CCR5 and CXCR4 dimers and in turn their activity, with therapeutic potential against HIV, cancer, and immune-inflammatory diseases.
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Affiliation(s)
- Daniele Di Marino
- Department of Life and Environmental Sciences - New York-Marche Structural Biology Centre (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
- Neuronal Death and Neuroprotection Unit, Department of Neuroscience, Mario Negri Institute for Pharmacological Research-IRCCS, Via Mario Negri 2, 20156, Milan, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Paolo Conflitti
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Euler Institute, Via G. Buffi 13, CH-6900, Lugano, Switzerland
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, 20126, Milan, Italy
| | - Vittorio Limongelli
- Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, Euler Institute, Via G. Buffi 13, CH-6900, Lugano, Switzerland.
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34
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Goßen J, Ribeiro RP, Bier D, Neumaier B, Carloni P, Giorgetti A, Rossetti G. AI-based identification of therapeutic agents targeting GPCRs: introducing ligand type classifiers and systems biology. Chem Sci 2023; 14:8651-8661. [PMID: 37592985 PMCID: PMC10430665 DOI: 10.1039/d3sc02352d] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/20/2023] [Indexed: 08/19/2023] Open
Abstract
Identifying ligands targeting G protein coupled receptors (GPCRs) with novel chemotypes other than the physiological ligands is a challenge for in silico screening campaigns. Here we present an approach that identifies novel chemotype ligands by combining structural data with a random forest agonist/antagonist classifier and a signal-transduction kinetic model. As a test case, we apply this approach to identify novel antagonists of the human adenosine transmembrane receptor type 2A, an attractive target against Parkinson's disease and cancer. The identified antagonists were tested here in a radio ligand binding assay. Among those, we found a promising ligand whose chemotype differs significantly from all so-far reported antagonists, with a binding affinity of 310 ± 23.4 nM. Thus, our protocol emerges as a powerful approach to identify promising ligand candidates with novel chemotypes while preserving antagonistic potential and affinity in the nanomolar range.
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Affiliation(s)
- Jonas Goßen
- Institute for Computational Biomedicine (INM-9/IAS-5) Forschungszentrum Jülich Wilhelm-Johnen-Straße 52428 Jülich Germany
- Faculty of Mathematics, Computer Science and Natural Sciences RWTH Aachen University Aachen Germany
| | - Rui Pedro Ribeiro
- Institute for Computational Biomedicine (INM-9/IAS-5) Forschungszentrum Jülich Wilhelm-Johnen-Straße 52428 Jülich Germany
| | - Dirk Bier
- Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Forschungszentrum Jülich GmbH Wilhelm-Johnen-Straße 52428 Jülich Germany
| | - Bernd Neumaier
- Institute of Neuroscience and Medicine, Nuclear Chemistry (INM-5), Forschungszentrum Jülich GmbH Wilhelm-Johnen-Straße 52428 Jülich Germany
- Institute of Radiochemistry and Experimental Molecular Imaging, University of Cologne, Faculty of Medicine and University Hospital Cologne Kerpener Straße 62 50937 Cologne Germany
| | - Paolo Carloni
- Institute for Computational Biomedicine (INM-9/IAS-5) Forschungszentrum Jülich Wilhelm-Johnen-Straße 52428 Jülich Germany
- Faculty of Mathematics, Computer Science and Natural Sciences RWTH Aachen University Aachen Germany
- JARA-Institut Molecular Neuroscience and Neuroimaging (INM-11) Forschungszentrum Jülich Wilhelm-Johnen-Straße 52428 Jülich Germany
| | - Alejandro Giorgetti
- Institute for Computational Biomedicine (INM-9/IAS-5) Forschungszentrum Jülich Wilhelm-Johnen-Straße 52428 Jülich Germany
- Department of Biotechnology University of Verona Verona Italy
| | - Giulia Rossetti
- Institute for Computational Biomedicine (INM-9/IAS-5) Forschungszentrum Jülich Wilhelm-Johnen-Straße 52428 Jülich Germany
- Jülich Supercomputing Centre (JSC) Forschungszentrum Jülich Jülich Germany
- Department of Neurology University Hospital Aachen (UKA), RWTH Aachen University Aachen Germany
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35
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Xu P, Huang S, Krumm BE, Zhuang Y, Mao C, Zhang Y, Wang Y, Huang XP, Liu YF, He X, Li H, Yin W, Jiang Y, Zhang Y, Roth BL, Xu HE. Structural genomics of the human dopamine receptor system. Cell Res 2023; 33:604-616. [PMID: 37221270 PMCID: PMC10397222 DOI: 10.1038/s41422-023-00808-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 03/30/2023] [Indexed: 05/25/2023] Open
Abstract
The dopaminergic system, including five dopamine receptors (D1R to D5R), plays essential roles in the central nervous system (CNS); and ligands that activate dopamine receptors have been used to treat many neuropsychiatric disorders, including Parkinson's Disease (PD) and schizophrenia. Here, we report cryo-EM structures of all five subtypes of human dopamine receptors in complex with G protein and bound to the pan-agonist, rotigotine, which is used to treat PD and restless legs syndrome. The structures reveal the basis of rotigotine recognition in different dopamine receptors. Structural analysis together with functional assays illuminate determinants of ligand polypharmacology and selectivity. The structures also uncover the mechanisms of dopamine receptor activation, unique structural features among the five receptor subtypes, and the basis of G protein coupling specificity. Our work provides a comprehensive set of structural templates for the rational design of specific ligands to treat CNS diseases targeting the dopaminergic system.
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Affiliation(s)
- Peiyu Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sijie Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Brian E Krumm
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, USA
| | - Youwen Zhuang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Chunyou Mao
- Center for Structural Pharmacology and Therapeutics Development, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yumu Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yue Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, USA
| | - Yong-Feng Liu
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, USA
| | - Xinheng He
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Huadong Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Wanchao Yin
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yi Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yan Zhang
- Center for Structural Pharmacology and Therapeutics Development, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- MOE Frontier Science Center for Brain Research and Brain-Machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China.
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, USA.
| | - H Eric Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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36
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Tajiri M, Imai S, Konuma T, Shimamoto K, Shimada I, Akashi S. Evaluation of Drug Responses to Human β 2AR Using Native Mass Spectrometry. ACS OMEGA 2023; 8:24544-24551. [PMID: 37457453 PMCID: PMC10339329 DOI: 10.1021/acsomega.3c02737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023]
Abstract
We aimed to develop a platform to rapidly investigate the responses of agonists and antagonists to G-protein-coupled receptors (GPCRs) using native mass spectrometry (MS). We successfully observed the ligand-bound human β2 adrenergic receptor (hβ2AR); however, it was challenging to quantitatively discuss drug efficacy from MS data alone. Since ligand-bound GPCRs are stabilized by the Gα subunit of G proteins on the membrane, mini-Gs and nanobody80 (Nb80) that can mimic the Gα interface of the GPCR were utilized. Ternary complexes of hβ2AR, ligand, and mini-Gs or Nb80 were prepared and subjected to native MS. We found a strong correlation between the hβ2AR-mini-Gs or -Nb80 complex ratio observed in the mass spectra and agonist/antagonist efficacy obtained using a cell-based assay. This method does not require radioisotope labeling and would be applicable to the analysis of other GPCRs, facilitating the characterization of candidate compounds as GPCR agonists and antagonists.
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Affiliation(s)
- Michiko Tajiri
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shunsuke Imai
- Biosystems
Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tsuyoshi Konuma
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Keiko Shimamoto
- Suntory
Foundation for Life Sciences, 8-1-1 Seikadai, Seika-cho, Soraku-gun, Kyoto 619-0284, Japan
| | - Ichio Shimada
- Biosystems
Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Graduate
School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi, Hiroshima City, Hiroshima 739-8528, Japan
| | - Satoko Akashi
- Graduate
School of Medical Life Science, Yokohama
City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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37
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Ray AP, Thakur N, Pour NG, Eddy MT. Dual mechanisms of cholesterol-GPCR interactions that depend on membrane phospholipid composition. Structure 2023; 31:836-847.e6. [PMID: 37236187 PMCID: PMC10330489 DOI: 10.1016/j.str.2023.05.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/25/2023] [Accepted: 05/01/2023] [Indexed: 05/28/2023]
Abstract
Cholesterol is a critical component of mammalian cell membranes and an allosteric modulator of G protein-coupled receptors (GPCRs), but divergent views exist on the mechanisms by which cholesterol influences receptor functions. Leveraging the benefits of lipid nanodiscs, i.e., quantitative control of lipid composition, we observe distinct impacts of cholesterol in the presence and absence of anionic phospholipids on the function-related conformational dynamics of the human A2A adenosine receptor (A2AAR). Direct receptor-cholesterol interactions drive activation of agonist-bound A2AAR in membranes containing zwitterionic phospholipids. Intriguingly, the presence of anionic lipids attenuates cholesterol's impact through direct interactions with the receptor, highlighting a more complex role for cholesterol that depends on membrane phospholipid composition. Targeted amino acid replacements at two frequently predicted cholesterol interaction sites showed distinct impacts of cholesterol at different receptor locations, demonstrating the ability to delineate different roles of cholesterol in modulating receptor signaling and maintaining receptor structural integrity.
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Affiliation(s)
- Arka Prabha Ray
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Naveen Thakur
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Niloofar Gopal Pour
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA
| | - Matthew T Eddy
- Department of Chemistry, University of Florida, 126 Sisler Hall, Gainesville, FL 32611, USA.
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38
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Mafi A, Kim SK, Goddard WA. The dynamics of agonist-β 2-adrenergic receptor activation induced by binding of GDP-bound Gs protein. Nat Chem 2023:10.1038/s41557-023-01238-6. [PMID: 37349378 DOI: 10.1038/s41557-023-01238-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 05/12/2023] [Indexed: 06/24/2023]
Abstract
There is considerable uncertainty about the mechanism by which the β2-adrenergic receptor (β2AR) is activated. Here we use molecular metadynamics computations to predict the mechanism by which an agonist induces the activation of the β2AR and its cognate Gs protein. We found that binding agonist alone to the inactive β2AR does not break the ionic lock and hence does not drive the β2AR towards the activated conformation. However, we found that attaching the inactive Gs protein to the agonist-bound inactive β2AR (containing the ionic lock) leads to partial insertion of Gαs-α5 into the core of β2AR, which breaks the ionic lock, leading to activation of the Gs protein coupled to β2AR. Upon activation, the Gαs protein undergoes a remarkable opening of the GDP binding pocket, making the GDP available for exchange or release. Concomitantly, Gαs-α5 undergoes a remarkable expansion in the β2AR cytoplasmic region after the ionic lock is broken, inducing TM6 to displace outward by ~5 Å from TM3.
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Affiliation(s)
- Amirhossein Mafi
- Materials and Process Simulation Center, Caltech, Pasadena, CA, USA
- California Institute of Technology, Pasadena, CA, USA
| | - Soo-Kyung Kim
- Materials and Process Simulation Center, Caltech, Pasadena, CA, USA
- California Institute of Technology, Pasadena, CA, USA
| | - William A Goddard
- Materials and Process Simulation Center, Caltech, Pasadena, CA, USA.
- California Institute of Technology, Pasadena, CA, USA.
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39
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Tzortzini E, Kolocouris A. Molecular Biophysics of Class A G Protein Coupled Receptors-Lipids Interactome at a Glance-Highlights from the A 2A Adenosine Receptor. Biomolecules 2023; 13:957. [PMID: 37371538 DOI: 10.3390/biom13060957] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/28/2023] [Indexed: 06/29/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipid membrane bilayers with cholesterol representing 34% of the total lipid content in mammalian plasma membranes. Membrane lipids interact with GPCRs structures and modulate their function and drug-stimulated signaling through conformational selection. It has been shown that anionic phospholipids form strong interactions between positively charged residues in the G protein and the TM5-TM6-TM 7 cytoplasmic interface of class A GPCRs stabilizing the signaling GPCR-G complex. Cholesterol with a high content in plasma membranes can be identified in more specific sites in the transmembrane region of GPCRs, such as the Cholesterol Consensus Motif (CCM) and Cholesterol Recognition Amino Acid Consensus (CRAC) motifs and other receptor dependent and receptor state dependent sites. Experimental biophysical methods, atomistic (AA) MD simulations and coarse-grained (CG) molecular dynamics simulations have been applied to investigate these interactions. We emphasized here the impact of phosphatidyl inositol-4,5-bisphosphate (PtdIns(4,5)P2 or PIP2), a minor phospholipid component and of cholesterol on the function-related conformational equilibria of the human A2A adenosine receptor (A2AR), a representative receptor in class A GPCR. Several GPCRs of class A interacted with PIP2 and cholesterol and in many cases the mechanism of the modulation of their function remains unknown. This review provides a helpful comprehensive overview for biophysics that enter the field of GPCRs-lipid systems.
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Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, 15771 Athens, Greece
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40
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Kobayashi K, Kawakami K, Kusakizako T, Tomita A, Nishimura M, Sawada K, Okamoto HH, Hiratsuka S, Nakamura G, Kuwabara R, Noda H, Muramatsu H, Shimizu M, Taguchi T, Inoue A, Murata T, Nureki O. Class B1 GPCR activation by an intracellular agonist. Nature 2023; 618:1085-1093. [PMID: 37286611 PMCID: PMC10307627 DOI: 10.1038/s41586-023-06169-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 05/04/2023] [Indexed: 06/09/2023]
Abstract
G protein-coupled receptors (GPCRs) generally accommodate specific ligands in the orthosteric-binding pockets. Ligand binding triggers a receptor allosteric conformational change that leads to the activation of intracellular transducers, G proteins and β-arrestins. Because these signals often induce adverse effects, the selective activation mechanism for each transducer must be elucidated. Thus, many orthosteric-biased agonists have been developed, and intracellular-biased agonists have recently attracted broad interest. These agonists bind within the receptor intracellular cavity and preferentially tune the specific signalling pathway over other signalling pathways, without allosteric rearrangement of the receptor from the extracellular side1-3. However, only antagonist-bound structures are currently available1,4-6, and there is no evidence to support that biased agonist binding occurs within the intracellular cavity. This limits the comprehension of intracellular-biased agonism and potential drug development. Here we report the cryogenic electron microscopy structure of a complex of Gs and the human parathyroid hormone type 1 receptor (PTH1R) bound to a PTH1R agonist, PCO371. PCO371 binds within an intracellular pocket of PTH1R and directly interacts with Gs. The PCO371-binding mode rearranges the intracellular region towards the active conformation without extracellularly induced allosteric signal propagation. PCO371 stabilizes the significantly outward-bent conformation of transmembrane helix 6, which facilitates binding to G proteins rather than β-arrestins. Furthermore, PCO371 binds within the highly conserved intracellular pocket, activating 7 out of the 15 class B1 GPCRs. Our study identifies a new and conserved intracellular agonist-binding pocket and provides evidence of a biased signalling mechanism that targets the receptor-transducer interface.
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Affiliation(s)
- Kazuhiro Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Tsukasa Kusakizako
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Atsuhiro Tomita
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Preferred Networks, Tokyo, Japan
| | - Michihiro Nishimura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Sawada
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki H Okamoto
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Suzune Hiratsuka
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Gaku Nakamura
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Riku Kuwabara
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Hiroshi Noda
- Research Division, Chugai Pharmaceutical, Shizuoka, Japan
| | | | - Masaru Shimizu
- Research Division, Chugai Pharmaceutical, Shizuoka, Japan
| | - Tomohiko Taguchi
- Laboratory of Organelle Pathophysiology, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan.
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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41
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Guo L, Cheng J, Lian S, Liu Q, Lu Y, Zheng Y, Zhu K, Zhang M, Kong Y, Zhang C, Rong N, Zhuang Y, Fang G, Jiang J, Zhang T, Han X, Liu Z, Xia M, Liu S, Zhang L, Liberles SD, Yu X, Xu Y, Yang F, Li Q, Sun JP. Structural basis of amine odorant perception by a mammal olfactory receptor. Nature 2023; 618:193-200. [PMID: 37225986 DOI: 10.1038/s41586-023-06106-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/20/2023] [Indexed: 05/26/2023]
Abstract
Odorants are detected as smell in the nasal epithelium of mammals by two G-protein-coupled receptor families, the odorant receptors and the trace amine-associated receptors1,2 (TAARs). TAARs emerged following the divergence of jawed and jawless fish, and comprise a large monophyletic family of receptors that recognize volatile amine odorants to elicit both intraspecific and interspecific innate behaviours such as attraction and aversion3-5. Here we report cryo-electron microscopy structures of mouse TAAR9 (mTAAR9) and mTAAR9-Gs or mTAAR9-Golf trimers in complex with β-phenylethylamine, N,N-dimethylcyclohexylamine or spermidine. The mTAAR9 structures contain a deep and tight ligand-binding pocket decorated with a conserved D3.32W6.48Y7.43 motif, which is essential for amine odorant recognition. In the mTAAR9 structure, a unique disulfide bond connecting the N terminus to ECL2 is required for agonist-induced receptor activation. We identify key structural motifs of TAAR family members for detecting monoamines and polyamines and the shared sequence of different TAAR members that are responsible for recognition of the same odour chemical. We elucidate the molecular basis of mTAAR9 coupling to Gs and Golf by structural characterization and mutational analysis. Collectively, our results provide a structural basis for odorant detection, receptor activation and Golf coupling of an amine olfactory receptor.
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MESH Headings
- Animals
- Mice
- Biogenic Amines/analysis
- Biogenic Amines/chemistry
- Biogenic Amines/metabolism
- Cryoelectron Microscopy
- GTP-Binding Protein alpha Subunits, Gs/chemistry
- GTP-Binding Protein alpha Subunits, Gs/metabolism
- GTP-Binding Protein alpha Subunits, Gs/ultrastructure
- Odorants/analysis
- Olfactory Perception/physiology
- Polyamines/analysis
- Polyamines/chemistry
- Polyamines/metabolism
- Receptors, Biogenic Amine/chemistry
- Receptors, Biogenic Amine/genetics
- Receptors, Biogenic Amine/metabolism
- Receptors, Biogenic Amine/ultrastructure
- Receptors, Odorant/chemistry
- Receptors, Odorant/genetics
- Receptors, Odorant/metabolism
- Receptors, Odorant/ultrastructure
- Smell/physiology
- Spermidine/analysis
- Spermidine/chemistry
- Spermidine/metabolism
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Affiliation(s)
- Lulu Guo
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Jie Cheng
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, China
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Shandong University, Jinan, China
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Shuo Lian
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Qun Liu
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Yan Lu
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Yuan Zheng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China
| | - Kongkai Zhu
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Minghui Zhang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Yalei Kong
- Songjiang Institute and Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chao Zhang
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Naikang Rong
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Yuming Zhuang
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Guoxing Fang
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Jingjing Jiang
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Tianyao Zhang
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Xiang Han
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Zili Liu
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China
| | - Ming Xia
- Department of Otolaryngology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong, China
| | - Shangming Liu
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, China
| | - Stephen D Liberles
- Howard Hughes Medical Institute, Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Xiao Yu
- Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Yunfei Xu
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, China.
| | - Fan Yang
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, China.
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China.
| | - Qian Li
- Songjiang Institute and Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Center for Brain Science, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Department of Anatomy and Physiology, Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health in Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, China.
| | - Jin-Peng Sun
- Advanced Medical Research Institute, Meili Lake Translational Research Park, Cheeloo College of Medicine, Shandong University, Jinan, China.
- Department of Biochemistry and Molecular Biology, Shandong University School of Medicine, Jinan, China.
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Key Laboratory of Molecular Cardiovascular Science, Ministry of Education, Beijing, China.
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42
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Matricon P, Nguyen AT, Vo DD, Baltos JA, Jaiteh M, Luttens A, Kampen S, Christopoulos A, Kihlberg J, May LT, Carlsson J. Structure-based virtual screening discovers potent and selective adenosine A 1 receptor antagonists. Eur J Med Chem 2023; 257:115419. [PMID: 37301076 DOI: 10.1016/j.ejmech.2023.115419] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 06/12/2023]
Abstract
Development of subtype-selective leads is essential in drug discovery campaigns targeting G protein-coupled receptors (GPCRs). Herein, a structure-based virtual screening approach to rationally design subtype-selective ligands was applied to the A1 and A2A adenosine receptors (A1R and A2AR). Crystal structures of these closely related subtypes revealed a non-conserved subpocket in the binding sites that could be exploited to identify A1R selective ligands. A library of 4.6 million compounds was screened computationally against both receptors using molecular docking and 20 A1R selective ligands were predicted. Of these, seven antagonized the A1R with micromolar activities and several compounds displayed slight selectivity for this subtype. Twenty-seven analogs of two discovered scaffolds were designed, resulting in antagonists with nanomolar potency and up to 76-fold A1R-selectivity. Our results show the potential of structure-based virtual screening to guide discovery and optimization of subtype-selective ligands, which could facilitate the development of safer drugs.
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Affiliation(s)
- Pierre Matricon
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Anh Tn Nguyen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Duc Duy Vo
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Jo-Anne Baltos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Mariama Jaiteh
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Andreas Luttens
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Stefanie Kampen
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, SE-751 23, Uppsala, Sweden
| | - Lauren Therese May
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, 3052, Australia.
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.
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43
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He L, Zhao Q, Qi J, Wang Y, Han W, Chen Z, Cong Y, Wang S. Structural insights into constitutive activity of 5-HT 6 receptor. Proc Natl Acad Sci U S A 2023; 120:e2209917120. [PMID: 36989299 PMCID: PMC10083584 DOI: 10.1073/pnas.2209917120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 02/16/2023] [Indexed: 03/30/2023] Open
Abstract
While most therapeutic research on G-protein-coupled receptors (GPCRs) focuses on receptor activation by (endogenous) agonists, significant therapeutic potential exists through agonist-independent intrinsic constitutive activity that can occur in various physiological and pathophysiological settings. For example, inhibiting the constitutive activity of 5-HT6R-a receptor that is found almost exclusively in the brain and mediates excitatory neurotransmission-has demonstrated a therapeutic effect on cognitive/memory impairment associated with several neuropsychiatric disorders. However, the structural basis of such constitutive activity remains unclear. Here, we present a cryo-EM structure of serotonin-bound human 5-HT6R-Gs heterotrimer at 3.0-Å resolution. Detailed analyses of the structure complemented by comprehensive interrogation of signaling illuminate key structural determinants essential for constitutive 5-HT6R activity. Additional structure-guided mutagenesis leads to a nanobody mimic Gαs for 5-HT6R that can reduce its constitutive activity. Given the importance of 5-HT6R for a large number of neuropsychiatric disorders, insights derived from these studies will accelerate the design of more effective medications, and shed light on the molecular basis of constitutive activity.
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Affiliation(s)
- Licong He
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Qiaoyu Zhao
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Jianzhong Qi
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Yifan Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Wenyu Han
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Zhangcheng Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Yao Cong
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
| | - Sheng Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai200031, China
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44
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Maslov I, Volkov O, Khorn P, Orekhov P, Gusach A, Kuzmichev P, Gerasimov A, Luginina A, Coucke Q, Bogorodskiy A, Gordeliy V, Wanninger S, Barth A, Mishin A, Hofkens J, Cherezov V, Gensch T, Hendrix J, Borshchevskiy V. Sub-millisecond conformational dynamics of the A 2A adenosine receptor revealed by single-molecule FRET. Commun Biol 2023; 6:362. [PMID: 37012383 PMCID: PMC10070357 DOI: 10.1038/s42003-023-04727-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
The complex pharmacology of G-protein-coupled receptors (GPCRs) is defined by their multi-state conformational dynamics. Single-molecule Förster Resonance Energy Transfer (smFRET) is well suited to quantify dynamics for individual protein molecules; however, its application to GPCRs is challenging. Therefore, smFRET has been limited to studies of inter-receptor interactions in cellular membranes and receptors in detergent environments. Here, we performed smFRET experiments on functionally active human A2A adenosine receptor (A2AAR) molecules embedded in freely diffusing lipid nanodiscs to study their intramolecular conformational dynamics. We propose a dynamic model of A2AAR activation that involves a slow (>2 ms) exchange between the active-like and inactive-like conformations in both apo and antagonist-bound A2AAR, explaining the receptor's constitutive activity. For the agonist-bound A2AAR, we detected faster (390 ± 80 µs) ligand efficacy-dependent dynamics. Our work establishes a general smFRET platform for GPCR investigations that can potentially be used for drug screening and/or mechanism-of-action studies.
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Affiliation(s)
- Ivan Maslov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | | | - Polina Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Philipp Orekhov
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China
| | - Anastasiia Gusach
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Pavel Kuzmichev
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Andrey Gerasimov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
- Vyatka State University, Kirov, Russia
| | - Aleksandra Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Quinten Coucke
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Andrey Bogorodskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Valentin Gordeliy
- Institut de Biologie Structurale J.-P. Ebel, Université Grenoble Alpes-CEA-CNRS, Grenoble, France
| | - Simon Wanninger
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany
| | - Anders Barth
- Physical Chemistry, Department of Chemistry, Center for Nano Science (CENS), Center for Integrated Protein Science (CIPSM) and Nanosystems Initiative München (NIM), Ludwig-Maximilians-Universität Munich, Munich, Germany
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, HZ, Delft, The Netherlands
| | - Alexey Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
- Max Plank Institute for Polymer Research, Mainz, Germany
| | - Vadim Cherezov
- Bridge Institute, Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Thomas Gensch
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, Diepenbeek, Belgium.
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, Leuven, Belgium.
| | - Valentin Borshchevskiy
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.
- Joint Institute for Nuclear Research, Dubna, Russian Federation.
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Yang Y, Kang HJ, Gao R, Wang J, Han GW, DiBerto JF, Wu L, Tong J, Qu L, Wu Y, Pileski R, Li X, Zhang XC, Zhao S, Kenakin T, Wang Q, Stevens RC, Peng W, Roth BL, Rao Z, Liu ZJ. Structural insights into the human niacin receptor HCA2-G i signalling complex. Nat Commun 2023; 14:1692. [PMID: 36973264 PMCID: PMC10043007 DOI: 10.1038/s41467-023-37177-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
The hydroxycarboxylic acid receptor 2 (HCA2) agonist niacin has been used as treatment for dyslipidemia for several decades albeit with skin flushing as a common side-effect in treated individuals. Extensive efforts have been made to identify HCA2 targeting lipid lowering agents with fewer adverse effects, despite little being known about the molecular basis of HCA2 mediated signalling. Here, we report the cryo-electron microscopy structure of the HCA2-Gi signalling complex with the potent agonist MK-6892, along with crystal structures of HCA2 in inactive state. These structures, together with comprehensive pharmacological analysis, reveal the ligand binding mode and activation and signalling mechanisms of HCA2. This study elucidates the structural determinants essential for HCA2 mediated signalling and provides insights into ligand discovery for HCA2 and related receptors.
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Affiliation(s)
- Yang Yang
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hye Jin Kang
- Department of Pharmacology, and NIMH Psychoactive Drug Screening Program University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, 27514, USA
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Ruogu Gao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingjing Wang
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Gye Won Han
- Departments of Biological Sciences and Chemistry, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Jeffrey F DiBerto
- Department of Pharmacology, and NIMH Psychoactive Drug Screening Program University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, 27514, USA
| | - Lijie Wu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Jiahui Tong
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Lu Qu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Yiran Wu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Ryan Pileski
- Department of Pharmacology, and NIMH Psychoactive Drug Screening Program University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, 27514, USA
- Department of Obstetrics and Gynecology, Duke University, Durham, NC, USA
| | - Xuemei Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuejun Cai Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Terry Kenakin
- Department of Pharmacology, and NIMH Psychoactive Drug Screening Program University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, 27514, USA
| | - Quan Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | | | - Wei Peng
- Innovation Center for Pathogen Research, Guangzhou Laboratory, Guangzhou, 510320, China.
| | - Bryan L Roth
- Department of Pharmacology, and NIMH Psychoactive Drug Screening Program University of North Carolina Chapel Hill Medical School, Chapel Hill, NC, 27514, USA.
| | - Zihe Rao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhi-Jie Liu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China.
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Salkin H, Satir-Basaran G, Korkmaz S, Burcin Gonen Z, Erdem Basaran K. Mesenchymal stem cell-derived conditioned medium and Methysergide give rise to crosstalk inhibition of 5-HT2A and 5-HT7 receptors in neuroblastoma cells. Brain Res 2023; 1808:148354. [PMID: 36997105 DOI: 10.1016/j.brainres.2023.148354] [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: 07/23/2022] [Revised: 12/04/2022] [Accepted: 03/26/2023] [Indexed: 03/30/2023]
Abstract
OBJECTIVE (s): We aimed to investigate the effects of mesenchymal stem cell secretome and methysergide combination on 5-hydroxytryptamine 2A, (5-HT2AR), 5-hydroxytryptamine 7 (5-HT7R), adenosine 2A (A2AR) receptors and CD73 on neuroblastoma cell line and how they affect biological characteristics. Methysergide was used as a serotonin antagonist on the neuroblastoma cells. MATERIALS AND METHODS Human dental pulp-derived stem cells (hDPSCs) used to obtain conditioned medium (CM). Methysergide drug was prepared in CM and applied to neuroblastoma cells. Analysis of 5-HT7R, 5-HT2AR, A2AR and CD73 expressions was performed by western blot and immunofluorescence staining. Total apoptosis, mitochondrial membrane depolarization, Ki-67 proliferation test, viability analysis, DNA damage and cell cycle analysis were performed in accordance with the product procedure by using biological activity test kits. RESULTS Our results showed that neuroblastoma cancer cells are normally on the Gs signaling axis via the serotonin 7 receptor and the adenosine 2A receptor. CM and Methysergide inhibited the 5-HT7 and A2A receptor levels in neuroblastoma cells. We found that CM and methysergide formed crosstalk inhibition between 5-HT2AR, 5-HT7R, A2AR and CD73. CM and Methysergide increased the total apoptosis in neuroblastoma cells and induced the mitochondrial membrane depolarization. CM and Methysergide induced the DNA damage and arrested in G0/G1 phase of cell cycle of the neuroblastoma cells. CONCLUSION These findings suggest that the combination of CM and methysergite may exert a therapeutic effect on neuroblastoma cancer cells, and future in vivo studies may be important in area of neuroblastoma research to support the findings.
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Affiliation(s)
- Hasan Salkin
- Beykent University, Vocational School, Department of Medical Services and Techniques, Program of Pathology Laboratory Techniques, Istanbul, Turkey; Erciyes University, Genome and Stem Cell Center, Kayseri, Turkey.
| | - Guzide Satir-Basaran
- Erciyes University, Faculty of Pharmacy, Department of Biochemistry, Kayseri, Turkey
| | - Seyda Korkmaz
- Erciyes University, Genome and Stem Cell Center, Kayseri, Turkey
| | - Zeynep Burcin Gonen
- Erciyes University, Genome and Stem Cell Center, Kayseri, Turkey; Erciyes University, Faculty of Dentistry, Department of Oral and Maxillofacial Surgery, Kayseri, Turkey
| | - Kemal Erdem Basaran
- Erciyes University, Faculty of Medicine, Department of Physiology, Kayseri, Turkey
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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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Thakur N, Ray AP, Sharp L, Jin B, Duong A, Pour NG, Obeng S, Wijesekara AV, Gao ZG, McCurdy CR, Jacobson KA, Lyman E, Eddy MT. Anionic phospholipids control mechanisms of GPCR-G protein recognition. Nat Commun 2023; 14:794. [PMID: 36781870 PMCID: PMC9925817 DOI: 10.1038/s41467-023-36425-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are embedded in phospholipids that strongly influence drug-stimulated signaling. Anionic lipids are particularly important for GPCR signaling complex formation, but a mechanism for this role is not understood. Using NMR spectroscopy, we explore the impact of anionic lipids on the function-related conformational equilibria of the human A2A adenosine receptor (A2AAR) in bilayers containing defined mixtures of zwitterionic and anionic phospholipids. Anionic lipids prime the receptor to form complexes with G proteins through a conformational selection process. Without anionic lipids, signaling complex formation proceeds through a less favorable induced fit mechanism. In computational models, anionic lipids mimic interactions between a G protein and positively charged residues in A2AAR at the receptor intracellular surface, stabilizing a pre-activated receptor conformation. Replacing these residues strikingly alters the receptor response to anionic lipids in experiments. High sequence conservation of the same residues among all GPCRs supports a general role for lipid-receptor charge complementarity in signaling.
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Affiliation(s)
- Naveen Thakur
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Arka P Ray
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Liam Sharp
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, USA
| | - Beining Jin
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Alexander Duong
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Niloofar Gopal Pour
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Samuel Obeng
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL, USA
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Anuradha V Wijesekara
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Christopher R McCurdy
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, USA
- Translational Drug Development Core, Clinical and Translational Sciences Institute, University of Florida, Gainesville, Florida, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, USA
| | - Edward Lyman
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware, USA
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, USA
| | - Matthew T Eddy
- Department of Chemistry, College of Liberal Arts & Sciences, University of Florida, 126 Sisler Hall, Gainesville, FL, USA.
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Tzortzini E, Corey RA, Kolocouris A. Comparative Study of Receptor-, Receptor State-, and Membrane-Dependent Cholesterol Binding Sites in A 2A and A 1 Adenosine Receptors Using Coarse-Grained Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:928-949. [PMID: 36637988 DOI: 10.1021/acs.jcim.2c01181] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
We used coarse-grained molecular dynamics (CG MD) simulations to study protein-cholesterol interactions for different activation states of the A2A adenosine receptor (A2AR) and the A1 adenosine receptor (A1R) and predict new cholesterol binding sites indicating amino acid residues with a high residence time in three biologically relevant membranes. Compared to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)-cholesterol and POPC-phosphatidylinositol-bisphosphate (PIP2)-cholesterol, the plasma mimetic membrane best described the cholesterol binding sites previously detected for the inactive state of A2AR and revealed the binding sites with long-lasting amino acid residues. We observed that using the plasma mimetic membrane and plotting residues with cholesterol residence time ≥2 μs, our CG MD simulations captured most obviously the cholesterol-protein interactions. For the inactive A2AR, we identified one more binding site in which cholesterol is bound to residues with a long residence time compared to the previously detected, for the active A1R, three binding sites, and for the inactive A1R, two binding sites. We calculated that for the active states, cholesterol binds to residues with a much longer residence time compared to the inactive state for both A2AR and A1R. The stability of the identified binding sites to A1R or A2AR with CG MD simulations was additionally investigated with potential of mean force calculations using umbrella sampling. We observed that the binding sites with residues to which cholesterol has a long residence time in A2AR have shallow binding free energy minima compared to the related binding sites in A1R, suggesting a stronger binding for cholesterol to A1R. The differences in binding sites in which cholesterol is stabilized and interacts with residues with a long residence time between active and inactive states of A1R and A2AR can be important for differences in functional activity and orthosteric agonist or antagonist affinity and can be used for the design of allosteric modulators, which can bind through lipid pathways. We observed a stronger binding for cholesterol to A1R (i.e., generally higher association rates) compared to A2AR, which remains to be demonstrated. For the active states, cholesterol binds to residues with much longer residence times compared to the inactive state for both A2AR and A1R. Taken together, binding sites of active A1R may be considered as promising allosteric targets.
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Affiliation(s)
- Efpraxia Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771Athens, Greece
| | - Robin A Corey
- Department of Biochemistry, University of Oxford, OxfordOX1 3QU, United Kingdom
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, 15771Athens, Greece
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50
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Min X, Sun N, Wang S, Zhang X, Kim KM. Sequestration of Gβγ by deubiquitinated arrestins into the nucleus as a novel desensitization mechanism of G protein-coupled receptors. Cell Commun Signal 2023; 21:11. [PMID: 36658650 PMCID: PMC9854190 DOI: 10.1186/s12964-022-01013-z] [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: 09/26/2022] [Accepted: 12/10/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Desensitization of G protein-coupled receptors (GPCRs) refers to a rapid attenuation of responsiveness that occurs with repeated or continuous exposure to agonists. GRK-mediated phosphorylation and subsequent binding with arrestins in the activated receptor cytoplasmic cavity in competition with G proteins has been suggested as the conventional mechanism of desensitization. Along with widely accepted conventional mechanism of desensitization, studies of various GPCRs including dopamine D2-like receptors (D2R, D3R, D4R) have suggested the existence of another desensitization mechanism. In this study, loss-of-function approaches and D2-like receptor mutants that display different desensitization properties were used to elucidate the molecular mechanisms responsible for desensitization. RESULTS Desensitization development entailed the signaling cascade composed of Src, PDK1, and Akt, the latter of which in turn interacted with USP33, an arrestin deubiquitinase, to promote arrestin deubiquitination. The deubiquitinated arrestin subsequently formed a complex with Gβγ and translocated to the nucleus via an importin complex, wherein it sequestered Gβγ from the receptor and Gα, thereby attenuating receptor signaling. As in D2-like receptors, both USP33 and importin β1 were involved in the desensitization of the β2 adrenoceptor. CONCLUSIONS In addition to the conventional mechanism of desensitization, which occurs on the plasma membrane and in the cytosol, this study provides a new insight that another desensitization pathway in which nuclear trafficking plays a critical role is operating. It is plausible that multiple, complementary desensitization measures are in place to properly induce desensitization depending on receptor characteristics or the surrounding environment. Video Abstract.
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Affiliation(s)
- Xiao Min
- grid.14005.300000 0001 0356 9399Department of Pharmacology, College of Pharmacy, Chonnam National University, Gwangju, 61186 Republic of Korea
| | - Ningning Sun
- grid.14005.300000 0001 0356 9399Department of Pharmacology, College of Pharmacy, Chonnam National University, Gwangju, 61186 Republic of Korea
| | - Shujie Wang
- grid.14005.300000 0001 0356 9399Department of Pharmacology, College of Pharmacy, Chonnam National University, Gwangju, 61186 Republic of Korea
| | - Xiaohan Zhang
- grid.14005.300000 0001 0356 9399Department of Pharmacology, College of Pharmacy, Chonnam National University, Gwangju, 61186 Republic of Korea ,grid.443382.a0000 0004 1804 268XCollege of Pharmaceutical Sciences, Guizhou University, Guiyang, 550025 Guizhou China
| | - Kyeong-Man Kim
- grid.14005.300000 0001 0356 9399Department of Pharmacology, College of Pharmacy, Chonnam National University, Gwangju, 61186 Republic of Korea
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