101
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Structure of an allosteric modulator bound to the CB1 cannabinoid receptor. Nat Chem Biol 2019; 15:1199-1205. [PMID: 31659318 DOI: 10.1038/s41589-019-0387-2] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 09/09/2019] [Indexed: 02/05/2023]
Abstract
The CB1 receptor mediates the central nervous system response to cannabinoids, and is a drug target for pain, anxiety and seizures. CB1 also responds to allosteric modulators, which influence cannabinoid binding and efficacy. To understand the mechanism of these compounds, we solved the crystal structure of CB1 with the negative allosteric modulator (NAM) ORG27569 and the agonist CP55940. The structure reveals that the NAM binds to an extrahelical site within the inner leaflet of the membrane, which overlaps with a conserved site of cholesterol interaction in many G protein-coupled receptors (GPCRs). The ternary structure with ORG27569 and CP55940 captures an intermediate state of the receptor, in which aromatic residues at the base of the agonist-binding pocket adopt an inactive conformation despite the large contraction of the orthosteric pocket. The structure illustrates a potential strategy for drug modulation of CB1 and other class A GPCRs.
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102
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Yu X, Plotnikova O, Bonin PD, Subashi TA, McLellan TJ, Dumlao D, Che Y, Dong YY, Carpenter EP, West GM, Qiu X, Culp JS, Han S. Cryo-EM structures of the human glutamine transporter SLC1A5 (ASCT2) in the outward-facing conformation. eLife 2019; 8:e48120. [PMID: 31580259 PMCID: PMC6800002 DOI: 10.7554/elife.48120] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/02/2019] [Indexed: 12/17/2022] Open
Abstract
Alanine-serine-cysteine transporter 2 (ASCT2, SLC1A5) is the primary transporter of glutamine in cancer cells and regulates the mTORC1 signaling pathway. The SLC1A5 function involves finely tuned orchestration of two domain movements that include the substrate-binding transport domain and the scaffold domain. Here, we present cryo-EM structures of human SLC1A5 and its complex with the substrate, L-glutamine in an outward-facing conformation. These structures reveal insights into the conformation of the critical ECL2a loop which connects the two domains, thus allowing rigid body movement of the transport domain throughout the transport cycle. Furthermore, the structures provide new insights into substrate recognition, which involves conformational changes in the HP2 loop. A putative cholesterol binding site was observed near the domain interface in the outward-facing state. Comparison with the previously determined inward-facing structure of SCL1A5 provides a basis for a more integrated understanding of substrate recognition and transport mechanism in the SLC1 family.
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Affiliation(s)
- Xiaodi Yu
- Medicine DesignPfizer IncGrotonUnited States
| | | | | | | | | | | | - Ye Che
- Medicine DesignPfizer IncGrotonUnited States
| | - Yin Yao Dong
- Structural Genomics ConsortiumUniversity of OxfordOxfordUnited Kingdom
| | | | | | - Xiayang Qiu
- Medicine DesignPfizer IncGrotonUnited States
| | | | - Seungil Han
- Medicine DesignPfizer IncGrotonUnited States
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103
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Hao J, Beck JP, Schaus JM, Krushinski JH, Chen Q, Beadle CD, Vidal P, Reinhard MR, Dressman BA, Massey SM, Boulet SL, Cohen MP, Watson BM, Tupper D, Gardinier KM, Myers J, Johansson AM, Richardson J, Richards DS, Hembre EJ, Remick DM, Coates DA, Bhardwaj RM, Diseroad BA, Bender D, Stephenson G, Wolfangel CD, Diaz N, Getman BG, Wang XS, Heinz BA, Cramer JW, Zhou X, Maren DL, Falcone JF, Wright RA, Mitchell SN, Carter G, Yang CR, Bruns RF, Svensson KA. Synthesis and Pharmacological Characterization of 2-(2,6-Dichlorophenyl)-1-((1 S,3 R)-5-(3-hydroxy-3-methylbutyl)-3-(hydroxymethyl)-1-methyl-3,4-dihydroisoquinolin-2(1 H)-yl)ethan-1-one (LY3154207), a Potent, Subtype Selective, and Orally Available Positive Allosteric Modulator of the Human Dopamine D1 Receptor. J Med Chem 2019; 62:8711-8732. [PMID: 31532644 DOI: 10.1021/acs.jmedchem.9b01234] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Clinical development of catechol-based orthosteric agonists of the dopamine D1 receptor has thus far been unsuccessful due to multiple challenges. To address these issues, we identified LY3154207 (3) as a novel, potent, and subtype selective human D1 positive allosteric modulator (PAM) with minimal allosteric agonist activity. Conformational studies showed LY3154207 adopts an unusual boat conformation, and a binding pose with the human D1 receptor was proposed based on this observation. In contrast to orthosteric agonists, LY3154207 showed a distinct pharmacological profile without a bell-shaped dose-response relationship or tachyphylaxis in preclinical models. Identification of a crystalline form of free LY3154207 from the discovery lots was not successful. Instead, a novel cocrystal form with superior solubility was discovered and determined to be suitable for development. This cocrystal form was advanced to clinical development as a potential first-in-class D1 PAM and is now in phase 2 studies for Lewy body dementia.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Daniel S Richards
- AMRI UK Ltd , Erl Wood Manor, Sunninghill Road , Windlesham , Surrey , GU20 6PH , United Kingdom
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104
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Duncan AL, Song W, Sansom MSP. Lipid-Dependent Regulation of Ion Channels and G Protein-Coupled Receptors: Insights from Structures and Simulations. Annu Rev Pharmacol Toxicol 2019; 60:31-50. [PMID: 31506010 DOI: 10.1146/annurev-pharmtox-010919-023411] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ion channels and G protein-coupled receptors (GPCRs) are regulated by lipids in their membrane environment. Structural studies combined with biophysical and molecular simulation investigations reveal interaction sites for specific lipids on membrane protein structures. For K channels, PIP2 plays a key role in regulating Kv and Kir channels. Likewise, several recent cryo-EM structures of TRP channels have revealed bound lipids, including PIP2 and cholesterol. Among the pentameric ligand-gated ion channel family, structural and biophysical studies suggest the M4 TM helix may act as a lipid sensor, e.g., forming part of the binding sites for neurosteroids on the GABAA receptor. Structures of GPCRs have revealed multiple cholesterol sites, which may modulate both receptor dynamics and receptor oligomerization. PIP2 also interacts with GPCRs and may modulate their interactions with G proteins. Overall, it is evident that multiple lipid binding sites exist on channels and receptors that modulate their function allosterically and are potential druggable sites.
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Affiliation(s)
- Anna L Duncan
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom;
| | - Wanling Song
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom;
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom;
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105
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Targeting GPCRs Activated by Fatty Acid-Derived Lipids in Type 2 Diabetes. Trends Mol Med 2019; 25:915-929. [PMID: 31377146 DOI: 10.1016/j.molmed.2019.07.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 04/28/2019] [Accepted: 07/08/2019] [Indexed: 12/20/2022]
Abstract
G protein-coupled receptors (GPCRs) are the most intensively studied drug targets, because of their diversity, cell-specific expression, and druggable sites accessible at the cell surface. Preclinical and clinical studies suggest that targeting GPCRs activated by fatty acid-derived lipids may have potential to improve glucose homeostasis and reduce complications in patients with type 2 diabetes (T2D). Despite the discontinued development of fasiglifam (TAK-875), the first FFA1 agonist to reach late-stage clinical trials, lipid-sensing receptors remain a viable target, albeit with a need for further characterization of their binding mode, intracellular signaling, and toxicity. Herein, we analyze general discovery trends, various signaling pathways, as well as possible challenges following activation of GPCRs that have been validated clinically to control blood glucose levels.
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106
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Carullo G, Perri M, Manetti F, Aiello F, Caroleo MC, Cione E. Quercetin-3-oleoyl derivatives as new GPR40 agonists: Molecular docking studies and functional evaluation. Bioorg Med Chem Lett 2019; 29:1761-1764. [DOI: 10.1016/j.bmcl.2019.05.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/07/2019] [Accepted: 05/11/2019] [Indexed: 11/26/2022]
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107
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Design, synthesis and biological evaluation of indane derived GPR40 agoPAMs. Bioorg Med Chem Lett 2019; 29:1842-1848. [DOI: 10.1016/j.bmcl.2019.04.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/16/2019] [Accepted: 04/30/2019] [Indexed: 01/21/2023]
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108
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Liu X, Masoudi A, Kahsai AW, Huang LY, Pani B, Staus DP, Shim PJ, Hirata K, Simhal RK, Schwalb AM, Rambarat PK, Ahn S, Lefkowitz RJ, Kobilka B. Mechanism of β 2AR regulation by an intracellular positive allosteric modulator. Science 2019; 364:1283-1287. [PMID: 31249059 DOI: 10.1126/science.aaw8981] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 06/10/2019] [Indexed: 12/17/2022]
Abstract
Drugs targeting the orthosteric, primary binding site of G protein-coupled receptors are the most common therapeutics. Allosteric binding sites, elsewhere on the receptors, are less well-defined, and so less exploited clinically. We report the crystal structure of the prototypic β2-adrenergic receptor in complex with an orthosteric agonist and compound-6FA, a positive allosteric modulator of this receptor. It binds on the receptor's inner surface in a pocket created by intracellular loop 2 and transmembrane segments 3 and 4, stabilizing the loop in an α-helical conformation required to engage the G protein. Structural comparison explains the selectivity of the compound for β2- over the β1-adrenergic receptor. Diversity in location, mechanism, and selectivity of allosteric ligands provides potential to expand the range of receptor drugs.
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Affiliation(s)
- Xiangyu Liu
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ali Masoudi
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Alem W Kahsai
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Li-Yin Huang
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Biswaranjan Pani
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Dean P Staus
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Paul J Shim
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Kunio Hirata
- Advanced Photon Technology Division, Research Infrastructure Group, SR Life Science Instrumentation Unit, RIKEN/SPring-8 Center, 1-1-1 Kouto Sayo-cho Sayo-gun, Hyogo 679-5148, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Rishabh K Simhal
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Allison M Schwalb
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Paula K Rambarat
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Seungkirl Ahn
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Robert J Lefkowitz
- Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA. .,Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA.,Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Brian Kobilka
- Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Medicine, Tsinghua University, Beijing 100084, China. .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, 279 Campus Drive, Stanford, CA 94305, USA
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109
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Wink LH, Baker DL, Cole JA, Parrill AL. A benchmark study of loop modeling methods applied to G protein-coupled receptors. J Comput Aided Mol Des 2019; 33:573-595. [PMID: 31123958 PMCID: PMC6628340 DOI: 10.1007/s10822-019-00196-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/12/2019] [Indexed: 11/25/2022]
Abstract
G protein-coupled receptors (GPCR) are important drug discovery targets. Despite progress, many GPCR structures have not yet been solved. For these targets, comparative modeling is used in virtual ligand screening to prioritize experimental efforts. However, the structure of extracellular loop 2 (ECL2) is often poorly predicted. This is significant due to involvement of ECL2 in ligand binding for many Class A GPCR. Here we examine the performance of loop modeling protocols available in the Rosetta (cyclic coordinate descent [CCD], KIC with fragments [KICF] and next generation KIC [NGK]) and Molecular Operating Environment (MOE) software suites (de novo search). ECL2 from GPCR crystal structures served as the structure prediction targets and were divided into four sets depending on loop length. Results suggest that KICF and NGK sampled and scored more loop models with sub-angstrom and near-atomic accuracy than CCD or de novo search for loops of 24 or fewer residues. None of the methods were able to sample loop conformations with near-atomic accuracy for the longest targets ranging from 25 to 32 residues based on 1000 models generated. For these long loop targets, increased conformational sampling is necessary. The strongly conserved disulfide bond between Cys3.25 and Cys45.50 in ECL2 proved an effective filter. Setting an upper limit of 5.1 Å on the S-S distance improved the lowest RMSD model included in the top 10 scored structures in Groups 1-4 on average between 0.33 and 1.27 Å. Disulfide bond formation and geometry optimization of ECL2 provided an additional incremental benefit in structure quality.
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Affiliation(s)
- Lee H Wink
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Daniel L Baker
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA
| | - Judith A Cole
- Department of Biological Sciences, The University of Memphis, Memphis, TN, 38152, USA
| | - Abby L Parrill
- Department of Chemistry, The University of Memphis, Memphis, TN, 38152, USA.
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110
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Falomir-Lockhart LJ, Cavazzutti GF, Giménez E, Toscani AM. Fatty Acid Signaling Mechanisms in Neural Cells: Fatty Acid Receptors. Front Cell Neurosci 2019; 13:162. [PMID: 31105530 PMCID: PMC6491900 DOI: 10.3389/fncel.2019.00162] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/08/2019] [Indexed: 12/15/2022] Open
Abstract
Fatty acids (FAs) are typically associated with structural and metabolic roles, as they can be stored as triglycerides, degraded by β-oxidation or used in phospholipids’ synthesis, the main components of biological membranes. It has been shown that these lipids exhibit also regulatory functions in different cell types. FAs can serve as secondary messengers, as well as modulators of enzymatic activities and substrates for cytokines synthesis. More recently, it has been documented a direct activity of free FAs as ligands of membrane, cytosolic, and nuclear receptors, and cumulative evidence has emerged, demonstrating its participation in a wide range of physiological and pathological conditions. It has been long known that the central nervous system is enriched with poly-unsaturated FAs, such as arachidonic (C20:4ω-6) or docosohexaenoic (C22:6ω-3) acids. These lipids participate in the regulation of membrane fluidity, axonal growth, development, memory, and inflammatory response. Furthermore, a whole family of low molecular weight compounds derived from FAs has also gained special attention as the natural ligands for cannabinoid receptors or key cytokines involved in inflammation, largely expanding the role of FAs as precursors of signaling molecules. Nutritional deficiencies, and alterations in lipid metabolism and lipid signaling have been associated with developmental and cognitive problems, as well as with neurodegenerative diseases. The molecular mechanism behind these effects still remains elusive. But in the last two decades, different families of proteins have been characterized as receptors mediating FAs signaling. This review focuses on different receptors sensing and transducing free FAs signals in neural cells: (1) membrane receptors of the family of G Protein Coupled Receptors known as Free Fatty Acid Receptors (FFARs); (2) cytosolic transport Fatty Acid-Binding Proteins (FABPs); and (3) transcription factors Peroxisome Proliferator-Activated Receptors (PPARs). We discuss how these proteins modulate and mediate direct regulatory functions of free FAs in neural cells. Finally, we briefly discuss the advantages of evaluating them as potential targets for drug design in order to manipulate lipid signaling. A thorough characterization of lipid receptors of the nervous system could provide a framework for a better understanding of their roles in neurophysiology and, potentially, help for the development of novel drugs against aging and neurodegenerative processes.
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Affiliation(s)
- Lisandro Jorge Falomir-Lockhart
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), Centro Científico Tecnológico - La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), La Plata, Argentina.,Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Gian Franco Cavazzutti
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), Centro Científico Tecnológico - La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), La Plata, Argentina.,Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Ezequiel Giménez
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), Centro Científico Tecnológico - La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), La Plata, Argentina.,Facultad de Ciencias Médicas, Universidad Nacional de La Plata (UNLP), La Plata, Argentina
| | - Andrés Martín Toscani
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), Centro Científico Tecnológico - La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), La Plata, Argentina.,Facultad de Ciencias Médicas, Universidad Nacional de La Plata (UNLP), La Plata, Argentina
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111
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Analysis of tractable allosteric sites in G protein-coupled receptors. Sci Rep 2019; 9:6180. [PMID: 30992500 PMCID: PMC6467999 DOI: 10.1038/s41598-019-42618-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/28/2019] [Indexed: 11/21/2022] Open
Abstract
Allosteric modulation of G protein-coupled receptors represent a promising mechanism of pharmacological intervention. Dramatic developments witnessed in the structural biology of membrane proteins continue to reveal that the binding sites of allosteric modulators are widely distributed, including along protein surfaces. Here we restrict consideration to intrahelical and intracellular sites together with allosteric conformational locks, and show that the protein mapping tools FTMap and FTSite identify 83% and 88% of such experimentally confirmed allosteric sites within the three strongest sites found. The methods were also able to find partially hidden allosteric sites that were not fully formed in X-ray structures crystallized in the absence of allosteric ligands. These results confirm that the intrahelical sites capable of binding druglike allosteric modulators are among the strongest ligand recognition sites in a large fraction of GPCRs and suggest that both FTMap and FTSite are useful tools for identifying allosteric sites and to aid in the design of such compounds in a range of GPCR targets.
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112
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Al-Zoubi R, Morales P, Reggio PH. Structural Insights into CB1 Receptor Biased Signaling. Int J Mol Sci 2019; 20:E1837. [PMID: 31013934 PMCID: PMC6515405 DOI: 10.3390/ijms20081837] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/09/2019] [Accepted: 04/11/2019] [Indexed: 12/21/2022] Open
Abstract
The endocannabinoid system has emerged as a promising target for the treatment of numerous diseases, including cancer, neurodegenerative disorders, and metabolic syndromes. Thus far, two cannabinoid receptors, CB1 and CB2, have been discovered, which are found predominantly in the central nervous system (CB1) or the immune system (CB2), among other organs and tissues. CB1 receptor ligands have been shown to induce a complex pattern of intracellular effects. The binding of a ligand induces distinct conformational changes in the receptor, which will eventually translate into distinct intracellular signaling pathways through coupling to specific intracellular effector proteins. These proteins can mediate receptor desensitization, trafficking, or signaling. Ligand specificity and selectivity, complex cellular components, and the concomitant expression of other proteins (which either regulate the CB1 receptor or are regulated by the CB1 receptor) will affect the therapeutic outcome of its targeting. With an increased interest in G protein-coupled receptors (GPCR) research, in-depth studies using mutations, biological assays, and spectroscopic techniques (such as NMR, EPR, MS, FRET, and X-ray crystallography), as well as computational modelling, have begun to reveal a set of concerted structural features in Class A GPCRs which relate to signaling pathways and the mechanisms of ligand-induced activation, deactivation, or activity modulation. This review will focus on the structural features of the CB1 receptor, mutations known to bias its signaling, and reported studies of CB1 receptor ligands to control its specific signaling.
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Affiliation(s)
- Rufaida Al-Zoubi
- Department of Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy, Jordan University of Science & Technology, P.O.BOX 3030, Irbid 22110, Jordan.
| | - Paula Morales
- Departamento de Química-Física Biológica, Instituto de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006 Madrid, Spain.
| | - Patricia H Reggio
- Chemistry and Biochemistry Department, UNC Greensboro, Greensboro, NC 27412, USA.
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113
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Szlenk CT, Gc JB, Natesan S. Does the Lipid Bilayer Orchestrate Access and Binding of Ligands to Transmembrane Orthosteric/Allosteric Sites of G Protein-Coupled Receptors? Mol Pharmacol 2019; 96:527-541. [PMID: 30967440 DOI: 10.1124/mol.118.115113] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/03/2019] [Indexed: 01/08/2023] Open
Abstract
The ligand-binding sites of many G protein-coupled receptors (GPCRs) are situated around and deeply embedded within the central pocket formed by their seven transmembrane-spanning α-helical domains. Generally, these binding sites are assumed accessible to endogenous ligands from the aqueous phase. Recent advances in the structural biology of GPCRs, along with biophysical and computational studies, suggest that amphiphilic and lipophilic molecules may gain access to these receptors by first partitioning into the membrane and then reaching the binding site via lateral diffusion through the lipid bilayer. In addition, several crystal structures of class A and class B GPCRs bound to their ligands offer unprecedented details on the existence of lipid-facing allosteric binding sites outside the transmembrane helices that can only be reached via lipid pathways. The highly organized structure of the lipid bilayer may direct lipophilic or amphiphilic drugs to a specific depth within the bilayer, changing local concentration of the drug near the binding site and affecting its binding kinetics. Additionally, the constraints of the lipid bilayer, including its composition and biophysical properties, may play a critical role in "pre-organizing" ligand molecules in an optimal orientation and conformation to facilitate receptor binding. Despite its clear involvement in molecular recognition processes, the critical role of the membrane in binding ligands to lipid-exposed transmembrane binding sites remains poorly understood and warrants comprehensive investigation. Understanding the mechanistic basis of the structure-membrane interaction relationship of drugs will not only provide useful insights about receptor binding kinetics but will also enhance our ability to take advantage of the apparent membrane contributions when designing drugs that target transmembrane proteins with improved efficacy and safety. In this minireview, we summarize recent structural and computational studies on membrane contributions to binding processes, elucidating both lipid pathways of ligand access and binding mechanisms for several orthosteric and allosteric ligands of class A and class B GPCRs.
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Affiliation(s)
- Christopher T Szlenk
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Jeevan B Gc
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Senthil Natesan
- College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
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114
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Abstract
Structures of G protein-coupled receptors (GPCRs) in complex with ligands mainly provide frozen pictures with little information about the actual molecular mechanism of action of the ligand in the normally highly dynamic receptor. Through computer-based molecular dynamics simulations of a receptor for long-chain fatty acids, free fatty acid receptor 1 (FFAR1), we discover that an unoccupied, solvent-exposed pocket closes on removal of the lipid-like agonist; that is, during a major conformational change of the receptor. Importantly, a compound designed to prevent closure of this previously unrecognized, dynamic pocket was identified through structure-based virtual screening and shown to function as an allosteric agonist for the receptor. The study demonstrates that molecular dynamics simulations can be used in drug discovery to identify different modes of stabilizing specific receptor states. The long-chain fatty acid receptor FFAR1/GPR40 binds agonists in both an interhelical site between the extracellular segments of transmembrane helix (TM)-III and TM-IV and a lipid-exposed groove between the intracellular segments of these helices. Molecular dynamics simulations of FFAR1 with agonist removed demonstrated a major rearrangement of the polar and charged anchor point residues for the carboxylic acid moiety of the agonist in the interhelical site, which was associated with closure of a neighboring, solvent-exposed pocket between the extracellular poles of TM-I, TM-II, and TM-VII. A synthetic compound designed to bind in this pocket, and thereby prevent its closure, was identified through structure-based virtual screening and shown to function both as an agonist and as an allosteric modulator of receptor activation. This discovery of an allosteric agonist for a previously unexploited, dynamic pocket in FFAR1 demonstrates both the power of including molecular dynamics in the drug discovery process and that this specific, clinically proven, but difficult, antidiabetes target can be addressed by chemotypes different from existing ligands.
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115
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Audet M, Stevens RC. Emerging structural biology of lipid G protein-coupled receptors. Protein Sci 2019; 28:292-304. [PMID: 30239054 PMCID: PMC6319753 DOI: 10.1002/pro.3509] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 01/14/2023]
Abstract
The first crystal structure of a G protein-coupled receptor (GPCR) was that of the bovine rhodopsin, solved in 2000, and is a light receptor within retina rode cells that enables vision by transducing a conformational signal from the light-induced isomerization of retinal covalently bound to the receptor. More than 7 years after this initial discovery and following more than 20 years of technological developments in GPCR expression, stabilization, and crystallography, the high-resolution structure of the adrenaline binding β2 -adrenergic receptor, a ligand diffusible receptor, was discovered. Since then, high-resolution structures of more than 53 unique GPCRs have been determined leading to a significant improvement in our understanding of the basic mechanisms of ligand-binding and ligand-mediated receptor activation that revolutionized the field of structural molecular pharmacology of GPCRs. Recently, several structures of eight unique lipid-binding receptors, one of the most difficult GPCR families to study, have been reported. This review presents the outstanding structural and pharmacological features that have emerged from these new lipid receptor structures. The impact of these findings goes beyond mechanistic insights, providing evidence of the fundamental role of GPCRs in the physiological integration of the lipid signaling system, and highlighting the importance of sustained research into the structural biology of GPCRs for the development of new therapeutics targeting lipid receptors.
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Affiliation(s)
- Martin Audet
- Departments of Biological Sciences and ChemistryBridge Institute, Michelson Center for Convergent Bioscience, University of Southern CaliforniaLos AngelesCalifornia90089
| | - Raymond C. Stevens
- Departments of Biological Sciences and ChemistryBridge Institute, Michelson Center for Convergent Bioscience, University of Southern CaliforniaLos AngelesCalifornia90089
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116
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Wold EA, Chen J, Cunningham KA, Zhou J. Allosteric Modulation of Class A GPCRs: Targets, Agents, and Emerging Concepts. J Med Chem 2019; 62:88-127. [PMID: 30106578 PMCID: PMC6556150 DOI: 10.1021/acs.jmedchem.8b00875] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
G-protein-coupled receptors (GPCRs) have been tractable drug targets for decades with over one-third of currently marketed drugs targeting GPCRs. Of these, the class A GPCR superfamily is highly represented, and continued drug discovery for this family of receptors may provide novel therapeutics for a vast range of diseases. GPCR allosteric modulation is an innovative targeting approach that broadens the available small molecule toolbox and is proving to be a viable drug discovery strategy, as evidenced by recent FDA approvals and clinical trials. Numerous class A GPCR allosteric modulators have been discovered recently, and emerging trends such as the availability of GPCR crystal structures, diverse functional assays, and structure-based computational approaches are improving optimization and development. This Perspective provides an update on allosterically targeted class A GPCRs and their disease indications and the medicinal chemistry approaches toward novel allosteric modulators and highlights emerging trends and opportunities in the field.
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Affiliation(s)
- Eric A. Wold
- Department of Pharmacology and Toxicology, Chemical Biology Program, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jianping Chen
- Department of Pharmacology and Toxicology, Chemical Biology Program, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Kathryn A. Cunningham
- Department of Pharmacology and Toxicology, Chemical Biology Program, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - Jia Zhou
- Department of Pharmacology and Toxicology, Chemical Biology Program, University of Texas Medical Branch, Galveston, Texas 77555, United States
- Department of Pharmacology and Toxicology, Center for Addiction Research, University of Texas Medical Branch, Galveston, Texas 77555, United States
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117
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Huang H, Meegalla SK, Lanter JC, Winters MP, Zhao S, Littrell J, Qi J, Rady B, Lee PS, Liu J, Martin T, Lam WW, Xu F, Lim HK, Wilde T, Silva J, Otieno M, Pocai A, Player MR. Discovery of a GPR40 Superagonist: The Impact of Aryl Propionic Acid α-Fluorination. ACS Med Chem Lett 2019; 10:16-21. [PMID: 30655940 PMCID: PMC6331191 DOI: 10.1021/acsmedchemlett.8b00444] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/03/2018] [Indexed: 12/11/2022] Open
Abstract
GPR40 is a G-protein-coupled receptor which mediates fatty acid-induced glucose-stimulated insulin secretion from pancreatic beta cells and incretion release from enteroendocrine cells of the small intestine. GPR40 full agonists exhibit superior glucose lowering compared to partial agonists in preclinical species due to increased insulin and GLP-1 secretion, with the added benefit of promoting weight loss. In our search for potent GPR40 full agonists, we discovered a superagonist which displayed excellent in vitro potency and superior efficacy in the Gαs-mediated signaling pathway. Most synthetic GPR40 agonists have a carboxylic acid headgroup, which may cause idiosyncratic toxicities, including drug-induced-liver-injury (DILI). With a methyl group and a fluorine atom substituted at the α-C of the carboxylic acid group, 19 is not only highly efficacious in lowering glucose and body weight in rodent models but also has a low DILI risk due to its stable acylglucuronide metabolite.
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Affiliation(s)
- Hui Huang
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Sanath K. Meegalla
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - James C. Lanter
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Michael P. Winters
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Shuyuan Zhao
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - James Littrell
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Jenson Qi
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Brian Rady
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Paul S. Lee
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Jianying Liu
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Tonya Martin
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Wing W. Lam
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Fran Xu
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Heng Keang Lim
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Thomas Wilde
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Jose Silva
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Monicah Otieno
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Alessandro Pocai
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
| | - Mark R. Player
- Departments
of Medicinal Chemistry, Cardiovascular & Metabolism in Vitro Biology, Cardiovascular &
Metabolism in Vivo Pharmacology, andPreclinical Drug Safety, Janssen Research & Development, Welsh and McKean Roads,Spring House, Pennsylvania 19477-0776, United States
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118
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New Binding Sites, New Opportunities for GPCR Drug Discovery. Trends Biochem Sci 2019; 44:312-330. [PMID: 30612897 DOI: 10.1016/j.tibs.2018.11.011] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/11/2018] [Accepted: 11/27/2018] [Indexed: 12/29/2022]
Abstract
Many central biological events rely on protein-ligand interactions. The identification and characterization of protein-binding sites for ligands are crucial for the understanding of functions of both endogenous ligands and synthetic drug molecules. G protein-coupled receptors (GPCRs) typically detect extracellular signal molecules on the cell surface and transfer these chemical signals across the membrane, inducing downstream cellular responses via G proteins or β-arrestin. GPCRs mediate many central physiological processes, making them important targets for modern drug discovery. Here, we focus on the most recent breakthroughs in finding new binding sites and binding modes of GPCRs and their potentials for the development of new medicines.
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119
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Wu Y, Tong J, Ding K, Zhou Q, Zhao S. GPCR Allosteric Modulator Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1163:225-251. [PMID: 31707706 DOI: 10.1007/978-981-13-8719-7_10] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
G protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology; about one-third of all marketed drugs target members of this family. GPCR allosteric ligands hold the promise of improved subtype selectivity, spatiotemporal sensitivity, and possible biased property over typical orthosteric ligands. However, only a small number of GPCR allosteric ligands have been approved as drugs or in clinical trials since the discovery process is very challenging. The rapid development of GPCR structural biology leads to the discovery of several allosteric sites and sheds light on understanding the mechanism of GPCR allosteric ligands, which is critical for discovering novel therapeutics. This book chapter summarized different GPCR allosteric modulating mechanisms and discussed validated mechanisms based on allosteric modulator-GPCR complex structures.
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Affiliation(s)
- Yiran Wu
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Jiahui Tong
- iHuman Institute, ShanghaiTech University, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Kang Ding
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Qingtong Zhou
- iHuman Institute, ShanghaiTech University, Shanghai, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, China. .,School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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120
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Chitre NM, Moniri NH, Murnane KS. Omega-3 Fatty Acids as Druggable Therapeutics for Neurodegenerative Disorders. CNS & NEUROLOGICAL DISORDERS DRUG TARGETS 2019; 18:735-749. [PMID: 31724519 PMCID: PMC7204890 DOI: 10.2174/1871527318666191114093749] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/07/2019] [Accepted: 10/22/2019] [Indexed: 12/19/2022]
Abstract
Neurodegenerative disorders are commonly associated with a complex pattern of pathophysiological hallmarks, including increased oxidative stress and neuroinflammation, which makes their treatment challenging. Omega-3 Fatty Acids (O3FA) are natural products with reported neuroprotective, anti-inflammatory, and antioxidant effects. These effects have been attributed to their incorporation into neuronal membranes or through the activation of intracellular or recently discovered cell-surface receptors (i.e., Free-Fatty Acid Receptors; FFAR). Molecular docking studies have investigated the roles of O3FA as agonists of FFAR and have led to the development of receptor-specific targeted agonists for therapeutic purposes. Moreover, novel formulation strategies for targeted delivery of O3FA to the brain have supported their development as therapeutics for neurodegenerative disorders. Despite the compelling evidence of the beneficial effects of O3FA for several neuroprotective functions, they are currently only available as unregulated dietary supplements, with only a single FDA-approved prescription product, indicated for triglyceride reduction. This review highlights the relative safety and efficacy of O3FA, their drug-like properties, and their capacity to be formulated in clinically viable drug delivery systems. Interestingly, the presence of cardiac conditions such as hypertriglyceridemia is associated with brain pathophysiological hallmarks of neurodegeneration, such as neuroinflammation, thereby further suggesting potential therapeutic roles of O3FA for neurodegenerative disorders. Taken together, this review article summarizes and integrates the compelling evidence regarding the feasibility of developing O3FA and their synthetic derivatives as potential drugs for neurodegenerative disorders.
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Affiliation(s)
- Neha M. Chitre
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, GA USA
| | - Nader H. Moniri
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, GA USA
| | - Kevin S. Murnane
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, GA USA
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121
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Luna-Vital DA, Gonzalez de Mejia E. Anthocyanins from purple corn activate free fatty acid-receptor 1 and glucokinase enhancing in vitro insulin secretion and hepatic glucose uptake. PLoS One 2018; 13:e0200449. [PMID: 29995924 PMCID: PMC6040766 DOI: 10.1371/journal.pone.0200449] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 06/26/2018] [Indexed: 11/21/2022] Open
Abstract
The objective of this study was to evaluate the ability of anthocyanins (ANC) present in purple corn to enhance insulin secretion and hepatic glucose uptake in pancreatic cells and hepatocytes, through activation of the free fatty acid receptor-1 (FFAR1) and glucokinase (GK), respectively. Using a dual-layer cell culture with Caco-2 cells, INS-1E or HepG2 cells were treated with an anthocyanin-rich extract from the pericarp of purple corn (PCW), as well as pure ANC cyanidin-3-O-glucoside (C3G), peonidin-3-O-glucoside, pelargonidin-3-O-glucoside. Delphinidin-3-O-glucoside (D3G) was used for comparative purposes. Semipurified C3G (C3G-P) and condensed forms (CF-P) isolated from PCW were also used. At 100 μM, the pure ANC enhanced glucose-stimulated insulin secretion (GSIS) in INS-1E cells ranging from 18% to 40% (p<0.05) compared to untreated cells. PCW increased GSIS by 51%. D3G was the most effective anthocyanin activating FFAR1 (EC50: 196.6 μM). PCW had activating potential on FFAR1 (EC50: 77 μg/mL). PCW, as well as C3G and D3G increased the expression of FFAR1, PLC, and phosphorylation of PKD, related to the FFAR1-dependent insulin secretory pathway. The treatment with 100 μM of P3G and C3G increased (p<0.05) glucose uptake in HepG2 cells by 19% and 31%. PCW increased the glucose uptake in HepG2 cells by 48%. It was determined that CF-P was the most effective for activating GK (EC50: 39.9 μM) and the PCW extracts had an efficacy of EC50: 44 μg/mL. The ANC in purple corn also reduced AMPK phosphorylation and PEPCK expression in HepG2 cells, known to be related to reduction in gluconeogenesis. It is demonstrated for the first time that dietary ANC can enhance the activity of novel biomarkers FFAR1 and GK and potentially ameliorate type-2 diabetes comorbidities.
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Affiliation(s)
- Diego A. Luna-Vital
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Elvira Gonzalez de Mejia
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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122
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Structural insights into G-protein-coupled receptor allostery. Nature 2018; 559:45-53. [DOI: 10.1038/s41586-018-0259-z] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 05/17/2018] [Indexed: 01/14/2023]
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123
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Stenkamp RE. Identifying G protein-coupled receptor dimers from crystal packings. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:655-670. [PMID: 29968675 DOI: 10.1107/s2059798318008136] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/01/2018] [Indexed: 12/20/2022]
Abstract
Dimers of G protein-coupled receptors (GPCRs) are believed to be important for signaling with their associated G proteins. Low-resolution electron microscopy has shown rhodopsin dimers in native retinal membranes, and CXCR4 dimers have been found in several different crystal structures. Evidence for dimers of other GPCRs is more indirect. An alternative to computational modeling studies is to search for parallel dimers in the packing environments of the reported crystal structures of GPCRs. Two major structural types of GPCR dimers exist (as predicted by others), but there is considerable structural variation within each cluster. The different structural variants described here might reflect different functional properties and should provide a range of model structures for computational and experimental examination.
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Affiliation(s)
- Ronald E Stenkamp
- Departments of Biological Structure and Biochemistry, Biomolecular Structure Center, University of Washington, Box 357420, Seattle, WA 98195, USA
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124
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Liu H, Kim HR, Deepak RNVK, Wang L, Chung KY, Fan H, Wei Z, Zhang C. Orthosteric and allosteric action of the C5a receptor antagonists. Nat Struct Mol Biol 2018; 25:472-481. [PMID: 29867214 DOI: 10.1038/s41594-018-0067-z] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/16/2018] [Indexed: 01/09/2023]
Abstract
The C5a receptor (C5aR) is a G-protein-coupled receptor (GPCR) that can induce strong inflammatory response to the anaphylatoxin C5a. Targeting C5aR has emerged as a novel anti-inflammatory therapeutic method. However, developing potent C5aR antagonists as drugs has proven difficult. Here, we report two crystal structures of human C5aR in ternary complexes with the peptide antagonist PMX53 and a non-peptide antagonist, either avacopan or NDT9513727. The structures, together with other biophysical, computational docking and cell-based signaling data, reveal the orthosteric action of PMX53 and its effect of stabilizing the C5aR structure, as well as the allosteric action of chemically diverse non-peptide C5aR antagonists with different binding poses. Structural comparison analysis suggests the presence of similar allosteric sites in other GPCRs. We also discuss critical structural features of C5aR in activation, including a novel conformation of helix 8. On the basis of our results, we suggest novel strategies for developing C5aR-targeting drugs.
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Affiliation(s)
- Heng Liu
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hee Ryung Kim
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - R N V Krishna Deepak
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lei Wang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Ka Young Chung
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Hao Fan
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zhiyi Wei
- Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Cheng Zhang
- Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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125
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Robertson N, Rappas M, Doré AS, Brown J, Bottegoni G, Koglin M, Cansfield J, Jazayeri A, Cooke RM, Marshall FH. Structure of the complement C5a receptor bound to the extra-helical antagonist NDT9513727. Nature 2018; 553:111-114. [PMID: 29300009 DOI: 10.1038/nature25025] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 11/07/2017] [Indexed: 11/09/2022]
Abstract
The complement system is a crucial component of the host response to infection and tissue damage. Activation of the complement cascade generates anaphylatoxins including C5a and C3a. C5a exerts a pro-inflammatory effect via the G-protein-coupled receptor C5a anaphylatoxin chemotactic receptor 1 (C5aR1, also known as CD88) that is expressed on cells of myeloid origin. Inhibitors of the complement system have long been of interest as potential drugs for the treatment of diseases such as sepsis, rheumatoid arthritis, Crohn's disease and ischaemia-reperfusion injuries. More recently, a role of C5a in neurodegenerative conditions such as Alzheimer's disease has been identified. Peptide antagonists based on the C5a ligand have progressed to phase 2 trials in psoriasis and rheumatoid arthritis; however, these compounds exhibited problems with off-target activity, production costs, potential immunogenicity and poor oral bioavailability. Several small-molecule competitive antagonists for C5aR1, such as W-54011 and NDT9513727, have been identified by C5a radioligand-binding assays. NDT9513727 is a non-peptide inverse agonist of C5aR1, and is highly selective for the primate and gerbil receptors over those of other species. Here, to study the mechanism of action of C5a antagonists, we determine the structure of a thermostabilized C5aR1 (known as C5aR1 StaR) in complex with NDT9513727. We found that the small molecule bound between transmembrane helices 3, 4 and 5, outside the helical bundle. One key interaction between the small molecule and residue Trp2135.49 seems to determine the species selectivity of the compound. The structure demonstrates that NDT9513727 exerts its inverse-agonist activity through an extra-helical mode of action.
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Affiliation(s)
- Nathan Robertson
- 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
| | - Andrew S Doré
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Jason Brown
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Giovanni Bottegoni
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Markus Koglin
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Julie Cansfield
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Ali Jazayeri
- 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
| | - Fiona H Marshall
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
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126
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Structural basis for GPR40 allosteric agonism and incretin stimulation. Nat Commun 2018; 9:1645. [PMID: 29695780 PMCID: PMC5917010 DOI: 10.1038/s41467-017-01240-w] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/30/2017] [Indexed: 12/23/2022] Open
Abstract
Activation of free fatty acid receptor 1 (GPR40) by synthetic partial and full agonists occur via distinct allosteric sites. A crystal structure of GPR40-TAK-875 complex revealed the allosteric site for the partial agonist. Here we report the 2.76-Å crystal structure of human GPR40 in complex with a synthetic full agonist, compound 1, bound to the second allosteric site. Unlike TAK-875, which acts as a Gαq-coupled partial agonist, compound 1 is a dual Gαq and Gαs-coupled full agonist. compound 1 binds in the lipid-rich region of the receptor near intracellular loop 2 (ICL2), in which the stabilization of ICL2 by the ligand is likely the primary mechanism for the enhanced G protein activities. The endogenous free fatty acid (FFA), γ-linolenic acid, can be computationally modeled in this site. Both γ-linolenic acid and compound 1 exhibit positive cooperativity with TAK-875, suggesting that this site could also serve as a FFA binding site. GPR40 is a G-protein coupled receptor that binds to free fatty acids, mediating insulin and incretin secretion. Here, the authors present the crystal structure of human GPR40 with an agonist bound to an allosteric site located near the lipid-rich region that suggests a mechanism for biased agonism.
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127
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Deganutti G, Salmaso V, Moro S. Could Adenosine Recognize its Receptors with a Stoichiometry Other than 1 : 1? Mol Inform 2018; 37:e1800009. [DOI: 10.1002/minf.201800009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/27/2018] [Indexed: 11/12/2022]
Affiliation(s)
- Giuseppe Deganutti
- Molecular Modeling Section (MMS); Department of Pharmaceutical and Pharmacological Sciences; University of Padova; via Marzolo 5 35131 Padova Italy
- School of Biological Sciences; University of Essex; Wivenhoe Park Colchester CO4 3SQ UK
| | - Veronica Salmaso
- Molecular Modeling Section (MMS); Department of Pharmaceutical and Pharmacological Sciences; University of Padova; via Marzolo 5 35131 Padova Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS); Department of Pharmaceutical and Pharmacological Sciences; University of Padova; via Marzolo 5 35131 Padova Italy
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128
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Rives ML, Rady B, Swanson N, Zhao S, Qi J, Arnoult E, Bakaj I, Mancini A, Breton B, Lee SP, Player MR, Pocai A. GPR40-Mediated G α12 Activation by Allosteric Full Agonists Highly Efficacious at Potentiating Glucose-Stimulated Insulin Secretion in Human Islets. Mol Pharmacol 2018; 93:581-591. [PMID: 29572336 DOI: 10.1124/mol.117.111369] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/20/2018] [Indexed: 12/25/2022] Open
Abstract
GPR40 is a clinically validated molecular target for the treatment of diabetes. Many GPR40 agonists have been identified to date, with the partial agonist fasiglifam (TAK-875) reaching phase III clinical trials before its development was terminated due to off-target liver toxicity. Since then, attention has shifted toward the development of full agonists that exhibit superior efficacy in preclinical models. Full agonists bind to a distinct binding site, suggesting conformational plasticity and a potential for biased agonism. Indeed, it has been suggested that alternative pharmacology may be required for meaningful efficacy. In this study, we described the discovery and characterization of Compound A, a newly identified GPR40 allosteric full agonist highly efficacious in human islets at potentiating glucose-stimulated insulin secretion. We compared Compound A-induced GPR40 activity to that induced by both fasiglifam and AM-1638, another allosteric full agonist previously reported to be highly efficacious in preclinical models, at a panel of G proteins. Compound A was a full agonist at both the Gαq and Gαi2 pathways, and in contrast to fasiglifam Compound A also induced Gα12 coupling. Compound A and AM-1638 displayed similar activity at all pathways tested. The Gα12/Gα13-mediated signaling pathway has been linked to protein kinase D activation as well as actin remodeling, well known to contribute to the release of insulin vesicles. Our data suggest that the pharmacology of GPR40 is complex and that Gα12/Gα13-mediated signaling, which may contribute to GPR40 agonists therapeutic efficacy, is a specific property of GPR40 allosteric full agonists.
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Affiliation(s)
- Marie-Laure Rives
- Molecular and Cellular Pharmacology, Janssen Research & Development, LLC, La Jolla, California (M.-L.R., N.S.); Cardiovascular and Metabolism (B.R., S.Z., J.Q., I.B., S.P.L., M.R.P., A.P.), and Computational Chemistry (E.A.), Janssen Research & Development, LLC, Spring House, Pennsylvania; and Domain Therapeutics NA Inc., Montreal, Quebec, Canada (A.M., B.B.)
| | - Brian Rady
- Molecular and Cellular Pharmacology, Janssen Research & Development, LLC, La Jolla, California (M.-L.R., N.S.); Cardiovascular and Metabolism (B.R., S.Z., J.Q., I.B., S.P.L., M.R.P., A.P.), and Computational Chemistry (E.A.), Janssen Research & Development, LLC, Spring House, Pennsylvania; and Domain Therapeutics NA Inc., Montreal, Quebec, Canada (A.M., B.B.)
| | - Nadia Swanson
- Molecular and Cellular Pharmacology, Janssen Research & Development, LLC, La Jolla, California (M.-L.R., N.S.); Cardiovascular and Metabolism (B.R., S.Z., J.Q., I.B., S.P.L., M.R.P., A.P.), and Computational Chemistry (E.A.), Janssen Research & Development, LLC, Spring House, Pennsylvania; and Domain Therapeutics NA Inc., Montreal, Quebec, Canada (A.M., B.B.)
| | - Shuyuan Zhao
- Molecular and Cellular Pharmacology, Janssen Research & Development, LLC, La Jolla, California (M.-L.R., N.S.); Cardiovascular and Metabolism (B.R., S.Z., J.Q., I.B., S.P.L., M.R.P., A.P.), and Computational Chemistry (E.A.), Janssen Research & Development, LLC, Spring House, Pennsylvania; and Domain Therapeutics NA Inc., Montreal, Quebec, Canada (A.M., B.B.)
| | - Jenson Qi
- Molecular and Cellular Pharmacology, Janssen Research & Development, LLC, La Jolla, California (M.-L.R., N.S.); Cardiovascular and Metabolism (B.R., S.Z., J.Q., I.B., S.P.L., M.R.P., A.P.), and Computational Chemistry (E.A.), Janssen Research & Development, LLC, Spring House, Pennsylvania; and Domain Therapeutics NA Inc., Montreal, Quebec, Canada (A.M., B.B.)
| | - Eric Arnoult
- Molecular and Cellular Pharmacology, Janssen Research & Development, LLC, La Jolla, California (M.-L.R., N.S.); Cardiovascular and Metabolism (B.R., S.Z., J.Q., I.B., S.P.L., M.R.P., A.P.), and Computational Chemistry (E.A.), Janssen Research & Development, LLC, Spring House, Pennsylvania; and Domain Therapeutics NA Inc., Montreal, Quebec, Canada (A.M., B.B.)
| | - Ivona Bakaj
- Molecular and Cellular Pharmacology, Janssen Research & Development, LLC, La Jolla, California (M.-L.R., N.S.); Cardiovascular and Metabolism (B.R., S.Z., J.Q., I.B., S.P.L., M.R.P., A.P.), and Computational Chemistry (E.A.), Janssen Research & Development, LLC, Spring House, Pennsylvania; and Domain Therapeutics NA Inc., Montreal, Quebec, Canada (A.M., B.B.)
| | - Arturo Mancini
- Molecular and Cellular Pharmacology, Janssen Research & Development, LLC, La Jolla, California (M.-L.R., N.S.); Cardiovascular and Metabolism (B.R., S.Z., J.Q., I.B., S.P.L., M.R.P., A.P.), and Computational Chemistry (E.A.), Janssen Research & Development, LLC, Spring House, Pennsylvania; and Domain Therapeutics NA Inc., Montreal, Quebec, Canada (A.M., B.B.)
| | - Billy Breton
- Molecular and Cellular Pharmacology, Janssen Research & Development, LLC, La Jolla, California (M.-L.R., N.S.); Cardiovascular and Metabolism (B.R., S.Z., J.Q., I.B., S.P.L., M.R.P., A.P.), and Computational Chemistry (E.A.), Janssen Research & Development, LLC, Spring House, Pennsylvania; and Domain Therapeutics NA Inc., Montreal, Quebec, Canada (A.M., B.B.)
| | - S Paul Lee
- Molecular and Cellular Pharmacology, Janssen Research & Development, LLC, La Jolla, California (M.-L.R., N.S.); Cardiovascular and Metabolism (B.R., S.Z., J.Q., I.B., S.P.L., M.R.P., A.P.), and Computational Chemistry (E.A.), Janssen Research & Development, LLC, Spring House, Pennsylvania; and Domain Therapeutics NA Inc., Montreal, Quebec, Canada (A.M., B.B.)
| | - Mark R Player
- Molecular and Cellular Pharmacology, Janssen Research & Development, LLC, La Jolla, California (M.-L.R., N.S.); Cardiovascular and Metabolism (B.R., S.Z., J.Q., I.B., S.P.L., M.R.P., A.P.), and Computational Chemistry (E.A.), Janssen Research & Development, LLC, Spring House, Pennsylvania; and Domain Therapeutics NA Inc., Montreal, Quebec, Canada (A.M., B.B.)
| | - Alessandro Pocai
- Molecular and Cellular Pharmacology, Janssen Research & Development, LLC, La Jolla, California (M.-L.R., N.S.); Cardiovascular and Metabolism (B.R., S.Z., J.Q., I.B., S.P.L., M.R.P., A.P.), and Computational Chemistry (E.A.), Janssen Research & Development, LLC, Spring House, Pennsylvania; and Domain Therapeutics NA Inc., Montreal, Quebec, Canada (A.M., B.B.)
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129
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Lu S, Zhang J. Small Molecule Allosteric Modulators of G-Protein-Coupled Receptors: Drug–Target Interactions. J Med Chem 2018; 62:24-45. [DOI: 10.1021/acs.jmedchem.7b01844] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
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130
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Structure-based discovery of selective positive allosteric modulators of antagonists for the M 2 muscarinic acetylcholine receptor. Proc Natl Acad Sci U S A 2018; 115:E2419-E2428. [PMID: 29453275 PMCID: PMC5877965 DOI: 10.1073/pnas.1718037115] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The orthosteric binding sites of the five muscarinic acetylcholine receptor (mAChR) subtypes are highly conserved, making the development of selective antagonists challenging. The allosteric sites of these receptors are more variable, allowing one to imagine allosteric modulators that confer subtype selectivity, which would reduce the major off-target effects of muscarinic antagonists. Accordingly, a large library docking campaign was prosecuted seeking unique positive allosteric modulators (PAMs) for antagonists, ultimately revealing a PAM that substantially potentiates antagonist binding leading to subtype selectivity at the M2 mAChR. This study supports the feasibility of discovering PAMs that can convert an armamentarium of potent but nonselective G-protein–coupled receptor (GPCR) antagonist drugs into subtype-selective reagents. Subtype-selective antagonists for muscarinic acetylcholine receptors (mAChRs) have long been elusive, owing to the highly conserved orthosteric binding site. However, allosteric sites of these receptors are less conserved, motivating the search for allosteric ligands that modulate agonists or antagonists to confer subtype selectivity. Accordingly, a 4.6 million-molecule library was docked against the structure of the prototypical M2 mAChR, seeking molecules that specifically stabilized antagonist binding. This led us to identify a positive allosteric modulator (PAM) that potentiated the antagonist N-methyl scopolamine (NMS). Structure-based optimization led to compound ’628, which enhanced binding of NMS, and the drug scopolamine itself, with a cooperativity factor (α) of 5.5 and a KB of 1.1 μM, while sparing the endogenous agonist acetylcholine. NMR spectral changes determined for methionine residues reflected changes in the allosteric network. Moreover, ’628 slowed the dissociation rate of NMS from the M2 mAChR by 50-fold, an effect not observed at the other four mAChR subtypes. The specific PAM effect of ’628 on NMS antagonism was conserved in functional assays, including agonist stimulation of [35S]GTPγS binding and ERK 1/2 phosphorylation. Importantly, the selective allostery between ’628 and NMS was retained in membranes from adult rat hypothalamus and in neonatal rat cardiomyocytes, supporting the physiological relevance of this PAM/antagonist approach. This study supports the feasibility of discovering PAMs that confer subtype selectivity to antagonists; molecules like ’628 can convert an armamentarium of potent but nonselective GPCR antagonist drugs into subtype-selective reagents, thus reducing their off-target effects.
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131
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Abstract
It is known but generally unappreciated that the fatty acid receptor FFAR1 (GPR40) is responsible for a major part of glucose-induced insulin secretion. This puzzling fact is now explained by Tunaru et al. (2018), who demonstrate that glucose-induced 20-hydroxyeicosatetraenoic acid (20-HETE) amplifies insulin secretion through autocrine activation of FFAR1.
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Affiliation(s)
- Mette Trauelsen
- Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Michael Lückmann
- Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Thomas M Frimurer
- Center for Basic Metabolic Research, University of Copenhagen, Denmark
| | - Thue W Schwartz
- Center for Basic Metabolic Research, University of Copenhagen, Denmark; Laboratory for Molecular Pharmacology, Department for Biomedical Research, Faculty of Health Sciences, University of Copenhagen, Denmark.
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132
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Discovery of a novel potent GPR40 full agonist. Bioorg Med Chem Lett 2018; 28:720-726. [DOI: 10.1016/j.bmcl.2018.01.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 11/18/2022]
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133
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Vass M, Kooistra AJ, Verhoeven S, Gloriam D, de Esch IJP, de Graaf C. A Structural Framework for GPCR Chemogenomics: What's In a Residue Number? Methods Mol Biol 2018; 1705:73-113. [PMID: 29188559 DOI: 10.1007/978-1-4939-7465-8_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The recent surge of crystal structures of G protein-coupled receptors (GPCRs), as well as comprehensive collections of sequence, structural, ligand bioactivity, and mutation data, has enabled the development of integrated chemogenomics workflows for this important target family. This chapter will focus on cross-family and cross-class studies of GPCRs that have pinpointed the need for, and the implementation of, a generic numbering scheme for referring to specific structural elements of GPCRs. Sequence- and structure-based numbering schemes for different receptor classes will be introduced and the remaining caveats will be discussed. The use of these numbering schemes has facilitated many chemogenomics studies such as consensus binding site definition, binding site comparison, ligand repurposing (e.g. for orphan receptors), sequence-based pharmacophore generation for homology modeling or virtual screening, and class-wide chemogenomics studies of GPCRs.
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Affiliation(s)
- Márton Vass
- Department of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands
| | - Albert J Kooistra
- Department of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands
- Centre for Molecular and Biomolecular Informatics (CMBI), Radboud University Medical Center, 6525 GA, Nijmegen, The Netherlands
| | - Stefan Verhoeven
- Netherlands eScience Center, 1098 XG, Amsterdam, The Netherlands
| | - David Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Iwan J P de Esch
- Department of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands
| | - Chris de Graaf
- Department of Medicinal Chemistry, Amsterdam Institute for Molecules Medicines and Systems, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HV, Amsterdam, The Netherlands.
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134
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Mahmud ZA, Jenkins L, Ulven T, Labéguère F, Gosmini R, De Vos S, Hudson BD, Tikhonova IG, Milligan G. Three classes of ligands each bind to distinct sites on the orphan G protein-coupled receptor GPR84. Sci Rep 2017; 7:17953. [PMID: 29263400 PMCID: PMC5738391 DOI: 10.1038/s41598-017-18159-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 12/05/2017] [Indexed: 12/18/2022] Open
Abstract
Medium chain fatty acids can activate the pro-inflammatory receptor GPR84 but so also can molecules related to 3,3′-diindolylmethane. 3,3′-Diindolylmethane and decanoic acid acted as strong positive allosteric modulators of the function of each other and analysis showed the affinity of 3,3′-diindolylmethane to be at least 100 fold higher. Methyl decanoate was not an agonist at GPR84. This implies a key role in binding for the carboxylic acid of the fatty acid. Via homology modelling we predicted and confirmed an integral role of arginine172, located in the 2nd extracellular loop, in the action of decanoic acid but not of 3,3′-diindolylmethane. Exemplars from a patented series of GPR84 antagonists were able to block agonist actions of both decanoic acid and 3,3′-diindolylmethane at GPR84. However, although a radiolabelled form of a related antagonist, [3H]G9543, was able to bind with high affinity to GPR84, this was not competed for by increasing concentrations of either decanoic acid or 3,3′-diindolylmethane and was not affected adversely by mutation of arginine172. These studies identify three separable ligand binding sites within GPR84 and suggest that if medium chain fatty acids are true endogenous regulators then co-binding with a positive allosteric modulator would greatly enhance their function in physiological settings.
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Affiliation(s)
- Zobaer Al Mahmud
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow, G12 8QQ, Scotland, United Kingdom
| | - Laura Jenkins
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow, G12 8QQ, Scotland, United Kingdom
| | - Trond Ulven
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Frédéric Labéguère
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230, Romainville, France.,Evotec, 195 Route d'Espagne, 31100, Toulouse, France
| | - Romain Gosmini
- Galapagos SASU, 102 Avenue Gaston Roussel, 93230, Romainville, France
| | - Steve De Vos
- Galapagos NV, Generaal De Wittelaan L11 A3, 2800, Mechelen, Belgium
| | - Brian D Hudson
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow, G12 8QQ, Scotland, United Kingdom
| | - Irina G Tikhonova
- School of Pharmacy, Medical Biology Centre, Queen's University Belfast, Belfast, BT9 7BL, United Kingdom
| | - Graeme Milligan
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow Glasgow, G12 8QQ, Scotland, United Kingdom.
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135
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Zhang XJ, Cheng X, Yan ZZ, Fang J, Wang X, Wang W, Liu ZY, Shen LJ, Zhang P, Wang PX, Liao R, Ji YX, Wang JY, Tian S, Zhu XY, Zhang Y, Tian RF, Wang L, Ma XL, Huang Z, She ZG, Li H. An ALOX12–12-HETE–GPR31 signaling axis is a key mediator of hepatic ischemia–reperfusion injury. Nat Med 2017; 24:73-83. [DOI: 10.1038/nm.4451] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/01/2017] [Indexed: 12/12/2022]
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136
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Loh YY, Nagao K, Hoover AJ, Hesk D, Rivera NR, Colletti SL, Davies IW, MacMillan DWC. Photoredox-catalyzed deuteration and tritiation of pharmaceutical compounds. Science 2017; 358:1182-1187. [PMID: 29123019 PMCID: PMC5907472 DOI: 10.1126/science.aap9674] [Citation(s) in RCA: 336] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 10/30/2017] [Indexed: 12/24/2022]
Abstract
Deuterium- and tritium-labeled pharmaceutical compounds are pivotal diagnostic tools in drug discovery research, providing vital information about the biological fate of drugs and drug metabolites. Herein we demonstrate that a photoredox-mediated hydrogen atom transfer protocol can efficiently and selectively install deuterium (D) and tritium (T) at α-amino sp3 carbon-hydrogen bonds in a single step, using isotopically labeled water (D2O or T2O) as the source of hydrogen isotope. In this context, we also report a convenient synthesis of T2O from T2, providing access to high-specific-activity T2O. This protocol has been successfully applied to the high incorporation of deuterium and tritium in 18 drug molecules, which meet the requirements for use in ligand-binding assays and absorption, distribution, metabolism, and excretion studies.
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Affiliation(s)
- Yong Yao Loh
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA
| | - Kazunori Nagao
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA
| | - Andrew J Hoover
- Labeled Compound Synthesis Group, Department of Process R&D, Merck Research Laboratories (MRL), Merck & Co., Inc., Rahway, NJ 07065, USA
| | - David Hesk
- Labeled Compound Synthesis Group, Department of Process R&D, Merck Research Laboratories (MRL), Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Nelo R Rivera
- Labeled Compound Synthesis Group, Department of Process R&D, Merck Research Laboratories (MRL), Merck & Co., Inc., Rahway, NJ 07065, USA
| | - Steven L Colletti
- Department of Discovery Chemistry, MRL, Merck & Co., Inc., Kenilworth, NJ 07033, USA
| | - Ian W Davies
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA
- Labeled Compound Synthesis Group, Department of Process R&D, Merck Research Laboratories (MRL), Merck & Co., Inc., Rahway, NJ 07065, USA
| | - David W C MacMillan
- Merck Center for Catalysis at Princeton University, Princeton, NJ 08544, USA.
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137
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Sergeev E, Hansen AH, Bolognini D, Kawakami K, Kishi T, Aoki J, Ulven T, Inoue A, Hudson BD, Milligan G. A single extracellular amino acid in Free Fatty Acid Receptor 2 defines antagonist species selectivity and G protein selection bias. Sci Rep 2017; 7:13741. [PMID: 29061999 PMCID: PMC5653858 DOI: 10.1038/s41598-017-14096-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 09/27/2017] [Indexed: 12/29/2022] Open
Abstract
Free Fatty Acid Receptor 2 is a GPCR activated by short chain fatty acids produced in high levels in the lower gut by microbial fermentation of non-digestible carbohydrates. A major challenge in studying this receptor is that the mouse ortholog does not have significant affinity for antagonists that are able to block the human receptor. Docking of exemplar antagonists from two chemical series to homology models of both human and mouse Free Fatty Acid Receptor 2 suggested that a single lysine - arginine variation at the extracellular face of the receptor might provide the basis for antagonist selectivity and mutational swap studies confirmed this hypothesis. Extending these studies to agonist function indicated that although the lysine - arginine variation between human and mouse orthologs had limited effect on G protein-mediated signal transduction, removal of positive charge from this residue produced a signalling-biased variant of Free Fatty Acid Receptor 2 in which Gi-mediated signalling by both short chain fatty acids and synthetic agonists was maintained whilst there was marked loss of agonist potency for signalling via Gq/11 and G12/13 G proteins. A single residue at the extracellular face of the receptor thus plays key roles in both agonist and antagonist function.
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Affiliation(s)
- Eugenia Sergeev
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, United Kingdom
| | - Anders Højgaard Hansen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Daniele Bolognini
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, United Kingdom
| | - Kouki Kawakami
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Takayuki Kishi
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan
| | - Junken Aoki
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.,Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (AMED-CREST), Tokyo, 100-0004, Japan
| | - Trond Ulven
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230, Odense M, Denmark
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, 6-3, Aoba, Aramaki, Aoba-ku, Sendai, 980-8578, Japan.,Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Kawaguchi, Saitama, 332-0012, Japan
| | - Brian D Hudson
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, United Kingdom
| | - Graeme Milligan
- Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, Scotland, United Kingdom.
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138
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Discovery of new GPCR ligands to illuminate new biology. Nat Chem Biol 2017; 13:1143-1151. [PMID: 29045379 DOI: 10.1038/nchembio.2490] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 08/30/2017] [Indexed: 12/12/2022]
Abstract
Although a plurality of drugs target G-protein-coupled receptors (GPCRs), most have emerged from classical medicinal chemistry and pharmacology programs and resemble one another structurally and functionally. Though effective, these drugs are often promiscuous. With the realization that GPCRs signal via multiple pathways, and with the emergence of crystal structures for this family of proteins, there is an opportunity to target GPCRs with new chemotypes and confer new signaling modalities. We consider structure-based and physical screening methods that have led to the discovery of new reagents, focusing particularly on the former. We illustrate their use against previously untargeted or orphan GPCRs, against allosteric sites, and against classical orthosteric sites that selectively activate one downstream pathway over others. The ligands that emerge are often chemically novel, which can lead to new biological effects.
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139
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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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