1
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Khorn PA, Luginina AP, Pospelov VA, Dashevsky DE, Khnykin AN, Moiseeva OV, Safronova NA, Belousov AS, Mishin AV, Borshchevsky VI. Rational Design of Drugs Targeting G-Protein-Coupled Receptors: A Structural Biology Perspective. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:747-764. [PMID: 38831510 DOI: 10.1134/s0006297924040138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 06/05/2024]
Abstract
G protein-coupled receptors (GPCRs) play a key role in the transduction of extracellular signals to cells and regulation of many biological processes, which makes these membrane proteins one of the most important targets for pharmacological agents. A significant increase in the number of resolved atomic structures of GPCRs has opened the possibility of developing pharmaceuticals targeting these receptors via structure-based drug design (SBDD). SBDD employs information on the structure of receptor-ligand complexes to search for selective ligands without the need for an extensive high-throughput experimental ligand screening and can significantly expand the chemical space for ligand search. In this review, we describe the process of deciphering GPCR structures using X-ray diffraction analysis and cryoelectron microscopy as an important stage in the rational design of drugs targeting this receptor class. Our main goal was to present modern developments and key features of experimental methods used in SBDD of GPCR-targeting agents to a wide range of specialists.
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Affiliation(s)
- Polina A Khorn
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Aleksandra P Luginina
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Vladimir A Pospelov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Andrey N Khnykin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Olga V Moiseeva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
- Scryabin Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Nadezhda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Anatolii S Belousov
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
| | - Valentin I Borshchevsky
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
- Joint Institute for Nuclear Research, Frank Laboratory of Neutron Physics, Dubna, Moscow Region, 141980, Russia
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2
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Hoare BL, Tippett DN, Kaur A, Cullum SA, Miljuš T, Koers EJ, Harwood CR, Dijon N, Holliday ND, Sykes DA, Veprintsev DB. ThermoBRET: A Ligand-Engagement Nanoscale Thermostability Assay Applied to GPCRs. Chembiochem 2024; 25:e202300459. [PMID: 37872746 DOI: 10.1002/cbic.202300459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Measurements of membrane protein thermostability reflect ligand binding. Current thermostability assays often require protein purification or rely on pre-existing radiolabelled or fluorescent ligands, limiting their application to established targets. Alternative methods, such as fluorescence-detection size exclusion chromatography thermal shift, detect protein aggregation but are not amenable to high-throughput screening. Here, we present a ThermoBRET method to quantify the relative thermostability of G protein coupled receptors (GPCRs), using cannabinoid receptors (CB1 and CB2 ) and the β2 -adrenoceptor (β2 AR) as model systems. ThermoBRET reports receptor unfolding, does not need labelled ligands and can be used with non-purified proteins. It uses Bioluminescence Resonance Energy Transfer (BRET) between Nanoluciferase (Nluc) and a thiol-reactive fluorescent dye that binds cysteines exposed by unfolding. We demonstrate that the melting point (Tm ) of Nluc-fused GPCRs can be determined in non-purified detergent solubilised membrane preparations or solubilised whole cells, revealing differences in thermostability for different solubilising conditions and in the presence of stabilising ligands. We extended the range of the assay by developing the thermostable tsNLuc by incorporating mutations from the fragments of split-Nluc (Tm of 87 °C versus 59 °C). ThermoBRET allows the determination of GPCR thermostability, which is useful for protein purification optimisation and drug discovery screening.
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Affiliation(s)
- Bradley L Hoare
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Current address, Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - David N Tippett
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Current address, Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Amandeep Kaur
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Sean A Cullum
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Tamara Miljuš
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Eline J Koers
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Clare R Harwood
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nicola Dijon
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nicholas D Holliday
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - David A Sykes
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Dmitry B Veprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
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3
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Ray M, Sayeed A, Ganshert M, Saha A. Direct Binding Methods to Measure Receptor-Ligand Interactions. J Phys Chem B 2024; 128:3-19. [PMID: 38134048 DOI: 10.1021/acs.jpcb.3c05041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
Abstract
G-protein-coupled receptors (GPCRs) contribute to numerous physiological processes via complex network mechanisms. While indirect signaling assays (Ca2+ mobilization, cAMP production, and GTPγS binding) have been useful in identifying and characterizing downstream signaling mechanisms of GPCRs, these methods lack measurements of direct binding affinities, kinetics, binding specificity, and selectivity that are important parameters in GPCR drug discovery. In comparison to existing direct methods that use radio- or fluorescent labels, label-free techniques can closely emulate the native interactions around binding partners. Surface plasmon resonance (SPR) is a label-free technique that utilizes the refractive index (RI) property and is applied widely in quantitative GPCR-ligand binding kinetics measurement including small molecules screening. However, purified GPCRs are further embedded in a synthetic lipid environment which is immobilized through different tags to the SPR sensor surface, resulting in a non-native environment. Here, we introduced a methodology that also uses the RI property to measure binding interactions in a label-free, immobilization-free arrangement. The free-solution technique is successfully applied in quantifying the interaction of bioactive lipids to cognate lipid GPCRs, which is not purified but rather present in near-native conditions, i.e., in milieu of other cytoplasmic lipids and proteins. To further consider the wide applicability of these free-solution approaches in biomolecular interaction research, additional applications on a variety of receptor-ligand pairs are imperative.
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Affiliation(s)
- Manisha Ray
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Aryana Sayeed
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Madeline Ganshert
- Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Road, Chicago, Illinois 60660, United States
| | - Arjun Saha
- Department of Chemistry and Biochemistry, University of Wisconsin, Milwaukee Chemistry Bldg, 144, 3210 N Cramer Street, Milwaukee, Wisconsin 53211, United States
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4
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Mattheisen JM, Limberakis C, Ruggeri RB, Dowling MS, Am Ende CW, Ceraudo E, Huber T, McClendon CL, Sakmar TP. Bioorthogonal Tethering Enhances Drug Fragment Affinity for G Protein-Coupled Receptors in Live Cells. J Am Chem Soc 2023; 145:11173-11184. [PMID: 37116188 DOI: 10.1021/jacs.3c00972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
G protein-coupled receptors (GPCRs) modulate diverse cellular signaling pathways and are important drug targets. Despite the availability of high-resolution structures, the discovery of allosteric modulators remains challenging due to the dynamic nature of GPCRs in native membranes. We developed a strategy to covalently tether drug fragments adjacent to allosteric sites in GPCRs to enhance their potency and enable fragment-based drug screening in cell-based systems. We employed genetic code expansion to site-specifically introduce noncanonical amino acids with reactive groups in C-C chemokine receptor 5 (CCR5) near an allosteric binding site for the drug maraviroc. We then used molecular dynamics simulations to design heterobifunctional maraviroc analogues consisting of a drug fragment connected by a flexible linker to a reactive moiety capable of undergoing a bioorthogonal coupling reaction. We synthesized a library of these analogues and employed the bioorthogonal inverse electron demand Diels-Alder reaction to couple the analogues to the engineered CCR5 in live cells, which were then assayed using cell-based signaling assays. Tetherable low-affinity maraviroc fragments displayed an increase in potency for CCR5 engineered with reactive unnatural amino acids that were adjacent to the maraviroc binding site. The strategy we describe to tether novel drug fragments to GPCRs should prove useful to probe allosteric or cryptic binding site functionality in fragment-based GPCR-targeted drug discovery.
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Affiliation(s)
- Jordan M Mattheisen
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
- Tri-Institutional PhD Program in Chemical Biology, New York, New York 10065, United States
| | - Chris Limberakis
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Roger B Ruggeri
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Matthew S Dowling
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Christopher W Am Ende
- Pfizer Worldwide Research, Development, and Medical, Groton, Connecticut 06340, United States
| | - Emilie Ceraudo
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
| | - Christopher L McClendon
- Pfizer Worldwide Research, Development, and Medical, Cambridge, Massachusetts 02139, United States
| | - Thomas P Sakmar
- Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065, United States
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5
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Walsh L, Erlanson DA, de Esch IJP, Jahnke W, Woodhead A, Wren E. Fragment-to-Lead Medicinal Chemistry Publications in 2021. J Med Chem 2023; 66:1137-1156. [PMID: 36622056 DOI: 10.1021/acs.jmedchem.2c01827] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
This Perspective is the seventh in an annual series that summarizes successful Fragment-to-Lead (F2L) case studies published in a given year. A tabulated summary of relevant articles published in 2021 is provided, and features such as target class, screening methods, and ligand efficiency are discussed, both for the 2021 examples and for the combined examples over the years 2015-2021. In addition, trends and new developments in the field are summarized. In particular, the use of structural information in fragment-based drug discovery is discussed.
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Affiliation(s)
- Louise Walsh
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Daniel A Erlanson
- Frontier Medicines, 151 Oyster Point Blvd., South San Francisco, California 94080, United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Andrew Woodhead
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
| | - Ella Wren
- Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, United Kingdom
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6
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Dmitrieva DA, Kotova TV, Safronova NA, Sadova AA, Dashevskii DE, Mishin AV. Protein Design Strategies for the Structural–Functional Studies of G Protein-Coupled Receptors. BIOCHEMISTRY (MOSCOW) 2023; 88:S192-S226. [PMID: 37069121 DOI: 10.1134/s0006297923140110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
G protein-coupled receptors (GPCRs) are an important family of membrane proteins responsible for many physiological functions in human body. High resolution GPCR structures are required to understand their molecular mechanisms and perform rational drug design, as GPCRs play a crucial role in a variety of diseases. That is difficult to obtain for the wild-type proteins because of their low stability. In this review, we discuss how this problem can be solved by using protein design strategies developed to obtain homogeneous stabilized GPCR samples for crystallization and cryoelectron microscopy.
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Affiliation(s)
- Daria A Dmitrieva
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Tatiana V Kotova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nadezda A Safronova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexandra A Sadova
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Dmitrii E Dashevskii
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Alexey V Mishin
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia.
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7
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Yao H, Cai H, Li D. Fluorescence-Detection Size-Exclusion Chromatography-Based Thermostability Assay for Membrane Proteins. Methods Mol Biol 2023; 2564:299-315. [PMID: 36107350 DOI: 10.1007/978-1-0716-2667-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Green fluorescent proteins (GFPs) have lightened up almost every aspect of biological research including protein sciences. In the field of membrane protein structural biology, GFPs have been used widely to monitor membrane protein localization, expression level, the purification process and yield, and the stability inside the cells and in the test tube. Of particular interest is the fluorescence-detector size-exclusion chromatography-based thermostability assay (FSEC-TS). By simple heating and FSEC, the generally applicable method allows rapid assessment of the thermostability of GFP-fused membrane proteins without purification. Here we describe the experimental details and some typical results for the FSEC-TS method.
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Affiliation(s)
| | | | - Dianfan Li
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.
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8
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Dragan P, Atzei A, Sanmukh SG, Latek D. Computational and experimental approaches to probe GPCR activation and signaling. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2022; 193:1-36. [PMID: 36357073 DOI: 10.1016/bs.pmbts.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
G protein-coupled receptors (GPCRs) regulate different physiological functions, e.g., sensation, growth, digestion, reproductivity, nervous and immune systems response, and many others. In eukaryotes, they are also responsible for intercellular communication in response to pathogens. The major primary messengers binding to these cell-surface receptors constitute small-molecule or peptide hormones and neurotransmitters, nucleotides, lipids as well as small proteins. The simplicity of the way how GPCR signaling can be regulated by their endogenous agonists prompted the usage of GPCRs as major drug targets in modern pharmacology. Drugs targeting GPCRs inhibit pathological processes at the very beginning. This enables to significantly reduce the occurrence of morphological changes caused by diseases. Until recently, X-ray crystallography was the method of the first choice to obtain high-resolution structural information about GPCRs. Following X-ray crystallography, cryo-EM gained attention in GPCR studies as a quick and low-cost alternative. FRET microscopy is also widely used for GPCRs in the analysis of protein-protein interactions (PPIs) in intact cells as well as for screening purposes. Regarding computational methods, molecular dynamics (MD) for many years has proven its usefulness in studying the GPCR activation. MODELLER and Rosetta were widely used to generate preliminary homology models of GPCRs for MD simulation systems. Apart from the conventional all-atom approach with explicitly defined solvent, also other techniques have been applied to GPCRs, e.g., MARTINI or hybrid methods involving the coarse-grained representation, less demanding regarding computational resources, and thus offering much larger simulation timescales.
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Affiliation(s)
- Paulina Dragan
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland
| | | | | | - Dorota Latek
- Faculty of Chemistry, University of Warsaw, Warsaw, Poland.
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9
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Shepherd C, Robinson S, Berizzi A, Thompson LEJ, Bird L, Culurgioni S, Varzandeh S, Rawlins PB, Olsen RHJ, Navratilova IH. Surface Plasmon Resonance Screening to Identify Active and Selective Adenosine Receptor Binding Fragments. ACS Med Chem Lett 2022; 13:1172-1181. [DOI: 10.1021/acsmedchemlett.2c00099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Claire Shepherd
- University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
- Kinetic Discovery Ltd., The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Sean Robinson
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Alice Berizzi
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Laura E. J. Thompson
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Louise Bird
- Kinetic Discovery Ltd., The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Simone Culurgioni
- Kinetic Discovery Ltd., The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Simon Varzandeh
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Philip B. Rawlins
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, United Kingdom
| | - Reid H. J. Olsen
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
| | - Iva Hopkins Navratilova
- University of Dundee, Dow Street, Dundee DD1 5EH, United Kingdom
- Kinetic Discovery Ltd., The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
- Exscientia plc, The Schrödinger
Building, Heatley Road, The Oxford Science Park, Oxford OX4 4GE, United Kingdom
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10
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Claff T, Klapschinski TA, Tiruttani Subhramanyam UK, Vaaßen VJ, Schlegel JG, Vielmuth C, Voß JH, Labahn J, Müller CE. Single Stabilizing Point Mutation Enables High-Resolution Co-Crystal Structures of the Adenosine A 2A Receptor with Preladenant Conjugates. Angew Chem Int Ed Engl 2022; 61:e202115545. [PMID: 35174942 PMCID: PMC9310709 DOI: 10.1002/anie.202115545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Indexed: 01/08/2023]
Abstract
The G protein-coupled adenosine A2A receptor (A2A AR) is an important new (potential) drug target in immuno-oncology, and for neurodegenerative diseases. Preladenant and its derivatives belong to the most potent A2A AR antagonists displaying exceptional selectivity. While crystal structures of the human A2A AR have been solved, mostly using the A2A -StaR2 protein that bears 9 point mutations, co-crystallization with Preladenant derivatives has so far been elusive. We developed a new A2A AR construct harboring a single point mutation (S913.39 K) which renders it extremely thermostable. This allowed the co-crystallization of two novel Preladenant derivatives, the polyethylene glycol-conjugated (PEGylated) PSB-2113, and the fluorophore-labeled PSB-2115. The obtained crystal structures (2.25 Å and 2.6 Å resolution) provide explanations for the high potency and selectivity of Preladenant derivatives. They represent the first crystal structures of a GPCR in complex with PEG- and fluorophore-conjugated ligands. The applied strategy is predicted to be applicable to further class A GPCRs.
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Affiliation(s)
- Tobias Claff
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Tim A Klapschinski
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Udaya K Tiruttani Subhramanyam
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607, Hamburg, Germany.,Research Centre Jülich, Institute of Complex Systems (IBI-7), Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Victoria J Vaaßen
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Jonathan G Schlegel
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Christin Vielmuth
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Jan H Voß
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
| | - Jörg Labahn
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607, Hamburg, Germany.,Research Centre Jülich, Institute of Complex Systems (IBI-7), Wilhelm-Johnen-Straße, 52425, Jülich, Germany
| | - Christa E Müller
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, 53121, Bonn, Germany
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11
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Yeast-based directed-evolution for high-throughput structural stabilization of G protein-coupled receptors (GPCRs). Sci Rep 2022; 12:8657. [PMID: 35606532 PMCID: PMC9126886 DOI: 10.1038/s41598-022-12731-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/10/2022] [Indexed: 11/08/2022] Open
Abstract
The immense potential of G protein-coupled receptors (GPCRs) as targets for drug discovery is not fully realized due to the enormous difficulties associated with structure elucidation of these profoundly unstable membrane proteins. The existing methods of GPCR stability-engineering are cumbersome and low-throughput; in addition, the scope of GPCRs that could benefit from these techniques is limited. Here, we present a yeast-based screening platform for a single-step isolation of GRCR variants stable in the presence of short-chain detergents, a feature essential for their successful crystallization using vapor diffusion method. The yeast detergent-resistant cell wall presents a unique opportunity for compartmentalization, to physically link the receptor's phenotype to its encoding DNA, and thus enable discovery of stable GPCR variants with unprecedent efficiency. The scope of mutations identified by the method reveals a surprising amenability of the GPCR scaffold to stabilization, and suggests an intriguing possibility of amending the stability properties of GPCR by varying the structural status of the C-terminus.
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12
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Claff T, Klapschinski TA, Tiruttani Subhramanyam UK, Vaaßen VJ, Schlegel JG, Vielmuth C, Voß JH, Labahn J, Müller CE. Eine einzige stabilisierende Punktmutation ermöglicht hochaufgelöste Co‐Kristallstrukturen des Adenosin‐A
2A
‐Rezeptors mit Preladenant‐Konjugaten. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202115545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tobias Claff
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Tim A. Klapschinski
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Udaya K. Tiruttani Subhramanyam
- Centre for Structural Systems Biology (CSSB) Notkestraße 85 22607 Hamburg Germany
- Research Centre Jülich Institute of Complex Systems (IBI-7) Wilhelm-Johnen-Straße 52425 Jülich Deutschland
| | - Victoria J. Vaaßen
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Jonathan G. Schlegel
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Christin Vielmuth
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Jan H. Voß
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Jörg Labahn
- Centre for Structural Systems Biology (CSSB) Notkestraße 85 22607 Hamburg Germany
- Research Centre Jülich Institute of Complex Systems (IBI-7) Wilhelm-Johnen-Straße 52425 Jülich Deutschland
| | - Christa E. Müller
- Pharmaceutical Institute Pharmaceutical & Medicinal Chemistry University of Bonn An der Immenburg 4 53121 Bonn Deutschland
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13
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Aertgeerts K, Ho TT, Yan YG. Optimization of Recombinant GPCR Proteins for Biophysical and Structural Studies Using Virus-like Particles. Methods Mol Biol 2022; 2507:327-336. [PMID: 35773590 DOI: 10.1007/978-1-0716-2368-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Overexpression of biologically functional GPCRs and homogeneous purified protein solutions are required to enable structural studies and protein-based biophysical assay development. Iterative and time-consuming optimization cycles of protein engineering, expression, and purification are often needed to achieve the desired protein quantity and quality. Here, we describe the reconstitution of GPCRs in virus-like particles (VLPs) and their use in biophysical assays to characterize protein yield, stability, and small molecule ligand binding. This approach prevents the need for time-consuming detergent solubilization and protein purification during recombinant GPCR protein optimization.
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Affiliation(s)
| | - Thao T Ho
- Biology Department, Vertex Pharmaceuticals, San Diego, CA, USA
| | - Yingzhou G Yan
- Neuroscience TRC, Bristol Myers Squibb, San Diego, CA, USA
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14
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Jespers W, Heitman LH, IJzerman AP, Sotelo E, van Westen GJP, Åqvist J, Gutiérrez-de-Terán H. Deciphering conformational selectivity in the A2A adenosine G protein-coupled receptor by free energy simulations. PLoS Comput Biol 2021; 17:e1009152. [PMID: 34818333 PMCID: PMC8654218 DOI: 10.1371/journal.pcbi.1009152] [Citation(s) in RCA: 4] [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: 05/19/2021] [Revised: 12/08/2021] [Accepted: 11/11/2021] [Indexed: 12/25/2022] Open
Abstract
Transmembranal G Protein-Coupled Receptors (GPCRs) transduce extracellular chemical signals to the cell, via conformational change from a resting (inactive) to an active (canonically bound to a G-protein) conformation. Receptor activation is normally modulated by extracellular ligand binding, but mutations in the receptor can also shift this equilibrium by stabilizing different conformational states. In this work, we built structure-energetic relationships of receptor activation based on original thermodynamic cycles that represent the conformational equilibrium of the prototypical A2A adenosine receptor (AR). These cycles were solved with efficient free energy perturbation (FEP) protocols, allowing to distinguish the pharmacological profile of different series of A2AAR agonists with different efficacies. The modulatory effects of point mutations on the basal activity of the receptor or on ligand efficacies could also be detected. This methodology can guide GPCR ligand design with tailored pharmacological properties, or allow the identification of mutations that modulate receptor activation with potential clinical implications. The design of new ligands as chemical modulators of G protein-coupled receptors (GPCRs) has benefited considerably during the last years of advances in both the structural and computational biology disciplines. Within the last area, the use of free energy calculation methods has arisen as a computational tool to predict ligand affinities to explain structure-affinity relationships and guide lead optimization campaigns. However, our comprehension of the structural determinants of ligands with different pharmacological profile is scarce, and knowledge of the chemical modifications associated with an agonistic or antagonistic profile would be extremely valuable. We herein report an original implementation of the thermodynamic cycles associated with free energy perturbation (FEP) simulations, to mimic the conformational equilibrium between active and inactive GPCRs, and establish a framework to describe pharmacological profiles as a function of the ligands selectivity for a given receptor conformation. The advantage of this method resides into its simplicity of use, and the only consideration of active and inactive conformations of the receptor, with no simulation of the transitions between them. This model can accurately predict the pharmacological profile of series of full and partial agonists as opposed to antagonists of the A2A adenosine receptor, and moreover, how certain mutations associated with modulation of basal activity can influence this pharmacological profiles, which enables our understanding of such clinically relevant mutations.
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Affiliation(s)
- Willem Jespers
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center (BMC), Uppsala, Sweden
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
- * E-mail: (WJ); (HGT)
| | - Laura H. Heitman
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
- Oncode Institute, Leiden, Leiden
| | - Adriaan P. IJzerman
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Eddy Sotelo
- Centro Singular de Investigación en Química Biolóxica y Materiais Moleculares (CIQUS), Santiago de Compostela, Spain
- Departamento de Química Orgánica, Facultade de Farmacia, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Gerard J. P. van Westen
- Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden, The Netherlands
| | - Johan Åqvist
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center (BMC), Uppsala, Sweden
| | - Hugo Gutiérrez-de-Terán
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center (BMC), Uppsala, Sweden
- Science for Life Laboratories, BMC, Uppsala, Sweden
- * E-mail: (WJ); (HGT)
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15
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Brown AJH, Bradley SJ, Marshall FH, Brown GA, Bennett KA, Brown J, Cansfield JE, Cross DM, de Graaf C, Hudson BD, Dwomoh L, Dias JM, Errey JC, Hurrell E, Liptrot J, Mattedi G, Molloy C, Nathan PJ, Okrasa K, Osborne G, Patel JC, Pickworth M, Robertson N, Shahabi S, Bundgaard C, Phillips K, Broad LM, Goonawardena AV, Morairty SR, Browning M, Perini F, Dawson GR, Deakin JFW, Smith RT, Sexton PM, Warneck J, Vinson M, Tasker T, Tehan BG, Teobald B, Christopoulos A, Langmead CJ, Jazayeri A, Cooke RM, Rucktooa P, Congreve MS, Weir M, Tobin AB. From structure to clinic: Design of a muscarinic M1 receptor agonist with potential to treatment of Alzheimer's disease. Cell 2021; 184:5886-5901.e22. [PMID: 34822784 DOI: 10.1016/j.cell.2021.11.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 04/29/2021] [Accepted: 11/01/2021] [Indexed: 12/31/2022]
Abstract
Current therapies for Alzheimer's disease seek to correct for defective cholinergic transmission by preventing the breakdown of acetylcholine through inhibition of acetylcholinesterase, these however have limited clinical efficacy. An alternative approach is to directly activate cholinergic receptors responsible for learning and memory. The M1-muscarinic acetylcholine (M1) receptor is the target of choice but has been hampered by adverse effects. Here we aimed to design the drug properties needed for a well-tolerated M1-agonist with the potential to alleviate cognitive loss by taking a stepwise translational approach from atomic structure, cell/tissue-based assays, evaluation in preclinical species, clinical safety testing, and finally establishing activity in memory centers in humans. Through this approach, we rationally designed the optimal properties, including selectivity and partial agonism, into HTL9936-a potential candidate for the treatment of memory loss in Alzheimer's disease. More broadly, this demonstrates a strategy for targeting difficult GPCR targets from structure to clinic.
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Affiliation(s)
- Alastair J H Brown
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Sophie J Bradley
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK; The Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Fiona H Marshall
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Giles A Brown
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Kirstie A Bennett
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Jason Brown
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Julie E Cansfield
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - David M Cross
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK; Cross Pharma Consulting Ltd, 20-22 Wenlock Road, London, N17GU, UK
| | - Chris de Graaf
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Brian D Hudson
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Louis Dwomoh
- The Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - João M Dias
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - James C Errey
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Edward Hurrell
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Jan Liptrot
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Giulio Mattedi
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Colin Molloy
- The Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Pradeep J Nathan
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK; Brain Mapping Unit, University of Cambridge, Department of Psychiatry, Herchel Smith Building, Cambridge, CB20SZ, UK
| | - Krzysztof Okrasa
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Greg Osborne
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Jayesh C Patel
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Mark Pickworth
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Nathan Robertson
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Shahram Shahabi
- Eli Lilly & Co, Neuroscience Discovery, Erl Wood Manor, Windlesham, Surrey, GU20 6PH, UK
| | - Christoffer Bundgaard
- Eli Lilly & Co, Neuroscience Discovery, Erl Wood Manor, Windlesham, Surrey, GU20 6PH, UK; H. Lundbeck A/S, Neuroscience Research, Ottiliavej 9, 2500 Valby, Copenhagen, Denmark
| | - Keith Phillips
- Eli Lilly & Co, Neuroscience Discovery, Erl Wood Manor, Windlesham, Surrey, GU20 6PH, UK
| | - Lisa M Broad
- Eli Lilly & Co, Neuroscience Discovery, Erl Wood Manor, Windlesham, Surrey, GU20 6PH, UK
| | - Anushka V Goonawardena
- Center for Neuroscience, Biosciences Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
| | - Stephen R Morairty
- Center for Neuroscience, Biosciences Division, SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA
| | - Michael Browning
- University Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX12JD, UK; P1vital, Manor house, Howbery Buisness Park, Wallingford, OX108BA, UK
| | - Francesca Perini
- Centre for Cognitive Neuroscience - Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Gerard R Dawson
- University Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, OX12JD, UK
| | - John F W Deakin
- Neuroscience and Psychiatry Unit, University of Manchester, Manchester, M139PT UK
| | - Robert T Smith
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville 3052, Victoria, Australia; ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville 3052, Victoria, Australia
| | - Julie Warneck
- Protogenia Consulting Ltd, PO-Box 289, Ely, CB79DR, UK
| | - Mary Vinson
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Tim Tasker
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Benjamin G Tehan
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Barry Teobald
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville 3052, Victoria, Australia
| | - Christopher J Langmead
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK; Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville 3052, Victoria, Australia
| | - Ali Jazayeri
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Robert M Cooke
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Prakash Rucktooa
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Miles S Congreve
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK
| | - Malcolm Weir
- Sosei-Heptares, Steinmetz Building, Granta Park, Cambridge, CB21 6DG, UK.
| | - Andrew B Tobin
- The Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
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16
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Mannes M, Martin C, Triest S, Pia Dimmito M, Mollica A, Laeremans T, Menet CJ, Ballet S. Development of Generic G Protein Peptidomimetics Able to Stabilize Active State G s Protein-Coupled Receptors for Application in Drug Discovery. Angew Chem Int Ed Engl 2021; 60:10247-10254. [PMID: 33596327 DOI: 10.1002/anie.202100180] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/05/2021] [Indexed: 11/06/2022]
Abstract
G protein-coupled receptors (GPCRs) represent an important group of membrane proteins that play a central role in modern medicine. Unfortunately, conformational promiscuity hampers full therapeutic exploitation of GPCRs, since the largest population of the receptor will adopt a basal conformation, which subsequently challenges screens for agonist drug discovery programs. Herein, we describe a set of peptidomimetics able to mimic the ability of G proteins in stabilizing the active state of the β2 adrenergic receptor (β2 AR) and the dopamine 1 receptor (D1R). During fragment-based screening efforts, these (un)constrained peptide analogues of the α5 helix in Gs proteins, were able to identify agonism pre-imprinted fragments for the examined GPCRs, and as such, they behave as a generic tool, enabling an engagement in agonist earmarked discovery programs.
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Affiliation(s)
- Morgane Mannes
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Charlotte Martin
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Sarah Triest
- Confo Therapeutics N.V., Technologiepark-Zwijnaarde 94, 9052, Ghent, Belgium
| | - Marilisa Pia Dimmito
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini 31, 66100, Chieti, Italy
| | - Adriano Mollica
- Department of Pharmacy, University "G. d'Annunzio" of Chieti-Pescara, Via dei Vestini 31, 66100, Chieti, Italy
| | - Toon Laeremans
- Confo Therapeutics N.V., Technologiepark-Zwijnaarde 94, 9052, Ghent, Belgium
| | - Christel J Menet
- Confo Therapeutics N.V., Technologiepark-Zwijnaarde 94, 9052, Ghent, Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
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17
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Mannes M, Martin C, Triest S, Pia Dimmito M, Mollica A, Laeremans T, Menet CJ, Ballet S. Development of Generic G Protein Peptidomimetics Able to Stabilize Active State G
s
Protein‐Coupled Receptors for Application in Drug Discovery. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202100180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Morgane Mannes
- Research Group of Organic Chemistry Vrije Universiteit Brussel Pleinlaan 2 1050 Brussels Belgium
| | - Charlotte Martin
- Research Group of Organic Chemistry Vrije Universiteit Brussel Pleinlaan 2 1050 Brussels Belgium
| | - Sarah Triest
- Confo Therapeutics N.V. Technologiepark-Zwijnaarde 94 9052 Ghent Belgium
| | - Marilisa Pia Dimmito
- Research Group of Organic Chemistry Vrije Universiteit Brussel Pleinlaan 2 1050 Brussels Belgium
- Department of Pharmacy University “G. d'Annunzio” of Chieti-Pescara Via dei Vestini 31 66100 Chieti Italy
| | - Adriano Mollica
- Department of Pharmacy University “G. d'Annunzio” of Chieti-Pescara Via dei Vestini 31 66100 Chieti Italy
| | - Toon Laeremans
- Confo Therapeutics N.V. Technologiepark-Zwijnaarde 94 9052 Ghent Belgium
| | - Christel J. Menet
- Confo Therapeutics N.V. Technologiepark-Zwijnaarde 94 9052 Ghent Belgium
| | - Steven Ballet
- Research Group of Organic Chemistry Vrije Universiteit Brussel Pleinlaan 2 1050 Brussels Belgium
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18
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Bennett KA, Sergeev E, MacSweeney CP, Bakker G, Cooper AE. Understanding Exposure-Receptor Occupancy Relationships for Metabotropic Glutamate Receptor 5 Negative Allosteric Modulators across a Range of Preclinical and Clinical Studies. J Pharmacol Exp Ther 2021; 377:157-168. [PMID: 33541889 DOI: 10.1124/jpet.120.000371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/26/2021] [Indexed: 01/17/2023] Open
Abstract
The metabotropic glutamate receptor 5 (mGlu5) is a recognized central nervous system therapeutic target for which several negative allosteric modulator (NAM) drug candidates have or are continuing to be investigated for various disease indications in clinical development. Direct measurement of target receptor occupancy (RO) is extremely useful to help design and interpret efficacy and safety in nonclinical and clinical studies. In the mGlu5 field, this has been successfully achieved by monitoring displacement of radiolabeled ligands, specifically binding to the mGlu5 receptor, in the presence of an mGlu5 NAM using in vivo and ex vivo binding in rodents and positron emission tomography imaging in cynomolgus monkeys and humans. The aim of this study was to measure the RO of the mGlu5 NAM HTL0014242 in rodents and cynomolgus monkeys and to compare its plasma and brain exposure-RO relationships with those of clinically tested mGlu5 NAMs dipraglurant, mavoglurant, and basimglurant. Potential sources of variability that may contribute to these relationships were explored. Distinct plasma exposure-response relationships were found for each mGlu5 NAM, with >100-fold difference in plasma exposure for a given level of RO. However, a unified exposure-response relationship was observed when both unbound brain concentration and mGlu5 affinity were considered. This relationship showed <10-fold overall difference, was fitted with a Hill slope that was not significantly different from 1, and appeared consistent with a simple Emax model. This is the first time this type of comparison has been conducted, demonstrating a unified brain exposure-RO relationship across several species and mGlu5 NAMs with diverse properties. SIGNIFICANCE STATEMENT: Despite the long history of mGlu5 as a therapeutic target and progression of multiple compounds to the clinic, no formal comparison of exposure-receptor occupancy relationships has been conducted. The data from this study indicate for the first time that a consistent, unified relationship can be observed between exposure and mGlu5 receptor occupancy when unbound brain concentration and receptor affinity are taken into account across a range of species for a diverse set of mGlu5 negative allosteric modulators, including a new drug candidate, HTL0014242.
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Affiliation(s)
| | | | | | - Geor Bakker
- Sosei Heptares, Cambridge, CB21 6DG, United Kingdom
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19
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Cai H, Yao H, Li T, Hutter CAJ, Li Y, Tang Y, Seeger MA, Li D. An improved fluorescent tag and its nanobodies for membrane protein expression, stability assay, and purification. Commun Biol 2020; 3:753. [PMID: 33303987 PMCID: PMC7729955 DOI: 10.1038/s42003-020-01478-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 11/12/2020] [Indexed: 01/08/2023] Open
Abstract
Green fluorescent proteins (GFPs) are widely used to monitor membrane protein expression, purification, and stability. An ideal reporter should be stable itself and provide high sensitivity and yield. Here, we demonstrate that a coral (Galaxea fascicularis) thermostable GFP (TGP) is by such reasons an improved tag compared to the conventional jellyfish GFPs. TGP faithfully reports membrane protein stability at temperatures near 90 °C (20-min heating). By contrast, the limit for the two popular GFPs is 64 °C and 74 °C. Replacing GFPs with TGP increases yield for all four test membrane proteins in four expression systems. To establish TGP as an affinity tag for membrane protein purification, several high-affinity synthetic nanobodies (sybodies), including a non-competing pair, are generated, and the crystal structure of one complex is solved. Given these advantages, we anticipate that TGP becomes a widely used tool for membrane protein structural studies.
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Affiliation(s)
- Hongmin Cai
- University of Chinese Academy of Sciences, National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Hebang Yao
- University of Chinese Academy of Sciences, National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Tingting Li
- University of Chinese Academy of Sciences, National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Cedric A J Hutter
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Yanfang Li
- University of Chinese Academy of Sciences, National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Yannan Tang
- University of Chinese Academy of Sciences, National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China
| | - Markus A Seeger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Dianfan Li
- University of Chinese Academy of Sciences, National Center for Protein Science Shanghai, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, 200031, Shanghai, China.
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20
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Wan S, Potterton A, Husseini FS, Wright DW, Heifetz A, Malawski M, Townsend-Nicholson A, Coveney PV. Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors. Interface Focus 2020; 10:20190128. [PMID: 33178414 PMCID: PMC7653344 DOI: 10.1098/rsfs.2019.0128] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/06/2020] [Indexed: 12/13/2022] Open
Abstract
We apply the hit-to-lead ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and lead-optimization TIES (thermodynamic integration with enhanced sampling) methods to compute the binding free energies of a series of ligands at the A1 and A2A adenosine receptors, members of a subclass of the GPCR (G protein-coupled receptor) superfamily. Our predicted binding free energies, calculated using ESMACS, show a good correlation with previously reported experimental values of the ligands studied. Relative binding free energies, calculated using TIES, accurately predict experimentally determined values within a mean absolute error of approximately 1 kcal mol-1. Our methodology may be applied widely within the GPCR superfamily and to other small molecule-receptor protein systems.
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Affiliation(s)
- Shunzhou Wan
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Andrew Potterton
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Fouad S. Husseini
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - David W. Wright
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
| | - Alexander Heifetz
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon OX14 4RZ, UK
| | - Maciej Malawski
- ACK Cyfronet, AGH University of Science and Technology, Nawojki 11, 30-950, Kraków, Poland
| | - Andrea Townsend-Nicholson
- Institute of Structural and Molecular Biology, Research Department of Structural and Molecular Biology, Division of Biosciences, University College London, London WC1E 6BT, UK
| | - Peter V. Coveney
- Centre for Computational Science, Department of Chemistry, University College London, London WC1H 0AJ, UK
- Computational Science Laboratory, Institute for Informatics, Faculty of Science, University of Amsterdam, 1098XH Amsterdam, The Netherlands
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21
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Borodovsky A, Barbon CM, Wang Y, Ye M, Prickett L, Chandra D, Shaw J, Deng N, Sachsenmeier K, Clarke JD, Linghu B, Brown GA, Brown J, Congreve M, Cheng RK, Dore AS, Hurrell E, Shao W, Woessner R, Reimer C, Drew L, Fawell S, Schuller AG, Mele DA. Small molecule AZD4635 inhibitor of A 2AR signaling rescues immune cell function including CD103 + dendritic cells enhancing anti-tumor immunity. J Immunother Cancer 2020; 8:jitc-2019-000417. [PMID: 32727810 PMCID: PMC7394305 DOI: 10.1136/jitc-2019-000417] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2020] [Indexed: 02/04/2023] Open
Abstract
Accumulation of extracellular adenosine within the microenvironment is a strategy exploited by tumors to escape detection by the immune system. Adenosine signaling through the adenosine 2A receptor (A2AR) on immune cells elicits a range of immunosuppressive effects which promote tumor growth and limit the efficacy of immune checkpoint inhibitors. Preclinical data with A2AR inhibitors have demonstrated tumor regressions in mouse models by rescuing T cell function; however, the mechanism and role on other immune cells has not been fully elucidated.
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Affiliation(s)
| | | | - Yanjun Wang
- Bioscience, AstraZeneca R&D Boston, Waltham, Massachusetts, USA
| | - Minwei Ye
- Bioscience, AstraZeneca R&D Boston, Waltham, Massachusetts, USA
| | - Laura Prickett
- Bioscience, AstraZeneca R&D Boston, Waltham, Massachusetts, USA
| | - Dinesh Chandra
- Bioscience, AstraZeneca R&D Boston, Waltham, Massachusetts, USA
| | - Joseph Shaw
- Discovery Sciences, AstraZeneca PLC, Cambridge, Cambridgeshire, UK
| | - Nanhua Deng
- Bioscience, AstraZeneca R&D Boston, Waltham, Massachusetts, USA
| | - Kris Sachsenmeier
- Translational Medicine, AstraZeneca R&D Boston, Waltham, Massachusetts, USA
| | - James D Clarke
- Drug Metabolism and Pharamcokinetics, AstraZeneca, Cambridge, Cambridgeshire, UK
| | - Bolan Linghu
- Translational Medicine, AstraZeneca R&D Boston, Waltham, Massachusetts, USA
| | - Giles A Brown
- Discovery, Omass Technologies Ltd, Oxford, United Kingdom
| | - James Brown
- Heptares Therapeutics, Welwyn Garden City, California, USA
| | - Miles Congreve
- Heptares Therapeutics, Welwyn Garden City, California, USA
| | | | - Andrew S Dore
- Heptares Therapeutics, Welwyn Garden City, California, USA
| | - Edward Hurrell
- Heptares Therapeutics, Welwyn Garden City, California, USA
| | - Wenlin Shao
- Oncology, AstraZeneca R&D Boston, Waltham, Massachusetts, USA
| | - Richard Woessner
- Pharmacology, Blueprint Medicines, Cambridge, Massachusetts, USA
| | - Corinne Reimer
- Bioscience, AstraZeneca R&D Boston, Waltham, Massachusetts, USA
| | - Lisa Drew
- Bioscience, AstraZeneca R&D Boston, Waltham, Massachusetts, USA
| | - Stephen Fawell
- Bioscience, AstraZeneca R&D Boston, Waltham, Massachusetts, USA
| | | | - Deanna A Mele
- Bioscience, AstraZeneca R&D Boston, Waltham, Massachusetts, USA
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22
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The discovery of a new antibody for BRIL-fused GPCR structure determination. Sci Rep 2020; 10:11669. [PMID: 32669569 PMCID: PMC7363855 DOI: 10.1038/s41598-020-68355-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 06/21/2020] [Indexed: 12/17/2022] Open
Abstract
G-protein-coupled receptors (GPCRs)—the largest family of cell-surface membrane proteins—mediate the intracellular signal transduction of many external ligands. Thus, GPCRs have become important drug targets. X-ray crystal structures of GPCRs are very useful for structure-based drug design (SBDD). Herein, we produced a new antibody (SRP2070) targeting the thermostabilised apocytochrome b562 from Escherichia coli M7W/H102I/R106L (BRIL). We found that a fragment of this antibody (SRP2070Fab) facilitated the crystallisation of the BRIL-tagged, ligand bound GPCRs, 5HT1B and AT2R. Furthermore, the electron densities of the ligands were resolved, suggesting that SPR2070Fab is versatile and adaptable for GPCR SBDD. We anticipate that this new tool will significantly accelerate structure determination of other GPCRs and the design of small molecular drugs targeting them.
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23
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Errey JC, Fiez-Vandal C. Production of membrane proteins in industry: The example of GPCRs. Protein Expr Purif 2020; 169:105569. [DOI: 10.1016/j.pep.2020.105569] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 01/07/2020] [Accepted: 01/12/2020] [Indexed: 01/08/2023]
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24
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Evaluation of chemical cross-linkers for in-depth structural analysis of G protein-coupled receptors through cross-linking mass spectrometry. Anal Chim Acta 2020; 1102:53-62. [DOI: 10.1016/j.aca.2019.12.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/12/2019] [Accepted: 12/15/2019] [Indexed: 01/05/2023]
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25
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Rappas M, Ali AAE, Bennett KA, Brown JD, Bucknell SJ, Congreve M, Cooke RM, Cseke G, de Graaf C, Doré AS, Errey JC, Jazayeri A, Marshall FH, Mason JS, Mould R, Patel JC, Tehan BG, Weir M, Christopher JA. Comparison of Orexin 1 and Orexin 2 Ligand Binding Modes Using X-ray Crystallography and Computational Analysis. J Med Chem 2020; 63:1528-1543. [PMID: 31860301 PMCID: PMC7050010 DOI: 10.1021/acs.jmedchem.9b01787] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Indexed: 12/20/2022]
Abstract
The orexin system, which consists of the two G protein-coupled receptors OX1 and OX2, activated by the neuropeptides OX-A and OX-B, is firmly established as a key regulator of behavioral arousal, sleep, and wakefulness and has been an area of intense research effort over the past two decades. X-ray structures of the receptors in complex with 10 new antagonist ligands from diverse chemotypes are presented, which complement the existing structural information for the system and highlight the critical importance of lipophilic hotspots and water molecules for these peptidergic GPCR targets. Learnings from the structural information regarding the utility of pharmacophore models and how selectivity between OX1 and OX2 can be achieved are discussed.
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Affiliation(s)
- Mathieu Rappas
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, U.K.
| | - Ammar A. E. Ali
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, U.K.
| | - Kirstie A. Bennett
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, U.K.
| | - Jason D. Brown
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, U.K.
| | - Sarah J. Bucknell
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, U.K.
| | - Miles Congreve
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, U.K.
| | - Robert M. Cooke
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, U.K.
| | - Gabriella Cseke
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, U.K.
| | - Chris de Graaf
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, U.K.
| | - Andrew S. Doré
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, U.K.
| | | | | | | | - Jonathan S. Mason
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, U.K.
| | | | - Jayesh C. Patel
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, U.K.
| | | | - Malcolm Weir
- Sosei Heptares, Steinmetz Building, Granta Park, Cambridge CB21 6DG, U.K.
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26
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García-Nafría J, Tate CG. Cryo-Electron Microscopy: Moving Beyond X-Ray Crystal Structures for Drug Receptors and Drug Development. Annu Rev Pharmacol Toxicol 2019; 60:51-71. [PMID: 31348870 DOI: 10.1146/annurev-pharmtox-010919-023545] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Electron cryo-microscopy (cryo-EM) has revolutionized structure determination of membrane proteins and holds great potential for structure-based drug discovery. Here we discuss the potential of cryo-EM in the rational design of therapeutics for membrane proteins compared to X-ray crystallography. We also detail recent progress in the field of drug receptors, focusing on cryo-EM of two protein families with established therapeutic value, the γ-aminobutyric acid A receptors (GABAARs) and G protein-coupled receptors (GPCRs). GABAARs are pentameric ion channels, and cryo-EM structures of physiological heteromeric receptors in a lipid environment have uncovered the molecular basis of receptor modulation by drugs such as diazepam. The structures of ten GPCR-G protein complexes from three different classes of GPCRs have now been determined by cryo-EM. These structures give detailed insights into molecular interactions with drugs, GPCR-G protein selectivity, how accessory membrane proteins alter receptor-ligand pharmacology, and the mechanism by which HIV uses GPCRs to enter host cells.
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Affiliation(s)
- Javier García-Nafría
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom; .,Current affiliation: Institute for Biocomputation and Physics of Complex Systems (BIFI) and Laboratorio de Microscopias Avanzadas, University of Zaragoza, 50018 Zaragoza, Spain;
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27
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Mahmod Al-Qattan MN, Mordi MN. Molecular Basis of Modulating Adenosine Receptors Activities. Curr Pharm Des 2019; 25:817-831. [DOI: 10.2174/1381612825666190304122624] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 02/26/2019] [Indexed: 01/04/2023]
Abstract
Modulating cellular processes through extracellular chemical stimuli is medicinally an attractive approach to control disease conditions. GPCRs are the most important group of transmembranal receptors that produce different patterns of activations using intracellular mediators (such as G-proteins and Beta-arrestins). Adenosine receptors (ARs) belong to GPCR class and are divided into A1AR, A2AAR, A2BAR and A3AR. ARs control different physiological activities thus considered valuable target to control neural, heart, inflammatory and other metabolic disorders. Targeting ARs using small molecules essentially works by binding orthosteric and/or allosteric sites of the receptors. Although targeting orthosteric site is considered typical to modulate receptor activity, allosteric sites provide better subtype selectivity, saturable modulation of activity and variable activation patterns. Each receptor exists in dynamical equilibrium between conformational ensembles. The equilibrium is affected by receptor interaction with other molecules. Changing the population of conformational ensembles of the receptor is the method by which orthosteric, allosteric and other cellular components control receptor signaling. Herein, the interactions of ARs with orthosteric, allosteric ligands as well as intracellular mediators are described. A quinary interaction model for the receptor is proposed and energy wells for major conformational ensembles are retrieved.
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Affiliation(s)
| | - Mohd Nizam Mordi
- Centre For Drug Research, Universiti Sains Malaysia, 11800 Gelugor, Penang, Malaysia
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28
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Therapeutic Monoclonal Antibodies to Complex Membrane Protein Targets: Antigen Generation and Antibody Discovery Strategies. BioDrugs 2019; 32:339-355. [PMID: 29934752 DOI: 10.1007/s40259-018-0289-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cell surface membrane proteins comprise a wide array of structurally and functionally diverse proteins involved in a variety of important physiological and homeostatic processes. Complex integral membrane proteins, which are embedded in the lipid bilayer by multiple transmembrane-spanning helices, are represented by families of proteins that are important target classes for drug discovery. Such protein families include G-protein-coupled receptors, ion channels and transporters. Although these targets have typically been the domain of small-molecule drugs, the exquisite specificity of monoclonal antibodies offers a significant opportunity to selectively modulate these target proteins. Nevertheless, the isolation of antibodies with desired pharmacological functions has proved difficult because of technical challenges in preparing membrane protein antigens for antibody drug discovery. In this review, we describe recent progress in defining strategies for the generation of membrane protein antigens. We also describe antibody-isolation strategies that identify antibodies that bind the membrane protein and modulate protein function.
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29
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Potterton A, Husseini FS, Southey MWY, Bodkin MJ, Heifetz A, Coveney PV, Townsend-Nicholson A. Ensemble-Based Steered Molecular Dynamics Predicts Relative Residence Time of A 2A Receptor Binders. J Chem Theory Comput 2019; 15:3316-3330. [PMID: 30893556 DOI: 10.1021/acs.jctc.8b01270] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Drug-target residence time, the length of time for which a small molecule stays bound to its receptor target, has increasingly become a key property for optimization in drug discovery programs. However, its in silico prediction has proven difficult. Here we describe a method, using atomistic ensemble-based steered molecular dynamics (SMD), to observe the dissociation of ligands from their target G protein-coupled receptor in a time scale suitable for drug discovery. These dissociation simulations accurately, precisely, and reproducibly identify ligand-residue interactions and quantify the change in ligand energy values for both protein and water. The method has been applied to 17 ligands of the A2A adenosine receptor, all with published experimental kinetic binding data. The residues that interact with the ligand as it dissociates are known experimentally to have an effect on binding affinities and residence times. There is a good correlation ( R2 = 0.79) between the computationally calculated change in water-ligand interaction energy and experimentally determined residence time. Our results indicate that ensemble-based SMD is a rapid, novel, and accurate semi-empirical method for the determination of drug-target relative residence time.
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Affiliation(s)
- Andrew Potterton
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences , University College London , London WC1E 6BT , United Kingdom
| | - Fouad S Husseini
- Centre for Computational Science, Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom
| | - Michelle W Y Southey
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park , Abingdon , Oxfordshire OX14 4RZ , United Kingdom
| | - Mike J Bodkin
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park , Abingdon , Oxfordshire OX14 4RZ , United Kingdom
| | - Alexander Heifetz
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences , University College London , London WC1E 6BT , United Kingdom.,Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park , Abingdon , Oxfordshire OX14 4RZ , United Kingdom
| | - Peter V Coveney
- Centre for Computational Science, Department of Chemistry , University College London , London WC1H 0AJ , United Kingdom.,Computational Science Laboratory, Institute for Informatics, Faculty of Science , University of Amsterdam , Amsterdam 1098XH , The Netherlands
| | - Andrea Townsend-Nicholson
- Institute of Structural & Molecular Biology, Research Department of Structural & Molecular Biology, Division of Biosciences , University College London , London WC1E 6BT , United Kingdom
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30
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Analysis of tractable allosteric sites in G protein-coupled receptors. Sci Rep 2019; 9:6180. [PMID: 30992500 PMCID: PMC6467999 DOI: 10.1038/s41598-019-42618-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 03/28/2019] [Indexed: 11/21/2022] Open
Abstract
Allosteric modulation of G protein-coupled receptors represent a promising mechanism of pharmacological intervention. Dramatic developments witnessed in the structural biology of membrane proteins continue to reveal that the binding sites of allosteric modulators are widely distributed, including along protein surfaces. Here we restrict consideration to intrahelical and intracellular sites together with allosteric conformational locks, and show that the protein mapping tools FTMap and FTSite identify 83% and 88% of such experimentally confirmed allosteric sites within the three strongest sites found. The methods were also able to find partially hidden allosteric sites that were not fully formed in X-ray structures crystallized in the absence of allosteric ligands. These results confirm that the intrahelical sites capable of binding druglike allosteric modulators are among the strongest ligand recognition sites in a large fraction of GPCRs and suggest that both FTMap and FTSite are useful tools for identifying allosteric sites and to aid in the design of such compounds in a range of GPCR targets.
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31
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Vass M, Podlewska S, de Esch IJP, Bojarski AJ, Leurs R, Kooistra AJ, de Graaf C. Aminergic GPCR-Ligand Interactions: A Chemical and Structural Map of Receptor Mutation Data. J Med Chem 2018; 62:3784-3839. [PMID: 30351004 DOI: 10.1021/acs.jmedchem.8b00836] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The aminergic family of G protein-coupled receptors (GPCRs) plays an important role in various diseases and represents a major drug discovery target class. Structure determination of all major aminergic subfamilies has enabled structure-based ligand design for these receptors. Site-directed mutagenesis data provides an invaluable complementary source of information for elucidating the structural determinants of binding of different ligand chemotypes. The current study provides a comparative analysis of 6692 mutation data points on 34 aminergic GPCR subtypes, covering the chemical space of 540 unique ligands from mutagenesis experiments and information from experimentally determined structures of 52 distinct aminergic receptor-ligand complexes. The integrated analysis enables detailed investigation of structural receptor-ligand interactions and assessment of the transferability of combined binding mode and mutation data across ligand chemotypes and receptor subtypes. An overview is provided of the possibilities and limitations of using mutation data to guide the design of novel aminergic receptor ligands.
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Affiliation(s)
- Márton Vass
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Sabina Podlewska
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , PL31-343 Kraków , Poland
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , PL31-343 Kraków , Poland
| | - Rob Leurs
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Albert J Kooistra
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands.,Department of Drug Design and Pharmacology , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Chris de Graaf
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands.,Sosei Heptares , Steinmetz Building, Granta Park, Great Abington , Cambridge CB21 6DG , U.K
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32
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Igonet S, Raingeval C, Cecon E, Pučić-Baković M, Lauc G, Cala O, Baranowski M, Perez J, Jockers R, Krimm I, Jawhari A. Enabling STD-NMR fragment screening using stabilized native GPCR: A case study of adenosine receptor. Sci Rep 2018; 8:8142. [PMID: 29802269 PMCID: PMC5970182 DOI: 10.1038/s41598-018-26113-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/23/2018] [Indexed: 12/27/2022] Open
Abstract
Structural studies of integral membrane proteins have been limited by the intrinsic conformational flexibility and the need to stabilize the proteins in solution. Stabilization by mutagenesis was very successful for structural biology of G protein-coupled receptors (GPCRs). However, it requires heavy protein engineering and may introduce structural deviations. Here we describe the use of specific calixarenes-based detergents for native GPCR stabilization. Wild type, full length human adenosine A2A receptor was used to exemplify the approach. We could stabilize native, glycosylated, non-aggregated and homogenous A2AR that maintained its ligand binding capacity. The benefit of the preparation for fragment screening, using the Saturation-Transfer Difference nuclear magnetic resonance (STD-NMR) experiment is reported. The binding of the agonist adenosine and the antagonist caffeine were observed and competition experiments with CGS-21680 and ZM241385 were performed, demonstrating the feasibility of the STD-based fragment screening on the native A2A receptor. Interestingly, adenosine was shown to bind a second binding site in the presence of the agonist CGS-21680 which corroborates published results obtained with molecular dynamics simulation. Fragment-like compounds identified using STD-NMR showed antagonistic effects on A2AR in the cAMP cellular assay. Taken together, our study shows that stabilization of native GPCRs represents an attractive approach for STD-based fragment screening and drug design.
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Affiliation(s)
| | - Claire Raingeval
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Erika Cecon
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,University Paris Descartes, Sorbonne Paris Cité, Paris, France
| | | | - Gordan Lauc
- GENOS, Borongajska cesta 83h, 10000, Zagreb, Croatia
| | - Olivier Cala
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Maciej Baranowski
- SWING Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, BP48, Saint-Aubin, Gif-sur-Yvette, F-91192, France
| | - Javier Perez
- SWING Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, BP48, Saint-Aubin, Gif-sur-Yvette, F-91192, France
| | - Ralf Jockers
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,University Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Isabelle Krimm
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Anass Jawhari
- CALIXAR, 60 avenue Rockefeller, 69008, Lyon, France.
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33
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Robertson N, Rappas M, Doré AS, Brown J, Bottegoni G, Koglin M, Cansfield J, Jazayeri A, Cooke RM, Marshall FH. Structure of the complement C5a receptor bound to the extra-helical antagonist NDT9513727. Nature 2018; 553:111-114. [PMID: 29300009 DOI: 10.1038/nature25025] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 11/07/2017] [Indexed: 11/09/2022]
Abstract
The complement system is a crucial component of the host response to infection and tissue damage. Activation of the complement cascade generates anaphylatoxins including C5a and C3a. C5a exerts a pro-inflammatory effect via the G-protein-coupled receptor C5a anaphylatoxin chemotactic receptor 1 (C5aR1, also known as CD88) that is expressed on cells of myeloid origin. Inhibitors of the complement system have long been of interest as potential drugs for the treatment of diseases such as sepsis, rheumatoid arthritis, Crohn's disease and ischaemia-reperfusion injuries. More recently, a role of C5a in neurodegenerative conditions such as Alzheimer's disease has been identified. Peptide antagonists based on the C5a ligand have progressed to phase 2 trials in psoriasis and rheumatoid arthritis; however, these compounds exhibited problems with off-target activity, production costs, potential immunogenicity and poor oral bioavailability. Several small-molecule competitive antagonists for C5aR1, such as W-54011 and NDT9513727, have been identified by C5a radioligand-binding assays. NDT9513727 is a non-peptide inverse agonist of C5aR1, and is highly selective for the primate and gerbil receptors over those of other species. Here, to study the mechanism of action of C5a antagonists, we determine the structure of a thermostabilized C5aR1 (known as C5aR1 StaR) in complex with NDT9513727. We found that the small molecule bound between transmembrane helices 3, 4 and 5, outside the helical bundle. One key interaction between the small molecule and residue Trp2135.49 seems to determine the species selectivity of the compound. The structure demonstrates that NDT9513727 exerts its inverse-agonist activity through an extra-helical mode of action.
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Affiliation(s)
- Nathan Robertson
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Mathieu Rappas
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Andrew S Doré
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Jason Brown
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Giovanni Bottegoni
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Markus Koglin
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Julie Cansfield
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Ali Jazayeri
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Robert M Cooke
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Fiona H Marshall
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
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34
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Morgan P, Brown DG, Lennard S, Anderton MJ, Barrett JC, Eriksson U, Fidock M, Hamrén B, Johnson A, March RE, Matcham J, Mettetal J, Nicholls DJ, Platz S, Rees S, Snowden MA, Pangalos MN. Impact of a five-dimensional framework on R&D productivity at AstraZeneca. Nat Rev Drug Discov 2018; 17:167-181. [DOI: 10.1038/nrd.2017.244] [Citation(s) in RCA: 225] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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35
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Brown DG, Brown GA, Centrella P, Certel K, Cooke RM, Cuozzo JW, Dekker N, Dumelin CE, Ferguson A, Fiez-Vandal C, Geschwindner S, Guié MA, Habeshian S, Keefe AD, Schlenker O, Sigel EA, Snijder A, Soutter HT, Sundström L, Troast DM, Wiggin G, Zhang J, Zhang Y, Clark MA. Agonists and Antagonists of Protease-Activated Receptor 2 Discovered within a DNA-Encoded Chemical Library Using Mutational Stabilization of the Target. SLAS DISCOVERY 2018; 23:429-436. [DOI: 10.1177/2472555217749847] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The discovery of ligands via affinity-mediated selection of DNA-encoded chemical libraries is driven by the quality and concentration of the protein target. G-protein-coupled receptors (GPCRs) and other membrane-bound targets can be difficult to isolate in their functional state and at high concentrations, and therefore have been challenging for affinity-mediated selection. Here, we report a successful selection campaign against protease-activated receptor 2 (PAR2). Using a thermo-stabilized mutant of PAR2, we conducted affinity selection using our >100-billion-compound DNA-encoded library. We observed a number of putative ligands enriched upon selection, and subsequent cellular profiling revealed these ligands to comprise both agonists and antagonists. The agonist series shared structural similarity with known agonists. The antagonists were shown to bind in a novel allosteric binding site on the PAR2 protein. This report serves to demonstrate that cell-free affinity selection against GPCRs can be achieved with mutant stabilized protein targets.
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Affiliation(s)
- Dean G. Brown
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Waltham, MA, USA
| | - Giles A. Brown
- Heptares Therapeutics Ltd., Welwyn Garden City, Hertfordshire, UK
| | | | - Kaan Certel
- X-Chem Pharmaceuticals, Waltham, MA, USA
- Novartis Institute for BioMedical Research, Cambridge, MA, USA
| | - Robert M. Cooke
- Heptares Therapeutics Ltd., Welwyn Garden City, Hertfordshire, UK
| | | | - Niek Dekker
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Mölndal, Sweden
| | - Christoph E. Dumelin
- X-Chem Pharmaceuticals, Waltham, MA, USA
- Novartis Institute for BioMedical Research, Basel, Switzerland
| | - Andrew Ferguson
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Waltham, MA, USA
- X-Chem, Inc., Waltham, MA, USA
| | | | - Stefan Geschwindner
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Mölndal, Sweden
| | | | - Sevan Habeshian
- X-Chem Pharmaceuticals, Waltham, MA, USA
- École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | | | - Oliver Schlenker
- Heptares Therapeutics Ltd., Welwyn Garden City, Hertfordshire, UK
| | | | - Arjan Snijder
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Mölndal, Sweden
| | | | - Linda Sundström
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Mölndal, Sweden
| | - Dawn M. Troast
- X-Chem Pharmaceuticals, Waltham, MA, USA
- Morphic Therapeutic, Waltham, MA
| | - Giselle Wiggin
- Heptares Therapeutics Ltd., Welwyn Garden City, Hertfordshire, UK
| | - Jing Zhang
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca R&D, Waltham, MA, USA
- Entasis Therapeutics, Waltham, MA
| | - Ying Zhang
- X-Chem Pharmaceuticals, Waltham, MA, USA
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36
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Rucktooa P, Cheng RKY, Segala E, Geng T, Errey JC, Brown GA, Cooke RM, Marshall FH, Doré AS. Towards high throughput GPCR crystallography: In Meso soaking of Adenosine A 2A Receptor crystals. Sci Rep 2018; 8:41. [PMID: 29311713 PMCID: PMC5758569 DOI: 10.1038/s41598-017-18570-w] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/08/2017] [Indexed: 01/14/2023] Open
Abstract
Here we report an efficient method to generate multiple co-structures of the A2A G protein-coupled receptor (GPCR) with small-molecules from a single preparation of a thermostabilised receptor crystallised in Lipidic Cubic Phase (LCP). Receptor crystallisation is achieved following purification using a low affinity “carrier” ligand (theophylline) and crystals are then soaked in solutions containing the desired (higher affinity) compounds. Complete datasets to high resolution can then be collected from single crystals and seven structures are reported here of which three are novel. The method significantly improves structural throughput for ligand screening using stabilised GPCRs, thereby actively driving Structure-Based Drug Discovery (SBDD).
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Affiliation(s)
- Prakash Rucktooa
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Robert K Y Cheng
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK.,LeadXpro, Park InnovAARE, 5232, Villigen, Switzerland
| | - Elena Segala
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Tian Geng
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - James C Errey
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Giles A Brown
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Robert M Cooke
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
| | - Fiona H Marshall
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK.
| | - Andrew S Doré
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire, AL7 3AX, UK
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37
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Structural Mapping of Adenosine Receptor Mutations: Ligand Binding and Signaling Mechanisms. Trends Pharmacol Sci 2018; 39:75-89. [DOI: 10.1016/j.tips.2017.11.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 11/06/2017] [Accepted: 11/06/2017] [Indexed: 12/16/2022]
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38
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Soave M, Cseke G, Hutchings CJ, Brown AJH, Woolard J, Hill SJ. A monoclonal antibody raised against a thermo-stabilised β 1-adrenoceptor interacts with extracellular loop 2 and acts as a negative allosteric modulator of a sub-set of β 1-adrenoceptors expressed in stable cell lines. Biochem Pharmacol 2017; 147:38-54. [PMID: 29102678 PMCID: PMC5770334 DOI: 10.1016/j.bcp.2017.10.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 10/31/2017] [Indexed: 11/30/2022]
Abstract
Recent interest has focused on antibodies that can discriminate between different receptor conformations. Here we have characterised the effect of a monoclonal antibody (mAb3), raised against a purified thermo-stabilised turkey β1-adrenoceptor (β1AR-m23 StaR), on β1-ARs expressed in CHO-K1 or HEK 293 cells. Immunohistochemical and radioligand-binding studies demonstrated that mAb3 was able to bind to ECL2 of the tβ1-AR, but not its human homologue. Specific binding of mAb3 to tβ1-AR was inhibited by a peptide based on the turkey, but not the human, ECL2 sequence. Studies with [3H]-CGP 12177 demonstrated that mAb3 prevented the binding of orthosteric ligands to a subset (circa 40%) of turkey β1-receptors expressed in both CHO K1 and HEK 293 cells. MAb3 significantly reduced the maximum specific binding capacity of [3H]-CGP-12177 without influencing its binding affinity. Substitution of ECL2 of tβ1-AR with its human equivalent, or mutation of residues D186S, P187D, Q188E prevented the inhibition of [3H]-CGP 12177 binding by mAb3. MAb3 also elicited a negative allosteric effect on agonist-stimulated cAMP responses. The identity of the subset of turkey β1-adrenoceptors influenced by mAb3 remains to be established but mAb3 should become an important tool to investigate the nature of β1-AR conformational states and oligomeric complexes.
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Affiliation(s)
- Mark Soave
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
| | - Gabriella Cseke
- Heptares Therapeutics Ltd., Bio Park, Welwyn Garden City AL7 3AX, UK
| | | | | | - Jeanette Woolard
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.
| | - Stephen J Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK.
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39
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Structures of Human A 1 and A 2A Adenosine Receptors with Xanthines Reveal Determinants of Selectivity. Structure 2017; 25:1275-1285.e4. [DOI: 10.1016/j.str.2017.06.012] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2017] [Revised: 04/13/2017] [Accepted: 06/15/2017] [Indexed: 01/06/2023]
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40
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Lee Y, Basith S, Choi S. Recent Advances in Structure-Based Drug Design Targeting Class A G Protein-Coupled Receptors Utilizing Crystal Structures and Computational Simulations. J Med Chem 2017; 61:1-46. [PMID: 28657745 DOI: 10.1021/acs.jmedchem.6b01453] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G protein-coupled receptors (GPCRs) represent the largest and most physiologically important integral membrane protein family, and these receptors respond to a wide variety of physiological and environmental stimuli. GPCRs are among the most critical therapeutic targets for numerous human diseases, and approximately one-third of the currently marketed drugs target this receptor family. The recent breakthroughs in GPCR structural biology have significantly contributed to our understanding of GPCR function, ligand binding, and pharmacological action as well as to the design of new drugs. This perspective highlights the latest advances in GPCR structures with a focus on the receptor-ligand interactions of each receptor family in class A nonrhodopsin GPCRs as well as the structural features for their activation, biased signaling, and allosteric mechanisms. The current state-of-the-art methodologies of structure-based drug design (SBDD) approaches in the GPCR research field are also discussed.
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Affiliation(s)
- Yoonji Lee
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Shaherin Basith
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
| | - Sun Choi
- National Leading Research Laboratory (NLRL) of Molecular Modeling & Drug Design, College of Pharmacy and Graduate School of Pharmaceutical Sciences, Ewha Womans University , Seoul 03760, Republic of Korea
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41
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Strege A, Carpenter B, Edwards PC, Tate CG. Strategy for the Thermostabilization of an Agonist-Bound GPCR Coupled to a G Protein. Methods Enzymol 2017; 594:243-264. [PMID: 28779842 DOI: 10.1016/bs.mie.2017.05.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Structure determination of G protein-coupled receptors (GPCRs) in the inactive state bound to high-affinity antagonists has been very successful through the implementation of a number of protein engineering and crystallization strategies. However, the structure determination of GPCRs in their fully active state coupled to a G protein is still very challenging. Recently, mini-G proteins were developed, which recapitulate the coupling of a full heterotrimeric G protein to a GPCR despite being less than one-third of the size. This allowed the structure determination of the agonist-bound adenosine A2A receptor (A2AR) coupled to mini-Gs. Although this is extremely encouraging, A2AR is very stable compared with many other GPCRs, particularly when an agonist is bound. In contrast, the agonist-bound conformation of the human corticotropin-releasing factor receptor is considerably less stable, impeding the formation of good quality crystals for structure determination. We have therefore developed a novel strategy for the thermostabilization of a GPCR-mini-G protein complex. In this chapter, we will describe the theoretical and practical principles of the thermostability assay for stabilizing this complex, discuss its strengths and weaknesses, and show some typical results from the thermostabilization process.
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Affiliation(s)
- Annette Strege
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Byron Carpenter
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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42
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Discovery of functional monoclonal antibodies targeting G-protein-coupled receptors and ion channels. Biochem Soc Trans 2017; 44:831-7. [PMID: 27284048 DOI: 10.1042/bst20160028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Indexed: 11/17/2022]
Abstract
The development of recombinant antibody therapeutics is a significant area of growth in the pharmaceutical industry with almost 50 approved monoclonal antibodies on the market in the US and Europe. Despite this growth, however, certain classes of important molecular targets have remained intractable to therapeutic antibodies due to complexity of the target molecules. These complex target molecules include G-protein-coupled receptors and ion channels which represent a large potential target class for therapeutic intervention with monoclonal antibodies. Although these targets have typically been addressed by small molecule approaches, the exquisite specificity of antibodies provides a significant opportunity to provide selective modulation of these target proteins. Given this opportunity, substantial effort has been applied to address the technical challenges of targeting these complex membrane proteins with monoclonal antibodies. In this review recent progress made in the strategies for discovery of functional monoclonal antibodies for these challenging membrane protein targets is addressed.
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43
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Huber S, Casagrande F, Hug MN, Wang L, Heine P, Kummer L, Plückthun A, Hennig M. SPR-based fragment screening with neurotensin receptor 1 generates novel small molecule ligands. PLoS One 2017; 12:e0175842. [PMID: 28510609 PMCID: PMC5433701 DOI: 10.1371/journal.pone.0175842] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 04/01/2017] [Indexed: 12/22/2022] Open
Abstract
The neurotensin receptor 1 represents an important drug target involved in various diseases of the central nervous system. So far, the full exploitation of potential therapeutic activities has been compromised by the lack of compounds with favorable physicochemical and pharmacokinetic properties which efficiently penetrate the blood-brain barrier. Recent progress in the generation of stabilized variants of solubilized neurotensin receptor 1 and its subsequent purification and successful structure determination presents a solid starting point to apply the approach of fragment-based screening to extend the chemical space of known neurotensin receptor 1 ligands. In this report, surface plasmon resonance was used as primary method to screen 6369 compounds. Thereby 44 hits were identified and confirmed in competition as well as dose-response experiments. Furthermore, 4 out of 8 selected hits were validated using nuclear magnetic resonance spectroscopy as orthogonal biophysical method. Computational analysis of the compound structures, taking the known crystal structure of the endogenous peptide agonist into consideration, gave insight into the potential fragment-binding location and interactions and inspires chemistry efforts for further exploration of the fragments.
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Affiliation(s)
- Sylwia Huber
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
- * E-mail: (SH); (MH)
| | - Fabio Casagrande
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
| | - Melanie N. Hug
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
| | - Lisha Wang
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
| | - Philipp Heine
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Lutz Kummer
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Andreas Plückthun
- Department of Biochemistry, University of Zurich, Zurich, Switzerland
| | - Michael Hennig
- Roche Innovation Center Basel, Pharmaceutical Research and Early Development, Basel, Switzerland
- * E-mail: (SH); (MH)
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44
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Abstract
Phage display has emerged as one of the leading technologies for the selection of highly specific monoclonal antibodies, offering a number of advantages over traditional methods of antibody generation. While there are various possibilities to conduct phage display (e.g., solution panning, solid-phase panning), whole cell panning is an elegant way to present membrane embedded target antigens in their natural environment and conformation to antibody-bearing phages. Here, a whole cell panning procedure using a Fab-based antibody library including primary cell based screening for selectivity is described.
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Affiliation(s)
- Yvonne Stark
- MorphoSys AG, Semmelweisstrasse 7, 82152, Planegg, Germany
| | - Sophie Venet
- MorphoSys AG, Semmelweisstrasse 7, 82152, Planegg, Germany
| | - Annika Schmid
- MorphoSys AG, Semmelweisstrasse 7, 82152, Planegg, Germany.
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45
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Oswald C, Rappas M, Kean J, Doré AS, Errey JC, Bennett K, Deflorian F, Christopher JA, Jazayeri A, Mason JS, Congreve M, Cooke RM, Marshall FH. Intracellular allosteric antagonism of the CCR9 receptor. Nature 2016; 540:462-465. [PMID: 27926729 DOI: 10.1038/nature20606] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/07/2016] [Indexed: 12/21/2022]
Abstract
Chemokines and their G-protein-coupled receptors play a diverse role in immune defence by controlling the migration, activation and survival of immune cells. They are also involved in viral entry, tumour growth and metastasis and hence are important drug targets in a wide range of diseases. Despite very significant efforts by the pharmaceutical industry to develop drugs, with over 50 small-molecule drugs directed at the family entering clinical development, only two compounds have reached the market: maraviroc (CCR5) for HIV infection and plerixafor (CXCR4) for stem-cell mobilization. The high failure rate may in part be due to limited understanding of the mechanism of action of chemokine antagonists and an inability to optimize compounds in the absence of structural information. CC chemokine receptor type 9 (CCR9) activation by CCL25 plays a key role in leukocyte recruitment to the gut and represents a therapeutic target in inflammatory bowel disease. The selective CCR9 antagonist vercirnon progressed to phase 3 clinical trials in Crohn's disease but efficacy was limited, with the need for very high doses to block receptor activation. Here we report the crystal structure of the CCR9 receptor in complex with vercirnon at 2.8 Å resolution. Remarkably, vercirnon binds to the intracellular side of the receptor, exerting allosteric antagonism and preventing G-protein coupling. This binding site explains the need for relatively lipophilic ligands and describes another example of an allosteric site on G-protein-coupled receptors that can be targeted for drug design, not only at CCR9, but potentially extending to other chemokine receptors.
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Affiliation(s)
- Christine Oswald
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Mathieu Rappas
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - James Kean
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Andrew S Doré
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - James C Errey
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Kirstie Bennett
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Francesca Deflorian
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - John A Christopher
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Ali Jazayeri
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Jonathan S Mason
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Miles Congreve
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Robert M Cooke
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Fiona H Marshall
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
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46
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Lee S, Mao A, Bhattacharya S, Robertson N, Grisshammer R, Tate CG, Vaidehi N. How Do Short Chain Nonionic Detergents Destabilize G-Protein-Coupled Receptors? J Am Chem Soc 2016; 138:15425-15433. [PMID: 27792324 PMCID: PMC5148649 DOI: 10.1021/jacs.6b08742] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Stability of detergent-solubilized G-protein-coupled receptors (GPCRs) is crucial for their purification in a biologically relevant state, and it is well-known that short chain detergents such as octylglucoside are more denaturing than long chain detergents such as dodecylmaltoside. However, the molecular basis for this phenomenon is poorly understood. To gain insights into the mechanism of detergent destabilization of GPCRs, we used atomistic molecular dynamics simulations of thermostabilized adenosine receptor (A2AR) mutants embedded in either a lipid bilayer or detergent micelles of alkylmaltosides and alkylglucosides. A2AR mutants in dodecylmaltoside or phospholipid showed low flexibility and good interhelical packing. In contrast, A2AR mutants in either octylglucoside or nonylglucoside showed decreased α-helicity in transmembrane regions, decreased α-helical packing, and the interpenetration of detergent molecules between transmembrane α-helices. This was not observed in octylglucoside containing phospholipid. Cholesteryl hemisuccinate in dodecylmaltoside increased the energetic stability of the receptor by wedging into crevices on the hydrophobic surface of A2AR, increasing packing interactions within the receptor and stiffening the detergent micelle. The data suggest a three-stage process for the initial events in the destabilization of GPCRs by octylglucoside: (i) highly mobile detergent molecules form small micelles around the receptor; (ii) loss of α-helicity and decreased interhelical packing interactions in transmembrane regions are promoted by increased receptor thermal motion; (iii) transient separation of transmembrane helices allowed penetration of detergent molecules into the core of the receptor. The relative hydration of the headgroup and alkyl chain correlates with detergent harshness and suggests new avenues to develop milder versions of octylglucoside for receptor crystallization.
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Affiliation(s)
- Sangbae Lee
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
| | - Allen Mao
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
| | - Supriyo Bhattacharya
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
| | - Nathan Robertson
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, AL7 3AX, UK
| | - Reinhard Grisshammer
- Membrane Protein Structure Function Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland 20852, USA
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Nagarajan Vaidehi
- Department of Molecular Immunology, Beckman Research Institute of the City of Hope, 1500 E. Duarte Road, Duarte, California 91010, USA
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47
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Calmet P, De Maria M, Harté E, Lamb D, Serrano-Vega M, Jazayeri A, Tschammer N, Alves ID. Real time monitoring of membrane GPCR reconstitution by plasmon waveguide resonance: on the role of lipids. Sci Rep 2016; 6:36181. [PMID: 27824122 PMCID: PMC5099921 DOI: 10.1038/srep36181] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 10/12/2016] [Indexed: 01/14/2023] Open
Abstract
G-protein coupled receptors (GPCRs) are important therapeutic targets since more than 40% of the drugs on the market exert their action through these proteins. To decipher the molecular mechanisms of activation and signaling, GPCRs often need to be isolated and reconstituted from a detergent-solubilized state into a well-defined and controllable lipid model system. Several methods exist to reconstitute membrane proteins in lipid systems but usually the reconstitution success is tested at the end of the experiment and often by an additional and indirect method. Irrespective of the method used, the reconstitution process is often an intractable and time-consuming trial-and-error procedure. Herein, we present a method that allows directly monitoring the reconstitution of GPCRs in model planar lipid membranes. Plasmon waveguide resonance (PWR) allows following GPCR lipid reconstitution process without any labeling and with high sensitivity. Additionally, the method is ideal to probe the lipid effect on receptor ligand binding as demonstrated by antagonist binding to the chemokine CCR5 receptor.
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Affiliation(s)
- Pierre Calmet
- Max Planck Institute for the Science of Light, Erlangen, Germany.,Friedrich Alexander University (FAU) Erlangen-Nürnberg, Erlangen, Germany.,Chemistry and Biology of Membranes and Nanoobjects, UMR 5248 CNRS, University of Bordeaux, Bat. B14 allée Geoffroy St. Hilaire, 33600 Pessac, France
| | - Monica De Maria
- Department of Developmental Biology, Friedrich Alexander University of Erlangen-Nürnberg, Erlangen, Germany
| | - Etienne Harté
- Chemistry and Biology of Membranes and Nanoobjects, UMR 5248 CNRS, University of Bordeaux, Bat. B14 allée Geoffroy St. Hilaire, 33600 Pessac, France
| | - Daniel Lamb
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Maria Serrano-Vega
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Ali Jazayeri
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK
| | - Nuska Tschammer
- Department of Developmental Biology, Friedrich Alexander University of Erlangen-Nürnberg, Erlangen, Germany.,NanoTemper Technologies GmbH, Munich, Germany
| | - Isabel D Alves
- Chemistry and Biology of Membranes and Nanoobjects, UMR 5248 CNRS, University of Bordeaux, Bat. B14 allée Geoffroy St. Hilaire, 33600 Pessac, France
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48
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McNeely PM, Naranjo AN, Forsten-Williams K, Robinson AS. A 2AR Binding Kinetics in the Ligand Depletion Regime. SLAS DISCOVERY 2016; 22:166-175. [PMID: 27577981 DOI: 10.1177/1087057116667256] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Ligand binding plays a fundamental role in stimulating the downstream signaling of membrane receptors. Here, ligand-binding kinetics of the full-length human adenosine A2A receptor (A2AR) reconstituted in detergent micelles were measured using a fluorescently labeled ligand via fluorescence anisotropy. Importantly, to optimize the signal-to-noise ratio, these experiments were conducted in the ligand depletion regime. In the ligand depletion regime, the assumptions used to determine analytical solutions for one-site binding models for either one or two ligands in competition are no longer valid. We therefore implemented a numerical solution approach to analyze kinetic binding data as experimental conditions approach the ligand depletion regime. By comparing the results from the numerical and the analytical solutions, we highlight the ligand-receptor ratios at which the analytical solution begins to lose predictive accuracy. Using the numerical solution approach, we determined the kinetic rate constants of the fluorescent ligand, FITC-APEC, and those for three unlabeled ligands using competitive association experiments. The association and dissociation rate constants of the unlabeled ligands determined from the competitive association experiments were then independently validated using competitive dissociation data. Based on this study, a numerical solution is recommended to determine kinetic ligand-binding parameters for experiments conducted in the ligand-depletion regime.
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Affiliation(s)
- Patrick M McNeely
- 1 Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Andrea N Naranjo
- 1 Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | | | - Anne Skaja Robinson
- 1 Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.,2 Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, LA, USA
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Shiroishi M, Moriya M, Ueda T. Micro-scale and rapid expression screening of highly expressed and/or stable membrane protein variants in Saccharomyces cerevisiae. Protein Sci 2016; 25:1863-72. [PMID: 27479358 DOI: 10.1002/pro.2993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 06/16/2016] [Accepted: 07/29/2016] [Indexed: 11/07/2022]
Abstract
Purification of milligram quantities of target proteins is required for structural and biophysical studies. However, mammalian membrane proteins, many of which are important therapeutic targets, are too unstable to be expressed in heterologous hosts and to be solubilized by detergents. One of the most promising ways to overcome these limitations is to stabilize the membrane proteins by generating variants via introduction of truncated flexible regions, fusion partners, and site-directed mutagenesis. Therefore, an effective screening strategy is a key to obtaining successful protein stabilization. Herein, we report the micro-scale and high-throughput screening of stabilized membrane protein variants using Saccharomyces cerevisiae as a host. All steps of the screening, including cultivation and disruption of cells, solubilization of the target protein, and the pretreatment for fluorescence-detected size exclusion chromatography (FSEC), could be performed in a 96-well microplate format. We demonstrated that the dispersion among wells was small, enabling detection of a small but important improvement in the protein stability. We also demonstrated that the thermally stable mutants of a human G protein-coupled receptor could be distinguished based on an increase of the peak height in the FSEC profile, which was well correlated with increased ligand binding activity of the protein. This strategy represents a significant platform for handling numerous mutants, similar to alanine scanning.
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Affiliation(s)
- Mitsunori Shiroishi
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan.
| | - Mai Moriya
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
| | - Tadashi Ueda
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-Ku, Fukuoka, 812-8582, Japan
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Magnani F, Serrano-Vega MJ, Shibata Y, Abdul-Hussein S, Lebon G, Miller-Gallacher J, Singhal A, Strege A, Thomas JA, Tate CG. A mutagenesis and screening strategy to generate optimally thermostabilized membrane proteins for structural studies. Nat Protoc 2016; 11:1554-71. [PMID: 27466713 PMCID: PMC5268090 DOI: 10.1038/nprot.2016.088] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The thermostability of an integral membrane protein (MP) in detergent solution is a key parameter that dictates the likelihood of obtaining well-diffracting crystals that are suitable for structure determination. However, many mammalian MPs are too unstable for crystallization. We developed a thermostabilization strategy based on systematic mutagenesis coupled to a radioligand-binding thermostability assay that can be applied to receptors, ion channels and transporters. It takes ∼6-12 months to thermostabilize a G-protein-coupled receptor (GPCR) containing 300 amino acid (aa) residues. The resulting thermostabilized MPs are more easily crystallized and result in high-quality structures. This methodology has facilitated structure-based drug design applied to GPCRs because it is possible to determine multiple structures of the thermostabilized receptors bound to low-affinity ligands. Protocols and advice are given on how to develop thermostability assays for MPs and how to combine mutations to make an optimally stable mutant suitable for structural studies. The steps in the procedure include the generation of ∼300 site-directed mutants by Ala/Leu scanning mutagenesis, the expression of each mutant in mammalian cells by transient transfection and the identification of thermostable mutants using a thermostability assay that is based on binding of an (125)I-labeled radioligand to the unpurified, detergent-solubilized MP. Individual thermostabilizing point mutations are then combined to make an optimally stable MP that is suitable for structural biology and other biophysical studies.
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Affiliation(s)
| | | | | | | | | | | | - Ankita Singhal
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Annette Strege
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Jennifer A. Thomas
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Christopher G. Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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