1
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Kotipalli A, Koulgi S, Jani V, Sonavane U, Joshi R. Early Events in β 2AR Dimer Dynamics Mediated by Activation-Related Microswitches. J Membr Biol 2024:10.1007/s00232-024-00324-1. [PMID: 39240374 DOI: 10.1007/s00232-024-00324-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 08/24/2024] [Indexed: 09/07/2024]
Abstract
G-Protein-Coupled Receptors (GPCRs) make up around 3-4% of the human genome and are the targets of one-third of FDA-approved drugs. GPCRs typically exist as monomers but also aggregate to form higher-order oligomers, including dimers. β2AR, a pharmacologically relevant GPCR, is known to be targeted for the treatment of asthma and cardiovascular diseases. The activation of β2AR at the dimer level remains under-explored. In the current study, molecular dynamics (MD) simulations have been performed to understand activation-related structural changes in β2AR at the dimer level. The transition from inactive to active and vice versa has been studied by starting the simulations in the apo, agonist-bound, and inverse agonist-bound β2AR dimers for PDB ID: 2RH1 and PDB ID: 3P0G, respectively. A cumulative total of around 21-μs simulations were performed. Residue-based distances, RMSD, and PCA calculations suggested that either of the one monomer attained activation-related features for the apo and agonist-bound β2AR dimers. The TM5 and TM6 helices within the two monomers were observed to be in significant variation in all the simulations. TM5 bulge and proximity of TM2 and TM7 helices may be contributing to one of the early events in activation. The dimeric interface between TM1 and helix 8 were observed to be well maintained in the apo and agonist-bound simulations. The presence of inverse agonists favored inactive features in both the monomers. These key features of activation known for monomers were observed to have an impact on β2AR dimers, thereby providing an insight into the oligomerization mechanism of GPCRs.
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Affiliation(s)
- Aneesh Kotipalli
- HPC-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, India, 411008
| | - Shruti Koulgi
- HPC-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, India, 411008
| | - Vinod Jani
- HPC-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, India, 411008
| | - Uddhavesh Sonavane
- HPC-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, India, 411008
| | - Rajendra Joshi
- HPC-Medical & Bioinformatics Applications Group, Centre for Development of Advanced Computing (C-DAC), Innovation Park, Panchawati, Pashan, Pune, India, 411008.
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2
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Isu UH, Polasa A, Moradi M. Differential Behavior of Conformational Dynamics in Active and Inactive States of Cannabinoid Receptor 1. J Phys Chem B 2024; 128:8437-8447. [PMID: 39169808 PMCID: PMC11382280 DOI: 10.1021/acs.jpcb.4c02828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Cannabinoid receptor 1 (CB1) is a G protein-coupled receptor that regulates critical physiological processes including pain, appetite, and cognition. Understanding the conformational dynamics of CB1 associated with transitions between inactive and active signaling states is imperative for developing targeted modulators. Using microsecond-level all-atom molecular dynamics simulations, we identified marked differences in the conformational ensembles of inactive and active CB1 in apo. The inactive state exhibited substantially increased structural heterogeneity and plasticity compared to the more rigidified active state in the absence of stabilizing ligands. Transmembrane helices TM3 and TM7 were identified as distinguishing factors modulating the state-dependent dynamics. TM7 displayed amplified fluctuations selectively in the inactive state simulations attributed to disruption of conserved electrostatic contacts anchoring it to surrounding helices in the active state. Additionally, we identified significant reorganizations in key salt bridge and hydrogen bond networks contributing to the CB1 activation/inactivation. For instance, D213-Y224 hydrogen bond and D184-K192 salt bridge showed marked rearrangements between the states. Collectively, these findings reveal the specialized role of TM7 in directing state-dependent CB1 dynamics through electrostatic switch mechanisms. By elucidating the intrinsic enhanced flexibility of inactive CB1, this study provides valuable insights into the conformational landscape enabling functional transitions. Our perspective advances understanding of CB1 activation mechanisms and offers opportunities for structure-based drug discovery targeting the state-specific conformational dynamics of this receptor.
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Affiliation(s)
- Ugochi H Isu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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3
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He Y, Cun S, Fan J, Wang J. Screening for promising multi-target bioactive components from Cortex Mori Radicis for the treatment of chronic cor pulmonale based on immobilized beta 1-adrenergic receptor and beta 2-adrenergic receptor chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1242:124175. [PMID: 38917653 DOI: 10.1016/j.jchromb.2024.124175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/15/2024] [Accepted: 05/25/2024] [Indexed: 06/27/2024]
Abstract
Cortex Morin Radicis (CMR) is the dried root bark of Morus alba. L. It has a variety of effects such as antibacterial, anti-tumour, treatment of cardiovascular diseases or upper respiratory tract disease and so on. The pursuit for drugs selected from Cortex Mori Radicis having improved therapeutic efficacy necessitates increasing research on new assays for screening bioactive compounds with multi-targets. In this work, we applied immobilized β1-AR and β2-AR as the stationary phase in chromatographic column to screen bioactive compounds from Cortex Morin Radicis. Specific ligands of the two receptors (e.g. esmolol, metoprolol, atenolol, salbutamol, methoxyphenamine, tulobuterol and clorprenaline) were utilized to characterize the specificity and bioactivity of the columns. We used high performance affinity chromatography coupled with ESI-MS to screen targeted compounds of Cortex Morin Radicis. By zonal elution, we identified morin as a bioactive compound simultaneously binding to β1-AR and β2-AR. The compound exhibited the association constants of 3.10 × 104 and 2.60 × 104 M-1 on the β1-AR and β2-AR column. On these sites, the dissociation rate constants were calculated to be 0.131 and 0.097 s-1. Molecular docking indicated that the binding of morin to the two receptors occurred on Asp200, Asp121, and Val122 of β1-AR, Asn312, Thr110, Asp113, Tyr316, Gly90, Phe193, Ile309, and Trp109 of β2-AR. Likewise, mulberroside C was identified as the bioactive compound binding to β2-AR. The association constants and dissociation rate constants were calculated to be 1.08 × 104 M-1 and 0.900 s-1. Molecular docking also indicated that mulberroside C could bind to β2-AR receptor on its agonist site. Taking together, we demonstrated that the chromatographic strategy to identify bioactive natural products based on the β1-AR and β2-AR immobilization, has potential for screening bioactive compounds with multi-targets from complex matrices including traditional Chinese medicines.
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MESH Headings
- Morus/chemistry
- Receptors, Adrenergic, beta-2/metabolism
- Receptors, Adrenergic, beta-2/chemistry
- Receptors, Adrenergic, beta-1/metabolism
- Receptors, Adrenergic, beta-1/chemistry
- Molecular Docking Simulation
- Plant Extracts/chemistry
- Chromatography, Affinity/methods
- Humans
- Chromatography, High Pressure Liquid/methods
- Flavonoids/analysis
- Flavonoids/chemistry
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Affiliation(s)
- Yunzhi He
- College of Life Sciences, Northwest University, Xi'an, China
| | - Sidi Cun
- College of Life Sciences, Northwest University, Xi'an, China
| | - Junni Fan
- College of Life Sciences, Northwest University, Xi'an, China
| | - Jing Wang
- College of Life Sciences, Northwest University, Xi'an, China
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4
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Manchanda Y, ElEid L, Oqua AI, Ramchunder Z, Choi J, Shchepinova MM, Rutter GA, Inoue A, Tate EW, Jones B, Tomas A. Engineered mini-G proteins block the internalization of cognate GPCRs and disrupt downstream intracellular signaling. Sci Signal 2024; 17:eabq7038. [PMID: 38954638 DOI: 10.1126/scisignal.abq7038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
Mini-G proteins are engineered, thermostable variants of Gα subunits designed to stabilize G protein-coupled receptors (GPCRs) in their active conformations. Because of their small size and ease of use, they are popular tools for assessing GPCR behaviors in cells, both as reporters of receptor coupling to Gα subtypes and for cellular assays to quantify compartmentalized signaling at various subcellular locations. Here, we report that overexpression of mini-G proteins with their cognate GPCRs disrupted GPCR endocytic trafficking and associated intracellular signaling. In cells expressing the Gαs-coupled GPCR glucagon-like peptide 1 receptor (GLP-1R), coexpression of mini-Gs, a mini-G protein derived from Gαs, blocked β-arrestin 2 recruitment and receptor internalization and disrupted endosomal GLP-1R signaling. These effects did not involve changes in receptor phosphorylation or lipid nanodomain segregation. Moreover, we found that mini-G proteins derived from Gαi and Gαq also inhibited the internalization of GPCRs that couple to them. Finally, we developed an alternative intracellular signaling assay for GLP-1R using a nanobody specific for active Gαs:GPCR complexes (Nb37) that did not affect GLP-1R internalization. Our results have important implications for designing methods to assess intracellular GPCR signaling.
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Affiliation(s)
- Yusman Manchanda
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | - Liliane ElEid
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | - Affiong I Oqua
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | - Zenouska Ramchunder
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | - Jiyoon Choi
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | - Maria M Shchepinova
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
- CR-CHUM, Université de Montréal, Montréal, QC, Canada
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Asuka Inoue
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Edward W Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, UK
| | - Ben Jones
- Section of Endocrinology and Investigative Medicine, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
| | - Alejandra Tomas
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion, and Reproduction, Imperial College London, London, UK
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5
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Gutiérrez-Mondragón MA, Vellido A, König C. A Study on the Robustness and Stability of Explainable Deep Learning in an Imbalanced Setting: The Exploration of the Conformational Space of G Protein-Coupled Receptors. Int J Mol Sci 2024; 25:6572. [PMID: 38928278 PMCID: PMC11203844 DOI: 10.3390/ijms25126572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
G-protein coupled receptors (GPCRs) are transmembrane proteins that transmit signals from the extracellular environment to the inside of the cells. Their ability to adopt various conformational states, which influence their function, makes them crucial in pharmacoproteomic studies. While many drugs target specific GPCR states to exert their effects-thereby regulating the protein's activity-unraveling the activation pathway remains challenging due to the multitude of intermediate transformations occurring throughout this process, and intrinsically influencing the dynamics of the receptors. In this context, computational modeling, particularly molecular dynamics (MD) simulations, may offer valuable insights into the dynamics and energetics of GPCR transformations, especially when combined with machine learning (ML) methods and techniques for achieving model interpretability for knowledge generation. The current study builds upon previous work in which the layer relevance propagation (LRP) technique was employed to interpret the predictions in a multi-class classification problem concerning the conformational states of the β2-adrenergic (β2AR) receptor from MD simulations. Here, we address the challenges posed by class imbalance and extend previous analyses by evaluating the robustness and stability of deep learning (DL)-based predictions under different imbalance mitigation techniques. By meticulously evaluating explainability and imbalance strategies, we aim to produce reliable and robust insights.
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Affiliation(s)
- Mario A. Gutiérrez-Mondragón
- Computer Science Department, Intelligent Data Science and Artificial Intelligence (IDEAI-UPC) Research Center, Universitat Politècnica de Catalunya, 08034 Barcelona, Spain; (M.A.G.-M.); (A.V.)
| | - Alfredo Vellido
- Computer Science Department, Intelligent Data Science and Artificial Intelligence (IDEAI-UPC) Research Center, Universitat Politècnica de Catalunya, 08034 Barcelona, Spain; (M.A.G.-M.); (A.V.)
- Centro de Investigacion Biomédica en Red (CIBER), 28029 Madrid, Spain
| | - Caroline König
- Computer Science Department, Intelligent Data Science and Artificial Intelligence (IDEAI-UPC) Research Center, Universitat Politècnica de Catalunya, 08034 Barcelona, Spain; (M.A.G.-M.); (A.V.)
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6
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Isu UH, Polasa A, Moradi M. Differential Behavior of Conformational Dynamics in Active and Inactive States of Cannabinoid Receptor 1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.17.589939. [PMID: 38659869 PMCID: PMC11042334 DOI: 10.1101/2024.04.17.589939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The cannabinoid receptor CB1 is a G protein-coupled receptor that regulates critical physiological processes including pain, appetite, and cognition. Understanding the conformational dynamics of CB1 associated with transitions between inactive and active signaling states is imperative for developing targeted modulators. Using microsecond-level all-atom molecular dynamics simulations, we identified marked differences in the conformational ensembles of inactive and active CB1 states in apo conditions. The inactive state exhibited substantially increased structural heterogeneity and plasticity compared to the more rigidified active state in the absence of stabilizing ligands. Transmembrane helices TM3 and TM7 were identified as distinguishing factors modulating the state-dependent dynamics. TM7 displayed amplified fluctuations selectively in the inactive state simulations attributed to disruption of conserved electrostatic contacts anchoring it to surrounding helices in the active state. Additionally, we identified significant reorganization of key salt bridge and hydrogen bond networks known to control CB1 activation between states. For instance, a conserved D213-Y224 hydrogen bond and D184-K192 salt bridge interactions showed marked rearrangements between the states. Collectively, these findings reveal the specialized role of TM7 in directing state-dependent CB1 dynamics through electrostatic switch mechanisms. By elucidating the intrinsic enhanced flexibility of inactive CB1, this study provides valuable insights into the conformational landscape enabling functional transitions. Our perspective advances understanding of CB1 activation mechanisms and offers opportunities for structure-based drug discovery targeting the state-specific conformational dynamics of this receptor.
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7
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Mitrovic D, Chen Y, Marciniak A, Delemotte L. Coevolution-Driven Method for Efficiently Simulating Conformational Changes in Proteins Reveals Molecular Details of Ligand Effects in the β2AR Receptor. J Phys Chem B 2023; 127:9891-9904. [PMID: 37947090 PMCID: PMC10683026 DOI: 10.1021/acs.jpcb.3c04897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/12/2023]
Abstract
With the advent of AI-powered structure prediction, the scientific community is inching closer to solving protein folding. An unresolved enigma, however, is to accurately, reliably, and deterministically predict alternative conformational states that are crucial for the function of, e.g., transporters, receptors, or ion channels where conformational cycling is innately coupled to protein function. Accurately discovering and exploring all conformational states of membrane proteins has been challenging due to the need to retain atomistic detail while enhancing the sampling along interesting degrees of freedom. The challenges include but are not limited to finding which degrees of freedom are relevant, how to accelerate the sampling along them, and then quantifying the populations of each micro- and macrostate. In this work, we present a methodology that finds relevant degrees of freedom by combining evolution and physics through machine learning and apply it to the conformational sampling of the β2 adrenergic receptor. In addition to predicting new conformations that are beyond the training set, we have computed free energy surfaces associated with the protein's conformational landscape. We then show that the methodology is able to quantitatively predict the effect of an array of ligands on the β2 adrenergic receptor activation through the discovery of new metastable states not present in the training set. Lastly, we also stake out the structural determinants of activation and inactivation pathway signaling through different ligands and compare them to functional experiments to validate our methodology and potentially gain further insights into the activation mechanism of the β2 adrenergic receptor.
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Affiliation(s)
- Darko Mitrovic
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
| | - Yue Chen
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
| | - Antoni Marciniak
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
| | - Lucie Delemotte
- Department of Applied Physics,
Science for Life Laboratory, KTH Royal Institute
of Technology, Sweden Tomtebodavägen 23, 171
65 Solna, Sweden
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8
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Ben-Shalom N, Sandbank E, Abramovitz L, Hezroni H, Levine T, Trachtenberg E, Fogel N, Mor M, Yefet R, Stoler-Barak L, Hagin D, Nakai A, Noda M, Suzuki K, Shulman Z, Ben-Eliyahu S, Freund NT. β2-adrenergic signaling promotes higher-affinity B cells and antibodies. Brain Behav Immun 2023; 113:66-82. [PMID: 37369341 DOI: 10.1016/j.bbi.2023.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/28/2023] [Accepted: 06/22/2023] [Indexed: 06/29/2023] Open
Abstract
Stress-induced β2-adrenergic receptor (β2AR) activation in B cells increases IgG secretion; however, the impact of this activation on antibody affinity and the underlying mechanisms remains unclear. In the current study, we demonstrate that stress in mice following ovalbumin (OVA) or SARS-CoV-2 RBD immunization significantly increases both serum and surface-expressed IgG binding to the immunogen, while concurrently reducing surface IgG expression and B cell clonal expansion. These effects were abolished by pharmacological β2AR blocking or when the experiments were conducted in β2AR -/- mice. In the second part of our study, we used single B cell sorting to characterize the monoclonal antibodies (mAbs) generated following β2AR activation in cultured RBD-stimulated B cells from convalescent SARS-CoV-2 donors. Ex vivo β2AR activation increased the affinities of the produced anti-RBD mAbs by 100-fold compared to mAbs produced by the same donor control cultures. Consistent with the mouse experiments, β2AR activation reduced both surface IgG levels and the frequency of expanded clones. mRNA sequencing revealed a β2AR-dependent upregulation of the PI3K pathway and B cell receptor (BCR) signaling through AKT phosphorylation, as well as an increased B cell motility. Overall, our study demonstrates that stress-mediated β2AR activation drives changes in B cells associated with BCR activation and higher affinity antibodies.
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Affiliation(s)
- Noam Ben-Shalom
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, 6997801 Israel
| | - Elad Sandbank
- The School of Psychological Sciences, Tel Aviv University, 6997801, Israel
| | - Lilach Abramovitz
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, 6997801 Israel
| | - Hadas Hezroni
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Talia Levine
- The School of Psychological Sciences, Tel Aviv University, 6997801, Israel
| | - Estherina Trachtenberg
- The Sagol School of Neurosciences, Gordon Faculty of Social Sciences, Tel Aviv University, Israel
| | - Nadav Fogel
- The School of Psychological Sciences, Tel Aviv University, 6997801, Israel
| | - Michael Mor
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, 6997801 Israel
| | - Ron Yefet
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, 6997801 Israel
| | - Liat Stoler-Barak
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - David Hagin
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, 6997801 Israel; Allergy and Clinical Immunology Unit, Department of Medicine, Tel Aviv Sourasky Medical Center, 623906, Israel
| | - Akiko Nakai
- Laboratory of Immune Response Dynamics, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan; Department of Immune Response Dynamics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan
| | - Masaki Noda
- Center for Stem Cell and Regenerative Medicine, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Kazuhiro Suzuki
- Laboratory of Immune Response Dynamics, WPI Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan; Department of Immune Response Dynamics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0871, Japan; Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka 565-0871, Japan
| | - Ziv Shulman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shamgar Ben-Eliyahu
- The School of Psychological Sciences, Tel Aviv University, 6997801, Israel; The Sagol School of Neurosciences, Gordon Faculty of Social Sciences, Tel Aviv University, Israel.
| | - Natalia T Freund
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, Tel Aviv University, 6997801 Israel.
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9
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Jin Y, Wang W, Zhang Z, Ou Y, Quan J, Zhao X. Stepwise Frontal Analysis Coupled with Affinity Chromatography: A Fast and Reliable Method for Potential Ligand Isolation and Evaluation from Mahuang-Fuzi-Xixin Decoction. Chem Biodivers 2023; 20:e202201057. [PMID: 36756691 DOI: 10.1002/cbdv.202201057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 02/10/2023]
Abstract
Mahuang-Fuzi-Xixin Decoction (MFXD) is widely used in the treatment of asthma, however, the functional components in the decoction targeting beta2-adrenoceptor (β2 -AR) remain unclear. Herein, we immobilized the haloalkane dehalogenase (Halo)-tagged β2 -AR on the 6-chlorocaproic acid-modified microspheres. Using the affinity stationary phase, the interactions of four ligands with the receptor were analyzed by stepwise frontal analysis. The association constants were (4.75±0.28)×104 M-1 for salbutamol, (2.93±0.15)×104 M-1 for terbutaline, (1.23±0.03)×104 M-1 for methoxyphenamine, (5.67±0.38)×104 M-1 for clorprenaline at high-affinity binding site, and (2.73±0.05)×103 M-1 at low-affinity binding site. These association constants showed the same rank order as the radioligand binding assay, demonstrating that immobilized β2 -AR had capacity to screen bioactive compounds binding to the receptor while stepwise frontal analysis could predict their binding affinities. Application of the immobilized receptor in analysis of MFXD by chromatographic method revealed that ephedrine, aconifine, karakoline, and chasmanine were the bioactive compounds targeting β2 -AR. Among them, ephedrine and chasmanine exhibited association constants of (2.94±0.02)×104 M-1 and (4.60±0.15)×104 M-1 to the receptor by stepwise frontal analysis. Molecular docking analysis demonstrated that ephedrine, chasmanine, and the other two compounds interact with β2 -AR through the same pocket involving the key amino acids such as Asn312, Asp113, Phe289, Trp286, Tyr316, and Val114. As such, we reasoned that the four compounds dominate the therapeutic effect of MFXD against asthma through β2 -AR mediating pathway. This work shed light on the potential of immobilized β2 -AR for drug discovery and provided a valuable methodology for rapid screening.
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Affiliation(s)
- Yahui Jin
- College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Wenwen Wang
- College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Zilong Zhang
- College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Yuanyuan Ou
- College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jia Quan
- College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Xinfeng Zhao
- College of Life Sciences, Northwest University, Xi'an, 710069, China
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10
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Yen HY, Liko I, Song W, Kapoor P, Almeida F, Toporowska J, Gherbi K, Hopper JTS, Charlton SJ, Politis A, Sansom MSP, Jazayeri A, Robinson CV. Mass spectrometry captures biased signalling and allosteric modulation of a G-protein-coupled receptor. Nat Chem 2022; 14:1375-1382. [PMID: 36357787 PMCID: PMC9758051 DOI: 10.1038/s41557-022-01041-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 08/09/2022] [Indexed: 11/12/2022]
Abstract
G-protein-coupled receptors signal through cognate G proteins. Despite the widespread importance of these receptors, their regulatory mechanisms for G-protein selectivity are not fully understood. Here we present a native mass spectrometry-based approach to interrogate both biased signalling and allosteric modulation of the β1-adrenergic receptor in response to various ligands. By simultaneously capturing the effects of ligand binding and receptor coupling to different G proteins, we probed the relative importance of specific interactions with the receptor through systematic changes in 14 ligands, including isoprenaline derivatives, full and partial agonists, and antagonists. We observed enhanced dynamics of the intracellular loop 3 in the presence of isoprenaline, which is capable of acting as a biased agonist. We also show here that endogenous zinc ions augment the binding in receptor-Gs complexes and propose a zinc ion-binding hotspot at the TM5/TM6 intracellular interface of the receptor-Gs complex. Further interrogation led us to propose a mechanism in which zinc ions facilitate a structural transition of the intermediate complex towards the stable state.
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Affiliation(s)
- Hsin-Yung Yen
- Chemical Research Laboratory, University of Oxford, Oxford, UK.
- OMass Therapeutics, Oxford, UK.
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
| | - Idlir Liko
- Chemical Research Laboratory, University of Oxford, Oxford, UK
- OMass Therapeutics, Oxford, UK
| | - Wanling Song
- Department of Biochemistry, University of Oxford, Oxford, UK
- Rahko, London, UK
| | | | | | | | | | | | - Steven J Charlton
- OMass Therapeutics, Oxford, UK
- School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Argyris Politis
- Department of Chemistry, King's College London, London, UK
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Carol V Robinson
- Chemical Research Laboratory, University of Oxford, Oxford, UK.
- Kavli Institute for Nanoscience Discovery, Oxford, UK.
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11
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L-DOPA and Droxidopa: From Force Field Development to Molecular Docking into Human β2-Adrenergic Receptor. Life (Basel) 2022; 12:life12091393. [PMID: 36143429 PMCID: PMC9501711 DOI: 10.3390/life12091393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/10/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
The increasing interest in the molecular mechanism of the binding of different agonists and antagonists to β2-adrenergic receptor (β2AR) inactive and active states has led us to investigate protein–ligand interactions using molecular docking calculations. To perform this study, the 3.2 Å X-ray crystal structure of the active conformation of human β2AR in the complex with the endogenous agonist adrenaline has been used as a template for investigating the binding of two exogenous catecholamines to this adrenergic receptor. Here, we show the derivation of L-DOPA and Droxidopa OPLS all atom (AA) force field (FF) parameters via quantum mechanical (QM) calculations, molecular dynamics (MD) simulations in aqueous solutions of the two catecholamines and the molecular docking of both ligands into rigid and flexible β2AR models. We observe that both ligands share with adrenaline similar experimentally observed binding anchor sites, which are constituted by Asp113/Asn312 and Ser203/Ser204/Ser207 side chains. Moreover, both L-DOPA and Droxidopa molecules exhibit binding affinities comparable to that predicted for adrenaline, which is in good agreement with previous experimental and computational results. L-DOPA and Droxidopa OPLS AA FFs have also been tested by performing MD simulations of these ligands docked into β2AR proteins embedded in lipid membranes. Both hydrogen bonds and hydrophobic interaction networks observed over the 1 μs MD simulation are comparable with those derived from molecular docking calculations and MD simulations performed with the CHARMM FF.
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12
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Evaluation of Neurotropic Activity and Molecular Docking Study of New Derivatives of pyrano[4″,3″:4',5']pyrido[3',2':4,5]thieno[3,2- d]pyrimidines on the Basis of pyrano[3,4- c]pyridines. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113380. [PMID: 35684318 PMCID: PMC9182472 DOI: 10.3390/molecules27113380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 11/20/2022]
Abstract
Background: Heterocyclic compounds and their fused analogs, which contain pharmacophore fragments such as pyridine, thiophene and pyrimidine rings, are of great interest due to their broad spectrum of biological activity. Chemical compounds containing two or more pharmacophore groups due to additional interactions with active receptor centers usually enhance biological activity and can even lead to a new type of activity. The search for new effective neurotropic drugs in the series of derivatives of heterocycles containing pharmacophore groups in organic, bioorganic and medical chemistry is a serious problem. Methods: Modern methodology of drugs involves synthesis, physicochemical study, molecular modeling and selection of active compounds through virtual screening and experimental evaluation of the biological activity of new chimeric compounds with pharmacophore fragments. For the synthesis of new compounds, classical organic methods were used and developed. For the evaluation of neurotropic activity of new synthesized compounds, some biological methods were used according to indicators characterizing anticonvulsant, sedative and antianxiety activity as well as side effects. For docking analysis, various soft ware packages and methods were used. Results: As a result of multistep reactions, 11 new, tri- and tetracyclic heterocyclic systems were obtained. The studied compounds exhibit protection against pentylenetetrazole (PTZ) seizures as well as some psychotropic effects. The biological assays evidenced that nine of the eleven studied compounds showed a high anticonvulsant activity by antagonism with pentylenetetrazole. The toxicity of the compounds is low, and they do not induce muscle relaxation in the studied doses. According to the study of psychotropic activity, it was found that the selected compounds have an activating behavior and anxiolytic effects on the “open field” and “elevated plus maze” (EPM) models. The data obtained indicate the anxiolytic (antianxiety) activity of the derivatives of tricyclic thieno[2,3-b]pyridines and tetracyclic pyridothieno[3,2-d]pyrimidin-8-ones, especially pronounced in compounds 3b–f and 4e. The studied compounds increase the latent time of first immobilization on the “forced swimming” (FS) model and exhibit antidepressant effects; compounds 3e and 3f especially exhibit these effects, similarly to diazepam. Docking studies revealed that compounds 3c and 4b bound tightly in the active site of γ-aminobutyric acid type A (GABAA) receptors with a value of the scoring function that estimates free energy of binding (∆G) at −10.0 ± 5 kcal/mol. Compound 4e showed the best affinity ((∆G) at −11.0 ± 0.54 kcal/mol) and seems to be an inhibitor of serotonin (SERT) transporter. Compounds 3c–f and 4e practically bound with the groove of T4L of 5HT_1A and blocked it completely, while the best affinity observed was in compound 3f ((∆G) at −9.3 ± 0.46 kcal/mol). Conclusions: The selected compounds have an anticonvulsant, activating behavior and anxiolytic effects and at the same time exhibit antidepressant effects.
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13
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Targeting ADRB2 enhances sensitivity of non-small cell lung cancer to VEGFR2 tyrosine kinase inhibitors. Cell Death Dis 2022; 8:36. [PMID: 35075132 PMCID: PMC8786837 DOI: 10.1038/s41420-022-00818-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 11/13/2021] [Accepted: 12/07/2021] [Indexed: 12/29/2022]
Abstract
Vascular Endothelial Growth Factor Receptor 2 (VEGFR2) tyrosine kinase inhibitors (TKIs) have achieved remarkable clinical progress in the treatment of non-small-cell lung cancer; however, resistance has limited their therapeutic efficacy. Therefore, understanding the mechanisms of VEGF-TKI and ICI resistance will help to develop effective treatment strategies for patients with advanced NSCLC. Our results suggested that treatment with VEGFR2-TKIs upregulated ADRB2 expression in NSCLC cells. Propranolol, a common ADRB2 antagonist, significantly enhanced the therapeutic effect of VEGFR2-TKIs by inhibiting the ADRB2 signaling pathway in NSCLC cells in vitro and in vivo. Mechanically, the treatment-induced ADRB2 upregulation and the enhancement of ADRB2/VEGFR2 interaction caused resistance to VEGFR2-TKIs in NSCLC. And the inhibition of the ADRB2/CREB/PSAT1 signaling pathway sensitized cells to VEGFR2-TKIs. We demonstrated that ADRB2 signaling is crucial in mediating resistance to VEGFR2-TKIs and provided a novel promising combinatory approach to enhance the antitumor effect of VEGFR2-TKIs in NSCLC combining with propranolol.
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14
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Chen Y, Fleetwood O, Pérez-Conesa S, Delemotte L. Allosteric Effect of Nanobody Binding on Ligand-Specific Active States of the β2 Adrenergic Receptor. J Chem Inf Model 2021; 61:6024-6037. [PMID: 34780174 PMCID: PMC8715506 DOI: 10.1021/acs.jcim.1c00826] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Nanobody binding
stabilizes G-protein-coupled receptors (GPCR)
in a fully active state and modulates their affinity for bound ligands.
However, the atomic-level basis for this allosteric regulation remains
elusive. Here, we investigate the conformational changes induced by
the binding of a nanobody (Nb80) on the active-like β2 adrenergic
receptor (β2AR) via enhanced sampling molecular dynamics simulations.
Dimensionality reduction analysis shows that Nb80 stabilizes structural
features of the β2AR with an ∼14 Å outward movement
of transmembrane helix 6 and a close proximity of transmembrane (TM)
helices 5 and 7, and favors the fully active-like conformation of
the receptor, independent of ligand binding, in contrast to the conditions
under which no intracellular binding partner is bound, in which case
the receptor is only stabilized in an intermediate-active state. This
activation is supported by the residues located at hotspots located
on TMs 5, 6, and 7, as shown by supervised machine learning methods.
Besides, ligand-specific subtle differences in the conformations assumed
by intracellular loop 2 and extracellular loop 2 are captured from
the trajectories of various ligand-bound receptors in the presence
of Nb80. Dynamic network analysis further reveals that Nb80 binding
triggers tighter and stronger local communication networks between
the Nb80 and the ligand-binding sites, primarily involving residues
around ICL2 and the intracellular end of TM3, TM5, TM6, as well as
ECL2, ECL3, and the extracellular ends of TM6 and TM7. In particular,
we identify unique allosteric signal transmission mechanisms between
the Nb80-binding site and the extracellular domains in conformations
modulated by a full agonist, BI167107, and a G-protein-biased partial
agonist, salmeterol, involving mainly TM1 and TM2, and TM5, respectively.
Altogether, our results provide insights into the effect of intracellular
binding partners on the GPCR activation mechanism, which should be
taken into account in structure-based drug discovery.
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Affiliation(s)
- Yue Chen
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Oliver Fleetwood
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Sergio Pérez-Conesa
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
| | - Lucie Delemotte
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, SE-17121 Solna, Sweden
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15
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Biswas AD, Catte A, Mancini G, Barone V. Analysis of L-DOPA and droxidopa binding to human β 2-adrenergic receptor. Biophys J 2021; 120:5631-5643. [PMID: 34767786 PMCID: PMC8715240 DOI: 10.1016/j.bpj.2021.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 12/29/2022] Open
Abstract
Over the last two decades, an increasing number of studies has been devoted to a deeper understanding of the molecular process involved in the binding of various agonists and antagonists to active and inactive conformations of β2-adrenergic receptor (β2AR). The 3.2 Å x-ray crystal structure of human β2AR active state in combination with the endogenous low affinity agonist adrenaline offers an ideal starting structure for studying the binding of various catecholamines to adrenergic receptors. We show that molecular docking of levodopa (L-DOPA) and droxidopa into rigid and flexible β2AR models leads for both ligands to binding anchor sites comparable to those experimentally reported for adrenaline, namely D113/N312 and S203/S204/S207 side chains. Both ligands have a hydrogen bond network that is extremely similar to those of noradrenaline and dopamine. Interestingly, redocking neutral and protonated versions of adrenaline to rigid and flexible β2AR models results in binding poses that are more energetically stable and distinct from the x-ray crystal structure. Similarly, lowest energy conformations of noradrenaline and dopamine generated by docking into flexible β2AR models had binding free energies lower than those of best poses in rigid receptor models. Furthermore, our findings show that L-DOPA and droxidopa molecules have binding affinities comparable to those predicted for adrenaline, noradrenaline, and dopamine, which are consistent with previous experimental and computational findings and supported by the molecular dynamics simulations of β2AR-ligand complexes performed here.
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16
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Harwood CR, Sykes DA, Hoare BL, Heydenreich FM, Uddin R, Poyner DR, Briddon SJ, Veprintsev DB. Functional solubilization of the β 2-adrenoceptor using diisobutylene maleic acid. iScience 2021; 24:103362. [PMID: 34825145 PMCID: PMC8605084 DOI: 10.1016/j.isci.2021.103362] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 07/16/2021] [Accepted: 10/25/2021] [Indexed: 12/16/2022] Open
Abstract
The β2-adrenoceptor (β2AR) is a well-established target in asthma and a prototypical G protein-coupled receptor for biophysical studies. Solubilization of membrane proteins has classically involved the use of detergents. However, the detergent environment differs from the native membrane environment and often destabilizes membrane proteins. Use of amphiphilic copolymers is a promising strategy to solubilize membrane proteins within their native lipid environment in the complete absence of detergents. Here we show the isolation of the β2AR in the polymer diisobutylene maleic acid (DIBMA). We demonstrate that β2AR remains functional in the DIBMA lipid particle and shows improved thermal stability compared with the n-dodecyl-β-D-maltopyranoside detergent-solubilized β2AR. This unique method of extracting β2AR offers significant advantages over previous methods routinely employed such as the introduction of thermostabilizing mutations and the use of detergents, particularly for functional biophysical studies.
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Affiliation(s)
- Clare R Harwood
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - David A Sykes
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Bradley L Hoare
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - Franziska M Heydenreich
- Laboratory of Biomolecular Research, Paul Scherrer Institute, PSI, 5232 Villigen, Switzerland.,Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Romez Uddin
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.,School of Life and Health Sciences, Aston University, Birmingham B47ET, UK
| | - David R Poyner
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.,School of Life and Health Sciences, Aston University, Birmingham B47ET, UK
| | - Stephen J Briddon
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
| | - D B Veprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, UK.,Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, Queen's Medical Centre, University of Nottingham, Nottingham NG7 2UH, UK
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17
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Rich TC, Leavesley SJ, Brandon AP, Evans CA, Raju SV, Wagener BM. Phosphodiesterase 4 mediates interleukin-8-induced heterologous desensitization of the β 2 -adrenergic receptor. FASEB J 2021; 35:e21946. [PMID: 34555226 DOI: 10.1096/fj.202002712rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 11/11/2022]
Abstract
Acute respiratory distress syndrome (ARDS) is a life-threatening illness characterized by decreased alveolar-capillary barrier function, pulmonary edema consisting of proteinaceous fluid, and inhibition of net alveolar fluid transport responsible for resolution of pulmonary edema. There is currently no pharmacotherapy that has proven useful to prevent or treat ARDS, and two trials using beta-agonist therapy to treat ARDS demonstrated no effect. Prior studies indicated that IL-8-induced heterologous desensitization of the beta2-adrenergic receptor (β2 -AR) led to decreased beta-agonist-induced mobilization of cyclic adenosine monophosphate (cAMP). Interestingly, phosphodiesterase (PDE) 4 inhibitors have been used in human airway diseases characterized by low intracellular cAMP levels and increases in specific cAMP hydrolyzing activity. Therefore, we hypothesized that PDE4 would mediate IL-8-induced heterologous internalization of the β2 -AR and that PDE4 inhibition would restore beta-agonist-induced functions. We determined that CINC-1 (a functional IL-8 analog in rats) induces internalization of β2 -AR from the cell surface, and arrestin-2, PDE4, and β2 -AR form a complex during this process. Furthermore, we determined that cAMP associated with the plasma membrane was adversely affected by β2 -AR heterologous desensitization. Additionally, we determined that rolipram, a PDE4 inhibitor, reversed CINC-1-induced derangements of cAMP and also caused β2 -AR to successfully recycle back to the cell surface. Finally, we demonstrated that rolipram could reverse CINC-1-mediated inhibition of beta-agonist-induced alveolar fluid clearance in a murine model of trauma-shock. These results indicate that PDE4 plays a role in CINC-1-induced heterologous internalization of the β2 -AR; PDE4 inhibition reverses these effects and may be a useful adjunct in particular ARDS patients.
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Affiliation(s)
- Thomas C Rich
- Department of Pharmacology, University of South Alabama, Mobile, Alabama, USA.,Center for Lung Biology, University of South Alabama, Mobile, Alabama, USA
| | - Silas J Leavesley
- Department of Pharmacology, University of South Alabama, Mobile, Alabama, USA.,Center for Lung Biology, University of South Alabama, Mobile, Alabama, USA.,Department of Chemical and Biomolecular Engineering, University of South Alabama, Mobile, Alabama, USA
| | - Angela P Brandon
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Cilina A Evans
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - S Vamsee Raju
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA.,UAB Lung Health Center, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Brant M Wagener
- Division of Molecular and Translational Biomedicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Division of Critical Care Medicine, Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Center for Free Radical Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
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18
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Predicting aptamer sequences that interact with target proteins using an aptamer-protein interaction classifier and a Monte Carlo tree search approach. PLoS One 2021; 16:e0253760. [PMID: 34170922 PMCID: PMC8232527 DOI: 10.1371/journal.pone.0253760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 06/14/2021] [Indexed: 11/19/2022] Open
Abstract
Oligonucleotide-based aptamers, which have a three-dimensional structure with a single-stranded fragment, feature various characteristics with respect to size, toxicity, and permeability. Accordingly, aptamers are advantageous in terms of diagnosis and treatment and are materials that can be produced through relatively simple experiments. Systematic evolution of ligands by exponential enrichment (SELEX) is one of the most widely used experimental methods for generating aptamers; however, it is highly expensive and time-consuming. To reduce the related costs, recent studies have used in silico approaches, such as aptamer-protein interaction (API) classifiers that use sequence patterns to determine the binding affinity between RNA aptamers and proteins. Some of these methods generate candidate RNA aptamer sequences that bind to a target protein, but they are limited to producing candidates of a specific size. In this study, we present a machine learning approach for selecting candidate sequences of various sizes that have a high binding affinity for a specific sequence of a target protein. We applied the Monte Carlo tree search (MCTS) algorithm for generating the candidate sequences using a score function based on an API classifier. The tree structure that we designed with MCTS enables nucleotide sequence sampling, and the obtained sequences are potential aptamer candidates. We performed a quality assessment using the scores of docking simulations. Our validation datasets revealed that our model showed similar or better docking scores in ZDOCK docking simulations than the known aptamers. We expect that our method, which is size-independent and easy to use, can provide insights into searching for an appropriate aptamer sequence for a target protein during the simulation step of SELEX.
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19
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Natwick DE, Collins SR. Optimized iLID Membrane Anchors for Local Optogenetic Protein Recruitment. ACS Synth Biol 2021; 10:1009-1023. [PMID: 33843200 DOI: 10.1021/acssynbio.0c00511] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Optogenetic protein dimerization systems are powerful tools to investigate the biochemical networks that cells use to make decisions and coordinate their activities. These tools, including the improved Light-Inducible Dimer (iLID) system, offer the ability to selectively recruit components to subcellular locations, such as micron-scale regions of the plasma membrane. In this way, the role of individual proteins within signaling networks can be examined with high spatiotemporal resolution. Currently, consistent recruitment is limited by heterogeneous optogenetic component expression, and spatial precision is diminished by protein diffusion, especially over long time scales. Here, we address these challenges within the iLID system with alternative membrane anchoring domains and fusion configurations. Using live cell imaging and mathematical modeling, we demonstrate that the anchoring strategy affects both component expression and diffusion, which in turn impact recruitment strength, kinetics, and spatial dynamics. Compared to the commonly used C-terminal iLID fusion, fusion proteins with large N-terminal anchors show stronger local recruitment, slower diffusion of recruited components, efficient recruitment over wider gene expression ranges, and improved spatial control over signaling outputs. We also define guidelines for component expression regimes for optimal recruitment for both cell-wide and subcellular recruitment strategies. Our findings highlight key sources of imprecision within light-inducible dimer systems and provide tools that allow greater control of subcellular protein localization across diverse cell biological applications.
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Affiliation(s)
- Dean E. Natwick
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, United States
| | - Sean R. Collins
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, California 95616, United States
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20
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The role of ADRB2 gene polymorphisms in malignancies. Mol Biol Rep 2021; 48:2741-2749. [PMID: 33675465 DOI: 10.1007/s11033-021-06250-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/24/2021] [Indexed: 12/30/2022]
Abstract
Beta-2-adrenergic receptor is a member of the G protein-coupled receptor superfamily, which is highly expressed in most malignancies. There is increasing evidence showing that beta-2-adrenergic receptors are associated with carcinogenesis, proliferation, immune regulation, invasion, angiogenesis, clinical prognosis and treatment resistance in malignancies. Polymorphisms of the ADRB2 gene have been confirmed to be associated with transcriptional activity, mRNA translation, and beta-2-adrenergic receptor expression and sensitivity. This review discusses clinically relevant examples of single nucleotide polymorphisms of ADRB2 in malignancies and the effects of these polymorphisms on cancer susceptibility, prognosis and treatment response of cancer patients.
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21
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Ružena Č, Jindra V, Renáta H. Chirality of β2-agonists. An overview of pharmacological activity, stereoselective analysis, and synthesis. OPEN CHEM 2020. [DOI: 10.1515/chem-2020-0056] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Abstractβ2-Agonists (β2-adrenergic agonists, bronchodilatants, and sympathomimetic drugs) are a group of drugs that are mainly used in asthma and obstructive pulmonary diseases. In practice, the substances used to contain one or more stereogenic centers in their structure and their enantiomers exhibit different pharmacological properties. In terms of bronchodilatory activity, (R)-enantiomers showed higher activity. The investigation of stereoselectivity in action and disposition of chiral drugs together with the preparation of pure enantiomer drugs calls for efficient stereoselective analytical methods. The overview focuses on the stereoselectivity in pharmacodynamics and pharmacokinetics of β2-agonists and summarizes the stereoselective analytical methods for the enantioseparation of racemic beta-agonists (HPLC, LC-MS, GC, TLC, CE). Some methods of the stereoselective synthesis for β2-agonists preparation are also presented.
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Affiliation(s)
- Čižmáriková Ružena
- Department of Chemical Theory of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, 832 32 Bratislava, Slovakia
| | - Valentová Jindra
- Department of Chemical Theory of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, 832 32 Bratislava, Slovakia
| | - Horáková Renáta
- Department of Chemical Theory of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, 832 32 Bratislava, Slovakia
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22
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Suresh R, Subramaniam V. Molecular dynamics simulation involved in expounding the activation of adrenoceptors by sympathetic nervous system signaling. Struct Chem 2020. [DOI: 10.1007/s11224-020-01553-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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23
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Preferential Coupling of Dopamine D 2S and D 2L Receptor Isoforms with G i1 and G i2 Proteins-In Silico Study. Int J Mol Sci 2020; 21:ijms21020436. [PMID: 31936673 PMCID: PMC7013695 DOI: 10.3390/ijms21020436] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 12/31/2019] [Accepted: 01/06/2020] [Indexed: 02/06/2023] Open
Abstract
The dopamine D2 receptor belongs to rhodopsin-like G protein-coupled receptors (GPCRs) and it is an important molecular target for the treatment of many disorders, including schizophrenia and Parkinson's disease. Here, computational methods were used to construct the full models of the dopamine D2 receptor short (D2S) and long (D2L) isoforms (differing with 29 amino acids insertion in the third intracellular loop, ICL3) and to study their coupling with Gi1 and Gi2 proteins. It was found that the D2L isoform preferentially couples with the Gi2 protein and D2S isoform with the Gi1 protein, which is in accordance with experimental data. Our findings give mechanistic insight into the interplay between isoforms of dopamine D2 receptors and Gi proteins subtypes, which is important to understand signaling by these receptors and their mediation by pharmaceuticals, in particular psychotic and antipsychotic agents.
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24
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Rambacher KM, Moniri NH. The β2-adrenergic receptor-ROS signaling axis: An overlooked component of β2AR function? Biochem Pharmacol 2019; 171:113690. [PMID: 31697929 DOI: 10.1016/j.bcp.2019.113690] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 10/31/2019] [Indexed: 02/07/2023]
Abstract
β2-Adrenergic receptor (β2AR) agonists are clinically used to elicit rapid bronchodilation for the treatment of bronchospasms in pulmonary diseases such as asthma and COPD, both of which exhibit characteristically high levels of reactive oxygen species (ROS); likely secondary to over-expression of ROS generating enzymes and chronically heightened inflammation. Interestingly, β2AR has long-been linked to ROS, yet the involvement of ROS in β2AR function has not been as vigorously studied as other aspects of β2AR signaling. Herein, we discuss the existing body of evidence linking β2AR activation to intracellular ROS generation and importantly, the role of ROS in regulating β2AR function. The reciprocal interplay of the β2AR and ROS appear to endow this receptor with the ability to self-regulate signaling efficacy and ligand binding, hereby unveiling a redox-axis that may be unfavorably altered in pathological states contributing to both disease progression and therapeutic drug responses.
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Affiliation(s)
- Kalyn M Rambacher
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, GA 30341, USA
| | - Nader H Moniri
- Department of Pharmaceutical Sciences, College of Pharmacy, Mercer University Health Sciences Center, Mercer University, Atlanta, GA 30341, USA.
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25
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Velmurugan BK, Baskaran R, Huang CY. Detailed insight on β-adrenoceptors as therapeutic targets. Biomed Pharmacother 2019; 117:109039. [PMID: 31176173 DOI: 10.1016/j.biopha.2019.109039] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 05/15/2019] [Accepted: 05/29/2019] [Indexed: 01/08/2023] Open
Abstract
Human G protein-coupled receptors (GPCRs), especially adrenoceptors, play a crucial role in maintaining important physiological activities including cardiovascular and pulmonary functions. Among all adrenoceptors, β-adrenoceptors are the best characterized GPCRs and possess distinctive features as drug targets. Similarly, ligands that activate/deactivate β-adrenoceptors also hold a significant position in the field of biomarker identification and drug discovery. Several studies regarding molecular characterization of the β-adrenoceptor ligands have revealed that ligands with abilities to inhibit basal or intrinsic receptor activity or prevent receptor desensitization are particularly important to efficiently manage detrimental health conditions, including chronic heart failure, asthma, chronic obstructive pulmonary disease, obesity, and diabetes. Given the importance of β-adrenoceptors as molecular targets for many pathological conditions, this review aims to provide a detailed insight on the structural and functional aspects of β-adrenoceptors, with a particular emphasis on their importance as biomarkers and therapeutic targets.
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Affiliation(s)
- Bharath Kumar Velmurugan
- Toxicology and Biomedicine Research group, Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Rathinasamy Baskaran
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
| | - Chih-Yang Huang
- Cardiovascular research center, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Tzu Chi University of Science and Technology, Hualien, Taiwan; Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan.
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Yang X, Zhao T, Feng L, Shi Y, Jiang J, Liang S, Sun B, Xu Q, Duan J, Sun Z. PM 2.5-induced ADRB2 hypermethylation contributed to cardiac dysfunction through cardiomyocytes apoptosis via PI3K/Akt pathway. ENVIRONMENT INTERNATIONAL 2019; 127:601-614. [PMID: 30986742 DOI: 10.1016/j.envint.2019.03.057] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/23/2019] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Long-term exposure to fine particulate matter (PM2.5) can causally contribute to progression of atherosclerosis, risk of ischemic heart disease and death, but the underlying mechanism is little known. Since DNA methylation impacts the process of heart disease, it might be useful in exploring potential mechanistic pathways linking PM2.5 exposure and heart disease. OBJECTIVES Here, we investigated the PM2.5-induced ADRB2 hypermethylation and the involving epigenetic mechanism of PM2.5-induced cardiomyocytes apoptosis and cardiac dysfunction. METHODS AND RESULTS In vitro, PM2.5 markedly augmented cardiotoxicity including oxidative damage and apoptosis in cardiomyocytes AC16 as well as epigenetic alteration. DNA methylation profiling revealed a significant gene-ADRB2 was involved in the cardiac relative GO and KEGG pathways. Methylation chip and Bisulfite Sequencing PCR (BSP) both identified the hypermethylation status of ADRB2 which encodes β2-Adrenergic receptor (β2AR). Mechanistic study showed ADRB2 hypermethylation-induced down-regulation of β2AR inhibited PI3K/Akt and then activated Bcl-2/BAX and p53 pathway in AC16. The transgenic cell lines showed over-expression of ADRB2 weakened the PM2.5-induced cardiomyocytes apoptosis in opposite way, but was augmented by PI3K inhibitor (LY294002). In vivo, echocardiography showed the heart contractile function was decreased after SD rats intratracheal instillation of PM2.5 for 30 days. The myocardial interstitial edema, myocardial gap expansion and myofibril disorder in PM2.5 treated group were observed in rats heart tissue. What's more, basal expression of β2AR and VEGFR2 decreased in heart tissue as the dosage of PM2.5 increasing, meanwhile PM2.5 markedly attenuated PI3K/Akt pathway followed by augmented Bcl-2/BAX and p53 pathway, thus caused a greater number of TUNEL positive cardiomyocytes resulted in cardiac dysfunction in vivo. CONCLUSIONS PM2.5 exposure could cause the myocardial ADRB2 hypermethylation and activate the β2AR/PI3K/Akt pathway, resulted in PM2.5-induced cardiomyocytes apoptosis and cardiac dysfunction. Our study suggested that the ADRB2 demethylation or ADRB2/β2AR activation may serve as a potential pathway to prevent cardiac dysfunction induced by PM2.5 exposure.
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Affiliation(s)
- Xiaozhe Yang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Tong Zhao
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Lin Feng
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Yanfeng Shi
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Jinjin Jiang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Shuang Liang
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Baiyang Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China
| | - Qing Xu
- Core Facilities for Electrophysiology, Core Facilities Center, Capital Medical University, Beijing 100069, PR China
| | - Junchao Duan
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China.
| | - Zhiwei Sun
- Department of Toxicology and Sanitary Chemistry, School of Public Health, Capital Medical University, Beijing 100069, PR China; Beijing Key Laboratory of Environmental Toxicology, Capital Medical University, Beijing 100069, PR China.
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27
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Wang T, Xing Y, Meng Q, Lu H, Liu W, Yan S, Song Y, Xu X, Huang J, Cui Y, Jia D, Cai L. Mammalian Eps15 homology domain 1 potentiates angiogenesis of non-small cell lung cancer by regulating β2AR signaling. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2019; 38:174. [PMID: 31023336 PMCID: PMC6482525 DOI: 10.1186/s13046-019-1162-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is a devastating disease with a heterogeneous prognosis, and the molecular mechanisms underlying tumor progression remain elusive. Mammalian Eps15 homology domain 1 (EHD1) plays a promotive role in tumor progression, but its role in cancer angiogenesis remains unknown. This study thus explored the role of EHD1 in angiogenesis in NSCLC. METHODS The changes in angiogenesis were evaluated through human umbilical vein endothelial cell (HUVEC) proliferation, migration and tube formation assays. The impact of EHD1 on β2-adrenoceptor (β2AR) signaling was evaluated by Western blotting, quantitative real-time polymerase chain reaction (qRT-PCR) analysis, and enzyme-linked immunosorbent assay (ELISA). The interaction between EHD1 and β2AR was confirmed by immunofluorescence (IF) and coimmunoprecipitation (Co-IP) experiments, and confocal microscopy immunofluorescence studies revealed that β2AR colocalized with the recycling endosome marker Rab11, which indicated β2AR endocytosis. Xenograft tumor models were used to investigate the role of EHD1 in NSCLC tumor growth. RESULTS The microarray analysis revealed that EHD1 was significantly correlated with tumor angiogenesis, and loss- and gain-of-function experiments demonstrated that EHD1 potentiates HUVEC proliferation, migration and tube formation. EHD1 knockdown inhibited β2AR signaling activity, and EHD1 upregulation promoted vascular endothelial growth factor A (VEGFA) and β2AR expression. Interestingly, EHD1 interacted with β2AR and played a novel and critical role in β2AR endocytic recycling to prevent receptor degradation. Aberrant VEGFA or β2AR expression significantly affected EHD1-mediated tumor angiogenesis. The proangiogenic role of EHD1 was confirmed in xenograft tumor models, and immunohistochemistry (IHC) analysis confirmed that EHD1 expression was positively correlated with VEGFA expression, microvessel density (MVD) and β2AR expression in patient specimens. CONCLUSION Collectively, the data obtained in this study suggest that EHD1 plays a critical role in NSCLC angiogenesis via β2AR signaling and highlight a potential target for antiangiogenic therapy.
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Affiliation(s)
- Ting Wang
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China
| | - Ying Xing
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China
| | - Qingwei Meng
- The Sixth Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China
| | - Hailing Lu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China
| | - Wei Liu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China
| | - Shi Yan
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China
| | - Yang Song
- Department of Orthopedic Surgery, The Second Affiliated Hospital of Harbin Medical University, Xuefu Road 246, Harbin, 150081, China
| | - Xinyuan Xu
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China
| | - Jian Huang
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China
| | - Yue Cui
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China
| | - Dexin Jia
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China
| | - Li Cai
- The Fourth Department of Medical Oncology, Harbin Medical University Cancer Hospital, 150 Haping Road, Harbin, 150040, China.
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Basavanhally T, Fonseca R, Uversky VN. Born This Way: Using Intrinsic Disorder to Map the Connections between SLITRKs, TSHR, and Male Sexual Orientation. Proteomics 2018; 18:e1800307. [PMID: 30156382 DOI: 10.1002/pmic.201800307] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 08/03/2018] [Indexed: 12/15/2022]
Abstract
Recently, genome-wide association study reveals a significant association between specific single nucleotide polymorphisms (SNPs) in men and their sexual orientation. These SNPs (rs9547443 and rs1035144) reside in the intergenic region between the SLITRK5 and SLITRK6 genes and in the intronic region of the TSHR gene and might affect functionality of SLITRK5, SLITRK6, and TSHR proteins that are engaged in tight control of key developmental processes, such as neurite outgrowth and modulation, cellular differentiation, and hormonal regulation. SLITRK5 and SLITRK6 are single-pass transmembrane proteins, whereas TSHR is a heptahelical G protein-coupled receptor (GPCR). Mutations in these proteins are associated with various diseases and are linked to phenotypes found at a higher rate in homosexual men. A bioinformatics analysis of SLITRK5, SLITRK6, and TSHR proteins is conducted to look at their structure, protein interaction networks, and propensity for intrinsic disorder. It is assumed that this information might improve understanding of the roles that SLITRK5, SLITRK6, and TSHR play within neuronal and thyroidal tissues and give insight into the phenotypes associated with male homosexuality.
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Affiliation(s)
- Tara Basavanhally
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Renée Fonseca
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.,USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.,Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, 142290, Pushchino, Moscow, Russia
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29
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Biophysical and functional characterization of Norrin signaling through Frizzled4. Proc Natl Acad Sci U S A 2018; 115:8787-8792. [PMID: 30104375 DOI: 10.1073/pnas.1805901115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Wnt signaling is initiated by Wnt ligand binding to the extracellular ligand binding domain, called the cysteine-rich domain (CRD), of a Frizzled (Fzd) receptor. Norrin, an atypical Fzd ligand, specifically interacts with Fzd4 to activate β-catenin-dependent canonical Wnt signaling. Much of the molecular basis that confers Norrin selectivity in binding to Fzd4 was revealed through the structural study of the Fzd4CRD-Norrin complex. However, how the ligand interaction, seemingly localized at the CRD, is transmitted across full-length Fzd4 to the cytoplasm remains largely unknown. Here, we show that a flexible linker domain, which connects the CRD to the transmembrane domain, plays an important role in Norrin signaling. The linker domain directly contributes to the high-affinity interaction between Fzd4 and Norrin as shown by ∼10-fold higher binding affinity of Fzd4CRD to Norrin in the presence of the linker. Swapping the Fzd4 linker with the Fzd5 linker resulted in the loss of Norrin signaling, suggesting the importance of the linker in ligand-specific cellular response. In addition, structural dynamics of Fzd4 associated with Norrin binding investigated by hydrogen/deuterium exchange MS revealed Norrin-induced conformational changes on the linker domain and the intracellular loop 3 (ICL3) region of Fzd4. Cell-based functional assays showed that linker deletion, L430A and L433A mutations at ICL3, and C-terminal tail truncation displayed reduced β-catenin-dependent signaling activity, indicating the functional significance of these sites. Together, our results provide functional and biochemical dissection of Fzd4 in Norrin signaling.
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30
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Yen HY, Hoi KK, Liko I, Hedger G, Horrell MR, Song W, Wu D, Heine P, Warne T, Lee Y, Carpenter B, Plückthun A, Tate CG, Sansom MSP, Robinson CV. PtdIns(4,5)P 2 stabilizes active states of GPCRs and enhances selectivity of G-protein coupling. Nature 2018; 559:423-427. [PMID: 29995853 PMCID: PMC6059376 DOI: 10.1038/s41586-018-0325-6] [Citation(s) in RCA: 206] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 05/14/2018] [Indexed: 11/21/2022]
Abstract
G-protein-coupled receptors (GPCRs) are involved in many physiological processes and are therefore key drug targets1. Although detailed structural information is available for GPCRs, the effects of lipids on the receptors, and on downstream coupling of GPCRs to G proteins are largely unknown. Here we use native mass spectrometry to identify endogenous lipids bound to three class A GPCRs. We observed preferential binding of phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) over related lipids and confirm that the intracellular surface of the receptors contain hotspots for PtdIns(4,5)P2 binding. Endogenous lipids were also observed bound directly to the trimeric Gαsβγ protein complex of the adenosine A2A receptor (A2AR) in the gas phase. Using engineered Gα subunits (mini-Gαs, mini-Gαi and mini-Gα12)2, we demonstrate that the complex of mini-Gαs with the β1 adrenergic receptor (β1AR) is stabilized by the binding of two PtdIns(4,5)P2 molecules. By contrast, PtdIns(4,5)P2 does not stabilize coupling between β1AR and other Gα subunits (mini-Gαi or mini-Gα12) or a high-affinity nanobody. Other endogenous lipids that bind to these receptors have no effect on coupling, highlighting the specificity of PtdIns(4,5)P2. Calculations of potential of mean force and increased GTP turnover by the activated neurotensin receptor when coupled to trimeric Gαiβγ complex in the presence of PtdIns(4,5)P2 provide further evidence for a specific effect of PtdIns(4,5)P2 on coupling. We identify key residues on cognate Gα subunits through which PtdIns(4,5)P2 forms bridging interactions with basic residues on class A GPCRs. These modulating effects of lipids on receptors suggest consequences for understanding function, G-protein selectivity and drug targeting of class A GPCRs.
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MESH Headings
- Animals
- GTP-Binding Protein alpha Subunits, Gi-Go/metabolism
- GTP-Binding Protein alpha Subunits, Gs/metabolism
- Heterotrimeric GTP-Binding Proteins/metabolism
- Humans
- Molecular Dynamics Simulation
- Phosphatidylinositol 4,5-Diphosphate/metabolism
- Protein Stability
- Rats
- Receptors, Adrenergic, alpha-2/chemistry
- Receptors, Adrenergic, alpha-2/genetics
- Receptors, Adrenergic, alpha-2/metabolism
- Receptors, Adrenergic, beta-1/chemistry
- Receptors, Adrenergic, beta-1/genetics
- Receptors, Adrenergic, beta-1/metabolism
- Receptors, G-Protein-Coupled/chemistry
- Receptors, G-Protein-Coupled/genetics
- Receptors, G-Protein-Coupled/metabolism
- Receptors, Neurotensin/chemistry
- Receptors, Neurotensin/genetics
- Receptors, Neurotensin/metabolism
- Single-Chain Antibodies/chemistry
- Single-Chain Antibodies/metabolism
- Substrate Specificity
- Turkeys
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Affiliation(s)
- Hsin-Yung Yen
- Chemical Research Laboratory, University of Oxford, Oxford, UK
- OMass Technologies, Kidlington, UK
| | - Kin Kuan Hoi
- Chemical Research Laboratory, University of Oxford, Oxford, UK
| | - Idlir Liko
- Chemical Research Laboratory, University of Oxford, Oxford, UK
- OMass Technologies, Kidlington, UK
| | - George Hedger
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Wanling Song
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - Di Wu
- Chemical Research Laboratory, University of Oxford, Oxford, UK
| | - Philipp Heine
- Biochemisches Institut, Universität Zürich, Zurich, Switzerland
| | - Tony Warne
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Yang Lee
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Byron Carpenter
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Warwick Integrative Synthetic Biology Centre, School of Life Sciences, The University of Warwick, Coventry, UK
| | | | | | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK.
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Abstract
Hepatitis C virus (HCV) is a leading cause of liver disease worldwide. Although several HCV protease/polymerase inhibitors were recently approved by U.S. FDA, the combination of antivirals targeting multiple processes of HCV lifecycle would optimize anti-HCV therapy and against potential drug-resistance. Viral entry is an essential target step for antiviral development, but FDA-approved HCV entry inhibitor remains exclusive. Here we identify serotonin 2A receptor (5-HT2AR) is a HCV entry factor amendable to therapeutic intervention by a chemical biology strategy. The silencing of 5-HT2AR and clinically available 5-HT2AR antagonist suppress cell culture-derived HCV (HCVcc) in different liver cells and primary human hepatocytes at late endocytosis process. The mechanism is related to regulate the correct plasma membrane localization of claudin 1 (CLDN1). Moreover, phenoxybenzamine (PBZ), an FDA-approved 5-HT2AR antagonist, inhibits all major HCV genotypes in vitro and displays synergy in combination with clinical used anti-HCV drugs. The impact of PBZ on HCV genotype 2a is documented in immune-competent humanized transgenic mice. Our results not only expand the understanding of HCV entry, but also present a promising target for the invention of HCV entry inhibitor.
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32
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Structural insights into positive and negative allosteric regulation of a G protein-coupled receptor through protein-lipid interactions. Sci Rep 2018. [PMID: 29535353 PMCID: PMC5849739 DOI: 10.1038/s41598-018-22735-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Lipids are becoming known as essential allosteric modulators of G protein-coupled receptor (GPCRs). However, how they exert their effects on GPCR conformation at the atomic level is still unclear. In light of recent experimental data, we have performed several long-timescale molecular dynamics (MD) simulations, totalling 24 μs, to rigorously map allosteric modulation and conformational changes in the β2 adrenergic receptor (β2AR) that occur as a result of interactions with three different phospholipids. In particular, we identify different sequential mechanisms behind receptor activation and deactivation, respectively, mediated by specific lipid interactions with key receptor regions. We show that net negatively charged lipids stabilize an active-like state of β2AR that is able to dock Gsα protein. Clustering of anionic lipids around the receptor with local distortion of membrane thickness is also apparent. On the other hand, net-neutral zwitterionic lipids inactivate the receptor, generating either fully inactive or intermediate states, with kinetics depending on lipid headgroup charge distribution and hydrophobicity. These chemical differences alter membrane thickness and density, which differentially destabilize the β2AR active state through lateral compression effects.
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Ligand binding modes from low resolution GPCR models and mutagenesis: chicken bitter taste receptor as a test-case. Sci Rep 2017; 7:8223. [PMID: 28811548 PMCID: PMC5557796 DOI: 10.1038/s41598-017-08344-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 07/10/2017] [Indexed: 11/08/2022] Open
Abstract
Bitter taste is one of the basic taste modalities, warning against consuming potential poisons. Bitter compounds activate members of the bitter taste receptor (Tas2r) subfamily of G protein-coupled receptors (GPCRs). The number of functional Tas2rs is species-dependent. Chickens represent an intriguing minimalistic model, because they detect the bitter taste of structurally different molecules with merely three bitter taste receptor subtypes. We investigated the binding modes of several known agonists of a representative chicken bitter taste receptor, ggTas2r1. Because of low sequence similarity between ggTas2r1 and crystallized GPCRs (~10% identity, ~30% similarity at most), the combination of computational approaches with site-directed mutagenesis was used to characterize the agonist-bound conformation of ggTas2r1 binding site between TMs 3, 5, 6 and 7. We found that the ligand interactions with N93 in TM3 and/or N247 in TM5, combined with hydrophobic contacts, are typically involved in agonist recognition. Next, the ggTas2r1 structural model was successfully used to identify three quinine analogues (epiquinidine, ethylhydrocupreine, quinidine) as new ggTas2r1 agonists. The integrated approach validated here may be applicable to additional cases where the sequence identity of the GPCR of interest and the existing experimental structures is low.
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34
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Wako H, Ishiuchi SI, Kato D, Féraud G, Dedonder-Lardeux C, Jouvet C, Fujii M. A conformational study of protonated noradrenaline by UV–UV and IR dip double resonance laser spectroscopy combined with an electrospray and a cold ion trap method. Phys Chem Chem Phys 2017; 19:10777-10785. [DOI: 10.1039/c6cp08426e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In protonated noradrenaline, 3 folded and 2 extended conformers were identified under the ultra-cold condition.
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Affiliation(s)
- Hiromichi Wako
- Laboratory for Chemistry and Life Science
- Institute of innovative research
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Shun-ichi Ishiuchi
- Laboratory for Chemistry and Life Science
- Institute of innovative research
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Daichi Kato
- Laboratory for Chemistry and Life Science
- Institute of innovative research
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Géraldine Féraud
- CNRS
- Aix-Marseille Université
- PIIM UMR 7365
- Avenue Escadrille Normandie-Niémen
- 13397 Marseille Cedex 20
| | - Claude Dedonder-Lardeux
- CNRS
- Aix-Marseille Université
- PIIM UMR 7365
- Avenue Escadrille Normandie-Niémen
- 13397 Marseille Cedex 20
| | - Christophe Jouvet
- CNRS
- Aix-Marseille Université
- PIIM UMR 7365
- Avenue Escadrille Normandie-Niémen
- 13397 Marseille Cedex 20
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute of innovative research
- Tokyo Institute of Technology
- Midori-ku
- Japan
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35
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Karaca S, Civelek E, Karaca M, Sahiner UM, Ozgul RK, Kocabas CN, Polimanti R, Sekerel BE. Allergy-specific Phenome-Wide Association Study for Immunogenes in Turkish Children. Sci Rep 2016; 6:33152. [PMID: 27624002 PMCID: PMC5021980 DOI: 10.1038/srep33152] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/10/2016] [Indexed: 01/06/2023] Open
Abstract
To dissect the role of immunogenetics in allergy and asthma, we performed a phenome-wide association study in 974 Turkish children selected from a cross-sectional study conducted using ISAAC (International Study of Asthma and Allergies in Children) Phase II tools. We investigated 9 loci involved in different immune functions (ADAM33, ADRB2, CD14, IL13, IL4, IL4R, MS4A2, SERPINE1, and TNF) with respect to 116 traits assessed through blood tests, hypertonic saline challenge tests, questionnaires, and skin prick tests. Multiple associations were observed for ADAM33: rs2280090 was associated with reduced MEF240% (i.e., the ratio of Mean Expiratory Flow after 240s of hypertonic saline inhalation with respect to the age- and ancestry-matched reference value) and with an increased risk of allergic bronchitis (p = 1.77*10−4 and p = 7.94*10−4, respectively); rs3918396 was associated with wheezing and eczema comorbidity (p = 3.41*10−4). IL4 rs2243250 was associated with increased FEV240 (Forced Expiratory Flow Volume after 240s of hypertonic saline inhalation; p = 4.81*10−4) and CD14 rs2569190 was associated with asthma diagnosis (p = 1.36*10−3). ADAM33 and IL4 appeared to play a role in the processes linked to allergic airway inflammation and lung function. Due to its association with wheezing and eczema comorbidity, ADAM33 may also be involved in the atopic march.
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Affiliation(s)
- Sefayet Karaca
- Aksaray University, Faculty of Health Science, Aksaray, Turkey
| | - Ersoy Civelek
- Ankara Child Health and Diseases Hematology Oncology Research Hospital, Pediatric Allergy and Immunology Clinic, Ankara, Turkey
| | - Mehmet Karaca
- Aksaray University, Faculty of Science and Arts, Department of Biology, Aksaray, Turkey
| | - Umit M Sahiner
- Hacettepe University, Faculty of Medicine, Pediatric Allergy and Asthma Unit, Ankara, Turkey
| | - Riza K Ozgul
- Hacettepe University, Faculty of Medicine, Pediatrics Department, Unit of Metabolism and Institute of Child Health, Ankara, Turkey
| | - Can N Kocabas
- Ankara Child Health and Diseases Hematology Oncology Research Hospital, Pediatric Allergy and Immunology Clinic, Ankara, Turkey
| | - Renato Polimanti
- Department of Psychiatry, Yale University School of Medicine and VA CT Healthcare Center, West Haven, CT, United States
| | - Bülent E Sekerel
- Hacettepe University, Faculty of Medicine, Pediatric Allergy and Asthma Unit, Ankara, Turkey
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36
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Lian P, Li L, Geng C, Zhen X, Fu W. Higher-Affinity Agonists of 5-HT1AR Discovered through Tuning the Binding-Site Flexibility. J Chem Inf Model 2015; 55:1616-27. [DOI: 10.1021/acs.jcim.5b00164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peng Lian
- Department of Medicinal Chemistry & Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - LinLang Li
- Jiangsu
Key Laboratory for Translational Research for Neuropsychiatric-Diseases,
Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Chuanrong Geng
- Department of Medicinal Chemistry & Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xuechu Zhen
- Jiangsu
Key Laboratory for Translational Research for Neuropsychiatric-Diseases,
Department of Pharmacology, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Wei Fu
- Department of Medicinal Chemistry & Key Laboratory of Smart Drug Delivery, Ministry of Education, School of Pharmacy, Fudan University, Shanghai 201203, China
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