151
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Wu H, Wacker D, Mileni M, Katritch V, Han GW, Vardy E, Liu W, Thompson AA, Huang XP, Carroll FI, Mascarella SW, Westkaemper RB, Mosier PD, Roth BL, Cherezov V, Stevens RC. Structure of the human κ-opioid receptor in complex with JDTic. Nature 2012; 485:327-32. [PMID: 22437504 PMCID: PMC3356457 DOI: 10.1038/nature10939] [Citation(s) in RCA: 701] [Impact Index Per Article: 58.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Accepted: 02/10/2012] [Indexed: 12/22/2022]
Abstract
Opioid receptors (ORs) mediate the actions of endogenous and exogenous opioids for many essential physiological processes including regulation of pain, respiratory drive, mood, and, in the case of κ-opioid receptors (KOR), dysphoria and psychotomimesis. Here we report the crystal structure of the human KOR (hKOR) in complex with the selective antagonist JDTic, arranged in parallel-dimers, at 2.9 angstrom resolution. The structure reveals important features of the ligand binding pocket that contribute to JDTic’s high affinity and subtype-selectivity for hKOR. Modeling of other important KOR-selective ligands, including the morphinan-derived antagonists nor-BNI and GNTI, and the diterpene agonist salvinorin A analog RB-64, reveals both common and distinct features for binding these diverse chemotypes. Analysis of site-directed mutagenesis and ligand structure-activity relationships confirms the interactions observed in the crystal structure, thereby providing a molecular explanation for hKOR subtype-selectivity along with insight essential for the design of hKOR compounds with new pharmacological properties.
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Affiliation(s)
- Huixian Wu
- Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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152
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Langmead CJ, Andrews SP, Congreve M, Errey JC, Hurrell E, Marshall FH, Mason JS, Richardson CM, Robertson N, Zhukov A, Weir M. Identification of novel adenosine A(2A) receptor antagonists by virtual screening. J Med Chem 2012; 55:1904-9. [PMID: 22250781 PMCID: PMC3308209 DOI: 10.1021/jm201455y] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Indexed: 12/15/2022]
Abstract
Virtual screening was performed against experimentally enabled homology models of the adenosine A(2A) receptor, identifying a diverse range of ligand efficient antagonists (hit rate 9%). By use of ligand docking and Biophysical Mapping (BPM), hits 1 and 5 were optimized to potent and selective lead molecules (11-13 from 5, pK(I) = 7.5-8.5, 13- to >100-fold selective versus adenosine A(1); 14-16 from 1, pK(I) = 7.9-9.0, 19- to 59-fold selective).
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Affiliation(s)
- Christopher J Langmead
- Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK.
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153
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Daval SB, Valant C, Bonnet D, Kellenberger E, Hibert M, Galzi JL, Ilien B. Fluorescent derivatives of AC-42 to probe bitopic orthosteric/allosteric binding mechanisms on muscarinic M1 receptors. J Med Chem 2012; 55:2125-43. [PMID: 22329602 DOI: 10.1021/jm201348t] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two fluorescent derivatives of the M1 muscarinic selective agonist AC-42 were synthesized by coupling the lissamine rhodamine B fluorophore (in ortho and para positions) to AC42-NH(2). This precursor, prepared according to an original seven-step procedure, was included in the study together with the LRB fluorophore (alone or linked to an alkyl chain). All these compounds are antagonists, but examination of their ability to inhibit or modulate orthosteric [(3)H]NMS binding revealed that para-LRB-AC42 shared several properties with AC-42. Carefully designed experiments allowed para-LRB-AC42 to be used as a FRET tracer on EGFP-fused M1 receptors. Under equilibrium binding conditions, orthosteric ligands, AC-42, and the allosteric modulator gallamine behaved as competitors of para-LRB-AC42 binding whereas other allosteric compounds such as WIN 51,708 and N-desmethylclozapine were noncompetitive inhibitors. Finally, molecular modeling studies focused on putative orthosteric/allosteric bitopic poses for AC-42 and para-LRB-AC42 in a 3D model of the human M1 receptor.
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Affiliation(s)
- Sandrine B Daval
- Unité Biotechnologie et Signalisation Cellulaire, UMR 7242 CNRS, Ecole Supérieure de Biotechnologie de Strasbourg, Université de Strasbourg, BP 10413, 67412 Illkirch, France
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154
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Rodríguez D, Bello X, Gutiérrez-de-Terán H. Molecular Modelling of G Protein-Coupled Receptors Through the Web. Mol Inform 2012; 31:334-41. [DOI: 10.1002/minf.201100162] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 01/06/2012] [Indexed: 11/07/2022]
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155
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Emerging role of surface plasmon resonance in fragment-based drug discovery. Future Med Chem 2012; 3:1809-20. [PMID: 22004086 DOI: 10.4155/fmc.11.128] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Surface plasmon resonance (SPR) offers a method of biophysical fragment screening that is fast, efficient, cost effective and accurate. SPR is increasingly being adopted as a secondary assay to validate fragment hits. Recently, technical advances have resulted in the emergence of SPR as a primary screening methodology for fragment-based drug discovery. Moreover, SPR biosensor assays can be developed for a wide range of proteins, including membrane proteins, such as G-protein-coupled receptors. In this review, we discuss the advantages and limitations of SPR fragment screening including experimental consideration of reducing false positive and false negative rates to a minimum. We discuss how ligand efficiency can be used both as a method to eliminate false positives and to understand which fragments in a library may be a source of false negatives.
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156
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Congreve M, Andrews SP, Doré AS, Hollenstein K, Hurrell E, Langmead CJ, Mason JS, Ng IW, Tehan B, Zhukov A, Weir M, Marshall FH. Discovery of 1,2,4-triazine derivatives as adenosine A(2A) antagonists using structure based drug design. J Med Chem 2012; 55:1898-903. [PMID: 22220592 PMCID: PMC3308197 DOI: 10.1021/jm201376w] [Citation(s) in RCA: 257] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Potent, ligand efficient, selective, and orally efficacious
1,2,4-triazine
derivatives have been identified using structure based drug design
approaches as antagonists of the adenosine A2A receptor.
The X-ray crystal structures of compounds 4e and 4g bound to the GPCR illustrate that the molecules bind deeply
inside the orthosteric binding cavity. In vivo pharmacokinetic and
efficacy data for compound 4k are presented, demonstrating
the potential of this series of compounds for the treatment of Parkinson’s
disease.
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Affiliation(s)
- Miles Congreve
- Heptares Therapeutics Limited, BioPark, Broadwater Road, Welwyn Garden City, Hertfordshire AL7 3AX, UK.
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157
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Bruno A, Costantino G. Molecular Dynamics Simulations of G Protein-Coupled Receptors. Mol Inform 2012; 31:222-30. [DOI: 10.1002/minf.201100138] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Accepted: 12/18/2011] [Indexed: 12/14/2022]
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158
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Soriano-Ursúa MA, McNaught-Flores DA, Nieto-Alamilla G, Segura-Cabrera A, Correa-Basurto J, Arias-Montaño JA, Trujillo-Ferrara JG. Cell-based and in-silico studies on the high intrinsic activity of two boron-containing salbutamol derivatives at the human β₂-adrenoceptor. Bioorg Med Chem 2012; 20:933-41. [PMID: 22182578 DOI: 10.1016/j.bmc.2011.11.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Revised: 11/16/2011] [Accepted: 11/23/2011] [Indexed: 02/07/2023]
Abstract
Salbutamol is a well-known β(2) adrenoceptor (β(2)AR) partial agonist. We synthesized two boron-containing salbutamol derivatives (BCSDs) with greater potency and efficacy, compared to salbutamol, for inducing β(2)AR-mediated smooth-muscle relaxation in guinea-pig tracheal rings. However, the mechanism involved in this pharmacological effect remains unclear. In order to gain insight, we carried out binding and functional assays for BCSDs in HEK-293T cells transfected with the human β(2)AR (hβ(2)AR). The transfected hβ(2)AR showed similar affinity for BCSDs and salbutamol, but adenosine 3',5'-cyclic phosphate (cAMP) accumulation induced by both BCSDs was similar to that elicited by isoproterenol and greater than that induced by salbutamol. The boron-containing precursors (boric and phenylboronic acids, 100 μM) had no significant effect on salbutamol binding or salbutamol-induced cAMP accumulation. These experimental results are in agreement with theoretical docking simulations on lipid bilayer membrane-embedded hβ(2)AR structures. These receptors showed slightly higher affinity for BCSDs than for salbutamol. An essential change between putative active and inactive conformational states depended on the interaction of the tested ligands with the fifth, sixth and seventh transmembrane domains. Overall, these data suggest that BCSDs induce and stabilize conformational states of the hβ(2)AR that are highly capable of stimulating cAMP production.
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Affiliation(s)
- Marvin A Soriano-Ursúa
- Departamentos de Fisiología, Bioquímica Médica y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina, Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón, Col. Casco de Santo Tomás, Del. Miguel Hidalgo, 11340 México, DF, Mexico.
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159
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Rdova-Sintjago TC, Villa N, Canal C, Booth R. Human Serotonin 5-HT 2C G Protein-Coupled Receptor Homology Model from the β2 Adrenoceptor Structure: Ligand Docking and Mutagenesis Studies. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2012; 112:10.1002/qua.23231. [PMID: 24244046 PMCID: PMC3826658 DOI: 10.1002/qua.23231] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Activation of the serotonin (5-hydroxytryptamine, 5-HT) 5HT2C G protein-coupled receptor (GPCR) is proposed as novel pharmacotherapy for obesity and neuropsychiatric disorders. In contrast, activation of the 5-HT2A and 5-HT2B GPCRs is associated with untoward hallucinogenic and cardiopulmonary effects, respectively. There is no crystal structure available to guide design of 5-HT2C receptor-specific ligands. For this reason, a homology model of the 5-HT2C receptor was built based on the crystal structure of the human β2 adrenoceptor GPCR to delineate molecular determinants of ligand-receptor interactions for drug design purposes. Computational and experimental studies were carried out to validate the model. Binding of N(CH3)2-PAT [(1R, 3S)-(-)-trans-1-phenyl-3-N,N-dimethylamino-1,2,3,4-tetrahydronaphthalene], a novel 5-HT2C agonist/5-HT2A/2B inverse agonist, and its secondary [NH(CH3)-PAT] and primary (NH2-PAT) amine analogs were studied at the 5-HT2C wild type (WT) and D3.32A, S3.36A, and Y7.43A 5-HT2C point-mutated receptors. Reference ligands included the tertiary amines lisuride and mesulergine and the primary amine 5-HT. Modeling results indicated that 5-HT2C residues D3.32, S3.36, and Y7.43 play a role in ligand binding. Experimental ligand binding results with WT and point-mutated receptors confirmed the impact of D3.32, S3.36, and Y7.43 on ligand affinity.
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Affiliation(s)
- Tania Có Rdova-Sintjago
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL 32610
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160
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Hughes AD, McNamara A, Steinfeld T. Multivalent dual pharmacology muscarinic antagonist and β₂ agonist (MABA) molecules for the treatment of COPD. PROGRESS IN MEDICINAL CHEMISTRY 2012; 51:71-95. [PMID: 22520472 DOI: 10.1016/b978-0-12-396493-9.00003-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Affiliation(s)
- Adam D Hughes
- Department of Medicinal Chemistry, Theravance, Inc., South San Francisco, CA, USA
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161
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Huang X, Zheng G, Zhan CG. Microscopic binding of M5 muscarinic acetylcholine receptor with antagonists by homology modeling, molecular docking, and molecular dynamics simulation. J Phys Chem B 2011; 116:532-41. [PMID: 22185605 DOI: 10.1021/jp210579b] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By performing homology modeling, molecular docking, and molecular dynamics (MD) simulations, we have developed three-dimensional (3D) structural models of the M5 muscarinic acetylcholine receptor (mAChR) and two complexes for M5 mAChR binding with antagonists SVT-40776 and solifenacin in the environment of lipid bilayer and solvent water. According to the simulated results, each of the antagonists is oriented horizontally in the binding pocket formed by transmembrane helices 2, 3, and 5-7. The cationic headgroup of each of the antagonists interacts with a negatively charged residue, Asp110, through electrostatic and hydrogen-bonding interactions. The simulated results also reveal some significant difference between the binding modes of SVT-40776 and solifenacin. In particular, SVT-40776 is persistently hydrogen bonded with the side chain of residue Tyr458, whereas solifenacin cannot form a similar hydrogen bond with residues around its carbonyl group. Such significant difference in the binding structures is consistent with the fact that SVT-40776 has a much higher binding affinity (K(d) = 0.4 nM) to M5 mAChR than that of solifenacin (K(d) = 31 nM) with the same reeptor. The calculated binding free energy change (-2.3 ± 0.3 kcal/mol) from solifenacin to SVT-40776 is in good agreement with the experimentally derived binding free energy change (-2.58 kcal/mol), suggesting that our modeled M5 mAChR structure and its complexes with the antagonists are reliable. The new structural insights obtained from this computational study are expected to stimulate further biochemical and pharmacological studies on the detailed structures of M5 and other subtypes of mAChRs.
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Affiliation(s)
- Xiaoqin Huang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, Kentucky 40536, United States
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162
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Gatica EA, Cavasotto CN. Ligand and decoy sets for docking to G protein-coupled receptors. J Chem Inf Model 2011; 52:1-6. [PMID: 22168315 DOI: 10.1021/ci200412p] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
We compiled a G protein-coupled receptor (GPCR) ligand library (GLL) for 147 targets, selecting for each ligand 39 decoy molecules, collected in the GPCR Decoy Database (GDD). Decoys were chosen ensuring a ligand-decoy similarity of six physical properties, while enforcing ligand-decoy chemical dissimilarity. The performance in docking of the GDD was evaluated on 19 GPCRs, showing a marked decrease in enrichment compared to bias-uncorrected decoy sets. Both the GLL and GDD are freely available for the scientific community.
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Affiliation(s)
- Edgar A Gatica
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, 7000 Fannin St., Houston, Texas 77030, USA
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163
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Costanzi S, Vilar S. In silico screening for agonists and blockers of the β(2) adrenergic receptor: implications of inactive and activated state structures. J Comput Chem 2011; 33:561-72. [PMID: 22170280 DOI: 10.1002/jcc.22893] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 09/28/2011] [Accepted: 10/30/2011] [Indexed: 11/07/2022]
Abstract
Ten crystal structures of the β(2) adrenergic receptor have been published, reflecting different signaling states. Here, through controlled-docking experiments, we examined the implications of using inactive or activated structures on the in silico screening for agonists and blockers of the receptor. Specifically, we targeted the crystal structures solved in complex with carazolol (2RH1), the neutral antagonist alprenalol, the irreversible agonist FAUC50 (3PDS), and the full agonist BI-167017 (3P0G). Our results indicate that activated structures favor agonists over blockers, whereas inactive structures favor blockers over agonists. This tendency is more marked for activated than for inactive structures. Additionally, agonists tend to receive more favorable docking scores when docked at activated rather than inactive structures, while blockers do the opposite. Hence, the difference between the docking scores attained with an activated and an inactive structure is an excellent means for the classification of ligands into agonists and blockers as we determined through receiver operating characteristic curves and linear discriminant analysis. With respect to virtual screening, all structures prioritized well agonists and blockers over nonbinders. However, inactive structures worked better for blockers and activated structures worked better for agonists, respectively. Notably, the combination of individual docking experiments through receptor ensemble docking resulted in an excellent performance in the retrieval of both agonists and blockers. Finally, we demonstrated that the induced-fit docking of agonists is a viable way of modifying an inactive crystal structure and bias it toward the in silico recognition of agonists rather than blockers.
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Affiliation(s)
- Stefano Costanzi
- Laboratory of Biological Modeling, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, Maryland 20892, USA.
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164
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de Graaf C, Kooistra AJ, Vischer HF, Katritch V, Kuijer M, Shiroishi M, Iwata S, Shimamura T, Stevens RC, de Esch IJP, Leurs R. Crystal structure-based virtual screening for fragment-like ligands of the human histamine H(1) receptor. J Med Chem 2011; 54:8195-206. [PMID: 22007643 DOI: 10.1021/jm2011589] [Citation(s) in RCA: 166] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The recent crystal structure determinations of druggable class A G protein-coupled receptors (GPCRs) have opened up excellent opportunities in structure-based ligand discovery for this pharmaceutically important protein family. We have developed and validated a customized structure-based virtual fragment screening protocol against the recently determined human histamine H(1) receptor (H(1)R) crystal structure. The method combines molecular docking simulations with a protein-ligand interaction fingerprint (IFP) scoring method. The optimized in silico screening approach was successfully applied to identify a chemically diverse set of novel fragment-like (≤22 heavy atoms) H(1)R ligands with an exceptionally high hit rate of 73%. Of the 26 tested fragments, 19 compounds had affinities ranging from 10 μM to 6 nM. The current study shows the potential of in silico screening against GPCR crystal structures to explore novel, fragment-like GPCR ligand space.
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Affiliation(s)
- Chris de Graaf
- Leiden/Amsterdam Center for Drug Research, Division of Medicinal Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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165
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Katritch V, Abagyan R. GPCR agonist binding revealed by modeling and crystallography. Trends Pharmacol Sci 2011; 32:637-43. [PMID: 21903279 PMCID: PMC3200445 DOI: 10.1016/j.tips.2011.08.001] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 08/05/2011] [Accepted: 08/08/2011] [Indexed: 10/17/2022]
Abstract
Despite recent progress in structural coverage of the G-protein-coupled receptor (GPCR) family, high plasticity of these membrane proteins poses additional challenges for crystallographic studies of their complexes with different classes of ligands, especially agonists. The ability to predict computationally the binding of natural and clinically relevant agonists and corresponding changes in the receptor pocket, starting from inactive GPCR structures, is therefore of great interest for understanding GPCR biology and drug action. Comparison of computational models published in 2009 and 2010 with recently determined agonist-bound structures of β-adrenergic and adenosine A(2A) receptors reveals high accuracy of the predicted agonist binding poses (0.8 Å and 1.7 Å respectively) and receptor interactions. In the case of the β(2)AR, energy-based models with limited backbone flexibility have also allowed characterization of side-chain rotations and a finite backbone shift in the pocket region as determinants of full, partial or inverse agonism. Development of accurate models of agonist binding for other GPCRs will be instrumental for functional and pharmacological studies, complementing biochemical and crystallographic techniques.
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Affiliation(s)
- Vsevolod Katritch
- Skaggs School of Pharmacy and Pharmaceutical Sciences and San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.
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166
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Katritch V, Cherezov V, Stevens RC. Diversity and modularity of G protein-coupled receptor structures. Trends Pharmacol Sci 2011; 33:17-27. [PMID: 22032986 DOI: 10.1016/j.tips.2011.09.003] [Citation(s) in RCA: 337] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Revised: 09/19/2011] [Accepted: 09/19/2011] [Indexed: 01/21/2023]
Abstract
G protein-coupled receptors (GPCRs) comprise the most 'prolific' family of cell membrane proteins, which share a general mechanism of signal transduction, but greatly vary in ligand recognition and function. Crystal structures are now available for rhodopsin, adrenergic, and adenosine receptors in both inactive and activated forms, as well as for chemokine, dopamine, and histamine receptors in inactive conformations. Here we review common structural features, outline the scope of structural diversity of GPCRs at different levels of homology, and briefly discuss the impact of the structures on drug discovery. Given the current set of GPCR crystal structures, a distinct modularity is now being observed between the extracellular (ligand-binding) and intracellular (signaling) regions. The rapidly expanding repertoire of GPCR structures provides a solid framework for experimental and molecular modeling studies, and helps to chart a roadmap for comprehensive structural coverage of the whole superfamily and an understanding of GPCR biological and therapeutic mechanisms.
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Affiliation(s)
- Vsevolod Katritch
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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