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Olson KM, Campbell A, Alt A, Traynor JR. Finding the Perfect Fit: Conformational Biosensors to Determine the Efficacy of GPCR Ligands. ACS Pharmacol Transl Sci 2022; 5:694-709. [PMID: 36110374 PMCID: PMC9469492 DOI: 10.1021/acsptsci.1c00256] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
G protein-coupled receptors (GPCRs) are highly druggable targets that adopt numerous conformations. A ligand's ability to stabilize specific conformation(s) of its cognate receptor determines its efficacy or ability to produce a biological response. Identifying ligands that produce different receptor conformations and potentially discrete pharmacological effects (e.g., biased agonists, partial agonists, antagonists, allosteric modulators) is a major goal in drug discovery and necessary to develop drugs with better effectiveness and fewer side effects. Fortunately, direct measurements of ligand efficacy, via receptor conformational changes are possible with the recent development of conformational biosensors. In this review, we discuss classical efficacy models, including the two-state model, the ternary-complex model, and multistate models. We describe how nanobody-, transducer-, and receptor-based conformational biosensors detect and/or stabilize specific GPCR conformations to identify ligands with different levels of efficacy. In particular, conformational biosensors provide the potential to identify and/or characterize therapeutically desirable but often difficult to measure conformations of receptors faster and better than current methods. For drug discovery/development, several recent proof-of-principle studies have optimized conformational biosensors for high-throughput screening (HTS) platforms. However, their widespread use is limited by the fact that few sensors are reliably capable of detecting low-frequency conformations and technically demanding assay conditions. Nonetheless, conformational biosensors do help identify desirable ligands such as allosteric modulators, biased ligands, or partial agonists in a single assay, representing a distinct advantage over classical methods.
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Affiliation(s)
- Keith M. Olson
- Department
of Pharmacology and Edward F Domino Research Center, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Andra Campbell
- Department
of Pharmacology and Edward F Domino Research Center, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Andrew Alt
- Department
of Pharmacology and Edward F Domino Research Center, University of Michigan, Ann Arbor, Michigan 48109, United States
- Life
Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - John R. Traynor
- Department
of Pharmacology and Edward F Domino Research Center, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department
of Medicinal Chemistry, College of Pharmacy, University of Michigan, 428 Church Street, Ann Arbor, Michigan 48109, United
States
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2
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Quirk S, Lieberman RL. Structure and activity of a thermally stable mutant of Acanthamoeba actophorin. Acta Crystallogr F Struct Biol Commun 2022; 78:150-160. [PMID: 35400667 PMCID: PMC8996146 DOI: 10.1107/s2053230x22002448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/02/2022] [Indexed: 11/10/2022] Open
Abstract
Actophorin, which was recently tested for crystallization under microgravity on the International Space Station, was subjected to mutagenesis to identify a construct with improved biophysical properties that were expected to improve the extent of diffraction. First, 20 mutations, including one C-terminal deletion of three residues, were introduced individually into actophorin, resulting in modest increases in thermal stability of between +0.5°C and +2.2°C. All but two of the stabilizing mutants increased both the rates of severing F-actin filaments and of spontaneous polymerization of pyrenyl G-actin in vitro. When the individual mutations were combined into a single actophorin variant, Acto-2, the overall thermal stability was 22°C higher than that of wild-type actophorin. When an inactivating S2P mutation in Acto-2 was restored, Acto-2/P2S was more stable by 20°C but was notably more active than the wild-type protein. The inactivating S2P mutation reaffirms the importance that Ser2 plays in the F-actin-severing reaction. The crystal structure of Acto-2 was solved to 1.7 Å resolution in a monoclinic space group, a first for actophorin. Surprisingly, despite the increase in thermal stability, the extended β-turn region, which is intimately involved in interactions with F-actin, is disordered in one copy of Acto-2 in the asymmetric unit. These observations emphasize the complex interplay among protein thermal stability, function and dynamics.
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Affiliation(s)
- Stephen Quirk
- Kimberly Clark, 1400 Holcomb Bridge Road, Roswell, GA 30076, USA
| | - Raquel L Lieberman
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive NW, Atlanta, GA 30332, USA
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3
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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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4
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García-Nafría J, Tate CG. Cryo-EM structures of GPCRs coupled to G s, G i and G o. Mol Cell Endocrinol 2019; 488:1-13. [PMID: 30930094 DOI: 10.1016/j.mce.2019.02.006] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 01/14/2023]
Abstract
Advances in electron cryo-microscopy (cryo-EM) now permit the structure determination of G protein-coupled receptors (GPCRs) coupled to heterotrimeric G proteins by single-particle imaging. A combination of G protein engineering and the development of antibodies that stabilise the heterotrimeric G protein facilitate the formation of stable GPCR-G protein complexes suitable for structural biology. Structures have been determined of GPCRs coupled to either heterotrimeric G proteins (Gs, Gi or Go) or mini-G proteins (mini-Gs or mini-Go) by single-particle cryo-EM and X-ray crystallography, respectively. This review describes the technical breakthroughs allowing their structure determination and compares the different techniques. In addition, we compare the structures of GPCRs coupled either to Gs, Gi or Go and analyse the contributions of amino acid residues to the GPCR-G protein interface. There is no unique set of interactions that specifies coupling either to Gs, Gi or Go. Instead, there is a common core of interactions between the C-terminal α-helix of the G protein α-subunit and helices H3, H5 and H6 of the receptor. In addition, there are varying degrees of interaction between all the other GPCR helices and intracellular loops to five regions of the α-subunit and four regions of the β-subunit. These data support the contention that there is not a simple linear barcode that defines the specificity of G protein coupling and thus how a G protein couples to a GPCR cannot currently be determined from simply analysing amino acid sequences. Although the overall architecture of GPCR-G protein complexes is conserved, there are significant differences in the molecular details. The number and type of molecular interactions between amino acid residues at the interfaces varies, resulting in subtly different orientation and position of the G protein with respect to the GPCR. This in turn affects the interface surface area that varies between 845 Å2 and 1490 Å2, which could impact upon the lifetime of signalling complexes in the cell.
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Affiliation(s)
- Javier García-Nafría
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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5
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Rues RB, Dong F, Dötsch V, Bernhard F. Systematic optimization of cell-free synthesized human endothelin B receptor folding. Methods 2018; 147:73-83. [DOI: 10.1016/j.ymeth.2018.01.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/18/2018] [Accepted: 01/22/2018] [Indexed: 12/16/2022] Open
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6
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Igonet S, Raingeval C, Cecon E, Pučić-Baković M, Lauc G, Cala O, Baranowski M, Perez J, Jockers R, Krimm I, Jawhari A. Enabling STD-NMR fragment screening using stabilized native GPCR: A case study of adenosine receptor. Sci Rep 2018; 8:8142. [PMID: 29802269 PMCID: PMC5970182 DOI: 10.1038/s41598-018-26113-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/23/2018] [Indexed: 12/27/2022] Open
Abstract
Structural studies of integral membrane proteins have been limited by the intrinsic conformational flexibility and the need to stabilize the proteins in solution. Stabilization by mutagenesis was very successful for structural biology of G protein-coupled receptors (GPCRs). However, it requires heavy protein engineering and may introduce structural deviations. Here we describe the use of specific calixarenes-based detergents for native GPCR stabilization. Wild type, full length human adenosine A2A receptor was used to exemplify the approach. We could stabilize native, glycosylated, non-aggregated and homogenous A2AR that maintained its ligand binding capacity. The benefit of the preparation for fragment screening, using the Saturation-Transfer Difference nuclear magnetic resonance (STD-NMR) experiment is reported. The binding of the agonist adenosine and the antagonist caffeine were observed and competition experiments with CGS-21680 and ZM241385 were performed, demonstrating the feasibility of the STD-based fragment screening on the native A2A receptor. Interestingly, adenosine was shown to bind a second binding site in the presence of the agonist CGS-21680 which corroborates published results obtained with molecular dynamics simulation. Fragment-like compounds identified using STD-NMR showed antagonistic effects on A2AR in the cAMP cellular assay. Taken together, our study shows that stabilization of native GPCRs represents an attractive approach for STD-based fragment screening and drug design.
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Affiliation(s)
| | - Claire Raingeval
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Erika Cecon
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,University Paris Descartes, Sorbonne Paris Cité, Paris, France
| | | | - Gordan Lauc
- GENOS, Borongajska cesta 83h, 10000, Zagreb, Croatia
| | - Olivier Cala
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Maciej Baranowski
- SWING Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, BP48, Saint-Aubin, Gif-sur-Yvette, F-91192, France
| | - Javier Perez
- SWING Beamline, Synchrotron SOLEIL, L'Orme des Merisiers, BP48, Saint-Aubin, Gif-sur-Yvette, F-91192, France
| | - Ralf Jockers
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,University Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Isabelle Krimm
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Université Lyon 1, ENS Lyon - 5, rue de la Doua, F-69100, Villeurbanne, France
| | - Anass Jawhari
- CALIXAR, 60 avenue Rockefeller, 69008, Lyon, France.
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7
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Functional characterisation of G protein-coupled receptors. Methods 2018; 147:213-220. [PMID: 29510249 DOI: 10.1016/j.ymeth.2018.02.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 02/26/2018] [Accepted: 02/27/2018] [Indexed: 12/11/2022] Open
Abstract
Characterisation of receptors can involve either assessment of their ability to bind ligands or measure receptor activation as a result of agonist or inverse agonist interactions. This review focuses on G protein-coupled receptors (GPCRs), examining techniques that can be applied to both receptors in membranes and after solubilisation. Radioligand binding remains a widely used technique, although there is increasing use of fluorescent ligands. These can be used in a variety of experimental designs, either directly monitoring ligand itself with techniques such as fluorescence polarisation or indirectly via resonance energy transfer (fluorescence/Forster resonance energy transfer, FRET and bioluminescence resonance energy transfer, BRET). Label free techniques such as isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR) are also increasingly being used. For GPCRs, the main measure of receptor activation is to investigate the association of the G protein with the receptor. The chief assay measures the receptor-stimulated binding of GTP or a suitable analogue to the receptor. The direct association of the G protein with the receptor has been investigated via resonance energy techniques. These have also been used to measure ligand-induced conformational changes within the receptor; a variety of experimental techniques are available to incorporate suitable donors and acceptors within the receptor.
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Hardy D, Desuzinges Mandon E, Rothnie AJ, Jawhari A. The yin and yang of solubilization and stabilization for wild-type and full-length membrane protein. Methods 2018; 147:118-125. [PMID: 29477816 DOI: 10.1016/j.ymeth.2018.02.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 02/12/2018] [Accepted: 02/18/2018] [Indexed: 11/16/2022] Open
Abstract
Membrane proteins (MP) are stable in their native lipid environment. To enable structural and functional investigations, MP need to be extracted from the membrane. This is a critical step that represents the main obstacle for MP biochemistry and structural biology. General guidelines and rules for membrane protein solubilization remain difficult to establish. This review aims to provide the reader with a comprehensive overview of the general concepts of MP solubilization and stabilization as well as recent advances in detergents innovation. Understanding how solubilization and stabilization are intimately linked is key to facilitate MP isolation toward fundamental structural and functional research as well as drug discovery applications. How to manage the tour de force of destabilizing the lipid bilayer and stabilizing MP at the same time is the holy grail of successful isolation and investigation of such a delicate and fascinating class of proteins.
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Affiliation(s)
- David Hardy
- CALIXAR, 60 Avenue Rockefeller, 69008 Lyon, France; Life & Health Sciences, Aston University, Birmingham B4 7ET, UK
| | | | - Alice J Rothnie
- Life & Health Sciences, Aston University, Birmingham B4 7ET, UK
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9
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Carpenter B. Current applications of mini G proteins to study the structure and function of G protein-coupled receptors. AIMS BIOENGINEERING 2018. [DOI: 10.3934/bioeng.2018.4.209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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10
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Carpenter B, Lebon G. Human Adenosine A 2A Receptor: Molecular Mechanism of Ligand Binding and Activation. Front Pharmacol 2017; 8:898. [PMID: 29311917 PMCID: PMC5736361 DOI: 10.3389/fphar.2017.00898] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Accepted: 11/24/2017] [Indexed: 11/29/2022] Open
Abstract
Adenosine receptors (ARs) comprise the P1 class of purinergic receptors and belong to the largest family of integral membrane proteins in the human genome, the G protein-coupled receptors (GPCRs). ARs are classified into four subtypes, A1, A2A, A2B, and A3, which are all activated by extracellular adenosine, and play central roles in a broad range of physiological processes, including sleep regulation, angiogenesis and modulation of the immune system. ARs are potential therapeutic targets in a variety of pathophysiological conditions, including sleep disorders, cancer, and dementia, which has made them important targets for structural biology. Over a decade of research and innovation has culminated with the publication of more than 30 crystal structures of the human adenosine A2A receptor (A2AR), making it one of the best structurally characterized GPCRs at the atomic level. In this review we analyze the structural data reported for A2AR that described for the first time the binding of mode of antagonists, including newly developed drug candidates, synthetic and endogenous agonists, sodium ions and an engineered G protein. These structures have revealed the key conformational changes induced upon agonist and G protein binding that are central to signal transduction by A2AR, and have highlighted both similarities and differences in the activation mechanism of this receptor compared to other class A GPCRs. Finally, comparison of A2AR with the recently solved structures of A1R has provided the first structural insight into the molecular determinants of ligand binding specificity in different AR subtypes.
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Affiliation(s)
- Byron Carpenter
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Guillaume Lebon
- Institut de Génomique Fonctionnelle, Neuroscience Department, UMR CNRS 5203, INSERM U1191, Université de Montpellier, Montpellier, France
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