51
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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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52
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Llinas Del Torrent C, Pérez-Benito L, Tresadern G. Computational Drug Design Applied to the Study of Metabotropic Glutamate Receptors. Molecules 2019; 24:molecules24061098. [PMID: 30897742 PMCID: PMC6470756 DOI: 10.3390/molecules24061098] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 11/16/2022] Open
Abstract
Metabotropic glutamate (mGlu) receptors are a family of eight GPCRs that are attractive drug discovery targets to modulate glutamate action and response. Here we review the application of computational methods to the study of this family of receptors. X-ray structures of the extracellular and 7-transmembrane domains have played an important role to enable structure-based modeling approaches, whilst we also discuss the successful application of ligand-based methods. We summarize the literature and highlight the areas where modeling and experiment have delivered important understanding for mGlu receptor drug discovery. Finally, we offer suggestions of future areas of opportunity for computational work.
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Affiliation(s)
- Claudia Llinas Del Torrent
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina, Universitat Autónoma de Barcelona, 08193 Bellaterra, Spain.
| | - Laura Pérez-Benito
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium.
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium.
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53
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Nakagita T, Ishida A, Matsuya T, Kobayashi T, Narukawa M, Hirokawa T, Hashimoto M, Misaka T. Structural insights into the differences among lactisole derivatives in inhibitory mechanisms against the human sweet taste receptor. PLoS One 2019; 14:e0213552. [PMID: 30883570 PMCID: PMC6422327 DOI: 10.1371/journal.pone.0213552] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 02/23/2019] [Indexed: 11/22/2022] Open
Abstract
Lactisole, an inhibitor of the human sweet taste receptor, has a 2-phenoxypropionic acid skeleton and has been shown to interact with the transmembrane domain of the T1R3 subunit (T1R3-TMD) of the receptor. Another inhibitor, 2,4-DP, which shares the same molecular skeleton as lactisole, was confirmed to be approximately 10-fold more potent in its inhibitory activity than lactisole; however the structural basis of their inhibitory mechanisms against the receptor remains to be elucidated. Crystal structures of the TMD of metabotropic glutamate receptors, which along with T1Rs are categorized as class C G-protein coupled receptors, have recently been reported and made it possible to create an accurate structural model for T1R3-TMD. In this study, the detailed structural mechanism underlying sweet taste inhibition was characterized by comparing the action of lactisole on T1R3-TMD with that of 2,4-DP. We first performed a series of experiments using cultured cells expressing the sweet taste receptor with mutations and examined the interactions with these inhibitors. Based on the results, we next performed docking simulations and then applied molecular dynamics-based energy minimization. Our analyses clearly revealed that the (S)-isomers of both lactisole and 2,4-DP, interacted with the same seven residues in T1R3-TMD and that the inhibitory potencies of those inhibitors were mainly due to stabilizing interactions mediated via their carboxyl groups in the vertical dimension of the ligand pocket of T1R3-TMD. In addition, 2,4-DP engaged in a hydrophobic interaction mediated by its o-Cl group, and this interaction may be chiefly responsible for the higher inhibitory potency of 2,4-DP.
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Affiliation(s)
- Tomoya Nakagita
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akiko Ishida
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Takumi Matsuya
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takuya Kobayashi
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masataka Narukawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery, National Institutes of Advanced Industrial Science and Technology, Tokyo, Japan
- Department of Chemical Biology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Makoto Hashimoto
- Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
| | - Takumi Misaka
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
- * E-mail:
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54
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Llinas Del Torrent C, Casajuana-Martin N, Pardo L, Tresadern G, Pérez-Benito L. Mechanisms Underlying Allosteric Molecular Switches of Metabotropic Glutamate Receptor 5. J Chem Inf Model 2019; 59:2456-2466. [PMID: 30811196 DOI: 10.1021/acs.jcim.8b00924] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The metabotropic glutamate 5 (mGlu5) receptor is a class C G protein-coupled receptor (GPCR) that is implicated in several CNS disorders making it a popular drug discovery target. Years of research have revealed allosteric mGlu5 ligands showing an unexpected complete switch in functional activity despite only small changes in their chemical structure, resulting in positive allosteric modulators (PAM) or negative allosteric modulators (NAM) for the same scaffold. Up to now, the origins of this effect are not understood, causing difficulties in a drug discovery context. In this work, experimental data was gathered and analyzed alongside docking and Molecular Dynamics (MD) calculations for three sets of PAM and NAM pairs. The results consistently show the role of specific interactions formed between ligand substituents and amino acid side chains that block or promote local movements associated with receptor activation. The work provides an explanation for how such small structural changes lead to remarkable differences in functional activity. While this work can greatly help drug discovery programs avoid these switches, it also provides valuable insight into the mechanisms of class C GPCR allosteric activation. Furthermore, the approach shows the value of applying MD to understand functional activity in drug design programs, even for such close structural analogues.
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Affiliation(s)
- Claudia Llinas Del Torrent
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina , Universitat Autonoma de Barcelona , 08193 Bellaterra , Spain
| | - Nil Casajuana-Martin
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina , Universitat Autonoma de Barcelona , 08193 Bellaterra , Spain
| | - Leonardo Pardo
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina , Universitat Autonoma de Barcelona , 08193 Bellaterra , Spain
| | - Gary Tresadern
- Computational Chemistry, Janssen Research & Development , Janssen Pharmaceutica N. V. , Turnhoutseweg 30 , B-2340 Beerse , Belgium
| | - Laura Pérez-Benito
- Laboratori de Medicina Computacional Unitat de Bioestadistica, Facultat de Medicina , Universitat Autonoma de Barcelona , 08193 Bellaterra , Spain.,Computational Chemistry, Janssen Research & Development , Janssen Pharmaceutica N. V. , Turnhoutseweg 30 , B-2340 Beerse , Belgium
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55
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Coughlin Q, Hopper AT, Blanco MJ, Tirunagaru V, Robichaud AJ, Doller D. Allosteric Modalities for Membrane-Bound Receptors: Insights from Drug Hunting for Brain Diseases. J Med Chem 2019; 62:5979-6002. [PMID: 30721063 DOI: 10.1021/acs.jmedchem.8b01651] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Medicinal chemists are accountable for embedding the appropriate drug target profile into the molecular architecture of a clinical candidate. An accurate characterization of the functional effects following binding of a drug to its biological target is a fundamental step in the discovery of new medicines, informing the translation of preclinical efficacy and safety observations into human trials. Membrane-bound proteins, particularly ion channels and G protein-coupled receptors (GPCRs), are biological targets prone to allosteric modulation. Investigations using allosteric drug candidates and chemical tools suggest that their functional effects may be tailored with a high degree of translational alignment, making them molecular tools to correct pathophysiological functional tone and enable personalized medicine when a causative target-to-disease link is known. We present select examples of functional molecular fine-tuning of allosterism and discuss consequences relevant to drug design.
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56
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How an activation signal is transmitted through an excitatory receptor. Nature 2019; 566:42-43. [DOI: 10.1038/d41586-018-07885-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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57
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Graziani D, Caligari S, Callegari E, De Toma C, Longhi M, Frigerio F, Dilernia R, Menegon S, Pinzi L, Pirona L, Tazzari V, Valsecchi AE, Vistoli G, Rastelli G, Riva C. Evaluation of Amides, Carbamates, Sulfonamides, and Ureas of 4-Prop-2-ynylidenecycloalkylamine as Potent, Selective, and Bioavailable Negative Allosteric Modulators of Metabotropic Glutamate Receptor 5. J Med Chem 2019; 62:1246-1273. [PMID: 30624919 DOI: 10.1021/acs.jmedchem.8b01226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Negative allosteric modulators (NAMs) of the metabotropic glutamate receptor 5 (mGlu5) hold great promise for the treatment of a variety of central nervous system disorders. We have recently reported that prop-2-ynylidenecycloalkylamine derivatives are potent and selective NAMs of the mGlu5 receptor. In this work, we explored the amide, carbamate, sulfonamide, and urea derivatives of prop-2-ynylidenecycloalkylamine compounds with the aim of improving solubility and metabolic stability. In silico and experimental analyses were performed on the synthesized series of compounds to investigate structure-activity relationships. Compounds 12, 32, and 49 of the carbamate, urea, and amide classes, respectively, showed the most suitable cytochrome inhibition and metabolic stability profiles. Among them, compound 12 showed excellent selectivity, solubility, and stability profiles as well as suitable in vitro and in vivo pharmacokinetic properties. It was highly absorbed in rats and dogs and was active in anxiety, neuropathic pain, and lower urinary tract models.
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Affiliation(s)
- Davide Graziani
- Drug Discovery Department , Recordati S.p.A. , Via M. Civitali 1 , 20148 Milan , Italy
| | - Silvia Caligari
- Drug Discovery Department , Recordati S.p.A. , Via M. Civitali 1 , 20148 Milan , Italy
| | - Elisa Callegari
- Drug Discovery Department , Recordati S.p.A. , Via M. Civitali 1 , 20148 Milan , Italy
| | - Carlo De Toma
- Drug Discovery Department , Recordati S.p.A. , Via M. Civitali 1 , 20148 Milan , Italy
| | - Matteo Longhi
- Drug Discovery Department , Recordati S.p.A. , Via M. Civitali 1 , 20148 Milan , Italy
| | - Fabio Frigerio
- Drug Discovery Department , Recordati S.p.A. , Via M. Civitali 1 , 20148 Milan , Italy
| | - Roberto Dilernia
- Drug Discovery Department , Recordati S.p.A. , Via M. Civitali 1 , 20148 Milan , Italy
| | - Sergio Menegon
- Drug Discovery Department , Recordati S.p.A. , Via M. Civitali 1 , 20148 Milan , Italy
| | - Luca Pinzi
- Department of Life Sciences , University of Modena and Reggio Emilia , Via Campi 103 , 41125 Modena , Italy
| | - Lorenza Pirona
- Drug Discovery Department , Recordati S.p.A. , Via M. Civitali 1 , 20148 Milan , Italy
| | - Valerio Tazzari
- Drug Discovery Department , Recordati S.p.A. , Via M. Civitali 1 , 20148 Milan , Italy
| | - Anna Elisa Valsecchi
- Drug Discovery Department , Recordati S.p.A. , Via M. Civitali 1 , 20148 Milan , Italy
| | - Giulio Vistoli
- Department of Pharmaceutical Sciences , Università degli Studi di Milano , Via Mangiagalli 25 , 20133 Milan , Italy
| | - Giulio Rastelli
- Department of Life Sciences , University of Modena and Reggio Emilia , Via Campi 103 , 41125 Modena , Italy
| | - Carlo Riva
- Drug Discovery Department , Recordati S.p.A. , Via M. Civitali 1 , 20148 Milan , Italy
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58
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Koehl A, Hu H, Feng D, Sun B, Zhang Y, Robertson MJ, Chu M, Kobilka TS, Laeremans T, Steyaert J, Tarrasch J, Dutta S, Fonseca R, Weis WI, Mathiesen JM, Skiniotis G, Kobilka BK. Structural insights into the activation of metabotropic glutamate receptors. Nature 2019; 566:79-84. [PMID: 30675062 PMCID: PMC6709600 DOI: 10.1038/s41586-019-0881-4] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 12/12/2018] [Indexed: 12/11/2022]
Abstract
Metabotropic glutamate receptors are family C G-protein-coupled receptors. They form obligate dimers and possess extracellular ligand-binding Venus flytrap domains, which are linked by cysteine-rich domains to their 7-transmembrane domains. Spectroscopic studies show that signalling is a dynamic process, in which large-scale conformational changes underlie the transmission of signals from the extracellular Venus flytraps to the G protein-coupling domains-the 7-transmembrane domains-in the membrane. Here, using a combination of X-ray crystallography, cryo-electron microscopy and signalling studies, we present a structural framework for the activation mechanism of metabotropic glutamate receptor subtype 5. Our results show that agonist binding at the Venus flytraps leads to a compaction of the intersubunit dimer interface, thereby bringing the cysteine-rich domains into close proximity. Interactions between the cysteine-rich domains and the second extracellular loops of the receptor enable the rigid-body repositioning of the 7-transmembrane domains, which come into contact with each other to initiate signalling.
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Affiliation(s)
- Antoine Koehl
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Hongli Hu
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Dan Feng
- ConfometRx, Santa Clara, CA, USA
| | | | - Yan Zhang
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Robertson
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Tong Sun Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,ConfometRx, Santa Clara, CA, USA
| | - Toon Laeremans
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jeffrey Tarrasch
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Somnath Dutta
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Rasmus Fonseca
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - William I Weis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Jesper M Mathiesen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Georgios Skiniotis
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. .,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. .,ConfometRx, Santa Clara, CA, USA.
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59
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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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