1
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Dengler DG, Sun Q, Holleran J, Pollari S, Beutel J, Brown BT, Shinoki Iwaya A, Ardecky R, Harikumar KG, Miller LJ, Sergienko EA. Development of a Testing Funnel for Identification of Small-Molecule Modulators Targeting Secretin Receptors. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:1-16. [PMID: 32749201 PMCID: PMC8278649 DOI: 10.1177/2472555220945284] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The secretin receptor (SCTR), a prototypical class B G protein-coupled receptor (GPCR), exerts its effects mainly by activating Gαs proteins upon binding of its endogenous peptide ligand secretin. SCTRs can be found in a variety of tissues and organs across species, including the pancreas, stomach, liver, heart, lung, colon, kidney, and brain. Beyond that, modulation of SCTR-mediated signaling has therapeutic potential for the treatment of multiple diseases, such as heart failure, obesity, and diabetes. However, no ligands other than secretin and its peptide analogs have been described to regulate SCTRs, probably due to inherent challenges in family B GPCR drug discovery. Here we report creation of a testing funnel that allowed targeted detection of SCTR small-molecule activators. Pursuing the strategy to identify positive allosteric modulators (PAMs), we established a unique primary screening assay employing a mixture of three orthosteric stimulators that was compared in a screening campaign testing 12,000 small-molecule compounds. Beyond that, we developed a comprehensive set of secondary assays, such as a radiolabel-free target engagement assay and a NanoBiT (NanoLuc Binary Technology)-based approach to detect β-arrestin-2 recruitment, all feasible in a high-throughput environment as well as capable of profiling ligands and hits regarding their effect on binding and receptor function. This combination of methods enabled the discovery of five promising scaffolds, four of which have been validated and further characterized with respect to their allosteric activities. We propose that our results may serve as starting points for developing the first in vivo active small molecules targeting SCTRs.
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Affiliation(s)
- Daniela G. Dengler
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Qing Sun
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - John Holleran
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Sirkku Pollari
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Jannis Beutel
- Department of Chemistry and Pharmacy, Chemikum, Friedrich-Alexander University Erlangen-Nuremberg, Erlangen, Germany
| | - Brock T. Brown
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Aki Shinoki Iwaya
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Robert Ardecky
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
| | - Kaleeckal G. Harikumar
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona, USA
| | - Laurence J. Miller
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona, USA
| | - Eduard A. Sergienko
- Conrad Prebys Center for Chemical Genomics, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California, USA
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2
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Odoemelam CS, Percival B, Wallis H, Chang MW, Ahmad Z, Scholey D, Burton E, Williams IH, Kamerlin CL, Wilson PB. G-Protein coupled receptors: structure and function in drug discovery. RSC Adv 2020; 10:36337-36348. [PMID: 35517958 PMCID: PMC9057076 DOI: 10.1039/d0ra08003a] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/22/2020] [Indexed: 12/13/2022] Open
Abstract
The G-protein coupled receptors (GPCRs) superfamily comprise similar proteins arranged into families or classes thus making it one of the largest in the mammalian genome. GPCRs take part in many vital physiological functions making them targets for numerous novel drugs. GPCRs share some distinctive features, such as the seven transmembrane domains, they also differ in the number of conserved residues in their transmembrane domain. Here we provide an introductory and accessible review detailing the computational advances in GPCR pharmacology and drug discovery. An overview is provided on family A-C GPCRs; their structural differences, GPCR signalling, allosteric binding and cooperativity. The dielectric constant (relative permittivity) of proteins is also discussed in the context of site-specific environmental effects.
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Affiliation(s)
| | - Benita Percival
- Nottingham Trent University 50 Shakespeare St Nottingham NG1 4FQ UK
| | - Helen Wallis
- Nottingham Trent University 50 Shakespeare St Nottingham NG1 4FQ UK
| | - Ming-Wei Chang
- Nanotechnology and Integrated Bioengineering Centre, University of Ulster Jordanstown Campus Newtownabbey BT37 0QB Northern Ireland UK
| | - Zeeshan Ahmad
- De Montfort University The Gateway Leicester LE1 9BH UK
| | - Dawn Scholey
- Nottingham Trent University 50 Shakespeare St Nottingham NG1 4FQ UK
| | - Emily Burton
- Nottingham Trent University 50 Shakespeare St Nottingham NG1 4FQ UK
| | - Ian H Williams
- Department of Chemistry, University of Bath Claverton Down Bath BA1 7AY UK
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3
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Wu F, Yang L, Hang K, Laursen M, Wu L, Han GW, Ren Q, Roed NK, Lin G, Hanson MA, Jiang H, Wang MW, Reedtz-Runge S, Song G, Stevens RC. Full-length human GLP-1 receptor structure without orthosteric ligands. Nat Commun 2020; 11:1272. [PMID: 32152292 PMCID: PMC7062719 DOI: 10.1038/s41467-020-14934-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/07/2020] [Indexed: 11/08/2022] Open
Abstract
Glucagon-like peptide-1 receptor (GLP-1R) is a class B G protein-coupled receptor that plays an important role in glucose homeostasis and treatment of type 2 diabetes. Structures of full-length class B receptors were determined in complex with their orthosteric agonist peptides, however, little is known about their extracellular domain (ECD) conformations in the absence of orthosteric ligands, which has limited our understanding of their activation mechanism. Here, we report the 3.2 Å resolution, peptide-free crystal structure of the full-length human GLP-1R in an inactive state, which reveals a unique closed conformation of the ECD. Disulfide cross-linking validates the physiological relevance of the closed conformation, while electron microscopy (EM) and molecular dynamic (MD) simulations suggest a large degree of conformational dynamics of ECD that is necessary for binding GLP-1. Our inactive structure represents a snapshot of the peptide-free GLP-1R and provides insights into the activation pathway of this receptor family.
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Affiliation(s)
- Fan Wu
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Linlin Yang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Kaini Hang
- iHuman Institute, ShanghaiTech University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mette Laursen
- Novo Nordisk A/S, Novo Nordisk Park, Copenhagen, Denmark
| | - Lijie Wu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Gye Won Han
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California, USA
| | | | | | - Guangyao Lin
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Hualiang Jiang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Ming-Wei Wang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- The National Center for Drug Screening, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
- School of Pharmacy, Fudan University, Shanghai, China
| | | | - Gaojie Song
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China.
| | - Raymond C Stevens
- iHuman Institute, ShanghaiTech University, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Departments of Biological Sciences and Chemistry, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, California, USA.
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4
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Dore AS, Bortolato A, Hollenstein K, Cheng RKY, Read RJ, Marshall FH. Decoding Corticotropin-Releasing Factor Receptor Type 1 Crystal Structures. Curr Mol Pharmacol 2018; 10:334-344. [PMID: 28183242 PMCID: PMC5684783 DOI: 10.2174/1874467210666170110114727] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 10/26/2015] [Accepted: 08/03/2016] [Indexed: 01/18/2023]
Abstract
The structural analysis of class B G protein-coupled receptors (GPCR), cell surface proteins responding to peptide hormones, has until recently been restricted to the extracellular domain (ECD). Cor-ticotropin-releasing factor receptor type 1 (CRF1R) is a class B receptor mediating stress response and also considered a drug target for depression and anxiety. Here we report the crystal structure of the trans-membrane domain of human CRF1R in complex with the small-molecule antagonist CP-376395 in a hex-agonal setting with translational non-crystallographic symmetry. Molecular dynamics and metadynamics simulations on this novel structure and the existing TMD structure for CRF1R provides insight as to how the small molecule ligand gains access to the induced-fit allosteric binding site with implications for the observed selectivity against CRF2R. Furthermore, molecular dynamics simulations performed using a full-length receptor model point to key interactions between the ECD and extracellular loop 3 of the TMD providing insight into the full inactive state of multidomain class B GPCRs.
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Affiliation(s)
- Andrew S Dore
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts, AL7 3AX. United Kingdom
| | - Andrea Bortolato
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts, AL7 3AX. United Kingdom
| | | | - Robert K Y Cheng
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts, AL7 3AX. United Kingdom
| | - Randy J Read
- Dept. of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Hills Road, Cambridge, CB2 0XY. United Kingdom
| | - Fiona H Marshall
- Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts, AL7 3AX. United Kingdom
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5
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A Novel G-Protein-Coupled Receptors Gene from Upland Cotton Enhances Salt Stress Tolerance in Transgenic Arabidopsis. Genes (Basel) 2018; 9:genes9040209. [PMID: 29649144 PMCID: PMC5924551 DOI: 10.3390/genes9040209] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 11/17/2022] Open
Abstract
Plants have developed a number of survival strategies which are significant for enhancing their adaptation to various biotic and abiotic stress factors. At the transcriptome level, G-protein-coupled receptors (GPCRs) are of great significance, enabling the plants to detect a wide range of endogenous and exogenous signals which are employed by the plants in regulating various responses in development and adaptation. In this research work, we carried out genome-wide analysis of target of Myb1 (TOM1), a member of the GPCR gene family. The functional role of TOM1 in salt stress tolerance was studied using a transgenic Arabidopsis plants over-expressing the gene. By the use of the functional domain PF06454, we obtained 16 TOM genes members in Gossypium hirsutum, 9 in Gossypium arboreum, and 11 in Gossypium raimondii. The genes had varying physiochemical properties, and it is significant to note that all the grand average of hydropathy (GRAVY) values were less than one, indicating that all are hydrophobic in nature. In all the genes analysed here, both the exonic and intronic regions were found. The expression level of Gh_A07G0747 (GhTOM) was significantly high in the transgenic lines as compared to the wild type; a similar trend in expression was observed in all the salt-related genes tested in this study. The study in epidermal cells confirmed the localization of the protein coded by the gene TOM1 in the plasma membrane. Analysis of anti-oxidant enzymes showed higher concentrations of antioxidants in transgenic lines and relatively lower levels of oxidant substances such as H₂O₂. The low malondialdehyde (MDA) level in transgenic lines indicated that the transgenic lines had relatively low level of oxidative damage compared to the wild types. The results obtained indicate that Gh_A07G0747 (GhTOM) can be a putative target gene for enhancing salt stress tolerance in plants and could be exploited in the future for the development of salt stress-tolerant cotton cultivars.
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6
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Extracellular loops 2 and 3 of the calcitonin receptor selectively modify agonist binding and efficacy. Biochem Pharmacol 2018; 150:214-244. [PMID: 29454620 PMCID: PMC5908784 DOI: 10.1016/j.bcp.2018.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 02/07/2018] [Indexed: 02/07/2023]
Abstract
Class B peptide hormone GPCRs are targets for the treatment of major chronic disease. Peptide ligands of these receptors display biased agonism and this may provide future therapeutic advantage. Recent active structures of the calcitonin (CT) and glucagon-like peptide-1 (GLP-1) receptors reveal distinct engagement of peptides with extracellular loops (ECLs) 2 and 3, and mutagenesis of the GLP-1R has implicated these loops in dynamics of receptor activation. In the current study, we have mutated ECLs 2 and 3 of the human CT receptor (CTR), to interrogate receptor expression, peptide affinity and efficacy. Integration of these data with insights from the CTR and GLP-1R active structures, revealed marked diversity in mechanisms of peptide engagement and receptor activation between the CTR and GLP-1R. While the CTR ECL2 played a key role in conformational propagation linked to Gs/cAMP signalling this was mechanistically distinct from that of GLP-1R ECL2. Moreover, ECL3 was a hotspot for distinct ligand- and pathway-specific effects, and this has implications for the future design of biased agonists of class B GPCRs.
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7
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Garelja ML, Walker CA, Siow A, Yang SH, Harris PWR, Brimble MA, Watkins HA, Gingell JJ, Hay DL. Receptor Activity Modifying Proteins Have Limited Effects on the Class B G Protein-Coupled Receptor Calcitonin Receptor-Like Receptor Stalk. Biochemistry 2018; 57:1410-1422. [PMID: 29388762 DOI: 10.1021/acs.biochem.7b01180] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The calcitonin receptor-like receptor (CLR) is a class B G protein-coupled receptor (GPCR) that forms the basis of three pharmacologically distinct receptors, the calcitonin gene-related peptide (CGRP) receptor, and two adrenomedullin (AM) receptors. These three receptors are created by CLR interacting with three receptor activity-modifying proteins (RAMPs). Class B GPCRs have an N-terminal extracellular domain (ECD) and transmembrane bundle that are both important for binding endogenous ligands. These two domains are joined together by a stretch of amino acids that is referred to as the "stalk". Studies of other class B GPCRs suggest that the stalk may act as hinge, allowing the ECD to adopt multiple conformations. It is unclear what the role of the stalk is within CLR and whether RAMPs can influence its function. Therefore, this study investigated the role of this region using an alanine scan. Effects of mutations were measured with all three RAMPs through cell surface expression, cAMP production and, in select cases, radioligand binding and total cell expression assays. Most mutants did not affect expression or cAMP signaling. CLR C127A, N140A, F142A, and L144A impaired cell surface expression with all three RAMPs. T125A decreased the potency of all peptides at all receptors. N128A, V135A, and L139A showed ligand-dependent effects. While the stalk appears to play a role in CLR function, the effect of RAMPs on this region seems limited, in contrast to their effects on the structure of CLR in other receptor regions.
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Affiliation(s)
- Michael L Garelja
- School of Biological Sciences, University of Auckland , 3A Symonds Street Auckland 1010, New Zealand
| | - Christina A Walker
- School of Biological Sciences, University of Auckland , 3A Symonds Street Auckland 1010, New Zealand
| | - Andrew Siow
- School of Biological Sciences, University of Auckland , 3A Symonds Street Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , 3A Symonds Street, Auckland 1010, New Zealand
| | - Sung H Yang
- School of Biological Sciences, University of Auckland , 3A Symonds Street Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , 3A Symonds Street, Auckland 1010, New Zealand
| | - Paul W R Harris
- School of Biological Sciences, University of Auckland , 3A Symonds Street Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , 3A Symonds Street, Auckland 1010, New Zealand
| | - Margaret A Brimble
- School of Biological Sciences, University of Auckland , 3A Symonds Street Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , 3A Symonds Street, Auckland 1010, New Zealand.,School of Chemical Sciences, The University of Auckland , 23 Symonds Street, Auckland 1010, New Zealand
| | - Harriet A Watkins
- School of Biological Sciences, University of Auckland , 3A Symonds Street Auckland 1010, New Zealand
| | - Joseph J Gingell
- School of Biological Sciences, University of Auckland , 3A Symonds Street Auckland 1010, New Zealand
| | - Debbie L Hay
- School of Biological Sciences, University of Auckland , 3A Symonds Street Auckland 1010, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland , 3A Symonds Street, Auckland 1010, New Zealand
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8
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Ramil CP, Dong M, An P, Lewandowski TM, Yu Z, Miller LJ, Lin Q. Spirohexene-Tetrazine Ligation Enables Bioorthogonal Labeling of Class B G Protein-Coupled Receptors in Live Cells. J Am Chem Soc 2017; 139:13376-13386. [PMID: 28876923 DOI: 10.1021/jacs.7b05674] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A new bioorthogonal reactant pair, spiro[2.3]hex-1-ene (Sph) and 3,6-di(2-pyridyl)-s-tetrazine (DpTz), for the strain-promoted inverse electron-demand Diels-Alder cycloaddition, that is, tetrazine ligation, is reported. As compared to the previously reported strained alkenes such as trans-cyclooctene (TCO) and 1,3-disubstituted cyclopropene, Sph exhibits balanced reactivity and stability in tetrazine ligation with the protein substrates. A lysine derivative of Sph, SphK, was site-selectively incorporated into the extracellular loop regions (ECLs) of GCGR and GLP-1R, two members of class B G protein-coupled receptors (GPCRs) in mammalian cells with the incorporation efficiency dependent on the location. Subsequent bioorthogonal reactions with the fluorophore-conjugated DpTz reagents afforded the fluorescently labeled GCGR and GLP-1R ECL mutants with labeling yield as high as 68%. A multitude of functional assays were performed with these GPCR mutants, including ligand binding, ligand-induced receptor internalization, and ligand-stimulated intracellular cAMP accumulation. Several positions in the ECL3s of GCGR and GLP-1R were identified that tolerate SphK mutagenesis and subsequent bioorthogonal labeling. The generation of functional, fluorescently labeled ECL3 mutants of GCGR and GLP-1R should allow biophysical studies of conformation dynamics of this important class of GPCRs in their native environment in live cells.
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Affiliation(s)
- Carlo P Ramil
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Maoqing Dong
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic , Scottsdale, Arizona 85259, United States
| | - Peng An
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Tracey M Lewandowski
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Zhipeng Yu
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
| | - Laurence J Miller
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic , Scottsdale, Arizona 85259, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260-3000, United States
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9
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Seidel L, Zarzycka B, Zaidi SA, Katritch V, Coin I. Structural insight into the activation of a class B G-protein-coupled receptor by peptide hormones in live human cells. eLife 2017; 6. [PMID: 28771403 PMCID: PMC5542768 DOI: 10.7554/elife.27711] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/17/2017] [Indexed: 12/22/2022] Open
Abstract
The activation mechanism of class B G-protein-coupled receptors (GPCRs) remains largely unknown. To characterize conformational changes induced by peptide hormones, we investigated interactions of the class B corticotropin-releasing factor receptor type 1 (CRF1R) with two peptide agonists and three peptide antagonists obtained by N-truncation of the agonists. Surface mapping with genetically encoded photo-crosslinkers and pair-wise crosslinking revealed distinct footprints of agonists and antagonists on the transmembrane domain (TMD) of CRF1R and identified numerous ligand-receptor contact sites, directly from the intact receptor in live human cells. The data enabled generating atomistic models of CRF- and CRF(12-41)-bound CRF1R, further explored by molecular dynamics simulations. We show that bound agonist and antagonist adopt different folds and stabilize distinct TMD conformations, which involves bending of helices VI and VII around flexible glycine hinges. Conservation of these glycine hinges among all class B GPCRs suggests their general role in activation of these receptors. DOI:http://dx.doi.org/10.7554/eLife.27711.001
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Affiliation(s)
- Lisa Seidel
- Institute of Biochemistry, Leipzig University, Leipzig, Germany
| | - Barbara Zarzycka
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, United States
| | - Saheem A Zaidi
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, United States
| | - Vsevolod Katritch
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, United States.,Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, United States
| | - Irene Coin
- Institute of Biochemistry, Leipzig University, Leipzig, Germany
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10
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Koole C, Reynolds CA, Mobarec JC, Hick C, Sexton PM, Sakmar TP. Genetically encoded photocross-linkers determine the biological binding site of exendin-4 peptide in the N-terminal domain of the intact human glucagon-like peptide-1 receptor (GLP-1R). J Biol Chem 2017; 292:7131-7144. [PMID: 28283573 PMCID: PMC5409479 DOI: 10.1074/jbc.m117.779496] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 03/09/2017] [Indexed: 12/25/2022] Open
Abstract
The glucagon-like peptide-1 receptor (GLP-1R) is a key therapeutic target in the management of type II diabetes mellitus, with actions including regulation of insulin biosynthesis and secretion, promotion of satiety, and preservation of β-cell mass. Like most class B G protein-coupled receptors (GPCRs), there is limited knowledge linking biological activity of the GLP-1R with the molecular structure of an intact, full-length, and functional receptor·ligand complex. In this study, we have utilized genetic code expansion to site-specifically incorporate the photoactive amino acid p-azido-l-phenylalanine (azF) into N-terminal residues of a full-length functional human GLP-1R in mammalian cells. UV-mediated photolysis of azF was then carried out to induce targeted photocross-linking to determine the proximity of the azido group in the mutant receptor with the peptide exendin-4. Cross-linking data were compared directly with the crystal structure of the isolated N-terminal extracellular domain of the GLP-1R in complex with exendin(9-39), revealing both similarities as well as distinct differences in the mode of interaction. Generation of a molecular model to accommodate the photocross-linking constraints highlights the potential influence of environmental conditions on the conformation of the receptor·peptide complex, including folding dynamics of the peptide and formation of dimeric and higher order oligomeric receptor multimers. These data demonstrate that crystal structures of isolated receptor regions may not give a complete reflection of peptide/receptor interactions and should be combined with additional experimental constraints to reveal peptide/receptor interactions occurring in the dynamic, native, and full-length receptor state.
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Affiliation(s)
- Cassandra Koole
- From the Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065
| | - Christopher A Reynolds
- the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Juan C Mobarec
- the School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom
| | - Caroline Hick
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia, and
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia, and
| | - Thomas P Sakmar
- From the Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University, New York, New York 10065,
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11
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Weaver RE, Mobarec JC, Wigglesworth MJ, Reynolds CA, Donnelly D. High affinity binding of the peptide agonist TIP-39 to the parathyroid hormone 2 (PTH 2) receptor requires the hydroxyl group of Tyr-318 on transmembrane helix 5. Biochem Pharmacol 2017; 127:71-81. [PMID: 28012961 PMCID: PMC5303546 DOI: 10.1016/j.bcp.2016.12.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/12/2016] [Indexed: 11/23/2022]
Abstract
TIP39 ("tuberoinfundibular peptide of 39 residues") acts via the parathyroid hormone 2 receptor, PTH2, a Family B G protein-coupled receptor (GPCR). Despite the importance of GPCRs in human physiology and pharmacotherapy, little is known about the molecular details of the TIP39-PTH2 interaction. To address this, we utilised the different pharmacological profiles of TIP39 and PTH(1-34) at PTH2 and its related receptor PTH1: TIP39 being an agonist at the former but an antagonist at the latter, while PTH(1-34) activates both. A total of 23 site-directed mutations of PTH2, in which residues were substituted to the equivalent in PTH1, were made and pharmacologically screened for agonist activity. Follow-up mutations were analysed by radioligand binding and cAMP assays. A model of the TIP39-PTH2 complex was built and analysed using molecular dynamics. Only Tyr318-Ile displayed reduced TIP39 potency, despite having increased PTH(1-34) potency, and further mutagenesis and analysis at this site demonstrated that this was due to reduced TIP39 affinity at Tyr318-Ile (pIC50=6.01±0.03) compared with wild type (pIC50=7.81±0.03). The hydroxyl group of the Tyr-318's side chain was shown to be important for TIP39 binding, with the Tyr318-Phe mutant displaying 13-fold lower affinity and 35-fold lower potency compared with wild type. TIP39 truncated by up to 5 residues at the N-terminus was still sensitive to the mutations at Tyr-318, suggesting that it interacts with a region within TIP39(6-39). Molecular modelling and molecular dynamics simulations suggest that the selectivity is based on an interaction between the Tyr-318 hydroxyl group with the carboxylate side chain of Asp-7 of the peptide.
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MESH Headings
- HEK293 Cells
- Humans
- Models, Molecular
- Mutation
- Neuropeptides/chemistry
- Neuropeptides/genetics
- Neuropeptides/pharmacology
- Protein Structure, Secondary
- Radioligand Assay
- Receptor, Parathyroid Hormone, Type 1/chemistry
- Receptor, Parathyroid Hormone, Type 1/metabolism
- Receptor, Parathyroid Hormone, Type 2/agonists
- Receptor, Parathyroid Hormone, Type 2/chemistry
- Receptor, Parathyroid Hormone, Type 2/metabolism
- Tyrosine/chemistry
- Tyrosine/genetics
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Affiliation(s)
- Richard E Weaver
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Juan C Mobarec
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Mark J Wigglesworth
- GlaxoSmithKline, New Frontiers Science Park North, Third Avenue, Harlow CM19 5AW, UK
| | - Christopher A Reynolds
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Dan Donnelly
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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12
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Wootten D, Miller LJ, Koole C, Christopoulos A, Sexton PM. Allostery and Biased Agonism at Class B G Protein-Coupled Receptors. Chem Rev 2016; 117:111-138. [PMID: 27040440 DOI: 10.1021/acs.chemrev.6b00049] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Class B G protein-coupled receptors (GPCRs) respond to paracrine or endocrine peptide hormones involved in control of bone homeostasis, glucose regulation, satiety, and gastro-intestinal function, as well as pain transmission. These receptors are targets for existing drugs that treat osteoporosis, hypercalcaemia, Paget's disease, type II diabetes, and obesity and are being actively pursued as targets for numerous other diseases. Exploitation of class B receptors has been limited by difficulties with small molecule drug discovery and development and an under appreciation of factors governing optimal therapeutic efficacy. Recently, there has been increasing awareness of novel attributes of GPCR function that offer new opportunity for drug development. These include the presence of allosteric binding sites on the receptor that can be exploited as drug binding pockets and the ability of individual drugs to enrich subpopulations of receptor conformations to selectively control signaling, a phenomenon termed biased agonism. In this review, current knowledge of biased signaling and small molecule allostery within class B GPCRs is discussed, highlighting areas that have progressed significantly over the past decade, in addition to those that remain largely unexplored with respect to these phenomena.
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Affiliation(s)
- Denise Wootten
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville 3052, Victoria, Australia
| | - Laurence J Miller
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic , Scottsdale, Arizona 85259, United States
| | - Cassandra Koole
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville 3052, Victoria, Australia.,Laboratory of Chemical Biology and Signal Transduction, The Rockefeller University , New York, New York 10065, United States
| | - Arthur Christopoulos
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville 3052, Victoria, Australia
| | - Patrick M Sexton
- Drug Discovery Biology and Department of Pharmacology, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville 3052, Victoria, Australia
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13
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Gardella TJ, Vilardaga JP. International Union of Basic and Clinical Pharmacology. XCIII. The parathyroid hormone receptors--family B G protein-coupled receptors. Pharmacol Rev 2015; 67:310-37. [PMID: 25713287 DOI: 10.1124/pr.114.009464] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The type-1 parathyroid hormone receptor (PTHR1) is a family B G protein-coupled receptor (GPCR) that mediates the actions of two polypeptide ligands; parathyroid hormone (PTH), an endocrine hormone that regulates the levels of calcium and inorganic phosphate in the blood by acting on bone and kidney, and PTH-related protein (PTHrP), a paracrine-factor that regulates cell differentiation and proliferation programs in developing bone and other tissues. The type-2 parathyroid hormone receptor (PTHR2) binds a peptide ligand, called tuberoinfundibular peptide-39 (TIP39), and while the biologic role of the PTHR2/TIP39 system is not as defined as that of the PTHR1, it likely plays a role in the central nervous system as well as in spermatogenesis. Mechanisms of action at these receptors have been explored through a variety of pharmacological and biochemical approaches, and the data obtained support a basic "two-site" mode of ligand binding now thought to be used by each of the family B peptide hormone GPCRs. Recent crystallographic studies on the family B GPCRs are providing new insights that help to further refine the specifics of the overall receptor architecture and modes of ligand docking. One intriguing pharmacological finding for the PTHR1 is that it can form surprisingly stable complexes with certain PTH/PTHrP ligand analogs and thereby mediate markedly prolonged cell signaling responses that persist even when the bulk of the complexes are found in internalized vesicles. The PTHR1 thus appears to be able to activate the Gα(s)/cAMP pathway not only from the plasma membrane but also from the endosomal domain. The cumulative findings could have an impact on efforts to develop new drug therapies for the PTH receptors.
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Affiliation(s)
- Thomas J Gardella
- Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts (T.J.G.); and Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (J.-P.V.)
| | - Jean-Pierre Vilardaga
- Endocrine Unit, Massachusetts General Hospital, Boston, Massachusetts (T.J.G.); and Laboratory for GPCR Biology, Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania (J.-P.V.)
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14
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Lee SM, Booe JM, Pioszak AA. Structural insights into ligand recognition and selectivity for classes A, B, and C GPCRs. Eur J Pharmacol 2015; 763:196-205. [PMID: 25981303 DOI: 10.1016/j.ejphar.2015.05.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 05/05/2015] [Accepted: 05/12/2015] [Indexed: 01/14/2023]
Abstract
The G protein-coupled receptor (GPCR) superfamily constitutes the largest collection of cell surface signaling proteins with approximately 800 members in the human genome. GPCRs regulate virtually all aspects of physiology and they are an important class of drug targets with ~30% of drugs on the market targeting a GPCR. Breakthroughs in GPCR structural biology in recent years have significantly expanded our understanding of GPCR structure and function and ushered in a new era of structure-based drug design for GPCRs. Crystal structures for nearly thirty distinct GPCRs are now available including receptors from each of the major classes, A, B, C, and F. These structures provide a foundation for understanding the molecular basis of GPCR pharmacology. Here, we review structural mechanisms of ligand recognition and selectivity of GPCRs with a focus on selected examples from classes A, B, and C, and we highlight major unresolved questions for future structural studies.
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Affiliation(s)
- Sang-Min Lee
- Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Jason M Booe
- Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Augen A Pioszak
- Department of Biochemistry and Molecular Biology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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15
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Milić D, Veprintsev DB. Large-scale production and protein engineering of G protein-coupled receptors for structural studies. Front Pharmacol 2015; 6:66. [PMID: 25873898 PMCID: PMC4379943 DOI: 10.3389/fphar.2015.00066] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 03/13/2015] [Indexed: 01/26/2023] Open
Abstract
Structural studies of G protein-coupled receptors (GPCRs) gave insights into molecular mechanisms of their action and contributed significantly to molecular pharmacology. This is primarily due to technical advances in protein engineering, production and crystallization of these important receptor targets. On the other hand, NMR spectroscopy of GPCRs, which can provide information about their dynamics, still remains challenging due to difficulties in preparation of isotopically labeled receptors and their low long-term stabilities. In this review, we discuss methods used for expression and purification of GPCRs for crystallographic and NMR studies. We also summarize protein engineering methods that played a crucial role in obtaining GPCR crystal structures.
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Affiliation(s)
- Dalibor Milić
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen Switzerland
| | - Dmitry B Veprintsev
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen Switzerland ; Department of Biology, Eidgenössische Technische Hochschule Zürich, Zürich Switzerland
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16
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Singh R, Ahalawat N, Murarka RK. Activation of corticotropin-releasing factor 1 receptor: insights from molecular dynamics simulations. J Phys Chem B 2015; 119:2806-17. [PMID: 25607803 DOI: 10.1021/jp509814n] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
G-protein-coupled receptors (GPCRs) constitute the largest family of membrane-bound proteins involved in translation of extracellular signals into intracellular responses. They regulate diverse physiological and pathophysiological processes, and hence, they are prime drug targets for therapeutic intervention. In spite of the recent advancements in membrane protein crystallography, limited information is available on the molecular signatures of activation of GPCRs. Although few studies have been reported for class A GPCRs, the activation mechanism of class B GPCRs remains unexplored. Corticotropin-releasing factor 1 receptor (CRF1R), a class B GPCR, is associated with various disease conditions including stress, anxiety, and irritable bowel syndrome. Here, we report the activation of CRF1R using accelerated molecular dynamics simulations of the apo receptor. The breakage of His155(2.50)-Glu209(3.50) and Glu209(3.50)-Thr316(6.42) interactions is found to be crucial in transition of the receptor to its active conformation. Compared to the inactive crystal structure, major structural rearrangements occurred in the intracellular region of the transmembrane (TM) domain upon activation: TM3 twisted away from TM2, and an opening of the G-protein binding site occurred as a result of the outward movements of TM5 and TM6 from the helical bundle. Further, an inward tilt of TM7 toward the helical core is observed at the extracellular side, in agreement with recent findings (Coin et al. Cell 2013, 155, 1258-1269), where it is proposed that this movement helps in establishing favorable interactions with peptide agonist. Moreover, different allosteric pathways in the inactive and active states are identified using the correlations in torsion angle space. The inactive state is found to be less dynamic as compared to the putative active state of the receptor. Results from the current study could present a model for class B GPCRs activation and aid in the design of CRF1R modulators against brain and metabolic disorders.
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Affiliation(s)
- Rajesh Singh
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal , Indore By-pass Road, Bhauri, Bhopal 462066, MP, India
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17
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Summers RJ. Editorial. Themed issue of the British Journal of Pharmacology. Br J Pharmacol 2014; 171:1069-72. [PMID: 24575818 DOI: 10.1111/bph.12587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
This themed issue of the British Journal of Pharmacology stems from the 7th in the series of meetings on the Molecular Pharmacology of G Protein-Coupled Receptors (MPGPCR) held at the Monash Institute of Pharmaceutical Sciences in Melbourne Australia from the 6th-8th December 2012.
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Affiliation(s)
- R J Summers
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Parkville, Vic, Australia; Department of Pharmacology, Monash University, Clayton, Vic, Australia
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18
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Yu Z, Lin Q. Design of spiro[2.3]hex-1-ene, a genetically encodable double-strained alkene for superfast photoclick chemistry. J Am Chem Soc 2014; 136:4153-6. [PMID: 24592808 PMCID: PMC3971965 DOI: 10.1021/ja5012542] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Reactive yet stable alkene reporters
offer a facile route to studying
fast biological processes via the cycloaddition-based bioorthogonal
reactions. Here, we report the design and synthesis of a strained
spirocyclic alkene, spiro[2.3]hex-1-ene (Sph), for an accelerated
photoclick chemistry, and its site-specific introduction into proteins
via amber codon suppression using the wild-type pyrrolysyl-tRNA synthetase/tRNACUA pair. Because of its high ring strain and reduced steric
hindrance, Sph exhibited fast reaction kinetics (k2 up to 34 000 M–1 s–1) in the photoclick chemistry and afforded rapid (<10 s) bioorthogonal
protein labeling.
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Affiliation(s)
- Zhipeng Yu
- Department of Chemistry, State University of New York at Buffalo , Buffalo, New York 14260, United States
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