151
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Flaumenhaft R, De Ceunynck K. Targeting PAR1: Now What? Trends Pharmacol Sci 2017; 38:701-716. [PMID: 28558960 PMCID: PMC5580498 DOI: 10.1016/j.tips.2017.05.001] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2017] [Revised: 05/01/2017] [Accepted: 05/04/2017] [Indexed: 12/30/2022]
Abstract
Protease-activated receptors (PARs) are a ubiquitously expressed class of G-protein-coupled receptors (GPCRs) that enable cells to respond to proteases in the extracellular environment in a nuanced and dynamic manner. PAR1 is the archetypal family member and has been the object of large-scale drug development programs since the 1990s. Vorapaxar and drotrecogin-alfa are approved PAR1-targeted therapeutics, but safety concerns have limited the clinical use of vorapaxar and questions regarding the efficacy of drotrecogin-alfa led to its withdrawal from the market. New understanding of mechanisms of PAR1 function, discovery of improved strategies for modifying PAR1 function, and identification of novel indications for PAR1 modulators have provided new opportunities for therapies targeting PAR1. In this review, we critically evaluate prospects for the next generation of PAR1-targeted therapeutics.
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Affiliation(s)
- Robert Flaumenhaft
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA.
| | - Karen De Ceunynck
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
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152
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Structures of Human A 1 and A 2A Adenosine Receptors with Xanthines Reveal Determinants of Selectivity. Structure 2017; 25:1275-1285.e4. [DOI: 10.1016/j.str.2017.06.012] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 04/13/2017] [Accepted: 06/15/2017] [Indexed: 01/06/2023]
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153
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Lee Y, Basith S, Choi S. Recent Advances in Structure-Based Drug Design Targeting Class A G Protein-Coupled Receptors Utilizing Crystal Structures and Computational Simulations. J Med Chem 2017; 61:1-46. [PMID: 28657745 DOI: 10.1021/acs.jmedchem.6b01453] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) represent the largest and most physiologically important integral membrane protein family, and these receptors respond to a wide variety of physiological and environmental stimuli. GPCRs are among the most critical therapeutic targets for numerous human diseases, and approximately one-third of the currently marketed drugs target this receptor family. The recent breakthroughs in GPCR structural biology have significantly contributed to our understanding of GPCR function, ligand binding, and pharmacological action as well as to the design of new drugs. This perspective highlights the latest advances in GPCR structures with a focus on the receptor-ligand interactions of each receptor family in class A nonrhodopsin GPCRs as well as the structural features for their activation, biased signaling, and allosteric mechanisms. The current state-of-the-art methodologies of structure-based drug design (SBDD) approaches in the GPCR research field are also discussed.
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Affiliation(s)
- Yoonji Lee
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Shaherin Basith
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Sun Choi
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
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154
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Strege A, Carpenter B, Edwards PC, Tate CG. Strategy for the Thermostabilization of an Agonist-Bound GPCR Coupled to a G Protein. Methods Enzymol 2017; 594:243-264. [PMID: 28779842 DOI: 10.1016/bs.mie.2017.05.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Structure determination of G protein-coupled receptors (GPCRs) in the inactive state bound to high-affinity antagonists has been very successful through the implementation of a number of protein engineering and crystallization strategies. However, the structure determination of GPCRs in their fully active state coupled to a G protein is still very challenging. Recently, mini-G proteins were developed, which recapitulate the coupling of a full heterotrimeric G protein to a GPCR despite being less than one-third of the size. This allowed the structure determination of the agonist-bound adenosine A2A receptor (A2AR) coupled to mini-Gs. Although this is extremely encouraging, A2AR is very stable compared with many other GPCRs, particularly when an agonist is bound. In contrast, the agonist-bound conformation of the human corticotropin-releasing factor receptor is considerably less stable, impeding the formation of good quality crystals for structure determination. We have therefore developed a novel strategy for the thermostabilization of a GPCR-mini-G protein complex. In this chapter, we will describe the theoretical and practical principles of the thermostability assay for stabilizing this complex, discuss its strengths and weaknesses, and show some typical results from the thermostabilization process.
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Affiliation(s)
- Annette Strege
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Byron Carpenter
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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155
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Sayama M, Inoue A, Nakamura S, Jung S, Ikubo M, Otani Y, Uwamizu A, Kishi T, Makide K, Aoki J, Hirokawa T, Ohwada T. Probing the Hydrophobic Binding Pocket of G-Protein-Coupled Lysophosphatidylserine Receptor GPR34/LPS 1 by Docking-Aided Structure-Activity Analysis. J Med Chem 2017; 60:6384-6399. [PMID: 28715213 DOI: 10.1021/acs.jmedchem.7b00693] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The ligands of certain G-protein-coupled receptors (GPCRs) have been identified as endogenous lipids, such as lysophosphatidylserine (LysoPS). Here, we analyzed the molecular basis of the structure-activity relationship of ligands of GPR34, one of the LysoPS receptor subtypes, focusing on recognition of the long-chain fatty acid moiety by the hydrophobic pocket. By introducing benzene ring(s) into the fatty acid moiety of 2-deoxy-LysoPS, we explored the binding site's preference for the hydrophobic shape. A tribenzene-containing fatty acid surrogate with modifications of the terminal aromatic moiety showed potent agonistic activity toward GPR34. Computational docking of these derivatives with a homology modeling/molecular dynamics-based virtual binding site of GPR34 indicated that a kink in the benzene-based lipid surrogates matches the L-shaped hydrophobic pocket of GPR34. A tetrabenzene-based lipid analogue bearing a bulky tert-butyl group at the 4-position of the terminal benzene ring exhibited potent GPR34 agonistic activity, validating the present hydrophobic binding pocket model.
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Affiliation(s)
- Misa Sayama
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Asuka Inoue
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University , 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan.,PRESTO, Japan Science and Technology Agency (JST) , 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Sho Nakamura
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Sejin Jung
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masaya Ikubo
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuko Otani
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akiharu Uwamizu
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University , 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Takayuki Kishi
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University , 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Kumiko Makide
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University , 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan.,PRESTO, Japan Science and Technology Agency (JST) , 4-1-8, Honcho, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Junken Aoki
- Laboratory of Molecular and Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Tohoku University , 6-3, Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8578, Japan.,AMED-CREST, Japan Agency for Medical Research and Development , 1-7-1 Otemachi, Chiyoda-ku, Tokyo 100-0004, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center of Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST) , 2-3-26 Aomi, Koto-ku, Tokyo 135-0064, Japan.,Division of Biomedical Science, Faculty of Medicine, University of Tsukuba , 1-1-1 Tennodai, Tsukuba-shi, Ibaraki 305-8575, Japan
| | - Tomohiko Ohwada
- Laboratory of Organic and Medicinal Chemistry, Graduate School of Pharmaceutical Sciences, The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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156
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Bartuzi D, Kaczor AA, Matosiuk D. Signaling within Allosteric Machines: Signal Transmission Pathways Inside G Protein-Coupled Receptors. Molecules 2017; 22:molecules22071188. [PMID: 28714871 PMCID: PMC6152049 DOI: 10.3390/molecules22071188] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 07/04/2017] [Accepted: 07/10/2017] [Indexed: 11/16/2022] Open
Abstract
In recent years, our understanding of function of G protein-coupled receptors (GPCRs) has changed from a picture of simple signal relays, transmitting only a particular signal to a particular G protein heterotrimer, to versatile machines, capable of various responses to different stimuli and being modulated by various factors. Some recent reports provide not only the data on ligands/modulators and resultant signals induced by them, but also deeper insights into exact pathways of signal migration and mechanisms of signal transmission through receptor structure. Combination of these computational and experimental data sheds more light on underlying mechanisms of signal transmission and signaling bias in GPCRs. In this review we focus on available clues on allosteric pathways responsible for complex signal processing within GPCRs structures, with particular emphasis on linking compatible in silico- and in vitro-derived data on the most probable allosteric connections.
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Affiliation(s)
- Damian Bartuzi
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., Lublin PL20093, Poland.
| | - Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., Lublin PL20093, Poland.
- School of Pharmacy, University of Eastern Finland, Yliopistonranta 1, P.O. Box 1627, Kuopio FI-70211, Finland.
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modelling Lab, Medical University of Lublin, 4A Chodźki Str., Lublin PL20093, Poland.
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157
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Abstract
The Reggio group has constructed computer models of the inactive and G-protein-activated states of the cannabinoid CB1 and CB2 receptors, as well as, several orphan receptors that recognize a subset of cannabinoid compounds, including GPR55 and GPR18. These models have been used to design ligands, mutations, and covalent labeling studies. The resultant second-generation models have been used to design ligands with improved affinity, efficacy, and subtype selectivity. Herein, we provide a guide for the development of GPCR models using the most recent orphan receptor studied in our lab, GPR3. GPR3 is an orphan receptor that belongs to the Class A family of G-protein-coupled receptors. It shares high sequence similarity with GPR6, GPR12, the lysophospholipid receptors, and the cannabinoid receptors. GPR3 is predominantly expressed in mammalian brain and oocytes and it is known as a Gαs-coupled receptor activated constitutively in cells. GPR3 represents a possible target for the treatment of different pathological conditions such as Alzheimer's disease, oocyte maturation, or neuropathic pain. However, the lack of potent and selective GPR3 ligands is delaying the exploitation of this promising therapeutic target. In this context, we aim to develop a homology model that helps us to elucidate the structural determinants governing ligand-receptor interactions at GPR3. In this chapter, we detail the methods and rationale behind the construction of the GPR3 active-and inactive-state models. These homology models will enable the rational design of novel ligands, which may serve as research tools for further understanding of the biological role of GPR3.
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Affiliation(s)
- Paula Morales
- University of North Carolina at Greensboro, Greensboro, NC, United States.
| | - Dow P Hurst
- University of North Carolina at Greensboro, Greensboro, NC, United States
| | - Patricia H Reggio
- University of North Carolina at Greensboro, Greensboro, NC, United States
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158
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Structure and Function of Peptide-Binding G Protein-Coupled Receptors. J Mol Biol 2017; 429:2726-2745. [PMID: 28705763 DOI: 10.1016/j.jmb.2017.06.022] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors and are important human drug targets. Of the 826 human GPCRs, 118 of them recognize endogenous peptide or protein ligands, and 30 of the 118 are targeted by approved drug molecules, including the very high-profile class B glucagon-like peptide 1 receptor. In this review, we analyze the 21 experimentally determined three-dimensional structures of the known peptide-binding GPCRs in relation to the endogenous peptides and drug molecules that modulate their cell signaling processes. Our integrated analyses reveal that half of the marketed drugs and most of the drugs in clinical trials that interact with peptide GPCRs are small molecules with a wide range of binding modes distinct from those of large peptide ligands. As we continue to collect additional data on these receptors from orthogonal approaches, including nuclear magnetic resonance and electron microscopy, we are beginning to understand how these receptors interact with their ligands at the molecular level and how improving the pharmacology of GPCR signal transduction requires us to study these receptors using multiple biophysical techniques.
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159
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Woolley MJ, Conner AC. Understanding the common themes and diverse roles of the second extracellular loop (ECL2) of the GPCR super-family. Mol Cell Endocrinol 2017; 449:3-11. [PMID: 27899324 DOI: 10.1016/j.mce.2016.11.023] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/02/2016] [Accepted: 11/24/2016] [Indexed: 11/16/2022]
Abstract
The extracellular loops (ECLs) of G protein-coupled receptors (GPCRs) can bind directly to docked orthosteric or allosteric ligands, they can contain transient contact points for ligand entry into the transmembrane (TM) bundle and they can regulate the activation of the receptor signalling pathways. Of the three ECLs, ECL2 is the largest and most structurally diverse reflecting its functional importance. This has been shown through biochemical techniques and has been supported by the many subsequent crystal structures of GPCRs bound to both agonists and antagonists. ECL2 shares common structural features between (and sometimes across) receptor sub-families and can facilitate ligand entry to the TM core or act directly as a surface of the ligand-binding pocket. Structural similarities seem to underpin common binding mechanisms; however, where these exist, variations in primary sequence ensure ligand-binding specificity. This review will compare current understanding of the structural themes and main functional roles of ECL2 in ligand binding, activation and regulation of the major families of GPCRs.
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Affiliation(s)
- Michael J Woolley
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Alex C Conner
- Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham, UK.
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160
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Muscarinic receptor regulates extracellular signal regulated kinase by two modes of arrestin binding. Proc Natl Acad Sci U S A 2017; 114:E5579-E5588. [PMID: 28652372 DOI: 10.1073/pnas.1700331114] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Binding of agonists to G-protein-coupled receptors (GPCRs) activates heterotrimeric G proteins and downstream signaling. Agonist-bound GPCRs are then phosphorylated by protein kinases and bound by arrestin to trigger desensitization and endocytosis. Arrestin plays another important signaling function. It recruits and regulates activity of an extracellular signal-regulated kinase (ERK) cascade. However, molecular details and timing of ERK activation remain fundamental unanswered questions that limit understanding of how arrestin-dependent GPCR signaling controls cell functions. Here we validate and model a system that tracks the dynamics of interactions of arrestin with receptors and of ERK activation using optical reporters. Our intermolecular FRET measurements in living cells are consistent with β-arrestin binding to M1 muscarinic acetylcholine receptors (M1Rs) in two different binding modes, transient and stable. The stable mode persists for minutes after agonist removal. The choice of mode is governed by phosphorylation on key residues in the third intracellular loop of the receptor. We detect a similar intramolecular conformational change in arrestin in either binding mode. It develops within seconds of arrestin binding to the M1 receptor, and it reverses within seconds of arrestin unbinding from the transient binding mode. Furthermore, we observed that, when stably bound to phosphorylated M1R, β-arrestin scaffolds and activates MEK-dependent ERK. In contrast, when transiently bound, β-arrestin reduces ERK activity via recruitment of a protein phosphatase. All this ERK signaling develops at the plasma membrane. In this scaffolding hypothesis, a shifting balance between the two arrestin binding modes determines the degree of ERK activation at the membrane.
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161
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Distinct activation modes of the Relaxin Family Peptide Receptor 2 in response to insulin-like peptide 3 and relaxin. Sci Rep 2017; 7:3294. [PMID: 28607406 PMCID: PMC5468325 DOI: 10.1038/s41598-017-03638-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/02/2017] [Indexed: 11/16/2022] Open
Abstract
Relaxin family peptide receptor 2 (RXFP2) is a GPCR known for its role in reproductive function. It is structurally related to the human relaxin receptor RXFP1 and can be activated by human gene-2 (H2) relaxin as well as its cognate ligand insulin-like peptide 3 (INSL3). Both receptors possess an N-terminal low-density lipoprotein type a (LDLa) module that is necessary for activation and is joined to a leucine-rich repeat domain by a linker. This linker has been shown to be important for H2 relaxin binding and activation of RXFP1 and herein we investigate the role of the equivalent region of RXFP2. We demonstrate that the linker’s highly-conserved N-terminal region is essential for activation of RXFP2 in response to both ligands. In contrast, the linker is necessary for H2 relaxin, but not INSL3, binding. Our results highlight the distinct mechanism by which INSL3 activates RXFP2 whereby ligand binding mediates reorientation of the LDLa module by the linker region to activate the RXFP2 transmembrane domains in conjunction with the INSL3 A-chain. In contrast, relaxin activation of RXFP2 involves a more RXFP1-like mechanism involving binding to the LDLa-linker, reorientation of the LDLa module and activation of the transmembrane domains by the LDLa alone.
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162
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A cluster of aspartic residues in the extracellular loop II of PAR 4 is important for thrombin interaction and activation of platelets. Thromb Res 2017; 154:84-92. [DOI: 10.1016/j.thromres.2017.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/29/2017] [Accepted: 04/10/2017] [Indexed: 12/25/2022]
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163
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Cheng RKY, Fiez-Vandal C, Schlenker O, Edman K, Aggeler B, Brown DG, Brown GA, Cooke RM, Dumelin CE, Doré AS, Geschwindner S, Grebner C, Hermansson NO, Jazayeri A, Johansson P, Leong L, Prihandoko R, Rappas M, Soutter H, Snijder A, Sundström L, Tehan B, Thornton P, Troast D, Wiggin G, Zhukov A, Marshall FH, Dekker N. Structural insight into allosteric modulation of protease-activated receptor 2. Nature 2017. [PMID: 28445455 DOI: 10.1038/nature2230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Protease-activated receptors (PARs) are a family of G-protein-coupled receptors (GPCRs) that are irreversibly activated by proteolytic cleavage of the N terminus, which unmasks a tethered peptide ligand that binds and activates the transmembrane receptor domain, eliciting a cellular cascade in response to inflammatory signals and other stimuli. PARs are implicated in a wide range of diseases, such as cancer and inflammation. PARs have been the subject of major pharmaceutical research efforts but the discovery of small-molecule antagonists that effectively bind them has proved challenging. The only marketed drug targeting a PAR is vorapaxar, a selective antagonist of PAR1 used to prevent thrombosis. The structure of PAR1 in complex with vorapaxar has been reported previously. Despite sequence homology across the PAR isoforms, discovery of PAR2 antagonists has been less successful, although GB88 has been described as a weak antagonist. Here we report crystal structures of PAR2 in complex with two distinct antagonists and a blocking antibody. The antagonist AZ8838 binds in a fully occluded pocket near the extracellular surface. Functional and binding studies reveal that AZ8838 exhibits slow binding kinetics, which is an attractive feature for a PAR2 antagonist competing against a tethered ligand. Antagonist AZ3451 binds to a remote allosteric site outside the helical bundle. We propose that antagonist binding prevents structural rearrangements required for receptor activation and signalling. We also show that a blocking antibody antigen-binding fragment binds to the extracellular surface of PAR2, preventing access of the tethered ligand to the peptide-binding site. These structures provide a basis for the development of selective PAR2 antagonists for a range of therapeutic uses.
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Affiliation(s)
- Robert K Y Cheng
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Cédric Fiez-Vandal
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Oliver Schlenker
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Karl Edman
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Birte Aggeler
- Bio-techne, 614 McKinley Place NE, Minneapolis, Minnesota 55413, USA
| | - Dean G Brown
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, 35 Gatehouse Dr, Waltham, Massachusetts 02451, USA
| | - Giles A Brown
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Robert M Cooke
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | | | - Andrew S Doré
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Stefan Geschwindner
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Christoph Grebner
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Nils-Olov Hermansson
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Ali Jazayeri
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Patrik Johansson
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Louis Leong
- Bio-techne, 614 McKinley Place NE, Minneapolis, Minnesota 55413, USA
| | - Rudi Prihandoko
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Mathieu Rappas
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Holly Soutter
- X-Chem Inc., 100 Beaver St., Waltham, Massachusetts 02453, USA
| | - Arjan Snijder
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Linda Sundström
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Benjamin Tehan
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Peter Thornton
- Neuroscience, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Granta Park, Cambridge CB21 6GH, UK
| | - Dawn Troast
- X-Chem Inc., 100 Beaver St., Waltham, Massachusetts 02453, USA
| | - Giselle Wiggin
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Andrei Zhukov
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Fiona H Marshall
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Niek Dekker
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Pepparedsleden 1, 431 83 Mölndal, Sweden
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164
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Structural insight into allosteric modulation of protease-activated receptor 2. Nature 2017; 545:112-115. [DOI: 10.1038/nature22309] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 03/28/2017] [Indexed: 02/06/2023]
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165
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Pappalardo M, Rayan M, Abu-Lafi S, Leonardi ME, Milardi D, Guccione S, Rayan A. Homology-based Modeling of Rhodopsin-like Family Members in the Inactive State: Structural Analysis and Deduction of Tips for Modeling and Optimization. Mol Inform 2017; 36. [PMID: 28375549 DOI: 10.1002/minf.201700014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/14/2017] [Indexed: 12/12/2022]
Abstract
Modeling G-Protein Coupled Receptors (GPCRs) is an emergent field of research, since utility of high-quality models in receptor structure-based strategies might facilitate the discovery of interesting drug candidates. The findings from a quantitative analysis of eighteen resolved structures of rhodopsin family "A" receptors crystallized with antagonists and 153 pairs of structures are described. A strategy termed endeca-amino acids fragmentation was used to analyze the structures models aiming to detect the relationship between sequence identity and Root Mean Square Deviation (RMSD) at each trans-membrane-domain. Moreover, we have applied the leave-one-out strategy to study the shiftiness likelihood of the helices. The type of correlation between sequence identity and RMSD was studied using the aforementioned set receptors as representatives of membrane proteins and 98 serine proteases with 4753 pairs of structures as representatives of globular proteins. Data analysis using fragmentation strategy revealed that there is some extent of correlation between sequence identity and global RMSD of 11AA width windows. However, spatial conservation is not always close to the endoplasmic side as was reported before. A comparative study with globular proteins shows that GPCRs have higher standard deviation and higher slope in the graph with correlation between sequence identity and RMSD. The extracted information disclosed in this paper could be incorporated in the modeling protocols while using technique for model optimization and refinement.
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Affiliation(s)
- Matteo Pappalardo
- Department of Drug Sciences.,Department of Chemical Sciences -, University of Catania -, V.le A.Doria 6, I-95125, Catania, Italy
| | - Mahmoud Rayan
- Institute of Applied Research - Galilee Society, Galeel street, Shefa-Amr, 20200, Israel
| | - Saleh Abu-Lafi
- Faculty of Pharmacy, Al-Quds University, Abu-Dies, Palestine
| | | | - Danilo Milardi
- National Research Council, Institute of Biostructures and Bioimages, Via. P. Gaifami 18, 95126, Catania, Italy
| | | | - Anwar Rayan
- Institute of Applied Research - Galilee Society, Galeel street, Shefa-Amr, 20200, Israel.,Drug Discovery Informatics Lab, Qasemi-Research Center, Al-Qasemi Academic College, Baka El-Garbiah, 30100, Israel
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166
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Boura E, Baumlova A, Chalupska D, Dubankova A, Klima M. Metal ions-binding T4 lysozyme as an intramolecular protein purification tag compatible with X-ray crystallography. Protein Sci 2017; 26:1116-1123. [PMID: 28342173 DOI: 10.1002/pro.3162] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/17/2017] [Indexed: 11/08/2022]
Abstract
Phage T4 lysozyme is a well folded and highly soluble protein that is widely used as an insertion tag to improve solubility and crystallization properties of poorly behaved recombinant proteins. It has been used in the fusion protein strategy to facilitate crystallization of various proteins including multiple G protein-coupled receptors, lipid kinases, or sterol binding proteins. Here, we present a structural and biochemical characterization of its novel, metal ions-binding mutant (mbT4L). We demonstrate that mbT4L can be used as a purification tag in the immobilized-metal affinity chromatography and that, in many respects, it is superior to the conventional hexahistidine tag. In addition, structural characterization of mbT4L suggests that mbT4L can be used as a purification tag compatible with X-ray crystallography.
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Affiliation(s)
- Evzen Boura
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Adriana Baumlova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Dominika Chalupska
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Anna Dubankova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
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167
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Waasdorp M, Duitman J, Spek CA. Plasmin reduces fibronectin deposition by mesangial cells in a protease-activated receptor-1 independent manner. Biochem Biophys Rep 2017; 10:152-156. [PMID: 29114573 PMCID: PMC5637235 DOI: 10.1016/j.bbrep.2017.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/17/2017] [Accepted: 03/28/2017] [Indexed: 12/31/2022] Open
Abstract
Background Protease-activated receptor-1 (PAR-1) potentiates diabetic nephropathy (DN) as evident from reduced kidney injury in diabetic PAR-1 deficient mice. Although thrombin is the prototypical PAR-1 agonist, anticoagulant treatment does not limit DN in experimental animal models suggesting that thrombin is not the endogenous PAR-1 agonist driving DN. Objectives To identify the endogenous PAR-1 agonist potentiating diabetes-induced nephropathy. Methods Unbiased protease expression profiling in glomeruli from human kidneys with DN was performed using publically available microarray data. The identified prime candidate PAR-1 agonist was subsequently analysed for PAR-1-dependent induction of fibrosis in vitro. Results Of the 553 proteases expressed in the human genome, 247 qualified as potential PAR-1 agonists of which 71 were significantly expressed above background in diabetic glomeruli. The recently identified PAR-1 agonist plasmin(ogen), together with its physiological activator tissue plasminogen activator, were among the highest expressed proteases. Plasmin did however not induce mesangial proliferation and/or fibronectin deposition in vitro. In a PAR-1 independent manner, plasmin even reduced fibronectin deposition. Conclusion Expression profiling identified plasmin as potential endogenous PAR-1 agonist driving DN. Instead of inducing fibronectin expression, plasmin however reduced mesangial fibronectin deposition in vitro. Therefore we conclude that plasmin may not be the endogenous PAR-1 agonist potentiating DN. Plasmin is highly expressed in kidneys of diabetic nephropathy patients. Plasmin limits fibronectin deposition by mesangial cells. Plasmin-dependent PAR-1 activation does not drive diabetic nephropathy.
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Affiliation(s)
- Maaike Waasdorp
- Center for Experimental and Molecular Medicine, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands
| | - JanWillem Duitman
- Center for Experimental and Molecular Medicine, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands.,INSERM, UMR1152, Medical School Xavier Bichat, Paris, France.,Paris Diderot University, Sorbonne Paris Cité, Département Hospitalo-Universitaire FIRE (Fibrosis, Inflammation and Remodeling), LabEx Inflamex, Paris, France
| | - C Arnold Spek
- Center for Experimental and Molecular Medicine, Academic Medical Center, Amsterdam 1105 AZ, The Netherlands
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168
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Sun X, Laroche G, Wang X, Ågren H, Bowman GR, Giguère PM, Tu Y. Propagation of the Allosteric Modulation Induced by Sodium in the δ-Opioid Receptor. Chemistry 2017; 23:4615-4624. [PMID: 28182309 DOI: 10.1002/chem.201605575] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Indexed: 11/07/2022]
Abstract
Allosteric sodium in the helix bundle of a G protein-coupled receptor (GPCR) can modulate the receptor activation on the intracellular side. This phenomenon has confounded the GPCR community for decades. In this work, we present a theoretical model that reveals the mechanism of the allosteric modulation induced by sodium in the δ-opioid receptor. We found that the allosteric sodium ion exploits a distinct conformation of the key residue Trp2746.48 to propagate the modulation to helices 5 and 6, which further transmits along the helices and regulates their positions on the intracellular side. This mechanism is supported by subsequent functional assays. Remarkably, our results highlight the contrast between the allosteric effects towards two GPCR partners, the G protein and β-arrestin, as indicated by the fact that the allosteric modulation initiated by the sodium ion significantly affects the β-arrestin recruitment, while it alters the G protein signaling only moderately. We believe that the mechanism revealed in this work can be used to explain allosteric effects initiated by sodium in other GPCRs since the allosteric sodium is highly conserved across GPCRs.
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Affiliation(s)
- Xianqiang Sun
- Pharmaceutical Research Center, School of Pharmacy, Guangzhou Medical University, 195 Dongfengxi Rd, Guangzhou, 510182, China
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, 106 91, Stockholm, Sweden
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Genevieve Laroche
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Rd, Ottawa, ON, Canada
| | - Xu Wang
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, 106 91, Stockholm, Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, 106 91, Stockholm, Sweden
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri, 63110, USA
| | - Patrick M Giguère
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Rd, Ottawa, ON, Canada
| | - Yaoquan Tu
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, 106 91, Stockholm, Sweden
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169
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Abstract
In addition to its procoagulant and proinflammatory functions mediated by cleavage of fibrinogen and PAR1, the trypsin-like protease thrombin activates the anticoagulant protein C in a reaction that requires the cofactor thrombomodulin and the endothelial protein C receptor. Once in the circulation, activated protein C functions as an anticoagulant, anti-inflammatory and regenerative factor. Hence, availability of a protein C activator would afford a therapeutic for patients suffering from thrombotic disorders and a diagnostic tool for monitoring the level of protein C in plasma. Here, we present a fusion protein where thrombin and the EGF456 domain of thrombomodulin are connected through a peptide linker. The fusion protein recapitulates the functional and structural properties of the thrombin-thrombomodulin complex, prolongs the clotting time by generating pharmacological quantities of activated protein C and effectively diagnoses protein C deficiency in human plasma. Notably, these functions do not require exogenous thrombomodulin, unlike other anticoagulant thrombin derivatives engineered to date. These features make the fusion protein an innovative step toward the development of protein C activators of clinical and diagnostic relevance.
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170
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Moschonas IC, Kellici TF, Mavromoustakos T, Stathopoulos P, Tsikaris V, Magafa V, Tzakos AG, Tselepis AD. Molecular requirements involving the human platelet protease-activated receptor-4 mechanism of activation by peptide analogues of its tethered-ligand. Platelets 2017; 28:812-821. [DOI: 10.1080/09537104.2017.1282607] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- I. C. Moschonas
- Atherothrombosis Research Centre/Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - T. F. Kellici
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, Greece
| | - T. Mavromoustakos
- Department of Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, Greece
- Department of Chemistry, York College and the Graduate Center of the City University of New York, Jamaica, NY, USA
| | - P. Stathopoulos
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - V. Tsikaris
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - V. Magafa
- Laboratory of Pharmacognosy and Chemistry of Natural Products, Department of Pharmacy, University of Patras, Patras, Greece
| | - A. G. Tzakos
- Sector of Organic Chemistry and Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - A. D. Tselepis
- Atherothrombosis Research Centre/Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
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171
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Koenen A, Babendreyer A, Schumacher J, Pasqualon T, Schwarz N, Seifert A, Deupi X, Ludwig A, Dreymueller D. The DRF motif of CXCR6 as chemokine receptor adaptation to adhesion. PLoS One 2017; 12:e0173486. [PMID: 28267793 PMCID: PMC5340378 DOI: 10.1371/journal.pone.0173486] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 02/21/2017] [Indexed: 12/23/2022] Open
Abstract
The CXC-chemokine receptor 6 (CXCR6) is a class A GTP-binding protein-coupled receptor (GPCRs) that mediates adhesion of leukocytes by interacting with the transmembrane cell surface-expressed chemokine ligand 16 (CXCL16), and also regulates leukocyte migration by interacting with the soluble shed variant of CXCL16. In contrast to virtually all other chemokine receptors with chemotactic activity, CXCR6 carries a DRF motif instead of the typical DRY motif as a key element in receptor activation and G protein coupling. In this work, modeling analyses revealed that the phenylalanine F3.51 in CXCR6 might have impact on intramolecular interactions including hydrogen bonds by this possibly changing receptor function. Initial investigations with embryonic kidney HEK293 cells and further studies with monocytic THP-1 cells showed that mutation of DRF into DRY does not influence ligand binding, receptor internalization, receptor recycling, and protein kinase B (AKT) signaling. Adhesion was slightly decreased in a time-dependent manner. However, CXCL16-induced calcium signaling and migration were increased. Vice versa, when the DRY motif of the related receptor CX3CR1 was mutated into DRF the migratory response towards CX3CL1 was diminished, indicating that the presence of a DRF motif generally impairs chemotaxis in chemokine receptors. Transmembrane and soluble CXCL16 play divergent roles in homeostasis, inflammation, and cancer, which can be beneficial or detrimental. Therefore, the DRF motif of CXCR6 may display a receptor adaptation allowing adhesion and cell retention by transmembrane CXCL16 but reducing the chemotactic response to soluble CXCL16. This adaptation may avoid permanent or uncontrolled recruitment of inflammatory cells as well as cancer metastasis.
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Affiliation(s)
- Andrea Koenen
- Institute of Pharmacology and Toxicology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Aaron Babendreyer
- Institute of Pharmacology and Toxicology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Julian Schumacher
- Institute of Pharmacology and Toxicology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Tobias Pasqualon
- Institute of Pharmacology and Toxicology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Nicole Schwarz
- Institute of Molecular and Cellular Anatomy, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Anke Seifert
- Institute of Pharmacology and Toxicology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Xavier Deupi
- Laboratory of Biomolecular Research and Condensed Matter Theory Group, Paul Scherrer Institute, Villigen, Switzerland
| | - Andreas Ludwig
- Institute of Pharmacology and Toxicology, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Daniela Dreymueller
- Institute of Pharmacology and Toxicology, Medical Faculty, RWTH Aachen University, Aachen, Germany
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172
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Suen J, Adams M, Lim J, Madala P, Xu W, Cotterell A, He Y, Yau M, Hooper J, Fairlie D. Mapping transmembrane residues of proteinase activated receptor 2 (PAR 2 ) that influence ligand-modulated calcium signaling. Pharmacol Res 2017; 117:328-342. [DOI: 10.1016/j.phrs.2016.12.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 12/07/2016] [Accepted: 12/07/2016] [Indexed: 12/22/2022]
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173
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7×7 RMSD matrix: A new method for quantitative comparison of the transmembrane domain structures in the G-protein coupled receptors. J Struct Biol 2017; 199:87-101. [PMID: 28223044 DOI: 10.1016/j.jsb.2017.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 02/13/2017] [Accepted: 02/15/2017] [Indexed: 01/14/2023]
Abstract
The G-protein coupled receptors (GPCRs) share a conserved heptahelical fold in the transmembrane (TM) region, but the exact arrangements of the seven TM helices vary with receptors and their activation states. The differences or the changes have been observed in the experimentally solved structures, but have not been systematically and quantitatively investigated due to lack of suitable methods. In this work, we describe a novel method, called 7×7 RMSD matrix that is proposed specifically for comparing the characteristic 7TM bundle structures of GPCRs. Compared to the commonly used overall TM bundle RMSD as a single parameter, a 7×7 RMSD matrix contains 49 parameters, which reveal changes of the relative orientations of the seven TMs. We demonstrate the novelty and advantages of this method by tackling two problems that are challenging for the existing methods. With this method, we are able to identify and quantify the helix movements in the activated receptor structures and reveal structural conservation and divergence as well as the structural relationships of different GPCRs in terms of the relative orientations of the seven TMs.
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174
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Coleman JLJ, Ngo T, Smith NJ. The G protein-coupled receptor N-terminus and receptor signalling: N-tering a new era. Cell Signal 2017; 33:1-9. [PMID: 28188824 DOI: 10.1016/j.cellsig.2017.02.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 02/06/2017] [Indexed: 01/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are a vast family of membrane-traversing proteins, essential to the ability of eukaryotic life to detect, and mount an intracellular response to, a diverse range of extracellular stimuli. GPCRs have evolved with archetypal features including an extracellular N-terminus and intracellular C-terminus that flank a transmembrane structure of seven sequential helices joined by intracellular and extracellular loops. These structural domains contribute to the ability of a GPCR to be correctly synthesised and inserted into the cell membrane, to interact with its cognate ligand(s) and to couple with signal-transducing heterotrimeric G proteins, allowing the activated receptor to selectively modulate a number of signalling cascades. Whilst well known for its importance in receptor translation and trafficking, the GPCR N-terminus is underexplored as a participant in receptor signalling. This review aims to discuss and integrate recent advances in knowledge of the vital roles of the GPCR N-terminus in receptor signalling.
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Affiliation(s)
- James L J Coleman
- Molecular Pharmacology Group, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia.
| | - Tony Ngo
- Molecular Pharmacology Group, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia
| | - Nicola J Smith
- Molecular Pharmacology Group, Victor Chang Cardiac Research Institute, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, University of New South Wales, Darlinghurst, NSW 2010, Australia.
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175
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Lingerfelt MA, Zhao P, Sharir HP, Hurst DP, Reggio PH, Abood ME. Identification of Crucial Amino Acid Residues Involved in Agonist Signaling at the GPR55 Receptor. Biochemistry 2017; 56:473-486. [PMID: 28005346 PMCID: PMC5338039 DOI: 10.1021/acs.biochem.6b01013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
GPR55 is a newly deorphanized class A G-protein-coupled receptor that has been implicated in inflammatory pain, neuropathic pain, metabolic disorder, bone development, and cancer. Few potent GPR55 ligands have been identified to date. This is largely due to an absence of information about salient features of GPR55, such as residues important for signaling and residues implicated in the GPR55 signaling cascade. The goal of this work was to identify residues that are key for the signaling of the GPR55 endogenous ligand, l-α-lysophosphatidylinositol (LPI), as well as the signaling of the GPR55 agonist, ML184 {CID 2440433, 3-[4-(2,3-dimethylphenyl)piperazine-1-carbonyl]-N,N-dimethyl-4-pyrrolidin-1-ylbenzenesulfonamide}. Serum response element (SRE) and serum response factor (SRF) luciferase assays were used as readouts for studying LPI and ML184 signaling at the GPR55 mutants. A GPR55 R* model based on the recent δ-opioid receptor (DOR) crystal structure was used to interpret the resultant mutation data. Two residues were found to be crucial for agonist signaling at GPR55, K2.60 and E3.29, suggesting that these residues form the primary interaction site for ML184 and LPI at GPR55. Y3.32F, H(170)F, and F6.55A/L mutation results suggested that these residues are part of the orthosteric binding site for ML184, while Y3.32F and H(170)F mutation results suggest that these two residues are part of the LPI binding pocket. Y3.32L, M3.36A, and F6.48A mutation results suggest the importance of a Y3.32/M3.36/F6.48 cluster in the GPR55 signaling cascade. C(10)A and C(260)A mutations suggest that these residues form a second disulfide bridge in the extracellular domain of GPR55, occluding ligand extracellular entry in the TMH1-TMH7 region of GPR55. Taken together, these results provide the first set of discrete information about GPR55 residues important for LPI and ML184 signaling and for GPR55 activation. This information should aid in the rational design of next-generation GPR55 ligands and the creation of the first high-affinity GPR55 radioligand, a tool that is sorely needed in the field.
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MESH Headings
- Amino Acid Motifs
- Binding Sites
- Crystallography, X-Ray
- Gene Expression
- HEK293 Cells
- Humans
- Kinetics
- Ligands
- Lysophospholipids/chemistry
- Lysophospholipids/pharmacology
- Molecular Docking Simulation
- Mutation
- Piperazines/chemistry
- Piperazines/pharmacology
- Protein Binding
- Pyrrolidines/chemistry
- Pyrrolidines/pharmacology
- Receptors, Cannabinoid
- Receptors, G-Protein-Coupled/agonists
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/genetics
- Receptors, G-Protein-Coupled/metabolism
- Receptors, Opioid, delta/chemistry
- Receptors, Opioid, delta/genetics
- Receptors, Opioid, delta/metabolism
- Recombinant Fusion Proteins/chemistry
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Serum Response Element
- Serum Response Factor/chemistry
- Serum Response Factor/genetics
- Serum Response Factor/metabolism
- Signal Transduction
- Glycine max
- Structural Homology, Protein
- Thermodynamics
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Affiliation(s)
- Mary A. Lingerfelt
- Department of Chemistry and Biochemistry, UNC-Greensboro, Greensboro, North Carolina 27402 United States
| | - Pingwei Zhao
- Center for Substance Abuse Research, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania 19140, United States
| | - Haleli P. Sharir
- Center for Substance Abuse Research, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania 19140, United States
| | - Dow P. Hurst
- Department of Chemistry and Biochemistry, UNC-Greensboro, Greensboro, North Carolina 27402 United States
| | - Patricia H. Reggio
- Department of Chemistry and Biochemistry, UNC-Greensboro, Greensboro, North Carolina 27402 United States
| | - Mary E. Abood
- Center for Substance Abuse Research, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania 19140, United States
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176
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Proteinase-activated receptors (PARs) as targets for antiplatelet therapy. Biochem Soc Trans 2016; 44:606-12. [PMID: 27068977 DOI: 10.1042/bst20150282] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Indexed: 01/07/2023]
Abstract
Since the identification of the proteinase-activated receptor (PAR) family as mediators of serine protease activity in the 1990s, there has been tremendous progress in the elucidation of their pathophysiological roles. The development of drugs that target PARs has been the focus of many laboratories for the potential treatment of thrombosis, cancer and other inflammatory diseases. Understanding the mechanisms of PAR activation and G protein signalling pathways evoked in response to the growing list of endogenous proteases has yielded great insight into receptor regulation at the molecular level. This has led to the development of new selective modulators of PAR activity, particularly PAR1. The mixed success of targeting PARs has been best exemplified in the context of inhibiting PAR1 as a new antiplatelet therapy. The development of the competitive PAR1 antagonist, vorapaxar (Zontivity), has clearly shown the value in targeting PAR1 in acute coronary syndrome (ACS); however the severity of associated bleeding with this drug has limited its use in the clinic. Due to the efficacy of thrombin acting via PAR1, strategies to selectively inhibit specific PAR1-mediated G protein signalling pathways or to target the second thrombin platelet receptor, PAR4, are being devised. The rationale behind these alternative approaches is to bias downstream thrombin activity via PARs to allow for inhibition of pro-thrombotic pathways but maintain other pathways that may preserve haemostatic balance and improve bleeding profiles for widespread clinical use. This review summarizes the structural determinants that regulate PARs and the modulators of PAR activity developed to date.
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177
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A novel mechanism regulating human platelet activation by MMP-2-mediated PAR1 biased signaling. Blood 2016; 129:883-895. [PMID: 28034890 DOI: 10.1182/blood-2016-06-724245] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 12/14/2016] [Indexed: 11/20/2022] Open
Abstract
Platelets contain and release several matrix metalloproteinases (MMPs). Among these, active MMP-2 enhances platelet aggregation by favoring the activation of phosphatidylinositol 3- kinase (PI3K) and contributes to arterial thrombosis. The platelet surface target of MMP-2 and the mechanism through which it primes platelets to respond to subsequent stimuli are still unknown. We show that active MMP-2 enhances platelet activation induced by weak stimuli by cleaving PAR1 at a noncanonical extracellular site different from the thrombin-cleavage site and thus initiates biased receptor signaling, triggering only some of the signaling pathways normally activated by full PAR1 agonism. The novel PAR1-tethered ligand exposed by MMP-2 stimulates PAR1-dependent Gq and G12/13 pathway activation, triggering p38-MAPK phosphorylation, Ca+2 fluxes, and PI3K activation, but not Gi signaling; this is insufficient to cause platelet aggregation, but it is enough to predispose platelets to fully respond to Gi-activating stimuli. Integrin αIIbβ3 is a necessary cofactor for PAR1 cleavage by MMP-2 by binding the MMP-2 hemopexin domain, thus favoring the interaction of the enzyme with PAR1. Our studies unravel a novel mechanism regulating platelet activation that involves the binding of MMP-2 to integrin αIIbβ3 and the subsequent cleavage of PAR1 by active MMP-2 at a noncanonical site, exposing a previously undescribed tethered ligand that triggers biased G-protein agonism and thus predisposes platelets to full activation by other stimuli. These results identify the MMP-2-αIIbβ3-PAR1 interaction as a potential target for the prevention of arterial thrombosis.
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178
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Hishinuma S, Kosaka K, Akatsu C, Uesawa Y, Fukui H, Shoji M. Asp73-dependent and -independent regulation of the affinity of ligands for human histamine H 1 receptors by Na . Biochem Pharmacol 2016; 128:46-54. [PMID: 28040476 DOI: 10.1016/j.bcp.2016.12.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 12/27/2016] [Indexed: 11/16/2022]
Abstract
The affinity of ligands for G-protein-coupled receptors (GPCRs) is allosterically regulated by Na+ via a highly conserved aspartate residue (Asp2.50) in the second transmembrane domain of GPCRs. In the present study, we examined the Na+-mediated regulation of the affinity of ligands for Gq/11-protein-coupled human histamine H1 receptors in Chinese hamster ovary cells. The affinities of 3 agonists and 20 antihistamines were evaluated by their displacement curves against the binding of [3H]-mepyramine to membrane preparations in the presence or absence of 100mM NaCl. The affinities of most drugs including histamine, an agonist, and d-chlorpheniramine, a first-generation antihistamine, were reduced by NaCl, with the extent of NaCl-mediated changes varying widely between drugs. In contrast, the affinities of some second-generation antihistamines such as fexofenadine were increased by NaCl. These changes were retained in intact cells. The mutation of Asp2.50 (Asp73) to asparagine abrogated NaCl-induced reductions in affinities for histamine and d-chlorpheniramine, but not NaCl-induced increases in the affinity for fexofenadine. Quantitative structure-activity relationship (QSAR) analyses showed that these Na+-mediated changes were explained and predicted by a combination of the molecular energies and implicit solvation energies of the compounds. These results suggest that Na+ diversely regulates the affinity of ligands for H1 receptors from the extracellular sites of receptors via Asp73-dependent and -independent mechanisms in a manner that depends on the physicochemical properties of ligands. These results may contribute to a deeper understanding of the fundamental mechanisms by which the affinity of ligands for their receptors is allosterically regulated by Na+.
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Affiliation(s)
- Shigeru Hishinuma
- Department of Pharmacodynamics, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan.
| | - Kiyoe Kosaka
- Department of Pharmacodynamics, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Chizuru Akatsu
- Department of Pharmacodynamics, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Yoshihiro Uesawa
- Department of Clinical Pharmaceutics, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
| | - Hiroyuki Fukui
- Department of Molecular Studies for Incurable Diseases, Institute of Biomedical Sciences, Tokushima University Graduate School, 3-18-15 Kuramoto, Tokushima 770-8503, Japan
| | - Masaru Shoji
- Department of Pharmacodynamics, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan
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179
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Jung SR, Seo JB, Deng Y, Asbury CL, Hille B, Koh DS. Contributions of protein kinases and β-arrestin to termination of protease-activated receptor 2 signaling. ACTA ACUST UNITED AC 2016; 147:255-71. [PMID: 26927499 PMCID: PMC4772372 DOI: 10.1085/jgp.201511477] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Systematic imaging studies and modeling reveal new details of the regulation of the Gq-coupled GPCR, protease-activated receptor 2, by phosphorylation and β-arrestin. Activated Gq protein–coupled receptors (GqPCRs) can be desensitized by phosphorylation and β-arrestin binding. The kinetics and individual contributions of these two mechanisms to receptor desensitization have not been fully distinguished. Here, we describe the shut off of protease-activated receptor 2 (PAR2). PAR2 activates Gq and phospholipase C (PLC) to hydrolyze phosphatidylinositol 4,5-bisphosphate (PIP2) into diacylglycerol and inositol trisphosphate (IP3). We used fluorescent protein–tagged optical probes to monitor several consequences of PAR2 signaling, including PIP2 depletion and β-arrestin translocation in real time. During continuous activation of PAR2, PIP2 was depleted transiently and then restored within a few minutes, indicating fast receptor activation followed by desensitization. Knockdown of β-arrestin 1 and 2 using siRNA diminished the desensitization, slowing PIP2 restoration significantly and even adding a delayed secondary phase of further PIP2 depletion. These effects of β-arrestin knockdown on PIP2 recovery were prevented when serine/threonine phosphatases that dephosphorylate GPCRs were inhibited. Thus, PAR2 may continuously regain its activity via dephosphorylation when there is insufficient β-arrestin to trap phosphorylated receptors. Similarly, blockers of protein kinase C (PKC) and G protein–coupled receptor kinase potentiated the PIP2 depletion. In contrast, an activator of PKC inhibited receptor activation, presumably by augmenting phosphorylation of PAR2. Our interpretations were strengthened by modeling. Simulations supported the conclusions that phosphorylation of PAR2 by protein kinases initiates receptor desensitization and that recruited β-arrestin traps the phosphorylated state of the receptor, protecting it from phosphatases. Speculative thinking suggested a sequestration of phosphatidylinositol 4-phosphate 5 kinase (PIP5K) to the plasma membrane by β-arrestin to explain why knockdown of β-arrestin led to secondary depletion of PIP2. Indeed, artificial recruitment of PIP5K removed the secondary loss of PIP2 completely. Altogether, our experimental and theoretical approaches demonstrate roles and dynamics of the protein kinases, β-arrestin, and PIP5K in the desensitization of PAR2.
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Affiliation(s)
- Seung-Ryoung Jung
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Jong Bae Seo
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Yi Deng
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Charles L Asbury
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Bertil Hille
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195
| | - Duk-Su Koh
- Department of Physiology and Biophysics, University of Washington, Seattle, WA 98195 Department of Physics, Pohang University of Science and Technology, Pohang, Kyungbuk, 790-784, Republic of Korea
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180
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Núñez Miguel R, Sanders J, Furmaniak J, Smith BR. Structure and activation of the TSH receptor transmembrane domain. AUTOIMMUNITY HIGHLIGHTS 2016; 8:2. [PMID: 27921237 PMCID: PMC5136658 DOI: 10.1007/s13317-016-0090-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/23/2016] [Indexed: 12/30/2022]
Abstract
PURPOSE The thyroid-stimulating hormone receptor (TSHR) is the target autoantigen for TSHR-stimulating autoantibodies in Graves' disease. The TSHR is composed of: a leucine-rich repeat domain (LRD), a hinge region or cleavage domain (CD) and a transmembrane domain (TMD). The binding arrangements between the TSHR LRD and the thyroid-stimulating autoantibody M22 or TSH have become available from the crystal structure of the TSHR LRD-M22 complex and a comparative model of the TSHR LRD in complex with TSH, respectively. However, the mechanism by which the TMD of the TSHR and the other glycoprotein hormone receptors (GPHRs) becomes activated is unknown. METHODS We have generated comparative models of the structures of the inactive (TMD_In) and active (TMD_Ac) conformations of the TSHR, follicle-stimulating hormone receptor (FSHR) and luteinizing hormone receptor (LHR) TMDs. The structures of TMD_Ac and TMD_In were obtained using class A GPCR crystal structures for which fully active and inactive conformations were available. RESULTS Most conserved motifs observed in GPCR TMDs are also observed in the amino acid sequences of GPHR TMDs. Furthermore, most GPCR TMD conserved helix distortions are observed in our models of the structures of GPHR TMDs. Analysis of these structures has allowed us to propose a mechanism for activation of GPHR TMDs. CONCLUSIONS Insight into the mechanism of activation of the TSHR by both TSH and TSHR autoantibodies is likely to be useful in the development of new treatments for Graves' disease.
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Affiliation(s)
| | - Jane Sanders
- FIRS Laboratories, RSR Ltd, Parc Ty Glas, Llanishen, Cardiff, CF14 5DU, UK
| | - Jadwiga Furmaniak
- FIRS Laboratories, RSR Ltd, Parc Ty Glas, Llanishen, Cardiff, CF14 5DU, UK
| | - Bernard Rees Smith
- FIRS Laboratories, RSR Ltd, Parc Ty Glas, Llanishen, Cardiff, CF14 5DU, UK.
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181
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Successful Strategies to Determine High-Resolution Structures of GPCRs. Trends Pharmacol Sci 2016; 37:1055-1069. [DOI: 10.1016/j.tips.2016.09.009] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/02/2016] [Accepted: 09/15/2016] [Indexed: 12/26/2022]
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182
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Tricoci P. Protease-Activated Receptor-1 Antagonists Post-Percutaneous Coronary Intervention. Interv Cardiol Clin 2016; 6:57-66. [PMID: 27886823 DOI: 10.1016/j.iccl.2016.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Thrombin is a potent platelet agonist, and protease-activated receptor-1 (PAR-1) is the main thrombin receptor in human platelets and thrombin. PAR-1 antagonism has attracted interest as a potential therapeutic target to reduce atherothrombotic events in patients with atherosclerotic disease, especially coronary artery disease. In this review, the author describes the rationale of PAR-1 antagonism for the reduction of atherothrombotic events and reviews the key phase 3 trial results, with special attention to analyses in percutaneous coronary intervention patients.
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Affiliation(s)
- Pierluigi Tricoci
- Division of Cardiology, Duke Clinical Research Institute, Duke University Medical Center, 2400 Pratt Street, 0311 Terrace Level, Box 3850 DUMC, Durham, NC 27705, USA.
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183
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Vibrational resonance, allostery, and activation in rhodopsin-like G protein-coupled receptors. Sci Rep 2016; 6:37290. [PMID: 27849063 PMCID: PMC5110974 DOI: 10.1038/srep37290] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 10/28/2016] [Indexed: 12/13/2022] Open
Abstract
G protein-coupled receptors are a large family of membrane proteins activated by a variety of structurally diverse ligands making them highly adaptable signaling molecules. Despite recent advances in the structural biology of this protein family, the mechanism by which ligands induce allosteric changes in protein structure and dynamics for its signaling function remains a mystery. Here, we propose the use of terahertz spectroscopy combined with molecular dynamics simulation and protein evolutionary network modeling to address the mechanism of activation by directly probing the concerted fluctuations of retinal ligand and transmembrane helices in rhodopsin. This approach allows us to examine the role of conformational heterogeneity in the selection and stabilization of specific signaling pathways in the photo-activation of the receptor. We demonstrate that ligand-induced shifts in the conformational equilibrium prompt vibrational resonances in the protein structure that link the dynamics of conserved interactions with fluctuations of the active-state ligand. The connection of vibrational modes creates an allosteric association of coupled fluctuations that forms a coherent signaling pathway from the receptor ligand-binding pocket to the G-protein activation region. Our evolutionary analysis of rhodopsin-like GPCRs suggest that specific allosteric sites play a pivotal role in activating structural fluctuations that allosterically modulate functional signals.
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184
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Eddy MT, Didenko T, Stevens RC, Wüthrich K. β 2-Adrenergic Receptor Conformational Response to Fusion Protein in the Third Intracellular Loop. Structure 2016; 24:2190-2197. [PMID: 27839952 DOI: 10.1016/j.str.2016.09.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/16/2016] [Accepted: 10/07/2016] [Indexed: 12/11/2022]
Abstract
Fluorine-19 nuclear magnetic resonance (NMR) was used to study conformational equilibria at the intracellular tips of helices VI and VII in a variant β2-adrenergic receptor (β2AR) containing T4-lysozyme fused into the third intracellular loop (β2AR-T4L), a G protein-coupled receptor (GPCR) modification widely used in crystal structure determination. G-protein signaling at helix VI showed nearly complete population of an active-like state for all ligand efficacies in the absence of an intracellular protein. For arrestin signaling at helix VII, a native-like equilibrium was observed, except for complexes with ligands devoid of a hydrophobic moiety at the ethanolamine end. These data confirm that response of G-protein and arrestin signaling to ligand efficacy is not coupled, and presents evidence for long-range effects between fusion protein and orthosteric binding cavity, which are suppressed by voluminous bound ligands. Solution NMR thus provides complementary information, which should be considered in functional interpretations of GPCR crystal structures obtained with ICL3 fusions.
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Affiliation(s)
- Matthew T Eddy
- Departments of Biological Sciences and Chemistry, Bridge Institute, The University of Southern California, South Vermont Avenue, MC 3303, Los Angeles, CA 90089, USA
| | - Tatiana Didenko
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Raymond C Stevens
- Departments of Biological Sciences and Chemistry, Bridge Institute, The University of Southern California, South Vermont Avenue, MC 3303, Los Angeles, CA 90089, USA
| | - Kurt Wüthrich
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA; Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
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185
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Zhong W, Liu P, Zhang Q, Li D, Lin J. Structure-based QSAR, molecule design and bioassays of protease-activated receptor 1 inhibitors. J Biomol Struct Dyn 2016; 35:2853-2867. [PMID: 27809674 DOI: 10.1080/07391102.2016.1234413] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Quantitative structure-activity relationship (QSAR) studies were performed on a series of protease-activated receptor 1 (PAR1) inhibitors to identify the key structural features responsible for their biological activity. Induced-fit docking (IFD) was used to explore the active mechanisms of all PAR1 inhibitors at the active pocket of PAR1, and the best plausible conformation was determined by IFD for further QSAR studies. Based on the best plausible conformation, structure-based descriptors and ligand descriptors incorporating the ligand-receptor interaction were calculated. The random forest method was used to select important descriptors and build the 2D-QSAR model. The results of the 2D-QSAR model gave a squared correlation coefficient (R2) of 0.937, a prediction squared correlation coefficient (R2pred) of 0.845 and a mean square error (MSE) of 0.056. Furthermore, a 3D-QSAR model was developed via topomer comparative molecular field analysis (Topomer CoMFA), resulting in an R2 of 0.938, a cross-validated Q2 of 0.503 and a R2pred of 0.758. Based on the developed QSAR model, Topomer search was used for virtual screening of the R2 fragment in lead-like inhibitors from the National Cancer Institute (NCI) database, which contains 260,000 molecules. Eighty-two compounds were designed with different R2 fragments, and four of these compounds were selected for further biological testing. All four compounds showed inhibitory potency against PAR1.
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Affiliation(s)
- Weilong Zhong
- a State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research , Nankai University , Tianjin 300071 , China
| | - Pi Liu
- b Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300000 , China
| | - Qiang Zhang
- a State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research , Nankai University , Tianjin 300071 , China
| | - Dongmei Li
- a State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research , Nankai University , Tianjin 300071 , China
| | - Jianping Lin
- a State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research , Nankai University , Tianjin 300071 , China.,b Tianjin Institute of Industrial Biotechnology , Chinese Academy of Sciences , Tianjin 300000 , China.,c Pharmaceutical Intelligence Platform, Tianjin Joint Academy of Biomedicine and Technology , Tianjin 300457 , China
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186
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Claes K, Vandewalle K, Laukens B, Laeremans T, Vosters O, Langer I, Parmentier M, Steyaert J, Callewaert N. Modular Integrated Secretory System Engineering in Pichia pastoris To Enhance G-Protein Coupled Receptor Expression. ACS Synth Biol 2016; 5:1070-1075. [PMID: 27176489 DOI: 10.1021/acssynbio.6b00032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Membrane protein research is still hampered by the generally very low levels at which these proteins are naturally expressed, necessitating heterologous expression. Protein degradation, folding problems, and undesired post-translational modifications often occur, together resulting in low expression levels of heterogeneous protein products that are unsuitable for structural studies. We here demonstrate how the integration of multiple engineering modules in Pichia pastoris can be used to increase both the quality and the quantity of overexpressed integral membrane proteins, with the human CXCR4 G-protein coupled receptor as an example. The combination of reduced proteolysis, enhanced ER folding capacity, GlycoDelete-based N-Glycan trimming, and nanobody-based fold stabilization improved the expression of this GPCR in P. pastoris from a low expression level of a heterogeneously glycosylated, proteolyzed product to substantial quantities (2-3 mg/L shake flask culture) of a nonproteolyzed, homogeneously glycosylated proteoform. We expect that this set of tools will contribute to successful expression of more membrane proteins in a quantity and quality suitable for functional and structural studies.
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Affiliation(s)
- Katrien Claes
- Unit
for Medical Biotechnology, Medical Biotechnology Center, VIB, Technologiepark 927, 9052 Ghent, Belgium
- Laboratory
for Protein Biochemistry and Biomolecular Engineering, Department
of Biochemistry and Microbiology, Ghent University, K.L.-Ledeganckstraat
35, 9000 Ghent, Belgium
| | - Kristof Vandewalle
- Unit
for Medical Biotechnology, Medical Biotechnology Center, VIB, Technologiepark 927, 9052 Ghent, Belgium
- Laboratory
for Protein Biochemistry and Biomolecular Engineering, Department
of Biochemistry and Microbiology, Ghent University, K.L.-Ledeganckstraat
35, 9000 Ghent, Belgium
| | - Bram Laukens
- Unit
for Medical Biotechnology, Medical Biotechnology Center, VIB, Technologiepark 927, 9052 Ghent, Belgium
- Laboratory
for Protein Biochemistry and Biomolecular Engineering, Department
of Biochemistry and Microbiology, Ghent University, K.L.-Ledeganckstraat
35, 9000 Ghent, Belgium
| | - Toon Laeremans
- Structural
Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Structural
Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Olivier Vosters
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Campus Erasme,
808 Route de Lennik, B-1070 Brussels, Belgium
| | - Ingrid Langer
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Campus Erasme,
808 Route de Lennik, B-1070 Brussels, Belgium
| | - Marc Parmentier
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Campus Erasme,
808 Route de Lennik, B-1070 Brussels, Belgium
- Welbio, Université Libre de Bruxelles (U.L.B.), Campus Erasme, 808 Route de Lennik, B-1070 Brussels, Belgium
| | - Jan Steyaert
- Structural
Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
- Structural
Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Nico Callewaert
- Unit
for Medical Biotechnology, Medical Biotechnology Center, VIB, Technologiepark 927, 9052 Ghent, Belgium
- Laboratory
for Protein Biochemistry and Biomolecular Engineering, Department
of Biochemistry and Microbiology, Ghent University, K.L.-Ledeganckstraat
35, 9000 Ghent, Belgium
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187
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Lu M, Wu B. Structural studies of G protein-coupled receptors. IUBMB Life 2016; 68:894-903. [PMID: 27766738 DOI: 10.1002/iub.1578] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 10/08/2016] [Indexed: 11/08/2022]
Abstract
G protein-coupled receptors (GPCRs) comprise the largest membrane protein family. These receptors sense a variety of signaling molecules, activate multiple intracellular signal pathways, and act as the targets of over 40% of marketed drugs. Recent progress on GPCR structural studies provides invaluable insights into the structure-function relationship of the GPCR superfamily, deepening our understanding about the molecular mechanisms of GPCR signal transduction. Here, we review recent breakthroughs on GPCR structure determination and the structural features of GPCRs, and take the structures of chemokine receptor CCR5 and purinergic receptors P2Y1 R and P2Y12 R as examples to discuss the importance of GPCR structures on functional studies and drug discovery. In addition, we discuss the prospect of GPCR structure-based drug discovery. © 2016 IUBMB Life, 68(11):894-903, 2016.
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Affiliation(s)
- Mengjie Lu
- CAS Key laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Beili Wu
- CAS Key laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, Pudong, Shanghai, China.
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188
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Costanzi S, Skorski M, Deplano A, Habermehl B, Mendoza M, Wang K, Biederman M, Dawson J, Gao J. Homology modeling of a Class A GPCR in the inactive conformation: A quantitative analysis of the correlation between model/template sequence identity and model accuracy. J Mol Graph Model 2016; 70:140-152. [PMID: 27723562 DOI: 10.1016/j.jmgm.2016.10.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/12/2016] [Accepted: 10/03/2016] [Indexed: 01/22/2023]
Abstract
With the present work we quantitatively studied the modellability of the inactive state of Class A G protein-coupled receptors (GPCRs). Specifically, we constructed models of one of the Class A GPCRs for which structures solved in the inactive state are available, namely the β2 AR, using as templates each of the other class members for which structures solved in the inactive state are also available. Our results showed a detectable linear correlation between model accuracy and model/template sequence identity. This suggests that the likely accuracy of the homology models that can be built for a given receptor can be generally forecasted on the basis of the available templates. We also probed whether sequence alignments that allow for the presence of gaps within the transmembrane domains to account for structural irregularities afford better models than the classical alignment procedures that do not allow for the presence of gaps within such domains. As our results indicated, although the overall differences are very subtle, the inclusion of internal gaps within the transmembrane domains has a noticeable a beneficial effect on the local structural accuracy of the domain in question.
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Affiliation(s)
- Stefano Costanzi
- Department of Chemistry, American University, Washington, DC 20016, USA; Center for Behavioral Neuroscience, American University, Washington, DC 20016, USA.
| | - Matthew Skorski
- Department of Chemistry, American University, Washington, DC 20016, USA
| | | | - Brett Habermehl
- Department of Chemistry, American University, Washington, DC 20016, USA
| | - Mary Mendoza
- Department of Chemistry, American University, Washington, DC 20016, USA
| | - Keyun Wang
- Department of Chemistry, American University, Washington, DC 20016, USA
| | | | - Jessica Dawson
- Department of Chemistry, American University, Washington, DC 20016, USA
| | - Jia Gao
- Department of Chemistry, American University, Washington, DC 20016, USA
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189
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Taudien S, Lausser L, Giamarellos-Bourboulis EJ, Sponholz C, Schöneweck F, Felder M, Schirra LR, Schmid F, Gogos C, Groth S, Petersen BS, Franke A, Lieb W, Huse K, Zipfel PF, Kurzai O, Moepps B, Gierschik P, Bauer M, Scherag A, Kestler HA, Platzer M. Genetic Factors of the Disease Course After Sepsis: Rare Deleterious Variants Are Predictive. EBioMedicine 2016; 12:227-238. [PMID: 27639823 PMCID: PMC5078585 DOI: 10.1016/j.ebiom.2016.08.037] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/19/2016] [Accepted: 08/24/2016] [Indexed: 12/20/2022] Open
Abstract
Sepsis is a life-threatening organ dysfunction caused by dysregulated host response to infection. For its clinical course, host genetic factors are important and rare genomic variants are suspected to contribute. We sequenced the exomes of 59 Greek and 15 German patients with bacterial sepsis divided into two groups with extremely different disease courses. Variant analysis was focusing on rare deleterious single nucleotide variants (SNVs). We identified significant differences in the number of rare deleterious SNVs per patient between the ethnic groups. Classification experiments based on the data of the Greek patients allowed discrimination between the disease courses with estimated sensitivity and specificity > 75%. By application of the trained model to the German patients we observed comparable discriminatory properties despite lower population-specific rare SNV load. Furthermore, rare SNVs in genes of cell signaling and innate immunity related pathways were identified as classifiers discriminating between the sepsis courses. Sepsis patients with favorable disease course after sepsis, even in the case of unfavorable preconditions, seem to be affected more often by rare deleterious SNVs in cell signaling and innate immunity related pathways, suggesting a protective role of impairments in these processes against a poor disease course. Rare SNV load is higher in the Greek vs. German population. Subsets of rare deleterious SNVs are predictive for the disease course after sepsis. Patients with favorable disease course seem to carry protective deleterious variants in sepsis related pathways.
Sepsis is a life-threatening disease caused by improper response to infection. Only little is known about the role of genetic factors. From > 4000 patients we selected the most extreme cases showing either a favorable or adverse disease course. We determined rare (< 1/200) protein-damaging genetic variants, as they may have a large effect. Using a computational model that includes knowledge on genes we can predict the disease course with > 75% accuracy. Surprisingly, favorable courses can be expected if defense mechanisms are damaged and prevented from overshooting. This underlines the relevance of rare variants for better understanding of sepsis and may offer new treatment options.
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Affiliation(s)
- Stefan Taudien
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Ludwig Lausser
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany; Institute of Medical Systems Biology, Ulm University, Germany
| | - Evangelos J Giamarellos-Bourboulis
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; 4th Department of Internal Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Christoph Sponholz
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany; Department of Anaesthesiology and Intensive Care Therapy, Jena University Hospital, Jena, Germany
| | - Franziska Schöneweck
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Research group Clinical Epidemiology, CSCC, Jena University Hospital, Jena, Germany
| | - Marius Felder
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | | | - Florian Schmid
- Institute of Medical Systems Biology, Ulm University, Germany
| | - Charalambos Gogos
- Department of Internal Medicine, University of Patras, Medical School, Greece
| | - Susann Groth
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Britt-Sabina Petersen
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrechts-Universität Kiel, Kiel, Germany
| | - Klaus Huse
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Peter F Zipfel
- Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany; Friedrich Schiller University Jena, Jena, Germany
| | - Oliver Kurzai
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Septomics Research Center Jena, Leibniz Institute for Natural Product Research and Infection Biology - Hans-Knöll-Institute, Jena, Germany
| | - Barbara Moepps
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany
| | - Peter Gierschik
- Institute of Pharmacology and Toxicology, Ulm University Medical Center, Ulm, Germany
| | - Michael Bauer
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Department of Anaesthesiology and Intensive Care Therapy, Jena University Hospital, Jena, Germany
| | - André Scherag
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany; Research group Clinical Epidemiology, CSCC, Jena University Hospital, Jena, Germany
| | - Hans A Kestler
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany; Institute of Medical Systems Biology, Ulm University, Germany; Friedrich Schiller University Jena, Jena, Germany.
| | - Matthias Platzer
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany.
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190
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Hamilton JR, Trejo J. Challenges and Opportunities in Protease-Activated Receptor Drug Development. Annu Rev Pharmacol Toxicol 2016; 57:349-373. [PMID: 27618736 DOI: 10.1146/annurev-pharmtox-011613-140016] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protease-activated receptors (PARs) are a unique class of G protein-coupled receptors (GPCRs) that transduce cellular responses to extracellular proteases. PARs have important functions in the vasculature, inflammation, and cancer and are important drug targets. A unique feature of PARs is their irreversible proteolytic mechanism of activation that results in the generation of a tethered ligand that cannot diffuse away. Despite the fact that GPCRs have proved to be the most successful class of druggable targets, the development of agents that target PARs specifically has been challenging. As a consequence, researchers have taken a remarkable diversity of approaches to develop pharmacological entities that modulate PAR function. Here, we present an overview of the diversity of therapeutic agents that have been developed against PARs. We further discuss PAR biased signaling and the influence of receptor compartmentalization, posttranslational modifications, and dimerization, which are important considerations for drug development.
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Affiliation(s)
- Justin R Hamilton
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria 3004, Australia
| | - JoAnn Trejo
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California 92093;
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191
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Cho NC, Seo SH, Kim D, Shin JS, Ju J, Seong J, Seo SH, Lee I, Lee KT, Kim YK, No KT, Pae AN. Pharmacophore-based virtual screening, biological evaluation and binding mode analysis of a novel protease-activated receptor 2 antagonist. J Comput Aided Mol Des 2016; 30:625-37. [DOI: 10.1007/s10822-016-9937-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/11/2016] [Indexed: 10/21/2022]
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192
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Moschonas IC, Tselepis AD. Increased Benefit With Vorapaxar Use in Patients With a History of Myocardial Infarction and Diabetes Mellitus: What the Data Show Us. J Cardiovasc Pharmacol Ther 2016; 22:133-141. [PMID: 27489245 DOI: 10.1177/1074248416662347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is a progressive and multifactorial metabolic disease mainly characterized by hyperglycemia and insulin resistance. Abnormal platelet reactivity associated with an increased risk of cardiovascular disease (CVD) is also a feature characteristic of patients with T2DM. Dual antiplatelet therapy consisting of aspirin and an adenosine diphosphate platelet P2Y12 receptor antagonist, such as clopidogrel, represents the standard antithrombotic regimen for the secondary prevention of CVD risk in T2DM. However, a high proportion of patients with T2DM exhibit high on-treatment platelet reactivity to aspirin and/or clopidogrel, associated with a greater risk of adverse cardiovascular events compared with nondiabetic patients. Consequently, novel antiplatelet therapeutic approaches may be required in order to avoid such events. Vorapaxar is a novel antiplatelet agent that targets the platelet protease-activated receptor 1 and inhibits thrombin-induced platelet activation. Vorapaxar has been studied in 2 phase III clinical trials and has been approved for use in the secondary prevention of atherothrombotic events in patients with a previous myocardial infarction (MI) or peripheral arterial disease. New data from the Thrombin-Receptor Antagonist in Secondary Prevention of Atherothrombotic Ischemic Events (TRA 2°P)-TIMI 50 trial MI cohort demonstrate that the subgroup of patients with T2DM exhibits increased benefit from vorapaxar use compared with non-T2DM patients. The aim of the present work is to critically review the current knowledge concerning vorapaxar use in patients with T2DM as well as to discuss the possible mechanism(s) underlying vorapaxar's beneficial effect in T2DM.
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Affiliation(s)
- Iraklis C Moschonas
- 1 Atherothrombosis Research Centre/Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
| | - Alexandros D Tselepis
- 1 Atherothrombosis Research Centre/Laboratory of Biochemistry, Department of Chemistry, University of Ioannina, Ioannina, Greece
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193
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Vaidehi N, Bhattacharya S. Allosteric communication pipelines in G-protein-coupled receptors. Curr Opin Pharmacol 2016; 30:76-83. [PMID: 27497048 DOI: 10.1016/j.coph.2016.07.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 11/29/2022]
Abstract
The binding of ligands to G-protein-coupled receptors (GPCRs) in the extracellular region transmits the signal to the intracellular region to initiate coupling to effector proteins. The mechanism of this allosteric communication remains largely unexplored. Knowledge of the residues involved in the pipeline of the allosteric communication from the extracellular to the intracellular region will provide means to (a) design ligands with bias in potency towards one signaling pathway over others, and (b) design allosteric modulators that show subtype selectivity in GPCRs. In this review we describe the current state of the computational methods that provide insights into the allosteric communication in GPCRs and elucidate how this information can be used to design allosteric modulators.
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Affiliation(s)
- Nagarajan Vaidehi
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA.
| | - Supriyo Bhattacharya
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
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194
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Wang Y, Liu J, Zhu T, Zhang L, He X, Zhang JZ. Predicted PAR1 inhibitors from multiple computational methods. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.07.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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195
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Vickery ON, Machtens JP, Zachariae U. Membrane potentials regulating GPCRs: insights from experiments and molecular dynamics simulations. Curr Opin Pharmacol 2016; 30:44-50. [PMID: 27474871 PMCID: PMC5080454 DOI: 10.1016/j.coph.2016.06.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 01/27/2023]
Abstract
G-protein coupled receptors (GPCRs) form the largest class of membrane proteins in humans and the targets of most present drugs. Membrane potential is one of the defining characteristics of living cells. Recent work has shown that the membrane voltage, and changes thereof, modulates signal transduction and ligand binding in GPCRs. As it may allow differential signalling patterns depending on tissue, cell type, and the excitation status of excitable cells, GPCR voltage sensitivity could have important implications for their pharmacology. This review summarises recent experimental insights on GPCR voltage regulation and the role of molecular dynamics simulations in identifying the structural basis of GPCR voltage-sensing. We discuss the potential significance for drug design on GPCR targets from excitable and non-excitable cells.
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Affiliation(s)
- Owen N Vickery
- Physics, School of Science and Engineering, University of Dundee, Nethergate Dundee DD1 4NH, UK; Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jan-Philipp Machtens
- Institute of Complex Systems, Zelluläre Biophysik (ICS-4), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Ulrich Zachariae
- Physics, School of Science and Engineering, University of Dundee, Nethergate Dundee DD1 4NH, UK; Computational Biology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
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196
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Structure of the adenosine A(2A) receptor bound to an engineered G protein. Nature 2016; 536:104-7. [PMID: 27462812 PMCID: PMC4979997 DOI: 10.1038/nature18966] [Citation(s) in RCA: 320] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/23/2016] [Indexed: 12/17/2022]
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197
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Park CM, Baek S, Kim S, Song JH, Lee S, Kim M. Trans-fused 5-[(tert-Butoxtycarbonyl)amino]octahydroindenes as a protease activated receptor-1 (PAR1) antagonist. Arch Pharm Res 2016; 39:1275-95. [PMID: 27406140 DOI: 10.1007/s12272-016-0788-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 06/28/2016] [Indexed: 12/01/2022]
Abstract
Protease activated receptor 1 (PAR1) has been considered as a promising antiplatelet target to prevent thrombotic cardiovascular events in patients with prior myocardial infarction or peripheral arterial diseases. Previously, we found a series of octahydroindene analogues to have high potency on PAR1 and no significant cytotoxicity but poor metabolic stability in human and rat liver microsomes. We designed and synthesized substituted analogues of octahydroindenes at C5 or C6 aiming to improvement of metabolic stability, and identified that trans-fused 5-[(tert-butoxtycarbonyl)amino]octahydroindene analogues showed improved metabolic stability with maintaining good activity on PAR1. Especially, 2-methanesulfonate 57 (IC50 = 0.006 μM; R50 = 126.3 min in human, 83.3 min in rat), sulfamate 58 (IC50 = 0.020 μM; R50 = 52.8 min in human, 106.0 min in rat), and N-(cyclopropyl)methylsufonamide 63 (IC50 = 0.010 μM; R50 = 51.4 min in human, 90.5 min in rat) exhibited excellent activity and metabolic stability both on human and rat liver microsomes, comparable to those obtained for varapaxar (IC50 = 0.0015 μM; R50 = 83.2 min in human, 32.4 min in rat). Additionally, these compounds (57, 58, and 63) represented significant efficacy (IC50 = 0.0022, 0.0062, and 0.015 μM, each) in human washed platelet aggregation (WPA) assay without cytotoxicity and CYP3A4 inhibitory activity.
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Affiliation(s)
- Chul Min Park
- Research Center for Medicinal Chemistry, Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong, Daejeon, 305-343, Republic of Korea
| | - Songhyun Baek
- Research Center for Medicinal Chemistry, Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong, Daejeon, 305-343, Republic of Korea.,Korea University of Science and Technology, 141 Gajeong-ro, Yuseong, Daejeon, 305-343, Republic of Korea
| | - Seongwoo Kim
- Research Center for Medicinal Chemistry, Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong, Daejeon, 305-343, Republic of Korea.,Department of Chemistry, Chungbuk National University, Chungdae-ro, Seowon-gu, Cheongju-si, 28644, Chungbuk, Republic of Korea
| | - Jong-Hwan Song
- Research Center for Medicinal Chemistry, Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong, Daejeon, 305-343, Republic of Korea
| | - Sunkyung Lee
- Research Center for Medicinal Chemistry, Division of Drug Discovery Research, Korea Research Institute of Chemical Technology, 141 Gajeong-ro, Yuseong, Daejeon, 305-343, Republic of Korea. .,Korea University of Science and Technology, 141 Gajeong-ro, Yuseong, Daejeon, 305-343, Republic of Korea.
| | - Min Kim
- Department of Chemistry, Chungbuk National University, Chungdae-ro, Seowon-gu, Cheongju-si, 28644, Chungbuk, Republic of Korea
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198
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Shahaf N, Pappalardo M, Basile L, Guccione S, Rayan A. How to Choose the Suitable Template for Homology Modelling of GPCRs: 5-HT7 Receptor as a Test Case. Mol Inform 2016; 35:414-23. [PMID: 27546045 DOI: 10.1002/minf.201501029] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 05/19/2016] [Indexed: 01/06/2023]
Abstract
G protein-coupled receptors (GPCRs) are a super-family of membrane proteins that attract great pharmaceutical interest due to their involvement in almost every physiological activity, including extracellular stimuli, neurotransmission, and hormone regulation. Currently, structural information on many GPCRs is mainly obtained by the techniques of computer modelling in general and by homology modelling in particular. Based on a quantitative analysis of eighteen antagonist-bound, resolved structures of rhodopsin family "A" receptors - also used as templates to build 153 homology models - it was concluded that a higher sequence identity between two receptors does not guarantee a lower RMSD between their structures, especially when their pair-wise sequence identity (within trans-membrane domain and/or in binding pocket) lies between 25 % and 40 %. This study suggests that we should consider all template receptors having a sequence identity ≤50 % with the query receptor. In fact, most of the GPCRs, compared to the currently available resolved structures of GPCRs, fall within this range and lack a correlation between structure and sequence. When testing suitability for structure-based drug design, it was found that choosing as a template the most similar resolved protein, based on sequence resemblance only, led to unsound results in many cases. Molecular docking analyses were carried out, and enrichment factors as well as attrition rates were utilized as criteria for assessing suitability for structure-based drug design.
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Affiliation(s)
- Nir Shahaf
- Drug Discovery Informatics Lab, Qasemi-Research Center, Al-Qasemi Academic College, Baka El-Garbiah, 30100, Israel
| | - Matteo Pappalardo
- Department of Drug Sciences . .,Department of Chemical Sciences -, University of Catania -, V.leA.Doria 6, I-95125, Catania, Italy.
| | | | | | - Anwar Rayan
- Drug Discovery Informatics Lab, Qasemi-Research Center, Al-Qasemi Academic College, Baka El-Garbiah, 30100, Israel, . .,Institute of Applied Research, Galilee Society, Shefa-Amr, 20200, Israel.
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199
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Tabit CE, Chen P, Kim GH, Fedson SE, Sayer G, Coplan MJ, Jeevanandam V, Uriel N, Liao JK. Elevated Angiopoietin-2 Level in Patients With Continuous-Flow Left Ventricular Assist Devices Leads to Altered Angiogenesis and Is Associated With Higher Nonsurgical Bleeding. Circulation 2016; 134:141-52. [PMID: 27354285 DOI: 10.1161/circulationaha.115.019692] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 05/18/2016] [Indexed: 02/03/2023]
Abstract
BACKGROUND Nonsurgical bleeding is the most common adverse event in patients with continuous-flow left ventricular assist devices (LVADs) and is caused by arteriovenous malformations. We hypothesized that deregulation of an angiogenic factor, angiopoietin-2 (Ang-2), in patients with LVADs leads to increased angiogenesis and higher nonsurgical bleeding. METHODS Ang-2 and thrombin levels were measured by ELISA and Western blotting, respectively, in blood samples from 101 patients with heart failure, LVAD, or orthotopic heart transplantation. Ang-2 expression in endothelial biopsy was quantified by immunofluorescence. Angiogenesis was determined by in vitro tube formation from serum from each patient with or without Ang-2-blocking antibody. Ang-2 gene expression was measured by reverse transcription-polymerase chain reaction in endothelial cells incubated with plasma from each patient with or without the thrombin receptor blocker vorapaxar. RESULTS Compared with patients with heart failure or those with orthotopic heart transplantation, serum levels and endothelial expression of Ang-2 were higher in LVAD patients (P=0.001 and P<0.001, respectively). This corresponded to an increased angiogenic potential of serum from patients with LVADs (P<0.001), which was normalized with Ang-2 blockade. Furthermore, plasma from LVAD patients contained higher amounts of thrombin (P=0.003), which was associated with activation of the contact coagulation system. Plasma from LVAD patients induced more Ang-2 gene expression in endothelial cells (P<0.001), which was reduced with thrombin receptor blockade (P=0.013). LVAD patients with Ang-2 levels above the mean (12.32 ng/mL) had more nonsurgical bleeding events compared with patients with Ang-2 levels below the mean (P=0.003). CONCLUSIONS Our findings indicate that thrombin-induced Ang-2 expression in LVAD patients leads to increased angiogenesis in vitro and may be associated with higher nonsurgical bleeding events. Ang-2 therefore may contribute to arteriovenous malformation formation and subsequent bleeding in LVAD patients.
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Affiliation(s)
- Corey E Tabit
- From the Department of Medicine, Section of Cardiology (C.E.T., P.C., G.H.K., G.S., M.J.C., N.U., J.K.L.) and Department of Surgery, Section of Cardiac and Thoracic Surgery (V.T.), University of Chicago, IL; and Section of Cardiology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX (S.E.F.)
| | - Phetcharat Chen
- From the Department of Medicine, Section of Cardiology (C.E.T., P.C., G.H.K., G.S., M.J.C., N.U., J.K.L.) and Department of Surgery, Section of Cardiac and Thoracic Surgery (V.T.), University of Chicago, IL; and Section of Cardiology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX (S.E.F.)
| | - Gene H Kim
- From the Department of Medicine, Section of Cardiology (C.E.T., P.C., G.H.K., G.S., M.J.C., N.U., J.K.L.) and Department of Surgery, Section of Cardiac and Thoracic Surgery (V.T.), University of Chicago, IL; and Section of Cardiology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX (S.E.F.)
| | - Savitri E Fedson
- From the Department of Medicine, Section of Cardiology (C.E.T., P.C., G.H.K., G.S., M.J.C., N.U., J.K.L.) and Department of Surgery, Section of Cardiac and Thoracic Surgery (V.T.), University of Chicago, IL; and Section of Cardiology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX (S.E.F.)
| | - Gabriel Sayer
- From the Department of Medicine, Section of Cardiology (C.E.T., P.C., G.H.K., G.S., M.J.C., N.U., J.K.L.) and Department of Surgery, Section of Cardiac and Thoracic Surgery (V.T.), University of Chicago, IL; and Section of Cardiology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX (S.E.F.)
| | - Mitchell J Coplan
- From the Department of Medicine, Section of Cardiology (C.E.T., P.C., G.H.K., G.S., M.J.C., N.U., J.K.L.) and Department of Surgery, Section of Cardiac and Thoracic Surgery (V.T.), University of Chicago, IL; and Section of Cardiology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX (S.E.F.)
| | - Valluvan Jeevanandam
- From the Department of Medicine, Section of Cardiology (C.E.T., P.C., G.H.K., G.S., M.J.C., N.U., J.K.L.) and Department of Surgery, Section of Cardiac and Thoracic Surgery (V.T.), University of Chicago, IL; and Section of Cardiology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX (S.E.F.)
| | - Nir Uriel
- From the Department of Medicine, Section of Cardiology (C.E.T., P.C., G.H.K., G.S., M.J.C., N.U., J.K.L.) and Department of Surgery, Section of Cardiac and Thoracic Surgery (V.T.), University of Chicago, IL; and Section of Cardiology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX (S.E.F.)
| | - James K Liao
- From the Department of Medicine, Section of Cardiology (C.E.T., P.C., G.H.K., G.S., M.J.C., N.U., J.K.L.) and Department of Surgery, Section of Cardiac and Thoracic Surgery (V.T.), University of Chicago, IL; and Section of Cardiology, Michael E. DeBakey Veterans Affairs Medical Center, Houston, TX (S.E.F.).
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200
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Kontogianni VG, Tsoumani ME, Kellici TF, Mavromoustakos T, Gerothanassis IP, Tselepis AD, Tzakos AG. Deconvoluting the Dual Antiplatelet Activity of a Plant Extract. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2016; 64:4511-4521. [PMID: 27161160 DOI: 10.1021/acs.jafc.6b00544] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A thorough evaluation of the antiplatelet activity profile of hexane olive leaf extract in human platelets indicated a potent activity accomplished through a two axis inhibition of platelet activation triggered both by ADP and thrombin. To delineate the extract components responsible for this dual activity, an NMR based method was established to determine and quantify the triterpenoid content leading to the characterization of uvaol, erythrodiol, and oleanolic acid. The antiplatelet profile of the total extract and of the 3 determined triterpenoids was evaluated against in vitro platelet aggregation induced by several platelet agonists as also on PAC-1 binding and P-selectin membrane expression both in healthy volunteers and in platelets from patients with an acute coronary syndrome receiving dual antiplatelet therapy with aspirin and ticagrelor. The extract was identified to inhibit ADP-induced platelet activation due to its erythrodiol content and TRAP-induced platelet activation due to the activity of uvaol and oleanolic acid.
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Affiliation(s)
- Vassiliki G Kontogianni
- Laboratory of Organic Chemistry, Department of Chemistry, University of Ioannina , 45110 Ioannina, Greece
| | - Maria E Tsoumani
- Atherothrombosis Research Centre/Laboratory of Biochemistry, Department of Chemistry, University of Ioannina , 45110 Ioannina, Greece
| | - Tahsin F Kellici
- Laboratory of Organic Chemistry, Department of Chemistry, University of Ioannina , 45110 Ioannina, Greece
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens , Athens, Greece
| | - Thomas Mavromoustakos
- Laboratory of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens , Athens, Greece
| | - Ioannis P Gerothanassis
- Laboratory of Organic Chemistry, Department of Chemistry, University of Ioannina , 45110 Ioannina, Greece
| | - Alexandros D Tselepis
- Atherothrombosis Research Centre/Laboratory of Biochemistry, Department of Chemistry, University of Ioannina , 45110 Ioannina, Greece
| | - Andreas G Tzakos
- Laboratory of Organic Chemistry, Department of Chemistry, University of Ioannina , 45110 Ioannina, Greece
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