1
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Watts SW, Townsend RR, Neubig RR. How New Developments in Pharmacology Receptor Theory Are Changing (Our Understanding of) Hypertension Therapy. Am J Hypertens 2024; 37:248-260. [PMID: 38150382 PMCID: PMC10941088 DOI: 10.1093/ajh/hpad121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/21/2023] [Indexed: 12/29/2023] Open
Abstract
BACKGROUND Many hypertension therapeutics were developed prior to major advances in drug receptor theory. Moreover, newer drugs may take advantage of some of the newly understood modalities of receptor function. GOAL The goal of this review is to provide an up-to-date summary of drug receptor theory. This is followed by a discussion of the drug classes recognized for treating hypertension to which new concepts in receptor theory apply. RESULTS We raise ideas for mechanisms of potential new antihypertensive drugs and whether they may take advantage of new theories in drug-receptor interaction.
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Affiliation(s)
- Stephanie W Watts
- Department of Pharmacology and Toxicology, College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan 48824-131, USA
| | - Raymond R Townsend
- Department of Nephrology and Hypertension, University of Pennsylvania Medical Center, Philadelphia, Pennsylvania 19104, USA
| | - Richard R Neubig
- Department of Pharmacology and Toxicology, College of Osteopathic Medicine, Michigan State University, East Lansing, Michigan 48824-131, USA
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2
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Harris JA, Faust B, Gondin AB, Dämgen MA, Suomivuori CM, Veldhuis NA, Cheng Y, Dror RO, Thal DM, Manglik A. Selective G protein signaling driven by substance P-neurokinin receptor dynamics. Nat Chem Biol 2022; 18:109-115. [PMID: 34711980 PMCID: PMC8712391 DOI: 10.1038/s41589-021-00890-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 08/27/2021] [Indexed: 12/20/2022]
Abstract
The neuropeptide substance P (SP) is important in pain and inflammation. SP activates the neurokinin-1 receptor (NK1R) to signal via Gq and Gs proteins. Neurokinin A also activates NK1R, but leads to selective Gq signaling. How two stimuli yield distinct G protein signaling at the same G protein-coupled receptor remains unclear. We determined cryogenic-electron microscopy structures of active NK1R bound to SP or the Gq-biased peptide SP6-11. Peptide interactions deep within NK1R are critical for receptor activation. Conversely, interactions between SP and NK1R extracellular loops are required for potent Gs signaling but not Gq signaling. Molecular dynamics simulations showed that these superficial contacts restrict SP flexibility. SP6-11, which lacks these interactions, is dynamic while bound to NK1R. Structural dynamics of NK1R agonists therefore depend on interactions with the receptor extracellular loops and regulate G protein signaling selectivity. Similar interactions between other neuropeptides and their cognate receptors may tune intracellular signaling.
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Affiliation(s)
- Julian A Harris
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, CA, USA
| | - Bryan Faust
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Biophysics Graduate Program, University of California, San Francisco, CA, USA
| | - Arisbel B Gondin
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash University, Parkville, Victoria, Australia
| | - Marc André Dämgen
- Department of Computer Science, Stanford University, Stanford, CA, USA
- 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
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Carl-Mikael Suomivuori
- Department of Computer Science, Stanford University, Stanford, CA, USA
- 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
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA
| | - Nicholas A Veldhuis
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash University, Parkville, Victoria, Australia
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA.
- Howard Hughes Medical Institute, University of California, San Francisco, CA, USA.
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA, USA.
- 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.
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia.
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA, USA.
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, CA, USA.
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3
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Thom C, Ehrenmann J, Vacca S, Waltenspühl Y, Schöppe J, Medalia O, Plückthun A. Structures of neurokinin 1 receptor in complex with G q and G s proteins reveal substance P binding mode and unique activation features. SCIENCE ADVANCES 2021; 7:eabk2872. [PMID: 34878828 PMCID: PMC8654284 DOI: 10.1126/sciadv.abk2872] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
The neurokinin 1 receptor (NK1R) is involved in inflammation and pain transmission. This pathophysiologically important G protein–coupled receptor is predominantly activated by its cognate agonist substance P (SP) but also by the closely related neurokinins A and B. Here, we report cryo–electron microscopy structures of SP-bound NK1R in complex with its primary downstream signal mediators, Gq and Gs. Our structures reveal how a polar network at the extracellular, solvent-exposed receptor surface shapes the orthosteric pocket and that NK1R adopts a noncanonical active-state conformation with an interface for G protein binding, which is distinct from previously reported structures. Detailed comparisons with antagonist-bound NK1R crystal structures reveal that insurmountable antagonists induce a distinct and long-lasting receptor conformation that sterically blocks SP binding. Together, our structures provide important structural insights into ligand and G protein promiscuity, the lack of basal signaling, and agonist- and antagonist-induced conformations in the neurokinin receptor family.
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4
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Louet M, Casiraghi M, Damian M, Costa MG, Renault P, Gomes AA, Batista PR, M'Kadmi C, Mary S, Cantel S, Denoyelle S, Ben Haj Salah K, Perahia D, Bisch PM, Fehrentz JA, Catoire LJ, Floquet N, Banères JL. Concerted conformational dynamics and water movements in the ghrelin G protein-coupled receptor. eLife 2021; 10:63201. [PMID: 34477105 PMCID: PMC8416020 DOI: 10.7554/elife.63201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 07/23/2021] [Indexed: 12/03/2022] Open
Abstract
There is increasing support for water molecules playing a role in signal propagation through G protein-coupled receptors (GPCRs). However, exploration of the hydration features of GPCRs is still in its infancy. Here, we combined site-specific labeling with unnatural amino acids to molecular dynamics to delineate how local hydration of the ghrelin receptor growth hormone secretagogue receptor (GHSR) is rearranged upon activation. We found that GHSR is characterized by a specific hydration pattern that is selectively remodeled by pharmacologically distinct ligands and by the lipid environment. This process is directly related to the concerted movements of the transmembrane domains of the receptor. These results demonstrate that the conformational dynamics of GHSR are tightly coupled to the movements of internal water molecules, further enhancing our understanding of the molecular bases of GPCR-mediated signaling.
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Affiliation(s)
- Maxime Louet
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Marina Casiraghi
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), Paris, France
| | | | - Mauricio Gs Costa
- Laboratoire de Biologie et Pharmacologie Appliquées, UMR 8113 CNRS, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France.,Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Pedro Renault
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Antoniel As Gomes
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France.,Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo R Batista
- Programa de Computação Científica, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Céline M'Kadmi
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Sophie Mary
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | - Sonia Cantel
- IBMM, Univ Montpellier, CNRS, ENSCM, Montpellier, France
| | | | | | - David Perahia
- Laboratoire de Biologie et Pharmacologie Appliquées, UMR 8113 CNRS, Ecole Normale Supérieure Paris-Saclay, Gif-sur-Yvette, France
| | - Paulo M Bisch
- Laboratório de Física Biológica, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Laurent J Catoire
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, UMR 7099, CNRS, Université de Paris, Institut de Biologie Physico-Chimique (FRC 550), Paris, France
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5
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Satarker S, Maity S, Mudgal J, Nampoothiri M. In silico screening of neurokinin receptor antagonists as a therapeutic strategy for neuroinflammation in Alzheimer's disease. Mol Divers 2021; 26:443-466. [PMID: 34331670 PMCID: PMC8885547 DOI: 10.1007/s11030-021-10276-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/07/2021] [Indexed: 02/08/2023]
Abstract
Neuroinflammation is one of the detrimental factors leading to neurodegeneration in Alzheimer’s disease (AD) and other neurodegenerative disorders. The activation of microglial neurokinin 1 receptor (NK1R) by substance P (SP) enhances neuroinflammation which is mediated through pro-inflammatory pathways involving NFkB, ERK1/2, and P38 and thus projects the scope and importance of NK1R inhibitors. Emphasizing the inhibitory role of N Acetyl l Tryptophan (l-NAT) on NK1R, this is the first in silico screening of l-NAT mediated NK1R antagonism. In addition, FDA- approved ligands were screened for their potential NK1R antagonism. The l-NAT was docked in XP (Extra Precision) mode while FDA-approved ligands were screened in HTVS (High Throughput Virtual Screening), SP (Standard Precision), and XP mode onto NK1R (PDB:6HLO). The l-NAT and top 3 compounds FDA-approved ligands were subjected to molecular dynamics (MD) studies of 100 ns simulation time. The XP docking of l-NAT, indacaterol, modafinil and alosetron showed good docking scores. Their 100 ns MD showed brief protein–ligand interactions with an acceptable root mean square deviation. The protein–ligand contacts depicted pi-pi stacking, pi-cation, hydrogen bonds, and water bridges with the amino acids necessary for NK1R inhibition. The variable colour band intensities on the protein–ligand contact map indicated their binding strength with amino acids. The molecular mechanics/generalized born surface area (MM-GBSA) scores suggested favourable binding free energy of the complexes. Thus, our study predicted the ability of l-NAT, indacaterol, modafinil, and alosetron as capable NK1R inhibitors that can aid to curb neuroinflammation in conditions of AD which could be further ascertained in subsequent studies.
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Affiliation(s)
- Sairaj Satarker
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Swastika Maity
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Jayesh Mudgal
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Madhavan Nampoothiri
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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6
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Receptor-Arrestin Interactions: The GPCR Perspective. Biomolecules 2021; 11:biom11020218. [PMID: 33557162 PMCID: PMC7913897 DOI: 10.3390/biom11020218] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/25/2021] [Accepted: 02/01/2021] [Indexed: 02/06/2023] Open
Abstract
Arrestins are a small family of four proteins in most vertebrates that bind hundreds of different G protein-coupled receptors (GPCRs). Arrestin binding to a GPCR has at least three functions: precluding further receptor coupling to G proteins, facilitating receptor internalization, and initiating distinct arrestin-mediated signaling. The molecular mechanism of arrestin–GPCR interactions has been extensively studied and discussed from the “arrestin perspective”, focusing on the roles of arrestin elements in receptor binding. Here, we discuss this phenomenon from the “receptor perspective”, focusing on the receptor elements involved in arrestin binding and emphasizing existing gaps in our knowledge that need to be filled. It is vitally important to understand the role of receptor elements in arrestin activation and how the interaction of each of these elements with arrestin contributes to the latter’s transition to the high-affinity binding state. A more precise knowledge of the molecular mechanisms of arrestin activation is needed to enable the construction of arrestin mutants with desired functional characteristics.
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7
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van Gastel J, Leysen H, Boddaert J, Vangenechten L, Luttrell LM, Martin B, Maudsley S. Aging-related modifications to G protein-coupled receptor signaling diversity. Pharmacol Ther 2020; 223:107793. [PMID: 33316288 DOI: 10.1016/j.pharmthera.2020.107793] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023]
Abstract
Aging is a highly complex molecular process, affecting nearly all tissue systems in humans and is the highest risk factor in developing neurodegenerative disorders such as Alzheimer's and Parkinson's disease, cardiovascular disease and Type 2 diabetes mellitus. The intense complexity of the aging process creates an incentive to develop more specific drugs that attenuate or even reverse some of the features of premature aging. As our current pharmacopeia is dominated by therapeutics that target members of the G protein-coupled receptor (GPCR) superfamily it may be prudent to search for effective anti-aging therapeutics in this fertile domain. Since the first demonstration of GPCR-based β-arrestin signaling, it has become clear that an enhanced appreciation of GPCR signaling diversity may facilitate the creation of therapeutics with selective signaling activities. Such 'biased' ligand signaling profiles can be effectively investigated using both standard molecular biological techniques as well as high-dimensionality data analyses. Through a more nuanced appreciation of the quantitative nature across the multiple dimensions of signaling bias that drugs possess, researchers may be able to further refine the efficacy of GPCR modulators to impact the complex aberrations that constitute the aging process. Identifying novel effector profiles could expand the effective pharmacopeia and assist in the design of precision medicines. This review discusses potential non-G protein effectors, and specifically their potential therapeutic suitability in aging and age-related disorders.
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Affiliation(s)
- Jaana van Gastel
- Receptor Biology Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Faculty of Pharmacy, Biomedical and Veterinary Science, University of Antwerp, Antwerp, Belgium
| | - Hanne Leysen
- Receptor Biology Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Faculty of Pharmacy, Biomedical and Veterinary Science, University of Antwerp, Antwerp, Belgium
| | - Jan Boddaert
- Molecular Pathology Group, Faculty of Medicine and Health Sciences, Laboratory of Cell Biology and Histology, Antwerp, Belgium
| | - Laura Vangenechten
- Receptor Biology Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Louis M Luttrell
- Division of Endocrinology, Diabetes & Medical Genetics, Medical University of South Carolina, USA
| | - Bronwen Martin
- Faculty of Pharmacy, Biomedical and Veterinary Science, University of Antwerp, Antwerp, Belgium
| | - Stuart Maudsley
- Receptor Biology Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium; Faculty of Pharmacy, Biomedical and Veterinary Science, University of Antwerp, Antwerp, Belgium.
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8
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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.
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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.
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9
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Wingler LM, Skiba MA, McMahon C, Staus DP, Kleinhenz ALW, Suomivuori CM, Latorraca NR, Dror RO, Lefkowitz RJ, Kruse AC. Angiotensin and biased analogs induce structurally distinct active conformations within a GPCR. Science 2020; 367:888-892. [PMID: 32079768 DOI: 10.1126/science.aay9813] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/23/2020] [Indexed: 12/13/2022]
Abstract
Biased agonists of G protein-coupled receptors (GPCRs) preferentially activate a subset of downstream signaling pathways. In this work, we present crystal structures of angiotensin II type 1 receptor (AT1R) (2.7 to 2.9 angstroms) bound to three ligands with divergent bias profiles: the balanced endogenous agonist angiotensin II (AngII) and two strongly β-arrestin-biased analogs. Compared with other ligands, AngII promotes more-substantial rearrangements not only at the bottom of the ligand-binding pocket but also in a key polar network in the receptor core, which forms a sodium-binding site in most GPCRs. Divergences from the family consensus in this region, which appears to act as a biased signaling switch, may predispose the AT1R and certain other GPCRs (such as chemokine receptors) to adopt conformations that are capable of activating β-arrestin but not heterotrimeric Gq protein signaling.
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Affiliation(s)
- Laura M Wingler
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Meredith A Skiba
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Conor McMahon
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Dean P Staus
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Alissa L W Kleinhenz
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA.,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carl-Mikael Suomivuori
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA.,Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Naomi R Latorraca
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA.,Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.,Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Ron O Dror
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA.,Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.,Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.,Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Robert J Lefkowitz
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA. .,Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA.,Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Andrew C Kruse
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
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10
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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.
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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
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12
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Abstract
Spinal projection neurons convey nociceptive signals to multiple brain regions including the parabrachial (PB) nucleus, which contributes to the emotional valence of pain perception. Despite the clear importance of projection neurons to pain processing, our understanding of the factors that shape their intrinsic membrane excitability remains limited. Here, we investigate a potential role for the Na leak channel NALCN in regulating the activity of spino-PB neurons in the developing rodent. Pharmacological reduction of NALCN current (INALCN), or the genetic deletion of NALCN channels, significantly reduced the intrinsic excitability of lamina I spino-PB neurons. In addition, substance P (SP) activated INALCN in ascending projection neurons through downstream Src kinase signaling, and the knockout of NALCN prevented SP-evoked action potential discharge in this neuronal population. These results identify, for the first time, NALCN as a strong regulator of neuronal activity within central pain circuits and also elucidate an additional ionic mechanism by which SP can modulate spinal nociceptive processing. Collectively, these findings indicate that the level of NALCN conductance within spino-PB neurons tightly governs ascending nociceptive transmission to the brain and thereby potentially influences pain perception.
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13
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Chen S, Lu M, Liu D, Yang L, Yi C, Ma L, Zhang H, Liu Q, Frimurer TM, Wang MW, Schwartz TW, Stevens RC, Wu B, Wüthrich K, Zhao Q. Human substance P receptor binding mode of the antagonist drug aprepitant by NMR and crystallography. Nat Commun 2019; 10:638. [PMID: 30733446 PMCID: PMC6367319 DOI: 10.1038/s41467-019-08568-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 01/11/2019] [Indexed: 12/30/2022] Open
Abstract
Neurokinin 1 receptor (NK1R) has key regulating functions in the central and peripheral nervous systems, and NK1R antagonists such as aprepitant have been approved for treating chemotherapy-induced nausea and vomiting. However, the lack of data on NK1R structure and biochemistry has limited further drug development targeting this receptor. Here, we combine NMR spectroscopy and X-ray crystallography to provide dynamic and static characterisation of the binding mode of aprepitant in complexes with human NK1R variants. 19F-NMR showed a slow off-rate in the binding site, where aprepitant occupies multiple substates that exchange with frequencies in the millisecond range. The environment of the bound ligand is affected by the amino acid in position 2.50, which plays a key role in ligand binding and receptor signaling in class A GPCRs. Crystal structures now reveal how receptor signaling relates to the conformation of the conserved NP7.50xxY motif in transmembrane helix VII. The FDA approved drug aprepitant is an antagonist of the Neurokinin 1 receptor (NK1R). Here the authors present aprepitant bound NK1R crystal structures and use NMR spectroscopy to gain further insights into the dynamics of aprepitant binding, which is of interest for further drug development.
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Affiliation(s)
- Shuanghong Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Mengjie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Dongsheng Liu
- iHuman Institute, Shanghai Tech University, 393 Hua Xia Zhong Road, Shanghai, 201210, China
| | - Lingyun Yang
- iHuman Institute, Shanghai Tech University, 393 Hua Xia Zhong Road, Shanghai, 201210, China
| | - Cuiying Yi
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Limin Ma
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hui Zhang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China.,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China
| | - Qing Liu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shou Jing Road, Pudong, Shanghai, 201203, China
| | - Thomas M Frimurer
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3b, Copenhagen, 2200, Denmark
| | - Ming-Wei Wang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China.,The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shou Jing Road, Pudong, Shanghai, 201203, China.,School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai, 201203, China.,School of Life Science and Technology, ShanghaiTech University, 393 Hua Xia Zhong Road, Pudong, Shanghai, 201210, China
| | - Thue W Schwartz
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3b, Copenhagen, 2200, Denmark
| | - Raymond C Stevens
- iHuman Institute, Shanghai Tech University, 393 Hua Xia Zhong Road, Shanghai, 201210, China.,School of Life Science and Technology, ShanghaiTech University, 393 Hua Xia Zhong Road, Pudong, Shanghai, 201210, China
| | - Beili Wu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China. .,School of Life Science and Technology, ShanghaiTech University, 393 Hua Xia Zhong Road, Pudong, Shanghai, 201210, China. .,CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Kurt Wüthrich
- iHuman Institute, Shanghai Tech University, 393 Hua Xia Zhong Road, Shanghai, 201210, China. .,School of Life Science and Technology, ShanghaiTech University, 393 Hua Xia Zhong Road, Pudong, Shanghai, 201210, China. .,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
| | - Qiang Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Pudong, Shanghai, 201203, China. .,CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China. .,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, 100049, China. .,CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China.
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14
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Schöppe J, Ehrenmann J, Klenk C, Rucktooa P, Schütz M, Doré AS, Plückthun A. Crystal structures of the human neurokinin 1 receptor in complex with clinically used antagonists. Nat Commun 2019; 10:17. [PMID: 30604743 PMCID: PMC6318301 DOI: 10.1038/s41467-018-07939-8] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/03/2018] [Indexed: 12/28/2022] Open
Abstract
Neurokinins (or tachykinins) are peptides that modulate a wide variety of human physiology through the neurokinin G protein-coupled receptor family, implicated in a diverse array of pathological processes. Here we report high-resolution crystal structures of the human NK1 receptor (NK1R) bound to two small-molecule antagonist therapeutics – aprepitant and netupitant and the progenitor antagonist CP-99,994. The structures reveal the detailed interactions between clinically approved antagonists and NK1R, which induce a distinct receptor conformation resulting in an interhelical hydrogen-bond network that cross-links the extracellular ends of helices V and VI. Furthermore, the high-resolution details of NK1R bound to netupitant establish a structural rationale for the lack of basal activity in NK1R. Taken together, these co-structures provide a comprehensive structural basis of NK1R antagonism and will facilitate the design of new therapeutics targeting the neurokinin receptor family. Neurokinin receptors are G protein-coupled receptors. Here the authors present three crystal structures of the neurokinin 1 receptor (NK1R) in complex with small-molecule antagonists including aprepitant and netupitant and observe that these clinically approved compounds induce a conformational change in the receptor.
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Affiliation(s)
- Jendrik Schöppe
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Janosch Ehrenmann
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Christoph Klenk
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Prakash Rucktooa
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Marco Schütz
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.,Heptares Therapeutics Zürich AG, Grabenstrasse 11a, 8952, Zürich, Switzerland
| | - Andrew S Doré
- Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, CB21 6DG, UK
| | - Andreas Plückthun
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland.
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15
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Di Pietrantonio C, Pandey A, Gould J, Hasabnis A, Prosser RS. Understanding Protein Function Through an Ensemble Description: Characterization of Functional States by 19F NMR. Methods Enzymol 2019; 615:103-130. [DOI: 10.1016/bs.mie.2018.09.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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16
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Taddese B, Deniaud M, Garnier A, Tiss A, Guissouma H, Abdi H, Henrion D, Chabbert M. Evolution of chemokine receptors is driven by mutations in the sodium binding site. PLoS Comput Biol 2018; 14:e1006209. [PMID: 29912865 PMCID: PMC6037435 DOI: 10.1371/journal.pcbi.1006209] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 07/09/2018] [Accepted: 05/16/2018] [Indexed: 12/22/2022] Open
Abstract
Chemokines and their receptors (members of the GPCR super-family) are involved in a wide variety of physiological processes and diseases; thus, understanding the specificity of the chemokine receptor family could help develop new receptor specific drugs. Here, we explore the evolutionary mechanisms that led to the emergence of the chemokine receptors. Based on GPCR hierarchical classification, we analyzed nested GPCR sets with an eigen decomposition approach of the sequence covariation matrix and determined three key residues whose mutation was crucial for the emergence of the chemokine receptors and their subsequent divergence into homeostatic and inflammatory receptors. These residues are part of the allosteric sodium binding site. Their structural and functional roles were investigated by molecular dynamics simulations of CXCR4 and CCR5 as prototypes of homeostatic and inflammatory chemokine receptors, respectively. This study indicates that the three mutations crucial for the evolution of the chemokine receptors dramatically altered the sodium binding mode. In CXCR4, the sodium ion is tightly bound by four protein atoms and one water molecule. In CCR5, the sodium ion is mobile within the binding pocket and moves between different sites involving from one to three protein atoms and two to five water molecules. Analysis of chemokine receptor evolution reveals that a highly constrained sodium binding site characterized most ancient receptors, and that the constraints were subsequently loosened during the divergence of this receptor family. We discuss the implications of these findings for the evolution of the chemokine receptor functions and mechanisms of action.
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Affiliation(s)
- Bruck Taddese
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Madeline Deniaud
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Antoine Garnier
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Asma Tiss
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
- Laboratoire de Génétique, Immunologie et Pathologies Humaines, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Hajer Guissouma
- Laboratoire de Génétique, Immunologie et Pathologies Humaines, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Hervé Abdi
- The University of Texas at Dallas, School of Behavioral and Brain Sciences, Dallas, Texas, United States of America
| | - Daniel Henrion
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
| | - Marie Chabbert
- Laboratoire MITOVASC, UMR CNRS 6015 – INSERM 1083, Université d’Angers, Angers, France
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17
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Kaiser A, Hempel C, Wanka L, Schubert M, Hamm HE, Beck-Sickinger AG. G Protein Preassembly Rescues Efficacy of W6.48 Toggle Mutations in Neuropeptide Y2 Receptor. Mol Pharmacol 2018; 93:387-401. [DOI: 10.1124/mol.117.110544] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Accepted: 02/02/2018] [Indexed: 12/19/2022] Open
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18
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Evolutionary action and structural basis of the allosteric switch controlling β 2AR functional selectivity. Nat Commun 2017; 8:2169. [PMID: 29255305 PMCID: PMC5735088 DOI: 10.1038/s41467-017-02257-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 11/15/2017] [Indexed: 12/18/2022] Open
Abstract
Functional selectivity of G-protein-coupled receptors is believed to originate from ligand-specific conformations that activate only subsets of signaling effectors. In this study, to identify molecular motifs playing important roles in transducing ligand binding into distinct signaling responses, we combined in silico evolutionary lineage analysis and structure-guided site-directed mutagenesis with large-scale functional signaling characterization and non-negative matrix factorization clustering of signaling profiles. Clustering based on the signaling profiles of 28 variants of the β2-adrenergic receptor reveals three clearly distinct phenotypical clusters, showing selective impairments of either the Gi or βarrestin/endocytosis pathways with no effect on Gs activation. Robustness of the results is confirmed using simulation-based error propagation. The structural changes resulting from functionally biasing mutations centered around the DRY, NPxxY, and PIF motifs, selectively linking these micro-switches to unique signaling profiles. Our data identify different receptor regions that are important for the stabilization of distinct conformations underlying functional selectivity. Ligand-induced biased signaling is thought to result in part from ligand-specific receptor conformations that cause the engagement of distinct effectors. Here the authors trace and evaluate the impact of mutations of the β2–adrenergic receptor on multiple signaling outputs to provide structural-level insight into the determinants of GPCR functional selectivity.
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19
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Montpas N, St-Onge G, Nama N, Rhainds D, Benredjem B, Girard M, Hickson G, Pons V, Heveker N. Ligand-specific conformational transitions and intracellular transport are required for atypical chemokine receptor 3-mediated chemokine scavenging. J Biol Chem 2017; 293:893-905. [PMID: 29180449 PMCID: PMC5777261 DOI: 10.1074/jbc.m117.814947] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 11/20/2017] [Indexed: 11/06/2022] Open
Abstract
The atypical chemokine receptor ACKR3 contributes to chemotaxis by binding, internalizing, and degrading the chemokines CXCL11 and CXCL12 to shape and terminate chemotactic gradients during development and immune responses. Although unable to trigger G protein activation, both ligands activate G protein-independent ACKR3 responses and prompt arrestin recruitment. This offers a model to specifically study ligand-specific receptor conformations leading to G protein-independent signaling and to functional parameters such as receptor transport and chemokine degradation. We here show chemokine specificity in arrestin recruitment, by different effects of single amino acid substitutions in ACKR3 on arrestin in response to CXCL12 or CXCL11. Chemokine specificity in receptor transport was also observed, as CXCL11 induced faster receptor internalization, slower recycling, and longer intracellular sojourn of ACKR3 than CXCL12. Internalization and recycling rates of the ACKR3 R1423.50A substitution in response to each chemokine were similar; however, ACKR3 R1423.50A degraded only CXCL12 and not CXCL11. This suggests that ligand-specific intracellular receptor transport is required for chemokine degradation. Remarkably, the failure of ACKR3 R1423.50A to degrade CXCL11 was not caused by the lack of arrestin recruitment; rather, arrestin was entirely dispensable for scavenging of either chemokine. This suggests the involvement of another, yet unidentified, ACKR3 effector in scavenging. In summary, our study correlates ACKR3 ligand-specific conformational transitions with chemokine-dependent receptor transport dynamics and points toward unexpected ligand specificity in the mechanisms of chemokine degradation.
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Affiliation(s)
- Nicolas Montpas
- From the Department of Biochemistry and Molecular Medicine, University of Montréal, Montréal, Quebec H3T 1J4, Canada.,the Research Centre, Saint-Justine Hospital, University of Montréal, Montréal, Quebec H3T 1C5, Canada
| | - Geneviève St-Onge
- the Research Centre, Saint-Justine Hospital, University of Montréal, Montréal, Quebec H3T 1C5, Canada
| | - Nassr Nama
- From the Department of Biochemistry and Molecular Medicine, University of Montréal, Montréal, Quebec H3T 1J4, Canada.,the Research Centre, Saint-Justine Hospital, University of Montréal, Montréal, Quebec H3T 1C5, Canada
| | - David Rhainds
- From the Department of Biochemistry and Molecular Medicine, University of Montréal, Montréal, Quebec H3T 1J4, Canada.,the Research Centre, Saint-Justine Hospital, University of Montréal, Montréal, Quebec H3T 1C5, Canada
| | - Besma Benredjem
- From the Department of Biochemistry and Molecular Medicine, University of Montréal, Montréal, Quebec H3T 1J4, Canada.,the Research Centre, Saint-Justine Hospital, University of Montréal, Montréal, Quebec H3T 1C5, Canada
| | - Mélanie Girard
- From the Department of Biochemistry and Molecular Medicine, University of Montréal, Montréal, Quebec H3T 1J4, Canada.,the Research Centre, Saint-Justine Hospital, University of Montréal, Montréal, Quebec H3T 1C5, Canada
| | - Gilles Hickson
- the Research Centre, Saint-Justine Hospital, University of Montréal, Montréal, Quebec H3T 1C5, Canada.,the Department of Pathology and Cell Biology, University of Montréal, Montréal, Quebec H3T 1J4, Canada, and
| | - Véronique Pons
- INSERM, UMR 1048, Institut des Maladies Métaboliques et Cardiovasculaires, Université de Toulouse, F-31432 Toulouse, France
| | - Nikolaus Heveker
- From the Department of Biochemistry and Molecular Medicine, University of Montréal, Montréal, Quebec H3T 1J4, Canada, .,the Research Centre, Saint-Justine Hospital, University of Montréal, Montréal, Quebec H3T 1C5, Canada
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20
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Lai JK, Ambia J, Wang Y, Barth P. Enhancing Structure Prediction and Design of Soluble and Membrane Proteins with Explicit Solvent-Protein Interactions. Structure 2017; 25:1758-1770.e8. [PMID: 28966016 PMCID: PMC5909693 DOI: 10.1016/j.str.2017.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/25/2017] [Accepted: 09/01/2017] [Indexed: 11/29/2022]
Abstract
Solvent molecules interact intimately with proteins and can profoundly regulate their structure and function. However, accurately and efficiently modeling protein solvation effects at the molecular level has been challenging. Here, we present a method that improves the atomic-level modeling of soluble and membrane protein structures and binding by efficiently predicting de novo protein-solvent molecule interactions. The method predicted with unprecedented accuracy buried water molecule positions, solvated protein conformations, and challenging mutational effects on protein binding. When applied to homology modeling, solvent-bound membrane protein structures, pockets, and cavities were recapitulated with near-atomic precision even from distant homologs. Blindly refined atomic-level structures of evolutionary distant G protein-coupled receptors imply strikingly different functional roles of buried solvent between receptor classes. The method should prove useful for refining low-resolution protein structures, accurately modeling drug-binding sites in structurally uncharacterized receptors, and designing solvent-mediated protein catalysis, recognition, ligand binding, and membrane protein signaling.
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Affiliation(s)
- Jason K Lai
- Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Joaquin Ambia
- Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Yumeng Wang
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Patrick Barth
- Department of Pharmacology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA; Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA.
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21
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Heterodimerization of the prostaglandin E2 receptor EP2 and the calcitonin receptor CTR. PLoS One 2017; 12:e0187711. [PMID: 29095955 PMCID: PMC5667882 DOI: 10.1371/journal.pone.0187711] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 10/24/2017] [Indexed: 12/14/2022] Open
Abstract
G protein-coupled receptors (GPCRs) have been found to form heterodimers and modulate or fine-tune the functions of GPCRs. However, the involvement of GPCR heterodimerization and its functional consequences in gonadal tissues, including granulosa cells, have been poorly investigated, mainly due to the lack of efficient method for identification of novel GPCR heterodimers. In this paper, we identified a novel GPCR heterodimer between prostaglandin E2 (PGE2) receptor 2 (EP2) and calcitonin (CT) receptor (CTR). High-resolution liquid chromatography (LC)-tandem mass spectrometry (MS/MS) of protease-digested EP2-coimmunoprecipitates detected protein fragments of CTR in an ovarian granulosa cell line, OV3121. Western blotting of EP2- and CTR-coimmunoprecipitates detected a specific band for EP2-CTR heterodimer. Specific heterodimerization between EP2 and CTR was also observed by fluorescence resonance energy transfer analysis in HEK293MSR cells expressing cyan- and yellow-fluorescent protein-fused EP2 and CTR, respectively. Collectively, these results provided evidence for heterodimerization between EP2 and CTR. Moreover, Ca2+ mobilization by CT was approximately 40% less potent in HEK293MSR cells expressing an EP2-CTR heterodimer, whereas cAMP production by EP2 or CT was not significantly altered compared with cells expressing EP2- or CTR alone. These functional analyses verified that CTR-mediated Ca2+ mobilization is specifically decreased via heterodimerization with EP2. Altogether, the present study suggests that a novel GPCR heterodimer, EP2-CTR, is involved in some functional regulation, and paves the way for investigation of novel biological roles of CTR and EP2 in various tissues.
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22
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Evaluation of a melanocortin-4 receptor (MC4R) agonist (Setmelanotide) in MC4R deficiency. Mol Metab 2017; 6:1321-1329. [PMID: 29031731 PMCID: PMC5641599 DOI: 10.1016/j.molmet.2017.06.015] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 06/26/2017] [Accepted: 06/28/2017] [Indexed: 01/08/2023] Open
Abstract
Objective Pro-opiomelanocortin (POMC)-derived peptides act on neurons expressing the Melanocortin 4 receptor (MC4R) to reduce body weight. Setmelanotide is a highly potent MC4R agonist that leads to weight loss in diet-induced obese animals and in obese individuals with complete POMC deficiency. While POMC deficiency is very rare, 1–5% of severely obese individuals harbor heterozygous mutations in MC4R. We sought to assess the efficacy of Setmelanotide in human MC4R deficiency. Methods We studied the effects of Setmelanotide on mutant MC4Rs in cells and the weight loss response to Setmelanotide administration in rodent studies and a human clinical trial. We annotated the functional status of 369 published MC4R variants. Results In cells, we showed that Setmelanotide is significantly more potent at MC4R than the endogenous ligand alpha-melanocyte stimulating hormone and can disproportionally rescue signaling by a subset of severely impaired MC4R mutants. Wild-type rodents appear more sensitive to Setmelanotide when compared to MC4R heterozygous deficient mice, while MC4R knockout mice fail to respond. In a 28-day Phase 1b clinical trial, Setmelanotide led to weight loss in obese MC4R variant carriers. Patients with POMC defects upstream of MC4R show significantly more weight loss with Setmelanotide than MC4R deficient patients or obese controls. Conclusions Setmelanotide led to weight loss in obese people with MC4R deficiency; however, further studies are justified to establish whether Setmelanotide can elicit clinically meaningful weight loss in a subset of the MC4R deficient obese population.
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Abstract
G-protein-coupled receptors (GPCRs) constitute a large group of integral membrane proteins that transduce extracellular signals from a wide range of agonists into targeted intracellular responses. Although the responses can vary depending on the category of G-proteins activated by a particular receptor, responses were also found to be triggered by interactions of the receptor with β-arrestins. It was subsequently discovered that for the same receptor molecule (e.g., the β-adrenergic receptor), some agonists have a propensity to specifically favor responses by G-proteins, others by β-arrestins, as has now been extensively studied. This feature of the GPCR system is known as biased agonism and is subject to various interpretations, including agonist-induced conformational change versus selective stabilization of preexisting active conformations. Here, we explore a complete allosteric framework for biased agonism based on alternative preexisting conformations that bind more strongly, but nonexclusively, either G-proteins or β-arrestins. The framework incorporates reciprocal effects among all interacting molecules. As a result, G-proteins and β-arrestins are in steric competition for binding to the cytoplasmic surface of either the G-protein-favoring or β-arrestin-favoring GPCR conformation. Moreover, through linkage relations, the strength of the interactions of G-proteins or β-arrestins with the corresponding active conformation potentiates the apparent affinity for the agonist, effectively equating these two proteins to allosteric modulators. The balance between response alternatives can also be influenced by the physiological concentrations of either G-proteins or β-arrestins, as well as by phosphorylation or interactions with positive or negative allosteric modulators. The nature of the interactions in the simulations presented suggests novel experimental tests to distinguish more fully among alternative mechanisms.
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24
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Sutcliffe KJ, Henderson G, Kelly E, Sessions RB. Drug Binding Poses Relate Structure with Efficacy in the μ Opioid Receptor. J Mol Biol 2017; 429:1840-1851. [PMID: 28502792 PMCID: PMC5472181 DOI: 10.1016/j.jmb.2017.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 05/07/2017] [Accepted: 05/08/2017] [Indexed: 12/18/2022]
Abstract
The μ-opioid receptor (MOPr) is a clinically important G protein-coupled receptor that couples to Gi/o proteins and arrestins. At present, the receptor conformational changes that occur following agonist binding and activation are poorly understood. This study has employed molecular dynamics simulations to investigate the binding mode and receptor conformational changes induced by structurally similar opioid ligands of widely differing intrinsic agonist efficacy, norbuprenorphine, buprenorphine, and diprenorphine. Bioluminescence resonance energy transfer assays for Gi activation and arrestin-3 recruitment in human embryonic kidney 293 cells confirmed that norbuprenorphine is a high efficacy agonist, buprenorphine a low efficacy agonist, and diprenorphine an antagonist at the MOPr. Molecular dynamics simulations revealed that these ligands adopt distinct binding poses and engage different subsets of residues, despite sharing a common morphinan scaffold. Notably, norbuprenorphine interacted with sodium ion-coordinating residues W2936.48 and N1503.35, whilst buprenorphine and diprenorphine did not. Principal component analysis of the movements of the receptor transmembrane domains showed that the buprenorphine-bound receptor occupied a distinct set of conformations to the norbuprenorphine-bound receptor. Addition of an allosteric sodium ion caused the receptor and ligand to adopt an inactive conformation. The differences in ligand-residue interactions and receptor conformations observed here may underlie the differing efficacies for cellular signalling outputs for these ligands.
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Affiliation(s)
- Katy J Sutcliffe
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol BS8 1TD, UK; School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK.
| | - Graeme Henderson
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol BS8 1TD, UK
| | - Eamonn Kelly
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol BS8 1TD, UK
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25
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Gaieb Z, Lo DD, Morikis D. Molecular Mechanism of Biased Ligand Conformational Changes in CC Chemokine Receptor 7. J Chem Inf Model 2016; 56:1808-22. [PMID: 27529431 DOI: 10.1021/acs.jcim.6b00367] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biased ligand binding to G protein-coupled receptors enables functional selectivity of intracellular effectors to mediate cellular function. Despite the significant advances made in characterizing the conformational states (transmembrane helical arrangements) capable of discriminating between G protein and arrestin binding, the role of the ligand in stabilizing such conformations remains unclear. To address this issue, we simulate microsecond dynamics of CC chemokine receptor 7 (CCR7) bound to its native biased ligands, CCL19 and CCL21, and detect a series of molecular switches that are mediated by various ligand-induced allosteric events. These molecular switches involve three tyrosine residues (Y112(3.32), Y255(6.51), and Y288(7.39)), three phenylalanine residues (F116(3.36), F208(5.47), and F248(6.44)), and a polar interaction between Q252(6.48) and R294(7.45) in the transmembrane domain of CCR7. Conformational changes within these switches, particularly hydrogen bond formation between Y112(3.32) and Y255(6.51), lead to global helical movements in the receptor's transmembrane helices and contribute to the transitioning of the receptor to distinct states. Ligand-induced helical movements in the receptor highlight the ability of biased ligands to stabilize the receptor in different states through a dynamic network of allosteric events.
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Affiliation(s)
- Zied Gaieb
- Department of Bioengineering, ‡Division of Biomedical Sciences, School of Medicine, University of California , Riverside, California 92521, United States
| | - David D Lo
- Department of Bioengineering, ‡Division of Biomedical Sciences, School of Medicine, University of California , Riverside, California 92521, United States
| | - Dimitrios Morikis
- Department of Bioengineering, ‡Division of Biomedical Sciences, School of Medicine, University of California , Riverside, California 92521, United States
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26
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Nederpelt I, Bleeker D, Tuijt B, IJzerman AP, Heitman LH. Kinetic binding and activation profiles of endogenous tachykinins targeting the NK1 receptor. Biochem Pharmacol 2016; 118:88-95. [PMID: 27501920 DOI: 10.1016/j.bcp.2016.08.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/02/2016] [Indexed: 02/01/2023]
Abstract
Ligand-receptor binding kinetics (i.e. association and dissociation rates) are emerging as important parameters for drug efficacy in vivo. Awareness of the kinetic behavior of endogenous ligands is pivotal, as drugs often have to compete with those. The binding kinetics of neurokinin 1 (NK1) receptor antagonists have been widely investigated while binding kinetics of endogenous tachykinins have hardly been reported, if at all. Therefore, the aim of this research was to investigate the binding kinetics of endogenous tachykinins and derivatives thereof and their role in the activation of the NK1 receptor. We determined the binding kinetics of seven tachykinins targeting the NK1 receptor. Dissociation rate constants (koff) ranged from 0.026±0.0029min-1 (Sar9,Met(O2)11-SP) to 0.21±0.015min-1 (septide). Association rate constants (kon) were more diverse: substance P (SP) associated the fastest with a kon value of 0.24±0.046nM-1min-1 while neurokinin A (NKA) had the slowest association rate constant of 0.001±0.0002nM-1min-1. Kinetic binding parameters were highly correlated with potency and maximal response values determined in label-free impedance-based experiments on U-251 MG cells. Our research demonstrates large variations in binding kinetics of tachykinins which correlate to receptor activation. These findings provide new insights into the ligand-receptor interactions of tachykinins and underline the importance of measuring binding kinetics of both drug candidates and competing endogenous ligands.
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Affiliation(s)
- I Nederpelt
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - D Bleeker
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - B Tuijt
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - A P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
| | - L H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research (LACDR), Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
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27
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Jiang Y, Yuan Y, Zhang X, Liang T, Guo Y, Li M, Pu X. Use of network model to explore dynamic and allosteric properties of three GPCR homodimers. RSC Adv 2016. [DOI: 10.1039/c6ra18243g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We used an elastic network model and protein structure network to study three class A GPCR homodimers.
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Affiliation(s)
- Yuanyuan Jiang
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Yuan Yuan
- College of Management
- Southwest University for Nationalities
- Chengdu 610064
- P. R. China
| | - Xi Zhang
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Tao Liang
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Yanzhi Guo
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Menglong Li
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Xumei Pu
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
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