Purinergic GPCR transmembrane residues involved in ligand recognition and dimerization
Tài liệu tham khảo
Al-Shar'i, 2019, Molecular dynamics simulations of adenosine receptors: Advances, applications and trends, Current Pharmaceutical Design, 25, 783, 10.2174/1381612825666190304123414
Attah, 2020, Ligand binding and activation of UTP-activated G protein-coupled P2Y2 and P2Y4 receptors elucidated by mutagenesis, pharmacological and computational studies, Biochimica et Biophysica Acta—General Subjects, 1864, 10.1016/j.bbagen.2019.129501
Ballante, 2020, Docking finds GPCR ligands in dark chemical matter, Journal of Medicinal Chemistry, 63, 613, 10.1021/acs.jmedchem.9b01560
Ballesteros, 1995, Integrated methods for the construction of three dimensional models and computational probing of structure function relations in G protein-coupled receptors, Methods in Neurosciences, 25, 366, 10.1016/S1043-9471(05)80049-7
Batyuk, 2016, Native phasing of x-ray free-electron laser data for a G protein-coupled receptor, Science Advances, 2, 10.1126/sciadv.1600292
Berman, 2000, The Protein Data Bank, Nucleic Acids Research, 28, 235, 10.1093/nar/28.1.235
Borodovsky, 2020, Small molecule AZD4635 inhibitor of A2AR signaling rescues immune cell function including CD103(+) dendritic cells enhancing anti-tumor immunity, Journal for Immunotherapy of Cancer, 8, 10.1136/jitc-2019-000417
Borroto-Escuela, 2020, Multiple adenosine-dopamine (A2A-D2 like) heteroreceptor complexes in the brain and their role in schizophrenia, Cell, 9
Borroto-Escuela, 2018, Mapping the Interface of a GPCR dimer: A structural model of the A2A adenosine and D2 dopamine receptor heteromer, Frontiers in Pharmacology, 9, 829, 10.3389/fphar.2018.00829
Broecker, 2018, High-throughput in situ X-ray screening of and data collection from protein crystals at room temperature and under cryogenic conditions, Nature Protocols, 13, 260, 10.1038/nprot.2017.135
Cao, 2018, Role of extracellular loops and membrane lipids for ligand recognition in the neuronal adenosine receptor type 2A: An enhanced sampling simulation study, Molecules, 23, 10.3390/molecules23102616
Carpenter, 2016, Structure of the adenosine A(2A) receptor bound to an engineered G protein, Nature, 536, 104, 10.1038/nature18966
Carpenter, 2017, Active state structures of G protein-coupled receptors highlight the similarities and differences in the G protein and arrestin coupling interfaces, Current Opinion in Structural Biology, 45, 124, 10.1016/j.sbi.2017.04.010
Cheng, 2017, Structures of human A1 and A2A adenosine receptors with xanthines reveal determinants of selectivity, Structure, 25, 1275, 10.1016/j.str.2017.06.012
Ciancetta, 2018, Breakthrough in GPCR crystallography and its impact on computer-aided drug design, Methods in Molecular Biology, 1705, 45, 10.1007/978-1-4939-7465-8_3
Ciancetta, 2019, A3 adenosine receptor activation mechanisms: Molecular dynamics analysis of inactive, active, and fully active states, Journal of Computer-Aided Molecular Design, 33, 983, 10.1007/s10822-019-00246-4
Congreve, 2012, Discovery of 1,2,4-triazine derivatives as adenosine A(2A) antagonists using structure based drug design, Journal of Medicinal Chemistry, 55, 1898, 10.1021/jm201376w
Congreve, 2020, Impact of GPCR structures on drug discovery, Cell, 181, 81, 10.1016/j.cell.2020.03.003
Dal Ben, 2014, Different efficacy of adenosine and NECA derivatives at the human A3 adenosine receptor: Insight into the receptor activation switch, Biochemical Pharmacology, 87, 321, 10.1016/j.bcp.2013.10.011
Dal Ben, 2019, Non-nucleoside agonists of the adenosine receptors: An overview, Pharmaceuticals (Basel, Switzerland), 12, 150, 10.3390/ph12040150
Doré, 2011, Structure of the adenosine A(2A) receptor in complex with ZM241385 and the xanthines XAC and caffeine, Structure, 19, 1283, 10.1016/j.str.2011.06.014
Draper-Joyce, 2018, Structure of the adenosine-bound human adenosine A1 receptor-Gi complex, Nature, 558, 559, 10.1038/s41586-018-0236-6
Eddy, 2018, Allosteric coupling of drug binding and intracellular signaling in the A2A adenosine receptor, Cell, 172, 68, 10.1016/j.cell.2017.12.004
Felce, 2017, Receptor quaternary organization explains G protein-coupled receptor family structure, Cell Reports, 20, 2654, 10.1016/j.celrep.2017.08.072
Fernandez-Duenas, 2012, Molecular determinants of A2AR-D2R allosterism: Role of the intracellular loop 3 of the D2R, Journal of Neurochemistry, 123, 373, 10.1111/j.1471-4159.2012.07956.x
Filipek, 2019, Molecular switches in GPCRs, Current Opinion in Structural Biology, 55, 114, 10.1016/j.sbi.2019.03.017
García-Nafría, 2018, Cryo-EM structure of the adenosine A2A receptor coupled to an engineered heterotrimeric G protein, elife, 7, 10.7554/eLife.35946
García-Recio, 2020, DIMERBOW: Exploring possible GPCR dimer interfaces, Bioinformatics, 36, 3271, 10.1093/bioinformatics/btaa117
Glukhova, 2017, Structure of the adenosine A1 receptor reveals the basis for subtype selectivity, Cell, 168, 867, 10.1016/j.cell.2017.01.042
Gutierrez-de-Teran, 2017, Structure-based rational design of adenosine receptor ligands, Current Topics in Medicinal Chemistry, 17, 40, 10.2174/1568026616666160719164207
Hill, 2014, Allosteric interactions at adenosine A(1) and A(3) receptors: New insights into the role of small molecules and receptor dimerization, British Journal of Pharmacology, 171, 1102, 10.1111/bph.12345
Hino, 2012, G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody, Nature, 482, 237, 10.1038/nature10750
Hinz, 2018, Adenosine A2A receptor ligand recognition and signaling is blocked by A2B receptors, Oncotarget, 9, 13593, 10.18632/oncotarget.24423
Huang, 2013, Crystal structure of oligomeric beta1-adrenergic G protein-coupled receptors in ligand-free basal state, Nature Structural & Molecular Biology, 20, 419, 10.1038/nsmb.2504
Ihara, 2020, Isoprenoid-chained lipid EROCOC17+4: A new matrix for membrane protein crystallization and a crystal delivery medium in serial femtosecond crystallography, Scientific Reports, 10, 19305, 10.1038/s41598-020-76277-x
Ishchenko, 2019, Toward G protein-coupled receptor structure-based drug design using X-ray lasers, IUCrJ, 6, 1106, 10.1107/S2052252519013137
Jaakola, 2008, The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist, Science, 322, 1211, 10.1126/science.1164772
Jacobson, 2009, Functionalized congener approach to the design of ligands for G protein–coupled receptors (GPCRs), Bioconjugate Chemistry, 20, 1816, 10.1021/bc9000596
Jacobson, 2020, Update of P2Y receptor pharmacology: IUPHAR Review 27, British Journal of Pharmacology, 177, 2413, 10.1111/bph.15005
Jacobson, 2021, Medicinal chemistry of P2 and adenosine receptors: Common scaffolds adapted for multiple targets, Biochemical Pharmacology, 187, 114311, 10.1016/j.bcp.2020.114311
Jespers, 2017, Structure-based design of potent and selective ligands at the four adenosine receptors, Molecules, 22, 10.3390/molecules22111945
Jespers, 2020, X-ray crystallography and free energy calculations reveal the binding mechanism of A2A adenosine receptor antagonists, Angewandte Chemie (International Ed. in English), 59, 16536, 10.1002/anie.202003788
Johnston, 2012, Assessing the relative stability of dimer interfaces in g protein-coupled receptors, PLoS Computational Biology, 8, 10.1371/journal.pcbi.1002649
Jung, 2020, Exploration of alternative scaffolds for P2Y14 receptor antagonists containing a biaryl core, Journal of Medicinal Chemistry, 63, 9563, 10.1021/acs.jmedchem.0c00745
Junker, 2016, Structure-based design of 3-(4-aryl-1H-1,2,3-triazol-1-yl)-biphenyl derivatives as P2Y14 receptor antagonists, Journal of Medicinal Chemistry, 59, 6149, 10.1021/acs.jmedchem.6b00044
Kim, 2006, Computational prediction of homodimerization of the A3 adenosine receptor, Journal of Molecular Graphics & Modelling, 25, 549, 10.1016/j.jmgm.2006.03.003
Kooistra, 2021, GPCRdb in 2021: Integrating GPCR sequence, structure and function, Nucleic Acids Research, 49, D335, 10.1093/nar/gkaa1080
Kose, 2018, Fluorescent-labeled selective adenosine A2B receptor antagonist enables competition binding assay by flow cytometry, Journal of Medicinal Chemistry, 61, 4301, 10.1021/acs.jmedchem.7b01627
Lebon, 2015, Molecular determinants of CGS21680 binding to the human adenosine A2A receptor, Molecular Pharmacology, 87, 907, 10.1124/mol.114.097360
Lebon, 2011, Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation, Nature, 474, 521, 10.1038/nature10136
Lee, 2020, Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase, IUCrJ, 7, 976, 10.1107/S2052252520012701
Liu, 2012, Structural basis for allosteric regulation of GPCRs by sodium ions, Science, 337, 232, 10.1126/science.1219218
Martin-Garcia, 2017, Serial millisecond crystallography of membrane and soluble protein microcrystals using synchrotron radiation, IUCrJ, 4, 439, 10.1107/S205225251700570X
Martin-Garcia, 2019, High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source, IUCrJ, 6, 412, 10.1107/S205225251900263X
Marullo, 2020, Mechanical GPCR activation by traction forces exerted on receptor N-glycans, ACS Pharmacology and Translational Science, 3, 171, 10.1021/acsptsci.9b00106
Matricon, 2021, Ligand design by targeting a binding site water, Chemical Science, 12, 960, 10.1039/D0SC04938G
May, 2011, Allosteric interactions across native adenosine-A3 receptor homodimers: Quantification using single-cell ligand-binding kinetics, The FASEB Journal, 25, 3465, 10.1096/fj.11-186296
Melnikov, 2017, Fast iodide-SAD phasing for high-throughput membrane protein structure determination, Science Advances, 3, 10.1126/sciadv.1602952
Moro, 1999, Role of the extracellular loops of G protein-coupled receptors in ligand recognition: A molecular modeling study of the human P2Y1 receptor, Biochemistry, 38, 3498, 10.1021/bi982369v
Nass, 2020, Advances in long-wavelength native phasing at X-ray free-electron lasers, IUCrJ, 7, 965, 10.1107/S2052252520011379
Navarro, 2016, Quaternary structure of a G-protein-coupled receptor heterotetramer in complex with Gi and Gs, BMC Biology, 14, 26, 10.1186/s12915-016-0247-4
Neumann, 2020, P2Y1-like nucleotide receptors—Structures, molecular modeling, mutagenesis, and oligomerization, WIREs Computational Molecular Science, 10, e1464, 10.1002/wcms.1464
Pedata, 2014, Adenosine A2A receptors modulate acute injury and neuroinflammation in brain ischemia, Mediators of Inflammation, 2014, 805198, 10.1155/2014/805198
Pin, 2019, GPCR interaction as a possible way for allosteric control between receptors, Molecular and Cellular Endocrinology, 486, 89, 10.1016/j.mce.2019.02.019
Qu, 2020, Chapter 1—Progress in GPCR structure determination, 3
Rodriguez, 2016, Structure-based screening of uncharted chemical space for atypical adenosine receptor agonists, ACS Chemical Biology, 11, 2763, 10.1021/acschembio.6b00357
Rodriguez-Espigares, 2020, GPCRmd uncovers the dynamics of the 3D-GPCRome, Nature Methods, 17, 777, 10.1038/s41592-020-0884-y
Rucktooa, 2018, Towards high throughput GPCR crystallography: In meso soaking of adenosine A2A receptor crystals, Scientific Reports, 8, 41, 10.1038/s41598-017-18570-w
Safdari, 2018, Illuminating GPCR signaling by cryo-EM, Trends in Cell Biology, 28, 591, 10.1016/j.tcb.2018.06.002
Salmaso, 2020, In silico drug design for purinergic GPCRs: Overview on molecular dynamics applied to adenosine and P2Y receptors, Biomolecules, 10, 10.3390/biom10060812
Salmaso, 2020, Purinergic signaling: Impact of GPCR structures on rational drug design, ChemMedChem, 15, 1958, 10.1002/cmdc.202000465
Segala, 2016, Controlling the dissociation of ligands from the adenosine A2A receptor through modulation of salt bridge strength, Journal of Medicinal Chemistry, 59, 6470, 10.1021/acs.jmedchem.6b00653
Shimazu, 2019, High-viscosity sample-injection device for serial femtosecond crystallography at atmospheric pressure, Journal of Applied Crystallography, 52, 1280, 10.1107/S1600576719012846
Sun, 2017, Crystal structure of the adenosine A2A receptor bound to an antagonist reveals a potential allosteric pocket, Proceedings of the National Academy of Sciences of the United States of America, 114, 2066, 10.1073/pnas.1621423114
Thevenin, 2005, Oligomerization of the fifth transmembrane domain from the adenosine A2A receptor, Protein Science, 14, 2177, 10.1110/ps.051409205
Tosh, 2012, Structure-guided design of A(3) adenosine receptor-selective nucleosides: Combination of 2-arylethynyl and bicyclo[3.1.0]hexane substitutions, Journal of Medicinal Chemistry, 55, 4847, 10.1021/jm300396n
Tosh, 2020, Truncated (N)-methanocarba nucleosides as partial agonists at mouse and human A3 adenosine receptors: Affinity enhancement by N(6)-(2-phenylethyl) substitution, Journal of Medicinal Chemistry, 63, 4334, 10.1021/acs.jmedchem.0c00235
Tosh, 2020, Direct comparison of (N)-methanocarba and ribose-containing 2-arylalkynyladenosine derivatives as A3 receptor agonists, ACS Medicinal Chemistry Letters, 11, 1935, 10.1021/acsmedchemlett.9b00637
Toti, 2017, Pyrimidine nucleotides containing a (S)-methanocarba ring as P2Y6 receptor agonists, Medicinal Chemistry Communications, 8, 1897, 10.1039/C7MD00397H
Townsend-Nicholson, 2019, Computational prediction of GPCR oligomerization, Current Opinion in Structural Biology, 55, 178, 10.1016/j.sbi.2019.04.005
van Rhee, 1996, Molecular architecture of G protein-coupled receptors, Drug Development Research, 37, 1, 10.1002/(SICI)1098-2299(199601)37:1<1::AID-DDR1>3.0.CO;2-S
Vasiliauskaite-Brooks, 2019, 7TM proteins are not necessarily GPCRs, Molecular and Cellular Endocrinology, 491, 10.1016/j.mce.2019.02.009
Velazhahan, 2021, Structure of the class D GPCR Ste2 dimer coupled to two G proteins, Nature, 589, 148, 10.1038/s41586-020-2994-1
Venkatakrishnan, 2013, Molecular signatures of G-protein-coupled receptors, Nature, 494, 185, 10.1038/nature11896
Venkatakrishnan, 2019, Diverse GPCRs exhibit conserved water networks for stabilization and activation, Proceedings of the National Academy of Sciences of the United States of America, 116, 3288, 10.1073/pnas.1809251116
Wacker, 2017, How ligands illuminate GPCR molecular pharmacology, Cell, 170, 414, 10.1016/j.cell.2017.07.009
Warne, 2019, Molecular basis for high-affinity agonist binding in GPCRs, Science, 364, 775, 10.1126/science.aau5595
Weinert, 2017, Serial millisecond crystallography for routine room-temperature structure determination at synchrotrons, Nature Communications, 8, 542, 10.1038/s41467-017-00630-4
White, 2018, Structural connection between activation microswitch and allosteric sodium site in GPCR signaling, Structure, 26, 259, 10.1016/j.str.2017.12.013
Wold, 2019, Allosteric modulation of class A GPCRs: Targets, agents, and emerging concepts, Journal of Medicinal Chemistry, 62, 88, 10.1021/acs.jmedchem.8b00875
Xu, 2011, Structure of an agonist-bound human A2A adenosine receptor, Science, 332, 322, 10.1126/science.1202793
Yu, 2018, Structure-guided modification of heterocyclic antagonists of the P2Y14 receptor, Journal of Medicinal Chemistry, 61, 4860, 10.1021/acs.jmedchem.8b00168
Zhang, 2015, Two disparate ligand-binding sites in the human P2Y1 receptor, Nature, 520, 317, 10.1038/nature14287
Zhang, 2014, Agonist-bound structure of the human P2Y12 receptor, Nature, 509, 119, 10.1038/nature13288
Zhang, 2014, Structure of the human P2Y12 receptor in complex with an antithrombotic drug, Nature, 509, 115, 10.1038/nature13083
Zhou, 2019, Common activation mechanism of class A GPCRs, eLife, 8, 10.7554/eLife.50279