1
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Goldberg A, Xie B, Shi L. The Molecular Mechanism of Positive Allosteric Modulation at the Dopamine D1 Receptor. Int J Mol Sci 2023; 24:12848. [PMID: 37629030 PMCID: PMC10454769 DOI: 10.3390/ijms241612848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
The dopamine D1 receptor (D1R) is a promising target for treating various psychiatric disorders. While upregulation of D1R activity has shown potential in alleviating motor and cognitive symptoms, orthosteric agonists have limitations, restricting their clinical applications. However, the discovery of several allosteric compounds specifically targeting the D1R, such as LY3154207, has opened new therapeutic avenues. Based on the cryo-EM structures of the D1R, we conducted molecular dynamics simulations to investigate the binding and allosteric mechanisms of LY3154207. Our simulations revealed that LY3154207 preferred the horizontal orientation above intracellular loop 2 (IL2) and stabilized the helical conformation of IL2. Moreover, LY3154207 binding induced subtle yet significant changes in key structural motifs and their neighboring residues. Notably, a cluster of residues centered around the Na+-binding site became more compact, while interactions involving the PIF motif and its neighboring residues were loosened upon LY3154207 binding, consistent with their role in opening the intracellular crevice for receptor activation. Additionally, we identified an allosteric pathway likely responsible for the positive allosteric effect of LY3154207 in enhancing Gs protein coupling. This mechanistic understanding of LY3154207's allosteric action at the D1R paves the way for the rational design of more potent and effective allosteric modulators.
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Affiliation(s)
| | | | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, MD 21224, USA
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2
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Goldberg A, Xie B, Shi L. The molecular mechanism of positive allosteric modulation at the dopamine D1 receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.27.550907. [PMID: 37546785 PMCID: PMC10402154 DOI: 10.1101/2023.07.27.550907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The dopamine D1 receptor (D1R) is a promising target for treating various psychiatric disorders. While upregulation of D1R activity has shown potential in alleviating motor and cognitive symptoms, orthosteric agonists have limitations, restricting their clinical applications. However, the discovery of several allosteric compounds specifically targeting the D1R, such as LY3154207, has opened new therapeutic avenues. Based on the cryo-EM structures of the D1R, we conducted molecular dynamics simulations to investigate the binding and allosteric mechanisms of LY3154207. Our simulations revealed that LY3154207 preferred the horizontal orientation above intracellular loop 2 (IL2) and stabilized the helical conformation of IL2. Moreover, LY3154207 binding induced subtle yet significant changes in key structural motifs and their neighboring residues. Notably, a cluster of residues centered around the Na + binding site became more compact, while interactions involving the PIF motif and its neighboring residues were loosened upon LY3154207 binding, consistent with their role in opening the intracellular crevice for receptor activation. Additionally, we identified an allosteric pathway likely responsible for the positive allosteric effect of LY3154207 in enhancing Gs protein coupling. This mechanistic understanding of LY3154207's allosteric action at the D1R pave the way for the rational design of more potent and effective allosteric modulators.
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Affiliation(s)
- Alexander Goldberg
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224
| | - Bing Xie
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, Baltimore, Maryland 21224
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3
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Jia L, Li S, Dai W, Guo L, Xu Z, Scott AM, Zhang Z, Ren J, Zhang Q, Dexheimer TS, Chung-Davidson YW, Neubig RR, Li Q, Li W. Convergent olfactory trace amine-associated receptors detect biogenic polyamines with distinct motifs via a conserved binding site. J Biol Chem 2021; 297:101268. [PMID: 34600890 PMCID: PMC8546428 DOI: 10.1016/j.jbc.2021.101268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 09/26/2021] [Accepted: 09/28/2021] [Indexed: 11/25/2022] Open
Abstract
Biogenic amines activate G-protein-coupled receptors (GPCRs) in the central nervous system in vertebrate animals. Several biogenic amines, when excreted, stimulate trace amine-associated receptors (TAARs), a group of GPCRs in the main olfactory epithelium, and elicit innate behaviors. How TAARs recognize amines with varying numbers of amino groups is largely unknown. We reasoned that a comparison between lamprey and mammalian olfactory TAARs, which are thought to have evolved independently but show convergent responses to polyamines, may reveal structural determinants of amine recognition. Here, we demonstrate that sea lamprey TAAR365 (sTAAR365) responds strongly to biogenic polyamines cadaverine, putrescine, and spermine, and shares a similar response profile as a mammalian TAAR (mTAAR9). Docking and site-directed mutagenesis analyses show that both sTAAR365 and mTAAR9 recognize the two amino groups of cadaverine with the conserved Asp3.32 and Tyr6.51 residues. sTAAR365, which has remarkable sensitivity for cadaverine (EC50 = 4 nM), uses an extra residue, Thr7.42, to stabilize ligand binding. These cadaverine recognition sites also interact with amines with four and three amino groups (spermine and spermidine, respectively). Glu7.36 of sTAAR365 cooperates with Asp3.32 and Thr7.42 to recognize spermine, whereas mTAAR9 recognizes spermidine through an additional aromatic residue, Tyr7.43. These results suggest a conserved mechanism whereby independently evolved TAAR receptors recognize amines with two, three, or four amino groups using the same recognition sites, at which sTAAR365 and mTAAR9 evolved distinct motifs. These motifs interact directly with the amino groups of the polyamines, a class of potent and ecologically important odorants, mediating olfactory signaling.
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Affiliation(s)
- Liang Jia
- Center for Brain Science, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA; College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Shengju Li
- Center for Brain Science, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenxuan Dai
- Center for Brain Science, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lingna Guo
- Center for Brain Science, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhengrong Xu
- Center for Brain Science, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Otolaryngology Head and Neck Surgery, Jiangsu Provincial Key Medical Discipline (Laboratory), Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Anne M Scott
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA
| | - Zhe Zhang
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA
| | - Jianfeng Ren
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Qinghua Zhang
- College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, China
| | - Thomas S Dexheimer
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, USA
| | - Yu-Wen Chung-Davidson
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA
| | - Richard R Neubig
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan, USA.
| | - Qian Li
- Center for Brain Science, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, China.
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, Michigan, USA.
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4
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Martínez A, Ibarra IA, Vargas R. A quantum chemical approach representing a new perspective concerning agonist and antagonist drugs in the context of schizophrenia and Parkinson's disease. PLoS One 2019; 14:e0224691. [PMID: 31830046 PMCID: PMC6907805 DOI: 10.1371/journal.pone.0224691] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/18/2019] [Indexed: 02/03/2023] Open
Abstract
Schizophrenia and Parkinson's disease can be controlled with dopamine antagonists and agonists. In order to improve the understanding of the reaction mechanism of these drugs, in this investigation we present a quantum chemical study of 20 antagonists and 10 agonists. Electron donor acceptor capacity and global hardness are analyzed using Density Functional Theory calculations. Following this theoretical approach, we provide new insights into the intrinsic response of these chemical species. In summary, antagonists generally prove to be better electron acceptors and worse electron donors than dopamine, whereas agonists present an electron donor-acceptor capacity similar to that of dopamine. The chemical hardness is a descriptor that captures the resistance of a chemical compound to change its number of electrons. Within this model, harder molecules are less polarizable and more stable systems. Our results show that the global hardness is similar for dopamine and agonists whilst antagonists present smaller values. Following the Hard and Soft Acid and Bases principle, it is possible to conclude that dopamine and agonists are hard bases while antagonists are soft acids, and this can be related to their activity. From the electronic point of view, we have evolved a new perspective for the classification of agonist and antagonist, which may help to analyze future results of chemical interactions triggered by these drugs.
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Affiliation(s)
- Ana Martínez
- Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, Circuito Exterior S. N., Ciudad Universitaria, CDMX, México
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, CDMX, México
| | - Ilich A Ibarra
- Laboratorio de Fisicoquímica y Reactividad de Superficies (LaFReS), Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, CDMX, Mexico
| | - Rubicelia Vargas
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, CDMX, México
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5
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Said ZS@AM, Arifi FAM, Salleh AB, Rahman RNZRA, Leow ATC, Latip W, Ali MSM. Unravelling protein -organic solvent interaction of organic solvent tolerant elastase from Pseudomonas aeruginosa strain K crystal structure. Int J Biol Macromol 2019; 127:575-584. [DOI: 10.1016/j.ijbiomac.2019.01.056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 01/11/2019] [Accepted: 01/11/2019] [Indexed: 10/27/2022]
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6
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Montgomery D, Campbell A, Sullivan HJ, Wu C. Molecular dynamics simulation of biased agonists at the dopamine D2 receptor suggests the mechanism of receptor functional selectivity. J Biomol Struct Dyn 2018; 37:3206-3225. [PMID: 30124143 DOI: 10.1080/07391102.2018.1513378] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The dopamine D2 receptor (D2R) is the primary target for antipsychotic drugs. Besides schizophrenia, this receptor is linked to dementia, Parkinson's disease, and depression. Recent studies have shown that β-arrestin biased agonists at this receptor treat schizophrenia with less side effects. Although the high resolution structure of this receptor exists, the mechanism of biased agonism at the receptor is unknown. In this study, dopamine, the endogenous unbiased G-protein agonist, MLS1547, a G-protein biased agonist, and UNC9975, a G-protein antagonist and a β-arrestin biased agonist, were docked to a homology model of the whole D2R including all flexible loops, and molecular dynamics simulations were conducted to study the potential mechanisms of biased agonism. Our thorough analysis on the protein-ligand interaction, secondary structure, tertiary structure, structure dynamics, and molecular switches of all three systems indicates that ligand binding to transmembrane 3 might be essential for G-protein recruitment, while ligand binding to transmembrane 6 might be essential for β-arrestin recruitment. Our analysis also suggests changes in both the secondary and the tertiary structures of TM5 and TM7, molecular switches and ICL3 flexibility are important in biased signaling. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- David Montgomery
- a College of Science and Mathematics , Rowan University , Glassboro , NJ , USA
| | - Alexandra Campbell
- a College of Science and Mathematics , Rowan University , Glassboro , NJ , USA
| | - Holli-Joi Sullivan
- a College of Science and Mathematics , Rowan University , Glassboro , NJ , USA
| | - Chun Wu
- a College of Science and Mathematics , Rowan University , Glassboro , NJ , USA
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7
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Salmas RE, Seeman P, Stein M, Durdagi S. Structural Investigation of the Dopamine-2 Receptor Agonist Bromocriptine Binding to Dimeric D2 HighR and D2 LowR States. J Chem Inf Model 2018. [PMID: 29537837 DOI: 10.1021/acs.jcim.7b00722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The active (D2HighR) and inactive (D2LowR) states of dimeric dopamine D2 receptor (D2R) models were investigated to clarify the binding mechanisms of the dopamine agonist bromocriptine, using Molecular Dynamics (MD) simulation. The aim of this comprehensive study was to investigate the critical effects of bromocriptine binding on each distinct receptor conformation. The different binding modes of the bromocriptine ligand in the active and inactive states have a significant effect on the conformational changes of the receptor. Based on the MM/GBSA approach, the calculated binding enthalpies of bromocriptine demonstrated selectivity toward the D2HighR active state. There is good agreement between the calculated and experimentally measured D2HighR selectivity. In the ligand-binding site, the key amino acids identified for D2HighR were Asp114(3.32) and Glu95(2.65), and for D2LowR, it was Ser193(5.42). Moreover, analysis of replicate MD trajectories demonstrated that the bromocriptine structure was more rigid at the D2HighR state and more flexible at the D2LowR state. However, the side chains of the ligand-receptor complex of D2HighR showed larger variations relative to the corresponding regions of D2LowR. The present study is part of an ongoing research program to study D2R conformational changes during ligand activation and to evaluate the conformational state selectivity for ligand binding.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine , Bahcesehir University , Istanbul 34349 , Turkey
| | - Philip Seeman
- Departments of Pharmacology and Psychiatry , University of Toronto , 260 Heath Street West, Unit 605 , M5P 3L6 Toronto , Ontario , Canada
| | - Matthias Stein
- Molecular Simulations and Design Group , Max Planck Institute for Dynamics of Complex Technical Systems , Sandtorstrasse 1 , 39106 Magdeburg , Germany
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine , Bahcesehir University , Istanbul 34349 , Turkey.,Neuroscience Program, Graduate School of Health Sciences , Bahcesehir University , Istanbul 34349 , Turkey
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8
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Draper-Joyce CJ, Verma RK, Michino M, Shonberg J, Kopinathan A, Klein Herenbrink C, Scammells PJ, Capuano B, Abramyan AM, Thal DM, Javitch JA, Christopoulos A, Shi L, Lane JR. The action of a negative allosteric modulator at the dopamine D 2 receptor is dependent upon sodium ions. Sci Rep 2018; 8:1208. [PMID: 29352161 PMCID: PMC5775417 DOI: 10.1038/s41598-018-19642-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 12/19/2017] [Indexed: 01/11/2023] Open
Abstract
Sodium ions (Na+) allosterically modulate the binding of orthosteric agonists and antagonists to many class A G protein-coupled receptors, including the dopamine D2 receptor (D2R). Experimental and computational evidences have revealed that this effect is mediated by the binding of Na+ to a conserved site located beneath the orthosteric binding site (OBS). SB269652 acts as a negative allosteric modulator (NAM) of the D2R that adopts an extended bitopic pose, in which the tetrahydroisoquinoline moiety interacts with the OBS and the indole-2-carboxamide moiety occupies a secondary binding pocket (SBP). In this study, we find that the presence of a Na+ within the conserved Na+-binding pocket is required for the action of SB269652. Using fragments of SB269652 and novel full-length analogues, we show that Na+ is required for the high affinity binding of the tetrahydroisoquinoline moiety within the OBS, and that the interaction of the indole-2-carboxamide moiety with the SBP determines the degree of Na+-sensitivity. Thus, we extend our understanding of the mode of action of this novel class of NAM by showing it acts synergistically with Na+ to modulate the binding of orthosteric ligands at the D2R, providing opportunities for fine-tuning of modulatory effects in future allosteric drug design efforts.
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Affiliation(s)
- Christopher J Draper-Joyce
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Ravi Kumar Verma
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland, 21224, United States
| | - Mayako Michino
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland, 21224, United States.,Tri-Institutional Therapeutics Discovery Institute, 413 E 69th St, New York, NY, 10021, United States
| | - Jeremy Shonberg
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Anitha Kopinathan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Carmen Klein Herenbrink
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Peter J Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Ben Capuano
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Ara M Abramyan
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland, 21224, United States
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Jonathan A Javitch
- Departments of Psychiatry and Pharmacology, New York State Psychiatric Institute, New York, New York, 10032, United States.,College of Physicians and Surgeons, Columbia University, and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York, 10032, United States
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland, 21224, United States.
| | - J Robert Lane
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, VIC 3052, Australia.
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9
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Ekhteiari Salmas R, Serhat Is Y, Durdagi S, Stein M, Yurtsever M. A QM protein–ligand investigation of antipsychotic drugs with the dopamine D2 Receptor (D2R). J Biomol Struct Dyn 2017; 36:2668-2677. [DOI: 10.1080/07391102.2017.1365772] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
| | - Yusuf Serhat Is
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
- Vocational School Department of Chemistry Technology, Istanbul Gedik University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Matthias Stein
- Molecular Simulations and Design Group, Max-Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Mine Yurtsever
- Department of Chemistry, Istanbul Technical University, Istanbul, Turkey
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10
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Salmas RE, Seeman P, Aksoydan B, Erol I, Kantarcioglu I, Stein M, Yurtsever M, Durdagi S. Analysis of the Glutamate Agonist LY404,039 Binding to Nonstatic Dopamine Receptor D2 Dimer Structures and Consensus Docking. ACS Chem Neurosci 2017; 8:1404-1415. [PMID: 28272861 DOI: 10.1021/acschemneuro.7b00070] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Dopamine receptor D2 (D2R) plays an important role in the human central nervous system and is a focal target of antipsychotic agents. The D2HighR and D2LowR dimeric models previously developed by our group are used to investigate the prediction of binding affinity of the LY404,039 ligand and its binding mechanism within the catalytic domain. The computational data obtained using molecular dynamics simulations fit well with the experimental results. The calculated binding affinities of LY404,039 using MM/PBSA for the D2HighR and D2LowR targets were -12.04 and -9.11 kcal/mol, respectively. The experimental results suggest that LY404,039 binds to D2HighR and D2LowR with binding affinities (Ki) of 8.2 and 1640 nM, respectively. The high binding affinity of LY404,039 in terms of binding to [3H]domperidone was inhibited by the presence of a guanine nucleotide, indicating an agonist action of the drug at D2HighR. The interaction analysis demonstrated that while Asp114 was among the most critical amino acids for D2HighR binding, residues Ser193 and Ser197 were significantly more important within the binding cavity of D2LowR. Molecular modeling analyses are extended to ensemble docking as well as structure-based pharmacophore model (E-pharmacophore) development using the bioactive conformation of LY404,039 at the binding pocket as a template and screening of small-molecule databases with derived pharmacophore models.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Philip Seeman
- Departments
of Pharmacology and Psychiatry, University of Toronto, 260 Heath
Street West, Unit 605, Toronto, Ontario M5P 3L6, Canada
| | - Busecan Aksoydan
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Ismail Erol
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
- Department
of Chemistry, Gebze Technical University, 41400, Kocaeli, Turkey
| | - Isik Kantarcioglu
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
| | - Matthias Stein
- Max-Planck Institute for Dynamics of Complex Technical Systems, Molecular Simulations and Design Group, Sandtorstrasse 1, 39106 Magdeburg, Germany
| | - Mine Yurtsever
- Department
of Chemistry, Istanbul Technical University, 34469 Istanbul, Turkey
| | - Serdar Durdagi
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahcesehir University, 34349 Istanbul, Turkey
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11
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Salmas RE, Stein M, Yurtsever M, Seeman P, Erol I, Mestanoglu M, Durdagi S. The signaling pathway of dopamine D2 receptor (D2R) activation using normal mode analysis (NMA) and the construction of pharmacophore models for D2R ligands. J Biomol Struct Dyn 2016; 35:2040-2048. [PMID: 27367058 DOI: 10.1080/07391102.2016.1206487] [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] [Indexed: 01/05/2023]
Abstract
G-protein-coupled receptors (GPCRs) are targets of more than 30% of marketed drugs. Investigation on the GPCRs may shed light on upcoming drug design studies. In the present study, we performed a combination of receptor- and ligand-based analysis targeting the dopamine D2 receptor (D2R). The signaling pathway of D2R activation and the construction of universal pharmacophore models for D2R ligands were also studied. The key amino acids, which contributed to the regular activation of the D2R, were in detail investigated by means of normal mode analysis (NMA). A derived cross-correlation matrix provided us an understanding of the degree of pair residue correlations. Although negative correlations were not observed in the case of the inactive D2R state, a high degree of correlation appeared between the residues in the active state. NMA results showed that the cytoplasmic side of the TM5 plays a significant role in promoting of residue-residue correlations in the active state of D2R. Tracing motions of the amino acids Arg219, Arg220, Val223, Asn224, Lys226, and Ser228 in the position of the TM5 are found to be critical in signal transduction. Complementing the receptor-based modeling, ligand-based modeling was also performed using known D2R ligands. The top-scored pharmacophore models were found as 5-sited (AADPR.671, AADRR.1398, AAPRR.3900, and ADHRR.2864) hypotheses from PHASE modeling from a pool consisting of more than 100 initial candidates. The constructed models using 38 D2R ligands (in the training set) were validated with 15 additional test set compounds. The resulting model correctly predicted the pIC50 values of an additional test set compounds as true unknowns.
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Affiliation(s)
- Ramin Ekhteiari Salmas
- a Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
| | - Matthias Stein
- b Molecular Simulations and Design Group , Max Planck Institute for Dynamics of Complex Technical System , Sandtorstrasse 1, 39106 Magdeburg , Germany
| | - Mine Yurtsever
- c Department of Chemistry , Istanbul Technical University , Istanbul , Turkey
| | - Philip Seeman
- d Department of Pharmacology and Psychiatry , University of Toronto , 260 Heath Street West, Unit 605, M5P 3L6 Toronto , Ontario , Canada
| | - Ismail Erol
- a Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey.,e Department of Chemistry , Gebze Technical University , Gebze , Turkey
| | - Mert Mestanoglu
- a Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
| | - Serdar Durdagi
- a Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
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12
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Investigating the structural impact of S311C mutation in DRD2 receptor by molecular dynamics & docking studies. Biochimie 2016; 123:52-64. [DOI: 10.1016/j.biochi.2016.01.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 01/16/2016] [Indexed: 01/11/2023]
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13
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Michino M, Free RB, Doyle TB, Sibley DR, Shi L. Structural basis for Na(+)-sensitivity in dopamine D2 and D3 receptors. Chem Commun (Camb) 2016; 51:8618-21. [PMID: 25896577 DOI: 10.1039/c5cc02204e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
To understand the structural basis for the Na(+)-sensitivity of ligand binding to dopamine D2-like receptors, using computational analysis in combination with binding assays, we identified interactions critical in propagating the impact of Na(+) on receptor conformations and on the ligand-binding site. Our findings expand the pharmacologically-relevant conformational spectrum of these receptors.
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Affiliation(s)
- Mayako Michino
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, USA.
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14
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Salmas RE, Yurtsever M, Stein M, Durdagi S. Modeling and protein engineering studies of active and inactive states of human dopamine D2 receptor (D2R) and investigation of drug/receptor interactions. Mol Divers 2015; 19:321-32. [DOI: 10.1007/s11030-015-9569-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 01/11/2015] [Indexed: 01/11/2023]
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15
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Sainsily X, Cabana J, Holleran BJ, Escher E, Lavigne P, Leduc R. Identification of transmembrane domain 1 & 2 residues that contribute to the formation of the ligand-binding pocket of the urotensin-II receptor. Biochem Pharmacol 2014; 92:280-8. [DOI: 10.1016/j.bcp.2014.08.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 11/15/2022]
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16
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Identification of transmembrane domain 3, 4 & 5 residues that contribute to the formation of the ligand-binding pocket of the urotensin-II receptor. Biochem Pharmacol 2013; 86:1584-93. [DOI: 10.1016/j.bcp.2013.09.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 09/17/2013] [Accepted: 09/18/2013] [Indexed: 11/19/2022]
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17
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Mugumbate G, Jackson GE, van der Spoel D. Open conformation of adipokinetic hormone receptor from the malaria mosquito facilitates hormone binding. Peptides 2011; 32:553-9. [PMID: 20804800 DOI: 10.1016/j.peptides.2010.08.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 08/19/2010] [Accepted: 08/22/2010] [Indexed: 11/20/2022]
Abstract
Insect flight requires rapid mobilization of energy reserves during flight, which is mediated and regulated by hormonal control via adipokinetic hormones. The structure of the G-protein receptors to which these hormones bind, are crucial in understanding many of the physiological processes in which they play a central role. To date no 3D structure of an insect G-protein coupled receptor (GPCR) is available. Here, the first models of the 3D structures of a GPCR from the malaria mosquito are presented. Homology modeling of the receptor identified from the genome of Anopheles gambiae was used to construct two models of the receptor. The 7 transmembrane helical bundles of these two models are based on the crystal structures of beta2-adrenergic receptor and rhodopsin. The flexible loop regions were modeled using high temperature simulated annealing and constrained molecular dynamic simulations. The two receptor models differ in a number of critical features, the most important of which is that the rhodopsin-based model has a 'closed' structure while the beta2-based structure is 'open'. The 'open' conformation provides easy access of the hormone to the binding pocket. Docking calculations with the insect adipokinetic hormones, AKH-1 (pGlu-Leu-Thr-Phe-Thr-Pro-Ala-Trp-NH(2)) from the malaria mosquito and Del-CC (pGlu-Lys-Asn-Phe-Ser-Pro-Asn-Trp-Gly-Asn-NH(2)) from the blister beetle showed that while the binding motif of the two is similar, AKH-1 has more than 30 times higher affinity than Del-CC, which strongly suggests that the binding is specific, and that the correct binding site was identified. Using these models it is possible to design antagonists, which block the binding site and are thus species-specific insecticides.
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Affiliation(s)
- Grace Mugumbate
- Department of Chemistry, University of Cape Town, Private Bag x3, Rondebosch, 7701, Cape Town, South Africa
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18
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Zhao Y, Lu X, Yang CY, Huang Z, Fu W, Hou T, Zhang J. Computational modeling toward understanding agonist binding on dopamine 3. J Chem Inf Model 2011; 50:1633-43. [PMID: 20695484 DOI: 10.1021/ci1002119] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dopamine 3 (D3) receptor is a promising therapeutic target for the treatment of nervous system disorders, such as Parkinson's disease, and current research interests primarily focus on the discovery/design of potent D3 agonists. Herein, a well-designed computational protocol, which combines pharmacophore identification, homology modeling, molecular docking, and molecular dynamics (MD) simulations, was employed to understand the agonist binding on D3 aiming to provide insights into the development of novel potent D3 agonists. We (1) identified the chemical features required in effective D3 agonists by pharmacophore modeling based upon 18 known diverse D3 agonists; (2) constructed the three-dimensional (3D) structure of D3 based on homology modeling and the pharmacophore hypothesis; (3) identified the binding modes of the agonists to D3 by the correlation between the predicted binding free energies and the experimental values; and (4) investigated the induced fit of D3 upon agonist binding through MD simulations. The pharmacophore models of the D3 agonists and the 3D structure of D3 can be used for either ligand- or receptor-based drug design. Furthermore, the MD simulations further give the insight that the long and flexible EL2 acts as a "door" for agonist binding, and the "ionic lock" at the bottom of TM3 and TM6 is essential to transduce the activation signal.
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Affiliation(s)
- Yaxue Zhao
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China
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19
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Ortore G, Tuccinardi T, Orlandini E, Martinelli A. Different Binding Modes of Structurally Diverse Ligands for Human D3DAR. J Chem Inf Model 2010; 50:2162-75. [DOI: 10.1021/ci100290f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gabriella Ortore
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Tiziano Tuccinardi
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Elisabetta Orlandini
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy
| | - Adriano Martinelli
- Dipartimento di Scienze Farmaceutiche, Università di Pisa, via Bonanno 6, 56126 Pisa, Italy
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20
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López L, Selent J, Ortega R, Masaguer CF, Domínguez E, Areias F, Brea J, Loza MI, Sanz F, Pastor M. Synthesis, 3D-QSAR, and structural modeling of benzolactam derivatives with binding affinity for the D(2) and D(3) receptors. ChemMedChem 2010; 5:1300-17. [PMID: 20544783 DOI: 10.1002/cmdc.201000101] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A series of 37 benzolactam derivatives were synthesized, and their respective affinities for the dopamine D(2) and D(3) receptors evaluated. The relationships between structures and binding affinities were investigated using both ligand-based (3D-QSAR) and receptor-based methods. The results revealed the importance of diverse structural features in explaining the differences in the observed affinities, such as the location of the benzolactam carbonyl oxygen, or the overall length of the compounds. The optimal values for such ligand properties are slightly different for the D(2) and D(3) receptors, even though the binding sites present a very high degree of homology. We explain these differences by the presence of a hydrogen bond network in the D(2) receptor which is absent in the D(3) receptor and limits the dimensions of the binding pocket, causing residues in helix 7 to become less accessible. The implications of these results for the design of more potent and selective benzolactam derivatives are presented and discussed.
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Affiliation(s)
- Laura López
- GRIB, IMIM, DCEXS, Universitat Pompeu Fabra, Barcelona, Spain
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21
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Tehan BG, Lloyd EJ, Wong MG, Chalmers DK. Analysis of agonism by dopamine at the dopaminergic D 2 G-protein coupled receptor based on comparative modelling of rhodopsin. MOLECULAR SIMULATION 2010. [DOI: 10.1080/0892702021000002548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Gkountelias K, Papadokostaki M, Javitch JA, Liapakis G. Exploring the binding site crevice of a family B G protein-coupled receptor, the type 1 corticotropin releasing factor receptor. Mol Pharmacol 2010; 78:785-93. [PMID: 20664003 DOI: 10.1124/mol.110.065474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Family B of G protein-coupled receptors (GPCRs) is composed of receptors that bind peptides, such as secretin, glucagon, parathyroid hormone, and corticotropin releasing factor (CRF), which play critical physiological roles. These receptors, like all GPCRs, share a common structural motif of seven membrane-spanning segments, which have been proposed to bind small ligands, such as antalarmin, a nonpeptide antagonist of the type 1 receptor for CRF (CRF(1)). This leads to the hypothesis that as for family A GPCRs, the binding sites of small ligands for family B GPCRs are on the surface of a water-accessible crevice, the binding-site crevice, which is formed by the membrane-spanning segments and extends from the extracellular surface of the receptor into the plane of the membrane. To test this hypothesis we have begun to obtain structural information about family B GPCRs, using as a prototype the CRF(1), by determining the ability of sulfhydryl-specific methanethiosulfonate derivatives, such as the methanethiosulfonate-ethylammonium (MTSEA), to react with CRF(1) and thus irreversibly inhibit (125)I-Tyr(0)-sauvagine binding. We found that MTSEA inhibited (125)I-Tyr(0)-sauvagine binding to CRF(1) and that antalarmin protected against this irreversible inhibition. To identify the susceptible cysteine(s), we mutated, one at a time, four endogenous cysteines to serine. Mutation to serine of Cys211, Cys233, or Cys364 decreased the susceptibility of sauvagine binding to irreversible inhibition by MTSEA. Thus, Cys211, Cys233, and Cys364 at the cytoplasmic ends of the third, fourth, and seventh membrane-spanning segments, respectively, are exposed in the binding site crevice of CRF(1).
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Affiliation(s)
- Kostas Gkountelias
- Department of Pharmacology, Faculty of Medicine, University of Crete, Heraklion 71003, Crete, Greece
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23
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McRobb FM, Capuano B, Crosby IT, Chalmers DK, Yuriev E. Homology Modeling and Docking Evaluation of Aminergic G Protein-Coupled Receptors. J Chem Inf Model 2010; 50:626-37. [DOI: 10.1021/ci900444q] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Fiona M. McRobb
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, VIC 3052 Australia
| | - Ben Capuano
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, VIC 3052 Australia
| | - Ian T. Crosby
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, VIC 3052 Australia
| | - David K. Chalmers
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, VIC 3052 Australia
| | - Elizabeth Yuriev
- Medicinal Chemistry and Drug Action, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, VIC 3052 Australia
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24
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Holleran BJ, Domazet I, Beaulieu ME, Yan LP, Guillemette G, Lavigne P, Escher E, Leduc R. Identification of transmembrane domain 6 & 7 residues that contribute to the binding pocket of the urotensin II receptor. Biochem Pharmacol 2009; 77:1374-82. [DOI: 10.1016/j.bcp.2009.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2008] [Revised: 01/20/2009] [Accepted: 01/21/2009] [Indexed: 11/16/2022]
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25
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Runyon SP, Mosier PD, Roth BL, Glennon RA, Westkaemper RB. Potential modes of interaction of 9-aminomethyl-9,10-dihydroanthracene (AMDA) derivatives with the 5-HT2A receptor: a ligand structure-affinity relationship, receptor mutagenesis and receptor modeling investigation. J Med Chem 2008; 51:6808-28. [PMID: 18847250 DOI: 10.1021/jm800771x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The effects of 3-position substitution of 9-aminomethyl-9,10-dihydroanthracene (AMDA) on 5-HT 2A receptor affinity were determined and compared to a parallel series of DOB-like 1-(2,5-dimethoxyphenyl)-2-aminopropanes substituted at the 4-position. The results were interpreted within the context of 5-HT 2A receptor models that suggest that members of the DOB-like series can bind to the receptor in two distinct modes that correlate with the compounds' functional activity. Automated ligand docking and molecular dynamics suggest that all of the AMDA derivatives, the parent of which is a 5-HT 2A antagonist, bind in a fashion analogous to that for the sterically demanding antagonist DOB-like compounds. The failure of the F340 (6.52)L mutation to adversely affect the affinity of AMDA and the 3-bromo derivative is consistent with the proposed modes of orientation. Evaluation of ligand-receptor complex models suggest that a valine/threonine exchange between the 5-HT 2A and D 2 receptors may be the origin of selectivity for AMDA and two substituted derivatives.
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Affiliation(s)
- Scott P Runyon
- Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, Virginia 23298, USA
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26
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Clément M, Chamberland C, Pérodin J, Leduc R, Guillemette G, Escher E. The Active and the Inactive Form of the hAT1Receptor Have an Identical Ligand-Binding Environment: An MPA Study on a Constitutively Active Angiotensin II Receptor Mutant. J Recept Signal Transduct Res 2008; 26:417-33. [PMID: 17118790 DOI: 10.1080/10799890600923195] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Several models of activation mechanisms were proposed for G protein-coupled receptors (GPCRs), yet no direct methods exist for their elucidation. The availability of constitutively active mutants has given an opportunity to study active receptor conformations within acceptable limits using models such as the angiotensin II type 1 (AT1)1 receptor mutant N111G-hAT1 which displays an important constitutive activity. Recently, by using methionine proximity assay, we showed for the hAT1 receptor that TMD III, VI, and VII form the ligand-binding pocket of the C-terminal amino acid of an antagonistic AngII analogue. In the present contribution, we investigated whether the same residues would also constitute the ligand-binding contacts in constitutively activated mutant (CAM) receptors. For this purpose, the same Met mutagenesis strategy was carried out on the N111G double mutants. Analysis of 43 receptors mutants in the N111G-hAT1 series, photolabeled and CNBr digested, showed that there were only subtle structural changes between the wt-receptor and its constitutively active form.
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Affiliation(s)
- Martin Clément
- Department of Pharmacology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
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27
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Dölker N, Deupi X, Pardo L, Campillo M. Charge-charge and cation-π interactions in ligand binding to G protein-coupled receptors. Theor Chem Acc 2007. [DOI: 10.1007/s00214-007-0341-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Goddard WA, Abrol R. 3-Dimensional structures of G protein-coupled receptors and binding sites of agonists and antagonists. J Nutr 2007; 137:1528S-1538S; discussion 1548S. [PMID: 17513420 DOI: 10.1093/jn/137.6.1528s] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
We summarize here recent progress in predicting the 3-dimensional (3D) structure of G protein-coupled receptors (GPCR) and in predicting the binding sites for various agonists and antagonists. These receptors play a critical role in cell communications (dopamine, histamine, epinephrine, and serotonin) and in sensing the outside world (vision, smell, taste, and pain). There are no experimental 3D structures available for human GPCR despite their vital function and importance as therapeutic targets. Indeed, considering every form of life, there is an experimental structure for only 1 GPCR: bovine rhodopsin. Consequently, we developed the MembStruk method to predict the 3D structure without using homology. We then validated our predicted structures by using them to predict their binding sites and binding energies for strongly binding agonists and antagonists. The results were in excellent agreement with available binding and mutation experiments. We will summarize the results for adrenergic receptors, dopamine receptors, chemokine receptors, muscarinic acetylcholine receptors, and a tetrapeptide receptor (mas-related gene C11).
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Affiliation(s)
- William A Goddard
- Materials and Process Simulation Center, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA.
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29
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Al-Fulaij MA, Ren Y, Beinborn M, Kopin AS. Identification of amino acid determinants of dopamine 2 receptor synthetic agonist function. J Pharmacol Exp Ther 2007; 321:298-307. [PMID: 17204745 DOI: 10.1124/jpet.106.116384] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The human dopamine 2 receptor (hD2R) modulates locomotor activity, hormone secretion, and neuropsychiatric function. Current knowledge of the hD2R structure is in large part derived from mutagenesis studies and molecular pharmacologic analysis together with homology modeling using bovine rhodopsin as a template. In this study, we utilized comparison of the Drosophila D2-like receptor (DD2R) with the hD2R as a novel approach for identifying candidate amino acids that are determinants of ligand potency and/or efficacy. We focused our studies on four dopaminergic ligands that are used in the treatment of Parkinson's disease: bromocriptine, pergolide, piribedil, and ropinirole. All four ligands are potent agonists at the wild-type hD2R, whereas only bromocriptine shows comparable function at the DD2R. We performed site-directed mutagenesis to replace hD2R amino acids (modeled to project into the ligand binding pocket) with corresponding fly residues, and vice versa. Substitution of three amino acids in the hD2R with the homologous DD2R residues (V91A, C118S, and L170I) led to a pronounced loss of pergolide potency and efficacy. A converse triple amino acid substitution of human residues into the fly receptor (DD2R-A133V/S160C/I211L) markedly enhanced pergolide efficacy and potency at the mutant DD2R. The same substitutions also converted piribedil and ropinirole, which lacked appreciable activity on the DD2R, to partial agonists. These findings show the important role of these three residues in drug-receptor interactions. Our study illustrates that comparison of a mammalian receptor with an invertebrate homolog complements previously described strategies for defining G protein-coupled receptor structure-function relationships.
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Affiliation(s)
- Munya A Al-Fulaij
- Program in Genetics, Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, USA
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30
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Chen L, Durkin KA, Casida JE. Spontaneous mobility of GABAA receptor M2 extracellular half relative to noncompetitive antagonist action. J Biol Chem 2006; 281:38871-8. [PMID: 17050528 DOI: 10.1074/jbc.m608301200] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The gamma-aminobutyric acid type A receptor beta(3) homopentamer is spontaneously open and highly sensitive to many noncompetitive antagonists(NCAs) and Zn(2+). Our earlier study of the M2 cytoplasmic half (-1' to 10') established a model in which NCAs bind at pore-lining residues Ala(2)', Thr(6)', and Leu(9)'. To further define transmembrane 2 (M2) structure relative to NCA action, we extended the Cys scanning to the extra cellular half of the beta(3) homopentamer (11' to 20'). Spontaneous disulfides formed with T13'C, L18'C, and E20'C from M2/M2 cross-linking and with I14'C (weak), H17'C, and R19'Con bridging M2/M3 intersubunits, based on single (M2 Cys only) and dual (M2 Cys plus M3 C289S) mutations. Induced disulfides also formed with T16'C, but there were few or none with M11'C, T12'C, and N15'C. These findings show conformational flexibility/mobility in the M2 extracellular half 17' to 20' region interpreted as a deformed beta-like conformation in the open channel. The NCA radioligands used were [(3)H]1-(4-ethynylphenyl)-4-n-propyl-2,6,7-trioxabicyclo[2.2.2]octane ([(3)H]EBOB) and [(3)H]3,3-bis-trifluoromethylbicyclo[2.2.1]heptane-2,2-dicarbonitrile with essentially the same results. NCA binding was disrupted by individual Cys substitutions at 13',14',16',17', and 19'. The inactivity of T13'C/T13'S may have been due to disturbance of the channel gate; I14'S and T16'S showed much better binding activity than their Cys counterparts, and the low activities of H17'C and R19'C were reversed by dithiothreitol. Zn(2+) potency for inhibition of [(3)H]EBOB binding was lowered 346-fold by the mutation H17'A. We propose that NCAs enter their binding site both directly, through the channel pore, and indirectly, through the water cavity of adjacent subunits.
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Affiliation(s)
- Ligong Chen
- Environmental Chemistry and Toxicology Laboratory, Department of Environmental Science, Policy, and Management, College of Chemistry, University of California-Berkeley, CA 94720, USA
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31
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Boeckler F, Gmeiner P. The structural evolution of dopamine D3 receptor ligands: structure-activity relationships and selected neuropharmacological aspects. Pharmacol Ther 2006; 112:281-333. [PMID: 16905195 DOI: 10.1016/j.pharmthera.2006.04.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Accepted: 04/13/2006] [Indexed: 01/13/2023]
Abstract
"Evolution consists largely of molecular tinkering."-Following the famous concept of the molecular geneticist and medicine Nobel laureate François Jacob, in this review we describe the structural evolution of dopamine D3 receptor ligands from the natural agonist dopamine (DA) to highly potent and subtype selective new agents by bioisosteric tinkering with well-established and privileged or novel and fancy chemical functionalities and scaffolds. Some of the more than 200 ligands presented herein have already achieved therapeutic or scientific value up to now, some will most likely achieve it in the future. Hence, great importance is not only attached to the relationship between structure and activity of the ligands, but also to their utility as pharmacological tools in animal models or as therapeutics in patients with neurological diseases or other disorders.
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Affiliation(s)
- Frank Boeckler
- Department of Medicinal Chemistry, Emil Fischer Center, Friedrich-Alexander University Erlangen-Nürnberg, Schuhstrasse 19, 91052 Erlangen, Germany.
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32
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Xu W, Campillo M, Pardo L, de Riel JK, Liu-Chen LY. The seventh transmembrane domains of the delta and kappa opioid receptors have different accessibility patterns and interhelical interactions. Biochemistry 2006; 44:16014-25. [PMID: 16331961 PMCID: PMC2688720 DOI: 10.1021/bi050938a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We applied the substituted cysteine accessibility method (SCAM) to map the residues of the transmembrane helices (TMs) 7 of delta and kappa opioid receptors (deltaOR and kappaOR) that are on the water-accessible surface of the binding-site crevices. A total of 25 consecutive residues (except C7.38) in the TMs 7 were mutated to Cys, one at a time, and each mutant was expressed in HEK 293 cells. Most mutants displayed similar binding affinity for [(3)H]diprenorphine, an antagonist, as the wild types. Pretreatment with (2-aminoethyl)methanethiosulfonate (MTSEA) inhibited [(3)H]diprenorphine binding to eight deltaOR and eight kappaOR mutants. All mutants except deltaOR L7.52(317)C were protected by naloxone from the MTSEA effect, indicating that the side chains of V7.31(296), A7.34(299), I7.39(304), L7.41(306), G7.42(307), P7.50(315), and Y7.53(318) of deltaOR and S7.34(311), F7.37(314), I7.39(316), A7.40(317), L7.41(318), G7.42(319), Y7.43(320), and N7.49(326) of kappaOR are on the water-accessible surface of the binding pockets. Combining the SCAM data with rhodopsin-based molecular models of the receptors led to the following conclusions. (i) The residues of the extracellular portion of TM7 predicted to face TM1 are sensitive to MTSEA in kappaOR but are not in deltaOR. Thus, TM1 may be closer to TM7 in deltaOR than in kappaOR. (ii) MTSEA-sensitive mutants start at position 7.31(296) in deltaOR and at 7.34(311) in kappaOR, suggesting that TM7 in deltaOR may have an additional helical turn (from 7.30 to 7.33). (iii) There is a conserved hydrogen-bond network linking D2.50 of the NLxxxD motif in TM2 with W6.48 of the CWxP motif in TM6. (iv) The NPxxY motif in TM7 interacts with TM2, TM6, and helix 8 to maintain receptors in inactive states. To the best of our knowledge, this represents the first such comparison of the structures of two highly homologous GPCRs.
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MESH Headings
- Amino Acid Sequence
- Animals
- Binding Sites
- Cattle
- Cell Line
- Cysteine/metabolism
- Humans
- Hydrogen Bonding
- Models, Molecular
- Molecular Sequence Data
- Protein Structure, Secondary
- Receptors, Opioid, delta/chemistry
- Receptors, Opioid, delta/genetics
- Receptors, Opioid, kappa/chemistry
- Receptors, Opioid, kappa/genetics
- Sequence Alignment
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Affiliation(s)
- Wei Xu
- Department of Pharmacology and Center for Substance Abuse Research, Temple University School of Medicine, Philadelphia, PA
| | - Mercedes Campillo
- Laboratori de Medicina Computacional, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - Leonardo Pardo
- Laboratori de Medicina Computacional, Unitat de Bioestadística and Institut de Neurociències, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain
| | - J. Kim de Riel
- Fels Institute for Molecular Biology and Cancer Research, Temple University School of Medicine, Philadelphia, PA
| | - Lee-Yuan Liu-Chen
- Department of Pharmacology and Center for Substance Abuse Research, Temple University School of Medicine, Philadelphia, PA
- Address correspondence to: Dr. Lee-Yuan Liu-Chen, Department of Pharmacology, Temple University School of Medicine, 3420 N. Broad St., Philadelphia, PA 19140, phone: (215) 707−4188; fax: (215) 707−7068; e-mail:
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Clément M, Martin SS, Beaulieu ME, Chamberland C, Lavigne P, Leduc R, Guillemette G, Escher E. Determining the Environment of the Ligand Binding Pocket of the Human Angiotensin II Type I (hAT1) Receptor Using the Methionine Proximity Assay. J Biol Chem 2005; 280:27121-9. [PMID: 15890659 DOI: 10.1074/jbc.m413653200] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The peptide hormone angiotensin II (AngII) binds to the AT0 (angiotensin type 1) receptor within the transmembrane domains in an extended conformation, and its C-terminal residue interacts with transmembrane domain VII at Phe-293/Asn-294. The molecular environment of this binding pocket remains to be elucidated. The preferential binding of benzophenone photolabels to methionine residues in the target structure has enabled us to design an experimental approach called the methionine proximity assay, which is based on systematic mutagenesis and photolabeling to determine the molecular environment of this binding pocket. A series of 44 transmembrane domain III, VI, and VII X --> Met mutants photolabeled either with 125I-[Sar1,p'-benzoyl-L-Phe8]AngII or with 125I-[Sar1,p''-methoxy-p'-benzoyl-L-Phe8]AngII were purified and digested with cyanogen bromide. Several mutants produced digestion patterns different from that observed with wild type human AT1, indicating that they had a new receptor contact with position 8 of AngII. The following residues form this binding pocket: L112M and Y113M in transmembrane domain (TMD) III; F249M, W253M, H256M, and T260M in TMD VI; and F293M, N294M, N295M, C296M, and L297M in TMD VII. Homology modeling and incorporation of these contacts allowed us to develop an evidence-based molecular model of interactions with human AT1 that is very similar to the rhodopsin-retinal interaction.
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Affiliation(s)
- Martin Clément
- Department of Pharmacology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Quebec J1H 5N4, Canada
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Cox A, Donnelly D, Kaur M, Cheetham SC, Cockcroft VB, Findlay JBC. MTSEA prevents ligand binding to the human melanocortin-4 receptor by modification of cysteine 130 in transmembrane helix 3. FEBS Lett 2005; 579:285-91. [PMID: 15620728 DOI: 10.1016/j.febslet.2004.11.087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2004] [Revised: 10/07/2004] [Accepted: 11/18/2004] [Indexed: 10/26/2022]
Abstract
We have investigated the effect of the sulfhydryl-reactive reagent, methyl thiosulfonate ethylammonium (MTSEA), on ligand binding to the human melanocortin-4 (MC4) receptor stably expressed in HEK-293 cells. MTSEA inhibited binding of the agonist, 125I-NDPalpha-MSH, and the antagonist, 125I-SHU9119, in a concentration-dependent manner. Pre-incubation of cells with either the agonist or antagonist protected from subsequent MTSEA inhibition of radioligand binding. Mutation of Cys130 in transmembrane helix 3 to alanine, whilst not affecting ligand binding, led to a complete loss of the inhibitory effect of MTSEA. Since other types of sulfhydryl-reactive reagents had no effect on ligand binding, we conclude that covalent modification of Cys130 by MTSEA disrupts ligand binding by neutralising a close-by negative charge, most likely on Asp126.
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Affiliation(s)
- Alan Cox
- School of Biochemistry and Microbiology, University of Leeds, Leeds LS2 9JT, UK.
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35
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Hjerde E, Dahl SG, Sylte I. Atypical and typical antipsychotic drug interactions with the dopamine D2 receptor. Eur J Med Chem 2005; 40:185-94. [PMID: 15694653 DOI: 10.1016/j.ejmech.2004.10.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Revised: 09/27/2004] [Accepted: 10/15/2004] [Indexed: 11/21/2022]
Abstract
A model of the dopamine D2 receptor was used to study the receptor interactions of dopamine, the typical antipsychotics haloperidol and loxapine, and the atypical antipsychotics clozapine and melperone. The atypical antipsychotics interacted with the halogen atom of the ring system in the direction of the transmembrane helices (TMHs) 2, 3 and 7, while the typical had the corresponding halogen atom in the direction of TMH5. Molecular dynamics simulations indicated that the average helical displacement upon binding increased in the order: typical < atypical < dopamine. Upon binding, the atypical induced larger displacements into TMH5 than did the typical. The typical had stronger non-bonded interactions with the receptor than had the atypical, which is in agreement with the experimental observation that the atypical antipsychotic drugs dissociate faster from the receptor than the typical antipsychotic drugs.
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Affiliation(s)
- Erik Hjerde
- Department of Pharmacology, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway
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36
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Gouldson PR, Kidley NJ, Bywater RP, Psaroudakis G, Brooks HD, Diaz C, Shire D, Reynolds CA. Toward the active conformations of rhodopsin and the beta2-adrenergic receptor. Proteins 2004; 56:67-84. [PMID: 15162487 DOI: 10.1002/prot.20108] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Using sets of experimental distance restraints, which characterize active or inactive receptor conformations, and the X-ray crystal structure of the inactive form of bovine rhodopsin as a starting point, we have constructed models of both the active and inactive forms of rhodopsin and the beta2-adrenergic G-protein coupled receptors (GPCRs). The distance restraints were obtained from published data for site-directed crosslinking, engineered zinc binding, site-directed spin-labeling, IR spectroscopy, and cysteine accessibility studies conducted on class A GPCRs. Molecular dynamics simulations in the presence of either "active" or "inactive" restraints were used to generate two distinguishable receptor models. The process for generating the inactive and active models was validated by the hit rates, yields, and enrichment factors determined for the selection of antagonists in the inactive model and for the selection of agonists in the active model from a set of nonadrenergic GPCR drug-like ligands in a virtual screen using ligand docking software. The simulation results provide new insights into the relationships observed between selected biochemical data, the crystal structure of rhodopsin, and the structural rearrangements that occur during activation.
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Kristiansen K. Molecular mechanisms of ligand binding, signaling, and regulation within the superfamily of G-protein-coupled receptors: molecular modeling and mutagenesis approaches to receptor structure and function. Pharmacol Ther 2004; 103:21-80. [PMID: 15251227 DOI: 10.1016/j.pharmthera.2004.05.002] [Citation(s) in RCA: 392] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The superfamily of G-protein-coupled receptors (GPCRs) could be subclassified into 7 families (A, B, large N-terminal family B-7 transmembrane helix, C, Frizzled/Smoothened, taste 2, and vomeronasal 1 receptors) among mammalian species. Cloning and functional studies of GPCRs have revealed that the superfamily of GPCRs comprises receptors for chemically diverse native ligands including (1) endogenous compounds like amines, peptides, and Wnt proteins (i.e., secreted proteins activating Frizzled receptors); (2) endogenous cell surface adhesion molecules; and (3) photons and exogenous compounds like odorants. The combined use of site-directed mutagenesis and molecular modeling approaches have provided detailed insight into molecular mechanisms of ligand binding, receptor folding, receptor activation, G-protein coupling, and regulation of GPCRs. The vast majority of family A, B, C, vomeronasal 1, and taste 2 receptors are able to transduce signals into cells through G-protein coupling. However, G-protein-independent signaling mechanisms have also been reported for many GPCRs. Specific interaction motifs in the intracellular parts of these receptors allow them to interact with scaffold proteins. Protein engineering techniques have provided information on molecular mechanisms of GPCR-accessory protein, GPCR-GPCR, and GPCR-scaffold protein interactions. Site-directed mutagenesis and molecular dynamics simulations have revealed that the inactive state conformations are stabilized by specific interhelical and intrahelical salt bridge interactions and hydrophobic-type interactions. Constitutively activating mutations or agonist binding disrupts such constraining interactions leading to receptor conformations that associates with and activate G-proteins.
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Affiliation(s)
- Kurt Kristiansen
- Department of Pharmacology, Institute of Medical Biology, University of Tromsø, N-9037 Tromsø, Norway.
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38
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Rivail L, Giner M, Gastineau M, Berthouze M, Soulier JL, Fischmeister R, Lezoualc'h F, Maigret B, Sicsic S, Berque-Bestel I. New insights into the human 5-HT4 receptor binding site: exploration of a hydrophobic pocket. Br J Pharmacol 2004; 143:361-70. [PMID: 15351779 PMCID: PMC1575351 DOI: 10.1038/sj.bjp.0705950] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
A body of evidences suggests that a hydrophobic pocket of the human 5-HT(4) receptor contributes to the high affinity of some bulky 5-HT(4) ligands. A thorough study of this pocket was performed using mutagenesis and molecular modeling. Ligand binding or competition studies with selected bulky ligands (RS39604, RS100235, [(3)H]GR113808 and ML11411) and small ligands (5-HT and ML10375) were carried out on wild-type and mutant receptors (W7.40A/F, Y7.43F, R3.28L) transiently transfected in COS-7 cells. The functional activity of the mutated receptors was evaluated by measuring the ability of 5-HT to stimulate adenylyl cyclase. For W7.40F mutation, no changes in the affinity of studied ligands and in the functional activity of the mutant receptor were observed, in contrary to W7.40A mutation, which abolished both binding of ligands and 5-HT-induced cAMP production. Mutation R3.28L revealed a totally silent receptor with a basal level of cAMP production similar to the mock control despite its ability to product cAMP in the presence of 5-HT. Moreover, a one order loss of affinity of RS39604 and a 45-fold increase of ML11411 affinity were observed. Mutation Y7.43F modified the affinity of GR113808, which displays a 13-fold lower affinity for the mutant than for the wild-type receptor. In conclusion, in the hydrophobic pocket, two polar amino acids are able to interact through hydrogen bonds with bulky ligands depending on their chemical properties. Moreover, these experimental data may validate the proposed new three-dimensional model of the human 5-HT(4) receptor.
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Affiliation(s)
- Lucie Rivail
- Biocis, UMR-8076 (CNRS), Faculté de Pharmacie, Université Paris-Sud, 5 rue JB Clément, 92296 Châtenay-Malabry, France
| | - Mireille Giner
- Biocis, UMR-8076 (CNRS), Faculté de Pharmacie, Université Paris-Sud, 5 rue JB Clément, 92296 Châtenay-Malabry, France
| | - Monique Gastineau
- Unité INSERM U-446, Laboratoire de Cardiologie Moléculaire et Cellulaire, Faculté de Pharmacie, 92296 Châtenay-Malabry, France
| | - Magali Berthouze
- Unité INSERM U-446, Laboratoire de Cardiologie Moléculaire et Cellulaire, Faculté de Pharmacie, 92296 Châtenay-Malabry, France
| | - Jean-Louis Soulier
- Biocis, UMR-8076 (CNRS), Faculté de Pharmacie, Université Paris-Sud, 5 rue JB Clément, 92296 Châtenay-Malabry, France
| | - Rodolphe Fischmeister
- Unité INSERM U-446, Laboratoire de Cardiologie Moléculaire et Cellulaire, Faculté de Pharmacie, 92296 Châtenay-Malabry, France
| | - Frank Lezoualc'h
- Unité INSERM U-446, Laboratoire de Cardiologie Moléculaire et Cellulaire, Faculté de Pharmacie, 92296 Châtenay-Malabry, France
| | - Bernard Maigret
- UMR-7565, Equipe de Dynamique des Assemblages Membranaires, Université Henri Poincaré, 54506 Vandœuvre, Nancy, France
| | - Sames Sicsic
- Biocis, UMR-8076 (CNRS), Faculté de Pharmacie, Université Paris-Sud, 5 rue JB Clément, 92296 Châtenay-Malabry, France
| | - Isabelle Berque-Bestel
- Biocis, UMR-8076 (CNRS), Faculté de Pharmacie, Université Paris-Sud, 5 rue JB Clément, 92296 Châtenay-Malabry, France
- Author for correspondence:
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Shim JY, Welsh WJ, Howlett AC. Homology model of the CB1 cannabinoid receptor: sites critical for nonclassical cannabinoid agonist interaction. Biopolymers 2004; 71:169-89. [PMID: 12767117 DOI: 10.1002/bip.10424] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Association of cannabimimetic compounds such as cannabinoids, aminoalkylindoles (AAIs), and arachidonylethanolamide (anandamide) with the brain cannabinoid (CB(1)) receptor activates G-proteins and relays signals to regulate neuronal functions. A CB(1) receptor homology model was constructed using the published x-ray crystal structure of bovine rhodopsin (Palczewski et al., Science, 2000, Vol. 289, pp. 739-745) in the conformation most likely to represent the "high-affinity" state for agonist binding to G-protein coupled receptors (GPCRs). A molecular docking approach that combined Monte Carlo and molecular dynamics simulations was used to identify the putative binding conformations of nonclassical cannabinoid agonists, including AC-bicyclic CP47497 and CP55940, and ACD-tricyclic CP55244. Placement of these ligands was based upon the assumption of a critical hydrogen bond between the A-ring OH and the side chain N of Lys192 in transmembrane helix 3. We evaluated two alternative binding conformations, C3-in and C3-out, denoting the directionality of the ligand C3 side chain within the receptor with respect to the inside or the outside of the cell. Assuming both the C3-in or C3-out conformation, the calculated ligand-receptor binding energy (DeltaE(bind)) was correlated with the experimentally observed binding affinity (K(i)) for a series of nonclassical cannabinoid agonists. The C3-in conformation was marginally better than the alternative C3-out conformation in predicting the rank order of the tested nonclassical cannabinoid analogs. Adopting the C3-in conformation due to the greater number of receptor interactions with known pharmacophoric elements of the ligand, key residues were identified comprising the presumed hydrophobic pocket that interacts with the C3 side chain of cannabinoid agonists. Key hydrogen bonds would form between both K3.28(192) and E(258) and the A-ring OH, and between Q(261) and the C-ring C-12 hydroxypropyl. In summary, the present study represents one of the first attempts to construct a homology model of the CB(1) cannabinoid receptor based upon the published bovine rhodopsin x-ray crystal structure and to elucidate the putative ligand binding site for nonclassical cannabinoid agonists. We postulated sites of the CB(1) receptor critical for the ligand interaction, including the hydrophobic pocket interacting with the key pharmacophoric moiety, the C3 side chain. More work is needed to delineate between two alternative (and possibly other) binding conformations of the nonclassical cannabinoid ligands within the CB(1) receptor. The present study provides a consistent framework for further investigation of the CB(1) receptor-ligand interaction and for the study of CB(1) receptor activation.
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Affiliation(s)
- Joong-Youn Shim
- Department of Basic Pharmaceutical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC 29208, USA.
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40
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Kalani MYS, Vaidehi N, Hall SE, Trabanino RJ, Freddolino PL, Kalani MA, Floriano WB, Kam VWT, Goddard WA. The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists. Proc Natl Acad Sci U S A 2004; 101:3815-20. [PMID: 14999101 PMCID: PMC374327 DOI: 10.1073/pnas.0400100101] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dopamine neurotransmitter and its receptors play a critical role in the cell signaling process responsible for information transfer in neurons functioning in the nervous system. Development of improved therapeutics for such disorders as Parkinson's disease and schizophrenia would be significantly enhanced with the availability of the 3D structure for the dopamine receptors and of the binding site for dopamine and other agonists and antagonists. We report here the 3D structure of the long isoform of the human D2 dopamine receptor, predicted from primary sequence using first-principles theoretical and computational techniques (i.e., we did not use bioinformatic or experimental 3D structural information in predicting structures). The predicted 3D structure is validated by comparison of the predicted binding site and the relative binding affinities of dopamine, three known dopamine agonists (antiparkinsonian), and seven known antagonists (antipsychotic) in the D2 receptor to experimentally determined values. These structures correctly predict the critical residues for binding dopamine and several antagonists, identified by mutation studies, and give relative binding affinities that correlate well with experiments. The predicted binding site for dopamine and agonists is located between transmembrane (TM) helices 3, 4, 5, and 6, whereas the best antagonists bind to a site involving TM helices 2, 3, 4, 6, and 7 with minimal contacts to TM helix 5. We identify characteristic differences between the binding sites of agonists and antagonists.
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Affiliation(s)
- M Yashar S Kalani
- Materials and Process Simulation Center, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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41
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Shi L, Javitch JA. The second extracellular loop of the dopamine D2 receptor lines the binding-site crevice. Proc Natl Acad Sci U S A 2004; 101:440-5. [PMID: 14704269 PMCID: PMC327166 DOI: 10.1073/pnas.2237265100] [Citation(s) in RCA: 170] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The binding site of the dopamine D(2) receptor (D2R), like those of homologous rhodopsin-like G protein-coupled receptors (GPCRs) that bind small molecules, is contained within a water-accessible crevice formed among its seven transmembrane segments (TMs). The high-resolution structure of bovine rhodopsin, however, revealed that the second extracellular loop (E2), which connects TM4 and TM5, folds down into the transmembrane domain and forms part of the ligand-binding surface for retinal. Whether E2 plays a related role in other rhodopsin-like GPCRs is unclear. To address this issue, we have now mutated to cysteine, one at a time, 10 consecutive residues in E2 of D2R. The reaction of five of these mutants with sulfhydryl reagents inhibited antagonist binding, and bound antagonist protected two, I184C and N186C, from reaction. The pattern of accessibility in E2 is consistent with a structure similar to that of bovine rhodopsin, in which the region C-terminal to the conserved disulfide bond is deeper in the binding-site crevice than is the N-terminal part of E2. Thus, E2 likely contributes to the binding site in the D2R and probably in other aminergic GPCRs as well. Knowledge of its detailed positioning and interactions with ligand would benefit GPCR molecular modeling and facilitate the design of novel drugs.
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Affiliation(s)
- Lei Shi
- Center for Molecular Recognition, Columbia University College of Physicians and Surgeons, 630 West 168th Street, New York, NY 10032, USA
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Ma C, Kotaria R, Mayor JA, Eriks LR, Dean AM, Walters DE, Kaplan RS. The Mitochondrial Citrate Transport Protein. J Biol Chem 2004; 279:1533-40. [PMID: 14561747 DOI: 10.1074/jbc.m310866200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mitochondrial citrate transport protein (CTP) has been investigated by mutating 28 consecutive residues within transmembrane domain III (TMDIII), one at a time, to cysteine. A cysteine-less CTP that retains wild-type functional properties, served as the starting template. The single Cys CTP mutants were abundantly expressed in Escherichia coli, isolated, and functionally reconstituted in a liposomal system. The accessibility of each single Cys mutant to two methanethiosulfonate reagents was evaluated by determining the rate constants for inhibition of CTP function. These rate constants varied by over five orders of magnitude. With two independent data sets we observed peaks and troughs in the rate constant data at identical amino acid positions and a periodicity of 4 was observed from residues 123-137. Based on the pattern of accessibility we conclude that residues 123-137 exist as an alpha-helix. Although less certain, a combination of the rate constant data and the specific activity data with the single Cys mutants suggests that the alpha-helical secondary structure may extend to residue 113. Furthermore, the rate constant data define water-accessible and water-inaccessible faces of the helix. We infer that the water-accessible face comprises a portion of the substrate translocation pathway through the CTP, whereas the water-inaccessible surface faces the lipid bilayer. Finally, based on a combination of the CTP inhibition rate constant data and the existence of significant sequence identity with a transmembrane segment within glycophorin A that forms a portion of its dimer interface, a model for a putative CTP TMDIII-TMDIII' dimer interface has been developed.
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Affiliation(s)
- Chunlong Ma
- Department of Biochemistry and Molecular Biology, Finch University of Health Sciences/The Chicago Medical School, North Chicago, Illinois 60064, USA
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Akabas MH. GABAA Receptor Structure–Function Studies: A Reexamination in Light of New Acetylcholine Receptor Structures. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2004; 62:1-43. [PMID: 15530567 DOI: 10.1016/s0074-7742(04)62001-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Myles H Akabas
- Department of Physiology and Biophysics, Albert Einstein College of Medicine, Yeshiva University, Bronx, New York 10461, USA
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Kulkarni AA, Haworth IS, Uchiyama T, Lee VHL. Analysis of Transmembrane Segment 7 of the Dipeptide Transporter hPepT1 by Cysteine-scanning Mutagenesis. J Biol Chem 2003; 278:51833-40. [PMID: 14532279 DOI: 10.1074/jbc.m308356200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To investigate the involvement of transmembrane segment 7 (TMS7) of hPepT1 in forming the putative central aqueous channel through which the substrate traverses, we individually mutated each of the 21 amino acids in TMS7 to a cysteine and analyzed the mutated transporters using the scanning cysteine accessibility method. Y287C- and M292C-hPepT1 did not express at the plasma membrane. Out of the remaining 19 transporters, three (F293C-, L296C-, and F297C-hPepT1) showed negligible glycyl-sarcosine (gly-sar) uptake activity and may play an important role in defining the overall hPepT1 structure. K278C-hPepT1 showed approximately 40% activity and the 15 other transporters exhibited more than 50% gly-sar uptake when compared with wild type (WT)-hPepT1. Gly-sar uptake for the 16 active transporters containing cysteine mutations was then measured in the presence of 2.5 mM 2-aminoethyl methanethiosulfonate hydrobromide (MTSEA) or 1 mM [2-(trimethylammonium) ethyl] methanethiosulfonate bromide (MTSET). Gly-sar uptake was significantly inhibited for each of the 16 single cysteine mutants in the presence of 2.5 mM MTSEA. In contrast, significant inhibition of uptake was only observed for K278C-, M279C-, V280C-, T281C-, M284C-, L286C-, P291C-, and D298C-hPepT1 in the presence of 1 mM MTSET. MTSET modification of R282C-hPepT1 resulted in a significant increase in gly-sar uptake. To investigate this further, we mutated WT-hPepT1 to R282A-, R282E-, and R282K-hPepT1. R282E-hPepT1 showed a 43% reduction in uptake activity, whereas R282A- and R282K-hPepT1 had activities comparable with WT-hPepT1, suggesting a role for the Arg-282 positive charge in substrate translocation. Most of the amino acids that were MTSET-sensitive upon cysteine mutation, including R282C, are located toward the intracellular end of TMS7. Hence, our results suggest that TMS7 of hPepT1 is relatively solvent-accessible along most of its length but that the intracellular end of the transmembrane domain is particularly so. From a structure-function perspective, we speculate that the extracellular end of TMS7 may shift following substrate binding, providing the basis for channel opening and substrate translocation.
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Affiliation(s)
- Ashutosh A Kulkarni
- Department of Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121, USA
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45
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Boucard AA, Roy M, Beaulieu ME, Lavigne P, Escher E, Guillemette G, Leduc R. Constitutive activation of the angiotensin II type 1 receptor alters the spatial proximity of transmembrane 7 to the ligand-binding pocket. J Biol Chem 2003; 278:36628-36. [PMID: 12842881 DOI: 10.1074/jbc.m305952200] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Activation of G protein-coupled receptors by agonists involves significant movement of transmembrane domains (TM) following binding of agonist. The underlying structural mechanism by which receptor activation takes place is largely unknown but can be inferred by detecting variability within the environment of the ligand-binding pocket, which constitutes a water-accessible crevice surrounded by the seven TM helices. Using the substituted cysteine accessibility method, we initially identified those residues within the seventh transmembrane domain (TM7) of wild type angiotensin II type 1 (AT1) receptor that contribute to forming the binding site pocket. We have substituted successively TM7 residues ranging from Ile276 to Tyr302 to cysteine. Treatment of A277C, V280C, T282C, A283C, I286C, A291C, and F301C mutant receptors with the charged sulfhydryl-specific alkylating agent MTSEA significantly inhibited ligand binding, which suggests that these residues orient themselves within the water-accessible binding pocket of the AT1 receptor. Interestingly, this pattern of acquired MTSEA sensitivity was greatly reduced for TM7 reporter cysteines engineered in a constitutively active mutant of the AT1 receptor. Our data suggest that upon activation, TM7 of the AT1 receptor goes through a pattern of helical movements that results in its distancing from the binding pocket per se. These studies support accumulating evidence whereby elements of TM7 of class A GPCRs promote activation of the receptor through structural rearrangements.
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Affiliation(s)
- Antony A Boucard
- Department of Pharmacology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec J1H 5N4, Canada
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46
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Kulkarni AA, Haworth IS, Lee VHL. Transmembrane segment 5 of the dipeptide transporter hPepT1 forms a part of the substrate translocation pathway. Biochem Biophys Res Commun 2003; 306:177-85. [PMID: 12788085 DOI: 10.1016/s0006-291x(03)00926-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This study is the first systematic attempt to investigate the role of transmembrane segment 5 of hPepT1, the most conserved segment across different species, in forming a part of the aqueous substrate translocation pathway. We used cysteine-scanning mutagenesis in conjunction with the sulfhydryl-specific reagents, MTSEA and MTSET. Neither of these reagents reduced wild-type-hPepT1 transport activity in HEK293 cells and Xenopus oocytes. Twenty-one single cysteine mutations in hPepT1 were created by replacing each residue within TMS5 with a cysteine. HEK293 cells were then transfected with each mutated protein and the steady-state protein level, [3H]Gly-Sar uptake activity, and sensitivity to the MTS reagents were measured. S164C-, L168C-, G173C-, and I179C-hPepT1 were not expressed on the plasma membrane. Y167C-, N171C-, and S174C-hPepT1 showed </=25% Gly-Sar uptake when compared with WT-hPepT1. P182C-hPepT1 showed approximately 40% specific activity whereas all the remaining transporters, although still sensitive to single cysteine mutations, exhibited more than 50% specific activity when compared to WT-hPepT1. The activity of F166C-, L176C-, S177C-, T178C-, I180C-, T181C-, and P182C-hPepT1 was partially inhibited, while the activity of F163C- and I170C-hPepT1 was completely inhibited by 2.5mM MTSEA. F163C, I165C, F166C, A169C, I170C, S177C, T181C, and P182C were clearly accessible to 1mM MTSET. Overall, these results suggest that TMS5 lines the putative aqueous channel and is slightly tilted from the vertical axis of the channel, with the exofacial half forming a classical amphipathic alpha-helix and the cytoplasmic half being highly solvent accessible.
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Affiliation(s)
- Ashutosh A Kulkarni
- Department of Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA
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Bera AK, Chatav M, Akabas MH. GABA(A) receptor M2-M3 loop secondary structure and changes in accessibility during channel gating. J Biol Chem 2002; 277:43002-10. [PMID: 12226083 DOI: 10.1074/jbc.m206321200] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The gamma-aminobutyric acid type A (GABA(A)) receptor M2-M3 loop structure and its role in gating were investigated using the substituted cysteine accessibility method. Residues from alpha(1)Arg-273 to alpha(1)Ile-289 were mutated to cysteine, one at a time. MTSET(+) or MTSES(-) reacted with all mutants from alpha(1)R273C to alpha(1)Y281C, except alpha(1)P277C, in the absence and presence of GABA. The MTSET(+) closed-state reaction rate was >1000 liters/mol-s at alpha(1)N274C, alpha(1)S275C, alpha(1)K278C, and alpha(1)Y281C and was <300 liters/mol-s at alpha(1)R273C, alpha(1)L276C, alpha(1)V279C, alpha(1)A280C, and alpha(1)A284C. These two groups of residues lie on opposite sides of an alpha-helix. The fast reacting group lies on a continuation of the M2 segment channel-lining helix face. This suggests that the M2 segment alpha-helix extends about two helical turns beyond alpha(1)N274 (20'), aligned with the extracellular ring of charge. At alpha(1)S275C, alpha(1)V279C, alpha(1)A280C, and alpha(1)A284C the reaction rate was faster in the presence of GABA. The reagents had no functional effect on the mutants from alpha(1)A282C to alpha(1)I289C, except alpha(1)A284C. Access may be sterically hindered possibly by close interaction with the extracellular domain. We suggest that the M2 segment alpha-helix extends beyond the predicted extracellular end of the M2 segment and that gating induces a conformational change in and/or around the N-terminal half of the M2-M3 loop. Implications for coupling ligand-evoked conformational changes in the extracellular domain to channel gating in the membrane-spanning domain are discussed.
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Affiliation(s)
- Amal K Bera
- Department of Physiology & Biophysics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Shi L, Javitch JA. The binding site of aminergic G protein-coupled receptors: the transmembrane segments and second extracellular loop. Annu Rev Pharmacol Toxicol 2002; 42:437-67. [PMID: 11807179 DOI: 10.1146/annurev.pharmtox.42.091101.144224] [Citation(s) in RCA: 270] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In the current chapter, we review approaches to the identification of the residues forming the binding sites for agonists, antagonists, and allosteric modulators in the family of aminergic G protein-coupled receptors (GPCRs). We then review the structural bases for ligand binding and pharmacological specificity based on the application of these methods to muscarinic cholinergic, adrenergic, dopaminergic, serotonergic, and histaminergic receptors, using the high resolution rhodopsin structure as a template. Furthermore, we propose a critical role of the second extracellular loop in forming the binding site for small molecular weight aminergic ligands, much as this loop dives down into the binding-site crevice and contacts retinal in rhodopsin.
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Affiliation(s)
- Lei Shi
- Center for Molecular Recognition and Department of Pharmacology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA.
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Javitch JA, Shi L, Liapakis G. Use of the substituted cysteine accessibility method to study the structure and function of G protein-coupled receptors. Methods Enzymol 2002; 343:137-56. [PMID: 11665562 DOI: 10.1016/s0076-6879(02)43131-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Jonathan A Javitch
- Center for Molecular Recognition and Departments of Psychiatry and Pharmacology, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
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Visiers I, Ballesteros JA, Weinstein H. Three-dimensional representations of G protein-coupled receptor structures and mechanisms. Methods Enzymol 2002; 343:329-71. [PMID: 11665578 DOI: 10.1016/s0076-6879(02)43145-x] [Citation(s) in RCA: 151] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Irache Visiers
- Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, New York 10029, USA
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