1
|
Barreto CAV, Vitorino JNM, Reis PBPS, Machuqueiro M, Moreira IS. p Ka Calculations of GPCRs: Understanding Protonation States in Receptor Activation. J Chem Inf Model 2024. [PMID: 39150719 DOI: 10.1021/acs.jcim.4c01125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
The increase in the available G protein-coupled receptor (GPCR) structures has been pivotal in helping to understand their activation process. However, the role of protonation-conformation coupling in GPCR activation still needs to be clarified. We studied the protonation behavior of the highly conserved Asp2.50 residue in five different class A GPCRs (active and inactive conformations) using a linear response approximation (LRA) pKa calculation protocol. We observed consistent differences (1.3 pK units) for the macroscopic pKa values between the inactive and active states of the A2AR and B2AR receptors, indicating the protonation of Asp2.50 during GPCR activation. This process seems to be specific and not conserved, as no differences were observed in the pKa values of the remaining receptors (CB1R, NT1R, and GHSR).
Collapse
Affiliation(s)
- Carlos A V Barreto
- PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Casa Costa Alemão, 3030-789 Coimbra, Portugal
- CNC─Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - João N M Vitorino
- BioSI─Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Pedro B P S Reis
- BioSI─Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Miguel Machuqueiro
- BioSI─Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Irina S Moreira
- CNC─Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, University of Coimbra, 3004-504 Coimbra, Portugal
- Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| |
Collapse
|
2
|
Wu Z, Sun X, Su J, Zhang X, Hu J, Li C. Revealing the graded activation mechanism of neurotensin receptor 1. Int J Biol Macromol 2024; 278:134488. [PMID: 39111461 DOI: 10.1016/j.ijbiomac.2024.134488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 08/02/2024] [Accepted: 08/02/2024] [Indexed: 08/16/2024]
Abstract
Graded activation contributes to the precise regulation of GPCR activity, presenting new opportunities for drug design. In this work, a total of 10 μs enhanced-sampling simulations are performed to provide molecular insights into the binding dynamics differences of the neurotensin receptor 1 (NTSR1) to the full agonist SRI-9829, partial agonist RTI-3a and inverse agonist SR48692. The possible graded activation mechanism of NTSR1 is revealed by an integrated analysis utilizing the reweighted potential of mean force (PMF), deep learning (DL) and transfer entropy (TE). Specifically, the orthosteric pocket is observed to undergo expansion and contraction, with the G-protein-binding site experiencing interconversions among the inactive, intermediate and active-like states. Detailed structural comparisons capture subtle conformational differences arising from ligand binding in allosteric signaling, which can well explain the graded activation. Critical microswitches that contribute to graded activation are efficiently identified with the DL model. TE calculations enable the visualization of allosteric communication networks within the receptor, elucidating the driver-responder relationships associated with signal transduction. Fortunately, the dissociation of the full agonist from the orthosteric pocket is observed. The current findings systematically reveal the mechanism of NTSR1 graded activation, and also provide implications for structure-based drug design.
Collapse
Affiliation(s)
- Zhixiang Wu
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Xiaohan Sun
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Jingjie Su
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Xinyu Zhang
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China.
| | - Chunhua Li
- College of Chemistry and Life Science, Beijing University of Technology, Beijing, China.
| |
Collapse
|
3
|
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.
Collapse
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.)
| |
Collapse
|
4
|
Bower JB, Robson SA, Ziarek JJ. Insights on the G protein-coupled receptor helix 8 solution structure and orientation using a neurotensin receptor 1 peptide. Protein Sci 2024; 33:e4976. [PMID: 38757374 PMCID: PMC11099793 DOI: 10.1002/pro.4976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/12/2024] [Accepted: 03/14/2024] [Indexed: 05/18/2024]
Abstract
G-protein coupled receptors (GPCRs) are the largest class of membrane proteins encoded in the human genome with high pharmaceutical relevance and implications to human health. These receptors share a prevalent architecture of seven transmembrane helices followed by an intracellular, amphipathic helix 8 (H8) and a disordered C-terminal tail (Ctail). Technological advancements have led to over 1000 receptor structures in the last two decades, yet frequently H8 and the Ctail are conformationally heterogeneous or altogether absent. Here we synthesize a peptide comprising the neurotensin receptor 1 (NTS1) H8 and Ctail (H8-Ctail) to investigate its structural stability, conformational dynamics, and orientation in the presence of detergent and phospholipid micelles, which mimic the membrane. Circular dichroism (CD) and nuclear magnetic resonance (NMR) measurements confirm that zwitterionic 1,2-diheptanoyl-sn-glycero-3-phosphocholine is a potent stabilizer of H8 structure, whereas the commonly-used branched detergent lauryl maltose neopentyl glycol (LMNG) is unable to completely stabilize the helix - even at amounts four orders of magnitude greater than its critical micellar concentration. We then used NMR spectroscopy to assign the backbone chemical shifts. A series of temperature and lipid titrations were used to define the H8 boundaries as F376-R392 from chemical shift perturbations, changes in resonance intensity, and chemical-shift-derived phi/psi angles. Finally, the H8 azimuthal and tilt angles, defining the helix orientation relative of the membrane normal were measured using paramagnetic relaxation enhancement NMR. Taken together, our studies reveal the H8-Ctail region is sensitive to membrane physicochemical properties and is capable of more adaptive behavior than previously suggested by static structural techniques.
Collapse
Affiliation(s)
- James B. Bower
- Molecular and Cellular Biochemistry DepartmentIndiana UniversityBloomingtonIndianaUSA
| | - Scott A. Robson
- Department of PharmacologyNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
| | - Joshua J. Ziarek
- Molecular and Cellular Biochemistry DepartmentIndiana UniversityBloomingtonIndianaUSA
- Department of PharmacologyNorthwestern University Feinberg School of MedicineChicagoIllinoisUSA
| |
Collapse
|
5
|
Asadollahi K, Rajput S, de Zhang LA, Ang CS, Nie S, Williamson NA, Griffin MDW, Bathgate RAD, Scott DJ, Weikl TR, Jameson GNL, Gooley PR. Unravelling the mechanism of neurotensin recognition by neurotensin receptor 1. Nat Commun 2023; 14:8155. [PMID: 38071229 PMCID: PMC10710507 DOI: 10.1038/s41467-023-44010-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
The conformational ensembles of G protein-coupled receptors (GPCRs) include inactive and active states. Spectroscopy techniques, including NMR, show that agonists, antagonists and other ligands shift the ensemble toward specific states depending on the pharmacological efficacy of the ligand. How receptors recognize ligands and the kinetic mechanism underlying this population shift is poorly understood. Here, we investigate the kinetic mechanism of neurotensin recognition by neurotensin receptor 1 (NTS1) using 19F-NMR, hydrogen-deuterium exchange mass spectrometry and stopped-flow fluorescence spectroscopy. Our results indicate slow-exchanging conformational heterogeneity on the extracellular surface of ligand-bound NTS1. Numerical analysis of the kinetic data of neurotensin binding to NTS1 shows that ligand recognition follows an induced-fit mechanism, in which conformational changes occur after neurotensin binding. This approach is applicable to other GPCRs to provide insight into the kinetic regulation of ligand recognition by GPCRs.
Collapse
Affiliation(s)
- Kazem Asadollahi
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sunnia Rajput
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Lazarus Andrew de Zhang
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Ching-Seng Ang
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Shuai Nie
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Nicholas A Williamson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ross A D Bathgate
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daniel J Scott
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Thomas R Weikl
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Guy N L Jameson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
- School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia.
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
| |
Collapse
|
6
|
Asadollahi K, Rajput S, Jameson GNL, Scott DJ, Gooley PR. Encounter Complexes Between the N-terminal of Neurotensin with the Extracellular Loop 2 of the Neurotensin Receptor 1 Steer Neurotensin to the Orthosteric Binding Pocket. J Mol Biol 2023; 435:168244. [PMID: 37625583 DOI: 10.1016/j.jmb.2023.168244] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
Neurotensin (NT) is a linear disordered peptide that activates two different class A GPCRs, neurotensin receptor 1 (NTS1) and NTS2. Resolved structures of the complex of the C-terminal fragment of NT, NT8-13, with NTS1 shows the peptide takes a well-defined structure in the bound state. However, the mechanisms underlying NT recognition of NTS1, and the conformational transition of NT upon binding NTS1 is an open question that if answered may aid discovery of highly selective drugs and reveal potential secondary binding sites on the surface of the receptor. Herein we investigated the interactions guiding NT to the orthosteric binding pocket of NTS1 by combining NMR experiments with kinetic analysis of the binding pathway using stopped-flow fluorescence and mutagenesis on both NT and NTS1. We show the presence of transient structures in the middle part of NT that kinetically regulate the binding of NT to NTS1. Moreover, our results indicate that the binding pathway of NT onto NTS1 is mediated via electrostatic interactions between the N-terminal region of NT with the extracellular loop 2 of NTS1. These interactions induce backbone conformational changes in neurotensin similar to the bound-state neurotensin, suggesting that the N-terminal region of NT and these interactions should be considered for development of selective drugs against NTS1.
Collapse
Affiliation(s)
- Kazem Asadollahi
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; The Florey, University of Melbourne, Parkville, VIC 3010, Australia. https://twitter.com/@KazemAsadollahi
| | - Sunnia Rajput
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
| | - Guy N L Jameson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia; School of Chemistry, University of Melbourne, Parkville, VIC 3010, Australia
| | - Daniel J Scott
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia; The Florey, University of Melbourne, Parkville, VIC 3010, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC 3010, Australia; Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia.
| |
Collapse
|
7
|
Smith AA, Pacull EM, Stecher S, Hildebrand PW, Vogel A, Huster D. Analysis of the Dynamics of the Human Growth Hormone Secretagogue Receptor Reveals Insights into the Energy Landscape of the Molecule. Angew Chem Int Ed Engl 2023; 62:e202302003. [PMID: 37205715 DOI: 10.1002/anie.202302003] [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: 02/09/2023] [Revised: 05/04/2023] [Accepted: 05/19/2023] [Indexed: 05/21/2023]
Abstract
G protein-coupled receptors initiate signal transduction in response to ligand binding. Growth hormone secretagogue receptor (GHSR), the focus of this study, binds the 28 residue peptide ghrelin. While structures of GHSR in different states of activation are available, dynamics within each state have not been investigated in depth. We analyze long molecular dynamics simulation trajectories using "detectors" to compare dynamics of the apo and ghrelin-bound states yielding timescale-specific amplitudes of motion. We identify differences in dynamics between apo and ghrelin-bound GHSR in the extracellular loop 2 and transmembrane helices 5-7. NMR of the GHSR histidine residues reveals chemical shift differences in these regions. We evaluate timescale specific correlation of motions between residues of ghrelin and GHSR, where binding yields a high degree of correlation for the first 8 ghrelin residues, but less correlation for the helical end. Finally, we investigate the traverse of GHSR over a rugged energy landscape via principal component analysis.
Collapse
Affiliation(s)
- Albert A Smith
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Emelyne M Pacull
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Sabrina Stecher
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Peter W Hildebrand
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Alexander Vogel
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| | - Daniel Huster
- Institute of Medical Physics and Biophysics, University of Leipzig, Härtelstr. 16/18, 04107, Leipzig, Germany
| |
Collapse
|
8
|
Kaipa JM, Krasnoselska G, Owens RJ, van den Heuvel J. Screening of Membrane Protein Production by Comparison of Transient Expression in Insect and Mammalian Cells. Biomolecules 2023; 13:biom13050817. [PMID: 37238687 DOI: 10.3390/biom13050817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Membrane proteins are difficult biomolecules to express and purify. In this paper, we compare the small-scale production of six selected eukaryotic integral membrane proteins in insect and mammalian cell expression systems using different techniques for gene delivery. The target proteins were C terminally fused to the green fluorescent marker protein GFP to enable sensitive monitoring. We show that the choice of expression systems makes a considerable difference to the yield and quality of the six selected membrane proteins. Virus-free transient gene expression (TGE) in insect High Five cells combined with solubilization in dodecylmaltoside plus cholesteryl hemisuccinate generated the most homogeneous samples for all six targets. Further, the affinity purification of the solubilized proteins using the Twin-Strep® tag improved protein quality in terms of yield and homogeneity compared to His-tag purification. TGE in High Five insect cells offers a fast and economically attractive alternative to the established methods that require either baculovirus construction and the infection of the insect cells or relatively expensive transient gene expression in mammalian cells for the production of integral membrane proteins.
Collapse
Affiliation(s)
| | - Ganna Krasnoselska
- Department of Biomedical Sciences, University of Copenhagen, Blegdamsvej 3B, 18.5, 42, 2200 Copenhagen, Denmark
| | - Raymond J Owens
- Structural Biology Division, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
- Rosalind Franklin Institute, Harwell Campus, Didcot OX11 0QX, UK
| | - Joop van den Heuvel
- Helmholtz Center for Infection Research, Department of Structure and Function of Proteins, Inhoffenstrasse 7, 38124 Braunschweig, Germany
| |
Collapse
|
9
|
Krumm BE, DiBerto JF, Olsen RHJ, Kang HJ, Slocum ST, Zhang S, Strachan RT, Huang XP, Slosky LM, Pinkerton AB, Barak LS, Caron MG, Kenakin T, Fay JF, Roth BL. Neurotensin Receptor Allosterism Revealed in Complex with a Biased Allosteric Modulator. Biochemistry 2023; 62:1233-1248. [PMID: 36917754 DOI: 10.1021/acs.biochem.3c00029] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The NTSR1 neurotensin receptor (NTSR1) is a G protein-coupled receptor (GPCR) found in the brain and peripheral tissues with neurotensin (NTS) being its endogenous peptide ligand. In the brain, NTS modulates dopamine neuronal activity, induces opioid-independent analgesia, and regulates food intake. Recent studies indicate that biasing NTSR1 toward β-arrestin signaling can attenuate the actions of psychostimulants and other drugs of abuse. Here, we provide the cryoEM structures of NTSR1 ternary complexes with heterotrimeric Gq and GoA with and without the brain-penetrant small-molecule SBI-553. In functional studies, we discovered that SBI-553 displays complex allosteric actions exemplified by negative allosteric modulation for G proteins that are Gα subunit selective and positive allosteric modulation and agonism for β-arrestin translocation at NTSR1. Detailed structural analysis of the allosteric binding site illuminated the structural determinants for biased allosteric modulation of SBI-553 on NTSR1.
Collapse
Affiliation(s)
- Brian E Krumm
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599-7365, United States
| | - Jeffrey F DiBerto
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599-7365, United States
| | - Reid H J Olsen
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599-7365, United States
| | - Hye Jin Kang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599-7365, United States
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), School of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599-7365, United States
| | - Samuel T Slocum
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599-7365, United States
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), School of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599-7365, United States
| | - Shicheng Zhang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599-7365, United States
| | - Ryan T Strachan
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599-7365, United States
| | - Xi-Ping Huang
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599-7365, United States
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), School of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599-7365, United States
| | - Lauren M Slosky
- Department of Pharmacology, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Anthony B Pinkerton
- Conrad Prebys Center for Chemical Genomics at Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037, United States
| | - Lawrence S Barak
- Department of Cell Biology, Duke University, Durham, North Carolina 27710, United States
| | - Marc G Caron
- Department of Cell Biology, Duke University, Durham, North Carolina 27710, United States
- Departments of Medicine and Neurobiology, Duke University, Durham, North Carolina 27710, United States
| | - Terry Kenakin
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599-7365, United States
| | - Jonathan F Fay
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599, United States
| | - Bryan L Roth
- Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599-7365, United States
- National Institute of Mental Health Psychoactive Drug Screening Program (NIMH PDSP), School of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina 27599-7365, United States
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-7360, United States
| |
Collapse
|
10
|
Klenk C, Scrivens M, Niederer A, Shi S, Mueller L, Gersz E, Zauderer M, Smith ES, Strohner R, Plückthun A. A Vaccinia-based system for directed evolution of GPCRs in mammalian cells. Nat Commun 2023; 14:1770. [PMID: 36997531 PMCID: PMC10063554 DOI: 10.1038/s41467-023-37191-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/06/2023] [Indexed: 04/03/2023] Open
Abstract
Directed evolution in bacterial or yeast display systems has been successfully used to improve stability and expression of G protein-coupled receptors for structural and biophysical studies. Yet, several receptors cannot be tackled in microbial systems due to their complex molecular composition or unfavorable ligand properties. Here, we report an approach to evolve G protein-coupled receptors in mammalian cells. To achieve clonality and uniform expression, we develop a viral transduction system based on Vaccinia virus. By rational design of synthetic DNA libraries, we first evolve neurotensin receptor 1 for high stability and expression. Second, we demonstrate that receptors with complex molecular architectures and large ligands, such as the parathyroid hormone 1 receptor, can be readily evolved. Importantly, functional receptor properties can now be evolved in the presence of the mammalian signaling environment, resulting in receptor variants exhibiting increased allosteric coupling between the ligand binding site and the G protein interface. Our approach thus provides insights into the intricate molecular interplay required for GPCR activation.
Collapse
Affiliation(s)
- Christoph Klenk
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| | - Maria Scrivens
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Anina Niederer
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Shuying Shi
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Loretta Mueller
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Elaine Gersz
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Maurice Zauderer
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Ernest S Smith
- Vaccinex, Inc., 1895 Mt. Hope Avenue, Rochester, New York, 14620, NY, USA
| | - Ralf Strohner
- MorphoSys AG, Semmelweisstr. 7, 82152, Planegg, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
| |
Collapse
|
11
|
Wang X, Wei S, Wang M, Xu Y, Hu W, Niu M, Wang S, Lei K, Ji L, Liu R, Ji G. Diphenyl Ether Derivatives as Novel GPR120 Agonists for the Treatment of Type 2 Diabetes Mellitus. Chem Biodivers 2023; 20:e202200814. [PMID: 36471492 DOI: 10.1002/cbdv.202200814] [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: 08/25/2022] [Revised: 12/04/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Diabetes mellitus (DM) is a serious disease affecting human health. Numerous attempts have been made to develop safe and effective new antidiabetic drugs. Recently, a series of G protein-coupled receptors for free fatty acids (FFAs) have been described and characterized, and small molecule agonists and antagonists of these receptors show considerable promise for managing diabetes and related complications. FFA-activated GPR120 could stimulate the release of glucagon-like peptide-1(GLP-1), which can enhance the glucose-dependent secretion of insulin from pancreatic β cells. GPR120 is a promising target for treating type 2 DM (T2DM). Herein we designed and synthesized a series of novel GPR120 agonists based on the structure of TUG-891, which was the first potent and selective GPR120 agonist. Among the designed compounds, 18 f showed excellent GPR120 activation activity and high selectivity for GPR40 in vitro. Compound 18 f dose-dependently improved glucose tolerance in normal mice, and no hypoglycemic side effects were observed at high dose. In addition, compound 18 f increased insulin release and displayed good antidiabetic effect in diet-induced obese mice. Molecular simulations illustrated that compound 18 f could enter the active site of GPR120 and interact with Arg99. Based on these observations, compound 18 f may be a promising lead compound for the design of novel GPR120 agonists to treat T2DM.
Collapse
Affiliation(s)
- Xuekun Wang
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng, Shandong 252059, China
| | - Shiting Wei
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng, Shandong 252059, China
| | - Min Wang
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng, Shandong 252059, China
| | - Yao Xu
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng, Shandong 252059, China
| | - Weidi Hu
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng, Shandong 252059, China
| | - Mingyue Niu
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng, Shandong 252059, China
| | - Shiben Wang
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng, Shandong 252059, China
| | - Kang Lei
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng, Shandong 252059, China
| | - Lusha Ji
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng, Shandong 252059, China
| | - Renmin Liu
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng, Shandong 252059, China
| | - Guoxia Ji
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng, Shandong 252059, China.,School of Chemistry and Chemical Engineering, Liaocheng University, 1 Hunan Street, Liaocheng, Shandong 252059, China
| |
Collapse
|
12
|
Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
Collapse
Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
| |
Collapse
|
13
|
Wang X, Li X, Wei S, Wang M, Xu Y, Hu W, Gao Z, Liu R, Wang S, Ji G. Discovery of Novel and Selective G-Protein Coupled Receptor 120 (GPR120) Agonists for the Treatment of Type 2 Diabetes Mellitus. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27249018. [PMID: 36558150 PMCID: PMC9781217 DOI: 10.3390/molecules27249018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/11/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Diabetes mellitus (DM), a chronic metabolic disorder characterized by high blood glucose, not only poses a serious threat to human life and health, but also places an economic burden on society. Currently available antidiabetic pharmacological agents have some adverse effects, which have stimulated researchers to explore novel antidiabetic agents with different mechanisms of action. G-protein Coupled Receptor 120 (GPR120), also known as free fatty acid receptor 4 (FFAR4), which is activated by medium-chain and long-chain fatty acids, has emerged as an interesting potential target for the treatment of metabolic disorders. Herein, we designed and synthesized a series of novel GPR120 agonists based on the structure of TUG-891, which is susceptible to β-oxidation and loses its GPR120 agonistic activity in vivo. Among the designed compounds, 14d showed excellent agonistic activity and selectivity and could improve glucose tolerance in normal mice in a dose-dependent manner. In addition, the compound 14d displayed good antidiabetic effects in diet-induced obese (DIO) mice and elevated insulin levels. Molecular simulations illustrated that compound 14d could enter the active site of GPR120 and interact with ARG99, which plays an important role in GPR120 activation. Based on these observations, compound 14d may be a promising lead compound deserving of further biological evaluation and structural modifications.
Collapse
Affiliation(s)
- Xuekun Wang
- Correspondence: (X.W.); (S.W.); (G.J.); Tel.: +86-0635-823-9087 (X.W.)
| | | | | | | | | | | | | | | | - Shiben Wang
- Correspondence: (X.W.); (S.W.); (G.J.); Tel.: +86-0635-823-9087 (X.W.)
| | - Guoxia Ji
- Correspondence: (X.W.); (S.W.); (G.J.); Tel.: +86-0635-823-9087 (X.W.)
| |
Collapse
|
14
|
Dixon AD, Inoue A, Robson SA, Culhane KJ, Trinidad JC, Sivaramakrishnan S, Bumbak F, Ziarek JJ. Effect of Ligands and Transducers on the Neurotensin Receptor 1 Conformational Ensemble. J Am Chem Soc 2022; 144:10241-10250. [PMID: 35647863 PMCID: PMC9936889 DOI: 10.1021/jacs.2c00828] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Using a discrete, intracellular 19F nuclear magnetic resonance (NMR) probe on transmembrane helix 6 of the neurotensin receptor 1 (NTS1), we aim to understand how ligands and transducers modulate the receptor's structural ensemble in a solution. For apo NTS1, 19F NMR spectra reveal an ensemble of at least three conformational substates (one inactive and two active-like) in equilibrium that exchange on the millisecond to second timescale. Dynamic NMR experiments reveal that these substates follow a linear three-site exchange process that is both thermodynamically and kinetically remodeled by orthosteric ligands. As previously observed in other G protein-coupled receptors (GPCRs), the full agonist is insufficient to completely stabilize the active-like state. The inactive substate is abolished upon coupling to β-arrestin-1 (βArr1) or the C-terminal helix of Gαq, which comprises ≳60% of the GPCR/G protein interface surface area. Whereas βArr1 exclusively selects for pre-existing active-like substates, the Gαq peptide induces a new substate. Both transducer molecules promote substantial line broadening of active-like states, suggesting contributions from additional microsecond to millisecond exchange processes. Together, our study suggests that (i) the NTS1 allosteric activation mechanism may be alternatively dominated by induced fit or conformational selection depending on the coupled transducer, and (ii) the available static structures do not represent the entire conformational ensemble observed in a solution.
Collapse
Affiliation(s)
- Austin D. Dixon
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578 Miyagi, Japan
| | - Scott A. Robson
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Kelly J. Culhane
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States,Present Address: Department of Chemistry, Lawrence University, Appleton, Wisconsin, 54911, United States
| | - Jonathan C. Trinidad
- Laboratory for Biological Mass Spectrometry, Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Fabian Bumbak
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States,Present Address: Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Joshua J. Ziarek
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| |
Collapse
|
15
|
Yadav P, Barati Farimani A. Activation Pathways of Neurotensin Receptor 1 Elucidated Using Statistical Machine Learning. ACS Chem Neurosci 2022; 13:1333-1341. [PMID: 35380784 DOI: 10.1021/acschemneuro.2c00154] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Neurotensin receptor 1 (NTSR1) is a G-protein coupled receptor (GPCR) that mediates many biological processes through its interaction with the neurotensin (NTS) peptide. The NTSR1 protein is a clinically significant target as it is involved in the proliferation of cancer cells. Understanding the activation mechanism of NTSR1 is an important prerequisite for exploring the therapeutic potential of targeting NTSR1 and the development of drug molecules specific to NTSR1. Previous studies have been aimed at elucidating the structure of NTSR1 in the active and inactive conformations; however, the intermediate molecular pathway for NTSR1 activation dynamics is largely unknown. In this study, we performed extensive molecular dynamics (MD) simulations of the NTSR1 protein and analyzed its kinetic conformational changes to determine the microswitches that drive NTSR1 activation. To biophysically interpret the high-dimensional simulation trajectories, we used Markov state models and machine learning to elucidate the important and detailed conformational changes in NTSR1. Through the analysis of identified microswitches, we propose a mechanistic pathway for NTSR1 activation.
Collapse
Affiliation(s)
- Prakarsh Yadav
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Amir Barati Farimani
- Department of Mechanical Engineering, Biomedical Engineering, Chemical Engineering and Machine Learning Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| |
Collapse
|
16
|
Molecular mechanism of agonism and inverse agonism in ghrelin receptor. Nat Commun 2022; 13:300. [PMID: 35027551 PMCID: PMC8758724 DOI: 10.1038/s41467-022-27975-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 12/29/2021] [Indexed: 02/05/2023] Open
Abstract
Much effort has been invested in the investigation of the structural basis of G protein-coupled receptors (GPCRs) activation. Inverse agonists, which can inhibit GPCRs with constitutive activity, are considered useful therapeutic agents, but the molecular mechanism of such ligands remains insufficiently understood. Here, we report a crystal structure of the ghrelin receptor bound to the inverse agonist PF-05190457 and a cryo-electron microscopy structure of the active ghrelin receptor-Go complex bound to the endogenous agonist ghrelin. Our structures reveal a distinct binding mode of the inverse agonist PF-05190457 in the ghrelin receptor, different from the binding mode of agonists and neutral antagonists. Combining the structural comparisons and cellular function assays, we find that a polar network and a notable hydrophobic cluster are required for receptor activation and constitutive activity. Together, our study provides insights into the detailed mechanism of ghrelin receptor binding to agonists and inverse agonists, and paves the way to design specific ligands targeting ghrelin receptors. Ghrelin receptor regulates energy homeostasis through constitutive activity or by the ghrelin. Here the authors report two structures of ghrelin receptor bound to agonist and inverse agonist, providing insights into the mechanism of inverse agonism, which is of interest for specific ligand design.
Collapse
|
17
|
Wang X, Ji G, Han X, Hao H, Liu W, Xue Q, Guo Q, Wang S, Lei K, Liu Y. Thiazolidinedione derivatives as novel GPR120 agonists for the treatment of type 2 diabetes. RSC Adv 2022; 12:5732-5742. [PMID: 35424534 PMCID: PMC8981563 DOI: 10.1039/d1ra08925k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/08/2022] [Indexed: 12/16/2022] Open
Abstract
GPR120, also called FFAR4, is preferentially expressed in the intestines, and can be stimulated by long-chain free fatty acids to increase the secretion of glucagon-like peptide-1 (GLP-1) from intestinal endocrine cells. It is known that GLP-1, as an incretin, can promote the insulin secretion from pancreatic cells in a glucose-dependent manner. Therefore, GPR120 is a potential drug target to treat type 2 diabetes. In this study, thiazolidinedione derivatives were found to be novel potent GPR120 agonists. Compound 5g, with excellent agonistic activity, selectivity, and metabolic stability, improved oral glucose tolerance in normal C57BL/6 mice in a dose-dependent manner. Moreover, compound 5g exhibited anti-diabetic activity by promoting insulin secretion in diet-induced obese mice. In summary, compound 5g might be a promising drug candidate for the treatment of type 2 diabetes. GPR120 has emerged as an attractive target for the treatment of type 2 diabetes and obesity. Thiazolidinedione derivatives were found to be novel potent GPR120 agonists.![]()
Collapse
Affiliation(s)
- Xuekun Wang
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng 252059, China
| | - Guoxia Ji
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng 252059, China
- School of Chemistry and Chemical Engineering, Liaocheng University, 1 Hunan Street, Liaocheng 252059, China
| | - Xinyu Han
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng 252059, China
| | - Huiran Hao
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng 252059, China
| | - Wenjing Liu
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng 252059, China
| | - Qidi Xue
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng 252059, China
| | - Qinghua Guo
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng 252059, China
| | - Shiben Wang
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng 252059, China
| | - Kang Lei
- School of Pharmaceutical Sciences, Liaocheng University, 1 Hunan Street, Liaocheng 252059, China
| | - Yadi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
18
|
Ballante F, Kooistra AJ, Kampen S, de Graaf C, Carlsson J. Structure-Based Virtual Screening for Ligands of G Protein-Coupled Receptors: What Can Molecular Docking Do for You? Pharmacol Rev 2021; 73:527-565. [PMID: 34907092 DOI: 10.1124/pharmrev.120.000246] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome and are important therapeutic targets. During the last decade, the number of atomic-resolution structures of GPCRs has increased rapidly, providing insights into drug binding at the molecular level. These breakthroughs have created excitement regarding the potential of using structural information in ligand design and initiated a new era of rational drug discovery for GPCRs. The molecular docking method is now widely applied to model the three-dimensional structures of GPCR-ligand complexes and screen for chemical probes in large compound libraries. In this review article, we first summarize the current structural coverage of the GPCR superfamily and the understanding of receptor-ligand interactions at atomic resolution. We then present the general workflow of structure-based virtual screening and strategies to discover GPCR ligands in chemical libraries. We assess the state of the art of this research field by summarizing prospective applications of virtual screening based on experimental structures. Strategies to identify compounds with specific efficacy and selectivity profiles are discussed, illustrating the opportunities and limitations of the molecular docking method. Our overview shows that structure-based virtual screening can discover novel leads and will be essential in pursuing the next generation of GPCR drugs. SIGNIFICANCE STATEMENT: Extraordinary advances in the structural biology of G protein-coupled receptors have revealed the molecular details of ligand recognition by this large family of therapeutic targets, providing novel avenues for rational drug design. Structure-based docking is an efficient computational approach to identify novel chemical probes from large compound libraries, which has the potential to accelerate the development of drug candidates.
Collapse
Affiliation(s)
- Flavio Ballante
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Albert J Kooistra
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Stefanie Kampen
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Chris de Graaf
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| | - Jens Carlsson
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (F.B., S.K., J.C.); Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark (A.J.K.); and Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, United Kingdom (C.d.G.)
| |
Collapse
|
19
|
Novel GPR120 Agonists with Improved Pharmacokinetic Profiles for the Treatment of Type 2 Diabetes. Molecules 2021; 26:molecules26226907. [PMID: 34833999 PMCID: PMC8624523 DOI: 10.3390/molecules26226907] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/16/2022] Open
Abstract
GPR120 is a promising target for the treatment of type 2 diabetes (T2DM), which is activated by free fatty acids (FFAs) and stimulates the release of glucagon-like peptide-1(GLP-1). GLP-1, as an incretin, can enhance glucose-dependent secretion of insulin from pancreatic beta cells and reduce blood glucose. In this study, a series of novel GPR120 agonists were designed and synthesized to improve the stability and hydrophilicity of the phenylpropanoic acid GPR120 agonist TUG-891. Compound 11b showed excellent GPR120 agonistic activity and pharmacokinetic properties, and could reduce the blood glucose of normal mice in a dose-dependent manner. In addition, no hypoglycemic side effects were observed even at a dose of 100 mg/kg. Moreover, 11b showed good anti-hyperglycemic effects in diet-induced obese (DIO) mice. Molecular simulation illustrated that compound 11b could enter the active site of GPR120 and interact with ARG99. Taken together, the results indicate that compound 11b might be a promising drug candidate for the treatment of T2DM.
Collapse
|
20
|
Casanovas M, Jiménez-Rosés M, Cordomí A, Lillo A, Vega-Quiroga I, Izquierdo J, Medrano M, Gysling K, Pardo L, Navarro G, Franco R. Discovery of a macromolecular complex mediating the hunger suppressive actions of cocaine: Structural and functional properties. Addict Biol 2021; 26:e13017. [PMID: 33559278 DOI: 10.1111/adb.13017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/14/2021] [Accepted: 01/18/2021] [Indexed: 12/16/2022]
Abstract
Cocaine not only increases brain dopamine levels but also activates the sigma1 receptor (σ1 R) that in turn regulates orexigenic receptor function. Identification of interactions involving dopamine D1 (D1 R), ghrelin (GHS-R1a ), and σ1 receptors have been addressed by biophysical techniques and a complementation approach using interfering peptides. The effect of cocaine on receptor functionality was assayed by measuring second messenger, cAMP and Ca2+ , levels. The effect of acute or chronic cocaine administration on receptor complex expression was assayed by in situ proximity ligation assay. In silico procedures were used for molecular model building. σ1 R KO mice were used for confirming involvement of this receptor. Upon identification of protomer interaction and receptor functionality, a unique structural model for the macromolecular complex formed by σ1 R, D1 R, and GHS-R1a is proposed. The functionality of the complex, able to couple to both Gs and Gq proteins, is affected by cocaine binding to the σ1 R, as confirmed using samples from σ1 R-/- mice. The expression of the macromolecular complex was differentially affected upon acute and chronic cocaine administration to rats. The constructed 3D model is consistent with biochemical, biophysical, and available structural data. The σ1 R, D1 R, and GHS-R1a complex constitutes a functional unit that is altered upon cocaine binding to the σ1 R. Remarkably, the heteromer can simultaneously couple to two G proteins, thus allowing dopamine to signal via Ca2+ and ghrelin via cAMP. The anorexic action of cocaine is mediated by such complex whose expression is higher after acute than after chronic administration regimens.
Collapse
Affiliation(s)
- Mireia Casanovas
- Department of Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain
| | - Mireia Jiménez-Rosés
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Autonomous University of Barcelona, Barcelona, Spain
| | - Arnau Cordomí
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Autonomous University of Barcelona, Barcelona, Spain
| | - Alejandro Lillo
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Ignacio Vega-Quiroga
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontifical Catholic University of Chile, Santiago, Chile
| | - Joan Izquierdo
- Department of Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, Barcelona, Spain
| | - Mireia Medrano
- Department of Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, Barcelona, Spain
- Department of Pharmaceutical Chemistry, Drug Analysis and Drug Information, Center for Neurosciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Katia Gysling
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontifical Catholic University of Chile, Santiago, Chile
| | - Leonardo Pardo
- Laboratory of Computational Medicine, Biostatistics Unit, Faculty of Medicine, Autonomous University of Barcelona, Barcelona, Spain
| | - Gemma Navarro
- Centro de Investigación Biomédica en Red, Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biology, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Spain
| | - Rafael Franco
- Department of Biochemistry and Molecular Biomedicine, School of Biology, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Neurodegenerativas, Instituto de Salud Carlos III, Madrid, Spain
| |
Collapse
|
21
|
Agamennone M, Nicoli A, Bayer S, Weber V, Borro L, Gupta S, Fantacuzzi M, Di Pizio A. Protein-protein interactions at a glance: Protocols for the visualization of biomolecular interactions. Methods Cell Biol 2021; 166:271-307. [PMID: 34752337 DOI: 10.1016/bs.mcb.2021.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Protein-protein interactions (PPIs) play a key role in many biological processes and are intriguing targets for drug discovery campaigns. Advancements in experimental and computational techniques are leading to a growth of data accessibility, and, with it, an increased need for the analysis of PPIs. In this respect, visualization tools are essential instruments to represent and analyze biomolecular interactions. In this chapter, we reviewed some of the available tools, highlighting their features, and describing their functions with practical information on their usage.
Collapse
Affiliation(s)
| | - Alessandro Nicoli
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Sebastian Bayer
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Verena Weber
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany
| | - Luca Borro
- Department of Imaging, Advanced Cardiovascular Imaging Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, Rostock, Germany
| | | | - Antonella Di Pizio
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Freising, Germany.
| |
Collapse
|
22
|
Bibbe JM, Vriend G. Motions around conserved helical weak spots facilitate GPCR activation. Proteins 2021; 89:1577-1586. [PMID: 34272892 PMCID: PMC9290982 DOI: 10.1002/prot.26179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 07/03/2021] [Accepted: 07/11/2021] [Indexed: 01/24/2023]
Abstract
G protein‐coupled receptors (GPCRs) participate in most physiological processes and are important drug targets in many therapeutic areas. Recently, many GPCR X‐ray structures became available, facilitating detailed studies of their sequence‐structure‐mobility‐function relations. We show that the functional role of many conserved GPCR sequence motifs is to create weak spots in the transmembrane helices that provide the structural plasticity necessary for ligand binding and signaling. Different receptor families use different conserved sequence motifs to obtain similar helix irregularities that allow for the same motions upon GPCR activation. These conserved motions come together to facilitate the timely release of the conserved sodium ion to the cytosol. Most GPCR crystal structures could be determined only after stabilization of the transmembrane helices by mutations that remove weak spots. These mutations often lead to diminished binding of agonists, but not antagonists, which logically agrees with the fact that large helix rearrangements occur only upon agonist binding. Upon activation, six of the seven TM helices in GPCRs undergo helix motions and/or deformations facilitated by weak spots in these helices. The location of these weak spots is much more conserved than the sequence motifs that cause them. Knowledge about these weak spots helps understand the activation process of GPCRs and thus helps design medicines.
Collapse
|
23
|
Hilger D. The role of structural dynamics in GPCR‐mediated signaling. FEBS J 2021; 288:2461-2489. [DOI: 10.1111/febs.15841] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/19/2021] [Accepted: 03/24/2021] [Indexed: 12/18/2022]
Affiliation(s)
- Daniel Hilger
- Department of Pharmaceutical Chemistry Philipps‐University Marburg Germany
| |
Collapse
|
24
|
Zhang M, Gui M, Wang ZF, Gorgulla C, Yu JJ, Wu H, Sun ZYJ, Klenk C, Merklinger L, Morstein L, Hagn F, Plückthun A, Brown A, Nasr ML, Wagner G. Cryo-EM structure of an activated GPCR-G protein complex in lipid nanodiscs. Nat Struct Mol Biol 2021; 28:258-267. [PMID: 33633398 PMCID: PMC8176890 DOI: 10.1038/s41594-020-00554-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 12/16/2020] [Indexed: 02/07/2023]
Abstract
G-protein-coupled receptors (GPCRs) are the largest superfamily of transmembrane proteins and the targets of over 30% of currently marketed pharmaceuticals. Although several structures have been solved for GPCR-G protein complexes, few are in a lipid membrane environment. Here, we report cryo-EM structures of complexes of neurotensin, neurotensin receptor 1 and Gαi1β1γ1 in two conformational states, resolved to resolutions of 4.1 and 4.2 Å. The structures, determined in a lipid bilayer without any stabilizing antibodies or nanobodies, reveal an extended network of protein-protein interactions at the GPCR-G protein interface as compared to structures obtained in detergent micelles. The findings show that the lipid membrane modulates the structure and dynamics of complex formation and provide a molecular explanation for the stronger interaction between GPCRs and G proteins in lipid bilayers. We propose an allosteric mechanism for GDP release, providing new insights into the activation of G proteins for downstream signaling.
Collapse
Affiliation(s)
- Meng Zhang
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Miao Gui
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Zi-Fu Wang
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Christoph Gorgulla
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of physics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - James J Yu
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Zhen-Yu J Sun
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Christoph Klenk
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Lisa Merklinger
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Lena Morstein
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Franz Hagn
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Garching, Germany
- Institute of Structural Biology, Helmholtz Center Munich, Neuherberg, Germany
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Alan Brown
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Mahmoud L Nasr
- Department of Medicine, Division of Renal Medicine, Division of Engineering in Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Gerhard Wagner
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
25
|
Chartier M, Desgagné M, Sousbie M, Côté J, Longpré JM, Marsault E, Sarret P. Design, Structural Optimization, and Characterization of the First Selective Macrocyclic Neurotensin Receptor Type 2 Non-opioid Analgesic. J Med Chem 2021; 64:2110-2124. [PMID: 33538583 DOI: 10.1021/acs.jmedchem.0c01726] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Neurotensin (NT) receptor type 2 (NTS2) represents an attractive target for the development of new NT-based analgesics. Here, we report the synthesis and functional in vivo characterization of the first constrained NTS2-selective macrocyclic NT analog. While most chemical optimization studies rely on the NT(8-13) fragment, we focused on NT(7-12) as a scaffold to design NTS2-selective macrocyclic peptides. Replacement of Ile12 by Leu, and Pro7/Pro10 by allylglycine residues followed by cyclization via ring-closing metathesis led to macrocycle 4, which exhibits good affinity for NTS2 (50 nM), high selectivity over NTS1 (>100 μM), and improved stability compared to NT(8-13). In vivo profiling in rats reveals that macrocycle 4 produces potent analgesia in three distinct rodent pain models, without causing the undesired effects associated with NTS1 activation. We further provide evidence of its non-opioid antinociceptive activity, therefore highlighting the strong therapeutic potential of NTS2-selective analogs for the management of acute and chronic pain.
Collapse
Affiliation(s)
- Magali Chartier
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Michael Desgagné
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Marc Sousbie
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Jérôme Côté
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Jean-Michel Longpré
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Eric Marsault
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Philippe Sarret
- Department of Pharmacology and Physiology, Faculty of Medicine and Health Sciences, Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| |
Collapse
|
26
|
Deluigi M, Klipp A, Klenk C, Merklinger L, Eberle SA, Morstein L, Heine P, Mittl PRE, Ernst P, Kamenecka TM, He Y, Vacca S, Egloff P, Honegger A, Plückthun A. Complexes of the neurotensin receptor 1 with small-molecule ligands reveal structural determinants of full, partial, and inverse agonism. SCIENCE ADVANCES 2021; 7:7/5/eabe5504. [PMID: 33571132 PMCID: PMC7840143 DOI: 10.1126/sciadv.abe5504] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 12/09/2020] [Indexed: 05/15/2023]
Abstract
Neurotensin receptor 1 (NTSR1) and related G protein-coupled receptors of the ghrelin family are clinically unexploited, and several mechanistic aspects of their activation and inactivation have remained unclear. Enabled by a new crystallization design, we present five new structures: apo-state NTSR1 as well as complexes with nonpeptide inverse agonists SR48692 and SR142948A, partial agonist RTI-3a, and the novel full agonist SRI-9829, providing structural rationales on how ligands modulate NTSR1. The inverse agonists favor a large extracellular opening of helices VI and VII, undescribed so far for NTSR1, causing a constriction of the intracellular portion. In contrast, the full and partial agonists induce a binding site contraction, and their efficacy correlates with the ability to mimic the binding mode of the endogenous agonist neurotensin. Providing evidence of helical and side-chain rearrangements modulating receptor activation, our structural and functional data expand the mechanistic understanding of NTSR1 and potentially other peptidergic receptors.
Collapse
Affiliation(s)
- Mattia Deluigi
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Alexander Klipp
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Christoph Klenk
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Lisa Merklinger
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Stefanie A Eberle
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Lena Morstein
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Philipp Heine
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Peer R E Mittl
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Patrick Ernst
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Theodore M Kamenecka
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #A2A, Jupiter, FL 33458, USA
| | - Yuanjun He
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, 130 Scripps Way #A2A, Jupiter, FL 33458, USA
| | - Santiago Vacca
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Pascal Egloff
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Annemarie Honegger
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
| |
Collapse
|
27
|
Goba I, Goricanec D, Schum D, Hillenbrand M, Plückthun A, Hagn F. Probing the Conformation States of Neurotensin Receptor 1 Variants by NMR Site-Directed Methyl Labeling. Chembiochem 2020; 22:139-146. [PMID: 32881260 PMCID: PMC7821118 DOI: 10.1002/cbic.202000541] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/02/2020] [Indexed: 12/11/2022]
Abstract
G protein‐coupled receptors (GPCRs) are key players in mediating signal transduction across the cell membrane. However, due to their intrinsic instability, many GPCRs are not suitable for structural investigations. Various approaches have been developed in recent years to remedy this situation, ranging from the use of more native membrane mimetics to protein‐stabilization methods. The latter approach typically results in GPCRs that contain various numbers of mutations. However, probing the functionality of such variants by in vitro and in vivo assays is often time consuming. In addition, to validate the suitability of such GPCRs for structural investigations, an assessment of their conformation state is required. NMR spectroscopy has been proven to be suitable to probe the conformation state of GPCRs in solution. Here, by using chemical labeling with an isotope‐labeled methyl probe, we show that the activity and the conformation state of stabilized neurotensin receptor 1 variants obtained from directed evolution can be efficiently assayed in 2D NMR experiments. This strategy enables the quantification of the active and inactive conformation states and the derivation of an estimation of the basal as well as agonist‐induced activity of the receptor. Furthermore, this assay can be used as a readout when re‐introducing agonist‐dependent signaling into a highly stabilized, and thus rigidified, receptor by mutagenesis. This approach will be useful in cases where low production yields do not permit the addition of labeled compounds to the growth medium and where 1D NMR spectra of selectively 19F‐labeled receptors are not sufficient to resolve signal overlap for a more detailed analysis.
Collapse
Affiliation(s)
- Inguna Goba
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85746, Oberschleißheim Neuherberg, Germany
| | - David Goricanec
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85747, Garching, Germany
| | - Dominik Schum
- Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85747, Garching, Germany
| | - Matthias Hillenbrand
- Biochemisches Institut, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Andreas Plückthun
- Biochemisches Institut, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Franz Hagn
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstrasse 1, 85746, Oberschleißheim Neuherberg, Germany.,Bavarian NMR Center at the Department of Chemistry, Technical University of Munich, Ernst-Otto-Fischer-Strasse 2, 85747, Garching, Germany
| |
Collapse
|
28
|
Bumbak F, Thomas T, Noonan-Williams BJ, Vaid TM, Yan F, Whitehead AR, Bruell S, Kocan M, Tan X, Johnson MA, Bathgate RAD, Chalmers DK, Gooley PR, Scott DJ. Conformational Changes in Tyrosine 11 of Neurotensin Are Required to Activate the Neurotensin Receptor 1. ACS Pharmacol Transl Sci 2020; 3:690-705. [PMID: 32832871 PMCID: PMC7432660 DOI: 10.1021/acsptsci.0c00026] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Indexed: 12/12/2022]
Abstract
Cell-cell communication via endogenous peptides and their receptors is vital for controlling all aspects of human physiology and most peptides signal through G protein-coupled receptors (GPCRs). Disordered peptides bind GPCRs through complex modes for which there are few representative crystal structures. The disordered peptide neurotensin (NT) is a neuromodulator of classical neurotransmitters such as dopamine and glutamate, through activation of neurotensin receptor 1 (NTS1). While several experimental structures show how NT binds NTS1, details about the structural dynamics of NT during and after binding NTS1, or the role of peptide dynamics on receptor activation, remain obscure. Here saturation transfer difference (STD) NMR revealed that the binding mode of NT fragment NT10-13 is heterogeneous. Epitope maps of NT10-13 at NTS1 suggested that tyrosine 11 (Y11) samples other conformations to those observed in crystal structures of NT-bound NTS1. Molecular dynamics (MD) simulations confirmed that when NT is bound to NTS1, residue Y11 can exist in two χ1 rotameric states, gauche plus (g+) or gauche minus (g-). Since only the g+ Y11 state is observed in all the structures solved to date, we asked if the g- state is important for receptor activation. NT analogues with Y11 replaced with 7-OH-Tic were synthesized to restrain the dynamics of the side chain. P(OH-TIC)IL bound NTS1 with the same affinity as NT10-13 but did not activate NTS1, instead acted as an antagonist. This study highlights that flexibility of Y11 in NT may be required for NT activation of NTS1.
Collapse
Affiliation(s)
- Fabian Bumbak
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Trayder Thomas
- Monash
Institute of Pharmaceutical Sciences, Monash
University, Parkville, Victoria 3052, Australia
| | - Billy J. Noonan-Williams
- Monash
Institute of Pharmaceutical Sciences, Monash
University, Parkville, Victoria 3052, Australia
| | - Tasneem M. Vaid
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Fei Yan
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alice R. Whitehead
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shoni Bruell
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Martina Kocan
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- The School
of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Xuan Tan
- Department
of Chemistry, The University of Alabama
at Birmingham, Birmingham, Alabama 35294-1240, United States
| | - Margaret A. Johnson
- Department
of Chemistry, The University of Alabama
at Birmingham, Birmingham, Alabama 35294-1240, United States
| | - Ross A. D. Bathgate
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
| | - David K. Chalmers
- Monash
Institute of Pharmaceutical Sciences, Monash
University, Parkville, Victoria 3052, Australia
| | - Paul R. Gooley
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Daniel J. Scott
- The
Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Victoria 3010, Australia
- Department
of Biochemistry and Molecular Biology, The
University of Melbourne, Parkville, Victoria 3010, Australia
| |
Collapse
|
29
|
Nakashima N, Nakashima K, Nakashima A, Takano M. Olfactory marker protein elevates basal cAMP concentration. Biochem Biophys Res Commun 2020; 531:203-208. [PMID: 32792198 DOI: 10.1016/j.bbrc.2020.07.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/08/2020] [Accepted: 07/19/2020] [Indexed: 01/25/2023]
Abstract
Olfactory marker protein (OMP), which is expressed abundantly in mature olfactory receptor neurons, operates as a cAMP-binding protein. OMP captures phasic cAMP surges induced by sensory stimuli and punctuates the downstream signalling in the cilia. On the other hand, OMP is also abundant in the soma. At equilibrium, OMP should exhibit association/dissociation reactions with cAMP. To examine the steady-state function of OMP, we expressed OMP in an HEK293 heterologous expression system and measured the activity of cAMP-dependent protein kinase (PKA) using a cAMP response element/luciferase reporter assay. In the presence of OMP, the basal activity level of PKA was elevated to approximately twice as much as that in the absence of OMP. Upon tonic stimulation by membrane-permeable cAMP, the PKA activity increased in a dose-dependent manner and was greater in the presence of OMP at all doses until saturation. These results indicate that OMP, a cytosolic cAMP-binding protein, operates as a cAMP reservoir by increases the basal cAMP concentration and enhances tonic cAMP actions. Together with the previous finding that OMP acutely sequesters cAMP-related responses, these results indicate that OMP can buffer acute surges in cAMP and tonic production, which stabilizes the basal cAMP pool in the long run.
Collapse
Affiliation(s)
- Noriyuki Nakashima
- Department of Physiology, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka, 830-0011, Japan.
| | - Kie Nakashima
- Laboratory of Developmental Neurobiology, Graduate School of Biostudies, Kyoto University, Yoshida Hon-machi, Kyoto, 606-8501, Japan
| | - Akiko Nakashima
- Department of Physiology, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka, 830-0011, Japan
| | - Makoto Takano
- Department of Physiology, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka, 830-0011, Japan
| |
Collapse
|
30
|
Dijkman PM, Muñoz-García JC, Lavington SR, Kumagai PS, dos Reis RI, Yin D, Stansfeld PJ, Costa-Filho AJ, Watts A. Conformational dynamics of a G protein-coupled receptor helix 8 in lipid membranes. SCIENCE ADVANCES 2020; 6:eaav8207. [PMID: 32851152 PMCID: PMC7428336 DOI: 10.1126/sciadv.aav8207] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 07/02/2020] [Indexed: 05/21/2023]
Abstract
G protein-coupled receptors (GPCRs) are the largest and pharmaceutically most important class of membrane proteins encoded in the human genome, characterized by a seven-transmembrane helix architecture and a C-terminal amphipathic helix 8 (H8). In a minority of GPCR structures solved to date, H8 either is absent or adopts an unusual conformation. The controversial existence of H8 of the class A GPCR neurotensin receptor 1 (NTS1) has been examined here for the nonthermostabilized receptor in a functionally supporting membrane environment using electron paramagnetic resonance, molecular dynamics simulations, and circular dichroism. Lipid-protein interactions with phosphatidylserine and phosphatidylethanolamine lipids, in particular, stabilize the residues 374 to 390 of NTS1 into forming a helix. Furthermore, introduction of a helix-breaking proline residue in H8 elicited an increase in ß-arrestin-NTS1 interactions observed in pull-down assays, suggesting that the structure and/or dynamics of H8 might play an important role in GPCR signaling.
Collapse
Affiliation(s)
- Patricia M. Dijkman
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Juan C. Muñoz-García
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Steven R. Lavington
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Patricia Suemy Kumagai
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-Carlense 400, C.P. 369, São Carlos SP 13560-970, Brazil
| | - Rosana I. dos Reis
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Daniel Yin
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Phillip J. Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- School of Life Sciences & Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Antonio José Costa-Filho
- Departamento de Física, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto SP 14040-901, Brazil
| | - Anthony Watts
- Biomembrane Structure Unit, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Corresponding author.
| |
Collapse
|
31
|
Schulze A, Kleinau G, Neumann S, Scheerer P, Schöneberg T, Brüser A. The intramolecular agonist is obligate for activation of glycoprotein hormone receptors. FASEB J 2020; 34:11243-11256. [PMID: 32648604 DOI: 10.1096/fj.202000100r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 01/15/2023]
Abstract
In contrast to most rhodopsin-like G protein-coupled receptors, the glycoprotein hormone receptors (GPHR) have a large extracellular N-terminus for hormone binding. The hormones do not directly activate the transmembrane domain but mediate their action via a, thus, far only partially known Tethered Agonistic LIgand (TALI). The existence of such an intramolecular agonist was initially indicated by site-directed mutation studies and activating peptides derived from the extracellular hinge region. It is still unknown precisely how TALI is involved in intramolecular signal transmission. We combined systematic mutagenesis studies at the luteinizing hormone receptor and the thyroid-stimulating hormone receptor (TSHR), stimulation with a drug-like agonist (E2) of the TSHR, and structural homology modeling to unravel the functional and structural properties defining the TALI region. Here, we report that TALI (a) is predisposed to constitutively activate GPHR, (b) can by itself rearrange GPHR into a fully active conformation, (c) stabilizes active GPHR conformation, and (d) is not involved in activation of the TSHR by E2. In the active state conformation, TALI forms specific interactions between the N-terminus and the transmembrane domain. We show that stabilization of an active state is dependent on TALI, including activation by hormones and constitutively activating mutations.
Collapse
Affiliation(s)
- Annelie Schulze
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Gunnar Kleinau
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Susanne Neumann
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Patrick Scheerer
- Group Protein X-ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Berlin Institute of Health, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Antje Brüser
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, University of Leipzig, Leipzig, Germany
| |
Collapse
|
32
|
Pope AL, Sanchez-Reyes OB, South K, Zaitseva E, Ziliox M, Vogel R, Reeves PJ, Smith SO. A Conserved Proline Hinge Mediates Helix Dynamics and Activation of Rhodopsin. Structure 2020; 28:1004-1013.e4. [PMID: 32470317 DOI: 10.1016/j.str.2020.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/24/2020] [Accepted: 05/11/2020] [Indexed: 01/05/2023]
Abstract
Despite high-resolution crystal structures of both inactive and active G protein-coupled receptors (GPCRs), it is still not known how ligands trigger the large structural change on the intracellular side of the receptor since the conformational changes that occur within the extracellular ligand-binding region upon activation are subtle. Here, we use solid-state NMR and Fourier transform infrared spectroscopy on rhodopsin to show that Trp2656.48 within the CWxP motif on transmembrane helix H6 constrains a proline hinge in the inactive state, suggesting that activation results in unraveling of the H6 backbone within this motif, a local change in dynamics that allows helix H6 to swing outward. Notably, Tyr3017.48 within activation switch 2 appears to mimic the negative allosteric sodium ion found in other family A GPCRs, a finding that is broadly relevant to the mechanism of receptor activation.
Collapse
Affiliation(s)
- Andreyah L Pope
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Omar B Sanchez-Reyes
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Kieron South
- School of Life Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK
| | - Ekaterina Zaitseva
- Biophysics Section, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Hermann Herder Strasse, 79104 Freiburg, Germany
| | - Martine Ziliox
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Reiner Vogel
- Biophysics Section, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, Freiburg, Hermann Herder Strasse, 79104 Freiburg, Germany
| | - Philip J Reeves
- School of Life Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
| |
Collapse
|
33
|
Doi T, Kikuta K, Tani K. Characterization of Critical Residues in the Extracellular and Transmembrane Domains of the Endothelin Type B Receptor for Propagation of the Endothelin-1 Signal. Biochemistry 2020; 59:1718-1727. [PMID: 32343134 DOI: 10.1021/acs.biochem.0c00158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have previously reported the crystal structures of endothelin-1 (ET-1)-bound, ligand-free, and antagonist bosentan-bound forms of the thermostabilized ET type B receptor (ETB). Although other agonist-bound structures of ETB have been determined, the interactions for high-affinity binding and ETB receptor activation, as well as the roles of rearrangement of the hydrogen-bond network surrounding the ligand in G protein activation, remain elusive. ET-1, a 21-amino acid residue peptide, plays fundamental roles in basal vascular tone, sodium balance, cell proliferation, and stress-responsive regulation. We studied the interactions between the ET-1(8-21) peptide and ETB in the ligand binding and activation of ETB using a series of Ala-substituted ET-1(8-21) analogues and the mutated ETB. We found that while D8, L17, D18, I20, and W21 were responsible for high-affinity binding and potent G protein activation, Y13 and F14 in the helical region of ET-1 are prerequisites for the full activation of ETB via interactions near the extracellular side. Furthermore, we introduced the mutation into the residues around the ET-1 binding pocket of ETB. The results showed that while S1843.35, W3366.48, N3787.45, and S3797.46 in a conserved polar network are required for full activation, N1191.50, D1472.50, and N3827.49 are essential for G protein activation via direct interactions after rearrangement upon ET-1 binding. These results demonstrate that both interactions near the extracellular side and within the transmembrane helices with ET-1 play crucial roles in the full activation of the ETB receptor.
Collapse
Affiliation(s)
- Tomoko Doi
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kohei Kikuta
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Kazutoshi Tani
- Graduate School of Medicine, Mie University, 2-174 Edobashi, Tsu, Mie 514-8507, Japan
| |
Collapse
|
34
|
Gahbauer S, Böckmann RA. Comprehensive Characterization of Lipid-Guided G Protein-Coupled Receptor Dimerization. J Phys Chem B 2020; 124:2823-2834. [DOI: 10.1021/acs.jpcb.0c00062] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Stefan Gahbauer
- Computational Biology, Friedrich-Alexander-University Erlangen-Nüremberg, Erlangen, Germany
| | - Rainer A. Böckmann
- Computational Biology, Friedrich-Alexander-University Erlangen-Nüremberg, Erlangen, Germany
| |
Collapse
|
35
|
Huang W, Masureel M, Qu Q, Janetzko J, Inoue A, Kato HE, Robertson MJ, Nguyen KC, Glenn JS, Skiniotis G, Kobilka BK. Structure of the neurotensin receptor 1 in complex with β-arrestin 1. Nature 2020; 579:303-308. [PMID: 31945771 PMCID: PMC7100716 DOI: 10.1038/s41586-020-1953-1] [Citation(s) in RCA: 219] [Impact Index Per Article: 54.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 01/08/2020] [Indexed: 01/14/2023]
Abstract
Arrestin proteins bind to active, phosphorylated G-protein-coupled receptors (GPCRs), thereby preventing G-protein coupling, triggering receptor internalization and affecting various downstream signalling pathways1,2. Although there is a wealth of structural information detailing the interactions between GPCRs and G proteins, less is known about how arrestins engage GPCRs. Here we report a cryo-electron microscopy structure of full-length human neurotensin receptor 1 (NTSR1) in complex with truncated human β-arrestin 1 (βarr1(ΔCT)). We find that phosphorylation of NTSR1 is critical for the formation of a stable complex with βarr1(ΔCT), and identify phosphorylated sites in both the third intracellular loop and the C terminus that may promote this interaction. In addition, we observe a phosphatidylinositol-4,5-bisphosphate molecule forming a bridge between the membrane side of NTSR1 transmembrane segments 1 and 4 and the C-lobe of arrestin. Compared with a structure of a rhodopsin-arrestin-1 complex, in our structure arrestin is rotated by approximately 85° relative to the receptor. These findings highlight both conserved aspects and plasticity among arrestin-receptor interactions.
Collapse
Affiliation(s)
- Weijiao Huang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthieu Masureel
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Qianhui Qu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - John Janetzko
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Hideaki E Kato
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Komaba Institute for Science, The University of Tokyo, Tokyo, Japan
| | - Michael J Robertson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Khanh C Nguyen
- Departments of Medicine and Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | - Jeffrey S Glenn
- Departments of Medicine and Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Photon Science, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
36
|
Yin W, Li Z, Jin M, Yin YL, de Waal PW, Pal K, Yin Y, Gao X, He Y, Gao J, Wang X, Zhang Y, Zhou H, Melcher K, Jiang Y, Cong Y, Edward Zhou X, Yu X, Eric Xu H. A complex structure of arrestin-2 bound to a G protein-coupled receptor. Cell Res 2019; 29:971-983. [PMID: 31776446 DOI: 10.1038/s41422-019-0256-2] [Citation(s) in RCA: 129] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 11/03/2019] [Indexed: 12/20/2022] Open
Abstract
Arrestins comprise a family of signal regulators of G-protein-coupled receptors (GPCRs), which include arrestins 1 to 4. While arrestins 1 and 4 are visual arrestins dedicated to rhodopsin, arrestins 2 and 3 (Arr2 and Arr3) are β-arrestins known to regulate many nonvisual GPCRs. The dynamic and promiscuous coupling of Arr2 to nonvisual GPCRs has posed technical challenges to tackle the basis of arrestin binding to GPCRs. Here we report the structure of Arr2 in complex with neurotensin receptor 1 (NTSR1), which reveals an overall assembly that is strikingly different from the visual arrestin-rhodopsin complex by a 90° rotation of Arr2 relative to the receptor. In this new configuration, intracellular loop 3 (ICL3) and transmembrane helix 6 (TM6) of the receptor are oriented toward the N-terminal domain of the arrestin, making it possible for GPCRs that lack the C-terminal tail to couple Arr2 through their ICL3. Molecular dynamics simulation and crosslinking data further support the assembly of the Arr2‒NTSR1 complex. Sequence analysis and homology modeling suggest that the Arr2‒NTSR1 complex structure may provide an alternative template for modeling arrestin-GPCR interactions.
Collapse
Affiliation(s)
- Wanchao Yin
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zhihai Li
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,Cryo-Electron Microscopy Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Mingliang Jin
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yu-Ling Yin
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Parker W de Waal
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Kuntal Pal
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.,Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Yanting Yin
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Xiang Gao
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Yuanzheng He
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.,Laboratory of Receptor Structure and Signaling, HIT Center for Life Science, Harbin Institute of Technology, Harbin, 150001, China
| | - Jing Gao
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiaoxi Wang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yan Zhang
- Department of Pathology of Sir Run Run Shaw Hospital and Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Hu Zhou
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Karsten Melcher
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Yi Jiang
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yao Cong
- National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
| | - X Edward Zhou
- Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.
| | - Xuekui Yu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,Cryo-Electron Microscopy Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - H Eric Xu
- The CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,Center for Cancer and Cell Biology, Program for Structural Biology, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.
| |
Collapse
|
37
|
Ciancetta A, Rubio P, Lieberman DI, Jacobson KA. A 3 adenosine receptor activation mechanisms: molecular dynamics analysis of inactive, active, and fully active states. J Comput Aided Mol Des 2019; 33:983-996. [PMID: 31758354 DOI: 10.1007/s10822-019-00246-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 11/02/2019] [Indexed: 12/12/2022]
Abstract
We investigated the Gi-coupled A3 adenosine receptor (A3AR) activation mechanism by running 7.2 µs of molecular dynamics (MD) simulations. Based on homology to G protein-coupled receptor (GPCR) structures, three constitutively active mutant (CAM) and the wild-type (WT) A3ARs in the apo form were modeled. Conformational signatures associated with three different receptor states (inactive R, active R*, and bound to Gi protein mimic) were predicted by analyzing and comparing the CAMs with WT receptor and by considering site-directed mutagenesis data. Detected signatures that were correlated with receptor state included: Persistent salt-bridges involving key charged residues for activation (including a novel, putative ionic lock), rotameric state of conserved W6.48, and Na+ ions and water molecules present. Active-coupled state signatures similar to the X-ray structures of β2 adrenergic receptor-Gs protein and A2AAR-mini-Gs and the recently solved cryo-EM A1AR-Gi complexes were found. Our MD analysis suggests that constitutive activation might arise from the D1073.49-R1083.50 ionic lock destabilization in R and the D1073.49-R1113.53 ionic lock stabilization in R* that presumably lowers the energy barrier associated with an R to R* transition. This study provides new opportunities to understand the underlying interactions of different receptor states of other Gi protein-coupled GPCRs.
Collapse
Affiliation(s)
- Antonella Ciancetta
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
- Sygnature Discovery, Nottingham, UK.
| | - Priscila Rubio
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - David I Lieberman
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA.
| |
Collapse
|
38
|
Zhang X, Sun H, Wen X, Yuan H. A Selectivity Study of FFAR4/FFAR1 Agonists by Molecular Modeling. J Chem Inf Model 2019; 59:4467-4474. [PMID: 31580060 DOI: 10.1021/acs.jcim.9b00735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
FFAR4 has been considered as a potential target for metabolic diseases, including diabetes. Some compounds with biphenyl scaffold, represented by compound SR13 reported by our group, showed significant FFAR4 selectivity. However, the molecular basis for their selectivity has not been definitely disclosed. This study provided insights into the protein-ligand interactions between agonists and FFAR4/FFAR1 by molecular modeling. The important residues identified were consistent with those found in experimental studies. Moreover, the results proposed that the selectivity of SR13 between FFAR4 and FFAR1 depended on whether it can enter the ligand-binding site through the entrance region by adopting its preferential conformation. The big difference between the preferential conformation of SR13 and the narrow entrance region determined its poor agonist activity against FFAR1. These findings will facilitate the further development of selective FFAR4 agonists.
Collapse
Affiliation(s)
- Xiangying Zhang
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing 210009 , P. R. China
| | - Hongbin Sun
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing 210009 , P. R. China
| | - Xiaoan Wen
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing 210009 , P. R. China
| | - Haoliang Yuan
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing 210009 , P. R. China
| |
Collapse
|
39
|
Zarzycka B, Zaidi SA, Roth BL, Katritch V. Harnessing Ion-Binding Sites for GPCR Pharmacology. Pharmacol Rev 2019; 71:571-595. [PMID: 31551350 PMCID: PMC6782022 DOI: 10.1124/pr.119.017863] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Endogenous ions play important roles in the function and pharmacology of G-protein coupled receptors (GPCRs). Historically the evidence for ionic modulation of GPCR function dates to 1973 with studies of opioid receptors, where it was demonstrated that physiologic concentrations of sodium allosterically attenuated agonist binding. This Na+-selective effect was distinct from effects of other monovalent and divalent cations, with the latter usually counteracting sodium's negative allosteric modulation of binding. Since then, numerous studies documenting the effects of mono- and divalent ions on GPCR function have been published. While ions can act selectively and nonselectively at many sites in different receptors, the discovery of the conserved sodium ion site in class A GPCR structures in 2012 revealed the unique nature of Na+ site, which has emerged as a near-universal site for allosteric modulation of class A GPCR structure and function. In this review, we synthesize and highlight recent advances in the functional, biophysical, and structural characterization of ions bound to GPCRs. Taken together, these findings provide a molecular understanding of the unique roles of Na+ and other ions as GPCR allosteric modulators. We will also discuss how this knowledge can be applied to the redesign of receptors and ligand probes for desired functional and pharmacological profiles. SIGNIFICANCE STATEMENT: The function and pharmacology of GPCRs strongly depend on the presence of mono and divalent ions in experimental assays and in living organisms. Recent insights into the molecular mechanism of this ion-dependent allosterism from structural, biophysical, biochemical, and computational studies provide quantitative understandings of the pharmacological effects of drugs in vitro and in vivo and open new avenues for the rational design of chemical probes and drug candidates with improved properties.
Collapse
Affiliation(s)
- Barbara Zarzycka
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Saheem A Zaidi
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Bryan L Roth
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Vsevolod Katritch
- Departments of Biological Sciences (B.Z., S.A.Z., V.K.) and Chemistry (V.K.), Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California; and Department of Pharmacology (B.L.R.) and Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy (B.L.R.), University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| |
Collapse
|
40
|
Jana S, Ghosh S, Muk S, Levy B, Vaidehi N. Prediction of Conformation Specific Thermostabilizing Mutations for Class A G Protein-Coupled Receptors. J Chem Inf Model 2019; 59:3744-3754. [PMID: 31408606 PMCID: PMC6944194 DOI: 10.1021/acs.jcim.9b00175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
G protein-coupled receptors (GPCRs) are highly flexible and prone to denaturation during protein extraction in detergents and purification. This poses a huge challenge to purify a conformationally homogeneous solution of GPCRs. Thermostabilizing mutations have been used widely to purify and obtain crystal structures of several GPCRs. However, identifying thermostabilizing mutations for GPCRs remains a tedious and expensive task as they are not transferable even among closely related GPCRs. Additionally, the mutations stabilizing one conformational state of a GPCR do not always stabilize other conformational state(s) of the same GPCR. Previously we developed a computational method, LiticonDesign, for rapid prediction of thermostabilizing mutations for a specific GPCR conformation. In this study, we have used LiticonDesign to predict thermostabilizing mutations for the agonist bound active-intermediate state of the human adenosine receptor (A2AR) using the structure of the inactive state of the same GPCR and vice versa. Our study shows that the thermostable mutation predictions using LiticonDesign, for an active-intermediate state of a GPCR (A2AR in our case), requires a homology model that is derived from an active/active-intermediate state GPCR structure as a template. Similarly, the homology models derived from inactive state GPCR conformations are better in predicting the thermostable mutations for the inactive state of A2AR. Overall, LiticonDesign method is not only efficient in predicting thermostabilizing mutations for a given GPCR sequence but also can recover conformation specific mutations for a state of interest, if a suitable starting structure of desired conformation is chosen.
Collapse
Affiliation(s)
- Suvamay Jana
- Department of Computation and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010
| | - Soumadwip Ghosh
- Department of Computation and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010
| | - Sanychen Muk
- Department of Computation and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010
| | - Benjamin Levy
- Department of Computation and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010
| | - Nagarajan Vaidehi
- Department of Computation and Quantitative Medicine, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, CA 91010
| |
Collapse
|
41
|
Kato HE, Zhang Y, Hu H, Suomivuori CM, Kadji FMN, Aoki J, Krishna Kumar K, Fonseca R, Hilger D, Huang W, Latorraca NR, Inoue A, Dror RO, Kobilka BK, Skiniotis G. Conformational transitions of a neurotensin receptor 1-G i1 complex. Nature 2019; 572:80-85. [PMID: 31243364 PMCID: PMC7065593 DOI: 10.1038/s41586-019-1337-6] [Citation(s) in RCA: 160] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/31/2019] [Indexed: 01/14/2023]
Abstract
Neurotensin receptor 1 (NTSR1) is a G-protein-coupled receptor (GPCR) that engages multiple subtypes of G protein, and is involved in the regulation of blood pressure, body temperature, weight and the response to pain. Here we present structures of human NTSR1 in complex with the agonist JMV449 and the heterotrimeric Gi1 protein, at a resolution of 3 Å. We identify two conformations: a canonical-state complex that is similar to recently reported GPCR-Gi/o complexes (in which the nucleotide-binding pocket adopts more flexible conformations that may facilitate nucleotide exchange), and a non-canonical state in which the G protein is rotated by about 45 degrees relative to the receptor and exhibits a more rigid nucleotide-binding pocket. In the non-canonical state, NTSR1 exhibits features of both active and inactive conformations, which suggests that the structure may represent an intermediate form along the activation pathway of G proteins. This structural information, complemented by molecular dynamics simulations and functional studies, provides insights into the complex process of G-protein activation.
Collapse
Affiliation(s)
- Hideaki E Kato
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Komaba Institute for Science, The University of Tokyo, Tokyo, Japan
| | - Yan Zhang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology of Sir Run Run Shaw Hospital, Department of Biophysics, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongli Hu
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Carl-Mikael Suomivuori
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | | | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Kaavya Krishna Kumar
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rasmus Fonseca
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Hilger
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Weijiao Huang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Naomi R Latorraca
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Ron O Dror
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
42
|
Wink LH, Baker DL, Cole JA, Parrill AL. A benchmark study of loop modeling methods applied to G protein-coupled receptors. J Comput Aided Mol Des 2019; 33:573-595. [PMID: 31123958 PMCID: PMC6628340 DOI: 10.1007/s10822-019-00196-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/12/2019] [Indexed: 11/25/2022]
Abstract
G protein-coupled receptors (GPCR) are important drug discovery targets. Despite progress, many GPCR structures have not yet been solved. For these targets, comparative modeling is used in virtual ligand screening to prioritize experimental efforts. However, the structure of extracellular loop 2 (ECL2) is often poorly predicted. This is significant due to involvement of ECL2 in ligand binding for many Class A GPCR. Here we examine the performance of loop modeling protocols available in the Rosetta (cyclic coordinate descent [CCD], KIC with fragments [KICF] and next generation KIC [NGK]) and Molecular Operating Environment (MOE) software suites (de novo search). ECL2 from GPCR crystal structures served as the structure prediction targets and were divided into four sets depending on loop length. Results suggest that KICF and NGK sampled and scored more loop models with sub-angstrom and near-atomic accuracy than CCD or de novo search for loops of 24 or fewer residues. None of the methods were able to sample loop conformations with near-atomic accuracy for the longest targets ranging from 25 to 32 residues based on 1000 models generated. For these long loop targets, increased conformational sampling is necessary. The strongly conserved disulfide bond between Cys3.25 and Cys45.50 in ECL2 proved an effective filter. Setting an upper limit of 5.1 Å on the S-S distance improved the lowest RMSD model included in the top 10 scored structures in Groups 1-4 on average between 0.33 and 1.27 Å. Disulfide bond formation and geometry optimization of ECL2 provided an additional incremental benefit in structure quality.
Collapse
Affiliation(s)
- Lee H Wink
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Daniel L Baker
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Judith A Cole
- Department of Biological Sciences, The University of Memphis, Memphis, TN, 38152, USA
| | - Abby L Parrill
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
| |
Collapse
|
43
|
Novel stable analogues of the neurotensin C-terminal hexapeptide containing unnatural amino acids. Amino Acids 2019; 51:1009-1022. [DOI: 10.1007/s00726-019-02741-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 05/02/2019] [Indexed: 10/26/2022]
|
44
|
Popov P, Kozlovskii I, Katritch V. Computational design for thermostabilization of GPCRs. Curr Opin Struct Biol 2019; 55:25-33. [PMID: 30909106 DOI: 10.1016/j.sbi.2019.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 02/19/2019] [Indexed: 10/27/2022]
Abstract
GPCR superfamily is the largest clinically relevant family of targets in human genome; however, low thermostability and high conformational plasticity of these integral membrane proteins make them notoriously hard to handle in biochemical, biophysical, and structural experiments. Here, we describe the recent advances in computational approaches to design stabilizing mutations for GPCR that take advantage of the structural and sequence conservation properties of the receptors, and employ machine learning on accumulated mutation data for the superfamily. The fast and effective computational tools can provide a viable alternative to existing experimental mutation screening and are poised for further improvements with expansion of thermostability datasets for training the machine learning models. The rapidly growing practical applications of computational stability design streamline GPCR structure determination and may contribute to more efficient drug discovery.
Collapse
Affiliation(s)
- Petr Popov
- Skolkovo Institute of Science and Technology, Moscow, Russia; Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Igor Kozlovskii
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Vsevolod Katritch
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia; Departments of Biological Sciences and Chemistry, Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA, USA.
| |
Collapse
|
45
|
Nagarajan S, Alkayed NJ, Kaul S, Barnes AP. Effect of thermostable mutations on the neurotensin receptor 1 (NTSR1) activation state. J Biomol Struct Dyn 2019; 38:340-353. [DOI: 10.1080/07391102.2019.1573705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Shanthi Nagarajan
- The Knight Cardiovascular Institute, Oregon Health Science University, Portland, OR, USA
- Medicinal Chemistry Core, Oregon Health Science University, Portland, OR, USA
| | - Nabil J. Alkayed
- The Knight Cardiovascular Institute, Oregon Health Science University, Portland, OR, USA
- Department of Anesthesiology & Perioperative Medicine, Oregon Health Science University Portland, Portland, OR, USA
| | - Sanjiv Kaul
- The Knight Cardiovascular Institute, Oregon Health Science University, Portland, OR, USA
| | - Anthony P. Barnes
- The Knight Cardiovascular Institute, Oregon Health Science University, Portland, OR, USA
| |
Collapse
|
46
|
Aguinaga D, Medrano M, Cordomí A, Jiménez-Rosés M, Angelats E, Casanovas M, Vega-Quiroga I, Canela EI, Petrovic M, Gysling K, Pardo L, Franco R, Navarro G. Cocaine Blocks Effects of Hunger Hormone, Ghrelin, Via Interaction with Neuronal Sigma-1 Receptors. Mol Neurobiol 2019; 56:1196-1210. [PMID: 29876881 DOI: 10.1007/s12035-018-1140-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 05/21/2018] [Indexed: 10/14/2022]
Abstract
Despite ancient knowledge on cocaine appetite-suppressant action, the molecular basis of such fact remains unknown. Addiction/eating disorders (e.g., binge eating, anorexia, bulimia) share a central control involving reward circuits. However, we here show that the sigma-1 receptor (σ1R) mediates cocaine anorectic effects by interacting in neurons with growth/hormone/secretagogue (ghrelin) receptors. Cocaine increases colocalization of σ1R and GHS-R1a at the cell surface. Moreover, in transfected HEK-293T and neuroblastoma SH-SY5Y cells, and in primary neuronal cultures, pretreatment with cocaine or a σ1R agonist inhibited ghrelin-mediated signaling, in a similar manner as the GHS-R1a antagonist YIL-781. Results were similar in G protein-dependent (cAMP accumulation and calcium release) and in partly dependent or independent (ERK1/2 phosphorylation and label-free) assays. We provide solid evidence for direct interaction between receptors and the functional consequences, as well as a reliable structural model of the macromolecular σ1R-GHS-R1a complex, which arises as a key piece in the puzzle of the events linking cocaine consumption and appetitive/consummatory behaviors.
Collapse
Affiliation(s)
- David Aguinaga
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biomedicine, School of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Mireia Medrano
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biomedicine, School of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Arnau Cordomí
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Mireia Jiménez-Rosés
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Edgar Angelats
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biomedicine, School of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Mireia Casanovas
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biomedicine, School of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Ignacio Vega-Quiroga
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Enric I Canela
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Department of Biochemistry and Molecular Biomedicine, School of Biology, Universitat de Barcelona, Barcelona, Spain
| | - Milos Petrovic
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, UK
| | - Katia Gysling
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Rafael Franco
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.
- Department of Biochemistry and Molecular Biomedicine, School of Biology, Universitat de Barcelona, Barcelona, Spain.
- School of Biology, Universitat de Barcelona, Diagonal 643, 08028, Barcelona, Spain.
| | - Gemma Navarro
- Centro de Investigación en Red, Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain.
- Department of Biochemistry and Physiology, Faculty of Pharmacy, Universitat de Barcelona, Barcelona, Spain.
- School of Biology, Universitat de Barcelona, Diagonal 643, 08028, Barcelona, Spain.
| |
Collapse
|
47
|
Ritler A, Shoshan MS, Deupi X, Wilhelm P, Schibli R, Wennemers H, Béhé M. Elucidating the Structure-Activity Relationship of the Pentaglutamic Acid Sequence of Minigastrin with Cholecystokinin Receptor Subtype 2. Bioconjug Chem 2019; 30:657-666. [PMID: 30608664 DOI: 10.1021/acs.bioconjchem.8b00849] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Derivatized minigastrin analogues make up a promising class of candidates for targeting cholecystokinin receptor subtype 2 (CCK2R), which is overexpressed on cancer cells of various neuroendocrine tumors. The pentaglutamic acid sequence of minigastrin influences its biological properties. In particular, it plays a crucial role in the kidney reuptake mechanism. However, the importance of the binding affinity and interaction of this region with the receptor on a molecular level remains unclear. To elucidate its structure-activity relationship with CCK2R, we replaced this sequence with various linkers differing in their amount of anionic charge, structural characteristics, and flexibility. Specifically, a flexible aliphatic linker, a linker with only three d-Glu residues, and a structured linker with four adjacent β3-glutamic acid residues were evaluated and compared to the lead compound PP-F11N (DOTA-[d-Glu1-6,Nle11]gastrin-13). 1,4,7,10-Tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) was conjugated to the minigastrin derivatives, which allowed radiolabeling with Lutetium-177. The levels of In vitro internalization into MZ-CRC1 cells and in vivo tumor uptake as well as human blood plasma stability increased in the following order: aliphatic linker < three d-Glu < (β3-Glu)4 < (d-Glu)6. The in vitro and in vivo behavior was therefore significantly improved with anionic charges. Computational modeling of a CCK2 receptor-ligand complex revealed ionic interactions between cationic residues (Arg and His) of the receptor and anionic residues of the ligand in the linker.
Collapse
Affiliation(s)
- Andreas Ritler
- Department of Chemistry and Applied Biosciences (D-CHAB), Laboratory of Organic Chemistry (LOC) , ETH , CH-8093 Zurich , Switzerland.,Department of Chemistry and Applied Biosciences (D-CHAB), Institute of Pharmaceutical Sciences (IPW) , ETH , CH-8093 Zurich , Switzerland.,Research Department of Biology and Chemistry, Center for Radiopharmaceutical Sciences (CRS) , Paul Scherrer Institute , CH-5232 Villigen , Switzerland
| | - Michal S Shoshan
- Department of Chemistry and Applied Biosciences (D-CHAB), Laboratory of Organic Chemistry (LOC) , ETH , CH-8093 Zurich , Switzerland
| | - Xavier Deupi
- Laboratory of Biomolecular Research and Condensed Matter Theory Group , Paul Scherrer Institute , CH-5232 Villigen , Switzerland
| | - Patrick Wilhelm
- Department of Chemistry and Applied Biosciences (D-CHAB), Laboratory of Organic Chemistry (LOC) , ETH , CH-8093 Zurich , Switzerland
| | - Roger Schibli
- Department of Chemistry and Applied Biosciences (D-CHAB), Institute of Pharmaceutical Sciences (IPW) , ETH , CH-8093 Zurich , Switzerland.,Research Department of Biology and Chemistry, Center for Radiopharmaceutical Sciences (CRS) , Paul Scherrer Institute , CH-5232 Villigen , Switzerland
| | - Helma Wennemers
- Department of Chemistry and Applied Biosciences (D-CHAB), Laboratory of Organic Chemistry (LOC) , ETH , CH-8093 Zurich , Switzerland
| | - Martin Béhé
- Research Department of Biology and Chemistry, Center for Radiopharmaceutical Sciences (CRS) , Paul Scherrer Institute , CH-5232 Villigen , Switzerland
| |
Collapse
|
48
|
Stenkamp RE. Identifying G protein-coupled receptor dimers from crystal packings. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:655-670. [PMID: 29968675 DOI: 10.1107/s2059798318008136] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/01/2018] [Indexed: 12/20/2022]
Abstract
Dimers of G protein-coupled receptors (GPCRs) are believed to be important for signaling with their associated G proteins. Low-resolution electron microscopy has shown rhodopsin dimers in native retinal membranes, and CXCR4 dimers have been found in several different crystal structures. Evidence for dimers of other GPCRs is more indirect. An alternative to computational modeling studies is to search for parallel dimers in the packing environments of the reported crystal structures of GPCRs. Two major structural types of GPCR dimers exist (as predicted by others), but there is considerable structural variation within each cluster. The different structural variants described here might reflect different functional properties and should provide a range of model structures for computational and experimental examination.
Collapse
Affiliation(s)
- Ronald E Stenkamp
- Departments of Biological Structure and Biochemistry, Biomolecular Structure Center, University of Washington, Box 357420, Seattle, WA 98195, USA
| |
Collapse
|
49
|
Dynamic tuneable G protein-coupled receptor monomer-dimer populations. Nat Commun 2018; 9:1710. [PMID: 29703992 PMCID: PMC5923235 DOI: 10.1038/s41467-018-03727-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 03/06/2018] [Indexed: 01/07/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are the largest class of membrane receptors, playing a key role in the regulation of processes as varied as neurotransmission and immune response. Evidence for GPCR oligomerisation has been accumulating that challenges the idea that GPCRs function solely as monomeric receptors; however, GPCR oligomerisation remains controversial primarily due to the difficulties in comparing evidence from very different types of structural and dynamic data. Using a combination of single-molecule and ensemble FRET, double electron–electron resonance spectroscopy, and simulations, we show that dimerisation of the GPCR neurotensin receptor 1 is regulated by receptor density and is dynamically tuneable over the physiological range. We propose a “rolling dimer” interface model in which multiple dimer conformations co-exist and interconvert. These findings unite previous seemingly conflicting observations, provide a compelling mechanism for regulating receptor signalling, and act as a guide for future physiological studies. Evidence suggests oligomerisation of G protein-coupled receptors in membranes, but this is controversial. Here, authors use single-molecule and ensemble FRET, and spectroscopy to show that the neurotensin receptor 1 forms multiple dimer conformations that interconvert - “rolling” interfaces.
Collapse
|
50
|
Heitkamp T, Grisshammer R, Börsch M. Towards monitoring conformational changes of the GPCR neurotensin receptor 1 by single-molecule FRET. PROCEEDINGS OF SPIE--THE INTERNATIONAL SOCIETY FOR OPTICAL ENGINEERING 2018; 10498. [PMID: 30013286 DOI: 10.1117/12.2286787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Neurotensin receptor 1 (NTSR1) is a G protein-coupled receptor that is important for signaling in the brain and the gut. Its agonist ligand neurotensin (NTS), a 13-amino-acid peptide, binds with nanomolar affinity from the extracellular side to NTSR1 and induces conformational changes that trigger intracellular signaling processes. Our goal is to monitor the conformational dynamics of single fluorescently labeled NTSR1. For this, we fused the fluorescent protein mNeonGreen to the C terminus of NTSR1, purified the receptor fusion protein from E. coli membranes, and reconstituted NTSR1 into liposomes with E. coli polar lipids. Using single-molecule anisotropy measurements, NTSR1 was found to be monomeric in liposomes, with a small fraction being dimeric and oligomeric, showing homoFRET. Similar results were obtained for NTSR1 in detergent solution. Furthermore, we demonstrated agonist binding to NTSR1 by time-resolved single-molecule Förster resonance energy transfer (smFRET), using neurotensin labeled with the fluorophore ATTO594.
Collapse
Affiliation(s)
- Thomas Heitkamp
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University Jena, Nonnenplan 2 - 4, 07743 Jena, Germany
| | - Reinhard Grisshammer
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, 50 South Drive, Bethesda, MD 20814, USA
| | - Michael Börsch
- Single-Molecule Microscopy Group, Jena University Hospital, Friedrich Schiller University Jena, Nonnenplan 2 - 4, 07743 Jena, Germany
| |
Collapse
|