51
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GPCR Activation States Induced by Nanobodies and Mini-G Proteins Compared by NMR Spectroscopy. MOLECULES (BASEL, SWITZERLAND) 2020; 25:molecules25245984. [PMID: 33348734 PMCID: PMC7767065 DOI: 10.3390/molecules25245984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/04/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022]
Abstract
In this work, we examine methyl nuclear magnetic resonance (NMR) spectra of the methionine ε-[13CH3] labelled thermostabilized β1 adrenergic receptor from turkey in association with a variety of different effectors, including mini-Gs and nanobody 60 (Nb60), which have not been previously studied in complex with β1 adrenergic receptor (β1AR) by NMR. Complexes with pindolol and Nb60 induce highly similar inactive states of the receptor, closely resembling the resting state conformational ensemble. We show that, upon binding of mini-Gs or nanobody 80 (Nb80), large allosteric changes throughout the receptor take place. The conformation of tβ1AR stabilized by the native-like mini-Gs protein is highly similar to the conformation induced by the currently used surrogate Nb80. Interestingly, in both cases residual dynamics are present, which were not observed in the resting states. Finally, we reproduce a pharmaceutically relevant situation, where an antagonist abolishes the interaction of the receptor with the mini-G protein in a competitive manner, validating the functional integrity of our preparation. The presented system is therefore well suited for reproducing the individual steps of the activation cycle of a G protein-coupled receptor (GPCR) in vitro and serves as a basis for functional and pharmacological characterizations of more native-like systems in the future.
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52
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Calebiro D, Koszegi Z, Lanoiselée Y, Miljus T, O'Brien S. G protein-coupled receptor-G protein interactions: a single-molecule perspective. Physiol Rev 2020; 101:857-906. [PMID: 33331229 DOI: 10.1152/physrev.00021.2020] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
G protein-coupled receptors (GPCRs) regulate many cellular and physiological processes, responding to a diverse range of extracellular stimuli including hormones, neurotransmitters, odorants, and light. Decades of biochemical and pharmacological studies have provided fundamental insights into the mechanisms of GPCR signaling. Thanks to recent advances in structural biology, we now possess an atomistic understanding of receptor activation and G protein coupling. However, how GPCRs and G proteins interact in living cells to confer signaling efficiency and specificity remains insufficiently understood. The development of advanced optical methods, including single-molecule microscopy, has provided the means to study receptors and G proteins in living cells with unprecedented spatio-temporal resolution. The results of these studies reveal an unexpected level of complexity, whereby GPCRs undergo transient interactions among themselves as well as with G proteins and structural elements of the plasma membrane to form short-lived signaling nanodomains that likely confer both rapidity and specificity to GPCR signaling. These findings may provide new strategies to pharmaceutically modulate GPCR function, which might eventually pave the way to innovative drugs for common diseases such as diabetes or heart failure.
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Affiliation(s)
- Davide Calebiro
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Zsombor Koszegi
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Yann Lanoiselée
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Tamara Miljus
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
| | - Shannon O'Brien
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, United Kingdom; Centre of Membrane Proteins and Receptors (COMPARE), Universities of Nottingham and Birmingham, Birmingham, United Kingdom
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53
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Velazhahan V, Ma N, Pándy-Szekeres G, Kooistra AJ, Lee Y, Gloriam DE, Vaidehi N, Tate CG. Structure of the class D GPCR Ste2 dimer coupled to two G proteins. Nature 2020; 589:148-153. [PMID: 33268889 PMCID: PMC7116888 DOI: 10.1038/s41586-020-2994-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/25/2020] [Indexed: 01/08/2023]
Abstract
G-protein-coupled receptors (GPCRs) are divided phylogenetically into six classes1,2, denoted A to F. More than 370 structures of vertebrate GPCRs (belonging to classes A, B, C and F) have been determined, leading to a substantial understanding of their function3. By contrast, there are no structures of class D GPCRs, which are found exclusively in fungi where they regulate survival and reproduction. Here we determine the structure of a class D GPCR, the Saccharomyces cerevisiae pheromone receptor Ste2, in an active state coupled to the heterotrimeric G protein Gpa1-Ste4-Ste18. Ste2 was purified as a homodimer coupled to two G proteins. The dimer interface of Ste2 is formed by the N terminus, the transmembrane helices H1, H2 and H7, and the first extracellular loop ECL1. We establish a class D1 generic residue numbering system (CD1) to enable comparisons with orthologues and with other GPCR classes. The structure of Ste2 bears similarities in overall topology to class A GPCRs, but the transmembrane helix H4 is shifted by more than 20 Å and the G-protein-binding site is a shallow groove rather than a cleft. The structure provides a template for the design of novel drugs to target fungal GPCRs, which could be used to treat numerous intractable fungal diseases4.
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Affiliation(s)
| | - Ning Ma
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
| | - Gáspár Pándy-Szekeres
- Department of Drug Design and Pharmacology, Universitetsparken 2, Copenhagen, Denmark.,Medicinal Chemistry Research Group, Research Center for Natural Sciences, Budapest, Hungary
| | - Albert J Kooistra
- Department of Drug Design and Pharmacology, Universitetsparken 2, Copenhagen, Denmark
| | - Yang Lee
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - David E Gloriam
- Department of Drug Design and Pharmacology, Universitetsparken 2, Copenhagen, Denmark
| | - Nagarajan Vaidehi
- Department of Computational and Quantitative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA
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54
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Yang F, Ling S, Zhou Y, Zhang Y, Lv P, Liu S, Fang W, Sun W, Hu LA, Zhang L, Shi P, Tian C. Different conformational responses of the β2-adrenergic receptor-Gs complex upon binding of the partial agonist salbutamol or the full agonist isoprenaline. Natl Sci Rev 2020. [DOI: 10.1093/nsr/nwaa284] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Abstract
G protein-coupled receptors (GPCRs) are responsible for most cytoplasmic signaling in response to extracellular ligands with different efficacy profiles. Various spectroscopic techniques have identified that agonists exhibiting varying efficacies can selectively stabilize a specific conformation of the receptor. However, the structural basis for activation of the GPCR-G protein complex by ligands with different efficacies is incompletely understood. To better understand the structural basis underlying the mechanisms by which ligands with varying efficacies differentially regulate the conformations of receptors and G proteins, we determined the structures of β2AR-Gαs$\beta $γ bound with partial agonist salbutamol or bound with full agonist isoprenaline using single-particle cryo-electron microscopy at resolutions of 3.26 Å and 3.80 Å, respectively. Structural comparisons between the β2AR-Gs-salbutamol and β2AR-Gs-isoprenaline complexes demonstrated that the decreased binding affinity and efficacy of salbutamol compared with those of isoprenaline might be attributed to weakened hydrogen bonding interactions, attenuated hydrophobic interactions in the orthosteric binding pocket and different conformational changes in the rotamer toggle switch in TM6. Moreover, the observed stronger interactions between the intracellular loop 2 or 3 (ICL2 or ICL3) of β2AR and Gαs with binding of salbutamol versus isoprenaline might decrease phosphorylation in the salbutamol-activated β2AR-Gs complex. From the observed structural differences between these complexes of β2AR, a mechanism of β2AR activation by partial and full agonists is proposed to provide structural insights into β2AR desensitization.
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Affiliation(s)
- Fan Yang
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Shenglong Ling
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Yingxin Zhou
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Yanan Zhang
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Pei Lv
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Sanling Liu
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Wei Fang
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Wenjing Sun
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Liaoyuan A Hu
- Amgen Asia R&D Center, Amgen Research, Shanghai 201210, China
| | - Longhua Zhang
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Pan Shi
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Changlin Tian
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei 230030, China
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55
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Giri R, Namballa HK, Sarker A, Alberts I, Harding WW. Synthesis and dopamine receptor pharmacological evaluations on ring C ortho halogenated 1-phenylbenzazepines. Bioorg Med Chem Lett 2020; 30:127305. [PMID: 32631525 DOI: 10.1016/j.bmcl.2020.127305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 05/27/2020] [Accepted: 06/01/2020] [Indexed: 01/11/2023]
Abstract
A series of 1-phenylbenzazepines containing bromine or chlorine substituents at the ortho position of the appended phenyl ring (2'-monosubstituted or 2',6'- disubstituted patterns) were synthesized and evaluated for affinity towards dopamine D1R, D2R and D5R. As is typical of the 1-phenylbenzazepine scaffold, the compounds displayed selectivity towards D1R and D5R; analogs generally lacked affinity for D2R. Interestingly, 2',6'-dichloro substituted analogs showed modest D5R versus D1R selectivity whereas this selectivity was reversed in compounds with a 2'-halo substitution pattern. Compound 10a was identified as a D1R antagonist (Ki = 14 nM; IC50 = 9.4 nM).
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Affiliation(s)
- Rajan Giri
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, NY 10065, USA; Program in Chemistry, CUNY Graduate Center, 365 5(th) Avenue, New York, NY 10016, USA
| | - Hari K Namballa
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, NY 10065, USA
| | - Ananta Sarker
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, NY 10065, USA
| | - Ian Alberts
- LaGuardia Community College, Department of Chemistry, 31-10 Thompson Avenue, LIC, NY 11104, USA
| | - Wayne W Harding
- Department of Chemistry, Hunter College, City University of New York, 695 Park Avenue, NY 10065, USA; Program in Chemistry, CUNY Graduate Center, 365 5(th) Avenue, New York, NY 10016, USA; Program in Biochemistry, CUNY Graduate Center, 365 5(th) Avenue, New York, NY 10016, USA.
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56
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Boulton S, Van K, VanSchouwen B, Augustine J, Akimoto M, Melacini G. Allosteric Mechanisms of Nonadditive Substituent Contributions to Protein-Ligand Binding. Biophys J 2020; 119:1135-1146. [PMID: 32882185 DOI: 10.1016/j.bpj.2020.07.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/30/2020] [Accepted: 07/06/2020] [Indexed: 02/07/2023] Open
Abstract
Quantifying chemical substituent contributions to ligand-binding free energies is challenging due to nonadditive effects. Protein allostery is a frequent cause of nonadditivity, but the underlying allosteric mechanisms often remain elusive. Here, we propose a general NMR-based approach to elucidate such mechanisms and we apply it to the HCN4 ion channel, whose cAMP-binding domain is an archetypal conformational switch. Using NMR, we show that nonadditivity arises not only from concerted conformational transitions, but also from conformer-specific effects, such as steric frustration. Our results explain how affinity-reducing functional groups may lead to affinity gains if combined. Surprisingly, our approach also reveals that nonadditivity depends markedly on the receptor conformation. It is negligible for the inhibited state but highly significant for the active state, opening new opportunities to tune potency and agonism of allosteric effectors.
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Affiliation(s)
- Stephen Boulton
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Katherine Van
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Bryan VanSchouwen
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Jerry Augustine
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
| | - Madoka Akimoto
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada
| | - Giuseppe Melacini
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada; Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Canada.
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57
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Zhang Y, Yang F, Ling S, Lv P, Zhou Y, Fang W, Sun W, Zhang L, Shi P, Tian C. Single-particle cryo-EM structural studies of the β 2AR-Gs complex bound with a full agonist formoterol. Cell Discov 2020; 6:45. [PMID: 32655881 PMCID: PMC7338445 DOI: 10.1038/s41421-020-0176-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 05/07/2020] [Indexed: 01/19/2023] Open
Affiliation(s)
- Yanan Zhang
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Fan Yang
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Shenglong Ling
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Pei Lv
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Yingxin Zhou
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Wei Fang
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Wenjing Sun
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Longhua Zhang
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Pan Shi
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
| | - Changlin Tian
- Hefei National Laboratory of Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, 230026 Hefei, Anhui China
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 230030 Hefei, Anhui China
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58
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Waltenspühl Y, Schöppe J, Ehrenmann J, Kummer L, Plückthun A. Crystal structure of the human oxytocin receptor. SCIENCE ADVANCES 2020; 6:eabb5419. [PMID: 32832646 PMCID: PMC7439316 DOI: 10.1126/sciadv.abb5419] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/29/2020] [Indexed: 05/24/2023]
Abstract
The peptide hormone oxytocin modulates socioemotional behavior and sexual reproduction via the centrally expressed oxytocin receptor (OTR) across several species. Here, we report the crystal structure of human OTR in complex with retosiban, a nonpeptidic antagonist developed as an oral drug for the prevention of preterm labor. Our structure reveals insights into the detailed interactions between the G protein-coupled receptor (GPCR) and an OTR-selective antagonist. The observation of an extrahelical cholesterol molecule, binding in an unexpected location between helices IV and V, provides a structural rationale for its allosteric effect and critical influence on OTR function. Furthermore, our structure in combination with experimental data allows the identification of a conserved neurohypophyseal receptor-specific coordination site for Mg2+ that acts as potent, positive allosteric modulator for agonist binding. Together, these results further our molecular understanding of the oxytocin/vasopressin receptor family and will facilitate structure-guided development of new therapeutics.
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59
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Lee Y, Warne T, Nehmé R, Pandey S, Dwivedi-Agnihotri H, Chaturvedi M, Edwards PC, García-Nafría J, Leslie AGW, Shukla AK, Tate CG. Molecular basis of β-arrestin coupling to formoterol-bound β 1-adrenoceptor. Nature 2020; 583:862-866. [PMID: 32555462 DOI: 10.1038/s41586-020-2419-1] [Citation(s) in RCA: 144] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 04/07/2020] [Indexed: 12/15/2022]
Abstract
The β1-adrenoceptor (β1AR) is a G-protein-coupled receptor (GPCR) that couples1 to the heterotrimeric G protein Gs. G-protein-mediated signalling is terminated by phosphorylation of the C terminus of the receptor by GPCR kinases (GRKs) and by coupling of β-arrestin 1 (βarr1, also known as arrestin 2), which displaces Gs and induces signalling through the MAP kinase pathway2. The ability of synthetic agonists to induce signalling preferentially through either G proteins or arrestins-known as biased agonism3-is important in drug development, because the therapeutic effect may arise from only one signalling cascade, whereas the other pathway may mediate undesirable side effects4. To understand the molecular basis for arrestin coupling, here we determined the cryo-electron microscopy structure of the β1AR-βarr1 complex in lipid nanodiscs bound to the biased agonist formoterol5, and the crystal structure of formoterol-bound β1AR coupled to the G-protein-mimetic nanobody6 Nb80. βarr1 couples to β1AR in a manner distinct to that7 of Gs coupling to β2AR-the finger loop of βarr1 occupies a narrower cleft on the intracellular surface, and is closer to transmembrane helix H7 of the receptor when compared with the C-terminal α5 helix of Gs. The conformation of the finger loop in βarr1 is different from that adopted by the finger loop of visual arrestin when it couples to rhodopsin8. β1AR coupled to βarr1 shows considerable differences in structure compared with β1AR coupled to Nb80, including an inward movement of extracellular loop 3 and the cytoplasmic ends of H5 and H6. We observe weakened interactions between formoterol and two serine residues in H5 at the orthosteric binding site of β1AR, and find that formoterol has a lower affinity for the β1AR-βarr1 complex than for the β1AR-Gs complex. The structural differences between these complexes of β1AR provide a foundation for the design of small molecules that could bias signalling in the β-adrenoceptors.
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Affiliation(s)
- Yang Lee
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Tony Warne
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Rony Nehmé
- MRC Laboratory of Molecular Biology, Cambridge, UK.,Creoptix AG, Wädenswil, Switzerland
| | - Shubhi Pandey
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | | | - Madhu Chaturvedi
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
| | | | - Javier García-Nafría
- Institute for Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, BIFI-IQFR (CSIC), Zaragoza, Spain.,Laboratorio de Microscopías Avanzadas, University of Zaragoza, Zaragoza, Spain
| | | | - Arun K Shukla
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India
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60
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Smith DGA, Burns LA, Simmonett AC, Parrish RM, Schieber MC, Galvelis R, Kraus P, Kruse H, Di Remigio R, Alenaizan A, James AM, Lehtola S, Misiewicz JP, Scheurer M, Shaw RA, Schriber JB, Xie Y, Glick ZL, Sirianni DA, O’Brien JS, Waldrop JM, Kumar A, Hohenstein EG, Pritchard BP, Brooks BR, Schaefer HF, Sokolov AY, Patkowski K, DePrince AE, Bozkaya U, King RA, Evangelista FA, Turney JM, Crawford TD, Sherrill CD. Psi4 1.4: Open-source software for high-throughput quantum chemistry. J Chem Phys 2020; 152:184108. [PMID: 32414239 PMCID: PMC7228781 DOI: 10.1063/5.0006002] [Citation(s) in RCA: 331] [Impact Index Per Article: 82.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/12/2020] [Indexed: 12/13/2022] Open
Abstract
PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.
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Affiliation(s)
| | - Lori A. Burns
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Andrew C. Simmonett
- National Institutes of Health – National Heart,
Lung and Blood Institute, Laboratory of Computational Biology, Bethesda,
Maryland 20892, USA
| | - Robert M. Parrish
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Matthew C. Schieber
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | | | - Peter Kraus
- School of Molecular and Life Sciences, Curtin
University, Kent St., Bentley, Perth, Western Australia 6102,
Australia
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of
Sciences, Královopolská 135, 612 65 Brno, Czech
Republic
| | - Roberto Di Remigio
- Department of Chemistry, Centre for Theoretical
and Computational Chemistry, UiT, The Arctic University of Norway, N-9037
Tromsø, Norway
| | - Asem Alenaizan
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Andrew M. James
- Department of Chemistry, Virginia
Tech, Blacksburg, Virginia 24061, USA
| | - Susi Lehtola
- Department of Chemistry, University of
Helsinki, P.O. Box 55 (A. I. Virtasen aukio 1), FI-00014 Helsinki,
Finland
| | - Jonathon P. Misiewicz
- Center for Computational Quantum Chemistry,
University of Georgia, Athens, Georgia 30602, USA
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific
Computing, Heidelberg University, D-69120 Heidelberg,
Germany
| | - Robert A. Shaw
- ARC Centre of Excellence in Exciton Science,
School of Science, RMIT University, Melbourne, VIC 3000,
Australia
| | - Jeffrey B. Schriber
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Yi Xie
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Zachary L. Glick
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Dominic A. Sirianni
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Joseph Senan O’Brien
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
| | - Jonathan M. Waldrop
- Department of Chemistry and Biochemistry, Auburn
University, Auburn, Alabama 36849, USA
| | - Ashutosh Kumar
- Department of Chemistry, Virginia
Tech, Blacksburg, Virginia 24061, USA
| | - Edward G. Hohenstein
- SLAC National Accelerator Laboratory, Stanford
PULSE Institute, Menlo Park, California 94025,
USA
| | | | - Bernard R. Brooks
- National Institutes of Health – National Heart,
Lung and Blood Institute, Laboratory of Computational Biology, Bethesda,
Maryland 20892, USA
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry,
University of Georgia, Athens, Georgia 30602, USA
| | - Alexander Yu. Sokolov
- Department of Chemistry and Biochemistry, The
Ohio State University, Columbus, Ohio 43210, USA
| | - Konrad Patkowski
- Department of Chemistry and Biochemistry, Auburn
University, Auburn, Alabama 36849, USA
| | - A. Eugene DePrince
- Department of Chemistry and Biochemistry,
Florida State University, Tallahassee, Florida 32306-4390,
USA
| | - Uğur Bozkaya
- Department of Chemistry, Hacettepe
University, Ankara 06800, Turkey
| | - Rollin A. King
- Department of Chemistry, Bethel
University, St. Paul, Minnesota 55112, USA
| | | | - Justin M. Turney
- Center for Computational Quantum Chemistry,
University of Georgia, Athens, Georgia 30602, USA
| | | | - C. David Sherrill
- Center for Computational Molecular Science and
Technology, School of Chemistry and Biochemistry, School of Computational Science and
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400,
USA
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Grahl A, Abiko LA, Isogai S, Sharpe T, Grzesiek S. A high-resolution description of β 1-adrenergic receptor functional dynamics and allosteric coupling from backbone NMR. Nat Commun 2020; 11:2216. [PMID: 32371991 PMCID: PMC7200737 DOI: 10.1038/s41467-020-15864-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 04/01/2020] [Indexed: 12/29/2022] Open
Abstract
Signal transmission and regulation of G-protein-coupled receptors (GPCRs) by extra- and intracellular ligands occurs via modulation of complex conformational equilibria, but their exact kinetic details and underlying atomic mechanisms are unknown. Here we quantified these dynamic equilibria in the β1-adrenergic receptor in its apo form and seven ligand complexes using 1H/15N NMR spectroscopy. We observe three major exchanging conformations: an inactive conformation (Ci), a preactive conformation (Cp) and an active conformation (Ca), which becomes fully populated in a ternary complex with a G protein mimicking nanobody. The Ci ↔ Cp exchange occurs on the microsecond scale, the Cp ↔ Ca exchange is slower than ~5 ms and only occurs in the presence of two highly conserved tyrosines (Y5.58, Y7.53), which stabilize the active conformation of TM6. The Cp→Ca chemical shift changes indicate a pivoting motion of the entire TM6 that couples the effector site to the orthosteric ligand pocket. Signal transmission and regulation of G-protein-coupled receptors (GPCRs) by ligands occurs via modulation of complex conformational equilibria. Here authors quantify these equilibria and their dynamics in the β1-adrenergic receptor in its apo form and seven ligand complexes using NMR.
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Affiliation(s)
- Anne Grahl
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Layara Akemi Abiko
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Shin Isogai
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Timothy Sharpe
- Biophysics Core Facility, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Stephan Grzesiek
- Focal Area Structural Biology and Biophysics, Biozentrum, University of Basel, 4056, Basel, Switzerland.
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62
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Tosh DK, Salmaso V, Rao H, Bitant A, Fisher CL, Lieberman DI, Vorbrüggen H, Reitman ML, Gavrilova O, Gao ZG, Auchampach JA, Jacobson KA. Truncated (N)-Methanocarba Nucleosides as Partial Agonists at Mouse and Human A 3 Adenosine Receptors: Affinity Enhancement by N6-(2-Phenylethyl) Substitution. J Med Chem 2020; 63:4334-4348. [PMID: 32271569 PMCID: PMC7443318 DOI: 10.1021/acs.jmedchem.0c00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Dopamine-derived N6-substituents, compared to N6-(2-phenylethyl), in truncated (N)-methanocarba (bicyclo[3.1.0]hexyl) adenosines favored high A3 adenosine receptor (AR) affinity/selectivity, e.g., C2-phenylethynyl analogue 15 (MRS7591, Ki = 10.9/17.8 nM, at human/mouse A3AR). 15 was a partial agonist in vitro (hA3AR, cAMP inhibition, 31% Emax; mA3AR, [35S]GTP-γ-S binding, 16% Emax) and in vivo and also antagonized hA3AR in vitro. Distal H-bonding substitutions of the N6-(2-phenylethyl) moiety particularly enhanced mA3AR affinity by polar interactions with the extracellular loops, predicted using docking and molecular dynamics simulation with newly constructed mA3AR and hA3AR homology models. These hybrid models were based on an inactive antagonist-bound hA1AR structure for the upper part of TM2 and an agonist-bound hA2AAR structure for the remaining TM portions. These species-independent A3AR-selective nucleosides are low efficacy partial agonists and novel, nuanced modulators of the A3AR, a drug target of growing interest.
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Affiliation(s)
| | | | | | - Amelia Bitant
- Department of Pharmacology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, USA 53226
| | - Courtney L. Fisher
- Department of Pharmacology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, USA 53226
| | | | - Helmut Vorbrüggen
- Institut für Chemie und Biochemie, Freie Universität, Takustr. 3, D-14195 Berlin, Germany
| | | | - Oksana Gavrilova
- Mouse Metabolism Core, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, 9000 Rockville Pike, Bethesda, MA, USA 20892
| | | | - John A. Auchampach
- Department of Pharmacology, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, USA 53226
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63
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Congreve M, de Graaf C, Swain NA, Tate CG. Impact of GPCR Structures on Drug Discovery. Cell 2020; 181:81-91. [DOI: 10.1016/j.cell.2020.03.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/03/2020] [Accepted: 03/03/2020] [Indexed: 12/21/2022]
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64
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Gahbauer S, Böckmann RA. Comprehensive Characterization of Lipid-Guided G Protein-Coupled Receptor Dimerization. J Phys Chem B 2020; 124:2823-2834. [DOI: 10.1021/acs.jpcb.0c00062] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Stefan Gahbauer
- Computational Biology, Friedrich-Alexander-University Erlangen-Nüremberg, Erlangen, Germany
| | - Rainer A. Böckmann
- Computational Biology, Friedrich-Alexander-University Erlangen-Nüremberg, Erlangen, Germany
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65
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The atomistic level structure for the activated human κ-opioid receptor bound to the full Gi protein and the MP1104 agonist. Proc Natl Acad Sci U S A 2020; 117:5836-5843. [PMID: 32127473 DOI: 10.1073/pnas.1910006117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The kappa opioid receptor (κOR) is an important target for pain therapeutics to reduce depression and other harmful side effects of existing medications. The analgesic activity is mediated by κOR signaling through the adenylyl cyclase-inhibitory family of Gi protein. Here, we report the three-dimensional (3D) structure for the active state of human κOR complexed with both heterotrimeric Gi protein and MP1104 agonist. This structure resulted from long molecular dynamics (MD) and metadynamics (metaMD) simulations starting from the 3.1-Å X-ray structure of κOR-MP1104 after replacing the nanobody with the activated Gi protein and from the 3.5-Å cryo-EM structure of μOR-Gi complex after replacing the 168 missing residues. Using MD and metaMD we discovered interactions to the Gi protein with strong anchors to two intracellular loops and transmembrane helix 6 of the κOR. These anchors strengthen the binding, contributing to a contraction in the binding pocket but an expansion in the cytoplasmic region of κOR to accommodate G protein. These remarkable changes in κOR structure reveal that the anchors are essential for activation.
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66
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Haloperidol bound D 2 dopamine receptor structure inspired the discovery of subtype selective ligands. Nat Commun 2020; 11:1074. [PMID: 32103023 PMCID: PMC7044277 DOI: 10.1038/s41467-020-14884-y] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 02/05/2020] [Indexed: 11/08/2022] Open
Abstract
The D2 dopamine receptor (DRD2) is one of the most well-established therapeutic targets for neuropsychiatric and endocrine disorders. Most clinically approved and investigational drugs that target this receptor are known to be subfamily-selective for all three D2-like receptors, rather than subtype-selective for only DRD2. Here, we report the crystal structure of DRD2 bound to the most commonly used antipsychotic drug, haloperidol. The structures suggest an extended binding pocket for DRD2 that distinguishes it from other D2-like subtypes. A detailed analysis of the structures illuminates key structural determinants essential for DRD2 activation and subtype selectivity. A structure-based and mechanism-driven screening combined with a lead optimization approach yield DRD2 highly selective agonists, which could be used as chemical probes for studying the physiological and pathological functions of DRD2 as well as promising therapeutic leads devoid of promiscuity. The D2 dopamine receptor (DRD2) is one of the most well-established therapeutic targets for neuropsychiatric and endocrine disorders. Here, the authors report the crystal structure of the antipsychotic drug haloperidol bound to DRD2 via an extended binding pocket that distinguishes it from other D2-like subtypes.
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67
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Conformational plasticity of ligand-bound and ternary GPCR complexes studied by 19F NMR of the β 1-adrenergic receptor. Nat Commun 2020; 11:669. [PMID: 32015348 PMCID: PMC6997182 DOI: 10.1038/s41467-020-14526-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 01/10/2020] [Indexed: 01/14/2023] Open
Abstract
G-protein-coupled receptors (GPCRs) are allosteric signaling proteins that transmit an extracellular stimulus across the cell membrane. Using 19F NMR and site-specific labelling, we investigate the response of the cytoplasmic region of transmembrane helices 6 and 7 of the β1-adrenergic receptor to agonist stimulation and coupling to a Gs-protein-mimetic nanobody. Agonist binding shows the receptor in equilibrium between two inactive states and a pre-active form, increasingly populated with higher ligand efficacy. Nanobody coupling leads to a fully active ternary receptor complex present in amounts correlating directly with agonist efficacy, consistent with partial agonism. While for different agonists the helix 6 environment in the active-state ternary complexes resides in a well-defined conformation, showing little conformational mobility, the environment of the highly conserved NPxxY motif on helix 7 remains dynamic adopting diverse, agonist-specific conformations, implying a further role of this region in receptor function. An inactive nanobody-coupled ternary receptor form is also observed.
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68
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Uchański T, Pardon E, Steyaert J. Nanobodies to study protein conformational states. Curr Opin Struct Biol 2020; 60:117-123. [DOI: 10.1016/j.sbi.2020.01.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 01/07/2023]
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69
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Stauch B, Johansson LC, Cherezov V. Structural insights into melatonin receptors. FEBS J 2019; 287:1496-1510. [PMID: 31693784 DOI: 10.1111/febs.15128] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/16/2019] [Accepted: 11/05/2019] [Indexed: 12/22/2022]
Abstract
The long-anticipated high-resolution structures of the human melatonin G protein-coupled receptors MT1 and MT2 , involved in establishing and maintaining circadian rhythm, were obtained in complex with two melatonin analogs and two approved anti-insomnia and antidepression drugs using X-ray free-electron laser serial femtosecond crystallography. The structures shed light on the overall conformation and unusual structural features of melatonin receptors, as well as their ligand binding sites and the melatonergic pharmacophore, thereby providing insights into receptor subtype selectivity. The structures revealed an occluded orthosteric ligand binding site with a membrane-buried channel for ligand entry in both receptors, and an additional putative ligand entry path in MT2 from the extracellular side. This unexpected ligand entry mode contributes to facilitating the high specificity with which melatonin receptors bind their cognate ligand and exclude structurally similar molecules such as serotonin, the biosynthetic precursor of melatonin. Finally, the MT2 structure allowed accurate mapping of type 2 diabetes-related single-nucleotide polymorphisms, where a clustering of residues in helices I and II on the protein-membrane interface was observed which could potentially influence receptor oligomerization. The role of receptor oligomerization is further discussed in light of the differential interaction of MT1 and MT2 with GPR50, a regulatory melatonin coreceptor. The melatonin receptor structures will facilitate design of selective tool compounds to further dissect the specific physiological function of each receptor subtype as well as provide a structural basis for next-generation sleeping aids and other drugs targeting these receptors with higher specificity and fewer side effects.
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Affiliation(s)
- Benjamin Stauch
- Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.,Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Linda C Johansson
- Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.,Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Vadim Cherezov
- Bridge Institute, USC Michelson Center for Convergent Biosciences, University of Southern California, Los Angeles, CA, USA.,Department of Chemistry, University of Southern California, Los Angeles, CA, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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70
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McKinstry-Wu AR, Woll KA, Joseph TT, Bu W, White ER, Bhanu NV, Garcia BA, Brannigan G, Dailey WP, Eckenhoff RG. Azi-medetomidine: Synthesis and Characterization of a Novel α2 Adrenergic Photoaffinity Ligand. ACS Chem Neurosci 2019; 10:4716-4728. [PMID: 31638765 DOI: 10.1021/acschemneuro.9b00484] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Agonists at the α2 adrenergic receptor produce sedation, increase focus, provide analgesia, and induce centrally mediated hypotension and bradycardia, yet neither their dynamic interactions with adrenergic receptors nor their modulation of neuronal circuit activity is completely understood. Photoaffinity ligands of α2 adrenergic agonists have the potential both to capture discrete moments of ligand-receptor interactions and to prolong naturalistic drug effects in discrete regions of tissue in vivo. We present here the synthesis and characterization of a novel α2 adrenergic agonist photolabel based on the imidazole medetomidine called azi-medetomidine. Azi-medetomidine shares protein association characteristics with its parent compound in experimental model systems and by molecular dynamics simulation of interactions with the α2A adrenergic receptor. Azi-medetomidine acts as an agonist at α2A adrenergic receptors, and produces hypnosis in Xenopus laevis tadpoles. Azi-medetomidine competes with the α2 agonist clonidine at α2A adrenergic receptors, which is potentiated by photolabeling, and azi-medetomidine labels moieties on the α2A adrenergic receptor as determined by mass spectrometry in a manner consistent with a simulated model. This novel α2 adrenergic agonist photolabel can serve as a powerful tool for in vitro and in vivo investigations of adrenergic signaling.
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Affiliation(s)
- Andrew R. McKinstry-Wu
- Department of Anesthesiology & Critical Care, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Kellie A. Woll
- Department of Anesthesiology & Critical Care, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Thomas T. Joseph
- Department of Anesthesiology & Critical Care, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Weiming Bu
- Department of Anesthesiology & Critical Care, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - E. Railey White
- Department of Anesthesiology & Critical Care, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Natarajan V. Bhanu
- Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A. Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Grace Brannigan
- Center for Computational and Integrative Biology, Department of Physics, Rutgers University, Camden, New Jersey 08102, United States
| | - William P. Dailey
- Department of Chemistry, University of Pennsylvania School of Arts and Sciences, 231 S. 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Roderic G. Eckenhoff
- Department of Anesthesiology & Critical Care, University of Pennsylvania Perelman School of Medicine, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
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71
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Zhang X, Sun H, Wen X, Yuan H. A Selectivity Study of FFAR4/FFAR1 Agonists by Molecular Modeling. J Chem Inf Model 2019; 59:4467-4474. [PMID: 31580060 DOI: 10.1021/acs.jcim.9b00735] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
FFAR4 has been considered as a potential target for metabolic diseases, including diabetes. Some compounds with biphenyl scaffold, represented by compound SR13 reported by our group, showed significant FFAR4 selectivity. However, the molecular basis for their selectivity has not been definitely disclosed. This study provided insights into the protein-ligand interactions between agonists and FFAR4/FFAR1 by molecular modeling. The important residues identified were consistent with those found in experimental studies. Moreover, the results proposed that the selectivity of SR13 between FFAR4 and FFAR1 depended on whether it can enter the ligand-binding site through the entrance region by adopting its preferential conformation. The big difference between the preferential conformation of SR13 and the narrow entrance region determined its poor agonist activity against FFAR1. These findings will facilitate the further development of selective FFAR4 agonists.
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Affiliation(s)
- Xiangying Zhang
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing 210009 , P. R. China
| | - Hongbin Sun
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing 210009 , P. R. China
| | - Xiaoan Wen
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing 210009 , P. R. China
| | - Haoliang Yuan
- Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease and State Key Laboratory of Natural Medicines , China Pharmaceutical University , Nanjing 210009 , P. R. China
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72
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Abiko LA, Grahl A, Grzesiek S. High Pressure Shifts the β 1-Adrenergic Receptor to the Active Conformation in the Absence of G Protein. J Am Chem Soc 2019; 141:16663-16670. [PMID: 31564099 DOI: 10.1021/jacs.9b06042] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
G protein-coupled receptors (GPCRs) are versatile chemical sensors, which transmit the signal of an extracellular binding event across the plasma membrane to the intracellular side. This function is achieved via the modulation of highly dynamical equilibria of various conformational receptor states. Here we have probed the effect of pressure on the conformational equilibria of a functional thermostabilized β1-adrenergic GPCR (β1AR) by solution NMR. High pressure induces a large shift in the conformational equilibrium (midpoint ∼600 bar) from the preactive conformation of agonist-bound β1AR to the fully active conformation, which under normal pressure is only populated when a G protein or a G protein-mimicking nanobody (Nb) binds to the intracellular side of the β1AR·agonist complex. No such large effects are observed for an antagonist-bound β1AR or the ternary β1AR·agonist·Nb80 complex. The detected structural changes of agonist-bound β1AR around the orthosteric ligand binding pocket indicate that the fully active receptor occupies an ∼100 Å3 smaller volume than that of its preactive form. Most likely, this volume reduction is caused by the compression of empty (nonhydrated) cavities in the ligand binding pocket and the center of the receptor, which increases the ligand receptor interactions and explains the ∼100-fold affinity increase of agonists in the presence of G protein. The finding that isotropic pressure induces a directed motion from the preactive to the fully active GPCR conformation provides evidence of the high mechanical robustness of this important functional switch.
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Affiliation(s)
- Layara Akemi Abiko
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , CH-4056 Basel , Switzerland
| | - Anne Grahl
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , CH-4056 Basel , Switzerland
| | - Stephan Grzesiek
- Focal Area Structural Biology and Biophysics, Biozentrum , University of Basel , CH-4056 Basel , Switzerland
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