51
|
Kleinau G, Worth CL, Kreuchwig A, Biebermann H, Marcinkowski P, Scheerer P, Krause G. Structural-Functional Features of the Thyrotropin Receptor: A Class A G-Protein-Coupled Receptor at Work. Front Endocrinol (Lausanne) 2017; 8:86. [PMID: 28484426 PMCID: PMC5401882 DOI: 10.3389/fendo.2017.00086] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 04/03/2017] [Indexed: 12/21/2022] Open
Abstract
The thyroid-stimulating hormone receptor (TSHR) is a member of the glycoprotein hormone receptors, a sub-group of class A G-protein-coupled receptors (GPCRs). TSHR and its endogenous ligand thyrotropin (TSH) are of essential importance for growth and function of the thyroid gland and proper function of the TSH/TSHR system is pivotal for production and release of thyroid hormones. This receptor is also important with respect to pathophysiology, such as autoimmune (including ophthalmopathy) or non-autoimmune thyroid dysfunctions and cancer development. Pharmacological interventions directly targeting the TSHR should provide benefits to disease treatment compared to currently available therapies of dysfunctions associated with the TSHR or the thyroid gland. Upon TSHR activation, the molecular events conveying conformational changes from the extra- to the intracellular side of the cell across the membrane comprise reception, conversion, and amplification of the signal. These steps are highly dependent on structural features of this receptor and its intermolecular interaction partners, e.g., TSH, antibodies, small molecules, G-proteins, or arrestin. For better understanding of signal transduction, pathogenic mechanisms such as autoantibody action and mutational modifications or for developing new pharmacological strategies, it is essential to combine available structural data with functional information to generate homology models of the entire receptor. Although so far these insights are fragmental, in the past few decades essential contributions have been made to investigate in-depth the involved determinants, such as by structure determination via X-ray crystallography. This review summarizes available knowledge (as of December 2016) concerning the TSHR protein structure, associated functional aspects, and based on these insights we suggest several receptor complex models. Moreover, distinct TSHR properties will be highlighted in comparison to other class A GPCRs to understand the molecular activation mechanisms of this receptor comprehensively. Finally, limitations of current knowledge and lack of information are discussed highlighting the need for intensified efforts toward TSHR structure elucidation.
Collapse
Affiliation(s)
- Gunnar Kleinau
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin, Berlin, Germany
- Group Protein X-Ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, Berlin, Germany
| | | | - Annika Kreuchwig
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
| | - Heike Biebermann
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin, Berlin, Germany
| | | | - Patrick Scheerer
- Group Protein X-Ray Crystallography and Signal Transduction, Institute of Medical Physics and Biophysics, Charité-Universitätsmedizin, Berlin, Germany
| | - Gerd Krause
- Leibniz-Institut für Molekulare Pharmakologie (FMP), Berlin, Germany
- *Correspondence: Gerd Krause,
| |
Collapse
|
52
|
Press O, Zvagelsky T, Vyazmensky M, Kleinau G, Engel S. Construction of Structural Mimetics of the Thyrotropin Receptor Intracellular Domain. Biophys J 2016; 111:2620-2628. [PMID: 28002738 PMCID: PMC5192603 DOI: 10.1016/j.bpj.2016.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/26/2016] [Accepted: 11/02/2016] [Indexed: 10/20/2022] Open
Abstract
The signaling of a G protein-coupled receptor (GPCR) is dictated by the complementary responsiveness of interacting intracellular effectors such as G proteins. Many GPCRs are known to couple to more than one G protein subtype and induce a multitude of signaling pathways, although the in vivo relevance of particular pathways is mostly unrecognized. Dissecting GPCR signaling in terms of the pathways that are activated will boost our understanding of the molecular fundamentals of hormone action. The structural determinants governing the selectivity of GPCR/G protein coupling, however, remain obscure. Here, we describe the design of soluble GPCR mimetics to study the details of the interplay between G-proteins and activators. We constructed functional mimetics of the intracellular domain of a model GPCR, the thyrotropin receptor. We based the construction on a unique scaffold, 6-Helix, an artificial protein that was derived from the elements of the trimer-of-hairpins structure of HIV gp41 and represents a bundle of six α-helices. The 6-Helix scaffold, which endowed the substituted thyrotropin receptor intracellular domain elements with spatial constraints analogous to those found in native receptors, enabled the reconstitution of a microdomain that consists of intracellular loops 2 and 3, and is capable of binding and activating Gα-(s). The 6-Helix-based mimetics could be used as a platform to study the molecular basis of GPCR/G protein recognition. Such knowledge could help investigators develop novel therapeutic strategies for GPCR-related disorders by targeting the GPCR/G protein interfaces and counteracting cellular dysfunctions via focused tuning of GPCR signaling.
Collapse
Affiliation(s)
- Olga Press
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Tatiana Zvagelsky
- Department of Chemistry, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Maria Vyazmensky
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Gunnar Kleinau
- Institute of Experimental Pediatric Endocrinology, Charité-Universitätsmedizin, Berlin, Germany
| | - Stanislav Engel
- Department of Clinical Biochemistry and Pharmacology, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel; National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel.
| |
Collapse
|
53
|
McRobb FM, Negri A, Beuming T, Sherman W. Molecular dynamics techniques for modeling G protein-coupled receptors. Curr Opin Pharmacol 2016; 30:69-75. [DOI: 10.1016/j.coph.2016.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/28/2016] [Accepted: 07/03/2016] [Indexed: 11/17/2022]
|
54
|
Kuhne S, Kooistra AJ, Bosma R, Bortolato A, Wijtmans M, Vischer HF, Mason JS, de Graaf C, de Esch IJP, Leurs R. Identification of Ligand Binding Hot Spots of the Histamine H1 Receptor following Structure-Based Fragment Optimization. J Med Chem 2016; 59:9047-9061. [DOI: 10.1021/acs.jmedchem.6b00981] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Sebastiaan Kuhne
- Amsterdam
Institute for Molecules, Medicines and Systems (AIMMS), Division of
Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Albert J. Kooistra
- Amsterdam
Institute for Molecules, Medicines and Systems (AIMMS), Division of
Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Reggie Bosma
- Amsterdam
Institute for Molecules, Medicines and Systems (AIMMS), Division of
Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Andrea Bortolato
- Heptares Therapeutics Ltd., BioPark,
Broadwater Road, Welwyn Garden City, Herts AL7 3AX, U.K
| | - Maikel Wijtmans
- Amsterdam
Institute for Molecules, Medicines and Systems (AIMMS), Division of
Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Henry F. Vischer
- Amsterdam
Institute for Molecules, Medicines and Systems (AIMMS), Division of
Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Jonathan S. Mason
- Heptares Therapeutics Ltd., BioPark,
Broadwater Road, Welwyn Garden City, Herts AL7 3AX, U.K
| | - Chris de Graaf
- Amsterdam
Institute for Molecules, Medicines and Systems (AIMMS), Division of
Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Iwan J. P. de Esch
- Amsterdam
Institute for Molecules, Medicines and Systems (AIMMS), Division of
Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Rob Leurs
- Amsterdam
Institute for Molecules, Medicines and Systems (AIMMS), Division of
Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| |
Collapse
|
55
|
Schneider G, Reker D, Chen T, Hauenstein K, Schneider P, Altmann KH. Deorphaning the Macromolecular Targets of the Natural Anticancer Compound Doliculide. Angew Chem Int Ed Engl 2016; 55:12408-11. [PMID: 27605391 DOI: 10.1002/anie.201605707] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/11/2016] [Indexed: 11/06/2022]
Abstract
The cyclodepsipeptide doliculide is a marine natural product with strong actin-polymerizing and anticancer activities. Evidence for doliculide acting as a potent and subtype-selective antagonist of prostanoid E receptor 3 (EP3) is presented. Computational target prediction suggested that this membrane receptor is a likely macromolecular target and enabled immediate in vitro validation. This proof-of-concept study demonstrates the in silico deorphanization of phenotypic screening hits as a viable concept for future natural-product-inspired chemical biology and drug discovery efforts.
Collapse
Affiliation(s)
- Gisbert Schneider
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zürich, Switzerland.
| | - Daniel Reker
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zürich, Switzerland
| | - Tao Chen
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zürich, Switzerland
| | - Kurt Hauenstein
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zürich, Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zürich, Switzerland.,inSili.com LLC, Zürich, Switzerland
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093, Zürich, Switzerland
| |
Collapse
|
56
|
Schneider G, Reker D, Chen T, Hauenstein K, Schneider P, Altmann KH. Deorphaning the Macromolecular Targets of the Natural Anticancer Compound Doliculide. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201605707] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Gisbert Schneider
- Department of Chemistry and Applied Biosciences; Institute of Pharmaceutical Sciences; ETH Zürich; Wolfgang-Pauli-Strasse 10 8093 Zürich Switzerland
| | - Daniel Reker
- Department of Chemistry and Applied Biosciences; Institute of Pharmaceutical Sciences; ETH Zürich; Wolfgang-Pauli-Strasse 10 8093 Zürich Switzerland
| | - Tao Chen
- Department of Chemistry and Applied Biosciences; Institute of Pharmaceutical Sciences; ETH Zürich; Wolfgang-Pauli-Strasse 10 8093 Zürich Switzerland
| | - Kurt Hauenstein
- Department of Chemistry and Applied Biosciences; Institute of Pharmaceutical Sciences; ETH Zürich; Wolfgang-Pauli-Strasse 10 8093 Zürich Switzerland
| | - Petra Schneider
- Department of Chemistry and Applied Biosciences; Institute of Pharmaceutical Sciences; ETH Zürich; Wolfgang-Pauli-Strasse 10 8093 Zürich Switzerland
- inSili.com LLC; Zürich Switzerland
| | - Karl-Heinz Altmann
- Department of Chemistry and Applied Biosciences; Institute of Pharmaceutical Sciences; ETH Zürich; Wolfgang-Pauli-Strasse 10 8093 Zürich Switzerland
| |
Collapse
|
57
|
Batyuk A, Galli L, Ishchenko A, Han GW, Gati C, Popov PA, Lee MY, Stauch B, White TA, Barty A, Aquila A, Hunter MS, Liang M, Boutet S, Pu M, Liu ZJ, Nelson G, James D, Li C, Zhao Y, Spence JCH, Liu W, Fromme P, Katritch V, Weierstall U, Stevens RC, Cherezov V. Native phasing of x-ray free-electron laser data for a G protein-coupled receptor. SCIENCE ADVANCES 2016; 2:e1600292. [PMID: 27679816 PMCID: PMC5035125 DOI: 10.1126/sciadv.1600292] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 08/01/2016] [Indexed: 05/23/2023]
Abstract
Serial femtosecond crystallography (SFX) takes advantage of extremely bright and ultrashort pulses produced by x-ray free-electron lasers (XFELs), allowing for the collection of high-resolution diffraction intensities from micrometer-sized crystals at room temperature with minimal radiation damage, using the principle of "diffraction-before-destruction." However, de novo structure factor phase determination using XFELs has been difficult so far. We demonstrate the ability to solve the crystallographic phase problem for SFX data collected with an XFEL using the anomalous signal from native sulfur atoms, leading to a bias-free room temperature structure of the human A2A adenosine receptor at 1.9 Å resolution. The advancement was made possible by recent improvements in SFX data analysis and the design of injectors and delivery media for streaming hydrated microcrystals. This general method should accelerate structural studies of novel difficult-to-crystallize macromolecules and their complexes.
Collapse
Affiliation(s)
- Alexander Batyuk
- Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Lorenzo Galli
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrii Ishchenko
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Gye Won Han
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Cornelius Gati
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Petr A Popov
- Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia.; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Ming-Yue Lee
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Benjamin Stauch
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA
| | - Thomas A White
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Anton Barty
- Center for Free-Electron Laser Science, Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mark S Hunter
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mengchen Pu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhi-Jie Liu
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.; iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Garrett Nelson
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Daniel James
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Chufeng Li
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Yun Zhao
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wei Liu
- Center for Applied Structural Discovery at the Biodesign Institute, School of Molecular Sciences, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
| | - Petra Fromme
- Center for Applied Structural Discovery at the Biodesign Institute, School of Molecular Sciences, Arizona State University, 727 East Tyler Street, Tempe, AZ 85287, USA
| | - Vsevolod Katritch
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Raymond C Stevens
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.; iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Vadim Cherezov
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA.; Bridge Institute, University of Southern California, Los Angeles, CA 90089, USA.; Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia.; Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.; Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
| |
Collapse
|
58
|
Tehan BG, Christopher JA. The use of conformationally thermostabilised GPCRs in drug discovery: application to fragment, structure and biophysical techniques. Curr Opin Pharmacol 2016; 30:8-13. [PMID: 27400445 DOI: 10.1016/j.coph.2016.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 06/16/2016] [Accepted: 06/28/2016] [Indexed: 11/19/2022]
Abstract
Recent developments in receptor stabilisation have facilitated major advances in G protein-coupled receptor (GPCR) research, notably structural biology, over the past eight years. Here we review the application of fragment, structure and biophysical techniques using stabilised GPCRs (StaR proteins), and their impact in the drug discovery process. These techniques have, most recently, been utilised in the discovery of the non-alkyne mGlu5 negative allosteric modulator HTL14242, in addition to the dual orexin receptor antagonist HTL6641, with differentiated residence time kinetics.
Collapse
Affiliation(s)
- Benjamin G Tehan
- Heptares Therapeutics, Biopark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom.
| | - John A Christopher
- Heptares Therapeutics, Biopark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, United Kingdom
| |
Collapse
|
59
|
Bodnarchuk MS. Water, water, everywhere… It's time to stop and think. Drug Discov Today 2016; 21:1139-46. [DOI: 10.1016/j.drudis.2016.05.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/15/2016] [Accepted: 05/13/2016] [Indexed: 12/11/2022]
|
60
|
Kleinau G, Müller A, Biebermann H. Oligomerization of GPCRs involved in endocrine regulation. J Mol Endocrinol 2016; 57:R59-80. [PMID: 27151573 DOI: 10.1530/jme-16-0049] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 05/04/2016] [Indexed: 12/27/2022]
Abstract
More than 800 different human membrane-spanning G-protein-coupled receptors (GPCRs) serve as signal transducers at biological barriers. These receptors are activated by a wide variety of ligands such as peptides, ions and hormones, and are able to activate a diverse set of intracellular signaling pathways. GPCRs are of central importance in endocrine regulation, which underpins the significance of comprehensively studying these receptors and interrelated systems. During the last decade, the capacity for multimerization of GPCRs was found to be a common and functionally relevant property. The interaction between GPCR monomers results in higher order complexes such as homomers (identical receptor subtype) or heteromers (different receptor subtypes), which may be present in a specific and dynamic monomer/oligomer equilibrium. It is widely accepted that the oligomerization of GPCRs is a mechanism for determining the fine-tuning and expansion of cellular processes by modification of ligand action, expression levels, and related signaling outcome. Accordingly, oligomerization provides exciting opportunities to optimize pharmacological treatment with respect to receptor target and tissue selectivity or for the development of diagnostic tools. On the other hand, GPCR heteromerization may be a potential reason for the undesired side effects of pharmacological interventions, faced with numerous and common mutual signaling modifications in heteromeric constellations. Finally, detailed deciphering of the physiological occurrence and relevance of specific GPCR/GPCR-ligand interactions poses a future challenge. This review will tackle the aspects of GPCR oligomerization with specific emphasis on family A GPCRs involved in endocrine regulation, whereby only a subset of these receptors will be discussed in detail.
Collapse
Affiliation(s)
- Gunnar Kleinau
- Institute of Experimental Pediatric Endocrinology (IEPE)Charité-Universitätsmedizin, Berlin, Germany
| | - Anne Müller
- Institute of Experimental Pediatric Endocrinology (IEPE)Charité-Universitätsmedizin, Berlin, Germany
| | - Heike Biebermann
- Institute of Experimental Pediatric Endocrinology (IEPE)Charité-Universitätsmedizin, Berlin, Germany
| |
Collapse
|
61
|
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.
Collapse
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
| |
Collapse
|
62
|
Dores MR, Grimsey NJ, Mendez F, Trejo J. ALIX Regulates the Ubiquitin-Independent Lysosomal Sorting of the P2Y1 Purinergic Receptor via a YPX3L Motif. PLoS One 2016; 11:e0157587. [PMID: 27301021 PMCID: PMC4907476 DOI: 10.1371/journal.pone.0157587] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/01/2016] [Indexed: 12/22/2022] Open
Abstract
Endocytic sorting and lysosomal degradation are integral to the regulation of G protein-coupled receptor (GPCR) function. Upon ligand binding, classical GPCRs are activated, internalized and recycled or sorted to lysosomes for degradation, a process that requires receptor ubiquitination. However, recent studies have demonstrated that numerous GPCRs are sorted to lysosomes independent of receptor ubiquitination. Here, we describe an ubiquitin-independent lysosomal sorting pathway for the purinergic GPCR P2Y1. After activation, P2Y1 sorts to lysosomes for degradation independent of direct ubiquitination that is mediated by a YPX3L motif within the second intracellular loop that serves as a binding site for the adaptor protein ALIX. Depletion of ALIX or site-directed mutation of the YPX3L motif inhibits P2Y1 sorting into the lumen of multivesicular endosomes/lysosomes and degradation. These findings confirm the function of YPX3L motifs as lysosomal targeting sequences for GPCRs and demonstrate that ALIX mediates the ubiquitin-independent degradation of certain GPCRs.
Collapse
Affiliation(s)
- Michael R. Dores
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States of America
- Department of Biology, Hofstra University, Hempstead, NY 11549, United States of America
| | - Neil J. Grimsey
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States of America
| | - Francisco Mendez
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States of America
| | - JoAnn Trejo
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States of America
- * E-mail:
| |
Collapse
|
63
|
Ichikawa O, Fujimoto K, Yamada A, Okazaki S, Yamazaki K. G-Protein/β-Arrestin-Linked Fluctuating Network of G-Protein-Coupled Receptors for Predicting Drug Efficacy and Bias Using Short-Term Molecular Dynamics Simulation. PLoS One 2016; 11:e0155816. [PMID: 27187591 PMCID: PMC4871340 DOI: 10.1371/journal.pone.0155816] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/04/2016] [Indexed: 01/14/2023] Open
Abstract
The efficacy and bias of signal transduction induced by a drug at a target protein are closely associated with the benefits and side effects of the drug. In particular, partial agonist activity and G-protein/β-arrestin-biased agonist activity for the G-protein-coupled receptor (GPCR) family, the family with the most target proteins of launched drugs, are key issues in drug discovery. However, designing GPCR drugs with appropriate efficacy and bias is challenging because the dynamic mechanism of signal transduction induced by ligand—receptor interactions is complicated. Here, we identified the G-protein/β-arrestin-linked fluctuating network, which initiates large-scale conformational changes, using sub-microsecond molecular dynamics (MD) simulations of the β2-adrenergic receptor (β2AR) with a diverse collection of ligands and correlation analysis of their G protein/β-arrestin efficacy. The G-protein-linked fluctuating network extends from the ligand-binding site to the G-protein-binding site through the connector region, and the β-arrestin-linked fluctuating network consists of the NPxxY motif and adjacent regions. We confirmed that the averaged values of fluctuation in the fluctuating network detected are good quantitative indexes for explaining G protein/β-arrestin efficacy. These results indicate that short-term MD simulation is a practical method to predict the efficacy and bias of any compound for GPCRs.
Collapse
Affiliation(s)
- Osamu Ichikawa
- Genomic Science Laboratories, Sumitomo Dainippon Pharma. Co. Ltd, Osaka, Osaka, Japan
| | - Kazushi Fujimoto
- Department of Applied Chemistry, Nagoya University, Nagoya, Aichi, Japan
| | - Atsushi Yamada
- Department of Applied Chemistry, Nagoya University, Nagoya, Aichi, Japan
| | - Susumu Okazaki
- Department of Applied Chemistry, Nagoya University, Nagoya, Aichi, Japan
| | - Kazuto Yamazaki
- Genomic Science Laboratories, Sumitomo Dainippon Pharma. Co. Ltd, Osaka, Osaka, Japan
| |
Collapse
|
64
|
Application of advanced X-ray methods in life sciences. Biochim Biophys Acta Gen Subj 2016; 1861:3671-3685. [PMID: 27156488 DOI: 10.1016/j.bbagen.2016.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Synchrotron radiation (SR) sources provide diverse X-ray methods for the investigation of structure-function relationships in biological macromolecules. SCOPE OF REVIEW Recent developments in SR sources and in the X-ray tools they offer for life sciences are reviewed. Specifically, advances in macromolecular crystallography, small angle X-ray solution scattering, X-ray absorption and fluorescence spectroscopy, and imaging are discussed with examples. MAJOR CONCLUSIONS SR sources offer a range of X-ray techniques that can be used in a complementary fashion in studies of biological systems at a wide range of resolutions from atomic to cellular scale. Emerging applications of X-ray techniques include the characterization of disordered proteins, noncrystalline and nonequilibrium systems, elemental imaging of tissues, cells and organs, and detection of time-resolved changes in molecular structures. GENERAL SIGNIFICANCE X-ray techniques are in the center of hybrid approaches that are used to gain insight into complex problems relating to biomolecular mechanisms, disease and possible therapeutic solutions. This article is part of a Special Issue entitled "Science for Life". Guest Editors: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
Collapse
|
65
|
Murphy RB, Repasky MP, Greenwood JR, Tubert-Brohman I, Jerome S, Annabhimoju R, Boyles NA, Schmitz CD, Abel R, Farid R, Friesner RA. WScore: A Flexible and Accurate Treatment of Explicit Water Molecules in Ligand–Receptor Docking. J Med Chem 2016; 59:4364-84. [DOI: 10.1021/acs.jmedchem.6b00131] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Robert B. Murphy
- Schrödinger, Inc., 101 SW Main Street, Portland Oregon 97204, United States
| | - Matthew P. Repasky
- Schrödinger, Inc., 101 SW Main Street, Portland Oregon 97204, United States
| | - Jeremy R. Greenwood
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ivan Tubert-Brohman
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Steven Jerome
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | | | - Nicholas A. Boyles
- Schrödinger, Inc., 101 SW Main Street, Portland Oregon 97204, United States
| | | | - Robert Abel
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Ramy Farid
- Schrödinger, Inc., 120 West 45th Street, New York, New York 10036, United States
| | - Richard A. Friesner
- Department of
Chemistry, Columbia University, New York, 3000 Broadway,
MC 3110, New York 10036, United States
| |
Collapse
|
66
|
Cohen LS, Arshava B, Kauffman S, Mathew E, Fracchiolla KE, Ding FX, Dumont ME, Becker JM, Naider F. Guided reconstitution of membrane protein fragments. Biopolymers 2016; 102:16-29. [PMID: 23897574 DOI: 10.1002/bip.22349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 06/13/2013] [Accepted: 06/26/2013] [Indexed: 11/12/2022]
Abstract
Structural analysis by NMR of G protein-coupled receptors (GPCRs) has proven to be extremely challenging. To reduce the number of peaks in the NMR spectra by segmentally labeling a GPCR, we have developed a Guided Reconstitution method that includes the use of charged residues and Cys activation to drive heterodimeric disulfide bond formation. Three different cysteine-activating reagents: 5-5'-dithiobis(2-nitrobenzoic acid) [DTNB], 2,2'-dithiobis(5-nitropyridine) [DTNP], and 4,4'-dipyridyl disulfide [4-PDS] were analyzed to determine their efficiency in heterodimer formation at different pHs. Short peptides representing the N-terminal (NT) and C-terminal (CT) regions of the first extracellular loop (EL1) of Ste2p, the Saccharomyces cerevisiae alpha-factor mating receptor, were activated using these reagents and the efficiencies of activation and rates of heterodimerization were analyzed. Activation of NT peptides with DTNP and 4-PDS resulted in about 60% yield, but heterodimerization was rapid and nearly quantitative. Double transmembrane domain protein fragments were biosynthesized and used in Guided Reconstitution reactions. A 102-residue fragment, 2TM-tail [Ste2p(G31-I120C)], was heterodimerized with CT-EL1-tail(DTNP) at pH 4.6 with a yield of ∼75%. A 132-residue fragment, 2TMlong-tail [Ste2p(M1-I120C)], was expressed in both unlabeled and (15)N-labeled forms and used with a peptide comprising the third transmembrane domain, to generate a 180-residue segmentally labeled 3TM protein that was found to be segmentally labeled using [(15)N,(1)H]-HSQC analysis. Our data indicate that the Guided Reconstitution method would be applicable to the segmental labeling of a membrane protein with 3 transmembrane domains and may prove useful in the preparation of an intact reconstituted GPCR for use in biophysical analysis and structure determination.
Collapse
Affiliation(s)
- Leah S Cohen
- Department of Chemistry, The College of Staten Island, City University of New York (CUNY), Staten Island, NY, 10314
| | | | | | | | | | | | | | | | | |
Collapse
|
67
|
Weiss DR, Bortolato A, Tehan B, Mason JS. GPCR-Bench: A Benchmarking Set and Practitioners' Guide for G Protein-Coupled Receptor Docking. J Chem Inf Model 2016; 56:642-51. [PMID: 26958710 DOI: 10.1021/acs.jcim.5b00660] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Virtual screening is routinely used to discover new ligands and in particular new ligand chemotypes for G protein-coupled receptors (GPCRs). To prepare for a virtual screen, we often tailor a docking protocol that will enable us to select the best candidates for further screening. To aid this, we created GPCR-Bench, a publically available docking benchmarking set in the spirit of the DUD and DUD-E reference data sets for validation studies, containing 25 nonredundant high-resolution GPCR costructures with an accompanying set of diverse ligands and computational decoy molecules for each target. Benchmarking sets are often used to compare docking protocols; however, it is important to evaluate docking methods not by "retrospective" hit rates but by the actual likelihood that they will produce novel prospective hits. Therefore, docking protocols must not only rank active molecules highly but also produce good poses that a chemist will select for purchase and screening. Currently, no simple objective machine-scriptable function exists that can do this; instead, docking hit lists must be subjectively examined in a consistent way to compare between docking methods. We present here a case study highlighting considerations we feel are of importance when evaluating a method, intended to be useful as a practitioners' guide.
Collapse
Affiliation(s)
- Dahlia R Weiss
- Heptares Therapeutics Ltd. , BioPark, Broadwater Road, Welwyn Garden City, Herts, AL7 3AX, U.K
| | - Andrea Bortolato
- Heptares Therapeutics Ltd. , BioPark, Broadwater Road, Welwyn Garden City, Herts, AL7 3AX, U.K
| | - Benjamin Tehan
- Heptares Therapeutics Ltd. , BioPark, Broadwater Road, Welwyn Garden City, Herts, AL7 3AX, U.K
| | - Jonathan S Mason
- Heptares Therapeutics Ltd. , BioPark, Broadwater Road, Welwyn Garden City, Herts, AL7 3AX, U.K
| |
Collapse
|
68
|
Di Bartolo N, Compton ELR, Warne T, Edwards PC, Tate CG, Schertler GFX, Booth PJ. Complete Reversible Refolding of a G-Protein Coupled Receptor on a Solid Support. PLoS One 2016; 11:e0151582. [PMID: 26982879 PMCID: PMC4794186 DOI: 10.1371/journal.pone.0151582] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 03/01/2016] [Indexed: 12/22/2022] Open
Abstract
The factors defining the correct folding and stability of integral membrane proteins are poorly understood. Folding of only a few select membrane proteins has been scrutinised, leaving considerable deficiencies in knowledge for large protein families, such as G protein coupled receptors (GPCRs). Complete reversible folding, which is problematic for any membrane protein, has eluded this dominant receptor family. Moreover, attempts to recover receptors from denatured states are inefficient, yielding at best 40–70% functional protein. We present a method for the reversible unfolding of an archetypal family member, the β1-adrenergic receptor, and attain 100% recovery of the folded, functional state, in terms of ligand binding, compared to receptor which has not been subject to any unfolding and retains its original, folded structure. We exploit refolding on a solid support, which could avoid unwanted interactions and aggregation that occur in bulk solution. We determine the changes in structure and function upon unfolding and refolding. Additionally, we employ a method that is relatively new to membrane protein folding; pulse proteolysis. Complete refolding of β1-adrenergic receptor occurs in n-decyl-β-D-maltoside (DM) micelles from a urea-denatured state, as shown by regain of its original helical structure, ligand binding and protein fluorescence. The successful refolding strategy on a solid support offers a defined method for the controlled refolding and recovery of functional GPCRs and other membrane proteins that suffer from instability and irreversible denaturation once isolated from their native membranes.
Collapse
Affiliation(s)
- Natalie Di Bartolo
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
- * E-mail:
| | - Emma L. R. Compton
- Organisational and Staff Development Unit, University of Strathclyde, Glasgow, United Kingdom
| | - Tony Warne
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Patricia C. Edwards
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom
| | | | - Paula J. Booth
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
| |
Collapse
|
69
|
Abstract
Schematic presentation of the overall adhesion G Protein-Coupled Receptor (aGPCR) structure and functional domains, covering an extracellular N-terminal fragment (NTF), a membrane-spanning C-terminal fragment (CTF) and a GPCR proteolysis site (GPS). (Left side) aGPCR model constructed based on the seven-transmembrane (7TM) structure (blue) of secretin family glucagon receptor (GCGR) (PDB, 4L6R) [11] and the GPCR autoproteolysis inducing (GAIN) domain (magenta) structure of latrophilin 1 (PDB, 4DLQ) [9]. The β-13 strand residues are depicted in green. (Right side) The experimentally validated full-length secretin family GCGR structure combining structural and experimental information from the GCGR 7TM crystal structure (PDB, 4L6R) (blue), the GCGR extracellular domain (ECD) structure (PDB, 4ERS) (magenta) and the ECD structure of glucagon-like peptide-1 (GLP-1)-bound glucagon-like peptide-1 receptor (GLP-1R) (PDB, 3IOL) (green), complemented by site-directed mutagenesis, electron microscopy (EM), hydrogen-deuterium exchange (HDX) and cross-linking studies [11-13]) Despite the recent breakthroughs in the elucidation of the three-dimensional structures of the seven transmembrane (7TM) domain of the G protein-coupled receptor (GPCR) superfamily, a corresponding structure of a member of the adhesion GPCR (aGPCR) family has not yet been solved. In this chapter, we give an overview of the current knowledge of the 7TM domain of aGPCRs by comparative structure-based sequence similarity analyses between aGPCRs and GPCRs with known crystal structure. Of the GPCR superfamily, only the secretin family shares some sequence similarity with aGPCRs. This chapter will therefore emphasize on the comparison of these two GPCR families. Two 7TM domain structures of secretin family GPCRs are known that provide insight into the structure-function relationships of conserved sequence motifs that play important roles and are also present in most aGPCRs. This suggests that the 7TM domains of aGPCRs and secretin family GPCRs share a similar structural fold and that the conserved residues in both families may be involved in similar intermolecular interaction networks and facilitate similar conformational changes. Comparison of the residues that line the large peptide hormone binding pocket in the 7TM domain of secretin family GPCRs with corresponding residues in aGPCRs indicates that in the latter, the corresponding pocket in the 7TM domain is relatively hydrophobic and may be even larger. Improved knowledge on these conserved sequence motifs will help to understand the interactions of the aGPCR 7TM domain with ligands and gain insight into the activation mechanism of aGPCRs.
Collapse
Affiliation(s)
- Chris de Graaf
- Department of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, 1081HV, The Netherlands.
| | - Saskia Nijmeijer
- Department of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, Vrije Universiteit Amsterdam, Amsterdam, 1081HV, The Netherlands
| | - Steffen Wolf
- Department of Biophysics, CAS-MPG Partner Institute for Computational Biology, Key Laboratory of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R. China
- Institute of Physics, Albert Ludwigs University, Freiburg, Germany
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, ON, Canada, M5S 1A8
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON, Canada, M5S 1A8
| |
Collapse
|
70
|
Tikhonova IG. Application of GPCR Structures for Modelling of Free Fatty Acid Receptors. Handb Exp Pharmacol 2016; 236:57-77. [PMID: 27757764 DOI: 10.1007/164_2016_52] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Five G protein-coupled receptors (GPCRs) have been identified to be activated by free fatty acids (FFA). Among them, FFA1 (GPR40) and FFA4 (GPR120) bind long-chain fatty acids, FFA2 (GPR43) and FFA3 (GPR41) bind short-chain fatty acids and GPR84 binds medium-chain fatty acids. Free fatty acid receptors have now emerged as potential targets for the treatment of diabetes, obesity and immune diseases. The recent progress in crystallography of GPCRs has now enabled the elucidation of the structure of FFA1 and provided reliable templates for homology modelling of other FFA receptors. Analysis of the crystal structure and improved homology models, along with mutagenesis data and structure activity, highlighted an unusual arginine charge-pairing interaction in FFA1-3 for receptor modulation, distinct structural features for ligand binding to FFA1 and FFA4 and an arginine of the second extracellular loop as a possible anchoring point for FFA at GPR84. Structural data will be helpful for searching novel small-molecule modulators at the FFA receptors.
Collapse
Affiliation(s)
- Irina G Tikhonova
- Molecular Therapeutics, School of Pharmacy, Medical Biology Centre, Queen's University Belfast, BT9 7BL, Northern Ireland, UK.
| |
Collapse
|
71
|
Thomas T, Chalmers DK, Yuriev E. Homology Modeling and Docking Evaluation of Human Muscarinic Acetylcholine Receptors. NEUROMETHODS 2016. [DOI: 10.1007/978-1-4939-2858-3_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
72
|
Biggin PC, Aldeghi M, Bodkin MJ, Heifetz A. Beyond Membrane Protein Structure: Drug Discovery, Dynamics and Difficulties. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 922:161-181. [PMID: 27553242 DOI: 10.1007/978-3-319-35072-1_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Most of the previous content of this book has focused on obtaining the structures of membrane proteins. In this chapter we explore how those structures can be further used in two key ways. The first is their use in structure based drug design (SBDD) and the second is how they can be used to extend our understanding of their functional activity via the use of molecular dynamics. Both aspects now heavily rely on computations. This area is vast, and alas, too large to consider in depth in a single book chapter. Thus where appropriate we have referred the reader to recent reviews for deeper assessment of the field. We discuss progress via the use of examples from two main drug target areas; G-protein coupled receptors (GPCRs) and ion channels. We end with a discussion of some of the main challenges in the area.
Collapse
Affiliation(s)
- Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.
| | - Matteo Aldeghi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Michael J Bodkin
- Evotec Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| | - Alexander Heifetz
- Evotec Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire, OX14 4RZ, UK
| |
Collapse
|
73
|
Heifetz A, Chudyk EI, Gleave L, Aldeghi M, Cherezov V, Fedorov DG, Biggin PC, Bodkin MJ. The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR–Ligand Interactions. J Chem Inf Model 2015; 56:159-72. [PMID: 26642258 DOI: 10.1021/acs.jcim.5b00644] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Our interpretation of ligand-protein interactions is often informed by high-resolution structures, which represent the cornerstone of structure-based drug design. However, visual inspection and molecular mechanics approaches cannot explain the full complexity of molecular interactions. Quantum Mechanics approaches are often too computationally expensive, but one method, Fragment Molecular Orbital (FMO), offers an excellent compromise and has the potential to reveal key interactions that would otherwise be hard to detect. To illustrate this, we have applied the FMO method to 18 Class A GPCR-ligand crystal structures, representing different branches of the GPCR genome. Our work reveals key interactions that are often omitted from structure-based descriptions, including hydrophobic interactions, nonclassical hydrogen bonds, and the involvement of backbone atoms. This approach provides a more comprehensive picture of receptor-ligand interactions than is currently used and should prove useful for evaluation of the chemical nature of ligand binding and to support structure-based drug design.
Collapse
Affiliation(s)
- Alexander Heifetz
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Ewa I. Chudyk
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Laura Gleave
- 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
| | - Vadim Cherezov
- Department
of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, United States
- Laboratory
for Structural Biology of GPCRs, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Dmitri G. Fedorov
- NMRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Philip C. Biggin
- 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
| |
Collapse
|
74
|
Ranganathan A, Stoddart LA, Hill SJ, Carlsson J. Fragment-Based Discovery of Subtype-Selective Adenosine Receptor Ligands from Homology Models. J Med Chem 2015; 58:9578-90. [PMID: 26592528 DOI: 10.1021/acs.jmedchem.5b01120] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fragment-based lead discovery (FBLD) holds great promise for drug discovery, but applications to G protein-coupled receptors (GPCRs) have been limited by a lack of sensitive screening techniques and scarce structural information. If virtual screening against homology models of GPCRs could be used to identify fragment ligands, FBLD could be extended to numerous important drug targets and contribute to efficient lead generation. Access to models of multiple receptors may further enable the discovery of fragments that bind specifically to the desired target. To investigate these questions, we used molecular docking to screen >500 000 fragments against homology models of the A3 and A1 adenosine receptors (ARs) with the goal to discover A3AR-selective ligands. Twenty-one fragments with predicted A3AR-specific binding were evaluated in live-cell fluorescence-based assays; of eight verified ligands, six displayed A3/A1 selectivity, and three of these had high affinities ranging from 0.1 to 1.3 μM. Subsequently, structure-guided fragment-to-lead optimization led to the identification of a >100-fold-selective antagonist with nanomolar affinity from commercial libraries. These results highlight that molecular docking screening can guide fragment-based discovery of selective ligands even if the structures of both the target and antitarget receptors are unknown. The same approach can be readily extended to a large number of pharmaceutically important targets.
Collapse
Affiliation(s)
- Anirudh Ranganathan
- Science for Life Laboratory, Department of Biochemistry and Biophysics, and Center for Biomembrane Research, Stockholm University , SE-106 91 Stockholm, Sweden
| | - Leigh A Stoddart
- Cell Signalling Research Group, School of Life Sciences, University of Nottingham , Nottingham NG7 2UH, U.K
| | - Stephen J Hill
- Cell Signalling Research Group, School of Life Sciences, University of Nottingham , Nottingham NG7 2UH, U.K
| | - Jens Carlsson
- Science for Life Laboratory, Department of Medicinal Chemistry, BMC, Uppsala University , P.O. Box 574, SE-751 23 Uppsala, Sweden
| |
Collapse
|
75
|
How Can Mutations Thermostabilize G-Protein-Coupled Receptors? Trends Pharmacol Sci 2015; 37:37-46. [PMID: 26547284 DOI: 10.1016/j.tips.2015.09.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/14/2015] [Accepted: 09/21/2015] [Indexed: 01/04/2023]
Abstract
Structures of over 30 different G-protein-coupled receptors (GPCRs) have advanced our understanding of cell signaling and have provided a foundation for structure-guided drug design. This exciting progress has required the development of three complementary methods to facilitate GPCR crystallization, one of which is the thermostabilization of receptors by systematic mutagenesis. However, the reason why a particular mutation, or combination of mutations, stabilizes the receptor is not always evident from a static crystal structure. Molecular dynamics (MD) simulations have been used to identify and estimate the energetic factors that affect thermostability through comparing the dynamics of the thermostabilized receptors with structure-based models of the wild-type receptor. The data indicate that receptors are stabilized through a combination of factors, including an increase in receptor rigidity, a decrease in collective motion, reduced stress at specific residues, and the presence of ordered water molecules. Predicting thermostabilizing mutations computationally represents a major challenge for the field.
Collapse
|
76
|
Cooke RM, Brown AJ, Marshall FH, Mason JS. Structures of G protein-coupled receptors reveal new opportunities for drug discovery. Drug Discov Today 2015; 20:1355-64. [DOI: 10.1016/j.drudis.2015.08.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Revised: 07/27/2015] [Accepted: 08/17/2015] [Indexed: 01/31/2023]
|
77
|
Dores MR, Lin H, J Grimsey N, Mendez F, Trejo J. The α-arrestin ARRDC3 mediates ALIX ubiquitination and G protein-coupled receptor lysosomal sorting. Mol Biol Cell 2015; 26:4660-73. [PMID: 26490116 PMCID: PMC4678022 DOI: 10.1091/mbc.e15-05-0284] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/16/2015] [Indexed: 01/21/2023] Open
Abstract
The novel ALIX-dependent GPCR sorting pathway is regulated by the a-arrestin ARRDC3. A critical role is also shown for the E3 ubiquitin ligase WWP2 in regulation of ALIX ubiquitination and lysosomal sorting of GPCRs. The sorting of G protein–coupled receptors (GPCRs) to lysosomes is critical for proper signaling and cellular responses. We previously showed that the adaptor protein ALIX regulates lysosomal degradation of protease-activated receptor-1 (PAR1), a GPCR for thrombin, independent of ubiquitin-binding ESCRTs and receptor ubiquitination. However, the mechanisms that regulate ALIX function during PAR1 lysosomal sorting are not known. Here we show that the mammalian α-arrestin arrestin domain–containing protein-3 (ARRDC3) regulates ALIX function in GPCR sorting via ubiquitination. ARRDC3 colocalizes with ALIX and is required for PAR1 sorting at late endosomes and degradation. Depletion of ARRDC3 by small interfering RNA disrupts ALIX interaction with activated PAR1 and the CHMP4B ESCRT-III subunit, suggesting that ARRDC3 regulates ALIX activity. We found that ARRDC3 is required for ALIX ubiquitination induced by activation of PAR1. A screen of nine mammalian NEDD4-family E3 ubiquitin ligases revealed a critical role for WWP2. WWP2 interacts with ARRDC3 and not ALIX. Depletion of WWP2 inhibited ALIX ubiquitination and blocked ALIX interaction with activated PAR1 and CHMP4B. These findings demonstrate a new role for the α-arrestin ARRDC3 and the E3 ubiquitin ligase WWP2 in regulation of ALIX ubiquitination and lysosomal sorting of GPCRs.
Collapse
Affiliation(s)
- Michael R Dores
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Huilan Lin
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Neil J Grimsey
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - Francisco Mendez
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA 92093
| | - JoAnn Trejo
- Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA 92093
| |
Collapse
|
78
|
Spyrakis F, Cavasotto CN. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description. Arch Biochem Biophys 2015; 583:105-19. [DOI: 10.1016/j.abb.2015.08.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 01/05/2023]
|
79
|
Biased signalling: the instinctive skill of the cell in the selection of appropriate signalling pathways. Biochem J 2015; 470:155-67. [DOI: 10.1042/bj20150358] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
GPCRs (G-protein-coupled receptors) are members of a family of proteins which are generally regarded as the largest group of therapeutic drug targets. Ligands of GPCRs do not usually activate all cellular signalling pathways linked to a particular seven-transmembrane receptor in a uniform manner. The fundamental idea behind this concept is that each ligand has its own ability, while interacting with the receptor, to activate different signalling pathways (or a particular set of signalling pathways) and it is this concept which is known as biased signalling. The importance of biased signalling is that it may selectively activate biological responses to favour therapeutically beneficial signalling pathways and to avoid adverse effects. There are two levels of biased signalling. First, bias can arise from the ability of GPCRs to couple to a subset of the available G-protein subtypes: Gαs, Gαq/11, Gαi/o or Gα12/13. These subtypes produce the diverse effects of GPCRs by targeting different effectors. Secondly, biased GPCRs may differentially activate G-proteins or β-arrestins. β-Arrestins are ubiquitously expressed and function to terminate or inhibit classic G-protein signalling and initiate distinct β-arrestin-mediated signalling processes. The interplay of G-protein and β-arrestin signalling largely determines the cellular consequences of the administration of GPCR-targeted drugs. In the present review, we highlight the particular functionalities of biased signalling and discuss its biological effects subsequent to GPCR activation. We consider that biased signalling is potentially allowing a choice between signalling through ‘beneficial’ pathways and the avoidance of ‘harmful’ ones.
Collapse
|
80
|
Bayden AS, Moustakas DT, Joseph-McCarthy D, Lamb ML. Evaluating Free Energies of Binding and Conservation of Crystallographic Waters Using SZMAP. J Chem Inf Model 2015; 55:1552-65. [DOI: 10.1021/ci500746d] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Alexander S. Bayden
- Oncology and Infection Innovative Medicines Units, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Demetri T. Moustakas
- Oncology and Infection Innovative Medicines Units, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Diane Joseph-McCarthy
- Oncology and Infection Innovative Medicines Units, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| | - Michelle L. Lamb
- Oncology and Infection Innovative Medicines Units, AstraZeneca R&D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States
| |
Collapse
|
81
|
The impact of binding thermodynamics on medicinal chemistry optimizations. Future Med Chem 2015; 7:1285-303. [DOI: 10.4155/fmc.15.63] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Ligand binding thermodynamics has been attracted considerable interest in the past decade owing to the recognized relation between binding thermodynamic profile and the physicochemical and druglike properties of compounds. In this review, the relation between optimization strategies and ligand properties is presented based on the structural and thermodynamic analysis of ligand–protein complex formation. The control of the binding thermodynamic profile is beneficial for the balanced affinity and physicochemical properties of drug candidates, and early phase optimization gives more opportunity to this control.
Collapse
|
82
|
Jazayeri A, Dias JM, Marshall FH. From G Protein-coupled Receptor Structure Resolution to Rational Drug Design. J Biol Chem 2015; 290:19489-95. [PMID: 26100628 DOI: 10.1074/jbc.r115.668251] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A number of recent technical solutions have led to significant advances in G protein-coupled receptor (GPCR) structural biology. Apart from a detailed mechanistic view of receptor activation, the new structures have revealed novel ligand binding sites. Together, these insights provide avenues for rational drug design to modulate the activities of these important drug targets. The application of structural data to GPCR drug discovery ushers in an exciting era with the potential to improve existing drugs and discover new ones. In this review, we focus on technical solutions that have accelerated GPCR crystallography as well as some of the salient findings from structures that are relevant to drug discovery. Finally, we outline some of the approaches used in GPCR structure based drug design.
Collapse
Affiliation(s)
- Ali Jazayeri
- From Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, United Kingdom
| | - Joao M Dias
- From Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, United Kingdom
| | - Fiona H Marshall
- From Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, United Kingdom
| |
Collapse
|
83
|
Chen Y, Palczewski K. Systems Pharmacology Links GPCRs with Retinal Degenerative Disorders. Annu Rev Pharmacol Toxicol 2015; 56:273-98. [PMID: 25839098 DOI: 10.1146/annurev-pharmtox-010715-103033] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In most biological systems, second messengers and their key regulatory and effector proteins form links between multiple cellular signaling pathways. Such signaling nodes can integrate the deleterious effects of genetic aberrations, environmental stressors, or both in complex diseases, leading to cell death by various mechanisms. Here we present a systems (network) pharmacology approach that, together with transcriptomics analyses, was used to identify different G protein-coupled receptors that experimentally protected against cellular stress and death caused by linked signaling mechanisms. We describe the application of this concept to degenerative and diabetic retinopathies in appropriate mouse models as an example. Systems pharmacology also provides an attractive framework for devising strategies to combat complex diseases by using (repurposing) US Food and Drug Administration-approved pharmacological agents.
Collapse
Affiliation(s)
- Yu Chen
- Yueyang Hospital and.,Clinical Research Institute of Integrative Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China
| | - Krzysztof Palczewski
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106;
| |
Collapse
|
84
|
Tao L, Zhu F, Qin C, Zhang C, Chen S, Zhang P, Zhang C, Tan C, Gao C, Chen Z, Jiang Y, Chen YZ. Clustered distribution of natural product leads of drugs in the chemical space as influenced by the privileged target-sites. Sci Rep 2015; 5:9325. [PMID: 25790752 PMCID: PMC5380136 DOI: 10.1038/srep09325] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/18/2015] [Indexed: 01/02/2023] Open
Abstract
Some natural product leads of drugs (NPLDs) have been found to congregate in the chemical space. The extent, detailed patterns, and mechanisms of this congregation phenomenon have not been fully investigated and their usefulness for NPLD discovery needs to be more extensively tested. In this work, we generated and evaluated the distribution patterns of 442 NPLDs of 749 pre-2013 approved and 263 clinical trial small molecule drugs in the chemical space represented by the molecular scaffold and fingerprint trees of 137,836 non-redundant natural products. In the molecular scaffold trees, 62.7% approved and 37.4% clinical trial NPLDs congregate in 62 drug-productive scaffolds/scaffold-branches. In the molecular fingerprint tree, 82.5% approved and 63.0% clinical trial NPLDs are clustered in 60 drug-productive clusters (DCs) partly due to their preferential binding to 45 privileged target-site classes. The distribution patterns of the NPLDs are distinguished from those of the bioactive natural products. 11.7% of the NPLDs in these DCs have remote-similarity relationship with the nearest NPLD in their own DC. The majority of the new NPLDs emerge from preexisting DCs. The usefulness of the derived knowledge for NPLD discovery was demonstrated by the recognition of the new NPLDs of 2013-2014 approved drugs.
Collapse
Affiliation(s)
- Lin Tao
- 1] Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, the Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen, Tsinghua University, Shenzhen, and Shenzhen Technology and Engineering Laboratory for Personalized Cancer Diagnostics and Therapeutics, PO Box 518000, P. R. China [2] Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore, Singapore 117543 [3] NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456
| | - Feng Zhu
- 1] Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, the Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen, Tsinghua University, Shenzhen, and Shenzhen Technology and Engineering Laboratory for Personalized Cancer Diagnostics and Therapeutics, PO Box 518000, P. R. China [2] Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore, Singapore 117543 [3] Innovative Drug Research Centre and College of Chemistry and Chemical Engineering, Chongqing University, Chongqing, P. R. China
| | - Chu Qin
- 1] Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore, Singapore 117543 [2] NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456
| | - Cheng Zhang
- Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore, Singapore 117543
| | - Shangying Chen
- Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore, Singapore 117543
| | - Peng Zhang
- Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore, Singapore 117543
| | - Cunlong Zhang
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, the Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen, Tsinghua University, Shenzhen, and Shenzhen Technology and Engineering Laboratory for Personalized Cancer Diagnostics and Therapeutics, PO Box 518000, P. R. China
| | - Chunyan Tan
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, the Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen, Tsinghua University, Shenzhen, and Shenzhen Technology and Engineering Laboratory for Personalized Cancer Diagnostics and Therapeutics, PO Box 518000, P. R. China
| | - Chunmei Gao
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, the Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen, Tsinghua University, Shenzhen, and Shenzhen Technology and Engineering Laboratory for Personalized Cancer Diagnostics and Therapeutics, PO Box 518000, P. R. China
| | - Zhe Chen
- Zhejiang Key Laboratory of Gastro-intestinal Pathophysiology, Zhejiang Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou, P. R. China
| | - Yuyang Jiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, the Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen, Tsinghua University, Shenzhen, and Shenzhen Technology and Engineering Laboratory for Personalized Cancer Diagnostics and Therapeutics, PO Box 518000, P. R. China
| | - Yu Zong Chen
- 1] Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, the Ministry-Province Jointly Constructed Base for State Key Lab-Shenzhen Key Laboratory of Chemical Biology, the Graduate School at Shenzhen, Tsinghua University, Shenzhen, and Shenzhen Technology and Engineering Laboratory for Personalized Cancer Diagnostics and Therapeutics, PO Box 518000, P. R. China [2] Bioinformatics and Drug Design Group, Department of Pharmacy, and Center for Computational Science and Engineering, National University of Singapore, Singapore 117543 [3] NUS Graduate School for Integrative Sciences and Engineering, Singapore 117456
| |
Collapse
|
85
|
Spielman SJ, Kumar K, Wilke CO. Comprehensive, structurally-informed alignment and phylogeny of vertebrate biogenic amine receptors. PeerJ 2015; 3:e773. [PMID: 25737813 PMCID: PMC4338800 DOI: 10.7717/peerj.773] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 01/26/2015] [Indexed: 01/29/2023] Open
Abstract
Biogenic amine receptors play critical roles in regulating behavior and physiology in both vertebrates and invertebrates, particularly within the central nervous system. Members of the G-protein coupled receptor (GPCR) family, these receptors interact with endogenous bioamine ligands such as dopamine, serotonin, and epinephrine, and are targeted by a wide array of pharmaceuticals. Despite the clear clinical and biological importance of these receptors, their evolutionary history remains poorly characterized. In particular, the relationships among biogenic amine receptors and any specific evolutionary constraints acting within distinct receptor subtypes are largely unknown. To advance and facilitate studies in this receptor family, we have constructed a comprehensive, high-quality sequence alignment of vertebrate biogenic amine receptors. In particular, we have integrated a traditional multiple sequence approach with robust structural domain predictions to ensure that alignment columns accurately capture the highly-conserved GPCR structural domains, and we demonstrate how ignoring structural information produces spurious inferences of homology. Using this alignment, we have constructed a structurally-partitioned maximum-likelihood phylogeny from which we deduce novel biogenic amine receptor relationships and uncover previously unrecognized lineage-specific receptor clades. Moreover, we find that roughly 1% of the 3039 sequences in our final alignment are either misannotated or unclassified, and we propose updated classifications for these receptors. We release our comprehensive alignment and its corresponding phylogeny as a resource for future research into the evolution and diversification of biogenic amine receptors.
Collapse
Affiliation(s)
| | - Keerthana Kumar
- Department of Integrative Biology, The University of Texas at Austin, Austin, USA
| | - Claus O. Wilke
- Department of Integrative Biology, The University of Texas at Austin, Austin, USA
| |
Collapse
|
86
|
Structures of mGluRs shed light on the challenges of drug development of allosteric modulators. Curr Opin Pharmacol 2015; 20:1-7. [DOI: 10.1016/j.coph.2014.09.022] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 09/24/2014] [Accepted: 09/27/2014] [Indexed: 01/06/2023]
|
87
|
Bortolato A, Doré AS, Hollenstein K, Tehan BG, Mason JS, Marshall FH. Structure of Class B GPCRs: new horizons for drug discovery. Br J Pharmacol 2015; 171:3132-45. [PMID: 24628305 DOI: 10.1111/bph.12689] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 03/04/2014] [Accepted: 03/10/2014] [Indexed: 01/15/2023] Open
Abstract
Class B GPCRs of the secretin family are important drug targets in many human diseases including diabetes, neurodegeneration, cardiovascular disease and psychiatric disorders. X-ray crystal structures for the glucagon receptor and corticotropin-releasing factor receptor 1 have now been published. In this review, we analyse the new structures and how they compare with each other and with Class A and F receptors. We also consider the differences in druggability and possible similarity in the activation mechanisms. Finally, we discuss the potential for the design of small-molecule modulators for these important targets in drug discovery. This new structural insight allows, for the first time, structure-based drug design methods to be applied to Class B GPCRs.
Collapse
Affiliation(s)
- Andrea Bortolato
- Heptares Therapeutics Limited, Welwyn Garden City, Hertfordshire, UK
| | | | | | | | | | | |
Collapse
|
88
|
Beuming T, Lenselink B, Pala D, McRobb F, Repasky M, Sherman W. Docking and Virtual Screening Strategies for GPCR Drug Discovery. Methods Mol Biol 2015; 1335:251-76. [PMID: 26260606 DOI: 10.1007/978-1-4939-2914-6_17] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Progress in structure determination of G protein-coupled receptors (GPCRs) has made it possible to apply structure-based drug design (SBDD) methods to this pharmaceutically important target class. The quality of GPCR structures available for SBDD projects fall on a spectrum ranging from high resolution crystal structures (<2 Å), where all water molecules in the binding pocket are resolved, to lower resolution (>3 Å) where some protein residues are not resolved, and finally to homology models that are built using distantly related templates. Each GPCR project involves a distinct set of opportunities and challenges, and requires different approaches to model the interaction between the receptor and the ligands. In this review we will discuss docking and virtual screening to GPCRs, and highlight several refinement and post-processing steps that can be used to improve the accuracy of these calculations. Several examples are discussed that illustrate specific steps that can be taken to improve upon the docking and virtual screening accuracy. While GPCRs are a unique target class, many of the methods and strategies outlined in this review are general and therefore applicable to other protein families.
Collapse
Affiliation(s)
- Thijs Beuming
- Schrödinger, Inc., 120 West 45th Street, New York, NY, 10036, USA,
| | | | | | | | | | | |
Collapse
|
89
|
Cavasotto CN, Palomba D. Expanding the horizons of G protein-coupled receptor structure-based ligand discovery and optimization using homology models. Chem Commun (Camb) 2015; 51:13576-94. [DOI: 10.1039/c5cc05050b] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We show the key role of structural homology models in GPCR structure-based lead discovery and optimization, highlighting methodological aspects, recent progress and future directions.
Collapse
Affiliation(s)
- Claudio N. Cavasotto
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society
- Buenos Aires
- Argentina
| | - Damián Palomba
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society
- Buenos Aires
- Argentina
| |
Collapse
|
90
|
Engineering G Protein-Coupled Receptors for Drug Design. MULTIFACETED ROLES OF CRYSTALLOGRAPHY IN MODERN DRUG DISCOVERY 2015. [DOI: 10.1007/978-94-017-9719-1_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
91
|
Goldfeld DA, Murphy R, Kim B, Wang L, Beuming T, Abel R, Friesner RA. Docking and free energy perturbation studies of ligand binding in the kappa opioid receptor. J Phys Chem B 2014; 119:824-35. [PMID: 25395044 DOI: 10.1021/jp5053612] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The kappa opioid receptor (KOR) is an important target for pain and depression therapeutics that lack harmful and addictive qualities of existing medications. We present a model for the binding of morphinan ligands and JDTic to the JDTic/KOR crystal structure based on an atomic level description of the water structure within its active site. The model contains two key interaction motifs that are supported by experimental evidence. The first is the formation of a salt bridge between the ligand and Asp 138(3.32) in transmembrane domain (TM) 3. The second is the stabilization by the ligand of two high energy, isolated, and ice-like waters near TM5 and TM6. This model is incorporated via energetic terms into a new empirical scoring function, WScore, designed to assess interactions between ligands and localized water in a binding site. Pairing WScore with the docking program Glide discriminates known active KOR ligands from large sets of decoy molecules much better than Glide's older generation scoring functions, SP and XP. We also use rigorous free energy perturbation calculations to provide evidence for the proposed mechanism of interaction between ligands and KOR. The molecular description of ligand binding in KOR should provide a good starting point for future drug discovery efforts for this receptor.
Collapse
Affiliation(s)
- Dahlia A Goldfeld
- Department of Chemistry, Columbia University , 3000 Broadway, MC 3110, New York, New York 10027, United States
| | | | | | | | | | | | | |
Collapse
|
92
|
Yuan S, Hu Z, Filipek S, Vogel H. W2466.48Opens a Gate for a Continuous Intrinsic Water Pathway during Activation of the Adenosine A2AReceptor. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409679] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
93
|
Yuan S, Hu Z, Filipek S, Vogel H. W246(6.48) opens a gate for a continuous intrinsic water pathway during activation of the adenosine A2A receptor. Angew Chem Int Ed Engl 2014; 54:556-9. [PMID: 25403323 DOI: 10.1002/anie.201409679] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Indexed: 01/21/2023]
Abstract
The question how G-protein-coupled receptors transduce an extracellular signal by a sequence of transmembrane conformational transitions into an intracellular response remains to be solved at molecular detail. Herein, we use molecular dynamics simulations to reveal distinct conformational transitions of the adenosine A2A receptor, and we found that the conserved W246(6.48) residue in transmembrane helix TM6 performs a key rotamer toggle switch. Agonist binding induces the sidechain of W246(6.48) to fluctuate between two distinct conformations enabling the diffusion of water molecules from the bulk into the center of the receptor. After passing the W246(6.48) gate, the internal water molecules induce another conserved residue, Y288(7.53), to switch to a distinct rotamer conformation establishing a continuous transmembrane water pathway. Further, structural changes of TM6 and TM7 induce local structural changes of the adjacent lipid bilayer.
Collapse
Affiliation(s)
- Shuguang Yuan
- Laboratory of Physical Chemistry of Polymers and Membranes, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne (Switzerland).
| | | | | | | |
Collapse
|
94
|
Don CG, Riniker S. Scents and sense:In silicoperspectives on olfactory receptors. J Comput Chem 2014; 35:2279-87. [DOI: 10.1002/jcc.23757] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 09/23/2014] [Accepted: 09/27/2014] [Indexed: 11/12/2022]
Affiliation(s)
- Charleen G. Don
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich; 8093 Zurich Switzerland
| | - Sereina Riniker
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich; 8093 Zurich Switzerland
| |
Collapse
|
95
|
Moyes AJ, Khambata RS, Villar I, Bubb KJ, Baliga RS, Lumsden NG, Xiao F, Gane PJ, Rebstock AS, Worthington RJ, Simone MI, Mota F, Rivilla F, Vallejo S, Peiró C, Sánchez Ferrer CF, Djordjevic S, Caulfield MJ, MacAllister RJ, Selwood DL, Ahluwalia A, Hobbs AJ. Endothelial C-type natriuretic peptide maintains vascular homeostasis. J Clin Invest 2014; 124:4039-51. [PMID: 25105365 PMCID: PMC4151218 DOI: 10.1172/jci74281] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 06/19/2014] [Indexed: 01/13/2023] Open
Abstract
The endothelium plays a fundamental role in maintaining vascular homeostasis by releasing factors that regulate local blood flow, systemic blood pressure, and the reactivity of leukocytes and platelets. Accordingly, endothelial dysfunction underpins many cardiovascular diseases, including hypertension, myocardial infarction, and stroke. Herein, we evaluated mice with endothelial-specific deletion of Nppc, which encodes C-type natriuretic peptide (CNP), and determined that this mediator is essential for multiple aspects of vascular regulation. Specifically, disruption of CNP leads to endothelial dysfunction, hypertension, atherogenesis, and aneurysm. Moreover, we identified natriuretic peptide receptor-C (NPR-C) as the cognate receptor that primarily underlies CNP-dependent vasoprotective functions and developed small-molecule NPR-C agonists to target this pathway. Administration of NPR-C agonists promotes a vasorelaxation of isolated resistance arteries and a reduction in blood pressure in wild-type animals that is diminished in mice lacking NPR-C. This work provides a mechanistic explanation for genome-wide association studies that have linked the NPR-C (Npr3) locus with hypertension by demonstrating the importance of CNP/NPR-C signaling in preserving vascular homoeostasis. Furthermore, these results suggest that the CNP/NPR-C pathway has potential as a disease-modifying therapeutic target for cardiovascular disorders.
Collapse
Affiliation(s)
- Amie J. Moyes
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Rayomand S. Khambata
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Inmaculada Villar
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Kristen J. Bubb
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Reshma S. Baliga
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Natalie G. Lumsden
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Fang Xiao
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Paul J. Gane
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Anne-Sophie Rebstock
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Roberta J. Worthington
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Michela I. Simone
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Filipa Mota
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Fernando Rivilla
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Susana Vallejo
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Concepción Peiró
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Carlos F. Sánchez Ferrer
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Snezana Djordjevic
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Mark J. Caulfield
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Raymond J. MacAllister
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - David L. Selwood
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Amrita Ahluwalia
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| | - Adrian J. Hobbs
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom. Wolfson Institute for Biomedical Research, University College London, London, United Kingdom. División de Cirugía Pediátrica, Hospital Universitario Ramón y Cajal, Madrid, Spain. Departamento de Farmacologia, Facultad de Medicina, Universidad Autonoma de Madrid, Madrid, Spain. Structural and Molecular Biology and Clinical Pharmacology, University College London, London, United Kingdom
| |
Collapse
|
96
|
Congreve M, Dias JM, Marshall FH. Structure-based drug design for G protein-coupled receptors. PROGRESS IN MEDICINAL CHEMISTRY 2014; 53:1-63. [PMID: 24418607 DOI: 10.1016/b978-0-444-63380-4.00001-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Our understanding of the structural biology of G protein-coupled receptors has undergone a transformation over the past 5 years. New protein-ligand complexes are described almost monthly in high profile journals. Appreciation of how small molecules and natural ligands bind to their receptors has the potential to impact enormously how medicinal chemists approach this major class of receptor targets. An outline of the key topics in this field and some recent examples of structure- and fragment-based drug design are described. A table is presented with example views of each G protein-coupled receptor for which there is a published X-ray structure, including interactions with small molecule antagonists, partial and full agonists. The possible implications of these new data for drug design are discussed.
Collapse
Affiliation(s)
- Miles Congreve
- Heptares Therapeutics Ltd, BioPark, Welwyn Garden City, Hertfordshire, United Kingdom
| | - João M Dias
- Heptares Therapeutics Ltd, BioPark, Welwyn Garden City, Hertfordshire, United Kingdom
| | - Fiona H Marshall
- Heptares Therapeutics Ltd, BioPark, Welwyn Garden City, Hertfordshire, United Kingdom
| |
Collapse
|
97
|
Scott DJ, Kummer L, Egloff P, Bathgate RAD, Plückthun A. Improving the apo-state detergent stability of NTS1 with CHESS for pharmacological and structural studies. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2817-24. [PMID: 25064156 DOI: 10.1016/j.bbamem.2014.07.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Revised: 07/13/2014] [Accepted: 07/14/2014] [Indexed: 11/18/2022]
Abstract
The largest single class of drug targets is the G protein-coupled receptor (GPCR) family. Modern high-throughput methods for drug discovery require working with pure protein, but this has been a challenge for GPCRs, and thus the success of screening campaigns targeting soluble, catalytic protein domains has not yet been realized for GPCRs. Therefore, most GPCR drug screening has been cell-based, whereas the strategy of choice for drug discovery against soluble proteins is HTS using purified proteins coupled to structure-based drug design. While recent developments are increasing the chances of obtaining GPCR crystal structures, the feasibility of screening directly against purified GPCRs in the unbound state (apo-state) remains low. GPCRs exhibit low stability in detergent micelles, especially in the apo-state, over the time periods required for performing large screens. Recent methods for generating detergent-stable GPCRs, however, offer the potential for researchers to manipulate GPCRs almost like soluble enzymes, opening up new avenues for drug discovery. Here we apply cellular high-throughput encapsulation, solubilization and screening (CHESS) to the neurotensin receptor 1 (NTS1) to generate a variant that is stable in the apo-state when solubilized in detergents. This high stability facilitated the crystal structure determination of this receptor and also allowed us to probe the pharmacology of detergent-solubilized, apo-state NTS1 using robotic ligand binding assays. NTS1 is a target for the development of novel antipsychotics, and thus CHESS-stabilized receptors represent exciting tools for drug discovery.
Collapse
Affiliation(s)
- Daniel J Scott
- Department of Biochemistry, The University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; The Florey Institute of Neuroscience and Mental Health, and The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lutz Kummer
- Department of Biochemistry, The University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Pascal Egloff
- Department of Biochemistry, The University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Ross A D Bathgate
- The Florey Institute of Neuroscience and Mental Health, and The Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Plückthun
- Department of Biochemistry, The University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| |
Collapse
|
98
|
Cohen LS, Fracchiolla KE, Becker J, Naider F. Invited review GPCR structural characterization: Using fragments as building blocks to determine a complete structure. Biopolymers 2014; 102:223-43. [DOI: 10.1002/bip.22490] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 03/24/2014] [Accepted: 03/27/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Leah S. Cohen
- Department of Chemistry; The College of Staten Island, City University of New York (CUNY); Staten Island NY 10314
| | - Katrina E. Fracchiolla
- Department of Chemistry; The College of Staten Island, City University of New York (CUNY); Staten Island NY 10314
| | - Jeff Becker
- Department of Microbiology; University of Tennessee; Knoxville TN 37996
| | - Fred Naider
- Department of Chemistry; The College of Staten Island, City University of New York (CUNY); Staten Island NY 10314
- Department of Biochemistry; The Graduate Center; CUNY NY 10016-4309
| |
Collapse
|
99
|
van der Kant R, Vriend G. Alpha-bulges in G protein-coupled receptors. Int J Mol Sci 2014; 15:7841-64. [PMID: 24806342 PMCID: PMC4057707 DOI: 10.3390/ijms15057841] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 04/02/2014] [Accepted: 04/09/2014] [Indexed: 12/31/2022] Open
Abstract
Agonist binding is related to a series of motions in G protein-coupled receptors (GPCRs) that result in the separation of transmembrane helices III and VI at their cytosolic ends and subsequent G protein binding. A large number of smaller motions also seem to be associated with activation. Most helices in GPCRs are highly irregular and often contain kinks, with extensive literature already available about the role of prolines in kink formation and the precise function of these kinks. GPCR transmembrane helices also contain many α-bulges. In this article we aim to draw attention to the role of these α-bulges in ligand and G-protein binding, as well as their role in several aspects of the mobility associated with GPCR activation. This mobility includes regularization and translation of helix III in the extracellular direction, a rotation of the entire helix VI, an inward movement of the helices near the extracellular side, and a concerted motion of the cytosolic ends of the helices that makes their orientation appear more circular and that opens up space for the G protein to bind. In several cases, α-bulges either appear or disappear as part of the activation process.
Collapse
Affiliation(s)
- Rob van der Kant
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands.
| | - Gert Vriend
- Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein 26-28, 6525 GA Nijmegen, The Netherlands.
| |
Collapse
|
100
|
Xia J, Jin H, Liu Z, Zhang L, Wang XS. An unbiased method to build benchmarking sets for ligand-based virtual screening and its application to GPCRs. J Chem Inf Model 2014; 54:1433-50. [PMID: 24749745 PMCID: PMC4038372 DOI: 10.1021/ci500062f] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Benchmarking data
sets have become common in recent years for the
purpose of virtual screening, though the main focus had been placed
on the structure-based virtual screening (SBVS) approaches. Due to
the lack of crystal structures, there is great need for unbiased benchmarking
sets to evaluate various ligand-based virtual screening (LBVS) methods
for important drug targets such as G protein-coupled receptors (GPCRs).
To date these ready-to-apply data sets for LBVS are fairly limited,
and the direct usage of benchmarking sets designed for SBVS could
bring the biases to the evaluation of LBVS. Herein, we propose an
unbiased method to build benchmarking sets for LBVS and validate it
on a multitude of GPCRs targets. To be more specific, our methods
can (1) ensure chemical diversity of ligands, (2) maintain the physicochemical
similarity between ligands and decoys, (3) make the decoys dissimilar
in chemical topology to all ligands to avoid false negatives, and
(4) maximize spatial random distribution of ligands and decoys. We
evaluated the quality of our Unbiased Ligand Set (ULS) and Unbiased
Decoy Set (UDS) using three common LBVS approaches, with Leave-One-Out
(LOO) Cross-Validation (CV) and a metric of average AUC of the ROC
curves. Our method has greatly reduced the “artificial enrichment”
and “analogue bias” of a published GPCRs benchmarking
set, i.e., GPCR Ligand Library (GLL)/GPCR Decoy Database (GDD). In
addition, we addressed an important issue about the ratio of decoys
per ligand and found that for a range of 30 to 100 it does not affect
the quality of the benchmarking set, so we kept the original ratio
of 39 from the GLL/GDD.
Collapse
Affiliation(s)
- Jie Xia
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University , Beijing 100191, China
| | | | | | | | | |
Collapse
|