1
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Rodriguez-Contreras D, García-Nafría J, Chan AE, Shinde U, Neve KA. Comparison of the function of two novel human dopamine D2 receptor variants identifies a likely mechanism for their pathogenicity. Biochem Pharmacol 2024:116228. [PMID: 38643909 DOI: 10.1016/j.bcp.2024.116228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/29/2024] [Accepted: 04/18/2024] [Indexed: 04/23/2024]
Abstract
Two recently discovered DRD2 mutations, c.634A > T, p.Ile212Phe and c.1121T > G, p.Met374Arg, cause hyperkinetic movement disorders that have overlapping features but apparently differ in severity. The two known carriers of the Met374Arg variant had early childhood disease onset and more severe motor, cognitive, and neuropsychiatric deficits than any known carriers of the Ile212Phe variant, whose symptoms were first apparent in adolescence. Here, we evaluated if differences in the function of the two variants in cultured cells could explain differing pathogenicity. Both variants were expressed less abundantly than the wild type receptor and exhibited loss of agonist-induced arrestin binding, but differences in expression and arrestin binding between the variants were minor. Basal and agonist-induced activation of heterotrimeric Gi/o/z proteins, however, showed clear differences; agonists were generally more potent at Met374Arg than at the Ile212Phe or wild type variants. Furthermore, all Gα subtypes tested were constitutively activated more by Met374Arg than by Ile212Phe. Met374Arg produced greater constitutive inhibition of cyclic AMP accumulation than Ile212Phe or the wild type D2 receptor. Met374Arg and Ile212Phe were more sensitive to thermal inactivation than the wild type D2 receptor, as reported for other constitutively active receptors, but Ile212Phe was affected more than Met374Arg. Additional pharmacological characterization suggested that the mutations differentially affect the shape of the agonist binding pocket and the potency of dopamine, norepinephrine, and tyramine. Molecular dynamics simulations provided a structural rationale for enhanced constitutive activation and agonist potency. Enhanced constitutive and agonist-induced G protein-mediated signaling likely contributes to the pathogenicity of these novel variants.
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Affiliation(s)
- Dayana Rodriguez-Contreras
- Research Service, Veterans Affairs Portland Health Care System, and Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA
| | - Javier García-Nafría
- Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratory of Advanced Microscopy (LMA), University of Zaragoza, 50018, Zaragoza, Spain
| | - Amy E Chan
- Research Service, Veterans Affairs Portland Health Care System, and Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA
| | - Ujwal Shinde
- Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kim A Neve
- Research Service, Veterans Affairs Portland Health Care System, and Department of Behavioral Neuroscience, Oregon Health & Science University, Portland, OR 97239, USA.
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2
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Buyanov I, Popov P. Characterizing conformational states in GPCR structures using machine learning. Sci Rep 2024; 14:1098. [PMID: 38212515 PMCID: PMC10784458 DOI: 10.1038/s41598-023-47698-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 11/17/2023] [Indexed: 01/13/2024] Open
Abstract
G protein-coupled receptors (GPCRs) play a pivotal role in signal transduction and represent attractive targets for drug development. Recent advances in structural biology have provided insights into GPCR conformational states, which are critical for understanding their signaling pathways and facilitating structure-based drug discovery. In this study, we introduce a machine learning approach for conformational state annotation of GPCRs. We represent GPCR conformations as high-dimensional feature vectors, incorporating information about amino acid residue pairs involved in the activation pathway. Using a dataset of GPCR conformations in inactive and active states obtained through molecular dynamics simulations, we trained machine learning models to distinguish between inactive-like and active-like conformations. The developed model provides interpretable predictions and can be used for the large-scale analysis of molecular dynamics trajectories of GPCRs.
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Affiliation(s)
- Ilya Buyanov
- iMolecule, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia
| | - Petr Popov
- iMolecule, Skolkovo Institute of Science and Technology, Moscow, 121205, Russia.
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3
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Kapur B, Baldessari F, Lazaratos M, Nar H, Schnapp G, Giorgetti A, Bondar AN. Protons taken hostage: Dynamic H-bond networks of the pH-sensing GPR68. Comput Struct Biotechnol J 2023; 21:4370-4384. [PMID: 37711190 PMCID: PMC10498176 DOI: 10.1016/j.csbj.2023.08.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/30/2023] [Accepted: 08/30/2023] [Indexed: 09/16/2023] Open
Abstract
Proton-sensing G Protein Coupled Receptors (GPCRs) sense changes in the extracellular pH to effect cell signaling for cellular homeostasis. They tend to be overexpressed in solid tumors associated with acidic extracellular pH, and are of direct interest as drug targets. How proton-sensing GPCRs sense extracellular acidification and activate upon protonation change is important to understand, because it may guide the design of therapeutics. Lack of publicly available experimental structures make it challenging to discriminate between conflicting mechanisms proposed for proton-binding, as main roles have been assigned to either an extracellular histidine cluster or to an internal carboxylic triad. Here we present a protocol to derive and evaluate structural models of the proton-sensing GPR68. This approach integrates state-of-the-art homology modeling with microsecond-timescale atomistic simulations, and with a detailed assessment of the compatibility of the structural models with known structural features of class A GPCRs. To decipher structural elements of potential interest for protonation-coupled conformational changes of GPR68, we used the best-compatible model as a starting point for independent atomistic simulations of GPR68 with different protonation states, and graph computations to characterize the response of GPR68 to changes in protonation. We found that GPR68 hosts an extended hydrogen-bond network that inter-connects the extracellular histidine cluster to the internal carboxylic triad, and which can even reach groups at the cytoplasmic G-protein binding site. Taken together, results suggest that GPR68 relies on dynamic, hydrogen-bond networks to inter-connect extracellular and internal proton-binding sites, and to elicit conformational changes at the cytoplasmic G-protein binding site.
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Affiliation(s)
- Bhav Kapur
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
- Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | | | - Michalis Lazaratos
- Department of Physics, Theoretical Molecular Biophysics Group, Freie Universität Berlin, Arnimallee 14, D-14195 Berlin, Germany
| | - Herbert Nar
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Gisela Schnapp
- Boehringer-Ingelheim Pharma GmbH & Co. KG, Birkendorfer Straße 65, 88397 Biberach an der Riß, Germany
| | - Alejandro Giorgetti
- University of Verona, Department of Biotechnology, 37134 Verona, Italy
- Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52525 Jülich, Germany
| | - Ana-Nicoleta Bondar
- Forschungszentrum Jülich, Institute for Neuroscience and Medicine and Institute for Advanced Simulations (IAS-5/INM-9), Computational Biomedicine, Wilhelm-Johnen Straße, 52525 Jülich, Germany
- University of Bucharest, Faculty of Physics, Str. Atomiştilor 405, 077125 Bucharest-Măgurele, Romania
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4
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Pham V, Habben Jansen MCC, Thompson G, Heitman LH, Christopoulos A, Thal DM, Valant C. Role of Conserved Tyrosine Lid Residues in the Activation of the M 2 Muscarinic Acetylcholine Receptor. Mol Pharmacol 2023; 104:92-104. [PMID: 37348914 DOI: 10.1124/molpharm.122.000661] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/10/2023] [Accepted: 06/06/2023] [Indexed: 06/24/2023] Open
Abstract
The development of subtype selective small molecule drugs for the muscarinic acetylcholine receptor (mAChR) family has been challenging. The design of more selective ligands can be improved by understanding the structure and function of key amino acid residues that line ligand binding sites. Here we study the role of three conserved key tyrosine residues [Y1043.33, Y4036.51, and Y4267.39 (Ballesteros and Weinstein numbers in superscript)] at the human M2 mAChR, located at the interface between the orthosteric and allosteric binding sites of the receptor. We specifically focused on the role of the three tyrosine hydroxyl groups in the transition between the inactive and active conformations of the receptor by making phenylalanine point mutants. Single-point mutation at either of the three positions was sufficient to reduce the affinity of agonists by ∼100-fold for the M2 mAChR, whereas the affinity of antagonists remained largely unaffected. In contrast, neither of the mutations affected the efficacy of orthosteric agonists. When mutations were combined into double and triple M2 mAChR mutants, the affinity of antagonists was reduced by more than 100-fold compared with the wild-type M2 receptor. In contrast, the affinity of allosteric modulators, either negative or positive, was retained at all single and multiple mutations, but the degree of allosteric effect exerted on the endogenous ligand acetylcholine was affected at all mutants containing Y4267.39F. These findings will provide insights to consider when designing future mAChR ligands. SIGNIFICANCE STATEMENT: Structural studies demonstrated that three tyrosine residues between the orthosteric and allosteric sites of the M2 muscarinic acetylcholine receptor (mAChR) had different hydrogen bonding networks in the inactive and active conformations. The role of hydroxyl groups of the tyrosine residues on orthosteric and allosteric ligand pharmacology was unknown. We found that hydroxyl groups of the tyrosine residues differentially affected the molecular pharmacology of orthosteric and allosteric ligands. These results provide insights to consider when designing future mAChR ligands.
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Affiliation(s)
- Vi Pham
- Drug Discovery Biology (V.P., G.T., A.C., D.M.T., C.V.), ARC Industrial Transformation Training Centre for Cryo-Electron Microscopy of Membrane Proteins (A.C., D.M.T.), Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia; Drug Discovery and Safety, Universiteit Leiden, Leiden, The Netherlands (M.C.C.H.J., L.H.H.); and Neuromedicines Discovery Center, Monash University, Parkville, Victoria, Australia (A.C.)
| | - Maria Clazina Cornelia Habben Jansen
- Drug Discovery Biology (V.P., G.T., A.C., D.M.T., C.V.), ARC Industrial Transformation Training Centre for Cryo-Electron Microscopy of Membrane Proteins (A.C., D.M.T.), Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia; Drug Discovery and Safety, Universiteit Leiden, Leiden, The Netherlands (M.C.C.H.J., L.H.H.); and Neuromedicines Discovery Center, Monash University, Parkville, Victoria, Australia (A.C.)
| | - Geoff Thompson
- Drug Discovery Biology (V.P., G.T., A.C., D.M.T., C.V.), ARC Industrial Transformation Training Centre for Cryo-Electron Microscopy of Membrane Proteins (A.C., D.M.T.), Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia; Drug Discovery and Safety, Universiteit Leiden, Leiden, The Netherlands (M.C.C.H.J., L.H.H.); and Neuromedicines Discovery Center, Monash University, Parkville, Victoria, Australia (A.C.)
| | - Laura H Heitman
- Drug Discovery Biology (V.P., G.T., A.C., D.M.T., C.V.), ARC Industrial Transformation Training Centre for Cryo-Electron Microscopy of Membrane Proteins (A.C., D.M.T.), Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia; Drug Discovery and Safety, Universiteit Leiden, Leiden, The Netherlands (M.C.C.H.J., L.H.H.); and Neuromedicines Discovery Center, Monash University, Parkville, Victoria, Australia (A.C.)
| | - Arthur Christopoulos
- Drug Discovery Biology (V.P., G.T., A.C., D.M.T., C.V.), ARC Industrial Transformation Training Centre for Cryo-Electron Microscopy of Membrane Proteins (A.C., D.M.T.), Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia; Drug Discovery and Safety, Universiteit Leiden, Leiden, The Netherlands (M.C.C.H.J., L.H.H.); and Neuromedicines Discovery Center, Monash University, Parkville, Victoria, Australia (A.C.)
| | - David M Thal
- Drug Discovery Biology (V.P., G.T., A.C., D.M.T., C.V.), ARC Industrial Transformation Training Centre for Cryo-Electron Microscopy of Membrane Proteins (A.C., D.M.T.), Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia; Drug Discovery and Safety, Universiteit Leiden, Leiden, The Netherlands (M.C.C.H.J., L.H.H.); and Neuromedicines Discovery Center, Monash University, Parkville, Victoria, Australia (A.C.)
| | - Celine Valant
- Drug Discovery Biology (V.P., G.T., A.C., D.M.T., C.V.), ARC Industrial Transformation Training Centre for Cryo-Electron Microscopy of Membrane Proteins (A.C., D.M.T.), Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia; Drug Discovery and Safety, Universiteit Leiden, Leiden, The Netherlands (M.C.C.H.J., L.H.H.); and Neuromedicines Discovery Center, Monash University, Parkville, Victoria, Australia (A.C.)
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5
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Vuckovic Z, Wang J, Pham V, Mobbs JI, Belousoff MJ, Bhattarai A, Burger WAC, Thompson G, Yeasmin M, Nawaratne V, Leach K, van der Westhuizen ET, Khajehali E, Liang YL, Glukhova A, Wootten D, Lindsley CW, Tobin A, Sexton P, Danev R, Valant C, Miao Y, Christopoulos A, Thal DM. Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics. eLife 2023; 12:83477. [PMID: 37248726 DOI: 10.7554/elife.83477] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 04/12/2023] [Indexed: 05/31/2023] Open
Abstract
Allosteric modulation of G protein-coupled receptors (GPCRs) is a major paradigm in drug discovery. Despite decades of research, a molecular-level understanding of the general principles that govern the myriad pharmacological effects exerted by GPCR allosteric modulators remains limited. The M4 muscarinic acetylcholine receptor (M4 mAChR) is a validated and clinically relevant allosteric drug target for several major psychiatric and cognitive disorders. In this study, we rigorously quantified the affinity, efficacy, and magnitude of modulation of two different positive allosteric modulators, LY2033298 (LY298) and VU0467154 (VU154), combined with the endogenous agonist acetylcholine (ACh) or the high-affinity agonist iperoxo (Ipx), at the human M4 mAChR. By determining the cryo-electron microscopy structures of the M4 mAChR, bound to a cognate Gi1 protein and in complex with ACh, Ipx, LY298-Ipx, and VU154-Ipx, and applying molecular dynamics simulations, we determine key molecular mechanisms underlying allosteric pharmacology. In addition to delineating the contribution of spatially distinct binding sites on observed pharmacology, our findings also revealed a vital role for orthosteric and allosteric ligand-receptor-transducer complex stability, mediated by conformational dynamics between these sites, in the ultimate determination of affinity, efficacy, cooperativity, probe dependence, and species variability. There results provide a holistic framework for further GPCR mechanistic studies and can aid in the discovery and design of future allosteric drugs.
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Affiliation(s)
- Ziva Vuckovic
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Jinan Wang
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Vi Pham
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Jesse I Mobbs
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Matthew J Belousoff
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Apurba Bhattarai
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Wessel A C Burger
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Geoff Thompson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Mahmuda Yeasmin
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Vindhya Nawaratne
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Katie Leach
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Emma T van der Westhuizen
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Elham Khajehali
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Yi-Lynn Liang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Alisa Glukhova
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Denise Wootten
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Craig W Lindsley
- Department of Pharmacology, Warren Center for Neuroscience Drug Discovery and Department of Chemistry, Warren Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, United States
| | - Andrew Tobin
- The Centre for Translational Pharmacology, Advanced Research Centre (ARC), College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Patrick Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Celine Valant
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | - Yinglong Miao
- Center for Computational Biology and Department of Molecular Biosciences, University of Kansas, Lawrence, United States
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- Neuromedicines Discovery Centre, Monash University, Parkville, Australia
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
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6
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den Hollander LS, Béquignon OJM, Wang X, van Wezel K, Broekhuis J, Gorostiola González M, de Visser KE, IJzerman AP, van Westen GJP, Heitman LH. Impact of cancer-associated mutations in CC chemokine receptor 2 on receptor function and antagonism. Biochem Pharmacol 2023; 208:115399. [PMID: 36581051 DOI: 10.1016/j.bcp.2022.115399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 12/27/2022]
Abstract
CC chemokine receptor 2 (CCR2), a G protein-coupled receptor, plays a role in many cancer-related processes such as metastasis formation and immunosuppression. Since ∼ 20 % of human cancers contain mutations in G protein-coupled receptors, ten cancer-associated CCR2 mutants obtained from the Genome Data Commons were investigated for their effect on receptor functionality and antagonist binding. Mutations were selected based on either their vicinity to CCR2's orthosteric or allosteric binding sites or their presence in conserved amino acid motifs. One of the mutant receptors, namely S101P2.63 with a mutation near the orthosteric binding site, did not express on the cell surface. All other studied mutants showed a decrease in or a lack of G protein activation in response to the main endogenous CCR2 ligand CCL2, but no change in potency was observed. Furthermore, INCB3344 and LUF7482 were chosen as representative orthosteric and allosteric antagonists, respectively. No change in potency was observed in a functional assay, but mutations located at F1163.28 impacted orthosteric antagonist binding significantly, while allosteric antagonist binding was abolished for L134Q3.46 and D137N3.49 mutants. As CC chemokine receptor 2 is an attractive drug target in cancer, the negative effect of these mutations on receptor functionality and drugability should be considered in the drug discovery process.
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Affiliation(s)
- L S den Hollander
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - O J M Béquignon
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - X Wang
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - K van Wezel
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - J Broekhuis
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - M Gorostiola González
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands; Oncode Institute, Leiden, The Netherlands
| | - K E de Visser
- Oncode Institute, Leiden, The Netherlands; Netherlands Cancer Institute, Division of Tumor Biology & Immunology, Amsterdam, The Netherlands; Leiden University, Department of Immunology, Medical Centre, Leiden, The Netherlands
| | - A P IJzerman
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - G J P van Westen
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands
| | - L H Heitman
- Leiden Academic Centre for Drug Research, Division of Drug Discovery and Safety, Leiden, The Netherlands; Oncode Institute, Leiden, The Netherlands.
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7
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Cary BP, Zhang X, Cao J, Johnson RM, Piper SJ, Gerrard EJ, Wootten D, Sexton PM. New insights into the structure and function of class B1 GPCRs. Endocr Rev 2022; 44:492-517. [PMID: 36546772 PMCID: PMC10166269 DOI: 10.1210/endrev/bnac033] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/07/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
G protein-coupled receptors (GPCRs) are the largest family of cell surface receptors. Class B1 GPCRs constitute a subfamily of 15 receptors that characteristically contain large extracellular domains (ECDs) and respond to long polypeptide hormones. Class B1 GPCRs are critical regulators of homeostasis, and as such, many are important drug targets. While most transmembrane proteins, including GPCRs, are recalcitrant to crystallization, recent advances in electron cryo-microscopy (cryo-EM) have facilitated a rapid expansion of the structural understanding of membrane proteins. As a testament to this success, structures for all the class B1 receptors bound to G proteins have been determined by cryo-EM in the past five years. Further advances in cryo-EM have uncovered dynamics of these receptors, ligands, and signalling partners. Here, we examine the recent structural underpinnings of the class B1 GPCRs with an emphasis on structure-function relationships.
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Affiliation(s)
- Brian P Cary
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Xin Zhang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Jianjun Cao
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Rachel M Johnson
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Sarah J Piper
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Elliot J Gerrard
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Denise Wootten
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.,ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
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8
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Chen Y, Fleetwood O, Pérez-Conesa S, Delemotte L. Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor. J Chem Inf Model 2021; 61:6024-6037. [PMID: 34780174 PMCID: PMC8715506 DOI: 10.1021/acs.jcim.1c00826] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Nanobody binding
stabilizes G-protein-coupled receptors (GPCR)
in a fully active state and modulates their affinity for bound ligands.
However, the atomic-level basis for this allosteric regulation remains
elusive. Here, we investigate the conformational changes induced by
the binding of a nanobody (Nb80) on the active-like β2 adrenergic
receptor (β2AR) via enhanced sampling molecular dynamics simulations.
Dimensionality reduction analysis shows that Nb80 stabilizes structural
features of the β2AR with an ∼14 Å outward movement
of transmembrane helix 6 and a close proximity of transmembrane (TM)
helices 5 and 7, and favors the fully active-like conformation of
the receptor, independent of ligand binding, in contrast to the conditions
under which no intracellular binding partner is bound, in which case
the receptor is only stabilized in an intermediate-active state. This
activation is supported by the residues located at hotspots located
on TMs 5, 6, and 7, as shown by supervised machine learning methods.
Besides, ligand-specific subtle differences in the conformations assumed
by intracellular loop 2 and extracellular loop 2 are captured from
the trajectories of various ligand-bound receptors in the presence
of Nb80. Dynamic network analysis further reveals that Nb80 binding
triggers tighter and stronger local communication networks between
the Nb80 and the ligand-binding sites, primarily involving residues
around ICL2 and the intracellular end of TM3, TM5, TM6, as well as
ECL2, ECL3, and the extracellular ends of TM6 and TM7. In particular,
we identify unique allosteric signal transmission mechanisms between
the Nb80-binding site and the extracellular domains in conformations
modulated by a full agonist, BI167107, and a G-protein-biased partial
agonist, salmeterol, involving mainly TM1 and TM2, and TM5, respectively.
Altogether, our results provide insights into the effect of intracellular
binding partners on the GPCR activation mechanism, which should be
taken into account in structure-based drug discovery.
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Affiliation(s)
- Yue Chen
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Oliver Fleetwood
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Sergio Pérez-Conesa
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
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9
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Hernández-Alvarado RB, Madariaga-Mazón A, Cosme-Vela F, Marmolejo-Valencia AF, Nefzi A, Martinez-Mayorga K. Encoding mu-opioid receptor biased agonism with interaction fingerprints. J Comput Aided Mol Des 2021; 35:1081-1093. [PMID: 34713377 DOI: 10.1007/s10822-021-00422-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/07/2021] [Indexed: 10/20/2022]
Abstract
Opioids are potent painkillers, however, their therapeutic use requires close medical monitoring to diminish the risk of severe adverse effects. The G-protein biased agonists of the μ-opioid receptor (MOR) have shown safer therapeutic profiles than non-biased ligands. In this work, we performed extensive all-atom molecular dynamics simulations of two markedly biased ligands and a balanced reference molecule. From those simulations, we identified a protein-ligand interaction fingerprint that characterizes biased ligands. Then, we built and virtually screened a database containing 68,740 ligands with proven or potential GPCR agonistic activity. Exemplary molecules that fulfill the interacting pattern for biased agonism are showcased, illustrating the usefulness of this work for the search of biased MOR ligands and how this contributes to the understanding of MOR biased signaling.
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Affiliation(s)
| | | | - Fernando Cosme-Vela
- Instituto de Química, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - Adel Nefzi
- Center for Translational Science, Florida International University, Port St. Lucie, FL, USA.,Torrey Pines Institute for Molecular Studies, Port St. Lucie, FL, USA
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10
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Randáková A, Jakubík J. Functionally selective and biased agonists of muscarinic receptors. Pharmacol Res 2021; 169:105641. [PMID: 33951507 DOI: 10.1016/j.phrs.2021.105641] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 12/24/2022]
Abstract
Disruption of cholinergic signalling via muscarinic receptors is associated with various pathologies, like Alzheimer's disease or schizophrenia. Selective muscarinic agonists possess therapeutic potential in the treatment of diabetes, pain or Sjögren's syndrome. The orthosteric binding site of all subtypes of the muscarinic receptor is structurally identical, making the development of affinity-based selective agonists virtually impossible. Some agonists, however, are functionally selective; they activate only a subset of receptors or signalling pathways. Others may stabilise specific conformations of the receptor leading to non-uniform modulation of individual signalling pathways (biased agonists). Functionally selective and biased agonists represent a promising approach for selective activation of individual subtypes of muscarinic receptors. In this work we review chemical structures, receptor binding and agonist-specific conformations of currently known functionally selective and biased muscarinic agonists in the context of their intricate intracellular signalling. Further, we take a perspective on the possible use of biased agonists for tissue and organ-specific activation of muscarinic receptors.
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Affiliation(s)
- Alena Randáková
- Institute of Physiology Czech Academy of Sciences, Prague, Czech Republic.
| | - Jan Jakubík
- Institute of Physiology Czech Academy of Sciences, Prague, Czech Republic.
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11
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Jakubík J, El-Fakahany EE. Allosteric Modulation of GPCRs of Class A by Cholesterol. Int J Mol Sci 2021; 22:1953. [PMID: 33669406 PMCID: PMC7920425 DOI: 10.3390/ijms22041953] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/16/2022] Open
Abstract
G-protein coupled receptors (GPCRs) are membrane proteins that convey extracellular signals to the cellular milieu. They represent a target for more than 30% of currently marketed drugs. Here we review the effects of membrane cholesterol on the function of GPCRs of Class A. We review both the specific effects of cholesterol mediated via its direct high-affinity binding to the receptor and non-specific effects mediated by cholesterol-induced changes in the properties of the membrane. Cholesterol binds to many GPCRs at both canonical and non-canonical binding sites. It allosterically affects ligand binding to and activation of GPCRs. Additionally, it changes the oligomerization state of GPCRs. In this review, we consider a perspective of the potential for the development of new therapies that are targeted at manipulating the level of membrane cholesterol or modulating cholesterol binding sites on to GPCRs.
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Affiliation(s)
- Jan Jakubík
- Department of Neurochemistry, Institute of Physiology Czech Academy of Sciences, 142 20 Prague, Czech Republic
| | - Esam E. El-Fakahany
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, MN 55455, USA
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12
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Krug U, Gloge A, Schmidt P, Becker‐Baldus J, Bernhard F, Kaiser A, Montag C, Gauglitz M, Vishnivetskiy SA, Gurevich VV, Beck‐Sickinger AG, Glaubitz C, Huster D. The Conformational Equilibrium of the Neuropeptide Y2 Receptor in Bilayer Membranes. Angew Chem Int Ed Engl 2020; 59:23854-23861. [PMID: 32790043 PMCID: PMC7736470 DOI: 10.1002/anie.202006075] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/13/2020] [Indexed: 12/23/2022]
Abstract
Dynamic structural transitions within the seven-transmembrane bundle represent the mechanism by which G-protein-coupled receptors convert an extracellular chemical signal into an intracellular biological function. Here, the conformational dynamics of the neuropeptide Y receptor type 2 (Y2R) during activation was investigated. The apo, full agonist-, and arrestin-bound states of Y2R were prepared by cell-free expression, functional refolding, and reconstitution into lipid membranes. To study conformational transitions between these states, all six tryptophans of Y2R were 13 C-labeled. NMR-signal assignment was achieved by dynamic-nuclear-polarization enhancement and the individual functional states of the receptor were characterized by monitoring 13 C NMR chemical shifts. Activation of Y2R is mediated by molecular switches involving the toggle switch residue Trp2816.48 of the highly conserved SWLP motif and Trp3277.55 adjacent to the NPxxY motif. Furthermore, a conformationally preserved "cysteine lock"-Trp11623.50 was identified.
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Affiliation(s)
- Ulrike Krug
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Anika Gloge
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Peter Schmidt
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Johanna Becker‐Baldus
- Institute of Biophysical ChemistryGoethe University FrankfurtGermany
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtGermany
| | - Frank Bernhard
- Institute of Biophysical ChemistryGoethe University FrankfurtGermany
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtGermany
| | - Anette Kaiser
- Institute of BiochemistryUniversity of LeipzigLeipzigGermany
| | - Cindy Montag
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
| | - Marcel Gauglitz
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
- Berlin Joint Electron Paramagnetic Resonance LaboratoryFree University BerlinGermany
| | | | | | | | - Clemens Glaubitz
- Institute of Biophysical ChemistryGoethe University FrankfurtGermany
- Center for Biomolecular Magnetic ResonanceGoethe University FrankfurtGermany
| | - Daniel Huster
- Institute of Medical Physics and BiophysicsUniversity of LeipzigHärtelstr. 16–1804107LeipzigGermany
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13
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Krug U, Gloge A, Schmidt P, Becker‐Baldus J, Bernhard F, Kaiser A, Montag C, Gauglitz M, Vishnivetskiy SA, Gurevich VV, Beck‐Sickinger AG, Glaubitz C, Huster D. Das Konformationsgleichgewicht des Neuropeptid‐Y2‐Rezeptors in Lipidmembranen. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ulrike Krug
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Anika Gloge
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Peter Schmidt
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Johanna Becker‐Baldus
- Institut für Biophysikalische Chemie Goethe-Universität Frankfurt am Main Deutschland
- Zentrum für Biomolekulare Magnetresonanz Goethe-Universität Frankfurt am Main Deutschland
| | - Frank Bernhard
- Institut für Biophysikalische Chemie Goethe-Universität Frankfurt am Main Deutschland
- Zentrum für Biomolekulare Magnetresonanz Goethe-Universität Frankfurt am Main Deutschland
| | - Anette Kaiser
- Institut für Biochemie Universität Leipzig Deutschland
| | - Cindy Montag
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
| | - Marcel Gauglitz
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
- Berlin Joint Electron Paramagnetic Resonance Laboratory Freie Universität Berlin Deutschland
| | | | | | | | - Clemens Glaubitz
- Institut für Biophysikalische Chemie Goethe-Universität Frankfurt am Main Deutschland
- Zentrum für Biomolekulare Magnetresonanz Goethe-Universität Frankfurt am Main Deutschland
| | - Daniel Huster
- Institut für Medizinische Physik und Biophysik Universität Leipzig Härtelstr. 16–18 04107 Leipzig Deutschland
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14
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Jones EM, Lubock NB, Venkatakrishnan AJ, Wang J, Tseng AM, Paggi JM, Latorraca NR, Cancilla D, Satyadi M, Davis JE, Babu MM, Dror RO, Kosuri S. Structural and functional characterization of G protein-coupled receptors with deep mutational scanning. eLife 2020; 9:54895. [PMID: 33084570 PMCID: PMC7707821 DOI: 10.7554/elife.54895] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 10/16/2020] [Indexed: 01/14/2023] Open
Abstract
The >800 human G protein–coupled receptors (GPCRs) are responsible for transducing diverse chemical stimuli to alter cell state- and are the largest class of drug targets. Their myriad structural conformations and various modes of signaling make it challenging to understand their structure and function. Here, we developed a platform to characterize large libraries of GPCR variants in human cell lines with a barcoded transcriptional reporter of G protein signal transduction. We tested 7800 of 7828 possible single amino acid substitutions to the beta-2 adrenergic receptor (β2AR) at four concentrations of the agonist isoproterenol. We identified residues specifically important for β2AR signaling, mutations in the human population that are potentially loss of function, and residues that modulate basal activity. Using unsupervised learning, we identify residues critical for signaling, including all major structural motifs and molecular interfaces. We also find a previously uncharacterized structural latch spanning the first two extracellular loops that is highly conserved across Class A GPCRs and is conformationally rigid in both the inactive and active states of the receptor. More broadly, by linking deep mutational scanning with engineered transcriptional reporters, we establish a generalizable method for exploring pharmacogenomics, structure and function across broad classes of drug receptors.
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Affiliation(s)
- Eric M Jones
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Nathan B Lubock
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - A J Venkatakrishnan
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Jeffrey Wang
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Alex M Tseng
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Joseph M Paggi
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Naomi R Latorraca
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Daniel Cancilla
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Megan Satyadi
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - Jessica E Davis
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Ron O Dror
- Department of Computer Science, Stanford University, Department of Computer Science, Institute for Computational and Mathematical Engineering, Stanford University, Department of Computer Science, Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Department of Computer Science, Department of Structural Biology, Stanford University School of Medicine, Stanford, United States
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, and Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, United States
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15
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Kapoor A, Provasi D, Filizola M. Atomic-Level Characterization of the Methadone-Stabilized Active Conformation of µ-Opioid Receptor. Mol Pharmacol 2020; 98:475-486. [PMID: 32680919 PMCID: PMC7562981 DOI: 10.1124/mol.119.119339] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 06/09/2020] [Indexed: 12/15/2022] Open
Abstract
Methadone is a synthetic opioid agonist with notoriously unique properties, such as lower abuse liability and induced relief of withdrawal symptoms and drug cravings, despite acting on the same opioid receptors triggered by classic opioids-in particular the µ-opioid receptor (MOR). Its distinct pharmacologic properties, which have recently been attributed to the preferential activation of β-arrestin over G proteins, make methadone a standard-of-care maintenance medication for opioid addiction. Although a recent biophysical study suggests that methadone stabilizes different MOR active conformations from those stabilized by classic opioid drugs or G protein-biased agonists, how this drug modulates the conformational equilibrium of MOR and what specific active conformation of the receptor it stabilizes are unknown. Here, we report the results of submillisecond adaptive sampling molecular dynamics simulations of a predicted methadone-bound MOR complex and compare them with analogous data obtained for the classic opioid morphine and the G protein-biased ligand TRV130. The model, which is supported by existing experimental data, is analyzed using Markov state models and transfer entropy analysis to provide testable hypotheses of methadone-specific conformational dynamics and activation kinetics of MOR. SIGNIFICANCE STATEMENT: Opioid addiction has reached epidemic proportions in both industrialized and developing countries. Although methadone maintenance treatment represents an effective therapeutic approach for opioid addiction, it is not as widely used as needed. In this study, we contribute an atomic-level understanding of how methadone exerts its unique function in pursuit of more accessible treatments for opioid addiction. In particular, we present details of a methadone-specific active conformation of the µ-opioid receptor that has thus far eluded experimental structural characterization.
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Affiliation(s)
- Abhijeet Kapoor
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Davide Provasi
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
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16
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Kim M, Wei JD, Harmalkar DS, Goo JI, Lee K, Choi Y, Kim JH, Cho AE. Elucidation of Mechanism for Ligand Efficacy at Leukotriene B 4 Receptor 2 (BLT2). ACS Med Chem Lett 2020; 11:1529-1534. [PMID: 32832019 DOI: 10.1021/acsmedchemlett.0c00065] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) have always been important drug targets in the pharmaceutical industry. One major question for the current GPCR drug discovery is how drugs have distinct efficacies at the same GPCR target. Related to this question, we studied how different ligands can have disparate efficacies at Leukotriene B4 receptor (BLT2). By using molecular modeling studies, we predicted that Tyr2716.51 located at TM6 of BLT2 performs as a key trigger for its activation and verified the prediction by site-directed mutagenesis, chemotactic motility studies, which included a chemical derivative of agonist CAY10583. We further identified Asn2756.55 located at TM6 as a weak activation trigger in BLT2 and performed double mutation studies to confirm our computational results. Our results provide strong evidence for the exact mechanism of ligand efficacy at BLT2.
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Affiliation(s)
- Minsup Kim
- inCerebro Co., Ltd. Drug Discovery Institute, Seoul Technopark, 232 Gongneung-ro, Nowon-gu, Seoul 01811, Korea
| | - Jun-Dong Wei
- Department of Biochemistry, Medical College, Taizhou University, Taizhou, 318000, Zhejjang, China
| | - Dipesh S. Harmalkar
- College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- College of Pharmacy, Dongguk University, 32 Dongguk-ro,
Ilsandong-gu, Goyang-si 10326, Republic of Korea
| | - Ja-il Goo
- College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Kyeong Lee
- College of Pharmacy, Dongguk University, 32 Dongguk-ro,
Ilsandong-gu, Goyang-si 10326, Republic of Korea
| | - Yongseok Choi
- College of Life Sciences and Biotechnology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jae-Hong Kim
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Art E. Cho
- Department of Bioinformatics, Korea University, 2511 Sejong-ro, Sejong 30019, Republic of Korea
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17
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Randáková A, Nelic D, Doležal V, El-Fakahany EE, Boulos J, Jakubík J. Agonist-Specific Conformations of the M 2 Muscarinic Acetylcholine Receptor Assessed by Molecular Dynamics. J Chem Inf Model 2020; 60:2325-2338. [PMID: 32130001 DOI: 10.1021/acs.jcim.0c00041] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Binding of muscarinic ligands, both antagonists and agonists, and their effects on the conformation of the M2 acetylcholine receptor were modeled in silico and compared to experimental data. After docking of antagonists to the M2 receptor in an inactive conformation (3UON, 5ZK3, 5ZKB, or 5ZKB) and agonists in an active conformation (4MQS), 100 ns of conventional molecular dynamics (MD) followed by 500 ns of accelerated MD was run. Conventional MD revealed ligand-specific interactions with the receptor. Antagonists stabilized the receptor in an inactive conformation during accelerated MD. The receptor in complex with various agonists attained different conformations specific to individual agonists. The magnitude of the TM6 movement correlated with agonist efficacy at the non-preferential Gs pathway. The shape of the intracellular opening where the receptor interacts with a G-protein was different for the classical agonist carbachol, super-agonist iperoxo, and Gi/o-biased partial agonists JR-6 and JR-7, being compatible with experimentally observed agonist bias at the G-protein level. Moreover, a wash-resistant binding of the unique agonist xanomeline associated with interactions with membrane lipids was formed during accelerated MD. Thus, accelerated MD is suitable for modeling of ligand-specific receptor binding and receptor conformations that is essential for the design of experiments aimed at identification of the secondary binding sites and understanding molecular mechanisms underlying receptor activation.
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Affiliation(s)
- Alena Randáková
- Department of Neurochemistry, Institute of Physiology CAS, Prague, CZ 142 20, Czech Republic
| | - Dominik Nelic
- Department of Neurochemistry, Institute of Physiology CAS, Prague, CZ 142 20, Czech Republic
| | - Vladimír Doležal
- Department of Neurochemistry, Institute of Physiology CAS, Prague, CZ 142 20, Czech Republic
| | - Esam E El-Fakahany
- Department of Experimental and Clinical Pharmacology, University of Minnesota College of Pharmacy, Minneapolis, Minnesota 55455, United States
| | - John Boulos
- Department of Physical Sciences, Barry University, Miami Shores, Florida 33161, United States
| | - Jan Jakubík
- Department of Neurochemistry, Institute of Physiology CAS, Prague, CZ 142 20, Czech Republic
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18
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Zhou Q, Yang D, Wu M, Guo Y, Guo W, Zhong L, Cai X, Dai A, Jang W, Shakhnovich EI, Liu ZJ, Stevens RC, Lambert NA, Babu MM, Wang MW, Zhao S. Common activation mechanism of class A GPCRs. eLife 2019; 8:e50279. [PMID: 31855179 PMCID: PMC6954041 DOI: 10.7554/elife.50279] [Citation(s) in RCA: 292] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/19/2019] [Indexed: 12/26/2022] Open
Abstract
Class A G-protein-coupled receptors (GPCRs) influence virtually every aspect of human physiology. Understanding receptor activation mechanism is critical for discovering novel therapeutics since about one-third of all marketed drugs target members of this family. GPCR activation is an allosteric process that couples agonist binding to G-protein recruitment, with the hallmark outward movement of transmembrane helix 6 (TM6). However, what leads to TM6 movement and the key residue level changes of this movement remain less well understood. Here, we report a framework to quantify conformational changes. By analyzing the conformational changes in 234 structures from 45 class A GPCRs, we discovered a common GPCR activation pathway comprising of 34 residue pairs and 35 residues. The pathway unifies previous findings into a common activation mechanism and strings together the scattered key motifs such as CWxP, DRY, Na+ pocket, NPxxY and PIF, thereby directly linking the bottom of ligand-binding pocket with G-protein coupling region. Site-directed mutagenesis experiments support this proposition and reveal that rational mutations of residues in this pathway can be used to obtain receptors that are constitutively active or inactive. The common activation pathway provides the mechanistic interpretation of constitutively activating, inactivating and disease mutations. As a module responsible for activation, the common pathway allows for decoupling of the evolution of the ligand binding site and G-protein-binding region. Such an architecture might have facilitated GPCRs to emerge as a highly successful family of proteins for signal transduction in nature.
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Affiliation(s)
- Qingtong Zhou
- iHuman InstituteShanghaiTech UniversityShanghaiChina
| | - Dehua Yang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Meng Wu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Yu Guo
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Wanjing Guo
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Li Zhong
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Xiaoqing Cai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Antao Dai
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
| | - Wonjo Jang
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeUnited States
| | - Zhi-Jie Liu
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Raymond C Stevens
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
| | - Nevin A Lambert
- Department of Pharmacology and Toxicology, Medical College of GeorgiaAugusta UniversityAugustaUnited States
| | - M Madan Babu
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Ming-Wei Wang
- The CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- The National Center for Drug ScreeningShanghai Institute of Materia Medica, Chinese Academy of SciencesShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
- School of PharmacyFudan UniversityShanghaiChina
| | - Suwen Zhao
- iHuman InstituteShanghaiTech UniversityShanghaiChina
- School of Life Science and TechnologyShanghaiTech UniversityShanghaiChina
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19
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Zhou Y, Cao C, He L, Wang X, Zhang XC. Crystal structure of dopamine receptor D4 bound to the subtype selective ligand, L745870. eLife 2019; 8:e48822. [PMID: 31750832 PMCID: PMC6872212 DOI: 10.7554/elife.48822] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 11/06/2019] [Indexed: 12/12/2022] Open
Abstract
Multiple subtypes of dopamine receptors within the GPCR superfamily regulate neurological processes through various downstream signaling pathways. A crucial question about the dopamine receptor family is what structural features determine the subtype-selectivity of potential drugs. Here, we report the 3.5-angstrom crystal structure of mouse dopamine receptor D4 (DRD4) complexed with a subtype-selective antagonist, L745870. Our structure reveals a secondary binding pocket extended from the orthosteric ligand-binding pocket to a DRD4-specific crevice located between transmembrane helices 2 and 3. Additional mutagenesis studies suggest that the antagonist L745870 prevents DRD4 activation by blocking the relative movement between transmembrane helices 2 and 3. These results expand our knowledge of the molecular basis for the physiological functions of DRD4 and assist new drug design.
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Affiliation(s)
- Ye Zhou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Can Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
| | - Lingli He
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
| | - Xianping Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
| | - Xuejun Cai Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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20
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Wifling D, Pfleger C, Kaindl J, Ibrahim P, Kling RC, Buschauer A, Gohlke H, Clark T. Basal Histamine H 4 Receptor Activation: Agonist Mimicry by the Diphenylalanine Motif. Chemistry 2019; 25:14613-14624. [PMID: 31498478 PMCID: PMC7687114 DOI: 10.1002/chem.201902801] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 09/08/2019] [Indexed: 12/20/2022]
Abstract
Histamine H4 receptor (H4 R) orthologues are G-protein-coupled receptors (GPCRs) that exhibit species-dependent basal activity. In contrast to the basally inactive mouse H4 R (mH4 R), human H4 R (hH4 R) shows a high degree of basal activity. We have performed long-timescale molecular dynamics simulations and rigidity analyses on wild-type hH4 R, the experimentally characterized hH4 R variants S179M, F169V, F169V+S179M, F168A, and on mH4 R to investigate the molecular nature of the differential basal activity. H4 R variant-dependent differences between essential motifs of GPCR activation and structural stabilities correlate with experimentally determined basal activities and provide a molecular explanation for the differences in basal activation. Strikingly, during the MD simulations, F16945.55 dips into the orthosteric binding pocket only in the case of hH4 R, thus adopting the role of an agonist and contributing to the stabilization of the active state. The results shed new light on the molecular mechanism of basal H4 R activation that are of importance for other GPCRs.
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Affiliation(s)
- David Wifling
- Department of Pharmaceutical/Medicinal Chemistry IIInstitute of PharmacyUniversity of RegensburgUniversitätsstr. 3193053RegensburgGermany
| | - Christopher Pfleger
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
| | - Jonas Kaindl
- Computer Chemistry CenterDepartment of Chemistry and PharmacyUniversity of Erlangen-NürnbergNägelsbachstr. 2591052ErlangenGermany
| | - Passainte Ibrahim
- Computer Chemistry CenterDepartment of Chemistry and PharmacyUniversity of Erlangen-NürnbergNägelsbachstr. 2591052ErlangenGermany
| | - Ralf C. Kling
- Computer Chemistry CenterDepartment of Chemistry and PharmacyUniversity of Erlangen-NürnbergNägelsbachstr. 2591052ErlangenGermany
| | - Armin Buschauer
- Department of Pharmaceutical/Medicinal Chemistry IIInstitute of PharmacyUniversity of RegensburgUniversitätsstr. 3193053RegensburgGermany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal ChemistryHeinrich Heine University DüsseldorfUniversitätsstr. 140225DüsseldorfGermany
- John von Neumann Institute for Computing (NIC)Jülich Supercomputing Centre (JSC) &Institute for Complex Systems—Structural Biochemistry (ICS 6)Forschungszentrum Jülich GmbHWilhelm-Johnen-Str.52425JülichGermany
| | - Timothy Clark
- Computer Chemistry CenterDepartment of Chemistry and PharmacyUniversity of Erlangen-NürnbergNägelsbachstr. 2591052ErlangenGermany
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21
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Shebanits K, Vasile S, Xu B, Gutiérrez-de-Terán H, Larhammar D. Functional characterization in vitro of twelve naturally occurring variants of the human pancreatic polypeptide receptor NPY4R. Neuropeptides 2019; 76:101933. [PMID: 31230758 DOI: 10.1016/j.npep.2019.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 04/14/2019] [Accepted: 05/13/2019] [Indexed: 11/23/2022]
Abstract
Obesity has become a global health problem and therefore understanding of the mechanisms regulating hunger and satiety is of utmost importance for the development of new treatment strategies. The Y4 receptor, encoded by the NPY4R gene, and its ligand pancreatic polypeptide (PP) have been reported to mediate a satiety signal. Multiple genetic studies have reported an association between NPY4R copy number and body weight. The gene also displays several SNP variants, many of which lead to amino acid differences, making it interesting to study. We have investigated the functional properties of 12 naturally occurring amino acid sequence variants of the Y4 and interpret the results in relation to sequence conservation and our structural model of the human Y4 receptor protein. Three receptor variants, Cys201ECL2Tyr, Val2716.41Leu and Asn3187.49Asp, were found to completely lose functional response, measured as inositol phosphate turnover, while retaining membrane expression. They display high sequence conservation and have important roles in the receptor structure. For two receptor variants the potency of PP was significantly decreased, Cys34NTSer (EC50 = 2.9 nM, p < .001) and Val1353.46Met (EC50 = 3.0 nM, p < .01), compared to wild-type Y4 (EC50 = 0.68 nM). Cys34 forms a disulphide bond with Cys298, linking the N-terminal part to ECL3. The Val1353.46Met variant has an amino acid replacement located in the TM3 helix, one helix turn above the highly conserved ERH motif. This position has influence on the network of residues involved in receptor activation and subsequent inactivation. Sequence conservation and the structural model are consistent with these results. The remaining seven positions had no significant effect on the receptor's functional response compared to wild-type Y4. These positions display more variation during evolution. Understanding of the interactions between the Y4 receptor and its native PP agonist and the effects of amino acid variation on its functional response will hopefully lead to future therapeutic possibilities.
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Affiliation(s)
- Kateryna Shebanits
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-751 24 Uppsala, Sweden.
| | - Silvana Vasile
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden.
| | - Bo Xu
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Box 815, SE-751 08 Uppsala, Sweden.
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden.
| | - Dan Larhammar
- Department of Neuroscience, Science for Life Laboratory, Uppsala University, Box 593, SE-751 24 Uppsala, Sweden.
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22
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Abstract
This review provides a distillate of the advances in knowledge about the neurotransmitter functions of acetylcholine over the 50-year period between 1967 and 2017, together with incremental information about the cognate nicotinic and muscarinic acetylcholine receptors, and some brief comments on possible advances in the near future. The text is supplemented by a timelines figure indicating the dates of some key advances in knowledge about acetylcholine receptors and a box-figure providing a snapshot of selected papers about acetylcholine published in the year 1967.
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Affiliation(s)
- David A Brown
- Department of Neuroscience, Physiology & Pharmacology, University College London, London, UK
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23
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Lipiński PFJ, Kosson P, Matalińska J, Roszkowski P, Czarnocki Z, Jarończyk M, Misicka A, Dobrowolski JC, Sadlej J. Fentanyl Family at the Mu-Opioid Receptor: Uniform Assessment of Binding and Computational Analysis. Molecules 2019; 24:E740. [PMID: 30791394 PMCID: PMC6412969 DOI: 10.3390/molecules24040740] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/17/2022] Open
Abstract
Interactions of 21 fentanyl derivatives with μ-opioid receptor (μOR) were studied using experimental and theoretical methods. Their binding to μOR was assessed with radioligand competitive binding assay. A uniform set of binding affinity data contains values for two novel and one previously uncharacterized derivative. The data confirms trends known so far and thanks to their uniformity, they facilitate further comparisons. In order to provide structural hypotheses explaining the experimental affinities, the complexes of the studied derivatives with μOR were modeled and subject to molecular dynamics simulations. Five common General Features (GFs) of fentanyls' binding modes stemmed from these simulations. They include: GF1) the ionic interaction between D147 and the ligands' piperidine NH⁺ moiety; GF2) the N-chain orientation towards the μOR interior; GF3) the other pole of ligands is directed towards the receptor outlet; GF4) the aromatic anilide ring penetrates the subpocket formed by TM3, TM4, ECL1 and ECL2; GF5) the 4-axial substituent (if present) is directed towards W318. Except for the ionic interaction with D147, the majority of fentanyl-μOR contacts is hydrophobic. Interestingly, it was possible to find nonlinear relationships between the binding affinity and the volume of the N-chain and/or anilide's aromatic ring. This kind of relationships is consistent with the apolar character of interactions involved in ligand⁻receptor binding. The affinity reaches the optimum for medium size while it decreases for both large and small substituents. Additionally, a linear correlation between the volumes and the average dihedral angles of W293 and W133 was revealed by the molecular dynamics study. This seems particularly important, as the W293 residue is involved in the activation processes. Further, the Y326 (OH) and D147 (Cγ) distance found in the simulations also depends on the ligands' size. In contrast, neither RMSF measures nor D114/Y336 hydrations show significant structure-based correlations. They also do not differentiate studied fentanyl derivatives. Eventually, none of 14 popular scoring functions yielded a significant correlation between the predicted and observed affinity data (R < 0.30, n = 28).
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Affiliation(s)
- Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland.
| | - Piotr Kosson
- Toxicology Research Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland.
| | - Joanna Matalińska
- Department of Neuropeptides, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland.
| | - Piotr Roszkowski
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
| | | | | | - Aleksandra Misicka
- Department of Neuropeptides, Mossakowski Medical Research Centre, Polish Academy of Sciences, 02-106 Warsaw, Poland.
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Poland.
| | | | - Joanna Sadlej
- National Medicines Institute, 00-725 Warsaw, Poland.
- Faculty of Mathematics and Natural Sciences, University of Cardinal Stefan Wyszyński, 1/3 Wóycickiego-Str., 01-938 Warsaw, Poland.
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24
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Blaho VA, Chun J. 'Crystal' Clear? Lysophospholipid Receptor Structure Insights and Controversies. Trends Pharmacol Sci 2018; 39:953-966. [PMID: 30343728 PMCID: PMC6201317 DOI: 10.1016/j.tips.2018.08.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 08/11/2018] [Accepted: 08/27/2018] [Indexed: 12/29/2022]
Abstract
Lysophospholipids (LPLs), particularly sphingosine 1-phosphate (S1P) and lysophosphatidic acid (LPA), are bioactive lipid modulators of cellular homeostasis and pathology. The discovery and characterization of five S1P- and six LPA-specific G protein-coupled receptors (GPCRs), S1P1-5 and LPA1-6, have expanded their known involvement in all mammalian physiological systems. Resolution of the S1P1, LPA1, and LPA6 crystal structures has fueled the growing interest in these receptors and their ligands as targets for pharmacological manipulation. In this review, we have attempted to provide an integrated overview of the three crystallized LPL GPCRs with biochemical and physiological structure-function data. Finally, we provide a novel discussion of how chaperones for LPLs may be considered when extrapolating crystallographic and computational data toward understanding actual biological interactions and phenotypes.
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Affiliation(s)
- Victoria A Blaho
- Sanford Burnham Prebys Medical Discovery Institute, Degenerative Diseases Program, La Jolla, CA 92037, USA.
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, Degenerative Diseases Program, La Jolla, CA 92037, USA.
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25
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Wong LLL, Scott DJ, Hossain MA, Kaas Q, Rosengren KJ, Bathgate RAD. Distinct but overlapping binding sites of agonist and antagonist at the relaxin family peptide 3 (RXFP3) receptor. J Biol Chem 2018; 293:15777-15789. [PMID: 30131340 DOI: 10.1074/jbc.ra118.002645] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 08/09/2018] [Indexed: 12/22/2022] Open
Abstract
The relaxin-3 neuropeptide activates the relaxin family peptide 3 (RXFP3) receptor to modulate stress, appetite, and cognition. RXFP3 shows promise as a target for treating neurological disorders, but realization of its clinical potential requires development of smaller RXFP3-specific drugs that can penetrate the blood-brain barrier. Designing such drugs is challenging and requires structural knowledge of agonist- and antagonist-binding modes. Here, we used structure-activity data for relaxin-3 and a peptide RXFP3 antagonist termed R3 B1-22R to guide receptor mutagenesis and develop models of their binding modes. RXFP3 residues were alanine-substituted individually and in combination and tested in cell-based binding and functional assays to refine models of agonist and antagonist binding to active- and inactive-state homology models of RXFP3, respectively. These models suggested that both agonists and antagonists interact with RXFP3 via similar residues in their B-chain central helix. The models further suggested that the B-chain Trp27 inserts into the binding pocket of RXFP3 and interacts with Trp138 and Lys271, the latter through a salt bridge with the C-terminal carboxyl group of Trp27 in relaxin-3. R3 B1-22R, which does not contain Trp27, used a non-native Arg23 residue to form cation-π and salt-bridge interactions with Trp138 and Glu141 in RXFP3, explaining a key contribution of Arg23 to affinity. Overall, relaxin-3 and R3 B1-22R appear to share similar binding residues but may differ in binding modes, leading to active and inactive RXFP3 conformational states, respectively. These mechanistic insights may assist structure-based drug design of smaller relaxin-3 mimetics to manage neurological disorders.
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Affiliation(s)
| | - Daniel James Scott
- From the Florey Institute of Neuroscience and Mental Health.,Department of Biochemistry and Molecular Biology, and
| | - Mohammed Akhter Hossain
- From the Florey Institute of Neuroscience and Mental Health.,School of Chemistry, University of Melbourne, Parkville, Victoria 3052, Australia and
| | | | - K Johan Rosengren
- Faculty of Medicine, School of Biomedical Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ross A D Bathgate
- From the Florey Institute of Neuroscience and Mental Health, .,Department of Biochemistry and Molecular Biology, and
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26
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Full rescue of an inactive olfactory receptor mutant by elimination of an allosteric ligand-gating site. Sci Rep 2018; 8:9631. [PMID: 29941999 PMCID: PMC6018111 DOI: 10.1038/s41598-018-27790-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/31/2018] [Indexed: 11/25/2022] Open
Abstract
Ligand-gating has recently been proposed as a novel mechanism to regulate olfactory receptor sensitivity. TAAR13c, the zebrafish olfactory receptor activated by the death-associated odor cadaverine, appears to possess an allosteric binding site for cadaverine, which was assumed to block progress of the ligand towards the internal orthosteric binding-and-activation site. Here we have challenged the suggested gating mechanism by modeling the entry tunnel for the ligand as well as the ligand path inside the receptor. We report an entry tunnel, whose opening is blocked by occupation of the external binding site by cadaverine, confirming the hypothesized gating mechanism. A multistep docking algorithm suggested a plausible path for cadaverine from the allosteric to the orthosteric binding-and-activation site. Furthermore we have combined a gain-of-function gating site mutation and a loss-of-function internal binding site mutation in one recombinant receptor. This receptor had almost wildtype ligand affinities, consistent with modeling results that showed localized effects for each mutation. A novel mutation of the suggested gating site resulted in increased receptor ligand affinity. In summary both the experimental and the modeling results provide further evidence for the proposed gating mechanism, which surprisingly exhibits pronounced similarity to processes described for some metabotropic neurotransmitter receptors.
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27
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Zhang XC, Zhou Y, Cao C. Proton transfer during class-A GPCR activation: do the CWxP motif and the membrane potential act in concert? BIOPHYSICS REPORTS 2018. [DOI: 10.1007/s41048-018-0056-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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28
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Gao N, Liang T, Yuan Y, Xiao X, Zhao Y, Guo Y, Li M, Pu X. Exploring the mechanism of F282L mutation-caused constitutive activity of GPCR by a computational study. Phys Chem Chem Phys 2018; 18:29412-29422. [PMID: 27735961 DOI: 10.1039/c6cp03710k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
G-protein-coupled receptors (GPCRs) are important drug targets and generally activated by ligands. However, some experiments found that GPCRs also give rise to constitutive activity through some mutations (viz., CAM), which are usually associated with different kinds of diseases. However, the mechanisms of CAMs and their roles in interactions with drug-ligands are unclear in experiments. Herein, we used microsecond molecular dynamics simulations to study the effect of one important F282L mutation on β2AR in order to address the questions above. With the aid of principle component and correlation analysis, our results revealed that the F282L mutation could increase the instability of the overall structure, increase the dramatic fluctuations of NPxxY and extracellular loops, and decrease restraint of the helices through weakening interhelical H-bonding and correlations between residues, which could partly contribute to the constitutive activity reported by the experiments. The observations from the protein structure network (PSN) analysis indicate that the mutant exhibits less information flow than the wild β2AR and weakens the role of TM5 and TM6 in the signal transmission, but it enhances the impact of TM3 on the orthosteric pathway and TM4 on the allosteric one. In addition, the results from the virtual screening reveal that the mutant prefers to select agonists rather than antagonists, similar to the active state but opposite of the inactive state, further confirming that the F282L mutation advances the activation of β2AR. Our observations provide valuable information for understanding the mechanism of the mutation-caused constitutive activity of GPCR and related drug-design.
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Affiliation(s)
- Nan Gao
- Faculty of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Tao Liang
- Faculty of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu 610041, P. R. China
| | - Xiuchan Xiao
- Department of Architecture and Environmental Engineering, Chengdu Technological University, Chengdu, Sichuan 611730, China
| | - Yihuan Zhao
- Faculty of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Yanzhi Guo
- Faculty of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Menglong Li
- Faculty of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
| | - Xuemei Pu
- Faculty of Chemistry, Sichuan University, Chengdu, Sichuan 610064, People's Republic of China.
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29
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White KL, Eddy MT, Gao ZG, Han GW, Lian T, Deary A, Patel N, Jacobson KA, Katritch V, Stevens RC. Structural Connection between Activation Microswitch and Allosteric Sodium Site in GPCR Signaling. Structure 2018; 26:259-269.e5. [PMID: 29395784 DOI: 10.1016/j.str.2017.12.013] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/21/2017] [Accepted: 12/27/2017] [Indexed: 12/18/2022]
Abstract
Sodium ions are endogenous allosteric modulators of many G-protein-coupled receptors (GPCRs). Mutation of key residues in the sodium binding motif causes a striking effect on G-protein signaling. We report the crystal structures of agonist complexes for two variants in the first sodium coordination shell of the human A2A adenosine receptor, D522.50N and S913.39A. Both structures present an overall active-like conformation; however, the variants show key changes in the activation motif NPxxY. Changes in the hydrogen bonding network in this microswitch suggest a possible mechanism for modified G-protein signaling and enhanced thermal stability. These structures, signaling data, and thermal stability analysis with a panel of pharmacological ligands provide a basis for understanding the role of the sodium-coordinating residues on stability and G-protein signaling. Utilizing the D2.50N variant is a promising method for stabilizing class A GPCRs to accelerate structural efforts and drug discovery.
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Affiliation(s)
- Kate L White
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Matthew T Eddy
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Zhan-Guo Gao
- Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gye Won Han
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Tiffany Lian
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Alexander Deary
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Nilkanth Patel
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vsevolod Katritch
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA
| | - Raymond C Stevens
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center, University of Southern California, 1002 West Childs Way, Los Angeles, CA 90089, USA.
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30
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Abstract
Apelin and apela (ELABELA/ELA/Toddler) are two peptide ligands for a class A G-protein-coupled receptor named the apelin receptor (AR/APJ/APLNR). Ligand-AR interactions have been implicated in regulation of the adipoinsular axis, cardiovascular system, and central nervous system alongside pathological processes. Each ligand may be processed into a variety of bioactive isoforms endogenously, with apelin ranging from 13 to 55 amino acids and apela from 11 to 32, typically being cleaved C-terminal to dibasic proprotein convertase cleavage sites. The C-terminal region of the respective precursor protein is retained and is responsible for receptor binding and subsequent activation. Interestingly, both apelin and apela exhibit isoform-dependent variability in potency and efficacy under various physiological and pathological conditions, but most studies focus on a single isoform. Biophysical behavior and structural properties of apelin and apela isoforms show strong correlations with functional studies, with key motifs now well determined for apelin. Unlike its ligands, the AR has been relatively difficult to characterize by biophysical techniques, with most characterization to date being focused on effects of mutagenesis. This situation may improve following a recently reported AR crystal structure, but there are still barriers to overcome in terms of comprehensive biophysical study. In this review, we summarize the three components of the apelinergic system in terms of structure-function correlation, with a particular focus on isoform-dependent properties, underlining the potential for regulation of the system through multiple endogenous ligands and isoforms, isoform-dependent pharmacological properties, and biological membrane-mediated receptor interaction. © 2018 American Physiological Society. Compr Physiol 8:407-450, 2018.
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Affiliation(s)
- Kyungsoo Shin
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Calem Kenward
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jan K Rainey
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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31
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Cunningham MR, Aungraheeta R, Mundell SJ. Pathophysiological consequences of receptor mistraffic: Tales from the platelet P2Y 12 receptor. Mol Cell Endocrinol 2017; 449:74-81. [PMID: 28212842 DOI: 10.1016/j.mce.2017.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/10/2017] [Accepted: 02/10/2017] [Indexed: 12/12/2022]
Abstract
Genetic variations in G protein-coupled receptor (GPCR) genes can disrupt receptor function in a wide variety of human genetic diseases, including platelet bleeding disorders. Platelets are critical for haemostasis with inappropriate platelet activation leading to the development of arterial thrombosis, which can result in heart attack and stroke whilst decreased platelet activity is associated with an increased risk of bleeding. GPCRs expressed on the surface of platelets play key roles in regulating platelet activity and therefore function. Receptors include purinergic receptors (P2Y1 and P2Y12), proteinase-activated receptor (PAR1 and PAR4) and thromboxane receptors (TPα), among others. Pharmacological blockade of these receptors forms a powerful therapeutic tool in the treatment and prevention of arterial thrombosis. With the advance of genomic technologies, there has been a substantial increase in the identification of naturally occurring rare and common GPCR variants. These variants include single-nucleotide polymorphisms (SNPs) and insertion or deletions that have the potential to alter GPCR expression or function. A number of defects in platelet GPCRs that disrupt receptor function have now been characterized in patients with mild bleeding disorders. This review will focus on rare, function-disrupting variants of platelet GPCRs with particular emphasis upon mutations in the P2Y12 receptor gene that affect receptor traffic to modulate platelet function. Further this review will outline how the identification and characterization of function-disrupting GPCR mutations provides an essential link in translating our detailed understanding of receptor traffic and function in cell line studies into relevant human biological systems.
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Affiliation(s)
- Margaret R Cunningham
- Strathclyde Institute for Pharmacy and Biomedical Sciences (SIPBS), University of Strathclyde, Glasgow, UK
| | - Riyaad Aungraheeta
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol, UK
| | - Stuart J Mundell
- School of Physiology, Pharmacology and Neuroscience, Faculty of Biomedical Sciences, University of Bristol, Bristol, UK.
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32
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Harpsøe K, Boesgaard MW, Munk C, Bräuner-Osborne H, Gloriam DE. Structural insight to mutation effects uncover a common allosteric site in class C GPCRs. Bioinformatics 2017; 33:1116-1120. [PMID: 28011766 PMCID: PMC5408886 DOI: 10.1093/bioinformatics/btw784] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/07/2016] [Indexed: 01/08/2023] Open
Abstract
Motivation Class C G protein-coupled receptors (GPCRs) regulate important physiological functions and allosteric modulators binding to the transmembrane domain constitute an attractive and, due to a lack of structural insight, a virtually unexplored potential for therapeutics and the food industry. Combining pharmacological site-directed mutagenesis data with the recent class C GPCR experimental structures will provide a foundation for rational design of new therapeutics. Results We uncover one common site for both positive and negative modulators with different amino acid layouts that can be utilized to obtain selectivity. Additionally, we show a large potential for structure-based modulator design, especially for four orphan receptors with high similarity to the crystal structures. Availability and Implementation All collated mutagenesis data is available in the GPCRdb mutation browser at http://gpcrdb.org/mutations/ and can be analyzed online or downloaded in excel format. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Kasper Harpsøe
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael W Boesgaard
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Munk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bräuner-Osborne
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - David E Gloriam
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- To whom correspondence should be addressed.
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Rovati GE, Capra V, Shaw VS, Malik RU, Sivaramakrishnan S, Neubig RR. The DRY motif and the four corners of the cubic ternary complex model. Cell Signal 2017; 35:16-23. [PMID: 28347873 DOI: 10.1016/j.cellsig.2017.03.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/24/2017] [Indexed: 12/14/2022]
Abstract
Recent structural data on GPCRs using a variety of spectroscopic approaches suggest that GPCRs adopt a dynamic conformational landscape, with ligands stabilizing subsets of these states to activate one or more downstream signaling effectors. A key outstanding question posed by this emerging dynamic structural model of GPCRs is what states, active, inactive, or intermediate are captured by the numerous crystal structures of GPCRs complexed with a variety of agonists, partial agonists, and antagonists. In the early nineties the discovery of inverse agonists and constitutive activity led to the idea that the active receptor state (R⁎) is an intrinsic property of the receptor itself rather than of the RG complex, eventually leading to the formulation of the cubic ternary complex model (CTC). Here, by a careful analysis of a series of data obtained with a number of mutants of the highly conserved E/DRY motif, we show evidences for the existence of all the receptor states theorized by the CTC, four 'uncoupled (R, R⁎ and HR and HR⁎), and, consequently four 'coupled' (RG, R⁎G, HRG and HR⁎G). The E/DRY motif located at the cytosolic end of transmembrane helix III of Class A GPCRs has been widely studied and analyzed because it forms a network of interactions believed to lock receptors in the inactive conformation (R), and, thus, to play a key role in receptor activation. Our conclusions are supported by recent crystal and NMR spectra, as well as by results obtained with two prototypical GPCRs using a new FRET technology that de-couples G protein binding to the receptor from signal transduction. Thus, despite its complexity and limitations, we propose that the CTC is a useful framework to reconcile pharmacological, biochemical and structural data.
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Affiliation(s)
- G Enrico Rovati
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milano, Italy.
| | - Valérie Capra
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milano, Italy; Department of Health Science, University of Milan, Milano, Italy.
| | - Vincent S Shaw
- Department of Pharmacology & Toxicology, Michigan State University, East Lansing, MI, USA.
| | - Rabia U Malik
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota Twin Cities, Minneapolis, MN, USA.
| | - Sivaraj Sivaramakrishnan
- Department of Genetics, Cell Biology & Development, College of Biological Sciences, University of Minnesota Twin Cities, Minneapolis, MN, USA.
| | - Richard R Neubig
- Department of Pharmacology & Toxicology, Michigan State University, East Lansing, MI, USA.
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34
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Liu Y, Canal CE, Cordova-Sintjago TC, Zhu W, Booth RG. Mutagenesis Analysis Reveals Distinct Amino Acids of the Human Serotonin 5-HT 2C Receptor Underlying the Pharmacology of Distinct Ligands. ACS Chem Neurosci 2017; 8:28-39. [PMID: 27580242 DOI: 10.1021/acschemneuro.6b00124] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
While exploring the structure-activity relationship of 4-phenyl-2-dimethylaminotetralins (PATs) at serotonin 5-HT2C receptors, we discovered that relatively minor modification of PAT chemistry impacts function at 5-HT2C receptors. In HEK293 cells expressing human 5-HT2C-INI receptors, for example, (-)-trans-3'-Br-PAT and (-)-trans-3'-Cl-PAT are agonists regarding Gαq-inositol phosphate signaling, whereas (-)-trans-3'-CF3-PAT is an inverse agonist. To investigate the ligand-receptor interactions that govern this change in function, we performed site-directed mutagenesis of 14 amino acids of the 5-HT2C receptor based on molecular modeling and reported G protein-coupled receptor crystal structures, followed by molecular pharmacology studies. We found that S3.36, T3.37, and F5.47 in the orthosteric binding pocket are critical for affinity (Ki) of all PATs tested, we also found that F6.44, M6.47, C7.45, and S7.46 are primarily involved in regulating EC/IC50 functional potencies of PATs. We discovered that when residue S5.43, N6.55, or both are mutated to alanine, (-)-trans-3'-CF3-PAT switches from inverse agonist to agonist function, and when N6.55 is mutated to leucine, (-)-trans-3'-Br-PAT switches from agonist to inverse agonist function. Notably, most point-mutations that affected PAT pharmacology did not significantly alter affinity (KD) of the antagonist radioligand [3H]mesulergine, but every mutation tested negatively impacted serotonin binding. Also, amino acid mutations differentially affected the pharmacology of other commercially available 5-HT2C ligands tested. Collectively, the data show that functional outcomes shared by different ligands are mediated by different amino acids and that some 5-HT2C receptor residues important for pharmacology of one ligand are not necessarily important for another ligand.
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Affiliation(s)
- Yue Liu
- Center
for Drug Discovery, Department of Pharmaceutical Sciences, and Department
of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Clinton E. Canal
- Center
for Drug Discovery, Department of Pharmaceutical Sciences, and Department
of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Tania C. Cordova-Sintjago
- Center
for Drug Discovery, Department of Pharmaceutical Sciences, and Department
of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Department
of Medicinal Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Wanying Zhu
- Center
for Drug Discovery, Department of Pharmaceutical Sciences, and Department
of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Raymond G. Booth
- Center
for Drug Discovery, Department of Pharmaceutical Sciences, and Department
of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
- Department
of Medicinal Chemistry, University of Florida, Gainesville, Florida 32611, United States
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35
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Tateyama M, Kubo Y. Stabilizing effects of G protein on the active conformation of adenosine A 1 receptor differ depending on G protein type. Eur J Pharmacol 2016; 788:122-131. [DOI: 10.1016/j.ejphar.2016.06.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 06/15/2016] [Accepted: 06/15/2016] [Indexed: 01/07/2023]
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36
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Young A, Dandekar U, Pan C, Sader A, Zheng JJ, Lewis RA, Farber DB. GNAI3: Another Candidate Gene to Screen in Persons with Ocular Albinism. PLoS One 2016; 11:e0162273. [PMID: 27607449 PMCID: PMC5015898 DOI: 10.1371/journal.pone.0162273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 08/21/2016] [Indexed: 11/18/2022] Open
Abstract
Ocular albinism type 1 (OA), caused by mutations in the OA1 gene, encodes a G-protein coupled receptor, OA1, localized in melanosomal membranes of the retinal pigment epithelium (RPE). This disorder is characterized by both RPE macro-melanosomes and abnormal decussation of ganglion cell axons at the brain's optic chiasm. We demonstrated previously that Oa1 specifically activates Gαi3, which also signals in the Oa1 transduction pathway that regulates melanosomal biogenesis. In this study, we screened the human Gαi3 gene, GNAI3, in DNA samples from 26 patients who had all clinical characteristics of OA but in whom a specific mutation in the OA1 gene had not been found, and in 6 normal control individuals. Using the Agilent HaloPlex Target Enrichment System and next-generation sequencing (NGS) on the Illumina MiSeq platform, we identified 518 variants after rigorous filtering. Many of these variants were corroborated by Sanger sequencing. Overall, 98.8% coverage of the GNAI3 gene was obtained by the HaloPlex amplicons. Of all variants, 6 non-synonymous and 3 synonymous were in exons, 41 in a non-coding exon embedded in the 3' untranslated region (UTR), 6 in the 5' UTR, and 462 in introns. These variants included novel SNVs, insertions, deletions, and a frameshift mutation. All were found in at least one patient but none in control samples. Using computational methods, we modeled the GNAI3 protein and its non-synonymous exonic mutations and determined that several of these may be the cause of disease in the patients studied. Thus, we have identified GNAI3 as a second gene possibly responsible for X-linked ocular albinism.
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Affiliation(s)
- Alejandra Young
- Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States of America
- Molecular Biology Institute, UCLA, Los Angeles, CA, United States of America
| | - Uma Dandekar
- UCLA-GenoSeq Core, UCLA, Los Angeles, CA, United States of America
| | - Calvin Pan
- UCLA-GenoSeq Core, UCLA, Los Angeles, CA, United States of America
| | - Avery Sader
- Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States of America
| | - Jie J. Zheng
- Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States of America
| | - Richard A. Lewis
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Debora B. Farber
- Stein Eye Institute and Department of Ophthalmology, David Geffen School of Medicine, UCLA, Los Angeles, CA, United States of America
- Molecular Biology Institute, UCLA, Los Angeles, CA, United States of America
- Brain Research Institute, UCLA, Los Angeles, CA, United States of America
- * E-mail:
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37
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Use of Fluorescence Indicators in Receptor Ligands. Methods Mol Biol 2016; 1335:115-30. [PMID: 26260598 DOI: 10.1007/978-1-4939-2914-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fluorescence techniques can provide insights into the environment of fluorescence indicators incorporated within a ligand as it is bound to its receptor. Fluorescence indicators of different sizes and chemical characteristics can provide insights into the nature of the binding environment, the surrounding structures, and even into conformational changes associated with receptor activation. Methods for determining fluorescence spectral analysis, fluorescence quenching, fluorescence anisotropy, fluorescence lifetimes, and red edge excitation shifts of the ligand probes are described. The applications of these techniques to the CCK1 receptor occupied by alexa(488)-CCK and aladan-CCK, as examples of probes developed (1) by derivatization of an existing peptide and (2) by incorporation during peptide synthesis, are utilized as examples. These methods represent powerful tools to expand our understanding of the structure and molecular basis of ligand activation of G protein-coupled receptors.
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38
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Li Y, Sun J, Li D, Lin J. Activation and conformational dynamics of a class B G-protein-coupled glucagon receptor. Phys Chem Chem Phys 2016; 18:12642-50. [PMID: 27094704 DOI: 10.1039/c6cp00798h] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The human glucagon receptor (GCGR) is a class B G-protein-coupled receptor (GPCR). The GCGR can be activated by glucagon and regulates the release of glucose. The GCGR has been proposed to be an important drug target for type 2 diabetes. Based on the structural model of a full-length glucagon-bound GCGR (glu-GCGR), we performed accelerated molecular dynamics (aMD) simulations, potential of mean force (PMF) calculations, cross-correlation analysis and community network analysis to study the activation mechanism and the conformational dynamics during the activation process. The PMF map depicts three different conformational states of the GCGR: the inactive, intermediate and active states. The activation of the GCGR is characterized by the outward movement of the intracellular side of helix VI. In the active state of the GCGR, the Arg173(2.46)-Ser350(6.41) and Glu245(3.50)-Thr351(6.42) hydrogen bonds break, and the χ1 rotamer of Phe322(5.54) changes from perpendicular to parallel to helix VI. The binding of the agonist glucagon decreases the correlated motions of the extracellular loops (ELCs) and the helices around the glucagon-binding site. During the activation of the GCGR, the connections between the intracellular sides of helices become weaker, and the connections between glucagon and ECLs and the extracellular sides of helices become stronger. These facilitate G-protein coupling on the intracellular side and glucagon binding on the extracellular side, and stabilize the GCGR in the active state. We expect that this study can provide useful information on the activation mechanism of the GCGR and facilitate the future design of GCGR inhibitors.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Haihe Education Park, 38 Tongyan Road, Tianjin 300353, People's Republic of China.
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39
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Allosteric effects of sodium ion binding on activation of the m3 muscarinic g-protein-coupled receptor. Biophys J 2016; 108:1796-1806. [PMID: 25863070 DOI: 10.1016/j.bpj.2015.03.003] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/03/2015] [Accepted: 03/04/2015] [Indexed: 12/31/2022] Open
Abstract
G-protein-coupled receptors (GPCRs) are important membrane proteins that mediate cellular signaling and represent primary targets for about one-third of currently marketed drugs. Recent x-ray crystallographic studies identified distinct conformations of GPCRs in the active and inactive states. An allosteric sodium ion was found bound to a highly conserved D2.50 residue in inactive GPCRs, whereas the D2.50 allosteric pocket became collapsed in active GPCR structures. However, the dynamic mechanisms underlying these observations remain elusive. In this study, we aimed to understand the mechanistic effects of sodium ion binding on dynamic activation of the M3 muscarinic GPCR through long-timescale accelerated molecular dynamics (aMD) simulations. Results showed that with the D2.50 residue deprotonated, the M3 receptor is bound by an allosteric sodium ion and confined mostly in the inactive state with remarkably reduced flexibility. In contrast, the D2.50-protonated receptor does not exhibit sodium ion binding to the D2.50 allosteric site and samples a significantly larger conformational space. The receptor activation is captured and characterized by large-scale structural rearrangements of the transmembrane helices via dynamic hydrogen bond and salt bridge interactions. The residue motions are highly correlated during receptor activation. Further network analysis revealed that the allosteric signaling between residue D2.50 and key residues in the intracellular, extracellular, and orthosteric pockets is significantly weakened upon sodium ion binding.
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40
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How Can Mutations Thermostabilize G-Protein-Coupled Receptors? Trends Pharmacol Sci 2015; 37:37-46. [PMID: 26547284 DOI: 10.1016/j.tips.2015.09.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/14/2015] [Accepted: 09/21/2015] [Indexed: 01/04/2023]
Abstract
Structures of over 30 different G-protein-coupled receptors (GPCRs) have advanced our understanding of cell signaling and have provided a foundation for structure-guided drug design. This exciting progress has required the development of three complementary methods to facilitate GPCR crystallization, one of which is the thermostabilization of receptors by systematic mutagenesis. However, the reason why a particular mutation, or combination of mutations, stabilizes the receptor is not always evident from a static crystal structure. Molecular dynamics (MD) simulations have been used to identify and estimate the energetic factors that affect thermostability through comparing the dynamics of the thermostabilized receptors with structure-based models of the wild-type receptor. The data indicate that receptors are stabilized through a combination of factors, including an increase in receptor rigidity, a decrease in collective motion, reduced stress at specific residues, and the presence of ordered water molecules. Predicting thermostabilizing mutations computationally represents a major challenge for the field.
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41
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Rinne A, Mobarec JC, Mahaut-Smith M, Kolb P, Bünemann M. The mode of agonist binding to a G protein-coupled receptor switches the effect that voltage changes have on signaling. Sci Signal 2015; 8:ra110. [PMID: 26535008 DOI: 10.1126/scisignal.aac7419] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Signaling by many heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors (GPCRs) is either enhanced or attenuated by changes in plasma membrane potential. To identify structural correlates of the voltage sensitivity of GPCR signaling, we chose muscarinic acetylcholine receptors (the M1, M3, and M5 isoforms) as a model system. We combined molecular docking analysis with Förster resonance energy transfer (FRET)-based assays that monitored receptor activity under voltage clamp conditions. When human embryonic kidney (HEK) 293 cells expressing the individual receptors were stimulated with the agonist carbachol, membrane depolarization enhanced signaling by the M1 receptor but attenuated signaling by the M3 and M5 receptors. Furthermore, whether membrane depolarization enhanced or inhibited receptor signaling depended on the type of agonist. Membrane depolarization attenuated M3 receptor signaling when the receptor was bound to carbachol or acetylcholine, whereas depolarization enhanced signaling when the receptor was bound to either choline or pilocarpine. Docking calculations predicted that there were two distinct binding modes for these ligands, which were associated with the effect of depolarization on receptor function. From these calculations, we identified a residue in the M3 receptor that, when mutated, would alter the binding mode of carbachol to resemble that of pilocarpine in silico. Introduction of this mutated M3 receptor into cells confirmed that the membrane depolarization enhanced, rather than attenuated, signaling by the carbachol-bound receptor. Together, these data suggest that the directionality of the voltage sensitivity of GPCR signaling is defined by the specific binding mode of each ligand to the receptor.
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Affiliation(s)
- Andreas Rinne
- Department of Cardiovascular Physiology, Ruhr University Bochum, Universitätsstr. 150, D-44780 Bochum, Germany
| | - Juan Carlos Mobarec
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Martyn Mahaut-Smith
- Department of Cell Physiology and Pharmacology, University of Leicester, University Road, P. O. Box 138, Leicester LE1 9HN, UK
| | - Peter Kolb
- Department of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg 6, D-35032 Marburg, Germany
| | - Moritz Bünemann
- Department of Pharmacology and Clinical Pharmacy, Philipps University Marburg, Karl-von-Frisch-Str. 1, D-35043 Marburg, Germany.
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42
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Sergeev E, Hansen AH, Pandey SK, MacKenzie AE, Hudson BD, Ulven T, Milligan G. Non-equivalence of Key Positively Charged Residues of the Free Fatty Acid 2 Receptor in the Recognition and Function of Agonist Versus Antagonist Ligands. J Biol Chem 2015; 291:303-17. [PMID: 26518871 PMCID: PMC4697166 DOI: 10.1074/jbc.m115.687939] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 01/22/2023] Open
Abstract
Short chain fatty acids (SCFAs) are produced in the gut by bacterial fermentation of poorly digested carbohydrates. A key mediator of their actions is the G protein-coupled free fatty acid 2 (FFA2) receptor, and this has been suggested as a therapeutic target for the treatment of both metabolic and inflammatory diseases. However, a lack of understanding of the molecular determinants dictating how ligands bind to this receptor has hindered development. We have developed a novel radiolabeled FFA2 antagonist to probe ligand binding to FFA2, and in combination with mutagenesis and molecular modeling studies, we define how agonist and antagonist ligands interact with the receptor. Although both agonist and antagonist ligands contain negatively charged carboxylates that interact with two key positively charged arginine residues in transmembrane domains V and VII of FFA2, there are clear differences in how these interactions occur. Specifically, although agonists require interaction with both arginine residues to bind the receptor, antagonists require an interaction with only one of the two. Moreover, different chemical series of antagonist interact preferentially with different arginine residues. A homology model capable of rationalizing these observations was developed and provides a tool that will be invaluable for identifying improved FFA2 agonists and antagonists to further define function and therapeutic opportunities of this receptor.
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Affiliation(s)
- Eugenia Sergeev
- From the Molecular Pharmacology Group, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom and
| | - Anders Højgaard Hansen
- the Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Sunil K Pandey
- the Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Amanda E MacKenzie
- From the Molecular Pharmacology Group, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom and
| | - Brian D Hudson
- From the Molecular Pharmacology Group, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom and
| | - Trond Ulven
- the Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Graeme Milligan
- From the Molecular Pharmacology Group, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, Scotland, United Kingdom and
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43
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Weston C, Lu J, Li N, Barkan K, Richards GO, Roberts DJ, Skerry TM, Poyner D, Pardamwar M, Reynolds CA, Dowell SJ, Willars GB, Ladds G. Modulation of Glucagon Receptor Pharmacology by Receptor Activity-modifying Protein-2 (RAMP2). J Biol Chem 2015. [PMID: 26198634 PMCID: PMC4645630 DOI: 10.1074/jbc.m114.624601] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The glucagon and glucagon-like peptide-1 (GLP-1) receptors play important, opposing roles in regulating blood glucose levels. Consequently, these receptors have been identified as targets for novel diabetes treatments. However, drugs acting at the GLP-1 receptor, although having clinical efficacy, have been associated with severe adverse side-effects, and targeting of the glucagon receptor has yet to be successful. Here we use a combination of yeast reporter assays and mammalian systems to provide a more complete understanding of glucagon receptor signaling, considering the effect of multiple ligands, association with the receptor-interacting protein receptor activity-modifying protein-2 (RAMP2), and the role of individual G protein α-subunits. We demonstrate that RAMP2 alters both ligand selectivity and G protein preference of the glucagon receptor. Importantly, we also uncover novel cross-reactivity of therapeutically used GLP-1 receptor ligands at the glucagon receptor that is abolished by RAMP2 interaction. This study reveals the glucagon receptor as a previously unidentified target for GLP-1 receptor agonists and highlights a role for RAMP2 in regulating its pharmacology. Such previously unrecognized functions of RAMPs highlight the need to consider all receptor-interacting proteins in future drug development.
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Affiliation(s)
- Cathryn Weston
- From the Division of Biomedical Cell Biology, Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom,
| | - Jing Lu
- the Department of Cell Physiology and Pharmacology, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Naichang Li
- the Department of Cell Physiology and Pharmacology, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Kerry Barkan
- From the Division of Biomedical Cell Biology, Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gareth O Richards
- the Mellanby Centre for Bone Research, Department of Human Metabolism, University of Sheffield, Sheffield S10 2RX, United Kingdom
| | - David J Roberts
- the Mellanby Centre for Bone Research, Department of Human Metabolism, University of Sheffield, Sheffield S10 2RX, United Kingdom
| | - Timothy M Skerry
- the Mellanby Centre for Bone Research, Department of Human Metabolism, University of Sheffield, Sheffield S10 2RX, United Kingdom
| | - David Poyner
- the School of Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, United Kingdom
| | - Meenakshi Pardamwar
- the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom, and
| | - Christopher A Reynolds
- the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom, and
| | - Simon J Dowell
- the Department of Biological Sciences, Molecular Discovery Research, GlaxoSmithKline, Hertfordshire SG1 2NY, United Kingdom, and
| | - Gary B Willars
- the Department of Cell Physiology and Pharmacology, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Graham Ladds
- From the Division of Biomedical Cell Biology, Warwick Medical School, University of Warwick, Coventry CV4 7AL, United Kingdom, the Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
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44
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Randáková A, Dolejší E, Rudajev V, Zimčík P, Doležal V, El-Fakahany EE, Jakubík J. Classical and atypical agonists activate M1 muscarinic acetylcholine receptors through common mechanisms. Pharmacol Res 2015; 97:27-39. [DOI: 10.1016/j.phrs.2015.04.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 04/03/2015] [Accepted: 04/03/2015] [Indexed: 01/24/2023]
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45
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Dalton JAR, Lans I, Giraldo J. Quantifying conformational changes in GPCRs: glimpse of a common functional mechanism. BMC Bioinformatics 2015; 16:124. [PMID: 25902715 PMCID: PMC4422131 DOI: 10.1186/s12859-015-0567-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/09/2015] [Indexed: 12/12/2022] Open
Abstract
Background G-protein-coupled receptors (GPCRs) are important drug targets and a better understanding of their molecular mechanisms would be desirable. The crystallization rate of GPCRs has accelerated in recent years as techniques have become more sophisticated, particularly with respect to Class A GPCRs interacting with G-proteins. These developments have made it possible for a quantitative analysis of GPCR geometrical features and binding-site conformations, including a statistical comparison between Class A GPCRs in active (agonist-bound) and inactive (antagonist-bound) states. Results Here we implement algorithms for the analysis of interhelical angles, distances, interactions and binding-site volumes in the transmembrane domains of 25 Class A GPCRs (7 active and 18 inactive). Two interhelical angles change in a statistically significant way between average inactive and active states: TM3-TM6 (by -9°) and TM6-TM7 (by +12°). A third interhelical angle: TM5-TM6 shows a trend, changing by -9°. In the transition from inactive to active states, average van der Waals interactions between TM3 and TM7 significantly increase as the average distance between them decreases by >2 Å. Average H-bonding between TM3 and TM6 decreases but is seemingly compensated by an increase in H-bonding between TM5 and TM6. In five Class A GPCRs, crystallized in both active and inactive states, increased H-bonding of agonists to TM6 and TM7, relative to antagonists, is observed. These protein-agonist interactions likely favour a change in the TM6-TM7 angle, which creates a narrowing in the binding pocket of activated receptors and an average ~200 Å3 reduction in volume. Conclusions In terms of similar conformational changes and agonist binding pattern, Class A GPCRs appear to share a common mechanism of activation, which can be exploited in future drug development. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0567-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- James A R Dalton
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Isaias Lans
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
| | - Jesús Giraldo
- Laboratory of Molecular Neuropharmacology and Bioinformatics, Institut de Neurociències and Unitat de Bioestadística, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain.
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Yun JH, Kim M, Kim K, Lee D, Jung Y, Oh D, Ko YJ, Cho AE, Cho HS, Lee W. Solution structure of the transmembrane 2 domain of the human melanocortin-4 receptor in sodium dodecyl sulfate (SDS) micelles and the functional implication of the D90N mutant. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:1294-302. [PMID: 25753114 DOI: 10.1016/j.bbamem.2015.02.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 02/03/2015] [Accepted: 02/27/2015] [Indexed: 10/23/2022]
Abstract
The melanocortin receptors (MCRs) are members of the G protein-coupled receptor (GPCR) 1 superfamily with seven transmembrane (TM) domains. Among them, the melanocortin-4 receptor (MC4R) subtype has been highlighted recently by genetic studies in obese humans. In particular, in a patient with severe early-onset obesity, a novel heterozygous mutation in the MC4R gene was found in an exchange of Asp to Asn in the 90th amino acid residue located in the TM 2 domain (MC4RD90N). Mutations in the MC4R gene are the most frequent monogenic causes of severe obesity and are described as heterozygous with loss of function. We determine solution structures of the TM 2 domain of MC4R (MC4RTM2) and compared secondary structure of Asp90 mutant (MC4RTM2-D90N) in a micelle environment by nuclear magnetic resonance (NMR) spectroscopy. NMR structure shows that MC4RTM2 forms a long α-helix with a kink at Gly98. Interestingly, the structure of MC4RTM2-D90N is similar to that of MC4RTM2 based on data from CD and NMR spectrum. However, the thermal stability and homogeneity of MC4RD90N is quite different from those of MC4R. The structure from molecular modeling suggests that Asp90(2.50) plays a key role in allosteric sodium ion binding. Our data suggest that the sodium ion interaction of Asp90(2.50) in the allosteric pocket of MC4R is essential to its function, explaining the loss of function of the MC4RD90N mutant.
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Affiliation(s)
- Ji-Hye Yun
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Minsup Kim
- Department of Bioinformatics, Korea University, Sejong 136-701, Republic of Korea
| | - Kuglae Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Dongju Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Youngjin Jung
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Daeseok Oh
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Yoon-Joo Ko
- National Center for Inter-University Research Facilities, Seoul National University, Seoul 151-747, Republic of Korea
| | - Art E Cho
- Department of Bioinformatics, Korea University, Sejong 136-701, Republic of Korea
| | - Hyun-Soo Cho
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea
| | - Weontae Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea.
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Zhang XC, Cao C, Zhou Y, Zhao Y. Proton transfer-mediated GPCR activation. Protein Cell 2014; 6:12-7. [PMID: 25319942 PMCID: PMC4286134 DOI: 10.1007/s13238-014-0106-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 09/28/2014] [Indexed: 12/29/2022] Open
Abstract
G-protein coupled receptors (GPCRs) play essential roles in signal transduction from the environment into the cell. While many structural features have been elucidated in great detail, a common functional mechanism on how the ligand-binding signal is converted into a conformational change on the cytoplasmic face resulting in subsequent activation of downstream effectors remain to be established. Based on available structural and functional data of the activation process in class-A GPCRs, we propose here that a change in protonation status, together with proton transfer via conserved structural elements located in the transmembrane region, are the key elements essential for signal transduction across the membrane.
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Affiliation(s)
- Xuejun C Zhang
- National Laboratory of Macromolecules, National Center of Protein Science-Beijing, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China,
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Dong M, Vattelana AM, Lam PCH, Orry AJ, Abagyan R, Christopoulos A, Sexton PM, Haines DR, Miller LJ. Development of a highly selective allosteric antagonist radioligand for the type 1 cholecystokinin receptor and elucidation of its molecular basis of binding. Mol Pharmacol 2014; 87:130-40. [PMID: 25319540 DOI: 10.1124/mol.114.095430] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Understanding the molecular basis of ligand binding to receptors provides insights useful for rational drug design. This work describes development of a new antagonist radioligand of the type 1 cholecystokinin receptor (CCK1R), (2-fluorophenyl)-2,3-dihydro-3-[(3-isoquinolinylcarbonyl)amino]-6-methoxy-2-oxo-l-H-indole-3-propanoate (T-0632), and exploration of the molecular basis of its binding. This radioligand bound specifically with high affinity within an allosteric pocket of CCK1R. T-0632 fully inhibited binding and action of CCK at this receptor, while exhibiting no saturable binding to the closely related type 2 cholecystokinin receptor (CCK2R). Chimeric CCK1R/CCK2R constructs were used to explore the molecular basis of T-0632 binding. Exchanging exonic regions revealed the functional importance of CCK1R exon 3, extending from the bottom of transmembrane segment (TM) 3 to the top of TM5, including portions of the intramembranous pocket as well as the second extracellular loop region (ECL2). However, CCK1R mutants in which each residue facing the pocket was changed to that present in CCK2R had no negative impact on T-0632 binding. Extending the chimeric approach to ECL2 established the importance of its C-terminal region, and site-directed mutagenesis of each nonconserved residue in this region revealed the importance of Ser(208) at the top of TM5. A molecular model of T-0632-occupied CCK1R was consistent with these experimental determinants, also identifying Met(121) in TM3 and Arg(336) in TM6 as important. Although these residues are conserved in CCK2R, mutating them had a distinct impact on the two closely related receptors, suggesting differential orientation. This establishes the molecular basis of binding of a highly selective nonpeptidyl allosteric antagonist of CCK1R, illustrating differences in docking that extend beyond determinants attributable to distinct residues lining the intramembranous pocket in the two receptor subtypes.
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Affiliation(s)
- Maoqing Dong
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona (M.D., L.J.M.); Department of Chemistry, Wellesley College, Wellesley, Massachusetts (A.M.V., D.R.H.); Molsoft LLC, La Jolla, California (P.C.-H.L., A.J.O., R.A.); Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California (R.A.); and Department of Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (A.C., P.M.S.)
| | - Ashton M Vattelana
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona (M.D., L.J.M.); Department of Chemistry, Wellesley College, Wellesley, Massachusetts (A.M.V., D.R.H.); Molsoft LLC, La Jolla, California (P.C.-H.L., A.J.O., R.A.); Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California (R.A.); and Department of Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (A.C., P.M.S.)
| | - Polo C-H Lam
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona (M.D., L.J.M.); Department of Chemistry, Wellesley College, Wellesley, Massachusetts (A.M.V., D.R.H.); Molsoft LLC, La Jolla, California (P.C.-H.L., A.J.O., R.A.); Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California (R.A.); and Department of Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (A.C., P.M.S.)
| | - Andrew J Orry
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona (M.D., L.J.M.); Department of Chemistry, Wellesley College, Wellesley, Massachusetts (A.M.V., D.R.H.); Molsoft LLC, La Jolla, California (P.C.-H.L., A.J.O., R.A.); Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California (R.A.); and Department of Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (A.C., P.M.S.)
| | - Ruben Abagyan
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona (M.D., L.J.M.); Department of Chemistry, Wellesley College, Wellesley, Massachusetts (A.M.V., D.R.H.); Molsoft LLC, La Jolla, California (P.C.-H.L., A.J.O., R.A.); Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California (R.A.); and Department of Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (A.C., P.M.S.)
| | - Arthur Christopoulos
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona (M.D., L.J.M.); Department of Chemistry, Wellesley College, Wellesley, Massachusetts (A.M.V., D.R.H.); Molsoft LLC, La Jolla, California (P.C.-H.L., A.J.O., R.A.); Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California (R.A.); and Department of Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (A.C., P.M.S.)
| | - Patrick M Sexton
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona (M.D., L.J.M.); Department of Chemistry, Wellesley College, Wellesley, Massachusetts (A.M.V., D.R.H.); Molsoft LLC, La Jolla, California (P.C.-H.L., A.J.O., R.A.); Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California (R.A.); and Department of Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (A.C., P.M.S.)
| | - David R Haines
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona (M.D., L.J.M.); Department of Chemistry, Wellesley College, Wellesley, Massachusetts (A.M.V., D.R.H.); Molsoft LLC, La Jolla, California (P.C.-H.L., A.J.O., R.A.); Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California (R.A.); and Department of Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (A.C., P.M.S.)
| | - Laurence J Miller
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona (M.D., L.J.M.); Department of Chemistry, Wellesley College, Wellesley, Massachusetts (A.M.V., D.R.H.); Molsoft LLC, La Jolla, California (P.C.-H.L., A.J.O., R.A.); Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California (R.A.); and Department of Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, Australia (A.C., P.M.S.)
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Congreve M, Dias JM, Marshall FH. Structure-based drug design for G protein-coupled receptors. PROGRESS IN MEDICINAL CHEMISTRY 2014; 53:1-63. [PMID: 24418607 DOI: 10.1016/b978-0-444-63380-4.00001-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Our understanding of the structural biology of G protein-coupled receptors has undergone a transformation over the past 5 years. New protein-ligand complexes are described almost monthly in high profile journals. Appreciation of how small molecules and natural ligands bind to their receptors has the potential to impact enormously how medicinal chemists approach this major class of receptor targets. An outline of the key topics in this field and some recent examples of structure- and fragment-based drug design are described. A table is presented with example views of each G protein-coupled receptor for which there is a published X-ray structure, including interactions with small molecule antagonists, partial and full agonists. The possible implications of these new data for drug design are discussed.
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Affiliation(s)
- Miles Congreve
- Heptares Therapeutics Ltd, BioPark, Welwyn Garden City, Hertfordshire, United Kingdom
| | - João M Dias
- Heptares Therapeutics Ltd, BioPark, Welwyn Garden City, Hertfordshire, United Kingdom
| | - Fiona H Marshall
- Heptares Therapeutics Ltd, BioPark, Welwyn Garden City, Hertfordshire, United Kingdom
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50
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Zweemer AJ, Bunnik J, Veenhuizen M, Miraglia F, Lenselink EB, Vilums M, de Vries H, Gibert A, Thiele S, Rosenkilde MM, IJzerman AP, Heitman LH. Discovery and Mapping of an Intracellular Antagonist Binding Site at the Chemokine Receptor CCR2. Mol Pharmacol 2014; 86:358-68. [DOI: 10.1124/mol.114.093328] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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