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Abdul-Ridha A, López L, Keov P, Thal DM, Mistry SN, Sexton PM, Lane JR, Canals M, Christopoulos A. Molecular determinants of allosteric modulation at the M1 muscarinic acetylcholine receptor. J Biol Chem 2014; 289:6067-79. [PMID: 24443568 DOI: 10.1074/jbc.m113.539080] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Benzylquinolone carboxylic acid (BQCA) is an unprecedented example of a selective positive allosteric modulator of acetylcholine at the M1 muscarinic acetylcholine receptor (mAChR). To probe the structural basis underlying its selectivity, we utilized site-directed mutagenesis, analytical modeling, and molecular dynamics to delineate regions of the M1 mAChR that govern modulator binding and transmission of cooperativity. We identified Tyr-85(2.64) in transmembrane domain 2 (TMII), Tyr-179 and Phe-182 in the second extracellular loop (ECL2), and Glu-397(7.32) and Trp-400(7.35) in TMVII as residues that contribute to the BQCA binding pocket at the M1 mAChR, as well as to the transmission of cooperativity with the orthosteric agonist carbachol. As such, the BQCA binding pocket partially overlaps with the previously described "common" allosteric site in the extracellular vestibule of the M1 mAChR, suggesting that its high subtype selectivity derives from either additional contacts outside this region or through a subtype-specific cooperativity mechanism. Mutation of amino acid residues that form the orthosteric binding pocket caused a loss of carbachol response that could be rescued by BQCA. Two of these residues (Leu-102(3.29) and Asp-105(3.32)) were also identified as indirect contributors to the binding affinity of the modulator. This new insight into the structural basis of binding and function of BQCA can guide the design of new allosteric ligands with tailored pharmacological properties.
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202
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From Three-Dimensional GPCR Structure to Rational Ligand Discovery. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:129-57. [DOI: 10.1007/978-94-007-7423-0_7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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203
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Abstract
Structural genomics efforts focused on the human proteome have had three aims: to understand the structural and functional variations within protein families; to understand the structural basis of disease and genetic variation; and to determine the structures of human integral membrane proteins. The overarching theme is to advance the understanding of human health and to provide a structural platform to aid in the development of therapeutics. A decade or more of work in this field has identified optimal experimental strategies that can be used to expedite expression and crystallization of human proteins-and we provide some guidance to this end.
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Affiliation(s)
- Khan Tanjid Osman
- Structural Genomics Consortium, University of Toronto, 101 College Street, MaRS South Tower, Suite 706, Toronto, ON, Canada, M5G 1L7
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204
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Thomas T, McLean KC, McRobb FM, Manallack DT, Chalmers DK, Yuriev E. Homology modeling of human muscarinic acetylcholine receptors. J Chem Inf Model 2013; 54:243-53. [PMID: 24328076 DOI: 10.1021/ci400502u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We have developed homology models of the acetylcholine muscarinic receptors M₁R-M₅R, based on the β₂-adrenergic receptor crystal as the template. This is the first report of homology modeling of all five subtypes of acetylcholine muscarinic receptors with binding sites optimized for ligand binding. The models were evaluated for their ability to discriminate between muscarinic antagonists and decoy compounds using virtual screening using enrichment factors, area under the ROC curve (AUC), and an early enrichment measure, LogAUC. The models produce rational binding modes of docked ligands as well as good enrichment capacity when tested against property-matched decoy libraries, which demonstrates their unbiased predictive ability. To test the relative effects of homology model template selection and the binding site optimization procedure, we generated and evaluated a naïve M₂R model, using the M₃R crystal structure as a template. Our results confirm previous findings that binding site optimization using ligand(s) active at a particular receptor, i.e. including functional knowledge into the model building process, has a more pronounced effect on model quality than target-template sequence similarity. The optimized M₁R-M₅R homology models are made available as part of the Supporting Information to allow researchers to use these structures, compare them to their own results, and thus advance the development of better modeling approaches.
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Affiliation(s)
- Trayder Thomas
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) , 381 Royal Parade, Parkville, VIC 3052 Australia
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205
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Costanzi S. G protein-coupled receptors: computer-aided ligand discovery and computational structural analyses in the 2010s. In Silico Pharmacol 2013; 1:20. [PMID: 25505664 PMCID: PMC4215811 DOI: 10.1186/2193-9616-1-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 12/07/2013] [Indexed: 01/02/2023] Open
Abstract
G protein-coupled receptors, or GPCRs, are a large superfamily of proteins found on the plasma membrane of cells. They are involved in most physiological and pathophysiological functions and constitute the target of the majority of marketed drugs. Although these receptors have been historically elusive to attempts of structural determination, GPCR crystallography is now in full blossom, opening the way to structure-based drug discovery and enabling homology modeling. This thematic issue of the journal In Silico Pharmacology, which illustrates how the expanding body of structural knowledge is fostering complex computational analyses of the structure-function relationships of the receptors and their interactions with their ligands, stems from the 31st Camerino-Cyprus-Noordwijkerhout Symposium held in Italy, in May 2013, at the University of Camerino. Specifically, it originates from a session of the symposium entitled “Structure-Based Discovery of Ligands of G Protein-Coupled Receptors: Finally a Reality”, and features a mix of research articles and reviews on the application of computational modeling to the analysis of the structure of GPCRs and the interactions of the receptors with their ligands.
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Affiliation(s)
- Stefano Costanzi
- Department of Chemistry and Center for Behavioral Neuroscience, American University, 4400 Massachusetts Ave, NW, 20016 Washington, DC USA
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206
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Sheftel S, Muratore KE, Black M, Costanzi S. Graph analysis of β2 adrenergic receptor structures: a "social network" of GPCR residues. In Silico Pharmacol 2013; 1:16. [PMID: 25505660 PMCID: PMC4230308 DOI: 10.1186/2193-9616-1-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 11/25/2013] [Indexed: 02/07/2023] Open
Abstract
Purpose G protein-coupled receptors (GPCRs) are a superfamily of membrane proteins of vast pharmaceutical interest. Here, we describe a graph theory-based analysis of the structure of the β2 adrenergic receptor (β2 AR), a prototypical GPCR. In particular, we illustrate the network of direct and indirect interactions that link each amino acid residue to any other residue of the receptor. Methods Networks of interconnected amino acid residues in proteins are analogous to social networks of interconnected people. Hence, they can be studied through the same analysis tools typically employed to analyze social networks – or networks in general – to reveal patterns of connectivity, influential members, and dynamicity. We focused on the analysis of closeness-centrality, which is a measure of the overall connectivity distance of the member of a network to all other members. Results The residues endowed with the highest closeness-centrality are located in the middle of the seven transmembrane domains (TMs). In particular, they are mostly located in the middle of TM2, TM3, TM6 or TM7, while fewer of them are located in the middle of TM1, TM4 or TM5. At the cytosolic end of TM6, the centrality detected for the active structure is markedly lower than that detected for the corresponding residues in the inactive structures. Moreover, several residues acquire centrality when the structures are analyzed in the presence of ligands. Strikingly, there is little overlap between the residues that acquire centrality in the presence of the ligand in the blocker-bound structures and the agonist-bound structures. Conclusions Our results reflect the fact that the receptor resembles a bow tie, with a rather tight knot of closely interconnected residues and two ends that fan out in two opposite directions: one toward the extracellular space, which hosts the ligand binding cavity, and one toward the cytosol, which hosts the G protein binding cavity. Moreover, they underscore how interaction network is by the conformational rearrangements concomitant with the activation of the receptor and by the presence of agonists or blockers. Electronic supplementary material The online version of this article (doi:10.1186/2193-9616-1-16) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Samuel Sheftel
- Department of Chemistry, American University, 4400 Massachusetts Ave, Northwest, Washington, DC 20016 USA
| | - Kathryn E Muratore
- Department of Chemistry, American University, 4400 Massachusetts Ave, Northwest, Washington, DC 20016 USA
| | - Michael Black
- Department of Computer Science, American University, Northwest, Washington, DC 20016 USA
| | - Stefano Costanzi
- Department of Chemistry, American University, 4400 Massachusetts Ave, Northwest, Washington, DC 20016 USA ; Center for Behavioral Neuroscience, American University, Northwest, Washington, DC 20016 USA
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207
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Abstract
Class B G-protein-coupled receptors are exciting drug targets, yet the structure of a complete receptor bound to a peptide agonist has remained elusive. Coin et al. present a model of the receptor CRF1R bound to its native ligand based on partial structures and 44 spatial constraints revealed by new crosslinking approaches.
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208
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Soriano-Ursúa MA, Trujillo-Ferrara JG, Correa-Basurto J, Vilar S. Recent structural advances of β1 and β2 adrenoceptors yield keys for ligand recognition and drug design. J Med Chem 2013; 56:8207-23. [PMID: 23862978 DOI: 10.1021/jm400471z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Because they represent attractive drug targets, adrenoceptors have been widely studied. Recent progress in structural data of β-adrenoceptors allows us to understand and predict key interactions in ligand recognition and receptor activation. Nevertheless, an important aspect of this process has only begun to be explored: the stabilization of a conformational state of these receptors upon contact with a ligand and the capacity of a ligand to influence receptor conformation through allosteric modulation, biased signaling, and selectivity. The aim of the present Perspective is to identify the well-defined orthosteric binding site and possible allosteric sites and to analyze the importance of the ligand-receptor interaction in the stabilization of certain receptor conformations. For this purpose, we have reviewed recent advances made through the use of X-ray data from ligand-β-adrenoceptor (including ADRB1 and ADRB2) crystal structures. Most importantly, implications in the medicinal chemistry field are explored in relation to drug design.
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Affiliation(s)
- Marvin A Soriano-Ursúa
- Departments of Biochemistry and Physiology, Laboratory of Molecular Modeling and Bioinformatics, Postgraduate Research Section, Escuela Superior de Medicina, Instituto Politécnico Nacional , Plan de San Luis y Dı́az Mirón s/n, Mexico City, 11340, Mexico
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209
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Shonberg J, Herenbrink CK, López L, Christopoulos A, Scammells PJ, Capuano B, Lane JR. A structure-activity analysis of biased agonism at the dopamine D2 receptor. J Med Chem 2013; 56:9199-221. [PMID: 24138311 DOI: 10.1021/jm401318w] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Biased agonism offers an opportunity for the medicinal chemist to discover pathway-selective ligands for GPCRs. A number of studies have suggested that biased agonism at the dopamine D2 receptor (D2R) may be advantageous for the treatment of neuropsychiatric disorders, including schizophrenia. As such, it is of great importance to gain insight into the SAR of biased agonism at this receptor. We have generated SAR based on a novel D2R partial agonist, tert-butyl (trans-4-(2-(3,4-dihydroisoquinolin-2(1H)-yl)ethyl)cyclohexyl)carbamate (4). This ligand shares structural similarity to cariprazine (2), a drug awaiting FDA approval for the treatment of schizophrenia, yet displays a distinct bias toward two different signaling end points. We synthesized a number of derivatives of 4 with subtle structural modifications, including incorporation of cariprazine fragments. By combining pharmacological profiling with analytical methodology to identify and to quantify bias, we have demonstrated that efficacy and biased agonism can be finely tuned by minor structural modifications to the head group containing the tertiary amine, a tail group that extends away from this moiety, and the orientation and length of a spacer region between these two moieties.
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Affiliation(s)
- Jeremy Shonberg
- Medicinal Chemistry, ‡Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus) , 381 Royal Parade, Parkville, Victoria 3052, Australia
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210
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Reassessment of the unique mode of binding between angiotensin II type 1 receptor and their blockers. PLoS One 2013; 8:e79914. [PMID: 24260317 PMCID: PMC3832659 DOI: 10.1371/journal.pone.0079914] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 09/25/2013] [Indexed: 11/30/2022] Open
Abstract
While the molecular structures of angiotensin II (Ang II) type 1 (AT1) receptor blockers (ARBs) are very similar, they are also slightly different. Although each ARB has been shown to exhibit a unique mode of binding to AT1 receptor, different positions of the AT1 receptor have been analyzed and computational modeling has been performed using different crystal structures for the receptor as a template and different kinds of software. Therefore, we systematically analyzed the critical positions of the AT1 receptor, Tyr113, Tyr184, Lys199, His256 and Gln257 using a mutagenesis study, and subsequently performed computational modeling of the binding of ARBs to AT1 receptor using CXCR4 receptor as a new template and a single version of software. The interactions between Tyr113 in the AT1 receptor and the hydroxyl group of olmesartan, between Lys199 and carboxyl or tetrazole groups, and between His256 or Gln257 and the tetrazole group were studied. The common structure, a tetrazole group, of most ARBs similarly bind to Lys199, His256 and Gln257 of AT1 receptor. Lys199 in the AT1 receptor binds to the carboxyl group of EXP3174, candesartan and azilsartan, whereas oxygen in the amidecarbonyl group of valsartan may bind to Lys199. The benzimidazole portion of telmisartan may bind to a lipophilic pocket that includes Tyr113. On the other hand, the n-butyl group of irbesartan may bind to Tyr113. In conclusion, we confirmed that the slightly different structures of ARBs may be critical for binding to AT1 receptor and for the formation of unique modes of binding.
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211
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The complexity of G-protein coupled receptor-ligand interactions. Sci China Chem 2013. [DOI: 10.1007/s11426-013-4911-z] [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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212
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Martínez-Archundia M, Correa-Basurto J. Molecular dynamics simulations reveal initial structural and dynamic features for the A2AR as a result of ligand binding. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.835485] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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213
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Fluorine-19 NMR of integral membrane proteins illustrated with studies of GPCRs. Curr Opin Struct Biol 2013; 23:740-747. [PMID: 23932201 DOI: 10.1016/j.sbi.2013.07.011] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 07/02/2013] [Indexed: 01/26/2023]
Abstract
Fluorine-19 is a spin-½ NMR isotope with high sensitivity and large chemical shift dispersion, which makes it attractive for high resolution NMR spectroscopy in solution. For studies of membrane proteins it is further of interest that (19)F is rarely found in biological materials, which enables observation of extrinsic (19)F labels with minimal interference from background signals. Today, after a period with rather limited use of (19)F NMR in structural biology, we witness renewed interest in this technology for studies of complex supramolecular systems. Here we report on recent (19)F NMR studies with the G protein-coupled receptor family of membrane proteins.
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214
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Gater DL, Réat V, Czaplicki G, Saurel O, Jolibois F, Cherezov V, Milon A. Hydrogen bonding of cholesterol in the lipidic cubic phase. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:8031-8038. [PMID: 23763339 PMCID: PMC3758441 DOI: 10.1021/la401351w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The addition of cholesterol to the monoolein-based lipidic cubic phase (LCP) has been instrumental in obtaining high-resolution crystal structures of several G protein-coupled receptors. Here, we report the use of high-resolution magic angle spinning NMR spectroscopy to record and assign the isotropic (13)C chemical shifts of cholesterol in lipidic lamellar and cubic phases at different hydration levels with monoolein and chain-deuterated DMPC as host lipids. The hydrogen-bonding patterns of cholesterol in these phases were determined from the NMR data by quantum chemical calculations. The results are consistent with the normal orientation of cholesterol in lipid bilayers and with the cholesterol hydroxyl group located at the hydrophobic/hydrophilic interface. The (13)C chemical shifts of cholesterol are mostly affected by the host lipid identity with little or no dependency on the hydration (20% vs 40%) or the phase identity (lamellar vs LCP). In chain-deuterated DMPC bilayers, the hydroxyl group of cholesterol forms most of its hydrogen bonds with water, while in monoolein bilayers it predominately interacts with monoolein. Such differences in the hydrogen-bonding network of cholesterol may have implications for the design of experiments in monoolein-based LCP.
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Affiliation(s)
- Deborah L. Gater
- Institut de Pharmacologie et de Biologie Structurale, UMR 5089 CNRS - Université de Toulouse, UPS, BP 64182, 205 route de Narbonne, 31077 Toulouse Cedex04 (France)
| | - Valérie Réat
- Institut de Pharmacologie et de Biologie Structurale, UMR 5089 CNRS - Université de Toulouse, UPS, BP 64182, 205 route de Narbonne, 31077 Toulouse Cedex04 (France)
| | - Georges Czaplicki
- Institut de Pharmacologie et de Biologie Structurale, UMR 5089 CNRS - Université de Toulouse, UPS, BP 64182, 205 route de Narbonne, 31077 Toulouse Cedex04 (France)
| | - Olivier Saurel
- Institut de Pharmacologie et de Biologie Structurale, UMR 5089 CNRS - Université de Toulouse, UPS, BP 64182, 205 route de Narbonne, 31077 Toulouse Cedex04 (France)
| | - Franck Jolibois
- Laboratoire de Physique et Chimie des Nano Objets, UMR 5215, IRSAMC -Université de Toulouse, UPS, 135 Avenue de Rangueil, 31077 Toulouse Cedex04 (France)
| | - Vadim Cherezov
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla CA 92037 (USA)
| | - Alain Milon
- Institut de Pharmacologie et de Biologie Structurale, UMR 5089 CNRS - Université de Toulouse, UPS, BP 64182, 205 route de Narbonne, 31077 Toulouse Cedex04 (France)
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215
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Shim J, Coop A, MacKerell AD. Molecular details of the activation of the μ opioid receptor. J Phys Chem B 2013; 117:7907-17. [PMID: 23758404 DOI: 10.1021/jp404238n] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Molecular details of μ opioid receptor activations were obtained using molecular dynamics simulations of the receptor in the presence of three agonists, three antagonists, and a partial agonist and on the constitutively active T279K mutant. Agonists have a higher probability of direct interactions of their basic nitrogen (N) with Asp147 as compared with antagonists, indicating that direct ligand-Asp147 interactions modulate activation. Medium-size substituents on the basic N of antagonists lead to steric interactions that perturb N-Asp147 interactions, while additional favorable interactions occur with larger basic N substituents, such as in N-phenethylnormorphine, restoring N-Asp147 interactions, leading to agonism. With the orvinols, the increased size of the C19 substituent in buprenorphine over diprenorphine leads to increased interactions with residues adjacent to Asp147, partially overcoming the presence of the cyclopropyl N substituent, such that buprenorphine is a partial agonist. Results also indicate different conformational properties of the intracellular regions of the transmembrane helices in agonists versus antagonists.
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Affiliation(s)
- Jihyun Shim
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, USA
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216
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Rajarathnam K, Rösgen J. Isothermal titration calorimetry of membrane proteins - progress and challenges. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2013; 1838:69-77. [PMID: 23747362 DOI: 10.1016/j.bbamem.2013.05.023] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 05/16/2013] [Accepted: 05/20/2013] [Indexed: 11/20/2022]
Abstract
Integral membrane proteins, including G protein-coupled receptors (GPCR) and ion channels, mediate diverse biological functions that are crucial to all aspects of life. The knowledge of the molecular mechanisms, and in particular, the thermodynamic basis of the binding interactions of the extracellular ligands and intracellular effector proteins is essential to understand the workings of these remarkable nanomachines. In this review, we describe how isothermal titration calorimetry (ITC) can be effectively used to gain valuable insights into the thermodynamic signatures (enthalpy, entropy, affinity, and stoichiometry), which would be most useful for drug discovery studies, considering that more than 30% of the current drugs target membrane proteins. This article is part of a Special Issue entitled: Structural and biophysical characterisation of membrane protein-ligand binding.
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Affiliation(s)
- Krishna Rajarathnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555, USA.
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217
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Visegrády A, Keserű GM. Fragment-based lead discovery on G-protein-coupled receptors. Expert Opin Drug Discov 2013; 8:811-20. [PMID: 23621346 DOI: 10.1517/17460441.2013.794135] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION G-protein-coupled receptors (GPCRs) form one of the largest groups of potential targets for novel medications. Low druggability of many GPCR targets and inefficient sampling of chemical space in high-throughput screening expertise however often hinder discovery of drug discovery leads for GPCRs. Fragment-based drug discovery is an alternative approach to the conventional strategy and has proven its efficiency on several enzyme targets. Based on developments in biophysical screening techniques, receptor stabilization and in vitro assays, virtual and experimental fragment screening and fragment-based lead discovery recently became applicable for GPCR targets. AREAS COVERED This article provides a review of the biophysical as well as biological detection techniques suitable to study GPCRs together with their applications to screen fragment libraries and identify fragment-size ligands of cell surface receptors. The article presents several recent examples including both virtual and experimental protocols for fragment hit discovery and early hit to lead progress. EXPERT OPINION With the recent progress in biophysical detection techniques, the advantages of fragment-based drug discovery could be exploited for GPCR targets. Structural information on GPCRs will be more abundantly available for early stages of drug discovery projects, providing information on the binding process and efficiently supporting the progression of fragment hit to lead. In silico approaches in combination with biological assays can be used to address structurally challenging GPCRs and confirm biological relevance of interaction early in the drug discovery project.
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218
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Anighoro A, Rastelli G. Enrichment Factor Analyses on G-Protein Coupled Receptors with Known Crystal Structure. J Chem Inf Model 2013; 53:739-43. [DOI: 10.1021/ci4000745] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Andrew Anighoro
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 183, 41125 Modena,
Italy
| | - Giulio Rastelli
- Dipartimento di Scienze della Vita, Università di Modena e Reggio Emilia, Via Campi 183, 41125 Modena,
Italy
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219
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Seibt BF, Schiedel AC, Thimm D, Hinz S, Sherbiny FF, Müller CE. The second extracellular loop of GPCRs determines subtype-selectivity and controls efficacy as evidenced by loop exchange study at A2 adenosine receptors. Biochem Pharmacol 2013; 85:1317-29. [PMID: 23500543 DOI: 10.1016/j.bcp.2013.03.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 03/04/2013] [Accepted: 03/05/2013] [Indexed: 01/19/2023]
Abstract
The second extracellular loop (EL2) of G protein-coupled receptors (GPCRs), which represent important drug targets, may be involved in ligand recognition and receptor activation. We studied the closely related adenosine receptor (AR) subtypes A2A and A2B by exchanging the complete EL2 of the human A2BAR for the EL2 of the A2AAR. Furthermore, single amino acid residues (Asp148(45.27), Ser149(45.28), Thr151(45.30), Glu164(45.43), Ser165(45.44), and Val169(45.48)) in the EL2 of the A2BAR were exchanged for alanine. The single mutations did not lead to any major effects, except for the T151A mutant, at which NECA showed considerably increased efficacy. The loop exchange entailed significant effects: The A2A-selective agonist CGS21680, while being completely inactive at A2BARs, showed high affinity for the mutant A2B(EL2-A2A)AR, and was able to fully activate the receptor. Most strikingly, all agonists investigated (adenosine, NECA, BAY60-6583, CGS21680) showed strongly increased efficacies at the mutant A2B(EL2-A2A) as compared to the wt AR. Thus, the EL2 of the A2BAR appears to have multiple functions: besides its involvement in ligand binding and subtype selectivity it modulates agonist-bound receptor conformations thereby controlling signalling efficacy. This role of the EL2 is likely to extend to other members of the GPCR family, and the EL2 of GPCRs appears to be an attractive target structure for drugs.
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Affiliation(s)
- Benjamin F Seibt
- PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, 53121 Bonn, Germany
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220
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Roth BL. Impossible or merely difficult? Two grand challenges from a biologist's perspective. ACS Med Chem Lett 2013; 4:316-318. [PMID: 23544175 DOI: 10.1021/ml4000386] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Here I propose two grand challenges for medicinal chemists: the deorphanization of orphan GPCRs via in silico methods and the design of multi-target drugs with enhanced safety and efficacy over current medications.
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Affiliation(s)
- Bryan L. Roth
- Department of Pharmacology
and Division of Chemical
Biology and Medicinal Chemistry, University of North Carolina Chapel Hill Medical School, 4072 Genetic Medicine
Building, Chapel Hill, North Carolina 27514, United States
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221
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Kopra K, Kainulainen M, Mikkonen P, Rozwandowicz-Jansen A, Hänninen P, Härmä H. Multiparametric homogeneous method for identification of ligand binding to G protein-coupled receptors: receptor-ligand binding and β-arrestin assay. Anal Chem 2013; 85:2276-81. [PMID: 23330639 DOI: 10.1021/ac303215r] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two homogeneous assay systems have been combined to provide a new cell-based functional assay. The assay can be used to identify ligand binding to β(2)-adrenergic receptors, but also the downstream response can be determined in the same assay. Both the quenching resonance energy transfer (QRET) and the DiscoveRx PathHunter assay formats allow the use of intact cells. The homogeneous QRET technique is a single-label approach based on nonspecific quenching of the time-resolved luminescence, enabling agonist and antagonist receptor binding measurements. The commercial PathHunter assay is in turn based on enzyme fragment complementation, which can be detected on the basis of chemiluminescence signal. In the PathHunter technology the enzyme complementation is recorded immediately downstream of agonist-induced receptor activation. The new multiparametric detection technology combines these two assay methods enabling the identification of agonist, and antagonist binding to the receptor, and the agonist-induced response. Using the QRET and the PathHunter methods a panel of β(2)-adrenergic receptor ligands (epinephrine, terbutaline, metaproterenol, salmeterol, propranolol, alprenolol, bisoprolol, ICI 118,551, and bucindolol) was tested to prove the assay performance. The signal-to-background ratio for tested ligands ranged from 5 to 11 and from 6 to 18 with QRET and PathHunter, respectively. Combined homogeneous assay technique can provide an informative method for screening purposes and an efficient way to monitor receptor-ligand interaction, thus separating agonist from antagonist.
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Affiliation(s)
- Kari Kopra
- Laboratory of Biophysics, Department of Cell Biology and Anatomy, Institute of Biomedicine, University of Turku, Turku, Finland.
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Anighoro A, Rastelli G. BEAR, a Molecular Docking Refinement and Rescoring Method. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/cmb.2013.32004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Bruell S, Kong RCK, Petrie EJ, Hoare B, Wade JD, Scott DJ, Gooley PR, Bathgate RAD. Chimeric RXFP1 and RXFP2 Receptors Highlight the Similar Mechanism of Activation Utilizing Their N-Terminal Low-Density Lipoprotein Class A Modules. Front Endocrinol (Lausanne) 2013; 4:171. [PMID: 24273532 PMCID: PMC3822782 DOI: 10.3389/fendo.2013.00171] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 10/25/2013] [Indexed: 11/13/2022] Open
Abstract
Relaxin family peptide (RXFP) receptors 1 and 2 are unique G-protein coupled receptors in that they contain an N-terminal low-density lipoprotein type A (LDLa) module which is necessary for receptor activation. The current hypothesis suggests that upon ligand binding the LDLa module interacts with the transmembrane (TM) domain of a homodimer partner receptor to induce the active receptor conformations. We recently demonstrated that three residues in the N-terminus of the RXFP1 LDLa module are potentially involved in hydrophobic interactions with the receptor to drive activation. RXFP2 shares two out of three of the residues implicated, suggesting that the two LDLa modules could be interchanged without adversely affecting activity. However, in 2007 it was shown that a chimera consisting of the RXFP1 receptor with its LDLa swapped for that of RXFP2 did not signal. We noticed this construct also contained the RXFP2 region linking the LDLa to the leucine-rich repeats. We therefore constructed chimeric RXFP1 and RXFP2 receptors with their LDLa modules swapped immediately C-terminally to the final cysteine residue of the module, retaining the native linker. In addition, we exchanged the TM domains of the chimeras to explore if matching the LDLa module with the TM domain of its native receptor altered activity. All of the chimeras were expressed at the surface of HEK293T cells with ligand binding profiles similar to the wild-type receptors. Importantly, as predicted, ligand binding was able to induce cAMP-based signaling. Chimeras of RXFP1 with the LDLa of RXFP2 demonstrated reduced H2 relaxin potency with the pairing of the RXFP2 TM with the RXFP2 LDLa necessary for full ligand efficacy. In contrast the ligand-mediated potencies and efficacies on the RXFP2 chimeras were similar suggesting the RXFP1 LDLa module has similar efficacy on the RXFP2 TM domain. Our studies demonstrate the LDLa modules of RXFP1 and RXFP2 modulate receptor activation via a similar mechanism.
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Affiliation(s)
- Shoni Bruell
- Florey Department of Neuroscience and Mental Health, Florey Institute of Neuroscience and Mental Health , Melbourne, VIC , Australia ; Department of Biochemistry and Molecular Biology , Melbourne, VIC , Australia
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Kopra K, Shweta, Martikkala E, Hänninen P, Petäjä-Repo U, Härmä H. A homogeneous single-label quenching resonance energy transfer assay for a δ-opioid receptor–ligand using intact cells. Analyst 2013; 138:4907-14. [DOI: 10.1039/c3an00736g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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