51
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Using the fragment molecular orbital method to investigate agonist-orexin-2 receptor interactions. Biochem Soc Trans 2016; 44:574-81. [PMID: 27068972 PMCID: PMC5264495 DOI: 10.1042/bst20150250] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Indexed: 12/11/2022]
Abstract
The understanding of binding interactions between any protein and a small molecule plays a key role in the rationalization of affinity and selectivity and is essential for an efficient structure-based drug discovery (SBDD) process. Clearly, to begin SBDD, a structure is needed, and although there has been fantastic progress in solving G-protein-coupled receptor (GPCR) crystal structures, the process remains quite slow and is not currently feasible for every GPCR or GPCR-ligand complex. This situation significantly limits the ability of X-ray crystallography to impact the drug discovery process for GPCR targets in 'real-time' and hence there is still a need for other practical and cost-efficient alternatives. We present here an approach that integrates our previously described hierarchical GPCR modelling protocol (HGMP) and the fragment molecular orbital (FMO) quantum mechanics (QM) method to explore the interactions and selectivity of the human orexin-2 receptor (OX2R) and its recently discovered nonpeptidic agonists. HGMP generates a 3D model of GPCR structures and its complexes with small molecules by applying a set of computational methods. FMO allowsab initioapproaches to be applied to systems that conventional QM methods would find challenging. The key advantage of FMO is that it can reveal information on the individual contribution and chemical nature of each residue and water molecule to the ligand binding that normally would be difficult to detect without QM. We illustrate how the combination of both techniques provides a practical and efficient approach that can be used to analyse the existing structure-function relationships (SAR) and to drive forward SBDD in a real-world example for which there is no crystal structure of the complex available.
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52
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Liang D, Zhao M, Wang T, McManus DP, Cummins SF. GPCR and IR genes in Schistosoma mansoni miracidia. Parasit Vectors 2016; 9:563. [PMID: 27784323 PMCID: PMC5080760 DOI: 10.1186/s13071-016-1837-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/05/2016] [Indexed: 11/25/2022] Open
Abstract
Background Schistosoma species are responsible for the disease schistosomiasis, a highly prevalent helminthic disease that requires a freshwater snail as intermediate host. The S. mansoni free-living miracidium must utilize olfaction to find a suitable snail host, and certain types of rhodopsin G protein-coupled receptors (GPCRs) and ionotropic receptors (IRs) have been identified as olfactory receptors in other animal phyla. The Schistosoma genome project, together with the recent availability of proteomic databases, allowed for studies to explore receptors within S. mansoni, some of which may contribute to host finding. Results We have identified 17 rhodopsin-type GPCR sequences in S. mansoni belonging to four subclasses, including ligand-specific GPCRs (i.e. neuropeptide and opsin). RT-PCR demonstrated the expression of nine out of the 17 GPCRs in the free-living miracidia, each of which have been characterized for homology to S. haematobium. Among the nine GPCRs, two are predicted as Gq-opsins. We also describe the characterization of a Schistosoma-encoded IR based on similarity with other species IR and conservation of IR-like domains. Schistosoma mansoni IR is expressed in miracidia at 3 and 6 h post-hatch. Conclusions The identification of receptors in S. mansoni miracidia, presented here, contributes not only to further understanding of Schistosoma biology and signal transduction but also provides a basis for approaches that may modify parasite behaviour. Electronic supplementary material The online version of this article (doi:10.1186/s13071-016-1837-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Di Liang
- Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore, QLD, 4558, Australia
| | - Min Zhao
- Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore, QLD, 4558, Australia
| | - Tianfang Wang
- Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore, QLD, 4558, Australia
| | - Donald P McManus
- Molecular Parasitology Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Q4006, Australia
| | - Scott F Cummins
- Faculty of Science, Health and Education, University of the Sunshine Coast, Maroochydore, QLD, 4558, Australia.
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53
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Heifetz A, James T, Morao I, Bodkin MJ, Biggin PC. Guiding lead optimization with GPCR structure modeling and molecular dynamics. Curr Opin Pharmacol 2016; 30:14-21. [DOI: 10.1016/j.coph.2016.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/16/2016] [Accepted: 06/17/2016] [Indexed: 01/04/2023]
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54
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Lückmann M, Amarandi RM, Papargyri N, Jakobsen MH, Christiansen E, Jensen LJ, Pui A, Schwartz TW, Rosenkilde MM, Frimurer TM. Structure-based discovery of novel US28 small molecule ligands with different modes of action. Chem Biol Drug Des 2016; 89:289-296. [PMID: 27569905 DOI: 10.1111/cbdd.12848] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 08/02/2016] [Accepted: 08/25/2016] [Indexed: 12/11/2022]
Abstract
The human cytomegalovirus-encoded G protein-coupled receptor US28 is a constitutively active receptor, which can recognize various chemokines. Despite the recent determination of its 2.9 Å crystal structure, potent and US28-specific tool compounds are still scarce. Here, we used structural information from a refined US28:VUF2274 complex for virtual screening of >12 million commercially available small molecule compounds. Using a combined receptor- and ligand-based approach, we tested 98 of the top 0.1% ranked compounds, revealing novel chemotypes as compared to the ~1.45 million known ligands in the ChEMBL database. Two compounds were confirmed as agonist and inverse agonist, respectively, in both IP accumulation and Ca2+ mobilization assays. The screening setup presented in this work is computationally inexpensive and therefore particularly useful in an academic setting as it enables simultaneous testing in binding as well as in different functional assays and/or species without actual chemical synthesis.
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Affiliation(s)
- Michael Lückmann
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Roxana-Maria Amarandi
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Faculty of Chemistry, Alexandru Ioan Cuza University of Iaşi, Iaşi, Romania
| | - Natalia Papargyri
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Mette H Jakobsen
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Elisabeth Christiansen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Lars J Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Aurel Pui
- Faculty of Chemistry, Alexandru Ioan Cuza University of Iaşi, Iaşi, Romania
| | - Thue W Schwartz
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Mette M Rosenkilde
- Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Thomas M Frimurer
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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55
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Newton CL, Wood MD, Strange PG. Examining the Effects of Sodium Ions on the Binding of Antagonists to Dopamine D2 and D3 Receptors. PLoS One 2016; 11:e0158808. [PMID: 27379794 PMCID: PMC4933336 DOI: 10.1371/journal.pone.0158808] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 06/22/2016] [Indexed: 11/19/2022] Open
Abstract
Many G protein-coupled receptors have been shown to be sensitive to the presence of sodium ions (Na+). Using radioligand competition binding assays, we have examined and compared the effects of sodium ions on the binding affinities of a number of structurally diverse ligands at human dopamine D2 and dopamine D3 receptor subtypes, which are important therapeutic targets for the treatment of psychotic disorders. At both receptors, the binding affinities of the antagonists/inverse agonists SB-277011-A, L,741,626, GR 103691 and U 99194 were higher in the presence of sodium ions compared to those measured in the presence of the organic cation, N-methyl-D-glucamine, used to control for ionic strength. Conversely, the affinities of spiperone and (+)-butaclamol were unaffected by the presence of sodium ions. Interestingly, the binding of the antagonist/inverse agonist clozapine was affected by changes in ionic strength of the buffer used rather than the presence of specific cations. Similar sensitivities to sodium ions were seen at both receptors, suggesting parallel effects of sodium ion interactions on receptor conformation. However, no clear correlation between ligand characteristics, such as subtype selectivity, and sodium ion sensitivity were observed. Therefore, the properties which determine this sensitivity remain unclear. However these findings do highlight the importance of careful consideration of assay buffer composition for in vitro assays and when comparing data from different studies, and may indicate a further level of control for ligand binding in vivo.
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Affiliation(s)
- Claire L. Newton
- School of Pharmacy, University of Reading, Reading, RG6 6AJ, United Kingdom
- * E-mail:
| | - Martyn D. Wood
- Psychiatry CEDD, GlaxoSmithKline, Harlow, Essex, CM19 5AW, United Kingdom
| | - Philip G. Strange
- School of Pharmacy, University of Reading, Reading, RG6 6AJ, United Kingdom
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56
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Vrecl M, Jorgensen R, Pogacnik A, Heding A. Development of a BRET2 Screening Assay Using β-Arrestin 2 Mutants. ACTA ACUST UNITED AC 2016; 9:322-33. [PMID: 15191649 DOI: 10.1177/1087057104263212] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This study has focused on enhancing the signal generated from the interaction between a G-protein-coupled receptor (GPCR) and β-arrestin 2 (β-arr2), measured by the bioluminescence resonance energy transfer (BRET2) technology. Both class A (β2-adrenergic receptor [β2-AR]) and class B (neurokinin-type 1 receptor [NK1-R]) GPCRs, classified based on their internalization characteristics, have been analyzed. It was evaluated whether the BRET2 signal can be enhanced by using (1) β-arr2 phosphorylation-independent mutant (β-arr2 R169E) and (2) β-arr2 mutants deficient in their ability to interact with the components of the clathrin-coated vesicles (β-arr2 R393E, R395E and β-arr2 373 stop). For the class B receptor, there was no major difference in the agonist-promoted BRET2 signal when comparing results obtained with wild-type (wt) and mutant β-arr2. However, with the class A receptor, a more than 2-fold increase in the BRET2 signal was observed with β-arr2 mutants lacking the AP-2 or both AP-2 and clathrin binding sites. This set of data suggests that the inability of these β-arr2 mutants to interact with the components of the clathrin-coated vesicle probably prevents their rapid dissociation from the receptor, thus yielding an increased and more stable BRET2 signal. The β-arr2 R393E, R395E mutant also enhanced the signal window with other members of the GPCR family (neuropeptide Y type 2 receptor [NPY2-R] and TG1019 receptor) and was successfully applied in full-plate BRET2-based agonist and antagonist screening assays.
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Affiliation(s)
- Milka Vrecl
- Institute of Anatomy, Histology & Embryology, Veterinary Faculty, University of Ljubljana, Ljubljana, Slovenia
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57
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Kornienko O, Lacson R, Kunapuli P, Schneeweis J, Hoffman I, Smith T, Alberts M, Inglese J, Strulovici B. Miniaturization of Whole Live Cell-Based GPCR Assays Using Microdispensing and Detection Systems. ACTA ACUST UNITED AC 2016; 9:186-95. [PMID: 15140380 DOI: 10.1177/1087057103260070] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Cell-based β-lactamase reporter gene assays designed to measure the functional responses of G-protein-coupled receptors (GPCRs) were miniaturized to less than 2 μL total assay volume in a 3456-well microplate. Studies were done to evaluate both receptor agonists and antagonists. The pharmacology of agonists and antagonists for target GPCRs originally developed in a 96-well format was recapitulated in a 3456-well microplate format without compromising data quality or EC50/IC50 precision. These assays were employed in high-throughput screening campaigns, allowing the testing of more than 150,000 compounds in 8 h. The instrumentation used and practical aspects of the assay development are discussed.
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MESH Headings
- Animals
- Biological Assay/instrumentation
- Biological Assay/methods
- Combinatorial Chemistry Techniques
- Cricetinae
- Dose-Response Relationship, Drug
- Drug Evaluation, Preclinical/instrumentation
- Drug Evaluation, Preclinical/methods
- Genes, Reporter
- Humans
- Inhibitory Concentration 50
- Nanotechnology/methods
- Receptors, G-Protein-Coupled/agonists
- Receptors, G-Protein-Coupled/antagonists & inhibitors
- Receptors, Neurotensin/drug effects
- Receptors, Neurotensin/genetics
- Receptors, Oxytocin/agonists
- Receptors, Oxytocin/antagonists & inhibitors
- Receptors, Oxytocin/genetics
- Reproducibility of Results
- Spectrometry, Fluorescence
- beta-Lactamases/genetics
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Affiliation(s)
- Oleg Kornienko
- Merck Research Laboratories, Department of Automated Biotechnology, North Wales, PA 19454, USA.
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58
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Mishina YM, Wilson CJ, Bruett L, Smith JJ, Stoop-Myer C, Jong S, Amaral LP, Pedersen R, Lyman SK, Myer VE, Kreider BL, Thompson CM. Multiplex GPCR Assay in Reverse Transfection Cell Microarrays. ACTA ACUST UNITED AC 2016; 9:196-207. [PMID: 15140381 DOI: 10.1177/1087057103261880] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
G protein-coupled receptors (GPCRs) are a superfamily of proteins that include some of the most important drug targets in the pharmaceutical industry. Despite the success of this group of drugs, there remains a need to identify GPCR-targeted drugs with greater selectivity, to develop screening assays for validated targets, and to identify ligands for orphan receptors. To address these challenges, the authors have created a multiplexed GPCR assay that measures greater than 3000 receptor: ligand interactions in a single microplate. The multiplexed assay is generated by combining reverse transfection in a 96-well plate format with a calcium flux readout. This assay quantitatively measures receptor activation and inhibition and permits the determination of compound potency and selectivity for entire families of GPCRs in parallel. To expand the number of GPCR targets that may be screened in this system, receptors are cotransfected with plasmids encoding a promiscuous G protein, permitting the analysis of receptors that do not normally mobilize intracellular calcium upon activation. The authors demonstrate the utility of reverse transfection cell microarrays to GPCR-targeted drug discovery with examples of ligand selectivity screening against a panel of GPCRs as well as dose-dependent titrations of selected agonists and antagonists.
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59
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Abstract
SUMMARYCells must respond to a diverse, complex, and ever-changing mix of signals, using a fairly limited set of parts. Changes in protein level, protein localization, protein activity, and protein-protein interactions are critical aspects of signal transduction, allowing cells to respond highly specifically to a nearly limitless set of cues and also to vary the sensitivity, duration, and dynamics of the response. Signal-dependent changes in levels of gene expression and protein synthesis play an important role in regulation of protein levels, whereas posttranslational modifications of proteins regulate their degradation, localization, and functional interactions. Protein ubiquitylation, for example, can direct proteins to the proteasome for degradation or provide a signal that regulates their interactions and/or location within the cell. Similarly, protein phosphorylation by specific kinases is a key mechanism for augmenting protein activity and relaying signals to other proteins that possess domains that recognize the phosphorylated residues.
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Affiliation(s)
- Michael J Lee
- David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Michael B Yaffe
- David H. Koch Institute for Integrative Cancer Research at MIT, Department of Biology and Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
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60
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Regulating the effects of GPR21, a novel target for type 2 diabetes. Sci Rep 2016; 6:27002. [PMID: 27243589 PMCID: PMC4886680 DOI: 10.1038/srep27002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/12/2016] [Indexed: 01/06/2023] Open
Abstract
Type 2 diabetes is a chronic metabolic disorder primarily caused by insulin resistance to which obesity is a major contributor. Expression levels of an orphan G protein-coupled receptor (GPCR), GPR21, demonstrated a trend towards a significant increase in the epididymal fat pads of wild type high fat high sugar (HFHS)-fed mice. To gain further insight into the potential role this novel target may play in the development of obesity-associated type 2 diabetes, the signalling capabilities of the receptor were investigated. Overexpression studies in HEK293T cells revealed GPR21 to be a constitutively active receptor, which couples to Gαq type G proteins leading to the activation of mitogen activated protein kinases (MAPKs). Overexpression of GPR21 in vitro also markedly attenuated insulin signalling. Interestingly, the effect of GPR21 on the MAPKs and insulin signalling was reduced in the presence of serum, inferring the possibility of a native inhibitory ligand. Homology modelling and ligand docking studies led to the identification of a novel compound that inhibited GPR21 activity. Its effects offer potential as an anti-diabetic pharmacological strategy as it was found to counteract the influence of GPR21 on the insulin signalling pathway.
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61
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Tesmer JJG. Hitchhiking on the heptahelical highway: structure and function of 7TM receptor complexes. Nat Rev Mol Cell Biol 2016; 17:439-50. [PMID: 27093944 DOI: 10.1038/nrm.2016.36] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A revolution in the analysis of seven transmembrane domain (7TM) receptors has provided detailed information about how these physiologically important signalling proteins interact with extracellular cues. However, it has proved much more challenging to understand how 7TM receptors convey information to their principal intracellular targets: heterotrimeric G proteins, G protein-coupled receptor kinases and arrestins. Recent structures now suggest a common mechanism that enables these structurally diverse cytoplasmic proteins to 'hitch a ride' on hundreds of different activated 7TM receptors in order to instigate physiological change.
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Affiliation(s)
- John J G Tesmer
- Life Sciences Institute and Departments of Pharmacology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109-2216, USA
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62
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Kling RC, Plomer M, Lang C, Banerjee A, Hübner H, Gmeiner P. Development of Covalent Ligand-Receptor Pairs to Study the Binding Properties of Nonpeptidic Neurotensin Receptor 1 Antagonists. ACS Chem Biol 2016; 11:869-75. [PMID: 26808719 DOI: 10.1021/acschembio.5b00965] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The neurotensin receptor NTS1 has been suggested to be of pharmaceutical relevance, as it was found to exert modulatory effects on dopaminergic signal transduction and to be involved in tumor progression. Rational drug design of NTS1 receptor ligands requires molecular insights into the binding behavior of a particular lead compound. Although crystal structures of NTS1 have revealed the molecular determinants of peptide-agonist interactions, the binding mode of small-molecule antagonists remains largely unknown. Employing a disulfide-based tethering approach, we developed covalently binding molecular probes. The ligands 1 and 2 are based on the pharmacophore of the nonpeptidic NTS1 antagonist SR142948A, allowing the formation of a disulfide bond to an engineered cysteine residue of NTS1. The position of the covalent bond between Cys127(2.65) and the ligand was used to predict the binding mode of the covalent antagonist 1 and its parent compound SR142948A by molecular dynamics simulations.
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Affiliation(s)
- Ralf C. Kling
- Department
of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstr. 19, 91052 Erlangen, Germany
| | - Manuel Plomer
- Department
of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstr. 19, 91052 Erlangen, Germany
| | - Christopher Lang
- Department
of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstr. 19, 91052 Erlangen, Germany
| | - Ashutosh Banerjee
- Department
of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstr. 19, 91052 Erlangen, Germany
| | - Harald Hübner
- Department
of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstr. 19, 91052 Erlangen, Germany
| | - Peter Gmeiner
- Department
of Chemistry and Pharmacy, Emil Fischer Center, Friedrich Alexander University, Schuhstr. 19, 91052 Erlangen, Germany
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63
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Salmas RE, Yurtsever M, Durdagi S. Atomistic molecular dynamics simulations of typical and atypical antipsychotic drugs at the dopamine D2 receptor (D2R) elucidates their inhibition mechanism. J Biomol Struct Dyn 2016; 35:738-754. [DOI: 10.1080/07391102.2016.1159986] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
| | - Mine Yurtsever
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
| | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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64
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Nakamura Y, Hashimoto T, Ishii J, Kondo A. Dual-color reporter switching system to discern dimer formations of G-protein-coupled receptors using Cre/loxP
site-specific recombination in yeast. Biotechnol Bioeng 2016; 113:2178-90. [DOI: 10.1002/bit.25974] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Revised: 02/29/2016] [Accepted: 03/01/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Yasuyuki Nakamura
- Department of Chemical Science and Engineering, Graduate School of Engineering; Kobe University; Kobe Japan
| | - Takamichi Hashimoto
- Department of Chemical Science and Engineering, Graduate School of Engineering; Kobe University; Kobe Japan
| | - Jun Ishii
- Organization of Advanced Science and Technology; Kobe University, 1-1 Rokkodai, Nada; Kobe 657-8501 Japan
| | - Akihiko Kondo
- Department of Chemical Science and Engineering, Graduate School of Engineering; Kobe University; Kobe Japan
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65
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Jean-Charles PY, Snyder JC, Shenoy SK. Chapter One - Ubiquitination and Deubiquitination of G Protein-Coupled Receptors. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2016; 141:1-55. [PMID: 27378754 DOI: 10.1016/bs.pmbts.2016.05.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The seven-transmembrane containing G protein-coupled receptors (GPCRs) constitute the largest family of cell-surface receptors. Transmembrane signaling by GPCRs is fundamental to many aspects of physiology including vision, olfaction, cardiovascular, and reproductive functions as well as pain, behavior and psychomotor responses. The duration and magnitude of signal transduction is tightly controlled by a series of coordinated trafficking events that regulate the cell-surface expression of GPCRs at the plasma membrane. Moreover, the intracellular trafficking profiles of GPCRs can correlate with the signaling efficacy and efficiency triggered by the extracellular stimuli that activate GPCRs. Of the various molecular mechanisms that impart selectivity, sensitivity and strength of transmembrane signaling, ubiquitination of the receptor protein plays an important role because it defines both trafficking and signaling properties of the activated GPCR. Ubiquitination of proteins was originally discovered in the context of lysosome-independent degradation of cytosolic proteins by the 26S proteasome; however a large body of work suggests that ubiquitination also orchestrates the downregulation of membrane proteins in the lysosomes. In the case of GPCRs, such ubiquitin-mediated lysosomal degradation engenders long-term desensitization of transmembrane signaling. To date about 40 GPCRs are known to be ubiquitinated. For many GPCRs, ubiquitination plays a major role in postendocytic trafficking and sorting to the lysosomes. This chapter will focus on the patterns and functional roles of GPCR ubiquitination, and will describe various molecular mechanisms involved in GPCR ubiquitination.
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Affiliation(s)
- P-Y Jean-Charles
- Department of Medicine (Cardiology), Duke University Medical Center, Durham, NC, United States
| | - J C Snyder
- Department of Cell Biology, Duke University Medical Center, Durham, NC, United States
| | - S K Shenoy
- Department of Medicine (Cardiology), Duke University Medical Center, Durham, NC, United States; Department of Cell Biology, Duke University Medical Center, Durham, NC, United States.
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66
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Heifetz A, Chudyk EI, Gleave L, Aldeghi M, Cherezov V, Fedorov DG, Biggin PC, Bodkin MJ. The Fragment Molecular Orbital Method Reveals New Insight into the Chemical Nature of GPCR–Ligand Interactions. J Chem Inf Model 2015; 56:159-72. [PMID: 26642258 DOI: 10.1021/acs.jcim.5b00644] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Our interpretation of ligand-protein interactions is often informed by high-resolution structures, which represent the cornerstone of structure-based drug design. However, visual inspection and molecular mechanics approaches cannot explain the full complexity of molecular interactions. Quantum Mechanics approaches are often too computationally expensive, but one method, Fragment Molecular Orbital (FMO), offers an excellent compromise and has the potential to reveal key interactions that would otherwise be hard to detect. To illustrate this, we have applied the FMO method to 18 Class A GPCR-ligand crystal structures, representing different branches of the GPCR genome. Our work reveals key interactions that are often omitted from structure-based descriptions, including hydrophobic interactions, nonclassical hydrogen bonds, and the involvement of backbone atoms. This approach provides a more comprehensive picture of receptor-ligand interactions than is currently used and should prove useful for evaluation of the chemical nature of ligand binding and to support structure-based drug design.
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Affiliation(s)
- Alexander Heifetz
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Ewa I. Chudyk
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Laura Gleave
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Matteo Aldeghi
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Vadim Cherezov
- Department
of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, United States
- Laboratory
for Structural Biology of GPCRs, Moscow Institute of Physics and Technology, Dolgoprudny 141700, Russia
| | - Dmitri G. Fedorov
- NMRI, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Philip C. Biggin
- Department
of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Mike J. Bodkin
- Evotec (U.K.) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
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67
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Abstract
Since their discovery, G protein-coupled receptors (GPCRs) constitute one of the most studied proteins leading to important discoveries and perspectives in terms of their biology and implication in physiology and pathophysiology. This is mostly linked to the remarkable advances in the development and application of the biophysical resonance energy transfer (RET)-based approaches, including bioluminescence and fluorescence resonance energy transfer (BRET and FRET, respectively). Indeed, BRET and FRET have been extensively applied to study different aspects of GPCR functioning such as their activation and regulation either statically or dynamically, in real-time and intact cells. Consequently, our view on GPCRs has considerably changed opening new challenges for the study of GPCRs in their native tissues in the aim to get more knowledge on how these receptors control the biological responses. Moreover, the technological aspect of this field of research promises further developments for robust and reliable new RET-based assays that may be compatible with high-throughput screening as well as drug discovery programs.
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Affiliation(s)
- Mohammed Akli Ayoub
- Biologie et Bioinformatique des Systèmes de Signalisation, Institut National de la Recherche Agronomique, UMR85, Unité Physiologie de la Reproduction et des Comportements; CNRS, UMR7247, Nouzilly, France; LE STUDIUM(®) Loire Valley Institute for Advanced Studies, Orléans, France.
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68
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Li T, Cao C, Yang T, Zhang L, He L, Xi Z, Bian G, Liu N. A G-protein-coupled receptor regulation pathway in cytochrome P450-mediated permethrin-resistance in mosquitoes, Culex quinquefasciatus. Sci Rep 2015; 5:17772. [PMID: 26656663 PMCID: PMC4674712 DOI: 10.1038/srep17772] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/04/2015] [Indexed: 01/29/2023] Open
Abstract
Rhodopsin-like G protein-coupled receptors (GPCRs) are known to be involved in the GPCR signal transduction system and regulate many essential physiological processes in organisms. This study, for the first time, revealed that knockdown of the rhodopsin-like GPCR gene in resistant mosquitoes resulted in a reduction of mosquitoes’ resistance to permethrin, simultaneously reducing the expression of two cAMP-dependent protein kinase A genes (PKAs) and four resistance related cytochrome P450 genes. The function of rhodopsin-like GPCR was further confirmed using transgenic lines of Drosophila melanogaster, in which the tolerance to permethrin and the expression of Drosophila resistance P450 genes were both increased. The roles of GPCR signaling pathway second messenger cyclic adenosine monophosphate (cAMP) and downstream effectors PKAs in resistance were investigated using cAMP production inhibitor Bupivacaine HCl and the RNAi technique. Inhibition of cAMP production led to significant decreases in both the expression of four resistance P450 genes and two PKA genes and mosquito resistance to permethrin. Knockdown of the PKA genes had shown the similar effects on permethrin resistance and P450 gene expression. Taken together, our studies revealed, for the first time, the role of the GPCR/cAMP/PKA-mediated regulatory pathway governing P450 gene expression and P450-mediated resistance in Culex mosquitoes.
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Affiliation(s)
- Ting Li
- Department of Entomology and Plant Pathology, Auburn University, Auburn AL 36849
| | - Chuanwang Cao
- Department of Entomology and Plant Pathology, Auburn University, Auburn AL 36849
| | - Ting Yang
- Department of Entomology and Plant Pathology, Auburn University, Auburn AL 36849
| | - Lee Zhang
- Genomics Laboratory, Auburn University, Auburn, AL 36849
| | - Lin He
- Department of Entomology and Plant Pathology, Auburn University, Auburn AL 36849
| | - Zhiyong Xi
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824
| | - Guowu Bian
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824
| | - Nannan Liu
- Department of Entomology and Plant Pathology, Auburn University, Auburn AL 36849
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Mutation-Guided Unbiased Modeling of the Fat Sensor GPR119 for High-Yield Agonist Screening. Structure 2015; 23:2377-2386. [PMID: 26526849 DOI: 10.1016/j.str.2015.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 09/14/2015] [Accepted: 09/15/2015] [Indexed: 12/14/2022]
Abstract
Recent benchmark studies have demonstrated the difficulties in obtaining accurate predictions of ligand binding conformations to comparative models of G-protein-coupled receptors. We have developed a data-driven optimization protocol, which integrates mutational data and structural information from multiple X-ray receptor structures in combination with a fully flexible ligand docking protocol to determine the binding conformation of AR231453, a small-molecule agonist, in the GPR119 receptor. Resulting models converge to one conformation that explains the majority of data from mutation studies and is consistent with the structure-activity relationship for a large number of AR231453 analogs. Another key property of the refined models is their success in separating active ligands from decoys in a large-scale virtual screening. These results demonstrate that mutation-guided receptor modeling can provide predictions of practical value for describing receptor-ligand interactions and drug discovery.
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Rios S, Fernandez MF, Caltabiano G, Campillo M, Pardo L, Gonzalez A. GPCRtm: An amino acid substitution matrix for the transmembrane region of class A G Protein-Coupled Receptors. BMC Bioinformatics 2015; 16:206. [PMID: 26134144 PMCID: PMC4489126 DOI: 10.1186/s12859-015-0639-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/06/2015] [Indexed: 01/08/2023] Open
Abstract
Background Protein sequence alignments and database search methods use standard scoring matrices calculated from amino acid substitution frequencies in general sets of proteins. These general-purpose matrices are not optimal to align accurately sequences with marked compositional biases, such as hydrophobic transmembrane regions found in membrane proteins. In this work, an amino acid substitution matrix (GPCRtm) is calculated for the membrane spanning segments of the G protein-coupled receptor (GPCR) rhodopsin family; one of the largest transmembrane protein family in humans with great importance in health and disease. Results The GPCRtm matrix reveals the amino acid compositional bias distinctive of the GPCR rhodopsin family and differs from other standard substitution matrices. These membrane receptors, as expected, are characterized by a high content of hydrophobic residues with regard to globular proteins. On the other hand, the presence of polar and charged residues is higher than in average membrane proteins, displaying high frequencies of replacement within themselves. Conclusions Analysis of amino acid frequencies and values obtained from the GPCRtm matrix reveals patterns of residue replacements different from other standard substitution matrices. GPCRs prioritize the reactivity properties of the amino acids over their bulkiness in the transmembrane regions. A distinctive role is that charged and polar residues seem to evolve at different rates than other amino acids. This observation is related to the role of the transmembrane bundle in the binding of ligands, that in many cases involve electrostatic and hydrogen bond interactions. This new matrix can be useful in database search and for the construction of more accurate sequence alignments of GPCRs. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0639-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santiago Rios
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Marta F Fernandez
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Gianluigi Caltabiano
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Mercedes Campillo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Angel Gonzalez
- Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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Shi JP, Li XN, Zhang XY, Du B, Jiang WZ, Liu MY, Wang JJ, Wang ZG, Ren H, Qian M. Gpr97 Is Dispensable for Inflammation in OVA-Induced Asthmatic Mice. PLoS One 2015; 10:e0131461. [PMID: 26132811 PMCID: PMC4489018 DOI: 10.1371/journal.pone.0131461] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 06/02/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Asthma is a complex inflammatory disorder involving the activation and invasion of various immune cells. GPR97 is highly expressed in some immunocytes, including mast cells and eosinophils, which play critical roles in asthma development. However, the role of Gpr97 in regulating airway inflammation in asthma has rarely been reported. In this study, we investigated the potential role of Gpr97 in the development of allergic asthma in mice. METHODS Relevant airway asthmatic mouse models were constructed with both wild-type and Gpr97-/- mice sensitized to 250 μg ovalbumin (OVA). The levels of interleukin IL-4, IL-6 and IFN-γ, which are involved in OVA-induced asthma, in the bronchoalveolar lavage fluid (BALF) and the IgE level in the serum were examined by enzyme-linked immunosorbent assay (ELISA). The invasion of mast cells and eosinophils into lung tissues was assessed by immunohistochemical and eosinophil peroxidase activity assays, respectively. Goblet cell hyperplasia and mucus production were morphologically evaluated with periodic acid-Schiff (PAS) staining. RESULTS In our study, no obvious alteration in the inflammatory response or airway remodeling was found in the Gpr97-deficient mice with OVA-induced asthma. Neither the secretion of cytokines, including IL-4, IL-6 and IFN-γ, nor inflammatory cell recruitment was altered in the Gpr97-deficient mice. Moreover, Gpr97 deficiency did not affect airway remodeling or mucus production in the asthma mouse model. CONCLUSION Our findings imply that Gpr97 might not be required for the development of airway inflammation in OVA-induced allergic asthma in mice.
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Affiliation(s)
- Jue-ping Shi
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
- Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Xiao-ning Li
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
- Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Xiao-yu Zhang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
- Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Bing Du
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
- Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Wen-zheng Jiang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
- Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Ming-yao Liu
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
- Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Jin-jin Wang
- Shanghai Research Center for Model Organisms, Shanghai, China
| | - Zhu-gang Wang
- Shanghai Research Center for Model Organisms, Shanghai, China
| | - Hua Ren
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
- Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Min Qian
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, China
- Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
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Mizrachi D, Chen Y, Liu J, Peng HM, Ke A, Pollack L, Turner RJ, Auchus RJ, DeLisa MP. Making water-soluble integral membrane proteins in vivo using an amphipathic protein fusion strategy. Nat Commun 2015; 6:6826. [PMID: 25851941 PMCID: PMC4403311 DOI: 10.1038/ncomms7826] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/03/2015] [Indexed: 11/30/2022] Open
Abstract
Integral membrane proteins (IMPs) play crucial roles in all cells and represent attractive pharmacological targets. However, functional and structural studies of IMPs are hindered by their hydrophobic nature and the fact that they are generally unstable following extraction from their native membrane environment using detergents. Here we devise a general strategy for in vivo solubilization of IMPs in structurally relevant conformations without the need for detergents or mutations to the IMP itself, as an alternative to extraction and in vitro solubilization. This technique, called SIMPLEx (solubilization of IMPs with high levels of expression), allows the direct expression of soluble products in living cells by simply fusing an IMP target with truncated apolipoprotein A-I, which serves as an amphipathic proteic ‘shield' that sequesters the IMP from water and promotes its solubilization. The study of integral membrane proteins (IMPs) is hampered by yields and the difficulty in retaining activity once they have been solubilized. Here Mizrachi et al. develop a strategy for in vivo expression and solubilization of IMPs in functionally relevant states by fusing them to truncated apolipoprotein A-I.
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Affiliation(s)
- Dario Mizrachi
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA
| | - Yujie Chen
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Jiayan Liu
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Hwei-Ming Peng
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Ailong Ke
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
| | - Raymond J Turner
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | - Richard J Auchus
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Matthew P DeLisa
- School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA
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Takenaka M, Miyachi Y, Ishii J, Ogino C, Kondo A. The mapping of yeast's G-protein coupled receptor with an atomic force microscope. NANOSCALE 2015; 7:4956-4963. [PMID: 25690872 DOI: 10.1039/c4nr05940a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
An atomic force microscope (AFM) can measure the adhesion force between a sample and a cantilever while simultaneously applying a rupture force during the imaging of a sample. An AFM should be useful in targeting specific proteins on a cell surface. The present study proposes the use of an AFM to measure the adhesion force between targeting receptors and their ligands, and to map the targeting receptors. In this study, Ste2p, one of the G protein-coupled receptors (GPCRs), was chosen as the target receptor. The specific force between Ste2p on a yeast cell surface and a cantilever modified with its ligand, α-factor, was measured and found to be approximately 250 pN. In addition, through continuous measuring of the cell surface, a mapping of the receptors on the cell surface could be performed, which indicated the differences in the Ste2p expression levels. Therefore, the proposed AFM system is accurate for cell diagnosis.
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Affiliation(s)
- Musashi Takenaka
- Department of Chemical and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan.
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de Munnik SM, Smit MJ, Leurs R, Vischer HF. Modulation of cellular signaling by herpesvirus-encoded G protein-coupled receptors. Front Pharmacol 2015; 6:40. [PMID: 25805993 PMCID: PMC4353375 DOI: 10.3389/fphar.2015.00040] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/12/2015] [Indexed: 12/22/2022] Open
Abstract
Human herpesviruses (HHVs) are widespread infectious pathogens that have been associated with proliferative and inflammatory diseases. During viral evolution, HHVs have pirated genes encoding viral G protein-coupled receptors (vGPCRs), which are expressed on infected host cells. These vGPCRs show highest homology to human chemokine receptors, which play a key role in the immune system. Importantly, vGPCRs have acquired unique properties such as constitutive activity and the ability to bind a broad range of human chemokines. This allows vGPCRs to hijack human proteins and modulate cellular signaling for the benefit of the virus, ultimately resulting in immune evasion and viral dissemination to establish a widespread and lifelong infection. Knowledge on the mechanisms by which herpesviruses reprogram cellular signaling might provide insight in the contribution of vGPCRs to viral survival and herpesvirus-associated pathologies.
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Affiliation(s)
- Sabrina M de Munnik
- Amsterdam Institute for Molecules Medicines and Systems - Division of Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam Netherlands
| | - Martine J Smit
- Amsterdam Institute for Molecules Medicines and Systems - Division of Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam Netherlands
| | - Rob Leurs
- Amsterdam Institute for Molecules Medicines and Systems - Division of Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam Netherlands
| | - Henry F Vischer
- Amsterdam Institute for Molecules Medicines and Systems - Division of Medicinal Chemistry, Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam Netherlands
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Saetear P, Perrin AJ, Bartholdson SJ, Wanaguru M, Kussrow A, Bornhop DJ, Wright GJ. Quantification of Plasmodium-host protein interactions on intact, unmodified erythrocytes by back-scattering interferometry. Malar J 2015; 14:88. [PMID: 25889240 PMCID: PMC4349660 DOI: 10.1186/s12936-015-0553-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/06/2015] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Invasion of host erythrocytes by Plasmodium falciparum is central to the pathogenesis of malaria. Invasion involves recognition events between erythrocyte receptors and ligands on the merozoite, the invasive blood form of the parasite. Identifying and characterizing host-parasite interactions is impeded by the biochemical challenges of working with membrane-embedded glycoprotein receptors. For example, the interaction between P. falciparum erythrocyte binding antigen 175 (PfEBA175) and glycophorin A (GYPA) depends on post-translational modifications that are not easily added in recombinant expression systems, and the use of native GYPA is limited by the hydrophobic transmembrane region, making it difficult to biochemically manipulate. It would, therefore, be desirable to perform quantitative binding assays with receptors embedded within the membranes of intact human erythrocytes. METHODS The extracellular region of GYPA was over-expressed as a soluble protein in HEK293E cells. This protein was characterized, sialylated and evaluated for binding to the PfEBA175 protein. The label-free and free-solution assay, backscattering interferometry (BSI), was used to perform binding assays of two well-characterized P. falciparum invasion ligands to intact unmodified human erythrocytes. RESULTS Findings indicate that the post-translational modifications present on native GYPA are required for it to bind recombinant PfEBA175 and that these modifications cannot be recapitulated in vitro using mammalian overexpression methods. Here, BSI was used to obtain quantitative, high fidelity interaction determinations on intact, unmodified erythrocytes. Using BSI and purified recombinant proteins constituting the entire ectodomains of the P. falciparum merozoite ligands PfEBA175 and PfRH5, K Ds of 1.1 μM and 50 nM were measured for the PfRH5-BSG and PfEBA175-GYPA interactions, respectively, in good agreement with previous biophysical measurements of these interactions. CONCLUSIONS These results demonstrate that BSI can be used to detect and quantify the interactions of two merozoite invasion ligands with their receptors on intact human erythrocytes. BSI assays were performed on unlabelled, free-solution proteins in their native environment, requiring only nanomoles of recombinant protein. This study suggests that BSI can be used to investigate host-parasite protein interactions without the limitations of other assay platforms, and therefore represents a valuable new method to investigate the molecular mechanisms involved in erythrocyte invasion by P. falciparum.
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Affiliation(s)
- Phoonthawee Saetear
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand.
| | - Abigail J Perrin
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
| | - S Josefin Bartholdson
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
| | - Madushi Wanaguru
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
| | - Amanda Kussrow
- Department of Chemistry and the Vanderbilt Institute for Chemical Biology, Vanderbilt University, 4226 Stevenson Center, Nashville, Tennessee, 37235, USA.
| | - Darryl J Bornhop
- Department of Chemistry and the Vanderbilt Institute for Chemical Biology, Vanderbilt University, 4226 Stevenson Center, Nashville, Tennessee, 37235, USA.
| | - Gavin J Wright
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
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Ihara M, Inoue A, Hanamoto S, Zhang H, Aoki J, Tanaka H. Detection of physiological activities of G protein-coupled receptor-acting pharmaceuticals in wastewater. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:1903-1911. [PMID: 25556879 DOI: 10.1021/es505349s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Although pharmaceuticals are generally found at very low levels in aquatic environments, concern about their potential risks to humans and aquatic species has been raised because they are designed to be biologically active. To resolve this concern, we must know whether the biological activity of pharmaceuticals can be detected in waters. Nearly half of all marketed pharmaceuticals act by binding to the G protein-coupled receptors (GPCRs). In this study, we measured the physiological activity of pharmaceuticals in wastewater. We applied the in vitro transforming growth factor-α (TGFα) shedding assay, which accurately and sensitively detect GPCR activation, to investigate the agonistic/antagonistic activities of wastewater extracts against receptors for angiotensin (AT1), dopamine (D2, D4), adrenergic family members (α1B, α2A, β1, β3), acetylcholine (M1, M3), cannabinoid (CB1), vasopressin (V1A, V2), histamine (H1, H2, H3), 5-hydroxytryptamine (5-HT1A, 5-HT2C), prostanoid (EP3), and leukotriene (BLT1). As a result, antagonistic activity against AT1, D2, α1B, β1, M1, M3, H1, and V2 receptors was detected at up to several μg/L for the first time. Agonistic activity against α2A receptor was also detected. The TGFα shedding assay is useful for measuring the physiological activity of GPCR-acting pharmaceuticals in the aquatic environment.
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Affiliation(s)
- Masaru Ihara
- Research Center for Environmental Quality Management, Graduate School of Engineering, Kyoto University , Otsu, Shiga 520-0811, Japan
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Gadhe CG, Balupuri A, Cho SJ. In silico characterization of binding mode of CCR8 inhibitor: homology modeling, docking and membrane based MD simulation study. J Biomol Struct Dyn 2015; 33:2491-510. [PMID: 25617117 DOI: 10.1080/07391102.2014.1002006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Human CC-chemokine receptor 8 (CCR8) is a crucial drug target in asthma that belongs to G-protein-coupled receptor superfamily, which is characterized by seven transmembrane helices. To date, there is no X-ray crystal structure available for CCR8; this hampers active research on the target. Molecular basis of interaction mechanism of antagonist with CCR8 remains unclear. In order to provide binding site information and stable binding mode, we performed modeling, docking and molecular dynamics (MD) simulation of CCR8. Docking study of biaryl-ether-piperidine derivative (13C) was performed inside predefined CCR8 binding site to get the representative conformation of 13C. Further, MD simulations of receptor and complex (13C-CCR8) inside dipalmitoylphosphatidylcholine lipid bilayers were performed to explore the effect of lipids. Results analyses showed that the Gln91, Tyr94, Cys106, Val109, Tyr113, Cys183, Tyr184, Ser185, Lys195, Thr198, Asn199, Met202, Phe254, and Glu286 were conserved in both docking and MD simulations. This indicated possible role of these residues in CCR8 antagonism. However, experimental mutational studies on these identified residues could be effective to confirm their importance in CCR8 antagonism. Furthermore, calculated Coulombic interactions represented the crucial roles of Glu286, Lys195, and Tyr113 in CCR8 antagonism. Important residues identified in this study overlap with the previous non-peptide agonist (LMD-009) binding site. Though, the non-peptide agonist and currently studied inhibitor (13C) share common substructure, but they differ in their effects on CCR8. So, to get more insight into their agonist and antagonist effects, further side-by-side experimental studies on both agonist (LMD-009) and antagonist (13C) are suggested.
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Affiliation(s)
- Changdev G Gadhe
- a Department of Life Sciences, College of BioNano Technology , Gachon University , 1342 Seongnamdaero, Sujeong-gu, Seongnam-si , Gyeonggi-do 461-701 , Republic of Korea
| | - Anand Balupuri
- b Department of Bio-New Drug Development, College of Medicine , Chosun University , Gwangju 501-759 , Republic of Korea
| | - Seung Joo Cho
- b Department of Bio-New Drug Development, College of Medicine , Chosun University , Gwangju 501-759 , Republic of Korea.,c Department of Cellular Molecular Medicine, College of Medicine , Chosun University , Gwangju 501-759 , Republic of Korea
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Rymer JK, Hauser M, Bourdon AK, Campagna SR, Naider F, Becker JM. Novobiocin and peptide analogs of α-factor are positive allosteric modulators of the yeast G protein-coupled receptor Ste2p. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:916-24. [PMID: 25576192 DOI: 10.1016/j.bbamem.2014.12.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 12/23/2014] [Accepted: 12/30/2014] [Indexed: 10/24/2022]
Abstract
G protein-coupled receptors (GPCRs) are the target of many drugs prescribed for human medicine and are therefore the subject of intense study. It has been recognized that compounds called allosteric modulators can regulate GPCR activity by binding to the receptor at sites distinct from, or overlapping with, that occupied by the orthosteric ligand. The purpose of this study was to investigate the nature of the interaction between putative allosteric modulators and Ste2p, a model GPCR expressed in the yeast Saccharomyces cerevisiae that binds the tridecapeptide mating pheromone α-factor. Biological assays demonstrated that an eleven amino acid α-factor analog and the antibiotic novobiocin were positive allosteric modulators of Ste2p. Both compounds enhanced the biological activity of α-factor, but did not compete with α-factor binding to Ste2p. To determine if novobiocin and the 11-mer shared a common allosteric binding site, a biologically-active analog of the 11-mer peptide ([Bio-DOPA]11-mer) was chemically cross-linked to Ste2p in the presence and absence of novobiocin. Immunoblots probing for the Ste2p-[Bio-DOPA]11-mer complex revealed that novobiocin markedly decreased cross-linking of the [Bio-DOPA]11-mer to the receptor, but cross-linking of the α-factor analog [Bio-DOPA]13-mer, which interacts with the orthosteric binding site of the receptor, was minimally altered. This finding suggests that both novobiocin and [Bio-DOPA]11-mer compete for an allosteric binding site on the receptor. These results indicate that Ste2p may provide an excellent model system for studying allostery in a GPCR.
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Affiliation(s)
- Jeffrey K Rymer
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
| | - Melinda Hauser
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States
| | - Allen K Bourdon
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, United States
| | - Shawn R Campagna
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, United States
| | - Fred Naider
- Department of Chemistry and Macromolecular Assemblies Institute, College of Staten Island, CUNY, New York, NY 10314, United States; Graduate School and University Center, CUNY, New York, NY 10314, United States
| | - Jeffrey M Becker
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, United States.
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Nataraja SG, Yu HN, Palmer SS. Discovery and Development of Small Molecule Allosteric Modulators of Glycoprotein Hormone Receptors. Front Endocrinol (Lausanne) 2015; 6:142. [PMID: 26441832 PMCID: PMC4568768 DOI: 10.3389/fendo.2015.00142] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 08/31/2015] [Indexed: 11/30/2022] Open
Abstract
Glycoprotein hormones, follicle-stimulating hormone (FSH), luteinizing hormone (LH), and thyroid-stimulating hormone (TSH) are heterodimeric proteins with a common α-subunit and hormone-specific β-subunit. These hormones are dominant regulators of reproduction and metabolic processes. Receptors for the glycoprotein hormones belong to the family of G protein-coupled receptors. FSH receptor (FSHR) and LH receptor are primarily expressed in somatic cells in ovary and testis to promote egg and sperm production in women and men, respectively. TSH receptor is expressed in thyroid cells and regulates the secretion of T3 and T4. Glycoprotein hormones bind to the large extracellular domain of the receptor and cause a conformational change in the receptor that leads to activation of more than one intracellular signaling pathway. Several small molecules have been described to activate/inhibit glycoprotein hormone receptors through allosteric sites of the receptor. Small molecule allosteric modulators have the potential to be administered orally to patients, thus improving the convenience of treatment. It has been a challenge to develop a small molecule allosteric agonist for glycoprotein hormones that can mimic the agonistic effects of the large natural ligand to activate similar signaling pathways. However, in the past few years, there have been several promising reports describing distinct chemical series with improved potency in preclinical models. In parallel, proposal of new structural model for FSHR and in silico docking studies of small molecule ligands to glycoprotein hormone receptors provide a giant leap on the understanding of the mechanism of action of the natural ligands and new chemical entities on the receptors. This review will focus on the current status of small molecule allosteric modulators of glycoprotein hormone receptors, their effects on common signaling pathways in cells, their utility for clinical application as demonstrated in preclinical models, and use of these molecules as novel tools to dissect the molecular signaling pathways of these receptors.
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Affiliation(s)
- Selvaraj G. Nataraja
- TocopheRx Inc., Burlington, MA, USA
- *Correspondence: Selvaraj G. Nataraja, TocopheRx Inc., 15 New England Executive Park, Suite 1087, Burlington, MA 01803, USA,
| | - Henry N. Yu
- TocopheRx Inc., Burlington, MA, USA
- EMD Serono Research and Development Institute Inc., Billerica, MA, USA
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80
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Martínez-Muñoz L, Barroso R, Paredes AG, Mellado M, Rodríguez-Frade JM. Methods to immobilize GPCR on the surface of SPR sensors. Methods Mol Biol 2015; 1272:173-188. [PMID: 25563184 DOI: 10.1007/978-1-4939-2336-6_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The G protein-coupled receptors (GPCRs) form one of the largest membrane receptor families. The nature of the ligands that interact with these receptors is highly diverse; they include light, peptides and hormones, neurotransmitters, and small molecular weight compounds. The GPCRs are involved in a wide variety of physiological processes and thus hold considerable therapeutic potential.GPCR function is usually determined in cell-based assays, whose complexity nonetheless limits their use. The use of alternative, cell-free assays is hampered by the difficulties in purifying these seven-transmembrane domain receptors without altering their functional properties. Several methods have been proposed to immobilize GPCR on biosensor surfaces which use antibodies or avidin-/biotin-based capture procedures, alone or with reconstitution of the GPCR physiological microenvironment. Here we propose a method for GPCR immobilization in their native membrane microenvironment that requires no manipulation of the target receptor and maintains the many conformations GPCR can adopt in the cell membrane.
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Affiliation(s)
- Laura Martínez-Muñoz
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB/CSIC), Darwin 3, Campus de Cantoblanco, Madrid, 28049, Spain
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81
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Tautermann CS, Seeliger D, Kriegl JM. What can we learn from molecular dynamics simulations for GPCR drug design? Comput Struct Biotechnol J 2014; 13:111-21. [PMID: 25709761 PMCID: PMC4334948 DOI: 10.1016/j.csbj.2014.12.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 11/28/2014] [Accepted: 12/03/2014] [Indexed: 01/05/2023] Open
Abstract
Recent years have seen a tremendous progress in the elucidation of experimental structural information for G-protein coupled receptors (GPCRs). Although for the vast majority of pharmaceutically relevant GPCRs structural information is still accessible only by homology models the steadily increasing amount of structural information fosters the application of structure-based drug design tools for this important class of drug targets. In this article we focus on the application of molecular dynamics (MD) simulations in GPCR drug discovery programs. Typical application scenarios of MD simulations and their scope and limitations will be described on the basis of two selected case studies, namely the binding of small molecule antagonists to the human CC chemokine receptor 3 (CCR3) and a detailed investigation of the interplay between receptor dynamics and solvation for the binding of small molecules to the human muscarinic acetylcholine receptor 3 (hM3R).
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Affiliation(s)
| | | | - Jan M. Kriegl
- Boehringer Ingelheim Pharma GmbH & Co. KG, Lead Identification and Optimization Support, Birkendorfer Str. 65, D-88397 Biberach a.d. Riss, Germany
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82
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Greenberg RM. Ion channels and drug transporters as targets for anthelmintics. CURRENT CLINICAL MICROBIOLOGY REPORTS 2014; 1:51-60. [PMID: 25554739 PMCID: PMC4278637 DOI: 10.1007/s40588-014-0007-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Infections with parasitic helminths such as schistosomes and soil-transmitted nematodes are hugely prevalent and responsible for a major portion of the global health and economic burdens associated with neglected tropical diseases. In addition, many of these parasites infect livestock and plants used in agriculture, resulting in further impoverishment. Treatment and control of these pathogens rely on anthelmintic drugs, which are few in number, and against which drug resistance can develop rapidly. The neuromuscular system of the parasite, and in particular, the ion channels and associated receptors underlying excitation and signaling, have proven to be outstanding targets for anthelmintics. This review will survey the different ion channels found in helminths, focusing on their unique characteristics and pharmacological sensitivities. It will also briefly review the literature on helminth multidrug efflux that may modulate parasite susceptibility to anthelmintics and may prove useful targets for new or repurposed agents that can enhance parasite drug susceptibility and perhaps overcome drug resistance.
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Affiliation(s)
- Robert M Greenberg
- Department of Pathobiology School of Veterinary Medicine University of Pennsylvania 3800 Spruce Street Philadelphia PA 19104 Tel: 215-898-5678
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83
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Doyle JR, Harwood BN, Krishnaji ST, Krishnamurthy VM, Lin WE, Fortin JP, Kumar K, Kopin AS. A two-step strategy to enhance activity of low potency peptides. PLoS One 2014; 9:e110502. [PMID: 25391026 PMCID: PMC4229100 DOI: 10.1371/journal.pone.0110502] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 09/15/2014] [Indexed: 12/25/2022] Open
Abstract
Novel strategies are needed to expedite the generation and optimization of peptide probes targeting G protein-coupled receptors (GPCRs). We have previously shown that membrane tethered ligands (MTLs), recombinant proteins comprised of a membrane anchor, an extracellular linker, and a peptide ligand can be used to identify targeted receptor modulators. Although MTLs provide a useful tool to identify and/or modify functionally active peptides, a major limitation of this strategy is the reliance on recombinant protein expression. We now report the generation and pharmacological characterization of prototype peptide-linker-lipid conjugates, synthetic membrane anchored ligands (SMALs), which are designed as mimics of corresponding MTLs. In this study, we systematically compare the activity of selected peptides as MTLs versus SMALs. As prototypes, we focused on the precursor proteins of mature Substance P (SubP) and Cholecystokinin 4 (CCK4), specifically non-amidated SubP (SubP-COOH) and glycine extended CCK4 (CCK4-Gly-COOH). As low affinity soluble peptides these ligands each presented a challenging test case for assessment of MTL/SMAL technology. For each ligand, MTLs and corresponding SMALs showed agonist activity and comparable subtype selectivity. In addition, our results illustrate that membrane anchoring increases ligand potency. Furthermore, both MTL and SMAL induced signaling can be blocked by specific non-peptide antagonists suggesting that the anchored constructs may be orthosteric agonists. In conclusion, MTLs offer a streamlined approach for identifying low activity peptides which can be readily converted to higher potency SMALs. The ability to recapitulate MTL activity with SMALs extends the utility of anchored peptides as probes of GPCR function.
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Affiliation(s)
- Jamie R. Doyle
- Tufts Medical Center, Molecular Cardiology Research Institute, Molecular Pharmacology Research Center, Boston, Massachusetts, United States of America
| | - Benjamin N. Harwood
- Tufts Medical Center, Molecular Cardiology Research Institute, Molecular Pharmacology Research Center, Boston, Massachusetts, United States of America
- Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
| | | | - Vijay M. Krishnamurthy
- Tufts University, Department of Chemistry, Medford, Massachusetts, United States of America
| | - Wei-En Lin
- Tufts University, Department of Chemistry, Medford, Massachusetts, United States of America
| | - Jean-Philippe Fortin
- Tufts Medical Center, Molecular Cardiology Research Institute, Molecular Pharmacology Research Center, Boston, Massachusetts, United States of America
| | - Krishna Kumar
- Tufts University, Department of Chemistry, Medford, Massachusetts, United States of America
| | - Alan S. Kopin
- Tufts Medical Center, Molecular Cardiology Research Institute, Molecular Pharmacology Research Center, Boston, Massachusetts, United States of America
- Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University, Boston, Massachusetts, United States of America
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84
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Marciano DP, Dharmarajan V, Griffin PR. HDX-MS guided drug discovery: small molecules and biopharmaceuticals. Curr Opin Struct Biol 2014; 28:105-11. [PMID: 25179005 DOI: 10.1016/j.sbi.2014.08.007] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/24/2014] [Accepted: 08/13/2014] [Indexed: 12/24/2022]
Abstract
Hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS or DXMS) has emerged as an important tool for the development of small molecule therapeutics and biopharmaceuticals. Central to these advances have been improvements to automated HDX-MS platforms and software that allow for the rapid acquisition and processing of experimental data. Correlating the HDX-MS profile of large numbers of ligands with their functional outputs has enabled the development of structure activity relationships (SAR) and delineation of ligand classes based on functional selectivity. HDX-MS has also been applied to address many of the unique challenges posed by the continued emergence of biopharmaceuticals. Here we review the latest applications of HDX-MS to drug discovery, recent advances in technology and software, and provide perspective on future outlook.
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Affiliation(s)
- David P Marciano
- Molecular Therapeutics Department, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | | | - Patrick R Griffin
- Molecular Therapeutics Department, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States.
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85
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Wittmann HJ, Seifert R, Strasser A. Sodium binding to hH3R and hH4R — a molecular modeling study. J Mol Model 2014; 20:2394. [DOI: 10.1007/s00894-014-2394-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 07/22/2014] [Indexed: 11/27/2022]
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86
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Highly selective screening of the bioactive compounds in Huoxue capsule using immobilized β2-adrenoceptor affinity chromatography. Anal Biochem 2014; 457:1-7. [DOI: 10.1016/j.ab.2014.04.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/10/2014] [Accepted: 04/11/2014] [Indexed: 11/23/2022]
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87
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Wittmann HJ, Seifert R, Strasser A. Mathematical analysis of the sodium sensitivity of the human histamine H3 receptor. In Silico Pharmacol 2014; 2:1. [PMID: 27502620 PMCID: PMC4644138 DOI: 10.1186/s40203-014-0001-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 04/28/2014] [Indexed: 11/22/2022] Open
Abstract
Purpose It was shown by several experimental studies that some G protein coupled receptors (GPCR) are sensitive to sodium ions. Furthermore, mutagenesis studies or the determination of crystal structures of the adenosine A2A or δ-opioid receptor revealed an allosteric Na+ binding pocket near to the highly conserved Asp2.50. Within a previous study, the influence of NaCl concentration onto the steady-state GTPase activity at the human histamine H3 receptor (hH3R) in presence of the endogenous histamine or the inverse agonist thioperamide was analyzed. The purpose of the present study was to examine and quantify the Na+-sensitivity of hH3R on a molecular level. Methods To achieve this, we developed a set of equations, describing constitutive activity and the different ligand-receptor equilibria in absence or presence of sodium ions. Furthermore, in order to gain a better understanding of the ligand- and Na+-binding to hH3R on molecular level, we performed molecular dynamic (MD) simulations. Results The analysis of the previously determined experimental steady-state GTPase data with the set of equations presented within this study, reveals that thioperamide binds into the orthosteric binding pocket of the hH3R in absence or presence of a Na+ in its allosteric binding site. However, the data suggest that thioperamide binds preferentially into the hH3R in absence of a sodium ion in its allosteric site. These experimental results were supported by MD simulations of thioperamide in the binding pocket of the inactive hH3R. Furthermore, the MD simulations revealed two different binding modes for thioperamide in presence or absence of a Na+ in its allosteric site. Conclusion The mathematical model presented within this study describes the experimental data regarding the Na+-sensitivity of hH3R in an excellent manner. Although the present study is focused onto the Na+-sensitivity of the hH3R, the resulting equations, describing Na+- and ligand-binding to a GPCR, can be used for all other ion-sensitive GPCRs.
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Affiliation(s)
- Hans-Joachim Wittmann
- Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, Regensburg, 93040, Germany
| | - Roland Seifert
- Institute of Pharmacology, Medical School of Hannover, Carl-Neuberg-Straße 1, Hannover, 30625, Germany
| | - Andrea Strasser
- Department of Pharmaceutical and Medicinal Chemistry II, Faculty of Chemistry and Pharmacy, University of Regensburg, Universitätsstraße 31, Regensburg, 93040, Germany.
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88
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Bioinformatics tools for predicting GPCR gene functions. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:205-24. [PMID: 24158807 DOI: 10.1007/978-94-007-7423-0_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Abstract
The automatic classification of GPCRs by bioinformatics methodology can provide functional information for new GPCRs in the whole 'GPCR proteome' and this information is important for the development of novel drugs. Since GPCR proteome is classified hierarchically, general ways for GPCR function prediction are based on hierarchical classification. Various computational tools have been developed to predict GPCR functions; those tools use not simple sequence searches but more powerful methods, such as alignment-free methods, statistical model methods, and machine learning methods used in protein sequence analysis, based on learning datasets. The first stage of hierarchical function prediction involves the discrimination of GPCRs from non-GPCRs and the second stage involves the classification of the predicted GPCR candidates into family, subfamily, and sub-subfamily levels. Then, further classification is performed according to their protein-protein interaction type: binding G-protein type, oligomerized partner type, etc. Those methods have achieved predictive accuracies of around 90 %. Finally, I described the future subject of research of the bioinformatics technique about functional prediction of GPCR.
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89
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Discovery of new lead pyrimidines derivatives as potential cannabinoid CB1 receptor antagonistic through molecular modeling and pharmacophore approach. Med Chem Res 2014. [DOI: 10.1007/s00044-013-0808-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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90
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Jaeger WC, Armstrong SP, Hill SJ, Pfleger KDG. Biophysical Detection of Diversity and Bias in GPCR Function. Front Endocrinol (Lausanne) 2014; 5:26. [PMID: 24634666 PMCID: PMC3943086 DOI: 10.3389/fendo.2014.00026] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 02/19/2014] [Indexed: 12/27/2022] Open
Abstract
Guanine nucleotide binding protein (G protein)-coupled receptors (GPCRs) function in complexes with a range of molecules and proteins including ligands, G proteins, arrestins, ubiquitin, and other receptors. Elements of these complexes may interact constitutively or dynamically, dependent upon factors such as ligand binding, phosphorylation, and dephosphorylation. They may also be allosterically modulated by other proteins in a manner that changes temporally and spatially within the cell. Elucidating how these complexes function has been greatly enhanced by biophysical technologies that are able to monitor proximity and/or binding, often in real time and in live cells. These include resonance energy transfer approaches such as bioluminescence resonance energy transfer (BRET) and fluorescence resonance energy transfer (FRET). Furthermore, the use of fluorescent ligands has enabled novel insights into allosteric interactions between GPCRs. Consequently, biophysical approaches are helping to unlock the amazing diversity and bias in G protein-coupled receptor signaling.
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Affiliation(s)
- Werner C. Jaeger
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
| | - Stephen P. Armstrong
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
| | - Stephen J. Hill
- Cell Signalling Research Group, School of Life Sciences, Queen’s Medical Centre, University of Nottingham Medical School, Nottingham, UK
| | - Kevin D. G. Pfleger
- Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, Perth, WA, Australia
- Dimerix Bioscience Pty Ltd, Perth, WA, Australia
- *Correspondence: Kevin D. G. Pfleger, Molecular Endocrinology and Pharmacology, Harry Perkins Institute of Medical Research and Centre for Medical Research, The University of Western Australia, QEII Medical Centre, QQ Block, 6 Verdun Street, Nedlands, Perth, WA 6009, Australia e-mail:
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91
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Blanchetot C, Verzijl D, Mujić-Delić A, Bosch L, Rem L, Leurs R, Verrips CT, Saunders M, de Haard H, Smit MJ. Neutralizing nanobodies targeting diverse chemokines effectively inhibit chemokine function. J Biol Chem 2013; 288:25173-25182. [PMID: 23836909 PMCID: PMC3757181 DOI: 10.1074/jbc.m113.467969] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 06/29/2013] [Indexed: 12/19/2022] Open
Abstract
Chemokine receptors and their ligands play a prominent role in immune regulation but many have also been implicated in inflammatory diseases such as multiple sclerosis, rheumatoid arthritis, allograft rejection after transplantation, and also in cancer metastasis. Most approaches to therapeutically target the chemokine system involve targeting of chemokine receptors with low molecular weight antagonists. Here we describe the selection and characterization of an unprecedented large and diverse panel of neutralizing Nanobodies (single domain camelid antibodies fragment) directed against several chemokines. We show that the Nanobodies directed against CCL2 (MCP-1), CCL5 (RANTES), CXCL11 (I-TAC), and CXCL12 (SDF-1α) bind the chemokines with high affinity (at nanomolar concentration), thereby blocking receptor binding, inhibiting chemokine-induced receptor activation as well as chemotaxis. Together, we show that neutralizing Nanobodies can be selected efficiently for effective and specific therapeutic treatment against a wide range of immune and inflammatory diseases.
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Affiliation(s)
- Christophe Blanchetot
- From the Departments of Cellular Biology and Biology, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Dennis Verzijl
- the Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands, and
| | - Azra Mujić-Delić
- the Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands, and
| | - Leontien Bosch
- the Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands, and
| | - Louise Rem
- From the Departments of Cellular Biology and Biology, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | - Rob Leurs
- the Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands, and
| | - C Theo Verrips
- From the Departments of Cellular Biology and Biology, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands
| | | | - Hans de Haard
- From the Departments of Cellular Biology and Biology, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands,; Ablynx N.V., Technologiepark 21, 9052 Ghent, Belgium.
| | - Martine J Smit
- the Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands, and.
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92
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Evidence for a bacterial lipopolysaccharide-recognizing G-protein-coupled receptor in the bacterial engulfment by Entamoeba histolytica. EUKARYOTIC CELL 2013; 12:1433-8. [PMID: 23975887 DOI: 10.1128/ec.00150-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Entamoeba histolytica is the causative agent of amoebic dysentery, a worldwide protozoal disease that results in approximately 100,000 deaths annually. The virulence of E. histolytica may be due to interactions with the host bacterial flora, whereby trophozoites engulf colonic bacteria as a nutrient source. The engulfment process depends on trophozoite recognition of bacterial epitopes that activate phagocytosis pathways. E. histolytica GPCR-1 (EhGPCR-1) was previously recognized as a putative G-protein-coupled receptor (GPCR) used by Entamoeba histolytica during phagocytosis. In the present study, we attempted to characterize EhGPCR-1 by using heterologous GPCR expression in Saccharomyces cerevisiae. We discovered that bacterial lipopolysaccharide (LPS) is an activator of EhGPCR-1 and that LPS stimulates EhGPCR-1 in a concentration-dependent manner. Additionally, we demonstrated that Entamoeba histolytica prefers to engulf bacteria with intact LPS and that this engulfment process is sensitive to suramin, which prevents the interactions of GPCRs and G-proteins. Thus, EhGPCR-1 is an LPS-recognizing GPCR that is a potential drug target for treatment of amoebiasis, especially considering the well-established drug targeting to GPCRs.
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93
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Abstract
G-protein–coupled receptors (GPCRs) still offer enormous scope for new therapeutic targets. Currently marketed agents are dominated by those with activity at aminergic receptors and yet they account for only ~10% of the family. Progress up until now with other subfamilies, notably orphans, Family A/peptide, Family A/lipid, Family B, Family C, and Family F, has been, at best, patchy. This may be attributable to the heterogeneous nature of GPCRs, their endogenous ligands, and consequently their binding sites. Our appreciation of receptor similarity has arguably been too simplistic, and screening collections have not necessarily been well suited to identifying leads in new areas. Despite the relative shortage of high-quality tool molecules in a number of cases, there is an emerging, and increasingly substantial, body of evidence associating many as yet “undrugged” receptors with a very wide range of diseases. Significant advances in our understanding of receptor pharmacology and technical advances in screening, protein X-ray crystallography, and ligand design methods are paving the way for new successes in the area. Exploitation of allosteric mechanisms; alternative signaling pathways such as G12/13, Gβγ, and β-arrestin; the discovery of “biased” ligands; and the emergence of GPCR-protein complexes as potential drug targets offer scope for new and much improved drugs.
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94
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The importance of interactions with helix 5 in determining the efficacy of β-adrenoceptor ligands. Biochem Soc Trans 2013; 41:159-65. [PMID: 23356277 DOI: 10.1042/bst20120228] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Structures of the inactive state of the thermostabilized β1-adrenoceptor have been determined bound to eight different ligands, including full agonists, partial agonists, inverse agonists and biased agonists. Comparison of the structures shows distinct differences within the binding pocket that correlate with the pharmacological properties of the ligands. These data suggest that full agonists stabilize a structure with a contracted binding pocket and a rotamer change of serine (5.46) compared with when antagonists are bound. Inverse agonists may prevent both of these occurrences, whereas partial agonists stabilize a contraction of the binding pocket but not the rotamer change of serine (5.46). It is likely that subtle changes in the interactions between transmembrane helix 5 (H5) and H3/H4 on agonist binding promote the formation of the activated state.
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95
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Patra MC, Maharana J, Pradhan SK, Rath SN. Molecular dynamics simulation of neuropeptide B and neuropeptide W in the dipalmitoylphosphatidylcholine membrane bilayer. J Biomol Struct Dyn 2013; 32:1118-31. [DOI: 10.1080/07391102.2013.811699] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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96
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Nowling RJ, Abrudan JL, Shoue DA, Abdul-Wahid B, Wadsworth M, Stayback G, Collins FH, McDowell MA, Izaguirre JA. Identification of novel arthropod vector G protein-coupled receptors. Parasit Vectors 2013; 6:150. [PMID: 23705687 PMCID: PMC3680159 DOI: 10.1186/1756-3305-6-150] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 05/18/2013] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The control of vector-borne diseases, such as malaria, dengue fever, and typhus fever is often achieved with the use of insecticides. Unfortunately, insecticide resistance is becoming common among different vector species. There are currently no chemical alternatives to these insecticides because new human-safe classes of molecules have yet to be brought to the vector-control market. The identification of novel targets offer opportunities for rational design of new chemistries to control vector populations. One target family, G protein-coupled receptors (GPCRs), has remained relatively under explored in terms of insecticide development. METHODS A novel classifier, Ensemble*, for vector GPCRs was developed. Ensemble* was validated and compared to existing classifiers using a set of all known GPCRs from Aedes aegypti, Anopheles gambiae, Apis Mellifera, Drosophila melanogaster, Homo sapiens, and Pediculus humanus. Predictions for unidentified sequences from Ae. aegypti, An. gambiae, and Pe. humanus were validated. Quantitative RT-PCR expression analysis was performed on previously-known and newly discovered Ae. aegypti GPCR genes. RESULTS We present a new analysis of GPCRs in the genomes of Ae, aegypti, a vector of dengue fever, An. gambiae, a primary vector of Plasmodium falciparum that causes malaria, and Pe. humanus, a vector of epidemic typhus fever, using a novel GPCR classifier, Ensemble*, designed for insect vector species. We identified 30 additional putative GPCRs, 19 of which we validated. Expression of the newly discovered Ae. aegypti GPCR genes was confirmed via quantitative RT-PCR. CONCLUSION A novel GPCR classifier for insect vectors, Ensemble*, was developed and GPCR predictions were validated. Ensemble* and the validation pipeline were applied to the genomes of three insect vectors (Ae. aegypti, An. gambiae, and Pe. humanus), resulting in the identification of 52 GPCRs not previously identified, of which 11 are predicted GPCRs, and 19 are predicted and confirmed GPCRs.
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Affiliation(s)
- Ronald J Nowling
- Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Jenica L Abrudan
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46656, USA
- Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Douglas A Shoue
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46656, USA
- Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Badi’ Abdul-Wahid
- Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Mariha Wadsworth
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46656, USA
- Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Gwen Stayback
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46656, USA
- Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Frank H Collins
- Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN, 46656, USA
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46656, USA
- Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Mary Ann McDowell
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, 46656, USA
- Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN, 46656, USA
| | - Jesús A Izaguirre
- Department of Computer Science & Engineering, University of Notre Dame, Notre Dame, IN, 46656, USA
- Eck Institute of Global Health, University of Notre Dame, Notre Dame, IN, 46656, USA
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Hagiwara Y, Ohno K, Kamohara M, Takasaki J, Watanabe T, Fukunishi Y, Nakamura H, Orita M. Molecular modeling of vasopressin receptor and in silico screening of V1b receptor antagonists. Expert Opin Drug Discov 2013; 8:951-64. [PMID: 23682717 DOI: 10.1517/17460441.2013.799134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION G protein-coupled receptors (GPCRs) are integral membrane proteins which contain seven-transmembrane-spanning alpha-helices. GPCR-mediated signaling has been associated with various human diseases, positioning GPCRs as attractive targets in the drug discovery field. Recently, through advances in protein engineering and crystallography, the number of resolved GPCR structures has increased dramatically. This growing availability of GPCR structures has greatly accelerated structure-based drug design (SBDD) and in silico screening for GPCR-targeted drug discovery. AREAS COVERED The authors introduce the current status of X-ray crystallography of GPCRs and what has been revealed from the resolved crystal structures. They also review the recent advances in SBDD and in silico screening for GPCR-targeted drug discovery and discuss a docking study, using homology modeling, with the discovery of potent antagonists of the vasopressin 1b receptor. EXPERT OPINION Several innovative protein engineering techniques and crystallographic methods have greatly accelerated SBDD, not only for already-resolved GPCRs but also for those structures which remain unclear. These technological advances are expected to enable the determination of GPCR-fragment complexes, making it practical to perform fragment-based drug discovery. This paves the way for a new era of GPCR-targeted drug discovery.
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Affiliation(s)
- Yohsuke Hagiwara
- Drug Discovery Research, Astellas Pharma, Inc., 21, Miyukigaoka, Ibaraki 305-8585, Japan.
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Sonawani A, Niazi S, Idicula-Thomas S. In silico study on binding specificity of gonadotropins and their receptors: design of a novel and selective peptidomimetic for human follicle stimulating hormone receptor. PLoS One 2013; 8:e64475. [PMID: 23700481 PMCID: PMC3659097 DOI: 10.1371/journal.pone.0064475] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 04/15/2013] [Indexed: 01/13/2023] Open
Abstract
Gonadotropins bind to specific receptors in spite of sharing a high level of sequence and structural similarity. This specific binding is crucial for maintaining the reproductive health of an organism. In this study, residues that dictate the receptor binding specificity of the gonadotropins (FSH and LH) have been identified using combination of in silico methods. Docking studies (ZDOCK), based on the systematic replacement of these residues, confirmed its importance in receptor binding. An interesting observation is that the relative positioning of the residues conferring binding specificity varied for the gonadotropin-receptor complexes. This spatial difference of the key residues could be exploited for design of specific modulators. Based on the identified residues, we have rationally designed a peptidomimetic (FSHP) that displays good binding affinity and specificity for hFSHR. FSHP was developed by screening 3.9 million compounds using pharmacophore-shape similarity followed by fragment-based approach. It was observed that FSHP and hFSHâ can share the same receptor binding site thereby mimicking the native hFSHR-FSH interactions. FSHP also displayed higher binding affinity to hFSHR as compared to two reported hFSHR antagonists. MD simulation studies on hFSHR-FSHP complex revealed that FSHP is conformationally rigid and the intermolecular interactions are maintained during the course of simulation.
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Affiliation(s)
- Archana Sonawani
- Biomedical Informatics Center of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai, India
| | - Sarfaraj Niazi
- Biomedical Informatics Center of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai, India
| | - Susan Idicula-Thomas
- Biomedical Informatics Center of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai, India
- * E-mail:
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Sheth H, Gorey C, Roush N, Smallman S, Collantes E, Santoro M, Olson B, Fitzgerald L, Lee PH, Shen XJ. A Multiplexed Fluorescent Calcium and NFAT Reporter Gene Assay to Identify GPCR Agonists. Curr Chem Genom Transl Med 2013; 7:1-8. [PMID: 24396729 PMCID: PMC3854663 DOI: 10.2174/2213988501307010001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 12/20/2012] [Accepted: 12/31/2012] [Indexed: 11/30/2022] Open
Abstract
Intracellular calcium response and resulting calcium signaling to an agonist-GPCR interaction are important for the measurement of compound activity in the GPCR drug development. The increase in cytosol calcium concentration can be measured by the fluorescent calcium indicator dye such as Fluo-4 in a quick assay (in 3-5 minutes) using the fluorescence imaging plate reader. The calcium signaling through the transcription factors such as NFAT that induces gene expression can be measured by the reporter gene assay that links to the expression of reporter enzyme such as the beta-lactamase that requires 5-hour incubation. We have evaluated a multiplexed assay that sequentially measures the calcium response to a GPCR agonist in a rapid fluorescent calcium dye assay, followed by a NFAT beta-lactamase assay, and compared them in the single assay format. We found that the agonist activity determined in the multiplexed assay were comparable with these determined in the single assay format and the Z’ factors were all >0.5. Five active compounds were identified that were active in both calcium dye assay and beta-lactamase assay. Therefore, our results demonstrated the utility of this multiplexed calcium assay for screening of GPCR compounds that can cross validate the primary hits and help to eliminate the false positive compounds.
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Affiliation(s)
- Heeral Sheth
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Colleen Gorey
- Department of Chemical and Environmental Engineering, University of Toledo, Toledo OH 43606, USA
| | - Nicole Roush
- Pfizer Global Research and Development, Groton Laboratories, Groton, CT 06340, USA
| | - Shelly Smallman
- Pfizer Global Research and Development, Groton Laboratories, Groton, CT 06340, USA
| | - Elizabeth Collantes
- Pfizer Global Research and Development, Groton Laboratories, Groton, CT 06340, USA
| | - Maxine Santoro
- Pfizer Global Research and Development, Groton Laboratories, Groton, CT 06340, USA
| | - Barbara Olson
- Pfizer Global Research and Development, Groton Laboratories, Groton, CT 06340, USA
| | - Laura Fitzgerald
- Pfizer Global Research and Development, Groton Laboratories, Groton, CT 06340, USA
| | - Paul H Lee
- Amgen, Inc., Lead Discovery, Thousand Oaks, CA 91320, USA
| | - Xiqiang John Shen
- Pfizer Global Research and Development, Groton Laboratories, Groton, CT 06340, USA
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Gao J, Huang Q, Wu D, Zhang Q, Zhang Y, Chen T, Liu Q, Zhu R, Cao Z, He Y. Study on human GPCR–inhibitor interactions by proteochemometric modeling. Gene 2013; 518:124-31. [DOI: 10.1016/j.gene.2012.11.061] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 11/27/2012] [Indexed: 11/15/2022]
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