1
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Pan D, Ladds G, Rahman KM, Pitchford SC. Exploring bias in platelet P2Y 1 signalling: Host defence versus haemostasis. Br J Pharmacol 2024; 181:580-592. [PMID: 37442808 PMCID: PMC10952580 DOI: 10.1111/bph.16191] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
Platelets are necessary for maintaining haemostasis. Separately, platelets are important for the propagation of inflammation during the host immune response against infection. The activation of platelets also causes inappropriate inflammation in various disease pathologies, often in the absence of changes to haemostasis. The separate functions of platelets during inflammation compared with haemostasis are therefore varied and this will be reflected in distinct pathways of activation. The activation of platelets by the nucleotide adenosine diphosphate (ADP) acting on P2Y1 and P2Y12 receptors is important for the development of platelet thrombi during haemostasis. However, P2Y1 stimulation of platelets is also important during the inflammatory response and paradoxically in scenarios where no changes to haemostasis and platelet aggregation occur. In these events, Rho-GTPase signalling, rather than the canonical phospholipase Cβ (PLCβ) signalling pathway, is necessary. We describe our current understanding of these differences, reflecting on recent advances in knowledge of P2Y1 structure, and the possibility of biased agonism occurring from activation via other endogenous nucleotides compared with ADP. Knowledge arising from these different pathways of P2Y1 stimulation of platelets during inflammation compared with haemostasis may help therapeutic control of platelet function during inflammation or infection, while preserving essential haemostasis. LINKED ARTICLES: This article is part of a themed issue on Platelet purinergic receptor and non-thrombotic disease. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v181.4/issuetoc.
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Affiliation(s)
- Dingxin Pan
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical ScienceKing's College LondonLondonUK
| | - Graham Ladds
- Department of PharmacologyUniversity of CambridgeCambridgeUK
| | - Khondaker Miraz Rahman
- Chemical Biology Group, Institute of Pharmaceutical ScienceKing's College LondonLondonUK
| | - Simon C. Pitchford
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical ScienceKing's College LondonLondonUK
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2
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Neumann A, Attah I, Al-Hroub H, Namasivayam V, Müller CE. Discovery of P2Y 2 Receptor Antagonist Scaffolds through Virtual High-Throughput Screening. J Chem Inf Model 2022; 62:1538-1549. [DOI: 10.1021/acs.jcim.1c01235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Neumann
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, 53121 Bonn, Germany
- Research Training Group 1873, University of Bonn, 53127 Bonn, Germany
| | - Isaac Attah
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, 53121 Bonn, Germany
| | - Haneen Al-Hroub
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, 53121 Bonn, Germany
| | - Vigneshwaran Namasivayam
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, 53121 Bonn, Germany
| | - Christa E. Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical & Medicinal Chemistry, University of Bonn, 53121 Bonn, Germany
- Research Training Group 1873, University of Bonn, 53127 Bonn, Germany
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3
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Alberto AVP, da Silva Ferreira NC, Soares RF, Alves LA. Molecular Modeling Applied to the Discovery of New Lead Compounds for P2 Receptors Based on Natural Sources. Front Pharmacol 2020; 11:01221. [PMID: 33117147 PMCID: PMC7553047 DOI: 10.3389/fphar.2020.01221] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/27/2020] [Indexed: 12/24/2022] Open
Abstract
P2 receptors are a family of transmembrane receptors activated by nucleotides and nucleosides. Two classes have been described in mammals, P2X and P2Y, which are implicated in various diseases. Currently, only P2Y12 has medicines approved for clinical use as antiplatelet agents and natural products have emerged as a source of new drugs with action on P2 receptors due to the diversity of chemical structures. In drug discovery, in silico virtual screening (VS) techniques have become popular because they have numerous advantages, which include the evaluation of thousands of molecules against a target, usually proteins, faster and cheaper than classical high throughput screening (HTS). The number of studies using VS techniques has been growing in recent years and has led to the discovery of new molecules of natural origin with action on different P2X and P2Y receptors. Using different algorithms it is possible to obtain information on absorption, distribution, metabolism, toxicity, as well as predictions on biological activity and the lead-likeness of the selected hits. Selected biomolecules may then be tested by molecular dynamics and, if necessary, rationally designed or modified to improve their interaction for the target. The algorithms of these in silico tools are being improved to permit the precision development of new drugs and, in the future, this process will take the front of drug development against some central nervous system (CNS) disorders. Therefore, this review discusses the methodologies of in silico tools concerning P2 receptors, as well as future perspectives and discoveries, such as the employment of artificial intelligence in drug discovery.
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Affiliation(s)
- Anael Viana Pinto Alberto
- Laboratory of Cellular Communication, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | - Rafael Ferreira Soares
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Luiz Anastacio Alves
- Laboratory of Cellular Communication, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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4
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Jacobson KA, Delicado EG, Gachet C, Kennedy C, von Kügelgen I, Li B, Miras-Portugal MT, Novak I, Schöneberg T, Perez-Sen R, Thor D, Wu B, Yang Z, Müller CE. Update of P2Y receptor pharmacology: IUPHAR Review 27. Br J Pharmacol 2020; 177:2413-2433. [PMID: 32037507 DOI: 10.1111/bph.15005] [Citation(s) in RCA: 150] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 01/12/2020] [Accepted: 01/15/2020] [Indexed: 02/06/2023] Open
Abstract
Eight G protein-coupled P2Y receptor subtypes respond to extracellular adenine and uracil mononucleotides and dinucleotides. P2Y receptors belong to the δ group of rhodopsin-like GPCRs and contain two structurally distinct subfamilies: P2Y1 , P2Y2 , P2Y4 , P2Y6 , and P2Y11 (principally Gq protein-coupled P2Y1 -like) and P2Y12-14 (principally Gi protein-coupled P2Y12 -like) receptors. Brain P2Y receptors occur in neurons, glial cells, and vasculature. Endothelial P2Y1 , P2Y2 , P2Y4 , and P2Y6 receptors induce vasodilation, while smooth muscle P2Y2 , P2Y4 , and P2Y6 receptor activation leads to vasoconstriction. Pancreatic P2Y1 and P2Y6 receptors stimulate while P2Y13 receptors inhibits insulin secretion. Antagonists of P2Y12 receptors, and potentially P2Y1 receptors, are anti-thrombotic agents, and a P2Y2 /P2Y4 receptor agonist treats dry eye syndrome in Asia. P2Y receptor agonists are generally pro-inflammatory, and antagonists may eventually treat inflammatory conditions. This article reviews recent developments in P2Y receptor pharmacology (using synthetic agonists and antagonists), structure and biophysical properties (using X-ray crystallography, mutagenesis and modelling), physiological and pathophysiological roles, and present and potentially future therapeutic targeting.
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Affiliation(s)
- Kenneth A Jacobson
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Massachusetts
| | - Esmerilda G Delicado
- Dpto. Bioquimica y Biologia Molecular, Universidad Complutense de Madrid, Madrid, Spain
| | - Christian Gachet
- Université de Strasbourg INSERM, EFS Grand Est, BPPS UMR-S 1255, FMTS, Strasbourg, France
| | - Charles Kennedy
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Ivar von Kügelgen
- Biomedical Research Center, Department of Pharmacology and Toxicology, University of Bonn, Bonn, Germany
| | - Beibei Li
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | | | - Ivana Novak
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Torsten Schöneberg
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany
| | - Raquel Perez-Sen
- Dpto. Bioquimica y Biologia Molecular, Universidad Complutense de Madrid, Madrid, Spain
| | - Doreen Thor
- Rudolf Schönheimer Institute of Biochemistry, Molecular Biochemistry, Medical Faculty, Leipzig University, Leipzig, Germany.,IFB AdiposityDiseases, Leipzig University Medical Center, Leipzig, Germany
| | - Beili Wu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhenlin Yang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Christa E Müller
- Pharmaceutical Institute, Department of Pharmaceutical and Medicinal Chemistry, University of Bonn, Bonn, Germany
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5
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von Kügelgen I. Pharmacology of P2Y receptors. Brain Res Bull 2019; 151:12-24. [PMID: 30922852 DOI: 10.1016/j.brainresbull.2019.03.010] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 03/04/2019] [Accepted: 03/17/2019] [Indexed: 01/17/2023]
Abstract
P2Y receptors are G-protein-coupled receptors (GPCRs) for extracellular nucleotides. There are eight mammalian P2Y receptor subtypes divided into two subgroups (P2Y1, P2Y2, P2Y4, P2Y6, and P2Y11) and (P2Y12, P2Y13, and P2Y14). The P2Y receptors are expressed in various cell types and play important roles in physiology and pathophysiology including inflammatory responses and neuropathic pain. The antagonism of P2Y12 receptors is used in pharmacotherapy for the prevention and therapy of cardiovascular events. The nucleoside analogue ticagrelor and active metabolites of the thienopyridine compounds ticlopidine, clopidogrel and prasugrel inhibit platelet P2Y12 receptors and reduce thereby platelet aggregation. The P2Y2 receptor agonist diquafosol is used for the treatment of the dry eye syndrome. The P2Y receptor subtypes differ in their amino acid sequences, their pharmacological profiles and their signaling transduction pathways. Recently, selective receptor ligands have been developed for all subtypes. The published crystal structures of the human P2Y1 and P2Y12 receptors as well as receptor models will facilitate the development of novel drugs for pharmacotherapy.
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Affiliation(s)
- Ivar von Kügelgen
- Department of Pharmacology and Toxicology, Pharma Center, University of Bonn, D-53127, Bonn, Germany.
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6
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Moldovan RP, Wenzel B, Teodoro R, Neumann W, Dukic-Stefanovic S, Kraus W, Rong P, Deuther-Conrad W, Hey-Hawkins E, Krügel U, Brust P. Studies towards the development of a PET radiotracer for imaging of the P2Y 1 receptors in the brain: synthesis, 18F-labeling and preliminary biological evaluation. Eur J Med Chem 2019; 165:142-159. [PMID: 30665144 DOI: 10.1016/j.ejmech.2019.01.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/20/2018] [Accepted: 01/04/2019] [Indexed: 12/14/2022]
Abstract
Purine nucleotides such as ATP and ADP are important extracellular signaling molecules in almost all tissues activating various subtypes of purinoreceptors. In the brain, the P2Y1 receptor (P2Y1R) subtype mediates trophic functions like differentiation and proliferation, and modulates fast synaptic transmission, both suggested to be affected in diseases of the central nervous system. Research on P2Y1R is limited because suitable brain-penetrating P2Y1R-selective tracers are not yet available. Here, we describe the first efforts to develop an 18F-labeled PET tracer based on the structure of the highly affine and selective, non-nucleotidic P2Y1R allosteric modulator 1-(2-[2-(tert-butyl)phenoxy]pyridin-3-yl)-3-[4-(trifluoromethoxy)phenyl]urea (7). A small series of fluorinated compounds was developed by systematic modification of the p-(trifluoromethoxy)phenyl, the urea and the 2-pyridyl subunits of the lead compound 7. Additionally, the p-(trifluoromethoxy)phenyl subunit was substituted by carborane, a boron-rich cluster with potential applicability in boron neutron capture therapy (BNCT). By functional assays, the new fluorinated derivative 1-{2-[2-(tert-butyl)phenoxy]pyridin-3-yl}-3-[4-(2-fluoroethyl)phenyl]urea (18) was identified with a high P2Y1R antagonistic potency (IC50 = 10 nM). Compound [18F]18 was radiosynthesized by using tetra-n-butyl ammonium [18F]fluoride with high radiochemical purity, radiochemical yield and molar activities. Investigation of brain homogenates using hydrophilic interaction chromatography (HILIC) revealed [18F]fluoride as major radiometabolite. Although [18F]18 showed fast in vivo metabolization, the high potency and unique allosteric binding mode makes this class of compounds interesting for further optimizations and investigation of the theranostic potential as PET tracer and BNCT agent.
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Affiliation(s)
- Rareş-Petru Moldovan
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Permoserstraße 15, 04318, Leipzig, Germany.
| | - Barbara Wenzel
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Permoserstraße 15, 04318, Leipzig, Germany
| | - Rodrigo Teodoro
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Permoserstraße 15, 04318, Leipzig, Germany
| | - Wilma Neumann
- Institute of Inorganic Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103, Leipzig, Germany
| | - Sladjana Dukic-Stefanovic
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Permoserstraße 15, 04318, Leipzig, Germany
| | - Werner Kraus
- BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Str. 11, 12489, Berlin, Germany
| | - Peijing Rong
- Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, 100700, Beijing, China
| | - Winnie Deuther-Conrad
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Permoserstraße 15, 04318, Leipzig, Germany
| | - Evamarie Hey-Hawkins
- Institute of Inorganic Chemistry, Faculty of Chemistry and Mineralogy, Universität Leipzig, 04103, Leipzig, Germany
| | - Ute Krügel
- Rudolf Boehm Institute of Pharmacology and Toxicology, Medical Faculty, Universität Leipzig, 04107, Leipzig, Germany
| | - Peter Brust
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Radiopharmaceutical Cancer Research, Permoserstraße 15, 04318, Leipzig, Germany
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7
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Structural insights into serotonin receptor ligands polypharmacology. Eur J Med Chem 2018; 151:797-814. [DOI: 10.1016/j.ejmech.2018.04.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 02/03/2023]
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8
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Ciancetta A, O'Connor RD, Paoletta S, Jacobson KA. Demystifying P2Y 1 Receptor Ligand Recognition through Docking and Molecular Dynamics Analyses. J Chem Inf Model 2017; 57:3104-3123. [PMID: 29182323 DOI: 10.1021/acs.jcim.7b00528] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We performed a molecular modeling analysis of 100 nucleotide-like bisphosphates and 46 non-nucleotide arylurea derivatives previously reported as P2Y1R binders using the recently solved hP2Y1R structures. We initially docked the compounds at the X-ray structures and identified the binding modes of representative compounds highlighting key patterns in the structure-activity relationship (SAR). We subsequently subjected receptor complexes with selected key agonists (2MeSADP and MRS2268) and antagonists (MRS2500 and BPTU) to membrane molecular dynamics (MD) simulations (at least 200 ns run in triplicate, simulation time 0.6-1.6 μs per ligand system) while considering alternative protonation states of nucleotides. Comparing the temporal evolution of the ligand-protein interaction patterns with available site-directed mutagenesis (SDM) data and P2Y1R apo state simulation provided further SAR insights and suggested reasonable explanations for loss/gain of binding affinity as well as the most relevant charged species for nucleotide ligands. The MD analysis also predicted local conformational changes required for the receptor inactive state to accommodate nucleotide agonists.
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Affiliation(s)
- Antonella Ciancetta
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Robert D O'Connor
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Silvia Paoletta
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
| | - Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, United States
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9
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Rafehi M, Neumann A, Baqi Y, Malik EM, Wiese M, Namasivayam V, Müller CE. Molecular Recognition of Agonists and Antagonists by the Nucleotide-Activated G Protein-Coupled P2Y 2 Receptor. J Med Chem 2017; 60:8425-8440. [PMID: 28938069 DOI: 10.1021/acs.jmedchem.7b00854] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A homology model of the nucleotide-activated P2Y2R was created based on the X-ray structures of the P2Y1 receptor. Docking studies were performed, and receptor mutants were created to probe the identified binding interactions. Mutation of residues predicted to interact with the ribose (Arg110) and the phosphates of the nucleotide agonists (Arg265, Arg292) or that contribute indirectly to binding (Tyr288) abolished activity. The Y114F, R194A, and F261A mutations led to inactivity of diadenosine tetraphosphate and to a reduced response of UTP. Significant reduction in agonist potency was observed for all other receptor mutants (Phe111, His184, Ser193, Phe261, Tyr268, Tyr269) predicted to be involved in agonist recognition. An ionic lock between Asp185 and Arg292 that is probably involved in receptor activation interacts with the phosphate groups. The antagonist AR-C118925 and anthraquinones likely bind to the orthosteric site. The updated homology models will be useful for virtual screening and drug design.
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Affiliation(s)
- Muhammad Rafehi
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany
| | - Alexander Neumann
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany
| | - Younis Baqi
- Department of Chemistry, Faculty of Science, Sultan Qaboos University , PO Box 36, Postal Code 123, Muscat, Oman
| | - Enas M Malik
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany
| | - Michael Wiese
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry II, University of Bonn , 53121 Bonn, Germany
| | - Vigneshwaran Namasivayam
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany.,PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry II, University of Bonn , 53121 Bonn, Germany
| | - Christa E Müller
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Sciences Bonn (PSB), Pharmaceutical Chemistry I, University of Bonn , 53121 Bonn, Germany
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10
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11
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von Kügelgen I, Hoffmann K. Pharmacology and structure of P2Y receptors. Neuropharmacology 2015; 104:50-61. [PMID: 26519900 DOI: 10.1016/j.neuropharm.2015.10.030] [Citation(s) in RCA: 163] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 10/22/2015] [Accepted: 10/23/2015] [Indexed: 01/30/2023]
Abstract
P2Y receptors are G-protein-coupled receptors (GPCRs) for extracellular nucleotides. There are eight mammalian P2Y receptor subtypes (P2Y1, P2Y2, P2Y4, P2Y6, P2Y11, P2Y12, P2Y13, and P2Y14). P2Y receptors are widely expressed and play important roles in physiology and pathophysiology. One important example is the ADP-induced platelet aggregation mediated by P2Y1 and P2Y12 receptors. Active metabolites of the thienopyridine compounds ticlopidine, clopidogrel and prasugrel as well as the nucleoside analogue ticagrelor block P2Y12 receptors and thereby platelet aggregation. These drugs are used for the prevention and therapy of cardiovascular events. Moreover, P2Y receptors play important roles in the nervous system. Adenine nucleotides modulate neuronal activity and neuronal fibre outgrowth by activation of P2Y1 receptors and control migration of microglia by P2Y12 receptors. UDP stimulates microglial phagocytosis through activation of P2Y6 receptors. There is evidence for a role for P2Y2 receptors in Alzheimer's disease pathology. The P2Y receptor subtypes are highly diverse in both their amino acid sequences and their pharmacological profiles. Selective receptor ligands have been developed for the pharmacological characterization of the receptor subtypes. The recently published three-dimensional crystal structures of the human P2Y1 and P2Y12 receptors will facilitate the development of therapeutic agents that selectively target P2Y receptors. This article is part of the Special Issue entitled 'Purines in Neurodegeneration and Neuroregeneration'.
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Affiliation(s)
- Ivar von Kügelgen
- Department of Pharmacology and Toxicology, Pharma Center, University of Bonn, D-53127 Bonn, Germany.
| | - Kristina Hoffmann
- Department of Pharmacology and Toxicology, Pharma Center, University of Bonn, D-53127 Bonn, Germany
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12
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Beuming T, Lenselink B, Pala D, McRobb F, Repasky M, Sherman W. Docking and Virtual Screening Strategies for GPCR Drug Discovery. Methods Mol Biol 2015; 1335:251-76. [PMID: 26260606 DOI: 10.1007/978-1-4939-2914-6_17] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Progress in structure determination of G protein-coupled receptors (GPCRs) has made it possible to apply structure-based drug design (SBDD) methods to this pharmaceutically important target class. The quality of GPCR structures available for SBDD projects fall on a spectrum ranging from high resolution crystal structures (<2 Å), where all water molecules in the binding pocket are resolved, to lower resolution (>3 Å) where some protein residues are not resolved, and finally to homology models that are built using distantly related templates. Each GPCR project involves a distinct set of opportunities and challenges, and requires different approaches to model the interaction between the receptor and the ligands. In this review we will discuss docking and virtual screening to GPCRs, and highlight several refinement and post-processing steps that can be used to improve the accuracy of these calculations. Several examples are discussed that illustrate specific steps that can be taken to improve upon the docking and virtual screening accuracy. While GPCRs are a unique target class, many of the methods and strategies outlined in this review are general and therefore applicable to other protein families.
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Affiliation(s)
- Thijs Beuming
- Schrödinger, Inc., 120 West 45th Street, New York, NY, 10036, USA,
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13
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Yang W, Wang Y, Lai A, Qiao JX, Wang TC, Hua J, Price LA, Shen H, Chen XQ, Wong P, Crain E, Watson C, Huang CS, Seiffert DA, Rehfuss R, Wexler RR, Lam PYS. Discovery of 4-aryl-7-hydroxyindoline-based P2Y1 antagonists as novel antiplatelet agents. J Med Chem 2014; 57:6150-64. [PMID: 24931384 DOI: 10.1021/jm5006226] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Adenosine diphosphate (ADP)-mediated platelet aggregation is signaled through two distinct G protein-coupled receptors (GPCR) on the platelet surface: P2Y12 and P2Y1. Blocking P2Y12 receptor is a clinically well-validated strategy for antithrombotic therapy. P2Y1 antagonists have been shown to have the potential to provide equivalent antithrombotic efficacy as P2Y12 inhibitors with reduced bleeding in preclinical animal models. We have previously reported the discovery of a potent and orally bioavailable P2Y1 antagonist, 1. This paper describes further optimization of 1 by introducing 4-aryl groups at the hydroxylindoline in two series. In the neutral series, 10q was identified with excellent potency and desirable pharmacokinetic (PK) profile. It also demonstrated similar antithrombotic efficacy with less bleeding compared with the known P2Y12 antagonist prasugrel in rabbit efficacy/bleeding models. In the basic series, 20c (BMS-884775) was discovered with an improved PK and liability profile over 1. These results support P2Y1 antagonism as a promising new antiplatelet target.
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Affiliation(s)
- Wu Yang
- Discovery Chemistry, ‡Discovery Biology, and §Pharmaceutical Candidate Optimization, Bristol-Myers Squibb Research , Post Office Box 5400, Princeton, New Jersey 08643-5400, United States
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14
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Qiao JX, Wang TC, Hiebert S, Hu CH, Schumacher WA, Spronk SA, Clark CG, Han Y, Hua J, Price LA, Shen H, Chacko SA, Everlof G, Bostwick JS, Steinbacher TE, Li YX, Huang CS, Seiffert DA, Rehfuss R, Wexler RR, Lam PYS. 4-Benzothiazole-7-hydroxyindolinyl diaryl ureas are potent P2Y1 antagonists with favorable pharmacokinetics: low clearance and small volume of distribution. ChemMedChem 2014; 9:2327-43. [PMID: 24989964 DOI: 10.1002/cmdc.201402141] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Indexed: 11/10/2022]
Abstract
Current antithrombotic discovery efforts target compounds that are highly efficacious in thrombus reduction with less bleeding liability than the standard of care. Preclinical data suggest that P2Y1 antagonists may have lower bleeding liabilities than P2Y12 antagonists while providing similar antithrombotic efficacy. This article describes our continuous SAR efforts in a series of 7-hydroxyindolinyl diaryl ureas. When dosed orally, 4-trifluoromethyl-7-hydroxy-3,3-dimethylindolinyl analogue 4 was highly efficacious in a model of arterial thrombosis in rats with limited bleeding. The chemically labile CF3 group in 4 was then transformed to various groups via a novel one-step synthesis, yielding a series of potent P2Y1 antagonists. Among them, the 4-benzothiazole-substituted indolines had desirable PK properties in rats, specifically, low clearance and small volume of distribution. In addition, compound 40 had high i.v. exposure and modest bioavailability, giving it the best overall profile.
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Affiliation(s)
- Jennifer X Qiao
- Medicinal Chemistry, Molecular Sciences and Candidate Optimization, Bristol-Myers Squibb Company, Rt. 206 and Province Line Road, Princeton, NJ 08543 (USA).
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15
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From Three-Dimensional GPCR Structure to Rational Ligand Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:129-57. [DOI: 10.1007/978-94-007-7423-0_7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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16
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Qiao JX, Wang TC, Ruel R, Thibeault C, L'Heureux A, Schumacher WA, Spronk SA, Hiebert S, Bouthillier G, Lloyd J, Pi Z, Schnur DM, Abell LM, Hua J, Price LA, Liu E, Wu Q, Steinbacher TE, Bostwick JS, Chang M, Zheng J, Gao Q, Ma B, McDonnell PA, Huang CS, Rehfuss R, Wexler RR, Lam PYS. Conformationally constrained ortho-anilino diaryl ureas: discovery of 1-(2-(1'-neopentylspiro[indoline-3,4'-piperidine]-1-yl)phenyl)-3-(4-(trifluoromethoxy)phenyl)urea, a potent, selective, and bioavailable P2Y1 antagonist. J Med Chem 2013; 56:9275-95. [PMID: 24164581 DOI: 10.1021/jm4013906] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Preclinical antithrombotic efficacy and bleeding models have demonstrated that P2Y1 antagonists are efficacious as antiplatelet agents and may offer a safety advantage over P2Y12 antagonists in terms of reduced bleeding liabilities. In this article, we describe the structural modification of the tert-butyl phenoxy portion of lead compound 1 and the subsequent discovery of a novel series of conformationally constrained ortho-anilino diaryl ureas. In particular, spiropiperidine indoline-substituted diaryl ureas are described as potent, orally bioavailable small-molecule P2Y1 antagonists with improved activity in functional assays and improved oral bioavailability in rats. Homology modeling and rat PK/PD studies on benchmark compound 3l will also be presented. Compound 3l was our first P2Y1 antagonist to demonstrate a robust oral antithrombotic effect with mild bleeding liability in the rat thrombosis and hemostasis models.
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Affiliation(s)
- Jennifer X Qiao
- Research and Development, Bristol-Myers Squibb Company , 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States
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17
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Kruse AC, Weiss DR, Rossi M, Hu J, Hu K, Eitel K, Gmeiner P, Wess J, Kobilka BK, Shoichet BK. Muscarinic receptors as model targets and antitargets for structure-based ligand discovery. Mol Pharmacol 2013; 84:528-40. [PMID: 23887926 DOI: 10.1124/mol.113.087551] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
G protein-coupled receptors (GPCRs) regulate virtually all aspects of human physiology and represent an important class of therapeutic drug targets. Many GPCR-targeted drugs resemble endogenous agonists, often resulting in poor selectivity among receptor subtypes and restricted pharmacologic profiles. The muscarinic acetylcholine receptor family exemplifies these problems; thousands of ligands are known, but few are receptor subtype-selective and nearly all are cationic in nature. Using structure-based docking against the M2 and M3 muscarinic receptors, we screened 3.1 million molecules for ligands with new physical properties, chemotypes, and receptor subtype selectivities. Of 19 docking-prioritized molecules tested against the M2 subtype, 11 had substantial activity and 8 represented new chemotypes. Intriguingly, two were uncharged ligands with low micromolar to high nanomolar Ki values, an observation with few precedents among aminergic GPCRs. To exploit a single amino-acid substitution among the binding pockets between the M2 and M3 receptors, we selected molecules predicted by docking to bind to the M3 and but not the M2 receptor. Of 16 molecules tested, 8 bound to the M3 receptor. Whereas selectivity remained modest for most of these, one was a partial agonist at the M3 receptor without measurable M2 agonism. Consistent with this activity, this compound stimulated insulin release from a mouse β-cell line. These results support the ability of structure-based discovery to identify new ligands with unexplored chemotypes and physical properties, leading to new biologic functions, even in an area as heavily explored as muscarinic pharmacology.
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Affiliation(s)
- Andrew C Kruse
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California (A.C.K., B.K.K.); Department of Pharmaceutical Chemistry, University of California, San Francisco, California (D.R.W., B.K.S.); Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada (B.K.S.); Molecular Signaling Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland (M.R., J.H., K.H., J.W.); and Department of Chemistry and Pharmacy, Friedrich Alexander University, Erlangen, Germany (K.E., P.G.)
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18
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Jacobson KA. Structure-based approaches to ligands for G-protein-coupled adenosine and P2Y receptors, from small molecules to nanoconjugates. J Med Chem 2013; 56:3749-67. [PMID: 23597047 PMCID: PMC3701956 DOI: 10.1021/jm400422s] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Adenosine receptor (ARs) and P2Y receptors (P2YRs) that respond to extracellular nucleosides/nucleotides are associated with new directions for therapeutics. The X-ray structures of the A2AAR complexes with agonists and antagonists are examined in relationship to the G-protein-coupled receptor (GPCR) superfamily and applied to drug discovery. Much of the data on AR ligand structure from early SAR studies now are explainable from the A2AAR X-ray crystallography. The ligand-receptor interactions in related GPCR complexes can be identified by means of modeling approaches, e.g., molecular docking. Thus, molecular recognition in binding and activation processes has been studied effectively using homology modeling and applied to ligand design. Virtual screening has yielded new nonnucleoside AR antagonists, and existing ligands have been improved with knowledge of the receptor interactions. New agonists are being explored for central nervous system and peripheral therapeutics based on in vivo activity, such as chronic neuropathic pain. Ligands for receptors more distantly related to the X-ray template, i.e., P2YRs, have been introduced and are mainly used as pharmacological tools for elucidating the physiological role of extracellular nucleotides. Other ligand tools for drug discovery include fluorescent probes, radioactive probes, multivalent probes, and functionalized nanoparticles.
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Affiliation(s)
- Kenneth A Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892, USA.
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19
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Chao H, Turdi H, Herpin TF, Roberge JY, Liu Y, Schnur DM, Poss MA, Rehfuss R, Hua J, Wu Q, Price LA, Abell LM, Schumacher WA, Bostwick JS, Steinbacher TE, Stewart AB, Ogletree ML, Huang CS, Chang M, Cacace AM, Arcuri MJ, Celani D, Wexler RR, Lawrence RM. Discovery of 2-(phenoxypyridine)-3-phenylureas as small molecule P2Y1 antagonists. J Med Chem 2013; 56:1704-14. [PMID: 23368907 DOI: 10.1021/jm301708u] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Two distinct G protein-coupled purinergic receptors, P2Y1 and P2Y12, mediate ADP-driven platelet activation. The clinical effectiveness of P2Y12 blockade is well established. Recent preclinical data suggest that P2Y1 and P2Y12 inhibition provide equivalent antithrombotic efficacy, while targeting P2Y1 has the potential for reduced bleeding liability. In this account, the discovery of a 2-(phenoxypyridine)-3-phenylurea chemotype that inhibited ADP-mediated platelet aggregation in human blood samples is described. Optimization of this series led to the identification of compound 16, 1-(2-(2-tert-butylphenoxy)pyridin-3-yl)-3-4-(trifluoromethoxy)phenylurea, which demonstrated a 68 ± 7% thrombus weight reduction in an established rat arterial thrombosis model (10 mg/kg plus 10 mg/kg/h) while only prolonging cuticle and mesenteric bleeding times by 3.3- and 3.1-fold, respectively, in provoked rat bleeding time models. These results suggest that a P2Y1 antagonist could potentially provide a safe and efficacious antithrombotic profile.
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Affiliation(s)
- Hannguang Chao
- Bristol-Myers Squibb Research and Development, P.O. Box 5400, Princeton New Jersey 08543, United States.
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Jacobson KA, Jayasekara MS, Costanzi S. Molecular Structure of P2Y Receptors: Mutagenesis, Modeling, and Chemical Probes. WILEY INTERDISCIPLINARY REVIEWS. MEMBRANE TRANSPORT AND SIGNALING 2012; 1:WMTS68. [PMID: 23336097 PMCID: PMC3547624 DOI: 10.1002/wmts.68] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
There are eight subtypes of P2Y receptors (P2YRs) that are activated, and in some cases inhibited, by a range of extracellular nucleotides. These nucleotides are ubiquitous, but their extracellular concentration can rise dramatically in response to hypoxia, ischemia, or mechanical stress, injury, and release through channels and from vesicles. Two subclasses of P2YRs were defined based on clustering of sequences, second messengers, and receptor sequence analysis. The numbering system for P2YR subtypes is discontinuous; i.e., P2Y(1-14)Rs have been defined, but six of the intermediate-numbered cloned receptor sequences (e.g., P2y(3), P2y(5), P2y(7-10)) are not functional mammalian nucleotide receptors. Of these two clusters, the P2Y(12-14) subtypes couple via Gα(i) to inhibit adenylate cyclase, while the remaining subtypes couple through Gα(q) to activate phospholipase C. Collectively, the P2YRs respond to both purine and pyrimidine nucleotides, in the form of 5'-mono- and dinucleotides and nucleoside-5'-diphosphosugars. In recent years, the medicinal chemistry of P2Y receptors has advanced significantly, to provide selective agonists and antagonists for many but not all of the subtypes. Ligand design has been aided by insights from structural probing using molecular modelling and mutagenesis. Currently, the molecular modelling of the receptors is effectively based on the X-ray structure of the CXCR4 receptor, which is the closest to the P2Y receptors among all the currently crystallized receptors in terms of sequence similarity. It is now a challenge to develop novel and selective P2YR ligands for disease treatment (although antagonists of the P2Y(12)R are already widely used as antithrombotics).
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Affiliation(s)
- Kenneth A. Jacobson
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8A, Rm. B1A-19, Bethesda, Maryland 20892-0810, USA
| | - M.P. Suresh Jayasekara
- Molecular Recognition Section, Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bldg. 8A, Rm. 1A-20, Bethesda, Maryland 20892-0810, USA
| | - Stefano Costanzi
- Department of Chemistry, American University, Washington, DC 20016, USA
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