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Mohamud A, Zeghal M, Patel S, Laroche G, Blgacim N, Giguère PM. Functional Characterization of Sodium Channel Inhibitors at the Delta-Opioid Receptor. ACS OMEGA 2022; 7:16939-16951. [PMID: 35647460 PMCID: PMC9134235 DOI: 10.1021/acsomega.1c07226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Existing pharmacotherapies acting on the opioid receptor system have been extensively used to treat chronic pain and addictive disorders. Nevertheless, the adverse side effects associated with opioid therapy underscore the need for concerted measures to develop safer analgesics. A promising avenue of research stems from the characterization of a sodium-dependent allosteric regulation site housed within the delta-opioid receptor and several other G protein-coupled receptors (GPCRs), thereby revealing the presence of a cluster of sodium and water molecules lodged in a cavity thought to be present only in the inactive conformation of the receptor. Studies into the structure-function relationship of said pocket demonstrated its critical involvement in the functional control of GPCR signaling. While the sodium pocket has been proposed to be present in the majority of class A GPCRs, the shape of this allosteric cavity appears to have significant structural variation among crystallographically solved GPCRs, making this site optimal for the design of new allosteric modulators that will be selective for opioid receptors. The size of the sodium pocket supports the accommodation of small molecules, and it has been speculated that promiscuous amiloride and 5'-substituted amiloride-related derivatives could target this cavity within many GPCRs, including opioid receptors. Using pharmacological approaches, we have described the selectivities of 5'-substituted amiloride-related derivatives, as well as the hitherto undescribed activity of the NHE1 inhibitor zoniporide toward class A GPCRs. Our investigations into the structural features of the delta-opioid receptor and its ensuing signaling activities suggest a bitopic mode of overlapping interactions involving the orthosteric site and the juxtaposed Na+ pocket, but only at the active or partially active opioid receptor.
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Affiliation(s)
- Abdulhamid
O. Mohamud
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H8M5, Canada
| | - Manel Zeghal
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H8M5, Canada
| | - Shivani Patel
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H8M5, Canada
| | - Geneviève Laroche
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H8M5, Canada
| | - Nuria Blgacim
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H8M5, Canada
| | - Patrick M. Giguère
- Department
of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON K1H8M5, Canada
- Brain
and Mind Research Institute, University
of Ottawa, Ottawa, ON K1H8M5, Canada
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Massink A, Amelia T, Karamychev A, IJzerman AP. Allosteric modulation of G protein-coupled receptors by amiloride and its derivatives. Perspectives for drug discovery? Med Res Rev 2019; 40:683-708. [PMID: 31495942 PMCID: PMC7028016 DOI: 10.1002/med.21633] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/22/2019] [Accepted: 08/21/2019] [Indexed: 01/09/2023]
Abstract
The function of G protein‐coupled receptors (GPCRs) can be modulated by compounds that bind to other sites than the endogenous orthosteric binding site, so‐called allosteric sites. Structure elucidation of a number of GPCRs has revealed the presence of a sodium ion bound in a conserved allosteric site. The small molecule amiloride and analogs thereof have been proposed to bind in this same sodium ion site. Hence, this review seeks to summarize and reflect on the current knowledge of allosteric effects by amiloride and its analogs on GPCRs. Amiloride is known to modulate adenosine, adrenergic, dopamine, chemokine, muscarinic, serotonin, gonadotropin‐releasing hormone, GABAB, and taste receptors. Amiloride analogs with lipophilic substituents tend to be more potent modulators than amiloride itself. Adenosine, α‐adrenergic and dopamine receptors are most strongly modulated by amiloride analogs. In addition, for a few GPCRs, more than one binding site for amiloride has been postulated. Interestingly, the nature of the allosteric effect of amiloride and derivatives varies considerably between GPCRs, with both negative and positive allosteric modulation occurring. Since the sodium ion binding site is strongly conserved among class A GPCRs it is to be expected that amiloride also binds to class A GPCRs not evaluated yet. Investigating this typical amiloride‐GPCR interaction further may yield general insight in the allosteric mechanisms of GPCR ligand binding and function, and possibly provide new opportunities for drug discovery.
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Affiliation(s)
- Arnault Massink
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Tasia Amelia
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Alex Karamychev
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
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Massink A, Gutiérrez-de-Terán H, Lenselink EB, Ortiz Zacarías NV, Xia L, Heitman LH, Katritch V, Stevens RC, IJzerman AP. Sodium ion binding pocket mutations and adenosine A2A receptor function. Mol Pharmacol 2014; 87:305-13. [PMID: 25473121 DOI: 10.1124/mol.114.095737] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Recently we identified a sodium ion binding pocket in a high-resolution structure of the human adenosine A2A receptor. In the present study we explored this binding site through site-directed mutagenesis and molecular dynamics simulations. Amino acids in the pocket were mutated to alanine, and their influence on agonist and antagonist affinity, allosterism by sodium ions and amilorides, and receptor functionality was explored. Mutation of the polar residues in the Na(+) pocket were shown to either abrogate (D52A(2.50) and N284A(7.49)) or reduce (S91A(3.39), W246A(6.48), and N280A(7.45)) the negative allosteric effect of sodium ions on agonist binding. Mutations D52A(2.50) and N284A(7.49) completely abolished receptor signaling, whereas mutations S91A(3.39) and N280A(7.45) elevated basal activity and mutations S91A(3.39), W246A(6.48), and N280A(7.45) decreased agonist-stimulated receptor signaling. In molecular dynamics simulations D52A(2.50) directly affected the mobility of sodium ions, which readily migrated to another pocket formed by Glu13(1.39) and His278(7.43). The D52A(2.50) mutation also decreased the potency of amiloride with respect to ligand displacement but did not change orthosteric ligand affinity. In contrast, W246A(6.48) increased some of the allosteric effects of sodium ions and amiloride, whereas orthosteric ligand binding was decreased. These new findings suggest that the sodium ion in the allosteric binding pocket not only impacts ligand affinity but also plays a vital role in receptor signaling. Because the sodium ion binding pocket is highly conserved in other class A G protein-coupled receptors, our findings may have a general relevance for these receptors and may guide the design of novel synthetic allosteric modulators or bitopic ligands.
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Affiliation(s)
- Arnault Massink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Hugo Gutiérrez-de-Terán
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Eelke B Lenselink
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Natalia V Ortiz Zacarías
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Lizi Xia
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Vsevolod Katritch
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Raymond C Stevens
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands (A.M., E.B.L., N.V.O.Z., L.X., L.H.H., A.P.IJ.); Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden (H.G.T.); and Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California (V.K., R.C.S.)
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Ranganathan A, Dror RO, Carlsson J. Insights into the Role of Asp792.50 in β2 Adrenergic Receptor Activation from Molecular Dynamics Simulations. Biochemistry 2014; 53:7283-96. [DOI: 10.1021/bi5008723] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Anirudh Ranganathan
- Science for Life Laboratory, Box 1031, SE-171 21 Solna, Sweden
- Department
of Biochemistry and Biophysics and Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ron O. Dror
- Department
of Computer Science, Department of Molecular and Cellular Physiology,
and Institute for Computational and Mathematical Engineering, Stanford University, Stanford, California 94305, United States
| | - Jens Carlsson
- Science for Life Laboratory, Box 1031, SE-171 21 Solna, Sweden
- Department
of Biochemistry and Biophysics and Center for Biomembrane Research, Stockholm University, SE-106 91 Stockholm, Sweden
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Katritch V, Cherezov V, Stevens RC. Structure-function of the G protein-coupled receptor superfamily. Annu Rev Pharmacol Toxicol 2012; 53:531-56. [PMID: 23140243 DOI: 10.1146/annurev-pharmtox-032112-135923] [Citation(s) in RCA: 783] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
During the past few years, crystallography of G protein-coupled receptors (GPCRs) has experienced exponential growth, resulting in the determination of the structures of 16 distinct receptors-9 of them in 2012 alone. Including closely related subtype homology models, this coverage amounts to approximately 12% of the human GPCR superfamily. The adrenergic, rhodopsin, and adenosine receptor systems are also described by agonist-bound active-state structures, including a structure of the receptor-G protein complex for the β(2)-adrenergic receptor. Biochemical and biophysical techniques, such as nuclear magnetic resonance and hydrogen-deuterium exchange coupled with mass spectrometry, are providing complementary insights into ligand-dependent dynamic equilibrium between different functional states. Additional details revealed by high-resolution structures illustrate the receptors as allosteric machines that are controlled not only by ligands but also by ions, lipids, cholesterol, and water. This wealth of data is helping redefine our knowledge of how GPCRs recognize such a diverse array of ligands and how they transmit signals 30 angstroms across the cell membrane; it also is shedding light on a structural basis of GPCR allosteric modulation and biased signaling.
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Affiliation(s)
- Vsevolod Katritch
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA
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Liu W, Chun E, Thompson AA, Chubukov P, Xu F, Katritch V, Han GW, Roth CB, Heitman LH, IJzerman AP, Cherezov V, Stevens RC. Structural basis for allosteric regulation of GPCRs by sodium ions. Science 2012; 337:232-6. [PMID: 22798613 DOI: 10.1126/science.1219218] [Citation(s) in RCA: 746] [Impact Index Per Article: 62.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Pharmacological responses of G protein-coupled receptors (GPCRs) can be fine-tuned by allosteric modulators. Structural studies of such effects have been limited due to the medium resolution of GPCR structures. We reengineered the human A(2A) adenosine receptor by replacing its third intracellular loop with apocytochrome b(562)RIL and solved the structure at 1.8 angstrom resolution. The high-resolution structure allowed us to identify 57 ordered water molecules inside the receptor comprising three major clusters. The central cluster harbors a putative sodium ion bound to the highly conserved aspartate residue Asp(2.50). Additionally, two cholesterols stabilize the conformation of helix VI, and one of 23 ordered lipids intercalates inside the ligand-binding pocket. These high-resolution details shed light on the potential role of structured water molecules, sodium ions, and lipids/cholesterol in GPCR stabilization and function.
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Affiliation(s)
- Wei Liu
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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Gottlieb A, Olender T, Lancet D, Horn D. Common peptides shed light on evolution of Olfactory Receptors. BMC Evol Biol 2009; 9:91. [PMID: 19416542 PMCID: PMC2681464 DOI: 10.1186/1471-2148-9-91] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2008] [Accepted: 05/05/2009] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Olfactory Receptors (ORs) form the largest multigene family in vertebrates. Their evolution and their expansion in the vertebrate genomes was the subject of many studies. In this paper we apply a motif-based approach to this problem in order to uncover evolutionary characteristics. RESULTS We extract deterministic motifs from ORs belonging to ten species using the MEX (Motif Extraction) algorithm, thus defining Common Peptides (CPs) characteristic to ORs. We identify species-specific CPs and show that their relative abundance is high only in fish and frog, suggesting relevance to water-soluble odorants. We estimate the origins of CPs according to the tree of life and track the gains and losses of CPs through evolution. We identify major CP gain in tetrapods and major losses in reptiles. Although the number of human ORs is less than half of the number of ORs in other mammals, the fraction of lost CPs is only 11%.By examining the positions of CPs along the OR sequence, we find two regions that expanded only in tetrapods. Using CPs we are able to establish remote homology relations between ORs and non-OR GPCRs.Selecting CPs according to their evolutionary age, we bicluster ORs and CPs for each species. Clean biclustering emerges when using relatively novel CPs. Evolutionary age is used to track the history of CP acquisition in the collection of mammalian OR families within HORDE (Human Olfactory Receptor Data Explorer). CONCLUSION The CP method provides a novel perspective that reveals interesting traits in the evolution of olfactory receptors. It is consistent with previous knowledge, and provides finer details. Using available phylogenetic trees, evolution can be rephrased in terms of CP origins.
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Affiliation(s)
- Assaf Gottlieb
- School of Physics and Astronomy, Tel Aviv University, Tel Aviv, Israel.
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