51
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Vass M, Podlewska S, de Esch IJP, Bojarski AJ, Leurs R, Kooistra AJ, de Graaf C. Aminergic GPCR-Ligand Interactions: A Chemical and Structural Map of Receptor Mutation Data. J Med Chem 2018; 62:3784-3839. [PMID: 30351004 DOI: 10.1021/acs.jmedchem.8b00836] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The aminergic family of G protein-coupled receptors (GPCRs) plays an important role in various diseases and represents a major drug discovery target class. Structure determination of all major aminergic subfamilies has enabled structure-based ligand design for these receptors. Site-directed mutagenesis data provides an invaluable complementary source of information for elucidating the structural determinants of binding of different ligand chemotypes. The current study provides a comparative analysis of 6692 mutation data points on 34 aminergic GPCR subtypes, covering the chemical space of 540 unique ligands from mutagenesis experiments and information from experimentally determined structures of 52 distinct aminergic receptor-ligand complexes. The integrated analysis enables detailed investigation of structural receptor-ligand interactions and assessment of the transferability of combined binding mode and mutation data across ligand chemotypes and receptor subtypes. An overview is provided of the possibilities and limitations of using mutation data to guide the design of novel aminergic receptor ligands.
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Affiliation(s)
- Márton Vass
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Sabina Podlewska
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , PL31-343 Kraków , Poland
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , PL31-343 Kraków , Poland
| | - Rob Leurs
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Albert J Kooistra
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands.,Department of Drug Design and Pharmacology , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Chris de Graaf
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands.,Sosei Heptares , Steinmetz Building, Granta Park, Great Abington , Cambridge CB21 6DG , U.K
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52
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Yun JH, Li X, Park JH, Wang Y, Ohki M, Jin Z, Lee W, Park SY, Hu H, Li C, Zatsepin N, Hunter MS, Sierra RG, Koralek J, Yoon CH, Cho HS, Weierstall U, Tang L, Liu H, Lee W. Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency. J Biol Chem 2018; 294:794-804. [PMID: 30455349 DOI: 10.1074/jbc.ra118.004038] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 11/12/2018] [Indexed: 11/06/2022] Open
Abstract
Non-cryogenic protein structures determined at ambient temperature may disclose significant information about protein activity. Chloride-pumping rhodopsin (ClR) exhibits a trend to hyperactivity induced by a change in the photoreaction rate because of a gradual decrease in temperature. Here, to track the structural changes that explain the differences in CIR activity resulting from these temperature changes, we used serial femtosecond crystallography (SFX) with an X-ray free electron laser (XFEL) to determine the non-cryogenic structure of ClR at a resolution of 1.85 Å, and compared this structure with a cryogenic ClR structure obtained with synchrotron X-ray crystallography. The XFEL-derived ClR structure revealed that the all-trans retinal (ATR) region and positions of two coordinated chloride ions slightly differed from those of the synchrotron-derived structure. Moreover, the XFEL structure enabled identification of one additional water molecule forming a hydrogen bond network with a chloride ion. Analysis of the channel cavity and a difference distance matrix plot (DDMP) clearly revealed additional structural differences. B-factor information obtained from the non-cryogenic structure supported a motility change on the residual main and side chains as well as of chloride and water molecules because of temperature effects. Our results indicate that non-cryogenic structures and time-resolved XFEL experiments could contribute to a better understanding of the chloride-pumping mechanism of ClR and other ion pumps.
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Affiliation(s)
- Ji-Hye Yun
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Xuanxuan Li
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China.,Department of Engineering Physics, Tsinghua University, Beijing 100086, China
| | - Jae-Hyun Park
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Yang Wang
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China
| | - Mio Ohki
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Zeyu Jin
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Wonbin Lee
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea
| | - Sam-Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama 230-0045, Japan
| | - Hao Hu
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Chufeng Li
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Nadia Zatsepin
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Raymond G Sierra
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Jake Koralek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025, and
| | - Hyun-Soo Cho
- Department of Systems Biology and Division of Life Sciences, Yonsei University, Seoul 03722, South Korea
| | - Uwe Weierstall
- Physics Department, and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona 85287
| | - Leihan Tang
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Center, 10 East Xibeiwang Road, Haidian District, Beijing 100193, China,
| | - Weontae Lee
- From the Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul 03722, South Korea,
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53
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GPCR drug discovery: integrating solution NMR data with crystal and cryo-EM structures. Nat Rev Drug Discov 2018; 18:59-82. [PMID: 30410121 DOI: 10.1038/nrd.2018.180] [Citation(s) in RCA: 159] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The 826 G protein-coupled receptors (GPCRs) in the human proteome regulate key physiological processes and thus have long been attractive drug targets. With the crystal structures of more than 50 different human GPCRs determined over the past decade, an initial platform for structure-based rational design has been established for drugs that target GPCRs, which is currently being augmented with cryo-electron microscopy (cryo-EM) structures of higher-order GPCR complexes. Nuclear magnetic resonance (NMR) spectroscopy in solution is one of the key approaches for expanding this platform with dynamic features, which can be accessed at physiological temperature and with minimal modification of the wild-type GPCR covalent structures. Here, we review strategies for the use of advanced biochemistry and NMR techniques with GPCRs, survey projects in which crystal or cryo-EM structures have been complemented with NMR investigations and discuss the impact of this integrative approach on GPCR biology and drug discovery.
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54
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Zavrtanik U, Lukan J, Loris R, Lah J, Hadži S. Structural Basis of Epitope Recognition by Heavy-Chain Camelid Antibodies. J Mol Biol 2018; 430:4369-4386. [PMID: 30205092 DOI: 10.1016/j.jmb.2018.09.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Revised: 09/03/2018] [Accepted: 09/04/2018] [Indexed: 10/28/2022]
Abstract
Truncated versions of heavy-chain antibodies (HCAbs) from camelids, also termed nanobodies, comprise only one-tenth the mass of conventional antibodies, yet retain similar, high binding affinities for the antigens. Here we analyze a large data set of nanobody-antigen crystal structures and investigate how nanobody-antigen recognition compares to the one by conventional antibodies. We find that nanobody paratopes are enriched in aromatic residues just like conventional antibodies, but additionally, they also bear a more hydrophobic character. Most striking differences were observed in the characteristics of the antigen's epitope. Unlike conventional antibodies, nanobodies bind to more rigid, concave, conserved and structured epitopes enriched with aromatic residues. Nanobodies establish fewer interactions with the antigens compared to conventional antibodies, and we speculate that high binding affinities are achieved due to less unfavorable conformational and more favorable solvation entropy contributions. We observed that interactions with antigen are mediated not only by three CDR loops but also by numerous residues from the nanobody framework. These residues are not distributed uniformly; rather, they are concentrated into four structurally distinct regions and mediate mostly charged interactions. Our findings suggest that in some respects nanobody-antigen interactions are more similar to the general protein-protein interactions rather than antibody-antigen interactions.
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Affiliation(s)
- Uroš Zavrtanik
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Junoš Lukan
- Statistical Office of the Republic of Slovenia, Litostrojska cesta 54, 1000 Ljubljana, Slovenia
| | - Remy Loris
- Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050 Brussel, Belgium; VIB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, 1000 Ljubljana, Slovenia; Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, B-1050 Brussel, Belgium; VIB Center for Structural Biology, Vlaams Instituut voor Biotechnologie, B-1050 Brussel, Belgium.
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55
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Breakthrough in GPCR Crystallography and Its Impact on Computer-Aided Drug Design. Methods Mol Biol 2018; 1705:45-72. [PMID: 29188558 DOI: 10.1007/978-1-4939-7465-8_3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Recent crystallographic structures of G protein-coupled receptors (GPCRs) have greatly advanced our understanding of the recognition of their diverse agonist and antagonist ligands. We illustrate here how this applies to A2A adenosine receptors (ARs) and to P2Y1 and P2Y12 receptors (P2YRs) for ADP. These X-ray structures have impacted the medicinal chemistry aimed at discovering new ligands for these two receptor families, including receptors that have not yet been crystallized but are closely related to the known structures. In this Chapter, we discuss recent structure-based drug design projects that led to the discovery of: (a) novel A3AR agonists based on a highly rigidified (N)-methanocarba scaffold for the treatment of chronic neuropathic pain and other conditions, (b) fluorescent probes of the ARs and P2Y14R, as chemical tools for structural probing of these GPCRs and for improving assay capabilities, and (c) new more drug-like antagonists of the inflammation-related P2Y14R. We also describe the computationally enabled molecular recognition of positive (for A3AR) and negative (P2Y1R) allosteric modulators that in some cases are shown to be consistent with structure-activity relationship (SAR) data. Thus, computational modeling has become an essential tool for the design of purine receptor ligands.
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56
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Igonet S, Raingeval C, Cecon E, Pučić-Baković M, Lauc G, Cala O, Baranowski M, Perez J, Jockers R, Krimm I, Jawhari A. Enabling STD-NMR fragment screening using stabilized native GPCR: A case study of adenosine receptor. Sci Rep 2018; 8:8142. [PMID: 29802269 PMCID: PMC5970182 DOI: 10.1038/s41598-018-26113-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/23/2018] [Indexed: 12/27/2022] Open
Abstract
Structural studies of integral membrane proteins have been limited by the intrinsic conformational flexibility and the need to stabilize the proteins in solution. Stabilization by mutagenesis was very successful for structural biology of G protein-coupled receptors (GPCRs). However, it requires heavy protein engineering and may introduce structural deviations. Here we describe the use of specific calixarenes-based detergents for native GPCR stabilization. Wild type, full length human adenosine A2A receptor was used to exemplify the approach. We could stabilize native, glycosylated, non-aggregated and homogenous A2AR that maintained its ligand binding capacity. The benefit of the preparation for fragment screening, using the Saturation-Transfer Difference nuclear magnetic resonance (STD-NMR) experiment is reported. The binding of the agonist adenosine and the antagonist caffeine were observed and competition experiments with CGS-21680 and ZM241385 were performed, demonstrating the feasibility of the STD-based fragment screening on the native A2A receptor. Interestingly, adenosine was shown to bind a second binding site in the presence of the agonist CGS-21680 which corroborates published results obtained with molecular dynamics simulation. Fragment-like compounds identified using STD-NMR showed antagonistic effects on A2AR in the cAMP cellular assay. Taken together, our study shows that stabilization of native GPCRs represents an attractive approach for STD-based fragment screening and drug design.
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Affiliation(s)
| | - Claire Raingeval
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Erika Cecon
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,University Paris Descartes, Sorbonne Paris Cité, Paris, France
| | | | - Gordan Lauc
- GENOS, Borongajska cesta 83h, 10000, Zagreb, Croatia
| | - Olivier Cala
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Maciej Baranowski
- SWING Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, BP48, Saint-Aubin, Gif-sur-Yvette, F-91192, France
| | - Javier Perez
- SWING Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, BP48, Saint-Aubin, Gif-sur-Yvette, F-91192, France
| | - Ralf Jockers
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,University Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Isabelle Krimm
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Anass Jawhari
- CALIXAR, 60 avenue Rockefeller, 69008, Lyon, France.
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57
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Birch J, Axford D, Foadi J, Meyer A, Eckhardt A, Thielmann Y, Moraes I. The fine art of integral membrane protein crystallisation. Methods 2018; 147:150-162. [PMID: 29778646 DOI: 10.1016/j.ymeth.2018.05.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 05/13/2018] [Accepted: 05/15/2018] [Indexed: 11/29/2022] Open
Abstract
Integral membrane proteins are among the most fascinating and important biomolecules as they play a vital role in many biological functions. Knowledge of their atomic structures is fundamental to the understanding of their biochemical function and key in many drug discovery programs. However, over the years, structure determination of integral membrane proteins has proven to be far from trivial, hence they are underrepresented in the protein data bank. Low expression levels, insolubility and instability are just a few of the many hurdles one faces when studying these proteins. X-ray crystallography has been the most used method to determine atomic structures of membrane proteins. However, the production of high quality membrane protein crystals is always very challenging, often seen more as art than a rational experiment. Here we review valuable approaches, methods and techniques to successful membrane protein crystallisation.
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Affiliation(s)
- James Birch
- Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK; Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Danny Axford
- Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, UK
| | - James Foadi
- Department of Mathematical Sciences, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - Arne Meyer
- XtalConcepts GmbH, Schnackenburgallee 13, 22525 Hamburg, Germany
| | - Annette Eckhardt
- XtalConcepts GmbH, Schnackenburgallee 13, 22525 Hamburg, Germany
| | - Yvonne Thielmann
- Max Planck Institute of Biophysics, Molecular Membrane Biology, Max-von-Laue-Strasse 3, 60438 Frankfurt, Germany
| | - Isabel Moraes
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK; Diamond Light Source, Harwell Science and Innovation Campus, Oxfordshire OX11 0DE, UK; National Physical Laboratory, Hampton Road, Teddington TW11 0LW, UK.
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58
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Isolation of state-dependent monoclonal antibodies against the 12-transmembrane domain glucose transporter 4 using virus-like particles. Proc Natl Acad Sci U S A 2018; 115:E4990-E4999. [PMID: 29769329 DOI: 10.1073/pnas.1716788115] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The insulin-responsive 12-transmembrane transporter GLUT4 changes conformation between an inward-open state and an outward-open state to actively facilitate cellular glucose uptake. Because of the difficulties of generating conformational mAbs against complex and highly conserved membrane proteins, no reliable tools exist to measure GLUT4 at the cell surface, follow its trafficking, or detect the conformational state of the protein. Here we report the isolation and characterization of conformational mAbs that recognize the extracellular and intracellular domains of GLUT4, including mAbs that are specific for the inward-open and outward-open states of GLUT4. mAbs against GLUT4 were generated using virus-like particles to present this complex membrane protein in its native conformation and using a divergent host species (chicken) for immunization to overcome immune tolerance. As a result, the isolated mAbs recognize conformational epitopes on native GLUT4 in cells, with apparent affinities as high as 1 pM and with specificity for GLUT4 across the human membrane proteome. Epitope mapping using shotgun mutagenesis alanine scanning across the 509 amino acids of GLUT4 identified the binding epitopes for mAbs specific for the states of GLUT4 and allowed the comprehensive identification of the residues that functionally control the GLUT4 inward-open and outward-open states. The mAbs identified here will be valuable molecular tools for monitoring GLUT4 structure, function, and trafficking, for differentiating GLUT4 conformational states, and for the development of novel therapeutics for the treatment of diabetes.
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59
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Mitchell LS, Colwell LJ. Comparative analysis of nanobody sequence and structure data. Proteins 2018; 86:697-706. [PMID: 29569425 PMCID: PMC6033041 DOI: 10.1002/prot.25497] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 02/25/2018] [Accepted: 03/20/2018] [Indexed: 02/04/2023]
Abstract
Nanobodies are a class of antigen‐binding protein derived from camelids that achieve comparable binding affinities and specificities to classical antibodies, despite comprising only a single 15 kDa variable domain. Their reduced size makes them an exciting target molecule with which we can explore the molecular code that underpins binding specificity—how is such high specificity achieved? Here, we use a novel dataset of 90 nonredundant, protein‐binding nanobodies with antigen‐bound crystal structures to address this question. To provide a baseline for comparison we construct an analogous set of classical antibodies, allowing us to probe how nanobodies achieve high specificity binding with a dramatically reduced sequence space. Our analysis reveals that nanobodies do not diversify their framework region to compensate for the loss of the VL domain. In addition to the previously reported increase in H3 loop length, we find that nanobodies create diversity by drawing their paratope regions from a significantly larger set of aligned sequence positions, and by exhibiting greater structural variation in their H1 and H2 loops.
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Affiliation(s)
- Laura S Mitchell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
| | - Lucy J Colwell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, United Kingdom
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60
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Fungal G-protein-coupled receptors: mediators of pathogenesis and targets for disease control. Nat Microbiol 2018; 3:402-414. [DOI: 10.1038/s41564-018-0127-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/09/2018] [Indexed: 12/31/2022]
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61
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Menzel S, Schwarz N, Haag F, Koch-Nolte F. Nanobody-Based Biologics for Modulating Purinergic Signaling in Inflammation and Immunity. Front Pharmacol 2018; 9:266. [PMID: 29636685 PMCID: PMC5880931 DOI: 10.3389/fphar.2018.00266] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/09/2018] [Indexed: 12/18/2022] Open
Abstract
Adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide (NAD+) are released as danger signals from cells during infection and sterile inflammation. In the extracellular compartment ATP is converted by CD39, CD73, and other ecto-enzymes into metabolites that modulate the activity of T cells and macrophages. While ATP mediates pro-inflammatory signals via P2X7 and other P2 receptors, adenosine triggers anti-inflammatory signaling via the adenosine 2a receptor (Adora2a) and other P1 receptors. The latter also plays a role in maintaining an immunosuppressive tumor microenvironment. NAD+ is converted by CD38, CD203 and other ecto-enzymes to the Ca2+ mobilizing messengers cyclic ADP-ribose and ADP-ribose, and to adenosine. Recent findings on the roles of CD38, CD39, CD73, CD203, P2X7, and Adora2a in inflammation and immunity underscore the potential of these proteins as drug targets. However, available small molecule inhibitors often lack specificity and mediate unwanted off-target toxicity. Nanobodies – single domain antibodies derived from heavy chain antibodies that naturally occur in camelids – display a propensity to bind functional epitopes not accessible to conventional antibodies. Like conventional antibodies, nanobodies and nanobody-based biologics are highly specific and have well-understood, tunable in vivo pharmacodynamics with little if any toxicity. Nanobodies thus represent attractive alternatives to small molecule inhibitors for modulating purinergic signaling in inflammation and immunity. Here we review recent progress made in developing nanobodies against key targets of purinergic signaling.
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Affiliation(s)
- Stephan Menzel
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nicole Schwarz
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Haag
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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62
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Eichel K, von Zastrow M. Subcellular Organization of GPCR Signaling. Trends Pharmacol Sci 2018; 39:200-208. [PMID: 29478570 PMCID: PMC5830169 DOI: 10.1016/j.tips.2017.11.009] [Citation(s) in RCA: 156] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 11/26/2017] [Accepted: 11/27/2017] [Indexed: 01/09/2023]
Abstract
G protein-coupled receptors (GPCRs) comprise a large and diverse class of signal-transducing receptors that undergo dynamic and isoform-specific membrane trafficking. GPCRs thus have an inherent potential to initiate or regulate signaling reactions from multiple membrane locations. This review discusses emerging insights into the subcellular organization of GPCR function in mammalian cells, focusing on signaling transduced by heterotrimeric G proteins and β-arrestins. We summarize recent evidence indicating that GPCR-mediated activation of G proteins occurs not only from the plasma membrane (PM) but also from endosomes and Golgi membranes and that β-arrestin-dependent signaling can be transduced from the PM by β-arrestin trafficking to clathrin-coated pits (CCPs) after dissociation from a ligand-activated GPCR.
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Affiliation(s)
- Kelsie Eichel
- Program in Biochemistry and Molecular Biology, University of California, San Francisco School of Medicine, San Francisco, CA 94158, USA
| | - Mark von Zastrow
- Department of Psychiatry, University of California, San Francisco School of Medicine, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco School of Medicine, San Francisco, CA 94158, USA.
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63
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Eden T, Menzel S, Wesolowski J, Bergmann P, Nissen M, Dubberke G, Seyfried F, Albrecht B, Haag F, Koch-Nolte F. A cDNA Immunization Strategy to Generate Nanobodies against Membrane Proteins in Native Conformation. Front Immunol 2018; 8:1989. [PMID: 29410663 PMCID: PMC5787055 DOI: 10.3389/fimmu.2017.01989] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 12/21/2017] [Indexed: 12/20/2022] Open
Abstract
Nanobodies (Nbs) are soluble, versatile, single-domain binding modules derived from the VHH variable domain of heavy-chain antibodies naturally occurring in camelids. Nbs hold huge promise as novel therapeutic biologics. Membrane proteins are among the most interesting targets for therapeutic Nbs because they are accessible to systemically injected biologics. In order to be effective, therapeutic Nbs must recognize their target membrane protein in native conformation. However, raising Nbs against membrane proteins in native conformation can pose a formidable challenge since membrane proteins typically contain one or more hydrophobic transmembrane regions and, therefore, are difficult to purify in native conformation. Here, we describe a highly efficient genetic immunization strategy that circumvents these difficulties by driving expression of the target membrane protein in native conformation by cells of the immunized camelid. The strategy encompasses ballistic transfection of skin cells with cDNA expression plasmids encoding one or more orthologs of the membrane protein of interest and, optionally, other costimulatory proteins. The plasmid is coated onto 1 µm gold particles that are then injected into the shaved and depilated skin of the camelid. A gene gun delivers a helium pulse that accelerates the DNA-coated particles to a velocity sufficient to penetrate through multiple layers of cells in the skin. This results in the exposure of the extracellular domains of the membrane protein on the cell surface of transfected cells. Repeated immunization drives somatic hypermutation and affinity maturation of target-specific heavy-chain antibodies. The VHH/Nb coding region is PCR-amplified from B cells obtained from peripheral blood or a lymph node biopsy. Specific Nbs are selected by phage display or by screening of Nb-based heavy-chain antibodies expressed as secretory proteins in transfected HEK cells. Using this strategy, we have successfully generated agonistic and antagonistic Nbs against several cell surface ecto-enzymes and ligand-gated ion channels.
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Affiliation(s)
- Thomas Eden
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stephan Menzel
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Janusz Wesolowski
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Philine Bergmann
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marion Nissen
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gudrun Dubberke
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fabienne Seyfried
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Birte Albrecht
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Haag
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friedrich Koch-Nolte
- Institute of Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Liu ZH, Huang D, Fu XJ, Cheng P, Du EQ. Comparison of three commonly used fusion tags for the expression of nanobodies in the cytoplasm of Escherichia coli. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2017.1420426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Ze-hui Liu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A & F University, Xianyang, Shaanxi, PR China
| | - Di Huang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A & F University, Xianyang, Shaanxi, PR China
| | - Xiang-jing Fu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A & F University, Xianyang, Shaanxi, PR China
| | - Peng Cheng
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A & F University, Xianyang, Shaanxi, PR China
| | - En-qi Du
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A & F University, Xianyang, Shaanxi, PR China
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65
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Carpenter B, Lebon G. Human Adenosine A 2A Receptor: Molecular Mechanism of Ligand Binding and Activation. Front Pharmacol 2017; 8:898. [PMID: 29311917 PMCID: PMC5736361 DOI: 10.3389/fphar.2017.00898] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 11/24/2017] [Indexed: 11/29/2022] Open
Abstract
Adenosine receptors (ARs) comprise the P1 class of purinergic receptors and belong to the largest family of integral membrane proteins in the human genome, the G protein-coupled receptors (GPCRs). ARs are classified into four subtypes, A1, A2A, A2B, and A3, which are all activated by extracellular adenosine, and play central roles in a broad range of physiological processes, including sleep regulation, angiogenesis and modulation of the immune system. ARs are potential therapeutic targets in a variety of pathophysiological conditions, including sleep disorders, cancer, and dementia, which has made them important targets for structural biology. Over a decade of research and innovation has culminated with the publication of more than 30 crystal structures of the human adenosine A2A receptor (A2AR), making it one of the best structurally characterized GPCRs at the atomic level. In this review we analyze the structural data reported for A2AR that described for the first time the binding of mode of antagonists, including newly developed drug candidates, synthetic and endogenous agonists, sodium ions and an engineered G protein. These structures have revealed the key conformational changes induced upon agonist and G protein binding that are central to signal transduction by A2AR, and have highlighted both similarities and differences in the activation mechanism of this receptor compared to other class A GPCRs. Finally, comparison of A2AR with the recently solved structures of A1R has provided the first structural insight into the molecular determinants of ligand binding specificity in different AR subtypes.
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Affiliation(s)
- Byron Carpenter
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Guillaume Lebon
- Institut de Génomique Fonctionnelle, Neuroscience Department, UMR CNRS 5203, INSERM U1191, Université de Montpellier, Montpellier, France
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66
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Scholler P, Nevoltris D, de Bundel D, Bossi S, Moreno-Delgado D, Rovira X, Møller TC, El Moustaine D, Mathieu M, Blanc E, McLean H, Dupuis E, Mathis G, Trinquet E, Daniel H, Valjent E, Baty D, Chames P, Rondard P, Pin JP. Allosteric nanobodies uncover a role of hippocampal mGlu2 receptor homodimers in contextual fear consolidation. Nat Commun 2017; 8:1967. [PMID: 29213077 PMCID: PMC5719040 DOI: 10.1038/s41467-017-01489-1] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 09/15/2017] [Indexed: 11/09/2022] Open
Abstract
Antibodies have enormous therapeutic and biotechnology potential. G protein-coupled receptors (GPCRs), the main targets in drug development, are of major interest in antibody development programs. Metabotropic glutamate receptors are dimeric GPCRs that can control synaptic activity in a multitude of ways. Here we identify llama nanobodies that specifically recognize mGlu2 receptors, among the eight subtypes of mGluR subunits. Among these nanobodies, DN10 and 13 are positive allosteric modulators (PAM) on homodimeric mGlu2, while DN10 displays also a significant partial agonist activity. DN10 and DN13 have no effect on mGlu2-3 and mGlu2-4 heterodimers. These PAMs enhance the inhibitory action of the orthosteric mGlu2/mGlu3 agonist, DCG-IV, at mossy fiber terminals in the CA3 region of hippocampal slices. DN13 also impairs contextual fear memory when injected in the CA3 region of hippocampal region. These data highlight the potential of developing antibodies with allosteric actions on GPCRs to better define their roles in vivo.
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Affiliation(s)
- Pauline Scholler
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
- Cisbio Bioassays, F-30200, Codolet, France
| | - Damien Nevoltris
- Cisbio Bioassays, F-30200, Codolet, France
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, F-13009, Marseille, France
| | - Dimitri de Bundel
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Simon Bossi
- CNRS UMR9197, Université Paris-Sud, Institut des Neurosciences Paris-Saclay, F-91405, Orsay, France
| | - David Moreno-Delgado
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Xavier Rovira
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Thor C Møller
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Driss El Moustaine
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Michaël Mathieu
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Emilie Blanc
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Heather McLean
- CNRS UMR9197, Université Paris-Sud, Institut des Neurosciences Paris-Saclay, F-91405, Orsay, France
| | | | | | | | - Hervé Daniel
- CNRS UMR9197, Université Paris-Sud, Institut des Neurosciences Paris-Saclay, F-91405, Orsay, France
| | - Emmanuel Valjent
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France
| | - Daniel Baty
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, F-13009, Marseille, France
| | - Patrick Chames
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, F-13009, Marseille, France.
| | - Philippe Rondard
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France.
| | - Jean-Philippe Pin
- Institut de Génomique Fonctionnelle, CNRS, INSERM, Univ. Montpellier, F-34094, Montpellier, France.
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Coudrat T, Simms J, Christopoulos A, Wootten D, Sexton PM. Improving virtual screening of G protein-coupled receptors via ligand-directed modeling. PLoS Comput Biol 2017; 13:e1005819. [PMID: 29131821 PMCID: PMC5708846 DOI: 10.1371/journal.pcbi.1005819] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/30/2017] [Accepted: 10/12/2017] [Indexed: 11/22/2022] Open
Abstract
G protein-coupled receptors (GPCRs) play crucial roles in cell physiology and pathophysiology. There is increasing interest in using structural information for virtual screening (VS) of libraries and for structure-based drug design to identify novel agonist or antagonist leads. However, the sparse availability of experimentally determined GPCR/ligand complex structures with diverse ligands impedes the application of structure-based drug design (SBDD) programs directed to identifying new molecules with a select pharmacology. In this study, we apply ligand-directed modeling (LDM) to available GPCR X-ray structures to improve VS performance and selectivity towards molecules of specific pharmacological profile. The described method refines a GPCR binding pocket conformation using a single known ligand for that GPCR. The LDM method is a computationally efficient, iterative workflow consisting of protein sampling and ligand docking. We developed an extensive benchmark comparing LDM-refined binding pockets to GPCR X-ray crystal structures across seven different GPCRs bound to a range of ligands of different chemotypes and pharmacological profiles. LDM-refined models showed improvement in VS performance over origin X-ray crystal structures in 21 out of 24 cases. In all cases, the LDM-refined models had superior performance in enriching for the chemotype of the refinement ligand. This likely contributes to the LDM success in all cases of inhibitor-bound to agonist-bound binding pocket refinement, a key task for GPCR SBDD programs. Indeed, agonist ligands are required for a plethora of GPCRs for therapeutic intervention, however GPCR X-ray structures are mostly restricted to their inactive inhibitor-bound state. G protein-coupled receptors (GPCRs) are a major target for drug discovery. These receptors are highly dynamic membrane proteins, and have had limited tractability using with biophysical screens that are widely adopted for globular protein targets. Thus, structure-based virtual screening (SBVS) holds great promise as a complement to physical screening for rational design of novel drugs. Indeed, the increasing number of atomic-detail GPCR X-ray crystal structures has coincided with an increase in prospective SBVS studies that have identified novel compounds. However, experimentally solved GPCR structures do not meet the full demand for SBVS, as the GPCR structural landscape is incomplete, lacking both in coverage of available GPCRs, and diversity in both receptor conformations and the chemistry of co-crystalised ligands. Here we present a novel computational GPCR binding pocket refinement method that can generate predictive GPCR/ligand complexes with improved SBVS performance. This ligand-directed modeling workflow uses parallel processing and efficient algorithms to search the GPCR/ligand conformational space faster and more efficiently than the widely used protein refinement method molecular dynamics. In this study, the resulting models are evaluated both structurally, and in retrospective SBVS. We demonstrate improved performance of refined models over their starting structures in the majority of our test cases.
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Affiliation(s)
- Thomas Coudrat
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - John Simms
- School of Life and Health Sciences, Aston University, Birmingham, United Kingdom
| | - Arthur Christopoulos
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Denise Wootten
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- * E-mail: (DW); (PMS)
| | - Patrick M. Sexton
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
- * E-mail: (DW); (PMS)
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Holcomb J, Spellmon N, Zhang Y, Doughan M, Li C, Yang Z. Protein crystallization: Eluding the bottleneck of X-ray crystallography. AIMS BIOPHYSICS 2017; 4:557-575. [PMID: 29051919 PMCID: PMC5645037 DOI: 10.3934/biophy.2017.4.557] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
To date, X-ray crystallography remains the gold standard for the determination of macromolecular structure and protein substrate interactions. However, the unpredictability of obtaining a protein crystal remains the limiting factor and continues to be the bottleneck in determining protein structures. A vast amount of research has been conducted in order to circumvent this issue with limited success. No single method has proven to guarantee the crystallization of all proteins. However, techniques using antibody fragments, lipids, carrier proteins, and even mutagenesis of crystal contacts have been implemented to increase the odds of obtaining a crystal with adequate diffraction. In addition, we review a new technique using the scaffolding ability of PDZ domains to facilitate nucleation and crystal lattice formation. Although in its infancy, such technology may be a valuable asset and another method in the crystallography toolbox to further the chances of crystallizing problematic proteins.
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Affiliation(s)
- Joshua Holcomb
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Nicholas Spellmon
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Yingxue Zhang
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Maysaa Doughan
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
| | - Chunying Li
- Center for Molecular and Translational Medicine, Georgia State University, Atlanta, GA, USA
| | - Zhe Yang
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, MI, USA
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Desmyter A, Spinelli S, Boutton C, Saunders M, Blachetot C, de Haard H, Denecker G, Van Roy M, Cambillau C, Rommelaere H. Neutralization of Human Interleukin 23 by Multivalent Nanobodies Explained by the Structure of Cytokine-Nanobody Complex. Front Immunol 2017; 8:884. [PMID: 28871249 PMCID: PMC5566574 DOI: 10.3389/fimmu.2017.00884] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 07/11/2017] [Indexed: 11/26/2022] Open
Abstract
The heterodimeric cytokine interleukin (IL) 23 comprises the IL12-shared p40 subunit and an IL23-specific subunit, p19. Together with IL12 and IL27, IL23 sits at the apex of the regulatory mechanisms shaping adaptive immune responses. IL23, together with IL17, plays an important role in the development of chronic inflammation and autoimmune inflammatory diseases. In this context, we generated monovalent antihuman IL23 variable heavy chain domain of llama heavy chain antibody (VHH) domains (Nanobodies®) with low nanomolar affinity for human interleukin (hIL) 23. The crystal structure of a quaternary complex assembling hIL23 and several nanobodies against p19 and p40 subunits allowed identification of distinct epitopes and enabled rational design of a multivalent IL23-specific blocking nanobody. Taking advantage of the ease of nanobody formatting, multivalent IL23 nanobodies were assembled with properly designed linkers flanking an antihuman serum albumin nanobody, with improved hIL23 neutralization capacity in vitro and in vivo, as compared to the monovalent nanobodies. These constructs with long exposure time are excellent candidates for further developments targeting Crohn’s disease, rheumatoid arthritis, and psoriasis.
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Affiliation(s)
- Aline Desmyter
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Marseille, France.,Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix-Marseille Université, Marseille, France
| | - Silvia Spinelli
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Marseille, France.,Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix-Marseille Université, Marseille, France
| | | | | | | | | | | | | | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Centre National de la Recherche Scientifique (CNRS), Marseille, France.,Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, Aix-Marseille Université, Marseille, France
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70
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de Wit RH, Heukers R, Brink HJ, Arsova A, Maussang D, Cutolo P, Strubbe B, Vischer HF, Bachelerie F, Smit MJ. CXCR4-Specific Nanobodies as Potential Therapeutics for WHIM syndrome. J Pharmacol Exp Ther 2017; 363:35-44. [PMID: 28768817 DOI: 10.1124/jpet.117.242735] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 07/10/2017] [Indexed: 12/15/2022] Open
Abstract
WHIM syndrome is a rare congenital immunodeficiency disease, named after its main clinical manifestations: warts, hypogammaglobulinemia, infections, and myelokathexis, which refers to abnormal accumulation of mature neutrophils in the bone marrow. The disease is primarily caused by C-terminal truncation mutations of the chemokine receptor CXCR4, giving these CXCR4-WHIM mutants a gain of function in response to their ligand CXCL12. Considering the broad functions of CXCR4 in maintaining leukocyte homeostasis, patients are panleukopenic and display altered immune responses, likely as a consequence of impairment in the differentiation and trafficking of leukocytes. Treatment of WHIM patients currently consists of symptom relief, leading to unsatisfactory clinical responses. As an alternative and potentially more effective approach, we tested the potency and efficacy of CXCR4-specific nanobodies on inhibiting CXCR4-WHIM mutants. Nanobodies are therapeutic proteins based on the smallest functional fragments of heavy chain antibodies. They combine the advantages of small-molecule drugs and antibody-based therapeutics due to their relative small size, high stability, and high affinity. We compared the potential of monovalent and bivalent CXCR4-specific nanobodies to inhibit CXCL12-induced CXCR4-WHIM-mediated signaling with the small-molecule clinical candidate AMD3100. The CXCR4-targeting nanobodies displace CXCL12 binding and bind CXCR4-wild type and CXCR4-WHIM (R334X/S338X) mutants and with (sub-) nanomolar affinities. The nanobodies' epitope was mapped to extracellular loop 2 of CXCR4, overlapping with the binding site of CXCL12. Monovalent, and in particular bivalent, nanobodies were more potent than AMD3100 in reducing CXCL12-mediated G protein activation. In addition, CXCR4-WHIM-dependent calcium flux and wound healing of human papillomavirus-immortalized cell lines in response to CXCL12 was effectively inhibited by the nanobodies. Based on these in vitro results, we conclude that CXCR4 nanobodies hold significant potential as alternative therapeutics for CXCR4-associated diseases such as WHIM syndrome.
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Affiliation(s)
- Raymond H de Wit
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Raimond Heukers
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Hendrik J Brink
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Angela Arsova
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - David Maussang
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Pasquale Cutolo
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Beatrijs Strubbe
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Henry F Vischer
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Françoise Bachelerie
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
| | - Martine J Smit
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands (R.H.d.W., R.H., H.J.B., A.A., D.M., H.F.V, M.J.S.); Inflammation Chemokines and Immunopathology, INSERM, Faculté de Médicine-Université Paris-Sud, Université Paris-Saclay, Clamart, France (P.C., F.B.); and Ablynx N.V., Zwijnaarde, Belgrium (B.S.)
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Carpenter B, Tate CG. Active state structures of G protein-coupled receptors highlight the similarities and differences in the G protein and arrestin coupling interfaces. Curr Opin Struct Biol 2017; 45:124-132. [DOI: 10.1016/j.sbi.2017.04.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 04/17/2017] [Accepted: 04/20/2017] [Indexed: 10/19/2022]
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72
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Saleh N, Ibrahim P, Clark T. Differences between G-Protein-Stabilized Agonist-GPCR Complexes and their Nanobody-Stabilized Equivalents. Angew Chem Int Ed Engl 2017; 56:9008-9012. [DOI: 10.1002/anie.201702468] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/26/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Noureldin Saleh
- Computer-Chemie-Centrum; Friedrich-Alexander-Universität Erlangen-Nürnberg; Nägelsbachstr. 25 91052 Erlangen Germany
- Present address: Institut für Medizinische Physik und Biophysik; Charité Berlin; Charitéplatz 1 10117 Berlin Germany
| | - Passainte Ibrahim
- Computer-Chemie-Centrum; Friedrich-Alexander-Universität Erlangen-Nürnberg; Nägelsbachstr. 25 91052 Erlangen Germany
| | - Timothy Clark
- Computer-Chemie-Centrum; Friedrich-Alexander-Universität Erlangen-Nürnberg; Nägelsbachstr. 25 91052 Erlangen Germany
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Saleh N, Ibrahim P, Clark T. Differences between G-Protein-Stabilized Agonist-GPCR Complexes and their Nanobody-Stabilized Equivalents. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702468] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Noureldin Saleh
- Computer-Chemie-Centrum; Friedrich-Alexander-Universität Erlangen-Nürnberg; Nägelsbachstr. 25 91052 Erlangen Germany
- Present address: Institut für Medizinische Physik und Biophysik; Charité Berlin; Charitéplatz 1 10117 Berlin Germany
| | - Passainte Ibrahim
- Computer-Chemie-Centrum; Friedrich-Alexander-Universität Erlangen-Nürnberg; Nägelsbachstr. 25 91052 Erlangen Germany
| | - Timothy Clark
- Computer-Chemie-Centrum; Friedrich-Alexander-Universität Erlangen-Nürnberg; Nägelsbachstr. 25 91052 Erlangen Germany
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74
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Functional selectivity of GPCR-directed drug action through location bias. Nat Chem Biol 2017; 13:799-806. [PMID: 28553949 PMCID: PMC5733145 DOI: 10.1038/nchembio.2389] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 03/08/2017] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) are increasingly recognized to operate from intracellular membranes as well as the plasma membrane. The β2-adrenergic GPCR can activate Gs-linkedcyclic AMP (cAMP) signaling from endosomes. We show here that the homologous human β1-adrenergic receptor initiates an internal Gs-cAMP signal from the Golgi apparatus. By developing a chemical method to acutely squelch G protein coupling at defined membrane locations, we demonstrate that Golgi activation contributes significantly to the overall cellular cAMP response. Golgi signalling utilizes a pre-existing receptor pool rather than receptors delivered from the cell surface, requiring separate access of extracellular ligands. Epinephrine, a hydrophilic endogenous ligand, accesses the Golgi-localized receptor pool by facilitated transport requiring the organic cation transporter 3 (OCT3) whereas drugs can access the Golgi pool by passive diffusion according to hydrophobicity. We demonstrate marked differences among both agonist and antagonist drugs in Golgi-localized receptor access, and show that β-blocker drugs presently used in the clinic differ markedly in ability to antagonize the Golgi signal. We propose ’location bias’ as a new principle for achieving functional selectivity of GPCR-directed drug action.
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75
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Kufareva I, Gustavsson M, Zheng Y, Stephens BS, Handel TM. What Do Structures Tell Us About Chemokine Receptor Function and Antagonism? Annu Rev Biophys 2017; 46:175-198. [PMID: 28532213 PMCID: PMC5764094 DOI: 10.1146/annurev-biophys-051013-022942] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Chemokines and their cell surface G protein-coupled receptors are critical for cell migration, not only in many fundamental biological processes but also in inflammatory diseases and cancer. Recent X-ray structures of two chemokines complexed with full-length receptors provided unprecedented insight into the atomic details of chemokine recognition and receptor activation, and computational modeling informed by new experiments leverages these insights to gain understanding of many more receptor:chemokine pairs. In parallel, chemokine receptor structures with small molecules reveal the complicated and diverse structural foundations of small molecule antagonism and allostery, highlight the inherent physicochemical challenges of receptor:chemokine interfaces, and suggest novel epitopes that can be exploited to overcome these challenges. The structures and models promote unique understanding of chemokine receptor biology, including the interpretation of two decades of experimental studies, and will undoubtedly assist future drug discovery endeavors.
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Affiliation(s)
- Irina Kufareva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Yi Zheng
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Bryan S Stephens
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
| | - Tracy M Handel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093; ,
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76
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Schoonaert L, Rué L, Roucourt B, Timmers M, Little S, Chávez-Gutiérrez L, Dewilde M, Joyce P, Curnock A, Weber P, Haustraete J, Hassanzadeh-Ghassabeh G, De Strooper B, Van Den Bosch L, Van Damme P, Lemmens R, Robberecht W. Identification and characterization of Nanobodies targeting the EphA4 receptor. J Biol Chem 2017; 292:11452-11465. [PMID: 28526745 PMCID: PMC5500810 DOI: 10.1074/jbc.m116.774141] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 05/16/2017] [Indexed: 12/14/2022] Open
Abstract
The ephrin receptor A4 (EphA4) is one of the receptors in the ephrin system that plays a pivotal role in a variety of cell-cell interactions, mostly studied during development. In addition, EphA4 has been found to play a role in cancer biology as well as in the pathogenesis of several neurological disorders such as stroke, spinal cord injury, multiple sclerosis, amyotrophic lateral sclerosis (ALS), and Alzheimer's disease. Pharmacological blocking of EphA4 has been suggested to be a therapeutic strategy for these disorders. Therefore, the aim of our study was to generate potent and selective Nanobodies against the ligand-binding domain of the human EphA4 receptor. We identified two Nanobodies, Nb 39 and Nb 53, that bind EphA4 with affinities in the nanomolar range. These Nanobodies were most selective for EphA4, with residual binding to EphA7 only. Using Alphascreen technology, we found that both Nanobodies displaced all known EphA4-binding ephrins from the receptor. Furthermore, Nb 39 and Nb 53 inhibited ephrin-induced phosphorylation of the EphA4 protein in a cell-based assay. Finally, in a cortical neuron primary culture, both Nanobodies were able to inhibit endogenous EphA4-mediated growth-cone collapse induced by ephrin-B3. Our results demonstrate the potential of Nanobodies to target the ligand-binding domain of EphA4. These Nanobodies may deserve further evaluation as potential therapeutics in disorders in which EphA4-mediated signaling plays a role.
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Affiliation(s)
- Lies Schoonaert
- From the KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium.,VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Laura Rué
- From the KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium.,VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Bart Roucourt
- KU Leuven-University of Leuven, Laboratory for Signal Integration in Cell Fate Decision, 3000 Leuven, Belgium
| | - Mieke Timmers
- From the KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium.,VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Susan Little
- Vertex Pharmaceuticals (Europe) Ltd., Biology Department, OX14 4RW Abingdon, United Kingdom
| | - Lucía Chávez-Gutiérrez
- VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium
| | - Maarten Dewilde
- VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium
| | - Peter Joyce
- Vertex Pharmaceuticals (Europe) Ltd., Biology Department, OX14 4RW Abingdon, United Kingdom
| | - Adam Curnock
- Vertex Pharmaceuticals (Europe) Ltd., Biology Department, OX14 4RW Abingdon, United Kingdom
| | - Peter Weber
- Vertex Pharmaceuticals (Europe) Ltd., Biology Department, OX14 4RW Abingdon, United Kingdom
| | - Jurgen Haustraete
- Protein Service Facility, Inflammation Research Center, VIB, Ghent University, 9052 Ghent, Belgium
| | | | - Bart De Strooper
- VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium.,KU Leuven, Department of Neurosciences and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium.,Institute of Neurology, University College London, WC1E 6BT London, United Kingdom, and
| | - Ludo Van Den Bosch
- From the KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium.,VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium
| | - Philip Van Damme
- From the KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium.,VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium.,University Hospitals Leuven, Department of Neurology, 3000 Leuven, Belgium
| | - Robin Lemmens
- From the KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium.,VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, 3000 Leuven, Belgium.,University Hospitals Leuven, Department of Neurology, 3000 Leuven, Belgium
| | - Wim Robberecht
- From the KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), 3000 Leuven, Belgium, .,University Hospitals Leuven, Department of Neurology, 3000 Leuven, Belgium
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77
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Hofrnann L, Alexander NS, Sun W, Zhang J, Orban T, Palczewski K. Hydrogen/Deuterium Exchange Mass Spectrometry of Human Green Opsin Reveals a Conserved Pro-Pro Motif in Extracellular Loop 2 of Monostable Visual G Protein-Coupled Receptors. Biochemistry 2017; 56:2338-2348. [PMID: 28402104 PMCID: PMC5501310 DOI: 10.1021/acs.biochem.7b00165] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Opsins comprise the protein component of light sensitive G protein-coupled receptors (GPCRs) in the retina of the eye that are responsible for the transduction of light into a biochemical signal. Here, we used hydrogen/deuterium (H/D) exchange coupled with mass spectrometry to map conformational changes in green cone opsin upon light activation. We then compared these findings with those reported for rhodopsin. The extent of H/D exchange in green cone opsin was greater than in rhodopsin in the dark and bleached states, suggesting a higher structural heterogeneity for green cone opsin. Further analysis revealed that green cone opsin exists as a dimer in both dark (inactive) and bleached (active) states, and that the predicted glycosylation sites at N32 and N34 are indeed glycosylated. Comparison of deuterium uptake between inactive and active states of green cone opsin also disclosed a reduced solvent accessibility of the extracellular N-terminal region and an increased accessibility of the chromophore binding site. Increased H/D exchange at the extracellular side of transmembrane helix four (TM4) combined with an analysis of sequence alignments revealed a conserved Pro-Pro motif in extracellular loop 2 (EL2) of monostable visual GPCRs. These data present new insights into the locus of chromophore release at the extracellular side of TM4 and TM5 and provide a foundation for future functional evaluation.
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Affiliation(s)
- Lukas Hofrnann
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Nathan S. Alexander
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Wenyu Sun
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Jianye Zhang
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Tivadar Orban
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
| | - Krzysztof Palczewski
- Department of Pharmacology and Cleveland Center for Membrane and Structural Biology, School of Medicine, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, United States
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78
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Shi Q, Li M, Mika D, Fu Q, Kim S, Phan J, Shen A, Vandecasteele G, Xiang YK. Heterologous desensitization of cardiac β-adrenergic signal via hormone-induced βAR/arrestin/PDE4 complexes. Cardiovasc Res 2017; 113:656-670. [PMID: 28339772 PMCID: PMC5852637 DOI: 10.1093/cvr/cvx036] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Revised: 10/20/2017] [Accepted: 02/17/2017] [Indexed: 12/22/2022] Open
Abstract
AIMS Cardiac β-adrenergic receptor (βAR) signalling is susceptible to heterologous desensitization by different neurohormonal stimuli in clinical conditions associated with heart failure. We aim to examine the underlying mechanism of cross talk between βARs and a set of G-protein coupled receptors (GPCRs) activated by hormones/agonists. METHODS AND RESULTS Rat ventricular cardiomyocytes were used to determine heterologous phosphorylation of βARs under a series of GPCR agonists. Activation of Gs-coupled dopamine receptor, adenosine receptor, relaxin receptor and prostaglandin E2 receptor, and Gq-coupled α1 adrenergic receptor and angiotensin II type 1 receptor promotes phosphorylation of β1AR and β2AR at putative protein kinase A (PKA) phosphorylation sites; but activation of Gi-coupled α2 adrenergic receptor and activation of protease-activated receptor does not. The GPCR agonists that promote β2AR phosphorylation effectively inhibit βAR agonist isoproterenol-induced PKA phosphorylation of phospholamban and contractile function in ventricular cardiomyocytes. Heterologous GPCR stimuli have minimal to small effect on isoproterenol-induced β2AR activation and G-protein coupling for cyclic adenosine monophosphate (cAMP) production. However, these GPCR stimuli significantly promote phosphorylation of phosphodiesterase 4D (PDE4D), and recruit PDE4D to the phosphorylated β2AR in a β-arrestin 2 dependent manner without promoting β2AR endocytosis. The increased binding between β2AR and PDE4D effectively hydrolyzes cAMP signal generated by subsequent stimulation with isoproterenol. Mutation of PKA phosphorylation sites in β2AR, inhibition of PDE4, or genetic ablation of PDE4D or β-arrestin 2 abolishes this heterologous inhibitory effect. Ablation of β-arrestin 2 or PDE4D gene also rescues β-adrenergic stimuli-induced myocyte contractile function. CONCLUSIONS These data reveal essential roles of β-arrestin 2 and PDE4D in a common mechanism for heterologous desensitization of cardiac βARs under hormonal stimulation, which is associated with impaired cardiac function during the development of pathophysiological conditions.
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MESH Headings
- Animals
- Cells, Cultured
- Cyclic AMP-Dependent Protein Kinases/metabolism
- Cyclic Nucleotide Phosphodiesterases, Type 4/genetics
- Cyclic Nucleotide Phosphodiesterases, Type 4/metabolism
- Hormones/pharmacology
- Male
- Mice, Knockout
- Myocardial Contraction/drug effects
- Myocytes, Cardiac/drug effects
- Myocytes, Cardiac/metabolism
- Phosphorylation
- Protein Kinase C/metabolism
- Rats
- Receptor Cross-Talk
- Receptors, Adrenergic, beta-1/drug effects
- Receptors, Adrenergic, beta-1/genetics
- Receptors, Adrenergic, beta-1/metabolism
- Receptors, Adrenergic, beta-2/drug effects
- Receptors, Adrenergic, beta-2/genetics
- Receptors, Adrenergic, beta-2/metabolism
- Signal Transduction/drug effects
- Time Factors
- beta-Arrestin 1/genetics
- beta-Arrestin 1/metabolism
- beta-Arrestin 2/genetics
- beta-Arrestin 2/metabolism
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Affiliation(s)
- Qian Shi
- Department of Pharmacology, University of California at Davis, Davis, CA 95616, USA
| | - Minghui Li
- Department of Pharmacology, University of California at Davis, Davis, CA 95616, USA
- Department of Cardiology, Nanjing First Hospital, Nanjing Medical University, Nanjing 210001, China
| | - Delphine Mika
- INSERM UMR-S 1180, Univ. Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Qin Fu
- Department of Pharmacology, Tongji Medical College, Huazhong University of Technology and Sciences, Wuhan 430030, China
| | - Sungjin Kim
- Department of Pharmacology, University of California at Davis, Davis, CA 95616, USA
| | - Jason Phan
- Department of Pharmacology, University of California at Davis, Davis, CA 95616, USA
| | - Ao Shen
- Department of Pharmacology, University of California at Davis, Davis, CA 95616, USA
| | | | - Yang K. Xiang
- Department of Pharmacology, University of California at Davis, Davis, CA 95616, USA
- VA Northern California Health care system, Mather, CA 95655, USA
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79
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Structural basis of inhibition of lipid-linked oligosaccharide flippase PglK by a conformational nanobody. Sci Rep 2017; 7:46641. [PMID: 28422165 PMCID: PMC5395944 DOI: 10.1038/srep46641] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 03/21/2017] [Indexed: 12/16/2022] Open
Abstract
PglK is an ABC transporter that flips a lipid-linked oligosaccharide (LLO) that serves as a donor in protein N-glycosylation. Previous structures revealed two inward-facing conformations, both with very large separations of the nucleotide binding domains (NBDs), and a closed, ADP-bound state that featured an occluded cavity. To investigate additional states, we developed conformation-sensitive, single-domain camelid nanobodies (Nb) and studied their effect on PglK activity. Biochemical, structural, and mass spectrometric analyses revealed that one inhibitory Nb binds as a single copy to homodimeric PglK. The co-crystal structure of this Nb and ADP-bound PglK revealed a new, narrowly inward-open conformation. Rather than inducing asymmetry in the PglK homodimer, the binding of one Nb results in steric constraints that prevent a second Nb to access the symmetry-related site in PglK. The Nb performed its inhibitory role by a “sticky-doorstop” mechanism, where inhibition of ATP hydrolysis and LLO flipping activity occurs due to impaired closing of the NBD interface, which prevents PglK from converting to an outward-open conformation. This inhibitory mode suggests tight conformational coupling between the ATPase sites, which may apply to other ABC transporters.
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80
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Expression, Functional Characterization, and Solid-State NMR Investigation of the G Protein-Coupled GHS Receptor in Bilayer Membranes. Sci Rep 2017; 7:46128. [PMID: 28387359 PMCID: PMC5384189 DOI: 10.1038/srep46128] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 03/13/2017] [Indexed: 01/14/2023] Open
Abstract
The expression, functional reconstitution and first NMR characterization of the human growth hormone secretagogue (GHS) receptor reconstituted into either DMPC or POPC membranes is described. The receptor was expressed in E. coli. refolded, and reconstituted into bilayer membranes. The molecule was characterized by 15N and 13C solid-state NMR spectroscopy in the absence and in the presence of its natural agonist ghrelin or an inverse agonist. Static 15N NMR spectra of the uniformly labeled receptor are indicative of axially symmetric rotational diffusion of the G protein-coupled receptor in the membrane. In addition, about 25% of the 15N sites undergo large amplitude motions giving rise to very narrow spectral components. For an initial quantitative assessment of the receptor mobility, 1H-13C dipolar coupling values, which are scaled by molecular motions, were determined quantitatively. From these values, average order parameters, reporting the motional amplitudes of the individual receptor segments can be derived. Average backbone order parameters were determined with values between 0.56 and 0.69, corresponding to average motional amplitudes of 40–50° of these segments. Differences between the receptor dynamics in DMPC or POPC membranes were within experimental error. Furthermore, agonist or inverse agonist binding only insignificantly influenced the average molecular dynamics of the receptor.
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81
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Sha F, Salzman G, Gupta A, Koide S. Monobodies and other synthetic binding proteins for expanding protein science. Protein Sci 2017; 26:910-924. [PMID: 28249355 PMCID: PMC5405424 DOI: 10.1002/pro.3148] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 02/20/2017] [Accepted: 02/21/2017] [Indexed: 01/20/2023]
Abstract
Synthetic binding proteins are constructed using nonantibody molecular scaffolds. Over the last two decades, in‐depth structural and functional analyses of synthetic binding proteins have improved combinatorial library designs and selection strategies, which have resulted in potent platforms that consistently generate binding proteins to diverse targets with affinity and specificity that rival those of antibodies. Favorable attributes of synthetic binding proteins, such as small size, freedom from disulfide bond formation and ease of making fusion proteins, have enabled their unique applications in protein science, cell biology and beyond. Here, we review recent studies that illustrate how synthetic binding proteins are powerful probes that can directly link structure and function, often leading to new mechanistic insights. We propose that synthetic proteins will become powerful standard tools in diverse areas of protein science, biotechnology and medicine.
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Affiliation(s)
- Fern Sha
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637
| | - Gabriel Salzman
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637
| | - Ankit Gupta
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016
| | - Shohei Koide
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois, 60637.,Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, 10016.,Department of Biochemistry and Molecular Pharmacology New York University School of Medicine, New York, NY, 10016
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82
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Abstract
Ligand-induced activation of G protein-coupled receptors (GPCRs) is a key mechanism permitting communication between cells and organs. Enormous progress has recently elucidated the structural and dynamic features of GPCR transmembrane signaling. Nanobodies, the recombinant antigen-binding fragments of camelid heavy-chain-only antibodies, have emerged as important research tools to lock GPCRs in particular conformational states. Active-state stabilizing nanobodies have elucidated several agonist-bound structures of hormone-activated GPCRs and have provided insight into the dynamic character of receptors. Nanobodies have also been used to stabilize transient GPCR transmembrane signaling complexes, yielding the first structural insights into GPCR signal transduction across the cellular membrane. Beyond their in vitro uses, nanobodies have served as conformational biosensors in living systems and have provided novel ways to modulate GPCR function. Here, we highlight several examples of how nanobodies have enabled the study of GPCR function and give insights into potential future uses of these important tools.
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Affiliation(s)
- Aashish Manglik
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305; ,
| | - Brian K Kobilka
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, California 94305; ,
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium;
- VIB Structural Biology Research Center, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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83
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Abstract
The human orexin/hypocretin receptors (hOX1R and hOX2R) are G protein-coupled receptors (GPCRs) that mediate the diverse functions of the orexin/hypocretin neuropeptides. Orexins/hypocretins produced by neurons in the lateral hypothalamus stimulate their cognate GPCRs in multiple regions of the central nervous system to control sleep and arousal, circadian rhythms, metabolism, reward pathways, and other behaviors. Dysfunction of orexin/hypocretin signaling is associated with human disease, and the receptors are active targets in a number of therapeutic areas. To better understand the molecular mechanism of the orexin/hypocretin neuropeptides, high-resolution three-dimensional structures of hOX1R and hOX2R are critical. We have solved high-resolution crystal structures of both human orexin/hypocretin receptors bound to high-affinity antagonists. These atomic structures have elucidated how different small molecule antagonists bind with high potency and selectivity, and have also provided clues as to how the native ligands may associate with their receptors. The orexin/hypocretin receptor coordinates, now available to the broader academic and drug discovery community, will facilitate rational design of new therapeutics that modulate orexin/hypocretin signaling in humans.
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Affiliation(s)
- Jie Yin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Daniel M Rosenbaum
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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84
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Native Mass Spectrometry for the Characterization of Structure and Interactions of Membrane Proteins. Methods Mol Biol 2017; 1635:205-232. [PMID: 28755371 DOI: 10.1007/978-1-4939-7151-0_11] [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: 12/12/2022]
Abstract
Over the past years, native mass spectrometry and ion mobility have grown into techniques that are widely applicable to the study of aspects of protein structure. More recently, it has become apparent that this approach provides a very promising avenue for the investigation of integral membrane proteins in lipid or detergent environments.In this chapter, we discuss applications of native mass spectrometry and ion mobility in membrane protein research-what is important to take into consideration when working with membrane proteins, and what the requirements are for sample preparation for native mass spectrometry. Furthermore, we will discuss the types of information provided by the measurements, including the oligomeric state, subunit composition and stoichiometry, interactions with detergents or lipids, conformational transitions, and the binding and structural effect of ligands and drugs.
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85
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Crystal structure of a LacY-nanobody complex in a periplasmic-open conformation. Proc Natl Acad Sci U S A 2016; 113:12420-12425. [PMID: 27791182 DOI: 10.1073/pnas.1615414113] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The lactose permease of Escherichia coli (LacY), a dynamic polytopic membrane protein, catalyzes galactoside-H+ symport and operates by an alternating access mechanism that exhibits multiple conformations, the distribution of which is altered by sugar binding. We have developed single-domain camelid nanobodies (Nbs) against a mutant in an outward (periplasmic)-open conformation to stabilize this state of the protein. Here we describe an X-ray crystal structure of a complex between a double-Trp mutant (Gly46→Trp/Gly262→Trp) and an Nb in which free access to the sugar-binding site from the periplasmic cavity is observed. The structure confirms biochemical data indicating that the Nb binds stoichiometrically with nanomolar affinity to the periplasmic face of LacY primarily to the C-terminal six-helix bundle. The structure is novel because the pathway to the sugar-binding site is constricted and the central cavity containing the galactoside-binding site is empty. Although Phe27 narrows the periplasmic cavity, sugar is freely accessible to the binding site. Remarkably, the side chains directly involved in binding galactosides remain in the same position in the absence or presence of bound sugar.
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86
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Kahsai AW, Wisler JW, Lee J, Ahn S, Cahill TJ, Dennison SM, Staus DP, Thomsen ARB, Anasti KM, Pani B, Wingler LM, Desai H, Bompiani KM, Strachan RT, Qin X, Alam SM, Sullenger BA, Lefkowitz RJ. Conformationally selective RNA aptamers allosterically modulate the β2-adrenoceptor. Nat Chem Biol 2016; 12:709-16. [PMID: 27398998 PMCID: PMC4990464 DOI: 10.1038/nchembio.2126] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/09/2016] [Indexed: 01/08/2023]
Abstract
G-protein-coupled receptor (GPCR) ligands function by stabilizing multiple, functionally distinct receptor conformations. This property underlies the ability of 'biased agonists' to activate specific subsets of a given receptor's signaling profile. However, stabilizing distinct active GPCR conformations to enable structural characterization of mechanisms underlying GPCR activation remains difficult. These challenges have accentuated the need for receptor tools that allosterically stabilize and regulate receptor function through unique, previously unappreciated mechanisms. Here, using a highly diverse RNA library combined with advanced selection strategies involving state-of-the-art next-generation sequencing and bioinformatics analyses, we identify RNA aptamers that bind a prototypical GPCR, the β2-adrenoceptor (β2AR). Using biochemical, pharmacological, and biophysical approaches, we demonstrate that these aptamers bind with nanomolar affinity at defined surfaces of the receptor, allosterically stabilizing active, inactive, and ligand-specific receptor conformations. The discovery of RNA aptamers as allosteric GPCR modulators significantly expands the diversity of ligands available to study the structural and functional regulation of GPCRs.
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Affiliation(s)
- Alem W. Kahsai
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - James W. Wisler
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Jungmin Lee
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138
| | - Seungkirl Ahn
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Thomas J. Cahill
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710
| | - S. Moses Dennison
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710
| | - Dean P. Staus
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Alex R. B. Thomsen
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Kara M. Anasti
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710
| | - Biswaranjan Pani
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Laura M. Wingler
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
| | - Hemant Desai
- The University of North Carolina School of Medicine, Chapel Hill, NC 27516
| | - Kristin M. Bompiani
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710
- Duke Translational Research Institute, Duke University Medical Center, Durham, NC, 27710
- The University of California, San Diego, Moores Cancer Center, La Jolla, CA 92093
| | | | - Xiaoxia Qin
- Genome Sequencing and Analysis Core Resource, Duke University, Durham, NC, 27710
| | - S. Munir Alam
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC, 27710
| | - Bruce A. Sullenger
- Department of Surgery, Duke University Medical Center, Durham, NC, 27710
- Duke Translational Research Institute, Duke University Medical Center, Durham, NC, 27710
| | - Robert J. Lefkowitz
- Department of Medicine, Duke University Medical Center, Durham, NC, 27710
- Department of Biochemistry, Duke University Medical Center, Durham, NC, 27710
- Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC, 27710
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87
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Magnani F, Serrano-Vega MJ, Shibata Y, Abdul-Hussein S, Lebon G, Miller-Gallacher J, Singhal A, Strege A, Thomas JA, Tate CG. A mutagenesis and screening strategy to generate optimally thermostabilized membrane proteins for structural studies. Nat Protoc 2016; 11:1554-71. [PMID: 27466713 PMCID: PMC5268090 DOI: 10.1038/nprot.2016.088] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The thermostability of an integral membrane protein (MP) in detergent solution is a key parameter that dictates the likelihood of obtaining well-diffracting crystals that are suitable for structure determination. However, many mammalian MPs are too unstable for crystallization. We developed a thermostabilization strategy based on systematic mutagenesis coupled to a radioligand-binding thermostability assay that can be applied to receptors, ion channels and transporters. It takes ∼6-12 months to thermostabilize a G-protein-coupled receptor (GPCR) containing 300 amino acid (aa) residues. The resulting thermostabilized MPs are more easily crystallized and result in high-quality structures. This methodology has facilitated structure-based drug design applied to GPCRs because it is possible to determine multiple structures of the thermostabilized receptors bound to low-affinity ligands. Protocols and advice are given on how to develop thermostability assays for MPs and how to combine mutations to make an optimally stable mutant suitable for structural studies. The steps in the procedure include the generation of ∼300 site-directed mutants by Ala/Leu scanning mutagenesis, the expression of each mutant in mammalian cells by transient transfection and the identification of thermostable mutants using a thermostability assay that is based on binding of an (125)I-labeled radioligand to the unpurified, detergent-solubilized MP. Individual thermostabilizing point mutations are then combined to make an optimally stable MP that is suitable for structural biology and other biophysical studies.
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Affiliation(s)
| | | | | | | | | | | | - Ankita Singhal
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Annette Strege
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Jennifer A. Thomas
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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88
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Tian H, Fürstenberg A, Huber T. Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics. Chem Rev 2016; 117:186-245. [DOI: 10.1021/acs.chemrev.6b00084] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
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89
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Jazayeri A, Andrews SP, Marshall FH. Structurally Enabled Discovery of Adenosine A 2A Receptor Antagonists. Chem Rev 2016; 117:21-37. [PMID: 27333206 DOI: 10.1021/acs.chemrev.6b00119] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Over the past decade there has been a revolution in the field of G protein-coupled receptor (GPCR) structural biology. Many years of innovative research from different areas have come together to fuel this significant change in the fortunes of this field, which for many years was characterized by the paucity of high-resolution structures. The determination to succeed has been in part due to the recognized importance of these proteins as drug targets, and although the pharmaceutical industry has been focusing on these receptors, it can be justifiably argued and demonstrated that many of the approved and commercially successful GPCR drugs can be significantly improved to increase efficacy and/or reduce undesired side effects. In addition, many validated targets in this class remain to be drugged. It is widely recognized that application of structure-based drug design approaches can help medicinal chemists a long way toward discovering better drugs. The achievement of structural biologists in providing high-resolution insight is beginning to transform drug discovery efforts, and there are a number of GPCR drugs that have been discovered by use of structural information that are in clinical development. This review aims to highlight the key developments that have brought success to GPCR structure resolution efforts and exemplify the practical application of structural information for the discovery of adenosine A2A receptor antagonists that have potential to treat multiple conditions.
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Affiliation(s)
- Ali Jazayeri
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
| | - Stephen P Andrews
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
| | - Fiona H Marshall
- Heptares Therapeutics Limited , BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
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90
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Heifetz A, Storer RI, McMurray G, James T, Morao I, Aldeghi M, Bodkin MJ, Biggin PC. Application of an Integrated GPCR SAR-Modeling Platform To Explain the Activation Selectivity of Human 5-HT2C over 5-HT2B. ACS Chem Biol 2016; 11:1372-82. [PMID: 26900768 DOI: 10.1021/acschembio.5b01045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Agonism of the 5-HT2C serotonin receptor has been associated with the treatment of a number of diseases including obesity, psychiatric disorders, sexual health, and urology. However, the development of effective 5-HT2C agonists has been hampered by the difficulty in obtaining selectivity over the closely related 5-HT2B receptor, agonism of which is associated with irreversible cardiac valvulopathy. Understanding how to design selective agonists requires exploration of the structural features governing the functional uniqueness of the target receptor relative to related off targets. X-ray crystallography, the major experimental source of structural information, is a slow and challenging process for integral membrane proteins, and so is currently not feasible for every GPCR or GPCR-ligand complex. Therefore, the integration of existing ligand SAR data with GPCR modeling can be a practical alternative to provide this essential structural insight. To demonstrate this, we integrated SAR data from 39 azepine series 5-HT2C agonists, comprising both selective and unselective examples, with our hierarchical GPCR modeling protocol (HGMP). Through this work we have been able to demonstrate how relatively small differences in the amino acid sequences of GPCRs can lead to significant differences in secondary structure and function, as supported by experimental data. In particular, this study suggests that conformational differences in the tilt of TM7 between 5-HT2B and 5-HT2C, which result from differences in interhelical interactions, may be the major source of selectivity in G-protein activation between these two receptors. Our approach also demonstrates how the use of GPCR models in conjunction with SAR data can be used to explain activity cliffs.
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Affiliation(s)
- Alexander Heifetz
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom
| | | | | | - Tim James
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom
| | - Inaki Morao
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom
| | - Matteo Aldeghi
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Mike J. Bodkin
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, United Kingdom
| | - Philip C. Biggin
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
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91
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Burger D, Stihle M, Sharma A, Di Lello P, Benz J, D'Arcy B, Debulpaep M, Fry D, Huber W, Kremer T, Laeremans T, Matile H, Ross A, Rufer AC, Schoch G, Steinmetz MO, Steyaert J, Rudolph MG, Thoma R, Ruf A. Crystal Structures of the Human Doublecortin C- and N-terminal Domains in Complex with Specific Antibodies. J Biol Chem 2016; 291:16292-306. [PMID: 27226599 DOI: 10.1074/jbc.m116.726547] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/06/2022] Open
Abstract
Doublecortin is a microtubule-associated protein produced during neurogenesis. The protein stabilizes microtubules and stimulates their polymerization, which allows migration of immature neurons to their designated location in the brain. Mutations in the gene that impair doublecortin function and cause severe brain formation disorders are located on a tandem repeat of two doublecortin domains. The molecular mechanism of action of doublecortin is only incompletely understood. Anti-doublecortin antibodies, such as the rabbit polyclonal Abcam 18732, are widely used as neurogenesis markers. Here, we report the generation and characterization of antibodies that bind to single doublecortin domains. The antibodies were used as tools to obtain structures of both domains. Four independent crystal structures of the N-terminal domain reveal several distinct open and closed conformations of the peptide linking N- and C-terminal domains, which can be related to doublecortin function. An NMR assignment and a crystal structure in complex with a camelid antibody fragment show that the doublecortin C-terminal domain adopts the same well defined ubiquitin-like fold as the N-terminal domain, despite its reported aggregation and molten globule-like properties. The antibodies' unique domain specificity also renders them ideal research tools to better understand the role of individual domains in doublecortin function. A single chain camelid antibody fragment specific for the C-terminal doublecortin domain affected microtubule binding, whereas a monoclonal mouse antibody specific for the N-terminal domain did not. Together with steric considerations, this suggests that the microtubule-interacting doublecortin domain observed in cryo-electron micrographs is the C-terminal domain rather than the N-terminal one.
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Affiliation(s)
- Dominique Burger
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Martine Stihle
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Ashwani Sharma
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Paola Di Lello
- pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, Roche, Nutley, New Jersey 07110
| | - Jörg Benz
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Brigitte D'Arcy
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Maja Debulpaep
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, and the Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - David Fry
- pRED Pharma Research and Early Development, Small Molecule Research, Discovery Technologies, Roche, Nutley, New Jersey 07110
| | - Walter Huber
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Thomas Kremer
- Roche Pharmaceutical Research and Early Development, NORD Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Toon Laeremans
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, and the Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Hugues Matile
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Alfred Ross
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Arne C Rufer
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Guillaume Schoch
- Roche Pharmaceutical Research and Early Development, NORD Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd., Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Michel O Steinmetz
- the Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium, and the Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Markus G Rudolph
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Ralf Thoma
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
| | - Armin Ruf
- From the pRED Pharma Research and Early Development, Therapeutic Modalities, and
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92
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Stevenson HP, Lin G, Barnes CO, Sutkeviciute I, Krzysiak T, Weiss SC, Reynolds S, Wu Y, Nagarajan V, Makhov AM, Lawrence R, Lamm E, Clark L, Gardella TJ, Hogue BG, Ogata CM, Ahn J, Gronenborn AM, Conway JF, Vilardaga JP, Cohen AE, Calero G. Transmission electron microscopy for the evaluation and optimization of crystal growth. Acta Crystallogr D Struct Biol 2016; 72:603-15. [PMID: 27139624 PMCID: PMC4854312 DOI: 10.1107/s2059798316001546] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/25/2016] [Indexed: 11/10/2022] Open
Abstract
The crystallization of protein samples remains the most significant challenge in structure determination by X-ray crystallography. Here, the effectiveness of transmission electron microscopy (TEM) analysis to aid in the crystallization of biological macromolecules is demonstrated. It was found that the presence of well ordered lattices with higher order Bragg spots, revealed by Fourier analysis of TEM images, is a good predictor of diffraction-quality crystals. Moreover, the use of TEM allowed (i) comparison of lattice quality among crystals from different conditions in crystallization screens; (ii) the detection of crystal pathologies that could contribute to poor X-ray diffraction, including crystal lattice defects, anisotropic diffraction and crystal contamination by heavy protein aggregates and nanocrystal nuclei; (iii) the qualitative estimation of crystal solvent content to explore the effect of lattice dehydration on diffraction and (iv) the selection of high-quality crystal fragments for microseeding experiments to generate reproducibly larger sized crystals. Applications to X-ray free-electron laser (XFEL) and micro-electron diffraction (microED) experiments are also discussed.
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Affiliation(s)
- Hilary P. Stevenson
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Christopher O. Barnes
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Ieva Sutkeviciute
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, M240 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Troy Krzysiak
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Simon C. Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Shelley Reynolds
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Ying Wu
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | | | - Alexander M. Makhov
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Robert Lawrence
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287, USA
| | - Emily Lamm
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Lisa Clark
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Timothy J. Gardella
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Brenda G. Hogue
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85287, USA
| | - Craig M. Ogata
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Ave, Lemont, IL 60439, USA
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Angela M. Gronenborn
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - James F. Conway
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Jean-Pierre Vilardaga
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, M240 Scaife Hall, 3550 Terrace Street, Pittsburgh, PA 15261, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
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93
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O'Brien DE, Conn PJ. Neurobiological Insights from mGlu Receptor Allosteric Modulation. Int J Neuropsychopharmacol 2016; 19:pyv133. [PMID: 26647381 PMCID: PMC4886670 DOI: 10.1093/ijnp/pyv133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/15/2015] [Accepted: 12/02/2015] [Indexed: 12/25/2022] Open
Abstract
Allosteric modulation of metabotropic glutamate (mGlu) receptors offers a promising pharmacological approach to normalize neural circuit dysfunction associated with various psychiatric and neurological disorders. As mGlu receptor allosteric modulators progress through discovery and clinical development, both technical advances and novel tool compounds are providing opportunities to better understand mGlu receptor pharmacology and neurobiology. Recent advances in structural biology are elucidating the structural determinants of mGlu receptor-negative allosteric modulation and supplying the means to resolve active, allosteric modulator-bound mGlu receptors. The discovery and characterization of allosteric modulators with novel pharmacological profiles is uncovering the biological significance of their intrinsic agonist activity, biased mGlu receptor modulation, and novel mGlu receptor heterodimers. The development and exploitation of optogenetic and optopharmacological tools is permitting a refined spatial and temporal understanding of both mGlu receptor functions and their allosteric modulation in intact brain circuits. Together, these lines of research promise to provide a more refined understanding of mGlu receptors and their allosteric modulation that will inform the development of mGlu receptor allosteric modulators as neurotherapeutics in the years to come.
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Affiliation(s)
- Daniel E O'Brien
- Department of Pharmacology and Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, Tennessee (Drs O'Brien and Conn)
| | - P Jeffrey Conn
- Department of Pharmacology and Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University, Nashville, Tennessee (Drs O'Brien and Conn).
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94
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Busato M, Giorgetti A. Structural modeling of G-protein coupled receptors: An overview on automatic web-servers. Int J Biochem Cell Biol 2016; 77:264-74. [PMID: 27102413 DOI: 10.1016/j.biocel.2016.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/09/2016] [Accepted: 04/15/2016] [Indexed: 12/27/2022]
Abstract
Despite the significant efforts and discoveries during the last few years in G protein-coupled receptor (GPCR) expression and crystallization, the receptors with known structures to date are limited only to a small fraction of human GPCRs. The lack of experimental three-dimensional structures of the receptors represents a strong limitation that hampers a deep understanding of their function. Computational techniques are thus a valid alternative strategy to model three-dimensional structures. Indeed, recent advances in the field, together with extraordinary developments in crystallography, in particular due to its ability to capture GPCRs in different activation states, have led to encouraging results in the generation of accurate models. This, prompted the community of modelers to render their methods publicly available through dedicated databases and web-servers. Here, we present an extensive overview on these services, focusing on their advantages, drawbacks and their role in successful applications. Future challenges in the field of GPCR modeling, such as the predictions of long loop regions and the modeling of receptor activation states are presented as well.
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Affiliation(s)
- Mirko Busato
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - Alejandro Giorgetti
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biomedicine, Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Germany.
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95
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New Technologies for Elucidating Opioid Receptor Function. Trends Pharmacol Sci 2016; 37:279-289. [PMID: 26833118 DOI: 10.1016/j.tips.2016.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/22/2015] [Accepted: 01/04/2016] [Indexed: 01/25/2023]
Abstract
Recent advances in technology, including high resolution crystal structures of opioid receptors, novel chemical tools, and new genetic approaches have provided an unparalleled palette of tools for deconstructing opioid receptor actions in vitro and in vivo. Here we provide a brief description of our understanding of opioid receptor function from both molecular and atomic perspectives, as well as their role in neural circuits in vivo. We then show how insights into the molecular details of opioid actions can facilitate the creation of functionally selective (biased) and photoswitchable opioid ligands. Finally, we describe how newly engineered opioid receptor-based chemogenetic and optogenetic tools, and new mouse lines, are expanding and transforming our understanding of opioid function and, perhaps, paving the way for new therapeutics.
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96
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Abstract
The ancient and ubiquitous major facilitator superfamily (MFS) represents the largest secondary transporter family and plays a crucial role in a multitude of physiological processes. MFS proteins transport a broad spectrum of ions and solutes across membranes via facilitated diffusion, symport, or antiport. In recent years, remarkable advances in understanding the structural biology of the MFS transporters have been made. This article reviews the history, classification, and general features of the MFS proteins; summarizes recent structural progress with a focus on the sugar porter family transporters exemplified by GLUT1; and discusses the molecular mechanisms of substrate binding, alternating access, and cotransport coupling.
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Affiliation(s)
- Nieng Yan
- State Key Laboratory of Bio-membrane and Membrane Biotechnology, Center for Structural Biology, School of Medicine, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China;
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97
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Kohnhorst CL, Schmitt DL, Sundaram A, An S. Subcellular functions of proteins under fluorescence single-cell microscopy. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1864:77-84. [PMID: 26025769 PMCID: PMC5679394 DOI: 10.1016/j.bbapap.2015.05.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 05/08/2015] [Accepted: 05/18/2015] [Indexed: 11/25/2022]
Abstract
A cell is a highly organized, dynamic, and intricate biological entity orchestrated by a myriad of proteins and their self-assemblies. Because a protein's actions depend on its coordination in both space and time, our curiosity about protein functions has extended from the test tube into the intracellular space of the cell. Accordingly, modern technological developments and advances in enzymology have been geared towards analyzing protein functions within intact single cells. We discuss here how fluorescence single-cell microscopy has been employed to identify subcellular locations of proteins, detect reversible protein-protein interactions, and measure protein activity and kinetics in living cells. Considering that fluorescence single-cell microscopy has been only recently recognized as a primary technique in enzymology, its potentials and outcomes in studying intracellular protein functions are projected to be immensely useful and enlightening. We anticipate that this review would inspire many investigators to study their proteins of interest beyond the conventional boundary of specific disciplines. This article is part of a Special Issue entitled: Physiological Enzymology and Protein Functions.
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Affiliation(s)
- Casey L Kohnhorst
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Danielle L Schmitt
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Anand Sundaram
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Songon An
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD 21250, USA.
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98
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Nilvebrant J, Tessier PM, Sidhu SS. Engineered Autonomous Human Variable Domains. Curr Pharm Des 2016; 22:6527-6537. [PMID: 27655414 PMCID: PMC5326600 DOI: 10.2174/1381612822666160921143011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/16/2016] [Accepted: 09/20/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND The complex multi-chain architecture of antibodies has spurred interest in smaller derivatives that retain specificity but can be more easily produced in bacteria. Domain antibodies consisting of single variable domains are the smallest antibody fragments and have been shown to possess enhanced ability to target epitopes that are difficult to access using multidomain antibodies. However, in contrast to natural camelid antibody domains, human variable domains typically suffer from low stability and high propensity to aggregate. METHODS This review summarizes strategies to improve the biophysical properties of heavy chain variable domains from human antibodies with an emphasis on aggregation resistance. Several protein engineering approaches have targeted antibody frameworks and complementarity determining regions to stabilize the native state and prevent aggregation of the denatured state. CONCLUSION Recent findings enable the construction of highly diverse libraries enriched in aggregation-resistant variants that are expected to provide binders to diverse antigens. Engineered domain antibodies possess unique advantages in expression, epitope preference and flexibility of formatting over conventional immunoreagents and are a promising class of antibody fragments for biomedical development.
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Affiliation(s)
- Johan Nilvebrant
- Division of Protein Technology, School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Peter M. Tessier
- Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
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99
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Comparing Class A GPCRs to bitter taste receptors: Structural motifs, ligand interactions and agonist-to-antagonist ratios. Methods Cell Biol 2015; 132:401-27. [PMID: 26928553 DOI: 10.1016/bs.mcb.2015.10.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) are seven transmembrane (TM) proteins that play a key role in human physiology. The GPCR superfamily comprises about 800 members, classified into several classes, with rhodopsin-like Class A being the largest and most studied thus far. A huge component of the human repertoire consists of the chemosensory GPCRs, including ∼400 odorant receptors, 25 bitter taste receptors (TAS2Rs), which are thought to guard the organism from consuming poisons, and sweet and umami TAS1R heteromers, which indicate the nutritive value of food. The location of the binding site of TAS2Rs is similar to that of Class A GPCRs. However, most of the known bitter ligands are agonists, with only a few antagonists documented thus far. The agonist-to-antagonist ratios of Class A GPCRs vary, but in general are much lower than for TAS2Rs. For a set of well-studied GPCRs, a gradual change in agonists-to-antagonists ratios is observed when comparing low (10 μM)- and high (10 nM)-affinity ligand sets from ChEMBL and the DrugBank set of drugs. This shift reflects pharmaceutical bias toward the therapeutically desirable pharmacology for each of these GPCRs, while the 10 μM sets possibly represent the native tendency of the receptors toward either agonists or antagonists. Analyzing ligand-GPCR interactions in 56 X-ray structures representative of currently available structural data, we find that the N-terminus, TM1 and TM2 are more involved in binding of antagonists than of agonists. On the other hand, ECL2 tends to be more involved in binding of agonists. This is of interest, since TAS2Rs harbor variations on the typical Class A sequence motifs, including the absence of the ECL2-TM3 disulfide bridge. This suggests an alternative mode of regulation of conformational states for TAS2Rs, with potentially less stabilized inactive state. The comparison of TAS2Rs and Class A GPCRs structural features and the pharmacology of the their ligands highlights the intricacies of GPCR architecture and provides a framework for rational design of new ligands.
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100
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Gustavsson M, Zheng Y, Handel TM. Production of Chemokine/Chemokine Receptor Complexes for Structural Biophysical Studies. Methods Enzymol 2015; 570:233-60. [PMID: 26921949 DOI: 10.1016/bs.mie.2015.10.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
The development of methods for expression and purification of seven-transmembrane receptors has led to an increase in structural and biophysical data and greatly improved the understanding of receptor structure and function. For chemokine receptors, this has been highlighted by the determination of crystal structures of CXCR4 and CCR5 in complex with small-molecule antagonists, followed recently by two receptor/chemokine complexes; CXCR4 in complex with vMIP-II and US28 in complex with the CX3CL1. However, these studies cover only a few of the many chemokines and chemokine receptors and production of stable receptor/chemokine complexes remains a challenging task. Here, we present a method for producing purified complexes between chemokine receptors and chemokines by coexpression in Sf9 cells. Using the complex between atypical chemokine receptor 3 and its native chemokine CXCL12 as an example, we describe the virus production, protein expression, and purification process as well as reconstitution into different membrane mimics. This method provides an efficient way of producing pure receptor/chemokine complexes and has been used to successfully produce receptor/chemokine complexes for CXC as well as CC receptors.
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Affiliation(s)
- Martin Gustavsson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Yi Zheng
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA
| | - Tracy M Handel
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California, USA.
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