101
|
Zhang XJ, Cheng X, Yan ZZ, Fang J, Wang X, Wang W, Liu ZY, Shen LJ, Zhang P, Wang PX, Liao R, Ji YX, Wang JY, Tian S, Zhu XY, Zhang Y, Tian RF, Wang L, Ma XL, Huang Z, She ZG, Li H. An ALOX12–12-HETE–GPR31 signaling axis is a key mediator of hepatic ischemia–reperfusion injury. Nat Med 2017; 24:73-83. [DOI: 10.1038/nm.4451] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/01/2017] [Indexed: 12/12/2022]
|
102
|
Khan M, Huang T, Lin CY, Wu J, Fan BM, Bian ZX. Exploiting cancer's phenotypic guise against itself: targeting ectopically expressed peptide G-protein coupled receptors for lung cancer therapy. Oncotarget 2017; 8:104615-104637. [PMID: 29262666 PMCID: PMC5732832 DOI: 10.18632/oncotarget.18403] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 05/23/2017] [Indexed: 02/07/2023] Open
Abstract
Lung cancer, claiming millions of lives annually, has the highest mortality rate worldwide. This advocates the development of novel cancer therapies that are highly toxic for cancer cells but negligibly toxic for healthy cells. One of the effective treatments is targeting overexpressed surface receptors of cancer cells with receptor-specific drugs. The receptors-in-focus in the current review are the G-protein coupled receptors (GPCRs), which are often overexpressed in various types of tumors. The peptide subfamily of GPCRs is the pivot of the current article owing to the high affinity and specificity to and of their cognate peptide ligands, and the proven efficacy of peptide-based therapeutics. The article summarizes various ectopically expressed peptide GPCRs in lung cancer, namely, Cholecystokinin-B/Gastrin receptor, the Bombesin receptor family, Bradykinin B1 and B2 receptors, Arginine vasopressin receptors 1a, 1b and 2, and the Somatostatin receptor type 2. The autocrine growth and pro-proliferative pathways they mediate, and the distinct tumor-inhibitory effects of somatostatin receptors are then discussed. The next section covers how these pathways may be influenced or 'corrected' through therapeutics (involving agonists and antagonists) targeting the overexpressed peptide GPCRs. The review proceeds on to Nano-scaled delivery platforms, which enclose chemotherapeutic agents and are decorated with peptide ligands on their external surface, as an effective means of targeting cancer cells. We conclude that targeting these overexpressed peptide GPCRs is potentially evolving as a highly promising form of lung cancer therapy.
Collapse
Affiliation(s)
- Mahjabin Khan
- Laboratory of Brain-Gut Research, School of Chinese Medicine, Hong Kong Baptist University, HKSAR, Kowloon Tong, P.R. China
| | - Tao Huang
- Laboratory of Brain-Gut Research, School of Chinese Medicine, Hong Kong Baptist University, HKSAR, Kowloon Tong, P.R. China
| | - Cheng-Yuan Lin
- Laboratory of Brain-Gut Research, School of Chinese Medicine, Hong Kong Baptist University, HKSAR, Kowloon Tong, P.R. China
- YMU-HKBU Joint Laboratory of Traditional Natural Medicine, Yunnan Minzu University, Kunming, P.R. China
| | - Jiang Wu
- State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Bao-Min Fan
- YMU-HKBU Joint Laboratory of Traditional Natural Medicine, Yunnan Minzu University, Kunming, P.R. China
| | - Zhao-Xiang Bian
- Laboratory of Brain-Gut Research, School of Chinese Medicine, Hong Kong Baptist University, HKSAR, Kowloon Tong, P.R. China
| |
Collapse
|
103
|
Wu Z, Lu W, Yu W, Wang T, Li W, Liu G, Zhang H, Pang X, Huang J, Liu M, Cheng F, Tang Y. Quantitative and systems pharmacology 2. In silico polypharmacology of G protein-coupled receptor ligands via network-based approaches. Pharmacol Res 2017; 129:400-413. [PMID: 29133212 DOI: 10.1016/j.phrs.2017.11.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/07/2017] [Accepted: 11/07/2017] [Indexed: 02/06/2023]
Abstract
G protein-coupled receptors (GPCRs) are the largest super family with more than 800 membrane receptors. Currently, over 30% of the approved drugs target human GPCRs. However, only approximately 30 human GPCRs have been resolved three-dimensional crystal structures, which limits traditional structure-based drug discovery. Recent advances in network-based systems pharmacology approaches have demonstrated powerful strategies for identifying new targets of GPCR ligands. In this study, we proposed a network-based systems pharmacology framework for comprehensive identification of new drug-target interactions on GPCRs. Specifically, we reconstructed both global and local drug-target interaction networks for human GPCRs. Network analysis on the known drug-target networks showed rational strategies for designing new GPCR ligands and evaluating side effects of the approved GPCR drugs. We further built global and local network-based models for predicting new targets of the known GPCR ligands. The area under the receiver operating characteristic curve of more than 0.96 was obtained for the best network-based models in cross validation. In case studies, we identified that several network-predicted GPCR off-targets (e.g. ADRA2A, ADRA2C and CHRM2) were associated with cardiovascular complications (e.g. bradycardia and palpitations) of the approved GPCR drugs via an integrative analysis of drug-target and off-target-adverse drug event networks. Importantly, we experimentally validated that two newly predicted compounds, AM966 and Ki16425, showed high binding affinities on prostaglandin E2 receptor EP4 subtype with IC50=2.67μM and 6.34μM, respectively. In summary, this study offers powerful network-based tools for identifying polypharmacology of GPCR ligands in drug discovery and development.
Collapse
Affiliation(s)
- Zengrui Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weiqiang Lu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Weiwei Yu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Tianduanyi Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Hankun Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xiufeng Pang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jin Huang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Mingyao Liu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China; Institute of Biosciences and Technology, Department of Molecular and Cellular Medicine, Texas A&M University Health Science Center, Houston, TX 77030, USA.
| | - Feixiong Cheng
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA; Center for Complex Networks Research, Northeastern University, Boston, MA 02115, USA.
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| |
Collapse
|
104
|
Spatial encryption of G protein-coupled receptor signaling in endosomes; Mechanisms and applications. Biochem Pharmacol 2017; 143:1-9. [DOI: 10.1016/j.bcp.2017.04.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 04/25/2017] [Indexed: 01/14/2023]
|
105
|
Koo JH, Kim TH, Park SY, Joo MS, Han CY, Choi CS, Kim SG. Gα13 ablation reprograms myofibers to oxidative phenotype and enhances whole-body metabolism. J Clin Invest 2017; 127:3845-3860. [PMID: 28920922 DOI: 10.1172/jci92067] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 08/02/2017] [Indexed: 12/24/2022] Open
Abstract
Skeletal muscle is a key organ in energy homeostasis owing to its high requirement for nutrients. Heterotrimeric G proteins converge signals from cell-surface receptors to potentiate or blunt responses against environmental changes. Here, we show that muscle-specific ablation of Gα13 in mice promotes reprogramming of myofibers to the oxidative type, with resultant increases in mitochondrial biogenesis and cellular respiration. Mechanistically, Gα13 and its downstream effector RhoA suppressed nuclear factor of activated T cells 1 (NFATc1), a chief regulator of myofiber conversion, by increasing Rho-associated kinase 2-mediated (Rock2-mediated) phosphorylation at Ser243. Ser243 phosphorylation of NFATc1 was reduced after exercise, but was higher in obese animals. Consequently, Gα13 ablation in muscles enhanced whole-body energy metabolism and increased insulin sensitivity, thus affording protection from diet-induced obesity and hepatic steatosis. Our results define Gα13 as a switch regulator of myofiber reprogramming, implying that modulations of Gα13 and its downstream effectors in skeletal muscle are a potential therapeutic approach to treating metabolic diseases.
Collapse
Affiliation(s)
- Ja Hyun Koo
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, South Korea
| | - Tae Hyun Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, South Korea
| | - Shi-Young Park
- Korea Mouse Metabolic Phenotyping Center, Lee Gil Ya Cancer and Diabetes Institute, Gachon University School of Medicine, Incheon, South Korea
| | - Min Sung Joo
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, South Korea
| | - Chang Yeob Han
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, South Korea
| | - Cheol Soo Choi
- Korea Mouse Metabolic Phenotyping Center, Lee Gil Ya Cancer and Diabetes Institute, Gachon University School of Medicine, Incheon, South Korea.,Endocrinology, Internal Medicine, Gachon University Gil Medical Center, Incheon, South Korea
| | - Sang Geon Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, South Korea
| |
Collapse
|
106
|
Flavonoid allosteric modulation of mutated visual rhodopsin associated with retinitis pigmentosa. Sci Rep 2017; 7:11167. [PMID: 28894166 PMCID: PMC5593859 DOI: 10.1038/s41598-017-11391-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/22/2017] [Indexed: 11/08/2022] Open
Abstract
Dietary flavonoids exhibit many biologically-relevant functions and can potentially have beneficial effects in the treatment of pathological conditions. In spite of its well known antioxidant properties, scarce structural information is available on the interaction of flavonoids with membrane receptors. Advances in the structural biology of a specific class of membrane receptors, the G protein-coupled receptors, have significantly increased our understanding of drug action and paved the way for developing improved therapeutic approaches. We have analyzed the effect of the flavonoid quercetin on the conformation, stability and function of the G protein-coupled receptor rhodopsin, and the G90V mutant associated with the retinal degenerative disease retinitis pigmentosa. By using a combination of experimental and computational methods, we suggest that quercetin can act as an allosteric modulator of opsin regenerated with 9-cis-retinal and more importantly, that this binding has a positive effect on the stability and conformational properties of the G90V mutant associated with retinitis pigmentosa. These results open new possibilities to use quercetin and other flavonoids, in combination with specific retinoids like 9-cis-retinal, for the treatment of retinal degeneration associated with retinitis pigmentosa. Moreover, the use of flavonoids as allosteric modulators may also be applicable to other members of the G protein-coupled receptors superfamily.
Collapse
|
107
|
Babinsky VN, Hannan FM, Ramracheya RD, Zhang Q, Nesbit MA, Hugill A, Bentley L, Hough TA, Joynson E, Stewart M, Aggarwal A, Prinz-Wohlgenannt M, Gorvin CM, Kallay E, Wells S, Cox RD, Richards D, Rorsman P, Thakker RV. Mutant Mice With Calcium-Sensing Receptor Activation Have Hyperglycemia That Is Rectified by Calcilytic Therapy. Endocrinology 2017; 158:2486-2502. [PMID: 28575322 PMCID: PMC5551547 DOI: 10.1210/en.2017-00111] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/30/2017] [Indexed: 12/12/2022]
Abstract
The calcium-sensing receptor (CaSR) is a family C G-protein-coupled receptor that plays a pivotal role in extracellular calcium homeostasis. The CaSR is also highly expressed in pancreatic islet α- and β-cells that secrete glucagon and insulin, respectively. To determine whether the CaSR may influence systemic glucose homeostasis, we characterized a mouse model with a germline gain-of-function CaSR mutation, Leu723Gln, referred to as Nuclear flecks (Nuf). Heterozygous- (CasrNuf/+) and homozygous-affected (CasrNuf/Nuf) mice were shown to have hypocalcemia in association with impaired glucose tolerance and insulin secretion. Oral administration of a CaSR antagonist compound, known as a calcilytic, rectified the glucose intolerance and hypoinsulinemia of CasrNuf/+ mice and ameliorated glucose intolerance in CasrNuf/Nuf mice. Ex vivo studies showed CasrNuf/+ and CasrNuf/Nuf mice to have reduced pancreatic islet mass and β-cell proliferation. Electrophysiological analysis of isolated CasrNuf/Nuf islets showed CaSR activation to increase the basal electrical activity of β-cells independently of effects on the activity of the adenosine triphosphate (ATP)-sensitive K+ (KATP) channel. CasrNuf/Nuf mice also had impaired glucose-mediated suppression of glucagon secretion, which was associated with increased numbers of α-cells and a higher α-cell proliferation rate. Moreover, CasrNuf/Nuf islet electrophysiology demonstrated an impairment of α-cell membrane depolarization in association with attenuated α-cell basal KATP channel activity. These studies indicate that the CaSR activation impairs glucose tolerance by a combination of α- and β-cell defects and also influences pancreatic islet mass. Moreover, our findings highlight a potential application of targeted CaSR compounds for modulating glucose metabolism.
Collapse
Affiliation(s)
- Valerie N. Babinsky
- Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LE, United Kingdom
| | - Fadil M. Hannan
- Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LE, United Kingdom
- Department of Musculoskeletal Biology, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool L7 8TX, United Kingdom
| | - Reshma D. Ramracheya
- Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LE, United Kingdom
| | - Quan Zhang
- Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LE, United Kingdom
| | - M. Andrew Nesbit
- Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LE, United Kingdom
- Biomedical Sciences Research Institute, Ulster University, Coleraine BT52 1SA, United Kingdom
| | - Alison Hugill
- Medical Research Council Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Liz Bentley
- Medical Research Council Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Tertius A. Hough
- Medical Research Council Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Elizabeth Joynson
- Medical Research Council Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Michelle Stewart
- Medical Research Council Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Abhishek Aggarwal
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna A-1090, Austria
| | | | - Caroline M. Gorvin
- Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LE, United Kingdom
| | - Enikö Kallay
- Department of Pathophysiology and Allergy Research, Medical University of Vienna, Vienna A-1090, Austria
| | - Sara Wells
- Medical Research Council Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Roger D. Cox
- Medical Research Council Mammalian Genetics Unit and Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Science and Innovation Campus, Oxfordshire OX11 0RD, United Kingdom
| | - Duncan Richards
- GlaxoSmithKline Clinical Unit, Cambridge CB2 0GG, United Kingdom
| | - Patrik Rorsman
- Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LE, United Kingdom
| | - Rajesh V. Thakker
- Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Oxford OX3 7LE, United Kingdom
| |
Collapse
|
108
|
Salmas RE, Seeman P, Aksoydan B, Erol I, Kantarcioglu I, Stein M, Yurtsever M, Durdagi S. Analysis of the Glutamate Agonist LY404,039 Binding to Nonstatic Dopamine Receptor D2 Dimer Structures and Consensus Docking. ACS Chem Neurosci 2017; 8:1404-1415. [PMID: 28272861 DOI: 10.1021/acschemneuro.7b00070] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dopamine receptor D2 (D2R) plays an important role in the human central nervous system and is a focal target of antipsychotic agents. The D2HighR and D2LowR dimeric models previously developed by our group are used to investigate the prediction of binding affinity of the LY404,039 ligand and its binding mechanism within the catalytic domain. The computational data obtained using molecular dynamics simulations fit well with the experimental results. The calculated binding affinities of LY404,039 using MM/PBSA for the D2HighR and D2LowR targets were -12.04 and -9.11 kcal/mol, respectively. The experimental results suggest that LY404,039 binds to D2HighR and D2LowR with binding affinities (Ki) of 8.2 and 1640 nM, respectively. The high binding affinity of LY404,039 in terms of binding to [3H]domperidone was inhibited by the presence of a guanine nucleotide, indicating an agonist action of the drug at D2HighR. The interaction analysis demonstrated that while Asp114 was among the most critical amino acids for D2HighR binding, residues Ser193 and Ser197 were significantly more important within the binding cavity of D2LowR. Molecular modeling analyses are extended to ensemble docking as well as structure-based pharmacophore model (E-pharmacophore) development using the bioactive conformation of LY404,039 at the binding pocket as a template and screening of small-molecule databases with derived pharmacophore models.
Collapse
Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Philip Seeman
- Departments
of Pharmacology and Psychiatry, University of Toronto, 260 Heath
Street West, Unit 605, Toronto, Ontario M5P 3L6, Canada
| | - Busecan Aksoydan
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Ismail Erol
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
- Department
of Chemistry, Gebze Technical University, 41400, Kocaeli, Turkey
| | - Isik Kantarcioglu
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Matthias Stein
- Max-Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Mine Yurtsever
- Department
of Chemistry, Istanbul Technical University, 34469 Istanbul, Turkey
| | - Serdar Durdagi
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| |
Collapse
|
109
|
Cheng H, Schafer A, Soloveva V, Gharaibeh D, Kenny T, Retterer C, Zamani R, Bavari S, Peet NP, Rong L. Identification of a coumarin-based antihistamine-like small molecule as an anti-filoviral entry inhibitor. Antiviral Res 2017. [PMID: 28645623 DOI: 10.1016/j.antiviral.2017.06.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Filoviruses, consisting of Ebola virus, Marburg virus and Cuevavirus, cause severe hemorrhagic fevers in humans with high mortality rates up to 90%. Currently, there is no approved vaccine or therapy available for the prevention and treatment of filovirus infection in humans. The recent 2013-2015 West African Ebola epidemic underscores the urgency to develop antiviral therapeutics against these infectious diseases. Our previous study showed that GPCR antagonists, particularly histamine receptor antagonists (antihistamines) inhibit Ebola and Marburg virus entry. In this study, we screened a library of 1220 small molecules with predicted antihistamine activity, identified multiple compounds with potent inhibitory activity against entry of both Ebola and Marburg viruses in human cancer cell lines, and confirmed their anti-Ebola activity in human primary cells. These small molecules target a late-stage of Ebola virus entry. Further structure-activity relationship studies around one compound (cp19) reveal the importance of the coumarin fused ring structure, especially the hydrophobic substituents at positions 3 and/or 4, for its antiviral activity, and this identified scaffold represents a favorable starting point for the rapid development of anti-filovirus therapeutic agents.
Collapse
Affiliation(s)
- Han Cheng
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA.
| | - Adam Schafer
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | - Veronica Soloveva
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA
| | - Dima Gharaibeh
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA
| | - Tara Kenny
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA
| | - Cary Retterer
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA
| | - Rouzbeh Zamani
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA
| | - Sina Bavari
- US Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, 21702, USA
| | - Norton P Peet
- Chicago BioSolutions, Inc., 2242 West Harrison Suite 201, Chicago, IL, 60612, USA
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, IL, 60612, USA.
| |
Collapse
|
110
|
Abstract
Cells produce lipid membranes de novo through a complex sequence of enzymatic reactions that are difficult to reconstitute in a minimal system. We set out to take a different approach and mimic the synthesis of phospholipids using abiotic but highly selective bioconjugation reactions. Here, I outline several of our group's recent advances in exploring chemoselective reactions for stitching together lipid fragments to form membrane-forming lipids from non-membrane-forming precursors. Rapid chemical reactions can be harnessed to achieve facile de novo synthesis of lipid membranes, and spontaneous membrane formation can be applied for the reconstitution of membrane proteins, encapsulation and concentration of nanomaterials, and the study of lipid membrane remodeling. I conclude by briefly outlining future challenges and opportunities.
Collapse
Affiliation(s)
- Neal K Devaraj
- University of California, San Diego , La Jolla, California 92093, United States
| |
Collapse
|
111
|
Abstract
Membrane proteins are substantially more challenging than natively soluble proteins as subjects for structural analysis. Thus, membrane proteins are greatly underrepresented in structural databases. Recently, focused consortium efforts and advances in methodology for protein production, crystallographic analysis and cryo-EM analysis have accelerated the pace of atomic-level structure determination of membrane proteins.
Collapse
|
112
|
|
113
|
Computational design of ligand-binding membrane receptors with high selectivity. Nat Chem Biol 2017; 13:715-723. [PMID: 28459439 PMCID: PMC5478435 DOI: 10.1038/nchembio.2371] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 02/02/2017] [Indexed: 12/13/2022]
Abstract
Accurate modeling and design of protein-ligand
interactions have broad applications in cell, synthetic
biology and drug discovery but remain challenging without
experimental protein structures. Here we developed an
integrated protein homology modeling-ligand docking-protein
design approach that reconstructs protein-ligand binding
sites from homolog protein structures in the presence of
protein-bound ligand poses to capture conformational
selection and induced fit modes of ligand binding. In
structure modeling tests, we blindly predicted near-atomic
accuracy ligand conformations bound to G protein-coupled
receptors (GPCRs) that were rarely identified by traditional
approaches. We also quantitatively predicted the binding
selectivity of diverse ligands to
structurally-uncharacterized GPCRs. We then applied the
technique to design functional human dopamine receptors with
novel ligand binding selectivity. Most blindly predicted
ligand binding specificities closely agreed with
experimental validations. Our method should prove useful in
ligand discovery approaches and in reprogramming the ligand
binding profile of membrane receptors that remain difficult
to crystallize.
Collapse
|
114
|
Shilling PJ, Bumbak F, Scott DJ, Bathgate RAD, Gooley PR. Characterisation of a cell-free synthesised G-protein coupled receptor. Sci Rep 2017; 7:1094. [PMID: 28439124 PMCID: PMC5430785 DOI: 10.1038/s41598-017-01227-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/27/2017] [Indexed: 02/03/2023] Open
Abstract
G-protein coupled receptors are the largest family of integral membrane proteins found within the human genome. They function as receptors and modulators to a wide range of ligands and responses which are crucial for human health. GPCR study, specifically the investigation of structure and interaction to cognate ligands, is of high priority. Limitations for structural study can be traced in part, to obtaining suitable quantities of recombinant protein. We sought to address the limitations of traditional recombinant technologies by utilising an Escherichia coli based cell-free protein synthesis (CFPS) approach for production of a thermostable neurotensin receptor 1 (en2NTS1). Initial results were promising, with a high amount (up to 2 mg/mL) of en2NTS1 produced, that had attained correct secondary structure. Meanwhile, concurrent experiments indicated that CFPS produced en2NTS1 showed non-competitive binding to the peptide ligand neurotensin8-13 when compared to E. coli produced en2NTS1. 1H-13C HMQC SOFAST NMR spectra were indicative of disrupted tertiary structure for CFPS produced 13CH3-methionine labelled en2NTS1. The results obtained, indicate CFPS produced en2NTS1 is not forming a discrete tertiary structure and that further development of the CFPS technique needs to be carried out.
Collapse
Affiliation(s)
- Patrick J Shilling
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | - Fabian Bumbak
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, The University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, The University of Melbourne, Parkville, 3052, Victoria, Australia
| | - Daniel J Scott
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, The University of Melbourne, Parkville, 3052, Victoria, Australia
| | - Ross A D Bathgate
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey Institute of Neuroscience and Mental Health, 30 Royal Parade, The University of Melbourne, Parkville, 3052, Victoria, Australia
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Bio21 Molecular Science and Biotechnology Institute, 30 Flemington Road, The University of Melbourne, Parkville, VIC, 3010, Australia.
| |
Collapse
|
115
|
Ekhteiari Salmas R, Seeman P, Aksoydan B, Stein M, Yurtsever M, Durdagi S. Biological Insights of the Dopaminergic Stabilizer ACR16 at the Binding Pocket of Dopamine D2 Receptor. ACS Chem Neurosci 2017; 8:826-836. [PMID: 28001043 DOI: 10.1021/acschemneuro.6b00396] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The dopamine D2 receptor (D2R) plays an important part in the human central nervous system and it is considered to be a focal target of antipsychotic agents. It is structurally modeled in active and inactive states, in which homodimerization reaction of the D2R monomers is also applied. The ASP2314 (also known as ACR16) ligand, a D2R stabilizer, is used in tests to evaluate how dimerization and conformational changes may alter the ligand binding space and to provide information on alterations in inhibitory mechanisms upon activation. The administration of the D2R agonist ligand ACR16 [3H](+)-4-propyl-3,4,4a,5,6,10b-hexahydro-2H-naphtho[1,2-b][1,4]oxazin-9-ol ((+)PHNO) revealed Ki values of 32 nM for the D2highR and 52 μM for the D2lowR. The calculated binding affinities of ACR16 with post processing molecular dynamics (MD) simulations analyses using MM/PBSA for the monomeric and homodimeric forms of the D2highR were -9.46 and -8.39 kcal/mol, respectively. The data suggests that the dimerization of the D2R leads negative cooperativity for ACR16 binding. The dimerization reaction of the D2highR is energetically favorable by -22.95 kcal/mol. The dimerization reaction structurally and thermodynamically stabilizes the D2highR conformation, which may be due to the intermolecular forces formed between the TM4 of each monomer, and the result strongly demonstrates dimerization essential for activation of the D2R.
Collapse
Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Philip Seeman
- Departments
of Pharmacology and Psychiatry, University of Toronto, 260 Heath
Street West, Unit 605, M5P 3L6 Toronto, Ontario Canada
| | - Busecan Aksoydan
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Matthias Stein
- Max-Planck
Institute
for Dynamics of Complex Technical Systems, Molecular Simulations and
Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Mine Yurtsever
- Department
of Chemistry, Istanbul Technical University, 34467 Istanbul, Turkey
| | - Serdar Durdagi
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, Istanbul, Turkey
| |
Collapse
|
116
|
Waldschmidt HV, Homan KT, Cato MC, Cruz-Rodríguez O, Cannavo A, Wilson MW, Song J, Cheung JY, Koch WJ, Tesmer JJG, Larsen SD. Structure-Based Design of Highly Selective and Potent G Protein-Coupled Receptor Kinase 2 Inhibitors Based on Paroxetine. J Med Chem 2017; 60:3052-3069. [PMID: 28323425 DOI: 10.1021/acs.jmedchem.7b00112] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In heart failure, the β-adrenergic receptors (βARs) become desensitized and uncoupled from heterotrimeric G proteins. This process is initiated by G protein-coupled receptor kinases (GRKs), some of which are upregulated in the failing heart, making them desirable therapeutic targets. The selective serotonin reuptake inhibitor, paroxetine, was previously identified as a GRK2 inhibitor. Utilizing a structure-based drug design approach, we modified paroxetine to generate a small compound library. Included in this series is a highly potent and selective GRK2 inhibitor, 14as, with an IC50 of 30 nM against GRK2 and greater than 230-fold selectivity over other GRKs and kinases. Furthermore, 14as showed a 100-fold improvement in cardiomyocyte contractility assays over paroxetine and a plasma concentration higher than its IC50 for over 7 h. Three of these inhibitors, including 14as, were additionally crystallized in complex with GRK2 to give insights into the structural determinants of potency and selectivity of these inhibitors.
Collapse
Affiliation(s)
- Helen V Waldschmidt
- Department of Medicinal Chemistry, College of Pharmacy, ‡Departments of Pharmacology and Biological Chemistry, Life Sciences Institute, §Ph.D. Program in Chemical Biology, ⊥Vahlteich Medicinal Chemistry Core, University of Michigan , Ann Arbor, Michigan 48109, United States.,Center for Translational Medicine, Temple University , Philadelphia, Pennsylvania 19140, United States
| | - Kristoff T Homan
- Department of Medicinal Chemistry, College of Pharmacy, ‡Departments of Pharmacology and Biological Chemistry, Life Sciences Institute, §Ph.D. Program in Chemical Biology, ⊥Vahlteich Medicinal Chemistry Core, University of Michigan , Ann Arbor, Michigan 48109, United States.,Center for Translational Medicine, Temple University , Philadelphia, Pennsylvania 19140, United States
| | - Marilyn C Cato
- Department of Medicinal Chemistry, College of Pharmacy, ‡Departments of Pharmacology and Biological Chemistry, Life Sciences Institute, §Ph.D. Program in Chemical Biology, ⊥Vahlteich Medicinal Chemistry Core, University of Michigan , Ann Arbor, Michigan 48109, United States.,Center for Translational Medicine, Temple University , Philadelphia, Pennsylvania 19140, United States
| | - Osvaldo Cruz-Rodríguez
- Department of Medicinal Chemistry, College of Pharmacy, ‡Departments of Pharmacology and Biological Chemistry, Life Sciences Institute, §Ph.D. Program in Chemical Biology, ⊥Vahlteich Medicinal Chemistry Core, University of Michigan , Ann Arbor, Michigan 48109, United States.,Center for Translational Medicine, Temple University , Philadelphia, Pennsylvania 19140, United States
| | - Alessandro Cannavo
- Department of Medicinal Chemistry, College of Pharmacy, ‡Departments of Pharmacology and Biological Chemistry, Life Sciences Institute, §Ph.D. Program in Chemical Biology, ⊥Vahlteich Medicinal Chemistry Core, University of Michigan , Ann Arbor, Michigan 48109, United States.,Center for Translational Medicine, Temple University , Philadelphia, Pennsylvania 19140, United States
| | - Michael W Wilson
- Department of Medicinal Chemistry, College of Pharmacy, ‡Departments of Pharmacology and Biological Chemistry, Life Sciences Institute, §Ph.D. Program in Chemical Biology, ⊥Vahlteich Medicinal Chemistry Core, University of Michigan , Ann Arbor, Michigan 48109, United States.,Center for Translational Medicine, Temple University , Philadelphia, Pennsylvania 19140, United States
| | - Jianliang Song
- Department of Medicinal Chemistry, College of Pharmacy, ‡Departments of Pharmacology and Biological Chemistry, Life Sciences Institute, §Ph.D. Program in Chemical Biology, ⊥Vahlteich Medicinal Chemistry Core, University of Michigan , Ann Arbor, Michigan 48109, United States.,Center for Translational Medicine, Temple University , Philadelphia, Pennsylvania 19140, United States
| | - Joseph Y Cheung
- Department of Medicinal Chemistry, College of Pharmacy, ‡Departments of Pharmacology and Biological Chemistry, Life Sciences Institute, §Ph.D. Program in Chemical Biology, ⊥Vahlteich Medicinal Chemistry Core, University of Michigan , Ann Arbor, Michigan 48109, United States.,Center for Translational Medicine, Temple University , Philadelphia, Pennsylvania 19140, United States
| | - Walter J Koch
- Department of Medicinal Chemistry, College of Pharmacy, ‡Departments of Pharmacology and Biological Chemistry, Life Sciences Institute, §Ph.D. Program in Chemical Biology, ⊥Vahlteich Medicinal Chemistry Core, University of Michigan , Ann Arbor, Michigan 48109, United States.,Center for Translational Medicine, Temple University , Philadelphia, Pennsylvania 19140, United States
| | - John J G Tesmer
- Department of Medicinal Chemistry, College of Pharmacy, ‡Departments of Pharmacology and Biological Chemistry, Life Sciences Institute, §Ph.D. Program in Chemical Biology, ⊥Vahlteich Medicinal Chemistry Core, University of Michigan , Ann Arbor, Michigan 48109, United States.,Center for Translational Medicine, Temple University , Philadelphia, Pennsylvania 19140, United States
| | - Scott D Larsen
- Department of Medicinal Chemistry, College of Pharmacy, ‡Departments of Pharmacology and Biological Chemistry, Life Sciences Institute, §Ph.D. Program in Chemical Biology, ⊥Vahlteich Medicinal Chemistry Core, University of Michigan , Ann Arbor, Michigan 48109, United States.,Center for Translational Medicine, Temple University , Philadelphia, Pennsylvania 19140, United States
| |
Collapse
|
117
|
Sokolina K, Kittanakom S, Snider J, Kotlyar M, Maurice P, Gandía J, Benleulmi-Chaachoua A, Tadagaki K, Oishi A, Wong V, Malty RH, Deineko V, Aoki H, Amin S, Yao Z, Morató X, Otasek D, Kobayashi H, Menendez J, Auerbach D, Angers S, Pržulj N, Bouvier M, Babu M, Ciruela F, Jockers R, Jurisica I, Stagljar I. Systematic protein-protein interaction mapping for clinically relevant human GPCRs. Mol Syst Biol 2017; 13:918. [PMID: 28298427 PMCID: PMC5371730 DOI: 10.15252/msb.20167430] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
G‐protein‐coupled receptors (GPCRs) are the largest family of integral membrane receptors with key roles in regulating signaling pathways targeted by therapeutics, but are difficult to study using existing proteomics technologies due to their complex biochemical features. To obtain a global view of GPCR‐mediated signaling and to identify novel components of their pathways, we used a modified membrane yeast two‐hybrid (MYTH) approach and identified interacting partners for 48 selected full‐length human ligand‐unoccupied GPCRs in their native membrane environment. The resulting GPCR interactome connects 686 proteins by 987 unique interactions, including 299 membrane proteins involved in a diverse range of cellular functions. To demonstrate the biological relevance of the GPCR interactome, we validated novel interactions of the GPR37, serotonin 5‐HT4d, and adenosine ADORA2A receptors. Our data represent the first large‐scale interactome mapping for human GPCRs and provide a valuable resource for the analysis of signaling pathways involving this druggable family of integral membrane proteins.
Collapse
Affiliation(s)
- Kate Sokolina
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | | | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Max Kotlyar
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Pascal Maurice
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,Sorbonne Paris Cité, University of Paris Descartes, Paris, France.,UMR CNRS 7369 Matrice Extracellulaire et Dynamique Cellulaire (MEDyC), Université de Reims Champagne Ardenne (URCA), UFR Sciences Exactes et Naturelles, Reims, France
| | - Jorge Gandía
- Unitat de Farmacologia, Departament de Patologia i Terapèutica Experimental, Facultat de Medicina, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain.,Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Abla Benleulmi-Chaachoua
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,Sorbonne Paris Cité, University of Paris Descartes, Paris, France
| | - Kenjiro Tadagaki
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,Sorbonne Paris Cité, University of Paris Descartes, Paris, France
| | - Atsuro Oishi
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,Sorbonne Paris Cité, University of Paris Descartes, Paris, France
| | - Victoria Wong
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Ramy H Malty
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Viktor Deineko
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Hiroyuki Aoki
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Shahreen Amin
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Zhong Yao
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Xavier Morató
- Unitat de Farmacologia, Departament de Patologia i Terapèutica Experimental, Facultat de Medicina, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain.,Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - David Otasek
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Hiroyuki Kobayashi
- Department of Biochemistry, Institute for Research in Immunology & Cancer, Université de Montréal, Montréal, QC, Canada
| | | | | | - Stephane Angers
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy and Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - Natasa Pržulj
- Department of Computing, University College London, London, UK
| | - Michel Bouvier
- Department of Biochemistry, Institute for Research in Immunology & Cancer, Université de Montréal, Montréal, QC, Canada
| | - Mohan Babu
- Department of Biochemistry, Research and Innovation Centre, University of Regina, Regina, SK, Canada
| | - Francisco Ciruela
- Unitat de Farmacologia, Departament de Patologia i Terapèutica Experimental, Facultat de Medicina, IDIBELL, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain.,Institut de Neurociències, Universitat de Barcelona, Barcelona, Spain
| | - Ralf Jockers
- Inserm, U1016, Institut Cochin, Paris, France.,CNRS UMR 8104, Paris, France.,Sorbonne Paris Cité, University of Paris Descartes, Paris, France
| | - Igor Jurisica
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada.,Departments of Medical Biophysics and Computer Science, University of Toronto, Toronto, ON, Canada.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, ON, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
118
|
Fronik P, Gaiser BI, Sejer Pedersen D. Bitopic Ligands and Metastable Binding Sites: Opportunities for G Protein-Coupled Receptor (GPCR) Medicinal Chemistry. J Med Chem 2017; 60:4126-4134. [DOI: 10.1021/acs.jmedchem.6b01601] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Philipp Fronik
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Birgit I. Gaiser
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Daniel Sejer Pedersen
- Department of Drug Design
and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| |
Collapse
|
119
|
Di Giglio MG, Muttenthaler M, Harpsøe K, Liutkeviciute Z, Keov P, Eder T, Rattei T, Arrowsmith S, Wray S, Marek A, Elbert T, Alewood PF, Gloriam DE, Gruber CW. Development of a human vasopressin V 1a-receptor antagonist from an evolutionary-related insect neuropeptide. Sci Rep 2017; 7:41002. [PMID: 28145450 PMCID: PMC5286520 DOI: 10.1038/srep41002] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/13/2016] [Indexed: 01/27/2023] Open
Abstract
Characterisation of G protein-coupled receptors (GPCR) relies on the availability of a toolbox of ligands that selectively modulate different functional states of the receptors. To uncover such molecules, we explored a unique strategy for ligand discovery that takes advantage of the evolutionary conservation of the 600-million-year-old oxytocin/vasopressin signalling system. We isolated the insect oxytocin/vasopressin orthologue inotocin from the black garden ant (Lasius niger), identified and cloned its cognate receptor and determined its pharmacological properties on the insect and human oxytocin/vasopressin receptors. Subsequently, we identified a functional dichotomy: inotocin activated the insect inotocin and the human vasopressin V1b receptors, but inhibited the human V1aR. Replacement of Arg8 of inotocin by D-Arg8 led to a potent, stable and competitive V1aR-antagonist ([D-Arg8]-inotocin) with a 3,000-fold binding selectivity for the human V1aR over the other three subtypes, OTR, V1bR and V2R. The Arg8/D-Arg8 ligand-pair was further investigated to gain novel insights into the oxytocin/vasopressin peptide-receptor interaction, which led to the identification of key residues of the receptors that are important for ligand functionality and selectivity. These observations could play an important role for development of oxytocin/vasopressin receptor modulators that would enable clear distinction of the physiological and pathological responses of the individual receptor subtypes.
Collapse
Affiliation(s)
- Maria Giulia Di Giglio
- Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Markus Muttenthaler
- Institute for Molecular Bioscience, The University of Queensland, QLD 4072 Brisbane, Australia
| | - Kasper Harpsøe
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Zita Liutkeviciute
- Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Peter Keov
- School of Biomedical Sciences, The University of Queensland, QLD 4072 Brisbane, Australia
| | - Thomas Eder
- IST Austria (Institute of Science and Technology), Am Campus 1, 3400 Klosterneuburg, Austria
- CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Thomas Rattei
- CUBE-Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Sarah Arrowsmith
- Harris-Wellbeing Preterm Birth Research Centre, Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, L69 3BX, United Kingdom
| | - Susan Wray
- Harris-Wellbeing Preterm Birth Research Centre, Department of Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, L69 3BX, United Kingdom
| | - Ales Marek
- Laboratory of Radioisotopes, Institute of Organic Chemistry and Biochemistry CAS, Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic
| | - Tomas Elbert
- Laboratory of Radioisotopes, Institute of Organic Chemistry and Biochemistry CAS, Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic
| | - Paul F. Alewood
- Institute for Molecular Bioscience, The University of Queensland, QLD 4072 Brisbane, Australia
| | - David E. Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100 Copenhagen, Denmark
| | - Christian W. Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
- School of Biomedical Sciences, The University of Queensland, QLD 4072 Brisbane, Australia
| |
Collapse
|
120
|
Baker MS, Ahn SB, Mohamedali A, Islam MT, Cantor D, Verhaert PD, Fanayan S, Sharma S, Nice EC, Connor M, Ranganathan S. Accelerating the search for the missing proteins in the human proteome. Nat Commun 2017; 8:14271. [PMID: 28117396 PMCID: PMC5286205 DOI: 10.1038/ncomms14271] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 12/06/2016] [Indexed: 12/25/2022] Open
Abstract
The Human Proteome Project (HPP) aims to discover high-stringency data for all proteins encoded by the human genome. Currently, ∼18% of the proteins in the human proteome (the missing proteins) do not have high-stringency evidence (for example, mass spectrometry) confirming their existence, while much additional information is available about many of these missing proteins. Here, we present MissingProteinPedia as a community resource to accelerate the discovery and understanding of these missing proteins. The Human Proteome Project aims to catalogue the ∼20,000 proteins encoded by the human genome. In this review, Baker et al . focus on the missing proteins, proteins that lack high stringency proteomic evidence, and launch MissingProteinPedia, a database aimed at accelerating the search for missing proteins.
Collapse
Affiliation(s)
- Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, New South Wales 2109, Australia
| | - Seong Beom Ahn
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, New South Wales 2109, Australia
| | - Abidali Mohamedali
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, New South Wales 2109, Australia
- Department of Chemistry & Biomolecular Sciences, Macquarie University, New South Wales 2109, Australia
| | - Mohammad T. Islam
- Department of Chemistry & Biomolecular Sciences, Macquarie University, New South Wales 2109, Australia
| | - David Cantor
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, New South Wales 2109, Australia
| | | | - Susan Fanayan
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, New South Wales 2109, Australia
| | - Samridhi Sharma
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, New South Wales 2109, Australia
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
| | - Mark Connor
- Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, New South Wales 2109, Australia
| | - Shoba Ranganathan
- Department of Chemistry & Biomolecular Sciences, Macquarie University, New South Wales 2109, Australia
| |
Collapse
|
121
|
Pacifico S, Kerckhoffs A, Fallow AJ, Foreman RE, Guerrini R, McDonald J, Lambert DG, Jamieson AG. Urotensin-II peptidomimetic incorporating a non-reducible 1,5-triazole disulfide bond reveals a pseudo-irreversible covalent binding mechanism to the urotensin G-protein coupled receptor. Org Biomol Chem 2017; 15:4704-4710. [DOI: 10.1039/c7ob00959c] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
New high affinity peptidomimetic ligands have been developed that provided new insight into the mechanism of binding of U-II peptide with the urotensin-II receptor.
Collapse
Affiliation(s)
- Salvatore Pacifico
- Department of Chemical and Pharmaceutical Sciences and LTTA
- University of Ferrara
- Ferrara
- Italy
| | - Aidan Kerckhoffs
- School of Chemistry
- Joseph Black Building. University Avenue
- Glasgow
- UK
| | | | | | - Remo Guerrini
- Department of Chemical and Pharmaceutical Sciences and LTTA
- University of Ferrara
- Ferrara
- Italy
| | - John McDonald
- Department of Cardiovascular Sciences
- Division of Anaesthesia Critical Care & Pain Management
- Leicester
- UK
| | - David G. Lambert
- Department of Cardiovascular Sciences
- Division of Anaesthesia Critical Care & Pain Management
- Leicester
- UK
| | | |
Collapse
|
122
|
Bhattacharya S, Salomon-Ferrer R, Lee S, Vaidehi N. Conserved Mechanism of Conformational Stability and Dynamics in G-Protein-Coupled Receptors. J Chem Theory Comput 2016; 12:5575-5584. [PMID: 27709935 DOI: 10.1021/acs.jctc.6b00618] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
G-protein-coupled receptors (GPCRs) are transmembrane receptors involved in diverse biological functions. Despite the diversity in their amino acid sequences, class A GPCRs exhibit a conserved structural topology and possibly a common mechanism of receptor activation. To understand how this high sequence diversity translates to a conserved functional mechanism, we have compared the dynamic behavior of eight class A GPCRs comprised of six biogenic amine receptors, adenosine A2A, and the peptide receptor protease-activated receptor 1. Starting from the crystal structures of the inactive state of these receptors bound to inverse agonists or antagonists, we have performed multiple all-atom MD simulations adding up to several microseconds of simulation. We elucidated the similarities and differences in the dynamic behavior and the conformational ensembles sampled by these eight class A GPCRs. Among the six biogenic amine receptors studied here, β2-adrenergic receptor shows the highest level of fluctuation in the sixth and seventh transmembrane helices, possibly explaining its high basal activity. In contrast, the muscarinic acetylcholine receptors show the lowest fluctuations as well as tight packing and low hydration of the transmembrane domain. All eight GPCRs show several conserved allosteric communication pipelines from the residues in the agonist binding site with the G-protein interface. Positions of the residues along these pipelines that serve as major hubs of allosteric communication are conserved in their respective structures. These findings have important implications in understanding the dynamics and allosteric mechanism of communication in class A GPCRs and hence are useful for designing conformation-specific drugs.
Collapse
Affiliation(s)
- Supriyo Bhattacharya
- Beckman Research Institute, City of Hope National Medical Center , 1500 Duarte Road, Duarte, California 91010, United States
| | - Romelia Salomon-Ferrer
- Beckman Research Institute, City of Hope National Medical Center , 1500 Duarte Road, Duarte, California 91010, United States
| | - Sangbae Lee
- Beckman Research Institute, City of Hope National Medical Center , 1500 Duarte Road, Duarte, California 91010, United States
| | - Nagarajan Vaidehi
- Beckman Research Institute, City of Hope National Medical Center , 1500 Duarte Road, Duarte, California 91010, United States
| |
Collapse
|
123
|
May V, Parsons RL. G Protein-Coupled Receptor Endosomal Signaling and Regulation of Neuronal Excitability and Stress Responses: Signaling Options and Lessons From the PAC1 Receptor. J Cell Physiol 2016; 232:698-706. [DOI: 10.1002/jcp.25615] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 09/22/2016] [Indexed: 02/03/2023]
Affiliation(s)
- Victor May
- Department of Neurological Sciences; University of Vermont College of Medicine; Burlington Vermont
| | - Rodney L. Parsons
- Department of Neurological Sciences; University of Vermont College of Medicine; Burlington Vermont
| |
Collapse
|
124
|
Hanson J, Chevigné A. GPCRs in immunity: Atypical receptors and novel concepts. Biochem Pharmacol 2016; 114:1-2. [DOI: 10.1016/j.bcp.2016.06.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 06/27/2016] [Indexed: 12/22/2022]
|
125
|
Ciancetta A, Cuzzolin A, Deganutti G, Sturlese M, Salmaso V, Cristiani A, Sabbadin D, Moro S. New Trends in Inspecting GPCR-ligand Recognition Process: the Contribution of the Molecular Modeling Section (MMS) at the University of Padova. Mol Inform 2016; 35:440-8. [PMID: 27546048 DOI: 10.1002/minf.201501011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 05/10/2016] [Indexed: 11/07/2022]
Abstract
In this review, we present a survey of the recent advances carried out by our research groups in the field of ligand-GPCRs recognition process simulations recently implemented at the Molecular Modeling Section (MMS) of the University of Padova. We briefly describe a platform of tools we have tuned to aid the identification of novel GPCRs binders and the better understanding of their binding mechanisms, based on two extensively used computational techniques such as molecular docking and MD simulations. The developed methodologies encompass: (i) the selection of suitable protocols for docking studies, (ii) the exploration of the dynamical evolution of ligand-protein interaction networks, (iii) the detailed investigation of the role of water molecules upon ligand binding, and (iv) a glance at the way the ligand might go through prior reaching the binding site.
Collapse
Affiliation(s)
- Antonella Ciancetta
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy
| | - Alberto Cuzzolin
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy
| | - Giuseppe Deganutti
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy
| | - Mattia Sturlese
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy
| | - Veronica Salmaso
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy
| | - Andrea Cristiani
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy
| | - Davide Sabbadin
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy
| | - Stefano Moro
- Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy.
| |
Collapse
|
126
|
Bow EW, Rimoldi JM. The Structure-Function Relationships of Classical Cannabinoids: CB1/CB2 Modulation. PERSPECTIVES IN MEDICINAL CHEMISTRY 2016; 8:17-39. [PMID: 27398024 PMCID: PMC4927043 DOI: 10.4137/pmc.s32171] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 05/31/2016] [Accepted: 06/02/2016] [Indexed: 12/11/2022]
Abstract
The cannabinoids are members of a deceptively simple class of terpenophenolic secondary metabolites isolated from Cannabis sativa highlighted by (-)-Δ(9)-tetrahydrocannabinol (THC), eliciting distinct pharmacological effects mediated largely by cannabinoid receptor (CB1 or CB2) signaling. Since the initial discovery of THC and related cannabinoids, synthetic and semisynthetic classical cannabinoid analogs have been evaluated to help define receptor binding modes and structure-CB1/CB2 functional activity relationships. This perspective will examine the classical cannabinoids, with particular emphasis on the structure-activity relationship of five regions: C3 side chain, phenolic hydroxyl, aromatic A-ring, pyran B-ring, and cyclohexenyl C-ring. Cumulative structure-activity relationship studies to date have helped define the critical structural elements required for potency and selectivity toward CB1 and CB2 and, more importantly, ushered the discovery and development of contemporary nonclassical cannabinoid modulators with enhanced physicochemical and pharmacological profiles.
Collapse
Affiliation(s)
- Eric W. Bow
- Department of BioMolecular Sciences, Division of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, MS, USA
| | - John M. Rimoldi
- Department of BioMolecular Sciences, Division of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, MS, USA
| |
Collapse
|
127
|
Tian H, Fürstenberg A, Huber T. Labeling and Single-Molecule Methods To Monitor G Protein-Coupled Receptor Dynamics. Chem Rev 2016; 117:186-245. [DOI: 10.1021/acs.chemrev.6b00084] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- He Tian
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Alexandre Fürstenberg
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| | - Thomas Huber
- Laboratory of Chemical Biology
and Signal Transduction, The Rockefeller University, 1230 York
Avenue, New York, New York 10065, United States
| |
Collapse
|
128
|
G-protein coupled receptors: advances in simulation and drug discovery. Curr Opin Struct Biol 2016; 41:83-89. [PMID: 27344006 DOI: 10.1016/j.sbi.2016.06.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2016] [Accepted: 06/07/2016] [Indexed: 11/21/2022]
Abstract
G-protein coupled receptors (GPCRs), the largest family of human membrane proteins, mediate cellular signaling and represent primary targets of about one third of currently marketed drugs. GPCRs undergo highly dynamic structural transitions during signal transduction, from binding of extracellular ligands to coupling with intracellular effector proteins. Molecular dynamics (MD) simulations have been utilized to investigate GPCR signaling mechanisms (such as pathways of ligand binding and receptor activation/deactivation) and to design novel small-molecule drug candidates. Future research directions point towards modeling cooperative binding of multiple orthosteric and allosteric ligands to GPCRs, GPCR oligomerization and interactions of GPCRs with different intracellular signaling proteins. Through methodological and supercomputing advances, MD simulations will continue to provide important insights into GPCR signaling mechanisms and further facilitate structure-based drug design.
Collapse
|
129
|
Anighoro A, Bajorath J. Binding mode similarity measures for ranking of docking poses: a case study on the adenosine A2A receptor. J Comput Aided Mol Des 2016; 30:447-56. [DOI: 10.1007/s10822-016-9918-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 06/18/2016] [Indexed: 12/31/2022]
|
130
|
Dores MR, Grimsey NJ, Mendez F, Trejo J. ALIX Regulates the Ubiquitin-Independent Lysosomal Sorting of the P2Y1 Purinergic Receptor via a YPX3L Motif. PLoS One 2016; 11:e0157587. [PMID: 27301021 PMCID: PMC4907476 DOI: 10.1371/journal.pone.0157587] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 06/01/2016] [Indexed: 12/22/2022] Open
Abstract
Endocytic sorting and lysosomal degradation are integral to the regulation of G protein-coupled receptor (GPCR) function. Upon ligand binding, classical GPCRs are activated, internalized and recycled or sorted to lysosomes for degradation, a process that requires receptor ubiquitination. However, recent studies have demonstrated that numerous GPCRs are sorted to lysosomes independent of receptor ubiquitination. Here, we describe an ubiquitin-independent lysosomal sorting pathway for the purinergic GPCR P2Y1. After activation, P2Y1 sorts to lysosomes for degradation independent of direct ubiquitination that is mediated by a YPX3L motif within the second intracellular loop that serves as a binding site for the adaptor protein ALIX. Depletion of ALIX or site-directed mutation of the YPX3L motif inhibits P2Y1 sorting into the lumen of multivesicular endosomes/lysosomes and degradation. These findings confirm the function of YPX3L motifs as lysosomal targeting sequences for GPCRs and demonstrate that ALIX mediates the ubiquitin-independent degradation of certain GPCRs.
Collapse
Affiliation(s)
- Michael R. Dores
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States of America
- Department of Biology, Hofstra University, Hempstead, NY 11549, United States of America
| | - Neil J. Grimsey
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States of America
| | - Francisco Mendez
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States of America
| | - JoAnn Trejo
- Department of Pharmacology, School of Medicine, University of California San Diego, La Jolla, CA 92093, United States of America
- * E-mail:
| |
Collapse
|
131
|
Ichikawa O, Fujimoto K, Yamada A, Okazaki S, Yamazaki K. G-Protein/β-Arrestin-Linked Fluctuating Network of G-Protein-Coupled Receptors for Predicting Drug Efficacy and Bias Using Short-Term Molecular Dynamics Simulation. PLoS One 2016; 11:e0155816. [PMID: 27187591 PMCID: PMC4871340 DOI: 10.1371/journal.pone.0155816] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/04/2016] [Indexed: 01/14/2023] Open
Abstract
The efficacy and bias of signal transduction induced by a drug at a target protein are closely associated with the benefits and side effects of the drug. In particular, partial agonist activity and G-protein/β-arrestin-biased agonist activity for the G-protein-coupled receptor (GPCR) family, the family with the most target proteins of launched drugs, are key issues in drug discovery. However, designing GPCR drugs with appropriate efficacy and bias is challenging because the dynamic mechanism of signal transduction induced by ligand—receptor interactions is complicated. Here, we identified the G-protein/β-arrestin-linked fluctuating network, which initiates large-scale conformational changes, using sub-microsecond molecular dynamics (MD) simulations of the β2-adrenergic receptor (β2AR) with a diverse collection of ligands and correlation analysis of their G protein/β-arrestin efficacy. The G-protein-linked fluctuating network extends from the ligand-binding site to the G-protein-binding site through the connector region, and the β-arrestin-linked fluctuating network consists of the NPxxY motif and adjacent regions. We confirmed that the averaged values of fluctuation in the fluctuating network detected are good quantitative indexes for explaining G protein/β-arrestin efficacy. These results indicate that short-term MD simulation is a practical method to predict the efficacy and bias of any compound for GPCRs.
Collapse
Affiliation(s)
- Osamu Ichikawa
- Genomic Science Laboratories, Sumitomo Dainippon Pharma. Co. Ltd, Osaka, Osaka, Japan
| | - Kazushi Fujimoto
- Department of Applied Chemistry, Nagoya University, Nagoya, Aichi, Japan
| | - Atsushi Yamada
- Department of Applied Chemistry, Nagoya University, Nagoya, Aichi, Japan
| | - Susumu Okazaki
- Department of Applied Chemistry, Nagoya University, Nagoya, Aichi, Japan
| | - Kazuto Yamazaki
- Genomic Science Laboratories, Sumitomo Dainippon Pharma. Co. Ltd, Osaka, Osaka, Japan
| |
Collapse
|
132
|
Nowroozi A, Shahlaei M. A coupling of homology modeling with multiple molecular dynamics simulation for identifying representative conformation of GPCR structures: a case study on human bombesin receptor subtype-3. J Biomol Struct Dyn 2016; 35:250-272. [DOI: 10.1080/07391102.2016.1140593] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Amin Nowroozi
- Pharmaceutical Sciences Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Shahlaei
- Nano Drug Delivery Research Center, School of Pharmacy, Kermanshah University of Medical Sciences, Kermanshah, Iran
| |
Collapse
|
133
|
Application of advanced X-ray methods in life sciences. Biochim Biophys Acta Gen Subj 2016; 1861:3671-3685. [PMID: 27156488 DOI: 10.1016/j.bbagen.2016.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 05/03/2016] [Accepted: 05/04/2016] [Indexed: 12/19/2022]
Abstract
BACKGROUND Synchrotron radiation (SR) sources provide diverse X-ray methods for the investigation of structure-function relationships in biological macromolecules. SCOPE OF REVIEW Recent developments in SR sources and in the X-ray tools they offer for life sciences are reviewed. Specifically, advances in macromolecular crystallography, small angle X-ray solution scattering, X-ray absorption and fluorescence spectroscopy, and imaging are discussed with examples. MAJOR CONCLUSIONS SR sources offer a range of X-ray techniques that can be used in a complementary fashion in studies of biological systems at a wide range of resolutions from atomic to cellular scale. Emerging applications of X-ray techniques include the characterization of disordered proteins, noncrystalline and nonequilibrium systems, elemental imaging of tissues, cells and organs, and detection of time-resolved changes in molecular structures. GENERAL SIGNIFICANCE X-ray techniques are in the center of hybrid approaches that are used to gain insight into complex problems relating to biomolecular mechanisms, disease and possible therapeutic solutions. This article is part of a Special Issue entitled "Science for Life". Guest Editors: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
Collapse
|
134
|
Schneider S, Provasi D, Filizola M. The Dynamic Process of Drug-GPCR Binding at Either Orthosteric or Allosteric Sites Evaluated by Metadynamics. Methods Mol Biol 2016; 1335:277-94. [PMID: 26260607 DOI: 10.1007/978-1-4939-2914-6_18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Major advances in G Protein-Coupled Receptor (GPCR) structural biology over the past few years have yielded a significant number of high-resolution crystal structures for several different receptor subtypes. This dramatic increase in GPCR structural information has underscored the use of automated docking algorithms for the discovery of novel ligands that can eventually be developed into improved therapeutics. However, these algorithms are often unable to discriminate between different, yet energetically similar, poses because of their relatively simple scoring functions. Here, we describe a metadynamics-based approach to study the dynamic process of ligand binding to/unbinding from GPCRs with a higher level of accuracy and yet satisfying efficiency.
Collapse
Affiliation(s)
- Sebastian Schneider
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, P.O. Box 1677, New York, NY, 10029-6574, USA
| | | | | |
Collapse
|
135
|
Emery AC, Alvarez RA, Abboud P, Xu W, Westover CD, Eiden MV, Eiden LE. C-terminal amidation of PACAP-38 and PACAP-27 is dispensable for biological activity at the PAC1 receptor. Peptides 2016; 79:39-48. [PMID: 26976270 PMCID: PMC4842133 DOI: 10.1016/j.peptides.2016.03.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 01/30/2016] [Accepted: 03/09/2016] [Indexed: 01/29/2023]
Abstract
PACAP-27 and PACAP-38 are the exclusive physiological ligands for the mammalian PAC1 receptor. The role of C-terminal amidation of these ligands at that receptor was examined in neuroendocrine cells expressing the PAC1 receptor endogenously and in non-neuroendocrine cells in which the human and rat PAC1 receptors were expressed from stable single-copy genes driven by the CMV promoter, providing stoichiometrically appropriate levels of this Gs-coupled GPCR in order to examine the potency and intrinsic activity of PACAP ligands and their des-amidated congeners. We found that replacement of the C-terminal glycine residues of PACAP-27 and -38 with a free acid; or extension of either peptide with the two to three amino acids normally found at these positions in PACAP processing intermediates in vivo following endoproteolytic cleavage and after exoproteolytic trimming and glycine-directed amidated, were equivalent in potency to the fully processed peptides in a variety of cell-based assays. These included real-time monitoring of cyclic AMP generation in both NS-1 neuroendocrine cells and non-neuroendocrine HEK293 cells; PKA-dependent gene activation in HEK293 cells; and neuritogenesis and cell growth arrest in NS-1 cells. The specific implications for the role of amidation in arming of secretin-related neuropeptides for biological function, and the general implications for neuropeptide-based delivery in the context of gene therapy, are discussed.
Collapse
Affiliation(s)
- Andrew C Emery
- Section on Molecular Neuroscience, Laboratory of Cellular and Molecular Regulation, National Institute of Mental Health, Bethesda, MD 20892, USA
| | - Ryan A Alvarez
- Section on Molecular Neuroscience, Laboratory of Cellular and Molecular Regulation, National Institute of Mental Health, Bethesda, MD 20892, USA
| | - Philip Abboud
- Section on Molecular Neuroscience, Laboratory of Cellular and Molecular Regulation, National Institute of Mental Health, Bethesda, MD 20892, USA
| | - Wenqin Xu
- Section on Directed Gene Transfer, Laboratory of Cellular and Molecular Regulation, National Institute of Mental Health, Bethesda, MD 20892, USA
| | - Craig D Westover
- Section on Directed Gene Transfer, Laboratory of Cellular and Molecular Regulation, National Institute of Mental Health, Bethesda, MD 20892, USA
| | - Maribeth V Eiden
- Section on Directed Gene Transfer, Laboratory of Cellular and Molecular Regulation, National Institute of Mental Health, Bethesda, MD 20892, USA
| | - Lee E Eiden
- Section on Molecular Neuroscience, Laboratory of Cellular and Molecular Regulation, National Institute of Mental Health, Bethesda, MD 20892, USA.
| |
Collapse
|
136
|
Zha Z, Han XR, Smith MD, Lei QY, Guan KL, Xiong Y. Hypertension-associated C825T polymorphism impairs the function of Gβ3 to target GRK2 ubiquitination. Cell Discov 2016; 2:16005. [PMID: 27462452 PMCID: PMC4849471 DOI: 10.1038/celldisc.2016.5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/08/2016] [Indexed: 01/08/2023] Open
Abstract
Population-based and case-control studies in different ethnicities have linked a polymorphism, C825T, in exon 10 of GNB3 gene to hypertension and several additional diseases. The 825T allele is associated with alternative splicing and results in a shortened Gβ3 protein, referred to as Gβ3s, which loses 41 amino acids encompassing one WD40 repeat domain. The mechanism of how Gβ3 C825T polymorphism is associated with hypertension has remained unclear, but an impairment of its canonical function in G-protein-coupled receptor signaling has been ruled out. Here, we report that Gβ3, like other Gβ proteins, binds to DDB1 and assembles a DDB1-CUL4A-ROC1 E3 ubiquitin ligase (CRL4A(Gβ3)) to target GRK2 ubiquitination. The loss of the 41 amino-acid residues disrupts the Gβ3-DDB1 binding and impairs the function of Gβ3s to ubiquitinate GRK2. GRK2 ubiquitination levels were decreased and protein levels were accumulated in the blood samples of Gβ3 825T allele carriers. Deletion of Cul4a in mice resulted in systolic pressure increased and weakened heart function in male mice that can be partially rescued by the deletion of one Grk2 allele. These results reveal a mechanism explaining the link between Gβ3 C825T polymorphism and hypertension.
Collapse
Affiliation(s)
- Zhengyu Zha
- Key Laboratory of Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai, China
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- School of Life Sciences, Fudan University, Shanghai, China
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xiao-Ran Han
- Key Laboratory of Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai, China
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- School of Life Sciences, Fudan University, Shanghai, China
| | - Matthew D Smith
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qun-Ying Lei
- Key Laboratory of Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai, China
| | - Kun-Liang Guan
- Key Laboratory of Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai, China
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Pharmacology and Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Yue Xiong
- Key Laboratory of Molecular Medicine, Ministry of Education, and Department of Biochemistry and Molecular Biology, Fudan University Shanghai Medical College, Shanghai, China
- Molecular and Cell Biology Lab, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Department of Biochemistry and Biophysics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
137
|
Lv X, Liu J, Shi Q, Tan Q, Wu D, Skinner JJ, Walker AL, Zhao L, Gu X, Chen N, Xue L, Si P, Zhang L, Wang Z, Katritch V, Liu ZJ, Stevens RC. In vitro expression and analysis of the 826 human G protein-coupled receptors. Protein Cell 2016; 7:325-37. [PMID: 27085723 PMCID: PMC4853319 DOI: 10.1007/s13238-016-0263-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 03/09/2016] [Indexed: 01/24/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are involved in all human physiological systems where they are responsible for transducing extracellular signals into cells. GPCRs signal in response to a diverse array of stimuli including light, hormones, and lipids, where these signals affect downstream cascades to impact both health and disease states. Yet, despite their importance as therapeutic targets, detailed molecular structures of only 30 GPCRs have been determined to date. A key challenge to their structure determination is adequate protein expression. Here we report the quantification of protein expression in an insect cell expression system for all 826 human GPCRs using two different fusion constructs. Expression characteristics are analyzed in aggregate and among each of the five distinct subfamilies. These data can be used to identify trends related to GPCR expression between different fusion constructs and between different GPCR families, and to prioritize lead candidates for future structure determination feasibility.
Collapse
Affiliation(s)
- Xuechen Lv
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Junlin Liu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Qiaoyun Shi
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Qiwen Tan
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Dong Wu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - John J Skinner
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Angela L Walker
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Lixia Zhao
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Xiangxiang Gu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Na Chen
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Lu Xue
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Pei Si
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Lu Zhang
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Zeshi Wang
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Vsevolod Katritch
- Department of Biological Sciences, Bridge Institute, University of Southern California, Los Angeles, CA, 90089, USA
| | - Zhi-Jie Liu
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | | |
Collapse
|
138
|
Investigating the structural impact of S311C mutation in DRD2 receptor by molecular dynamics & docking studies. Biochimie 2016; 123:52-64. [DOI: 10.1016/j.biochi.2016.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/16/2016] [Indexed: 01/11/2023]
|
139
|
Attwood MM, Krishnan A, Pivotti V, Yazdi S, Almén MS, Schiöth HB. Topology based identification and comprehensive classification of four-transmembrane helix containing proteins (4TMs) in the human genome. BMC Genomics 2016; 17:268. [PMID: 27030248 PMCID: PMC4815072 DOI: 10.1186/s12864-016-2592-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 03/16/2016] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Membrane proteins are key components in a large spectrum of diverse functions and thus account for the major proportion of the drug-targeted portion of the genome. From a structural perspective, the α-helical transmembrane proteins can be categorized into major groups based on the number of transmembrane helices and these groups are often associated with specific functions. When compared to the well-characterized seven-transmembrane containing proteins (7TM), other TM groups are less explored and in particular the 4TM group. In this study, we identify the complete 4TM complement from the latest release of the human genome and assess the 4TM structure group as a whole. We functionally characterize this dataset and evaluate the resulting groups and ubiquitous functions, and furthermore describe disease and drug target involvement. RESULTS We classified 373 proteins, which represents ~7 % of the human membrane proteome, and includes 69 more proteins than our previous estimate. We have characterized the 4TM dataset based on functional, structural, and/or evolutionary similarities. Proteins that are involved in transport activity constitute 37 % of the dataset, 23 % are receptor-related, and 13 % have enzymatic functions. Intriguingly, proteins involved in transport are more than double the 15 % of transporters in the entire human membrane proteome, which might suggest that the 4TM topological architecture is more favored for transporting molecules over other functions. Moreover, we found an interesting exception to the ubiquitous intracellular N- and C-termini localization that is found throughout the entire membrane proteome and 4TM dataset in the neurotransmitter gated ion channel families. Overall, we estimate that 58 % of the dataset has a known association to disease conditions with 19 % of the genes possibly involved in different types of cancer. CONCLUSIONS We provide here the most robust and updated classification of the 4TM complement of the human genome as a platform to further understand the characteristics of 4TM functions and to explore pharmacological opportunities.
Collapse
Affiliation(s)
- Misty M. Attwood
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Arunkumar Krishnan
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Valentina Pivotti
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Samira Yazdi
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Markus Sällman Almén
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Helgi B. Schiöth
- />Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
- />Institutionen för neurovetenskap, BMC, Box 593, 751 24 Uppsala, Sweden
| |
Collapse
|
140
|
Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications. PLoS Comput Biol 2016; 12:e1004805. [PMID: 27028541 PMCID: PMC4814114 DOI: 10.1371/journal.pcbi.1004805] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Accepted: 02/11/2016] [Indexed: 11/23/2022] Open
Abstract
The understanding of G-protein coupled receptors (GPCRs) is undergoing a revolution due to increased information about their signaling and the experimental determination of structures for more than 25 receptors. The availability of at least one receptor structure for each of the GPCR classes, well separated in sequence space, enables an integrated superfamily-wide analysis to identify signatures involving the role of conserved residues, conserved contacts, and downstream signaling in the context of receptor structures. In this study, we align the transmembrane (TM) domains of all experimental GPCR structures to maximize the conserved inter-helical contacts. The resulting superfamily-wide GpcR Sequence-Structure (GRoSS) alignment of the TM domains for all human GPCR sequences is sufficient to generate a phylogenetic tree that correctly distinguishes all different GPCR classes, suggesting that the class-level differences in the GPCR superfamily are encoded at least partly in the TM domains. The inter-helical contacts conserved across all GPCR classes describe the evolutionarily conserved GPCR structural fold. The corresponding structural alignment of the inactive and active conformations, available for a few GPCRs, identifies activation hot-spot residues in the TM domains that get rewired upon activation. Many GPCR mutations, known to alter receptor signaling and cause disease, are located at these conserved contact and activation hot-spot residue positions. The GRoSS alignment places the chemosensory receptor subfamilies for bitter taste (TAS2R) and pheromones (Vomeronasal, VN1R) in the rhodopsin family, known to contain the chemosensory olfactory receptor subfamily. The GRoSS alignment also enables the quantification of the structural variability in the TM regions of experimental structures, useful for homology modeling and structure prediction of receptors. Furthermore, this alignment identifies structurally and functionally important residues in all human GPCRs. These residues can be used to make testable hypotheses about the structural basis of receptor function and about the molecular basis of disease-associated single nucleotide polymorphisms. G-protein coupled receptors (GPCRs) are a large superfamily of integral membrane proteins that share a characteristic 7 transmembrane helix fold. They detect various molecules outside of the cell and signal their presence to the inside of the cell. At least half of the 800 human GPCRs are potential drug targets, so understanding their structure and function is critical. Experimental structures are now available for at least one receptor from each GPCR class. The structure of the 7 helix fold is highly conserved even for receptors with very low sequence similarity. We analyze the available experimental structures and compare the common inter-helical contacts. Our analysis leads to a unified sequence-structure alignment of the GPCR superfamily that can then be used as the starting point for structure prediction of all other GPCRs. A key result of our analysis is a list of conserved contact residues and activation “hot-spots” residues that are critical for GPCR folding and function. We propose that mutations and natural variants of amino acids at these locations in the GPCRs can dramatically influence their activation state and alter intracellular signaling. This provides hypotheses for the molecular mechanisms underlying disease causing mutants for any GPCR.
Collapse
|
141
|
Verdonck R, De Haes W, Cardoen D, Menschaert G, Huhn T, Landuyt B, Baggerman G, Boonen K, Wenseleers T, Schoofs L. Fast and Reliable Quantitative Peptidomics with labelpepmatch. J Proteome Res 2016; 15:1080-9. [DOI: 10.1021/acs.jproteome.5b00845] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Gerben Menschaert
- Research
Group of Bio-informatics and Computational Genomics, Ghent University, Ghent, Belgium
| | - Thomas Huhn
- Chemistry
Department, University of Konstanz, Konstanz, Germany
| | | | - Geert Baggerman
- CFP/CeProMa, Antwerp University, Antwerp, Belgium
- Applied Bio & Molecular Systems, Vito, Mol, Belgium
| | - Kurt Boonen
- Biology
Department, KU Leuven, Leuven, Belgium
| | | | | |
Collapse
|
142
|
Chawla U, Jiang Y, Zheng W, Kuang L, Perera SMDC, Pitman MC, Brown MF, Liang H. A Usual G-Protein-Coupled Receptor in Unusual Membranes. Angew Chem Int Ed Engl 2016; 55:588-92. [PMID: 26633591 PMCID: PMC5233722 DOI: 10.1002/anie.201508648] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/02/2015] [Indexed: 12/30/2022]
Abstract
G-protein-coupled receptors (GPCRs) are the largest family of membrane-bound receptors and constitute about 50% of all known drug targets. They offer great potential for membrane protein nanotechnologies. We report here a charge-interaction-directed reconstitution mechanism that induces spontaneous insertion of bovine rhodopsin, the eukaryotic GPCR, into both lipid- and polymer-based artificial membranes. We reveal a new allosteric mode of rhodopsin activation incurred by the non-biological membranes: the cationic membrane drives a transition from the inactive MI to the activated MII state in the absence of high [H(+)] or negative spontaneous curvature. We attribute this activation to the attractive charge interaction between the membrane surface and the deprotonated Glu134 residue of the rhodopsin-conserved ERY sequence motif that helps break the cytoplasmic "ionic lock". This study unveils a novel design concept of non-biological membranes to reconstitute and harness GPCR functions in synthetic systems.
Collapse
Affiliation(s)
- Udeep Chawla
- Department of Chemistry & Biochemistry, Department of Physics University of Arizona, Tucson, AZ 85721 (USA)
| | - Yunjiang Jiang
- Department of Metallurgical & Materials Engineering, Colorado School of Mines, Golden, CO 80401 (USA)
- Current address: Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech, University Health Science Center, Lubbock, TX 79430 (USA)
| | - Wan Zheng
- Department of Metallurgical & Materials Engineering, Colorado School of Mines, Golden, CO 80401 (USA)
| | - Liangju Kuang
- Department of Metallurgical & Materials Engineering, Colorado School of Mines, Golden, CO 80401 (USA)
| | - Suchithranga M D C Perera
- Department of Chemistry & Biochemistry, Department of Physics University of Arizona, Tucson, AZ 85721 (USA)
| | - Michael C Pitman
- Department of Chemistry & Biochemistry, Department of Physics University of Arizona, Tucson, AZ 85721 (USA)
| | - Michael F Brown
- Department of Chemistry & Biochemistry, Department of Physics University of Arizona, Tucson, AZ 85721 (USA).
| | - Hongjun Liang
- Department of Metallurgical & Materials Engineering, Colorado School of Mines, Golden, CO 80401 (USA).
- Current address: Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech, University Health Science Center, Lubbock, TX 79430 (USA).
| |
Collapse
|
143
|
Urlacher E, Soustelle L, Parmentier ML, Verlinden H, Gherardi MJ, Fourmy D, Mercer AR, Devaud JM, Massou I. Honey Bee Allatostatins Target Galanin/Somatostatin-Like Receptors and Modulate Learning: A Conserved Function? PLoS One 2016; 11:e0146248. [PMID: 26741132 PMCID: PMC4704819 DOI: 10.1371/journal.pone.0146248] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 12/15/2015] [Indexed: 12/21/2022] Open
Abstract
Sequencing of the honeybee genome revealed many neuropeptides and putative neuropeptide receptors, yet functional characterization of these peptidic systems is scarce. In this study, we focus on allatostatins, which were first identified as inhibitors of juvenile hormone synthesis, but whose role in the adult honey bee (Apis mellifera) brain remains to be determined. We characterize the bee allatostatin system, represented by two families: allatostatin A (Apime-ASTA) and its receptor (Apime-ASTA-R); and C-type allatostatins (Apime-ASTC and Apime-ASTCC) and their common receptor (Apime-ASTC-R). Apime-ASTA-R and Apime-ASTC-R are the receptors in bees most closely related to vertebrate galanin and somatostatin receptors, respectively. We examine the functional properties of the two honeybee receptors and show that they are transcriptionally expressed in the adult brain, including in brain centers known to be important for learning and memory processes. Thus we investigated the effects of exogenously applied allatostatins on appetitive olfactory learning in the bee. Our results show that allatostatins modulate learning in this insect, and provide important insights into the evolution of somatostatin/allatostatin signaling.
Collapse
Affiliation(s)
- Elodie Urlacher
- Department of Zoology, Dunedin, Otago, New Zealand
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherches sur la Cognition Animale (UMR 5169), Toulouse, France
- Université de Toulouse, UPS Centre de Recherches sur la Cognition Animale (UMR 5169), Toulouse, France
- * E-mail:
| | - Laurent Soustelle
- CNRS, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U1191, Montpellier, France
- Université de Montpellier, UMR 5203, Montpellier, France
| | - Marie-Laure Parmentier
- CNRS, UMR 5203, Institut de Génomique Fonctionnelle, Montpellier, France
- INSERM, U1191, Montpellier, France
- Université de Montpellier, UMR 5203, Montpellier, France
| | - Heleen Verlinden
- Department of Animal Physiology and Neurobiology, Zoological Institute, KU Leuven, Leuven, Belgium
| | - Marie-Julie Gherardi
- EA 4552 Réceptorologie et ciblage thérapeutique en cancérologie, Université de Toulouse, UPS, Toulouse, France
| | - Daniel Fourmy
- EA 4552 Réceptorologie et ciblage thérapeutique en cancérologie, Université de Toulouse, UPS, Toulouse, France
| | | | - Jean-Marc Devaud
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherches sur la Cognition Animale (UMR 5169), Toulouse, France
- Université de Toulouse, UPS Centre de Recherches sur la Cognition Animale (UMR 5169), Toulouse, France
| | - Isabelle Massou
- Centre National de la Recherche Scientifique (CNRS), Centre de Recherches sur la Cognition Animale (UMR 5169), Toulouse, France
- Université de Toulouse, UPS Centre de Recherches sur la Cognition Animale (UMR 5169), Toulouse, France
| |
Collapse
|
144
|
Hattori M, Ozawa T. Live Cell Bioluminescence Imaging in Temporal Reaction of G Protein-Coupled Receptor for High-Throughput Screening and Analysis. Methods Mol Biol 2016; 1461:195-202. [PMID: 27424906 DOI: 10.1007/978-1-4939-3813-1_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
G protein-coupled receptors (GPCRs) are notable targets of basic therapeutics. Many screening methods have been established to identify novel agents for GPCR signaling in a high-throughput manner. However, information related to the temporal reaction of GPCR with specific ligands remains poor. We recently developed a bioluminescence method for the quantitative detection of the interaction between GPCR and β-arrestin using split luciferase complementation. To monitor time-course variation of the interactions, a new imaging system contributes to the accurate evaluation of drugs for GPCRs in a high-throughput manner.
Collapse
Affiliation(s)
- Mitsuru Hattori
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takeaki Ozawa
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| |
Collapse
|
145
|
Thomas T, Chalmers DK, Yuriev E. Homology Modeling and Docking Evaluation of Human Muscarinic Acetylcholine Receptors. NEUROMETHODS 2016. [DOI: 10.1007/978-1-4939-2858-3_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
146
|
Chawla U, Jiang Y, Zheng W, Kuang L, Perera SMDC, Pitman MC, Brown MF, Liang H. A Usual G-Protein-Coupled Receptor in Unusual Membranes. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508648] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
147
|
Advances in Computational Techniques to Study GPCR–Ligand Recognition. Trends Pharmacol Sci 2015; 36:878-890. [DOI: 10.1016/j.tips.2015.08.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/15/2015] [Accepted: 08/07/2015] [Indexed: 12/16/2022]
|
148
|
Dai SX, Li GH, Gao YD, Huang JF. Pharmacophore-Map-Pick: A Method to Generate Pharmacophore Models for All Human GPCRs. Mol Inform 2015; 35:81-91. [PMID: 27491793 DOI: 10.1002/minf.201500075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 09/21/2015] [Indexed: 01/04/2023]
Abstract
GPCR-based drug discovery is hindered by a lack of effective screening methods for most GPCRs that have neither ligands nor high-quality structures. With the aim to identify lead molecules for these GPCRs, we developed a new method called Pharmacophore-Map-Pick to generate pharmacophore models for all human GPCRs. The model of ADRB2 generated using this method not only predicts the binding mode of ADRB2-ligands correctly but also performs well in virtual screening. Findings also demonstrate that this method is powerful for generating high-quality pharmacophore models. The average enrichment for the pharmacophore models of the 15 targets in different GPCR families reached 15-fold at 0.5 % false-positive rate. Therefore, the pharmacophore models can be applied in virtual screening directly with no requirement for any ligand information or shape constraints. A total of 2386 pharmacophore models for 819 different GPCRs (99 % coverage (819/825)) were generated and are available at http://bsb.kiz.ac.cn/GPCRPMD.
Collapse
Affiliation(s)
- Shao-Xing Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, P. R. China phone/fax: + 86 087165199200/+ 86 087165199200.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Gong-Hua Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, P. R. China phone/fax: + 86 087165199200/+ 86 087165199200.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yue-Dong Gao
- Kunming Biological Diversity Regional Center of Instruments, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, P. R. China
| | - Jing-Fei Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, P. R. China phone/fax: + 86 087165199200/+ 86 087165199200. .,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100049, P. R. China. .,Kunming Institute of Zoology - Chinese University of Hongkong Joint Research Center for Bio-resources and Human Disease Mechanisms, Kunming 650223, P. R. China.
| |
Collapse
|
149
|
Culhane KJ, Liu Y, Cai Y, Yan ECY. Transmembrane signal transduction by peptide hormones via family B G protein-coupled receptors. Front Pharmacol 2015; 6:264. [PMID: 26594176 PMCID: PMC4633518 DOI: 10.3389/fphar.2015.00264] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 10/23/2015] [Indexed: 01/28/2023] Open
Abstract
Although family B G protein-coupled receptors (GPCRs) contain only 15 members, they play key roles in transmembrane signal transduction of hormones. Family B GPCRs are drug targets for developing therapeutics for diseases ranging from metabolic to neurological disorders. Despite their importance, the molecular mechanism of activation of family B GPCRs remains largely unexplored due to the challenges in expression and purification of functional receptors to the quantity for biophysical characterization. Currently, there is no crystal structure available of a full-length family B GPCR. However, structures of key domains, including the extracellular ligand binding regions and seven-helical transmembrane regions, have been solved by X-ray crystallography and NMR, providing insights into the mechanisms of ligand recognition and selectivity, and helical arrangements within the cell membrane. Moreover, biophysical and biochemical methods have been used to explore functions, key residues for signaling, and the kinetics and dynamics of signaling processes. This review summarizes the current knowledge of the signal transduction mechanism of family B GPCRs at the molecular level and comments on the challenges and outlook for mechanistic studies of family B GPCRs.
Collapse
Affiliation(s)
- Kelly J Culhane
- Department of Molecular Biophysics and Biochemistry, Yale University New Haven, CT, USA
| | - Yuting Liu
- Department of Chemistry, Yale University New Haven, CT, USA
| | - Yingying Cai
- Department of Chemistry, Yale University New Haven, CT, USA
| | - Elsa C Y Yan
- Department of Chemistry, Yale University New Haven, CT, USA
| |
Collapse
|
150
|
Blankenship E, Vahedi-Faridi A, Lodowski DT. The High-Resolution Structure of Activated Opsin Reveals a Conserved Solvent Network in the Transmembrane Region Essential for Activation. Structure 2015; 23:2358-2364. [PMID: 26526852 DOI: 10.1016/j.str.2015.09.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 08/27/2015] [Accepted: 09/06/2015] [Indexed: 11/15/2022]
Abstract
Rhodopsin, a light-activated G protein coupled receptor (GPCR), has been the subject of numerous biochemical and structural investigations, serving as a model receptor for GPCRs and their activation. We present the 2.3-Å resolution structure of native source rhodopsin stabilized in a conformation competent for G protein binding. An extensive water-mediated hydrogen bond network linking the chromophore binding site to the site of G protein binding is observed, providing connections to conserved motifs essential for GPCR activation. Comparison of this extensive solvent-mediated hydrogen-bonding network with the positions of ordered solvent in earlier crystallographic structures of rhodopsin photointermediates reveals both static structural and dynamic functional water-protein interactions present during the activation process. When considered along with observations that solvent occupies similar positions in the structures of other GPCRs, these analyses strongly support an integral role for this dynamic ordered water network in both rhodopsin and GPCR activation.
Collapse
Affiliation(s)
- Elise Blankenship
- Department of Nutrition, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Ardeschir Vahedi-Faridi
- Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - David T Lodowski
- Department of Nutrition, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Center for Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH 44106, USA.
| |
Collapse
|