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da Rocha MJ, Presa MH, Nunes GD, Zuge NP, Pires CS, Besckow EM, Gomes CS, Dapper LH, Lenardão EJ, Penteado F, Bortolatto CF, Brüning CA. 1-(Phenylselanyl)-2-(p-tolyl)indolizine: A selenoindolizine with potential antidepressant-like activity in mice mediated by the modulation of dopaminergic and noradrenergic systems. Brain Res 2024; 1834:148904. [PMID: 38561086 DOI: 10.1016/j.brainres.2024.148904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/19/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
1-(Phenylselanyl)-2-(p-tolyl)indolizine (MeSeI) is a selenoindolizine with an antidepressant-like effect in mice by regulation of the serotonergic system. This study investigated the involvement of dopaminergic and noradrenergic systems in the antidepressant-like action of MeSeI. For this purpose, Swiss male mice were pretreated with different antagonists, after 15 min, the MeSeI was administrated by intragastric (i.g.) via; after 30 min, the mouse behavior was assessed in the forced swimming test (FST). The action of MeSeI on the activity of monoamine oxidase (MAO) was determined. The pretreatment of mice with haloperidol (0.05 mg/kg, intraperitoneally, i.p.; non-selective dopamine receptor antagonist), sulpiride (50 mg/kg, i.p.; D2 receptor antagonist), yohimbine (1 mg/kg, i.p.; α2 receptor antagonist), and propranolol (2 mg/kg, i.p.; non-selective β receptor antagonist), inhibited the anti-immobility action of MeSeI (50 mg/kg, i.g.) in the FST. This blocking effect was not observed when SCH23390 (0.01 mg/kg, i.p.; D1 receptor antagonist), and prazosin (1 mg/kg, i.p.; α1 receptor antagonist) were administered. The coadministration of subeffective doses of bupropion (3 mg/kg. i.g.; dopamine and noradrenaline reuptake inhibitor) and MeSeI (0.5 mg/kg. i.g.) reduced the immobility time in the FST. Furthermore, MeSeI inhibited MAO-A and B activities in vitro and ex vivo tests. These results suggest that MeSeI exerts its antidepressant-like effect via regulation of the D2, α2, and β1 receptors and the inhibition of MAO-A and B activities. Molecular docking investigations corroborated these results. This study provides comprehensive insights into the antidepressant-like mechanism of MeSeI in mice, suggesting its potential as a novel antidepressant candidate.
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Affiliation(s)
- Marcia Juciele da Rocha
- Laboratory of Biochemistry and Molecular Neuropharmacology (LABIONEM), Graduate Program in Biochemistry and Bioprospecting (PPGBBio), Chemical, Pharmaceutical and Food Sciences Center (CCQFA), Federal University of Pelotas (UFPel), Pelotas, RS 96010‑900, Brazil
| | - Marcelo Heinemann Presa
- Laboratory of Biochemistry and Molecular Neuropharmacology (LABIONEM), Graduate Program in Biochemistry and Bioprospecting (PPGBBio), Chemical, Pharmaceutical and Food Sciences Center (CCQFA), Federal University of Pelotas (UFPel), Pelotas, RS 96010‑900, Brazil
| | - Gustavo D'Avila Nunes
- Laboratory of Biochemistry and Molecular Neuropharmacology (LABIONEM), Graduate Program in Biochemistry and Bioprospecting (PPGBBio), Chemical, Pharmaceutical and Food Sciences Center (CCQFA), Federal University of Pelotas (UFPel), Pelotas, RS 96010‑900, Brazil
| | - Narryman Pinto Zuge
- Laboratory of Biochemistry and Molecular Neuropharmacology (LABIONEM), Graduate Program in Biochemistry and Bioprospecting (PPGBBio), Chemical, Pharmaceutical and Food Sciences Center (CCQFA), Federal University of Pelotas (UFPel), Pelotas, RS 96010‑900, Brazil
| | - Camila Simões Pires
- Laboratory of Biochemistry and Molecular Neuropharmacology (LABIONEM), Graduate Program in Biochemistry and Bioprospecting (PPGBBio), Chemical, Pharmaceutical and Food Sciences Center (CCQFA), Federal University of Pelotas (UFPel), Pelotas, RS 96010‑900, Brazil
| | - Evelyn Mianes Besckow
- Laboratory of Biochemistry and Molecular Neuropharmacology (LABIONEM), Graduate Program in Biochemistry and Bioprospecting (PPGBBio), Chemical, Pharmaceutical and Food Sciences Center (CCQFA), Federal University of Pelotas (UFPel), Pelotas, RS 96010‑900, Brazil
| | - Caroline Signorini Gomes
- Laboratory of Clean Organic Synthesis (LASOL), Graduate Program in Chemistry (PPGQ), Chemical, Pharmaceutical and Food Sciences Center (CCQFA), Federal University of Pelotas (UFPel), Pelotas, RS 96010‑900, Brazil
| | - Luiz Henrique Dapper
- Laboratory of Clean Organic Synthesis (LASOL), Graduate Program in Chemistry (PPGQ), Chemical, Pharmaceutical and Food Sciences Center (CCQFA), Federal University of Pelotas (UFPel), Pelotas, RS 96010‑900, Brazil
| | - Eder João Lenardão
- Laboratory of Clean Organic Synthesis (LASOL), Graduate Program in Chemistry (PPGQ), Chemical, Pharmaceutical and Food Sciences Center (CCQFA), Federal University of Pelotas (UFPel), Pelotas, RS 96010‑900, Brazil
| | - Filipe Penteado
- Department of Chemistry, Federal University of Santa Maria, Santa Maria, Rio Grande do Sul, Brazil
| | - Cristiani Folharini Bortolatto
- Laboratory of Biochemistry and Molecular Neuropharmacology (LABIONEM), Graduate Program in Biochemistry and Bioprospecting (PPGBBio), Chemical, Pharmaceutical and Food Sciences Center (CCQFA), Federal University of Pelotas (UFPel), Pelotas, RS 96010‑900, Brazil.
| | - César Augusto Brüning
- Laboratory of Biochemistry and Molecular Neuropharmacology (LABIONEM), Graduate Program in Biochemistry and Bioprospecting (PPGBBio), Chemical, Pharmaceutical and Food Sciences Center (CCQFA), Federal University of Pelotas (UFPel), Pelotas, RS 96010‑900, Brazil.
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Lee KH, Manning JJ, Javitch J, Shi L. A Novel "Activation Switch" Motif Common to All Aminergic Receptors. J Chem Inf Model 2023; 63:5001-5017. [PMID: 37540602 PMCID: PMC10695015 DOI: 10.1021/acs.jcim.3c00732] [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] [Indexed: 08/06/2023]
Abstract
Aminergic receptors are G protein-coupled receptors (GPCRs) that transduce signals from small endogenous biogenic amines to regulate intracellular signaling pathways. Agonist binding in the ligand binding pocket on the extracellular side opens and prepares a cavity on the intracellular face of the receptors to interact with and activate G proteins and β-arrestins. Here, by reviewing and analyzing all available aminergic receptor structures, we seek to identify activation-related conformational changes that are independent of the specific scaffold of the bound agonist, which we define as "activation conformational changes" (ACCs). While some common intracellular ACCs have been well-documented, identifying common extracellular ACCs, including those in the ligand binding pocket, is complicated by local adjustments to different ligand scaffolds. Our analysis shows no common ACCs at the extracellular ends of the transmembrane helices. Furthermore, the restricted access to the ligand binding pocket identified previously in some receptors is not universal. Notably, the Trp6.48 toggle switch and the Pro5.50-Ile3.40-Phe6.44 (PIF) motif at the bottom of the ligand binding pocket have previously been proposed to mediate the conformational consequences of ligand binding to the intracellular side of the receptors. Our analysis shows that common ACCs in the ligand binding pocket are associated with the PIF motif and nearby residues, including Trp6.48, but fails to support a shared rotamer toggle associated with activation. However, we identify two common rearrangements between the extracellular and middle subsegments, and propose a novel "activation switch" motif common to all aminergic receptors. This motif includes the middle subsegments of transmembrane helices 3, 5, and 6 and integrates both the PIF motif and Trp6.48.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Jamie J. Manning
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Jonathan Javitch
- Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, USA
- Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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Wygas MM, Laugwitz JM, Schmidt P, Elgeti M, Kaiser A. Dynamics of the Second Extracellular Loop Control Transducer Coupling of Peptide-Activated GPCRs. Int J Mol Sci 2023; 24:12197. [PMID: 37569573 PMCID: PMC10419011 DOI: 10.3390/ijms241512197] [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: 06/26/2023] [Revised: 07/20/2023] [Accepted: 07/28/2023] [Indexed: 08/13/2023] Open
Abstract
Many peptide-activated rhodopsin-like GPCRs share a β-hairpin folding motif in the extracellular loop 2 (ECL2), which interacts with the peptide ligand while at the same time being connected to transmembrane helix 3 (TM3) via a highly conserved disulfide bond. Currently, it remains unknown whether the coupling of the specifically shaped ECL2 to TM3 influences the activation of peptide-activated GPCRs. We investigated this possibility in a selection of peptide GPCRs with known structures. Most of the receptors with cysteine to alanine mutations folded like the respective wild-type and resided in the cell membrane, challenging pure folding stabilization by the disulfide bridge. G-protein signaling of the disulfide mutants was retained to a greater extent in secretin-like GPCRs than in rhodopsin-like GPCRs, while recruitment of arrestin was completely abolished in both groups, which may be linked to alterations in ligand residence time. We found a correlation between receptor activity of the neuropeptide Y2 receptor and alterations in ECL2 dynamics using engineered disulfide bridges or site-directed spin labeling and EPR spectroscopy. These data highlight the functional importance of the TM3-ECL2 link for the activation of specific signaling pathways in peptide-activated GPCRs, which might have implications for future drug discovery.
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Affiliation(s)
- Marcel M. Wygas
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
| | - Jeannette M. Laugwitz
- Medical Faculty, Institute of Medical Physics and Biophysics, Leipzig University, Haertelstasse 16-18, 04107 Leipzig, Germany
| | - Peter Schmidt
- Medical Faculty, Institute of Medical Physics and Biophysics, Leipzig University, Haertelstasse 16-18, 04107 Leipzig, Germany
| | - Matthias Elgeti
- Medical Faculty, Institute of Medical Physics and Biophysics, Leipzig University, Haertelstasse 16-18, 04107 Leipzig, Germany
- Medical Faculty, Institute for Drug Discovery, Leipzig University, Haertelstasse 16-18, 04107 Leipzig, Germany
| | - Anette Kaiser
- Faculty of Life Sciences, Institute of Biochemistry, Leipzig University, Brüderstr. 34, 04103 Leipzig, Germany
- Medical Faculty, Department of Anesthesiology and Intensive Care, Leipzig University, Liebigstrasse 19, 04103 Leipzig, Germany
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Chowdhury AS, Oxford JT. Collagen a1(XI) structure prediction by Alphafold 2. PROCEEDINGS. INTERNATIONAL CONFERENCE ON COMPUTATIONAL SCIENCE AND COMPUTATIONAL INTELLIGENCE 2022; 2022:572-577. [PMID: 37860747 PMCID: PMC10586751 DOI: 10.1109/csci58124.2022.00108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Collagen α1(XI) is a minor fibrillar collagen involved in the critical regulation of collagen fibrils such as nucleation, assembly, and regulation of fibril diameter. The amino propeptide domain of the collagen α1(XI) is retained on the surface of the collagen fibril for an extended period of time and may play a crucial role in the interaction with extracellular matrix glycosaminoglycans and other proteins during the process of fibrillogenesis. Understanding the mechanism of action of this protein will ultimately help us understand the organization and assembly of the extracellular matrix that underlies the structural integrity of connective tissues.
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Affiliation(s)
- Abu Sayeed Chowdhury
- Biomolecular Sciences Graduate Program, Center of Biomedical Research Excellence, Boise State University, Boise, Idaho USA
| | - Julia Thom Oxford
- Department of Biological Sciences, Center of Biomedical Research Excellence, Boise State University, Boise, Idaho, USA
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5
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Stevens AO, He Y. Benchmarking the Accuracy of AlphaFold 2 in Loop Structure Prediction. Biomolecules 2022; 12:985. [PMID: 35883541 PMCID: PMC9312937 DOI: 10.3390/biom12070985] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/05/2022] [Accepted: 07/12/2022] [Indexed: 01/22/2023] Open
Abstract
The inhibition of protein-protein interactions is a growing strategy in drug development. In addition to structured regions, many protein loop regions are involved in protein-protein interactions and thus have been identified as potential drug targets. To effectively target such regions, protein structure is critical. Loop structure prediction is a challenging subgroup in the field of protein structure prediction because of the reduced level of conservation in protein sequences compared to the secondary structure elements. AlphaFold 2 has been suggested to be one of the greatest achievements in the field of protein structure prediction. The AlphaFold 2 predicted protein structures near the X-ray resolution in the Critical Assessment of protein Structure Prediction (CASP 14) competition in 2020. The purpose of this work is to survey the performance of AlphaFold 2 in specifically predicting protein loop regions. We have constructed an independent dataset of 31,650 loop regions from 2613 proteins (deposited after the AlphaFold 2 was trained) with both experimentally determined structures and AlphaFold 2 predicted structures. With extensive evaluation using our dataset, the results indicate that AlphaFold 2 is a good predictor of the structure of loop regions, especially for short loop regions. Loops less than 10 residues in length have an average Root Mean Square Deviation (RMSD) of 0.33 Å and an average the Template Modeling score (TM-score) of 0.82. However, we see that as the number of residues in a given loop increases, the accuracy of AlphaFold 2's prediction decreases. Loops more than 20 residues in length have an average RMSD of 2.04 Å and an average TM-score of 0.55. Such a correlation between accuracy and length of the loop is directly linked to the increase in flexibility. Moreover, AlphaFold 2 does slightly over-predict α-helices and β-strands in proteins.
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Affiliation(s)
- Amy O. Stevens
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA;
| | - Yi He
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131, USA;
- Translational Informatics Division, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA
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Adepu KK, Kachhap S, Anishkin A, Chintapalli SV. Structural and Energetic Insights Into the Interaction of Niacin With the GPR109A Receptor. Bioinform Biol Insights 2021; 15:11779322211056122. [PMID: 34866904 PMCID: PMC8637708 DOI: 10.1177/11779322211056122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/02/2021] [Indexed: 11/16/2022] Open
Abstract
The transmembrane G-protein coupled receptor GPR109A has been previously shown to function as a receptor for niacin in mediating antilipolytic effects. Although administration of high doses of niacin has shown beneficial effects on lipid metabolism, however, it is often accompanied by disturbing side effects such as flushing, liver damage, glucose intolerance, or gastrointestinal problems. Thus, it is important to understand niacin-GPR109A interactions, which can be beneficial for the development of alternate drugs having antilipolytic effects with less or no side effects. To get into the structural insights on niacin binding to GPR109A, we have performed 100 nanoseconds long all-atom MD simulations of five niacin-GPR109A complexes (automatically docked pose 0, and randomly placed niacin in poses 1 to 4 in the receptor crevice) and analyzed using binding free energy calculations and H-bond analysis. Steered MD simulations were used to get an average force for niacin translocation between the bulk and the external crevice of the wild type and mutant (N86Y, W91 S, S178I, and triple mutant of all three residues) GPR109A receptors, as well as GPR109B (as a control that does not bind niacin). The H-bond analysis revealed that TMH3 residue R111 interacts with niacin in a total of 4 (poses 0 to 3) complexes, while residues C177, S178, and S179 contact niacin in complex pose 4, and all these complexes were energetically stable. According to steered MD simulations, all the GPR109A mutants and GPR109B required greater force than that of wild-type GPR109A to translocate in the external crevice, suggesting increased sterical obstacles. Thus, the residues N86 (at the junction of TMH2/ECL2), W91 (ECL2), R111 (TMH3), and ECL3 residues (C177, S178, S179) play an important role for optimal routing of niacin entry and to bind GPR109A.
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Affiliation(s)
- Kiran Kumar Adepu
- Arkansas Children's Nutrition Center, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sangita Kachhap
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Krakow, Poland
| | - Andriy Anishkin
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Sree V Chintapalli
- Arkansas Children's Nutrition Center, Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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Neuronal Dopamine D3 Receptors: Translational Implications for Preclinical Research and CNS Disorders. Biomolecules 2021; 11:biom11010104. [PMID: 33466844 PMCID: PMC7830622 DOI: 10.3390/biom11010104] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 02/06/2023] Open
Abstract
Dopamine (DA), as one of the major neurotransmitters in the central nervous system (CNS) and periphery, exerts its actions through five types of receptors which belong to two major subfamilies such as D1-like (i.e., D1 and D5 receptors) and D2-like (i.e., D2, D3 and D4) receptors. Dopamine D3 receptor (D3R) was cloned 30 years ago, and its distribution in the CNS and in the periphery, molecular structure, cellular signaling mechanisms have been largely explored. Involvement of D3Rs has been recognized in several CNS functions such as movement control, cognition, learning, reward, emotional regulation and social behavior. D3Rs have become a promising target of drug research and great efforts have been made to obtain high affinity ligands (selective agonists, partial agonists and antagonists) in order to elucidate D3R functions. There has been a strong drive behind the efforts to find drug-like compounds with high affinity and selectivity and various functionality for D3Rs in the hope that they would have potential treatment options in CNS diseases such as schizophrenia, drug abuse, Parkinson’s disease, depression, and restless leg syndrome. In this review, we provide an overview and update of the major aspects of research related to D3Rs: distribution in the CNS and periphery, signaling and molecular properties, the status of ligands available for D3R research (agonists, antagonists and partial agonists), behavioral functions of D3Rs, the role in neural networks, and we provide a summary on how the D3R-related drug research has been translated to human therapy.
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Structure of the dopamine D 2 receptor in complex with the antipsychotic drug spiperone. Nat Commun 2020; 11:6442. [PMID: 33353947 PMCID: PMC7755896 DOI: 10.1038/s41467-020-20221-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 11/19/2020] [Indexed: 12/26/2022] Open
Abstract
In addition to the serotonin 5-HT2A receptor (5-HT2AR), the dopamine D2 receptor (D2R) is a key therapeutic target of antipsychotics for the treatment of schizophrenia. The inactive state structures of D2R have been described in complex with the inverse agonists risperidone (D2Rris) and haloperidol (D2Rhal). Here we describe the structure of human D2R in complex with spiperone (D2Rspi). In D2Rspi, the conformation of the extracellular loop (ECL) 2, which composes the ligand-binding pocket, was substantially different from those in D2Rris and D2Rhal, demonstrating that ECL2 in D2R is highly dynamic. Moreover, D2Rspi exhibited an extended binding pocket to accommodate spiperone’s phenyl ring, which probably contributes to the selectivity of spiperone to D2R and 5-HT2AR. Together with D2Rris and D2Rhal, the structural information of D2Rspi should be of value for designing novel antipsychotics with improved safety and efficacy. The dopamine D2 receptor (D2R) is a GPCR and an important drug target for schizophrenia treatment. Here, the authors present the crystal structure of human D2R in complex with the antipsychotic drug spiperone, which is of interest for designing antipsychotics with improved receptor selectivity.
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9
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Huang AY, Taylor AMW, Ghogha A, Pribadi M, Wang Q, Kim TSJ, Cahill CM, Coppola G, Evans CJ. Genetic and functional analysis of a Pacific hagfish opioid system. J Neurosci Res 2020; 100:19-34. [PMID: 32830380 DOI: 10.1002/jnr.24682] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 05/22/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022]
Abstract
The actions of endogenous opioids and nociceptin/orphanin FQ are mediated by four homologous G protein-coupled receptors that constitute the opioid receptor family. However, little is known about opioid systems in cyclostomes (living jawless fish) and how opioid systems might have evolved from invertebrates. Here, we leveraged de novo transcriptome and low-coverage whole-genome assembly in the Pacific hagfish (Eptatretus stoutii) to identify and characterize the first full-length coding sequence for a functional opioid receptor in a cyclostome. Additionally, we define two novel endogenous opioid precursors in this species that predict several novel opioid peptides. Bioinformatic analysis shows no closely related opioid receptor genes in invertebrates with regard either to the genomic organization or to conserved opioid receptor-specific sequences that are common in all vertebrates. Furthermore, no proteins analogous to vertebrate opioid precursors could be identified by genomic searches despite previous claims of protein or RNA-derived sequences in several invertebrate species. The presence of an expressed orthologous receptor and opioid precursors in the Pacific hagfish confirms that a functional opioid system was likely present in the common ancestor of all extant vertebrates some 550 million years ago, earlier than all previous authenticated accounts. We discuss the premise that the cyclostome and vertebrate opioid systems evolved from invertebrate systems concerned with antimicrobial defense and speculate that the high concentrations of opioid precursors in tissues such as the testes, gut, and activated immune cells are key remnants of this evolutionary role.
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Affiliation(s)
- Alden Y Huang
- Department of Psychiatry and Biobehavioral Sciences, Shirley and Stefan Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Anna M W Taylor
- Department of Psychiatry and Biobehavioral Sciences, Shirley and Stefan Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Atefeh Ghogha
- Department of Psychiatry and Biobehavioral Sciences, Shirley and Stefan Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Mochtar Pribadi
- Department of Psychiatry and Biobehavioral Sciences, Shirley and Stefan Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Qing Wang
- Department of Psychiatry and Biobehavioral Sciences, Shirley and Stefan Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Tanya S J Kim
- Department of Psychiatry and Biobehavioral Sciences, Shirley and Stefan Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Catherine M Cahill
- Department of Psychiatry and Biobehavioral Sciences, Shirley and Stefan Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Giovanni Coppola
- Department of Psychiatry and Biobehavioral Sciences, Shirley and Stefan Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Christopher J Evans
- Department of Psychiatry and Biobehavioral Sciences, Shirley and Stefan Hatos Center for Neuropharmacology, Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
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Yin J, Chen KYM, Clark MJ, Hijazi M, Kumari P, Bai XC, Sunahara RK, Barth P, Rosenbaum DM. Structure of a D2 dopamine receptor-G-protein complex in a lipid membrane. Nature 2020; 584:125-129. [PMID: 32528175 PMCID: PMC7415663 DOI: 10.1038/s41586-020-2379-5] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/08/2020] [Indexed: 12/28/2022]
Abstract
The D2 dopamine receptor (DRD2) is a therapeutic target for Parkinson’s disease1 and antipsychotic drugs2. DRD2 is activated by the endogenous neurotransmitter dopamine and synthetic agonist drugs such as bromocriptine3, leading to stimulation of Gi and inhibition of adenylyl cyclase. We used cryo-electron microscopy to elucidate the structure of an agonist-bound activated DRD2-Gi complex reconstituted into a phospholipid membrane. The extracellular ligand binding site of DRD2 is remodeled in response to agonist binding, with conformational changes in extracellular loop 2 (ECL2), transmembrane domain 5 (TM5), TM6, and TM7 propagating to opening of the intracellular Gi binding site. The DRD2-Gi structure represents the first experimental model of a GPCR-G protein complex embedded in a phospholipid bilayer, which serves as a benchmark to validate the interactions seen in previous detergent-bound structures. The structure also reveals interactions that are unique to the membrane-embedded complex, including helix 8 burial in the inner leaflet, ordered lysine and arginine sidechains in the membrane interfacial regions, and lipid anchoring of the G protein in the membrane. Our model of the activated DRD2 will help inform the design of subtype-selective DRD2 ligands for multiple human CNS disorders.
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Affiliation(s)
- Jie Yin
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kuang-Yui M Chen
- Institute of Bioengineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Mary J Clark
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Mahdi Hijazi
- Institute of Bioengineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Punita Kumari
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiao-Chen Bai
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Roger K Sunahara
- Department of Pharmacology, University of California San Diego School of Medicine, La Jolla, CA, USA.
| | - Patrick Barth
- Institute of Bioengineering, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland.
| | - Daniel M Rosenbaum
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Karami Y, Rey J, Postic G, Murail S, Tufféry P, de Vries SJ. DaReUS-Loop: a web server to model multiple loops in homology models. Nucleic Acids Res 2020; 47:W423-W428. [PMID: 31114872 PMCID: PMC6602439 DOI: 10.1093/nar/gkz403] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/20/2019] [Accepted: 05/06/2019] [Indexed: 02/07/2023] Open
Abstract
Loop regions in protein structures often have crucial roles, and they are much more variable in sequence and structure than other regions. In homology modeling, this leads to larger deviations from the homologous templates, and loop modeling of homology models remains an open problem. To address this issue, we have previously developed the DaReUS-Loop protocol, leading to significant improvement over existing methods. Here, a DaReUS-Loop web server is presented, providing an automated platform for modeling or remodeling loops in the context of homology models. This is the first web server accepting a protein with up to 20 loop regions, and modeling them all in parallel. It also provides a prediction confidence level that corresponds to the expected accuracy of the loops. DaReUS-Loop facilitates the analysis of the results through its interactive graphical interface and is freely available at http://bioserv.rpbs.univ-paris-diderot.fr/services/DaReUS-Loop/.
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Affiliation(s)
- Yasaman Karami
- Sorbonne Paris Cité, Université Paris Diderot, CNRS UMR 8251, INSERM ERL U1133, Paris, France.,Ressource Parisienne en Bioinformatique Structurale (RPBS), Paris, France
| | - Julien Rey
- Sorbonne Paris Cité, Université Paris Diderot, CNRS UMR 8251, INSERM ERL U1133, Paris, France.,Ressource Parisienne en Bioinformatique Structurale (RPBS), Paris, France
| | - Guillaume Postic
- Sorbonne Paris Cité, Université Paris Diderot, CNRS UMR 8251, INSERM ERL U1133, Paris, France.,Ressource Parisienne en Bioinformatique Structurale (RPBS), Paris, France.,Institut Français de Bioinformatique (IFB), UMS 3601-CNRS, Université Paris-Saclay, Orsay, France
| | - Samuel Murail
- Sorbonne Paris Cité, Université Paris Diderot, CNRS UMR 8251, INSERM ERL U1133, Paris, France
| | - Pierre Tufféry
- Sorbonne Paris Cité, Université Paris Diderot, CNRS UMR 8251, INSERM ERL U1133, Paris, France.,Ressource Parisienne en Bioinformatique Structurale (RPBS), Paris, France
| | - Sjoerd J de Vries
- Sorbonne Paris Cité, Université Paris Diderot, CNRS UMR 8251, INSERM ERL U1133, Paris, France.,Ressource Parisienne en Bioinformatique Structurale (RPBS), Paris, France
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12
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Kotarska A, Fernandes L, Kleene R, Schachner M. Cell adhesion molecule close homolog of L1 binds to the dopamine receptor D2 and inhibits the internalization of its short isoform. FASEB J 2020; 34:4832-4851. [PMID: 32052901 DOI: 10.1096/fj.201900577rrrr] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 12/05/2019] [Accepted: 12/05/2019] [Indexed: 02/05/2023]
Abstract
Cell adhesion molecule close homolog of L1 (CHL1) and the dopamine receptor D2 (DRD2) are associated with psychiatric and mental disorders. We here show that DRD2 interacts with CHL1 in mouse brain, as evidenced by co-immunostaining, proximity ligation assay, co-immunoprecipitation, and pull-down assay with recombinant extracellular CHL1 domain fused to Fc (CHL1-Fc). Direct binding of CHL1-Fc to the first extracellular loop of DRD2 was shown by ELISA. Using HEK cells transfected to co-express CHL1 and the short (DRD2-S) or long (DRD2-L) DRD2 isoforms, co-localization of CHL1 and both isoforms was observed by immunostaining and proximity ligation assay. Moreover, CHL1 inhibited agonist-triggered internalization of DRD2-S. Proximity ligation assay showed close interaction between CHL1 and DRD2 in neurons expressing dopamine- and cAMP-regulated phosphoprotein of 32 kDa (DARPP32) or tyrosine hydroxylase (TH) in tissue sections of adult mouse striatum. In cultures of striatum or ventral midbrain, CHL1 was also closely associated with DRD2 in DARPP32- or TH-immunopositive cells, respectively. In the dorsal striatum of CHL1-deficient mice, lower levels of DRD2 and phosphorylated TH were observed, when compared to wild-type littermates. In the ventral striatum of CHL1-deficient mice, levels of phosphorylated DARPP32 were reduced. We propose that CHL1 regulates DRD2-dependent presynaptic and postsynaptic functions.
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Affiliation(s)
- Agnieszka Kotarska
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Luciana Fernandes
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Ralf Kleene
- Zentrum für Molekulare Neurobiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Melitta Schachner
- Center for Neuroscience, Shantou University Medical College, Shantou, China
- Keck Center for Collaborative Neuroscience and Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, NJ, USA
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13
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Lane JR, Abramyan AM, Adhikari P, Keen AC, Lee KH, Sanchez J, Verma RK, Lim HD, Yano H, Javitch JA, Shi L. Distinct inactive conformations of the dopamine D2 and D3 receptors correspond to different extents of inverse agonism. eLife 2020; 9:e52189. [PMID: 31985399 PMCID: PMC7053997 DOI: 10.7554/elife.52189] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/24/2020] [Indexed: 01/07/2023] Open
Abstract
By analyzing and simulating inactive conformations of the highly homologous dopamine D2 and D3 receptors (D2R and D3R), we find that eticlopride binds D2R in a pose very similar to that in the D3R/eticlopride structure but incompatible with the D2R/risperidone structure. In addition, risperidone occupies a sub-pocket near the Na+ binding site, whereas eticlopride does not. Based on these findings and our experimental results, we propose that the divergent receptor conformations stabilized by Na+-sensitive eticlopride and Na+-insensitive risperidone correspond to different degrees of inverse agonism. Moreover, our simulations reveal that the extracellular loops are highly dynamic, with spontaneous transitions of extracellular loop 2 from the helical conformation in the D2R/risperidone structure to an extended conformation similar to that in the D3R/eticlopride structure. Our results reveal previously unappreciated diversity and dynamics in the inactive conformations of D2R. These findings are critical for rational drug discovery, as limiting a virtual screen to a single conformation will miss relevant ligands.
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Affiliation(s)
- J Robert Lane
- Division of Pharmacology, Physiology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of NottinghamNottinghamUnited Kingdom
- Centre of Membrane Protein and Receptors, Universities of Birmingham and NottinghamNottinghamUnited Kingdom
| | - Ara M Abramyan
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Pramisha Adhikari
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Alastair C Keen
- Division of Pharmacology, Physiology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of NottinghamNottinghamUnited Kingdom
- Centre of Membrane Protein and Receptors, Universities of Birmingham and NottinghamNottinghamUnited Kingdom
- Drug Discovery Biology, Department of Pharmacology and Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | - Kuo-Hao Lee
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Julie Sanchez
- Division of Pharmacology, Physiology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of NottinghamNottinghamUnited Kingdom
- Centre of Membrane Protein and Receptors, Universities of Birmingham and NottinghamNottinghamUnited Kingdom
| | - Ravi Kumar Verma
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Herman D Lim
- Drug Discovery Biology, Department of Pharmacology and Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash UniversityParkvilleAustralia
| | - Hideaki Yano
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
| | - Jonathan A Javitch
- Department of Psychiatry, Vagelos College of Physicians and Surgeons, Columbia UniversityNew YorkUnited States
- Division of Molecular Therapeutics, New York State Psychiatric InstituteNew YorkUnited States
- Department of PharmacologyVagelos College of Physicians and Surgeons, Columbia UniversityNew YorkUnited States
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse - Intramural Research Program, National Institutes of HealthBaltimoreUnited States
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14
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Pharmacological characterization, cellular localization and expression profile of NPY receptor subtypes Y2 and Y7 in large yellow croaker, Larimichthys crocea. Comp Biochem Physiol B Biochem Mol Biol 2019; 238:110347. [PMID: 31499219 DOI: 10.1016/j.cbpb.2019.110347] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/02/2019] [Accepted: 09/04/2019] [Indexed: 11/23/2022]
Abstract
Neuropeptide Y (NPY) receptors are suggested to mediate the multi-physiological functions of NPY family peptides, such as food intake, in teleost fish. However, the structure and signaling of fish NPY receptors are yet to be fully elucidated. In this study, we report the cloning and characterization of two neuropeptide Y receptor subtypes, Y2 (NPY2R) and Y7 (NPY7R), in yellow croaker Larimichthys crocea (L. crocea) (LcNPY2R, LcNPY7R). The gene structure, pharmacological characterization, cell location, and tissue expression of these two receptors were explored. The phylogenetic results showed that LcNPY2R and LcNPY7R had typical G protein-coupled receptor profiles, associated with the Y2 subfamily, with coding sequences that are highly conserved in vertebrates. The expression of both LcNPY2R and LcNPY7R could be activated by LcNPY in HEK293 cells. However, truncated LcNPY18-36 was only able to activate LcNPY2R at the same level as full length LcNPY. Expression analysis revealed that LcNPY2R mRNA was predominantly expressed in the intestine and liver, whereas LcNPY7R was expressed in the stomach, which indicated that both receptors were related to the digestive system. Overall, our data establishes a molecular basis to determine the actions of LcNPY2R and LcNPY7R, which could be used to elucidate the conserved roles of these receptor-ligand pairs in vertebrates.
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15
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Klein Herenbrink C, Verma R, Lim HD, Kopinathan A, Keen A, Shonberg J, Draper-Joyce CJ, Scammells PJ, Christopoulos A, Javitch JA, Capuano B, Shi L, Lane JR. Molecular Determinants of the Intrinsic Efficacy of the Antipsychotic Aripiprazole. ACS Chem Biol 2019; 14:1780-1792. [PMID: 31339684 DOI: 10.1021/acschembio.9b00342] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Partial agonists of the dopamine D2 receptor (D2R) have been developed to treat the symptoms of schizophrenia without causing the side effects elicited by antagonists. The receptor-ligand interactions that determine the intrinsic efficacy of such drugs, however, are poorly understood. Aripiprazole has an extended structure comprising a phenylpiperazine primary pharmacophore and a 1,2,3,4-tetrahydroquinolin-2-one secondary pharmacophore. We combined site-directed mutagenesis, analytical pharmacology, ligand fragments, and molecular dynamics simulations to identify the D2R-aripiprazole interactions that contribute to affinity and efficacy. We reveal that an interaction between the secondary pharmacophore of aripiprazole and a secondary binding pocket defined by residues at the extracellular portions of transmembrane segments 1, 2, and 7 determines the intrinsic efficacy of aripiprazole. Our findings reveal a hitherto unappreciated mechanism for fine-tuning the intrinsic efficacy of D2R agonists.
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Affiliation(s)
| | - Ravi 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
| | | | | | | | | | | | | | | | | | | | - 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
- Division of Pharmacology, Physiology and Neuroscience, School of Life Sciences, Queen’s Medical Centre, University of Nottingham, Nottingham NG7 2UH, U.K
- Centre of Membrane Protein and Receptors, Universities of Birmingham and Nottingham, Nottingham, United Kingdom
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16
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Vass M, Podlewska S, de Esch IJP, Bojarski AJ, Leurs R, Kooistra AJ, de Graaf C. Aminergic GPCR-Ligand Interactions: A Chemical and Structural Map of Receptor Mutation Data. J Med Chem 2018; 62:3784-3839. [PMID: 30351004 DOI: 10.1021/acs.jmedchem.8b00836] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The aminergic family of G protein-coupled receptors (GPCRs) plays an important role in various diseases and represents a major drug discovery target class. Structure determination of all major aminergic subfamilies has enabled structure-based ligand design for these receptors. Site-directed mutagenesis data provides an invaluable complementary source of information for elucidating the structural determinants of binding of different ligand chemotypes. The current study provides a comparative analysis of 6692 mutation data points on 34 aminergic GPCR subtypes, covering the chemical space of 540 unique ligands from mutagenesis experiments and information from experimentally determined structures of 52 distinct aminergic receptor-ligand complexes. The integrated analysis enables detailed investigation of structural receptor-ligand interactions and assessment of the transferability of combined binding mode and mutation data across ligand chemotypes and receptor subtypes. An overview is provided of the possibilities and limitations of using mutation data to guide the design of novel aminergic receptor ligands.
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Affiliation(s)
- Márton Vass
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Sabina Podlewska
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , PL31-343 Kraków , Poland
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Andrzej J Bojarski
- Department of Medicinal Chemistry, Institute of Pharmacology , Polish Academy of Sciences , Smętna 12 , PL31-343 Kraków , Poland
| | - Rob Leurs
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands
| | - Albert J Kooistra
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands.,Department of Drug Design and Pharmacology , University of Copenhagen , Universitetsparken 2 , 2100 Copenhagen , Denmark
| | - Chris de Graaf
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , VU University Amsterdam , 1081HZ Amsterdam , The Netherlands.,Sosei Heptares , Steinmetz Building, Granta Park, Great Abington , Cambridge CB21 6DG , U.K
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17
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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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18
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Karami Y, Guyon F, De Vries S, Tufféry P. DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins. Sci Rep 2018; 8:13673. [PMID: 30209260 PMCID: PMC6135855 DOI: 10.1038/s41598-018-32079-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/31/2018] [Indexed: 11/08/2022] Open
Abstract
Despite efforts during the past decades, loop modeling remains a difficult part of protein structure modeling. Several approaches have been developed in the framework of crystal structures. However, for homology models, the modeling of loops is still far from being solved. We propose DaReUS-Loop, a data-based approach that identifies loop candidates mining the complete set of experimental structures available in the Protein Data Bank. Candidate filtering relies on local conformation profile-profile comparison, together with physico-chemical scoring. Applied to three different template-based test sets, DaReUS-Loop shows significant increase in the number of high-accuracy loops, and significant enhancement for modeling long loops. A special advantage is that our method proposes a prediction confidence score that correlates well with the expected accuracy of the loops. Strikingly, over 50% of successful loop models are derived from unrelated proteins, indicating that fragments under similar constraints tend to adopt similar structure, beyond mere homology.
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Affiliation(s)
- Yasaman Karami
- Molécules Thérapeutiques in silico, UMR-S973, Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Diderot, Sorbonne Paris Cité, RPBS, 75013, Paris, France
| | - Frédéric Guyon
- Molécules Thérapeutiques in silico, UMR-S973, Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Diderot, Sorbonne Paris Cité, RPBS, 75013, Paris, France
| | - Sjoerd De Vries
- Molécules Thérapeutiques in silico, UMR-S973, Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Diderot, Sorbonne Paris Cité, RPBS, 75013, Paris, France.
| | - Pierre Tufféry
- Molécules Thérapeutiques in silico, UMR-S973, Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Diderot, Sorbonne Paris Cité, RPBS, 75013, Paris, France.
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19
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Zhang Q, Zhou M, Zhao L, Jiang H, Yang H. Dynamic States of the Ligand-Free Class A G Protein-Coupled Receptor Extracellular Side. Biochemistry 2018; 57:4767-4775. [PMID: 29999306 DOI: 10.1021/acs.biochem.8b00146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
G protein-coupled receptors (GPCRs) make up the largest family of drug targets. The second extracellular loop (ECL2) and extracellular end of the third transmembrane helix (TM3) are basic structural elements of the GPCR ligand binding site. Currently, the disulfide bond between the two conserved cysteines in the ECL2 and TM3 is considered to be a basic GPCR structural feature. This disulfide bond has a significant effect on receptor dynamics and ligand binding. Here, molecular dynamics simulations and experimental results show that the two cysteines are distant from one another in the highest-population conformational state of ligand-free class A GPCRs and do not form a disulfide bond, indicating that the dynamics of the GPCR extracellular side are different from our conventional understanding. These surprising dynamics should have important effects on the drug binding process. On the basis of the two distinct ligand-free states, we suggest two kinetic processes for binding of ligands to GPCRs. These results challenge our commonly held beliefs regarding both GPCR structural features and ligand binding.
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Affiliation(s)
- Qiansen Zhang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai 200241 , China
| | - Mang Zhou
- Shanghai Institute of Materia Medica , Chinese Academy of Sciences , Shanghai 201203 , China
| | - Lifen Zhao
- Shanghai Institute of Materia Medica , Chinese Academy of Sciences , Shanghai 201203 , China
| | - Hualiang Jiang
- Shanghai Institute of Materia Medica , Chinese Academy of Sciences , Shanghai 201203 , China
| | - Huaiyu Yang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences , East China Normal University , Shanghai 200241 , China
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20
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Won J, Lee GR, Park H, Seok C. GalaxyGPCRloop: Template-Based and Ab Initio Structure Sampling of the Extracellular Loops of G-Protein-Coupled Receptors. J Chem Inf Model 2018; 58:1234-1243. [DOI: 10.1021/acs.jcim.8b00148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Jonghun Won
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Gyu Rie Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Hahnbeom Park
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Chaok Seok
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
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21
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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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22
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Draper-Joyce CJ, Michino M, Verma RK, Klein Herenbrink C, Shonberg J, Kopinathan A, Scammells PJ, Capuano B, Thal DM, Javitch JA, Christopoulos A, Shi L, Lane JR. The structural determinants of the bitopic binding mode of a negative allosteric modulator of the dopamine D 2 receptor. Biochem Pharmacol 2018; 148:315-328. [PMID: 29325769 DOI: 10.1016/j.bcp.2018.01.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 01/02/2018] [Indexed: 01/11/2023]
Abstract
SB269652 is a negative allosteric modulator of the dopamine D2 receptor (D2R) yet possesses structural similarity to ligands with a competitive mode of interaction. In this study, we aimed to understand the ligand-receptor interactions that confer its allosteric action. We combined site-directed mutagenesis with molecular dynamics simulations using both SB269652 and derivatives from our previous structure activity studies. We identify residues within the conserved orthosteric binding site (OBS) and a secondary binding pocket (SBP) that determine affinity and cooperativity. Our results indicate that interaction with the SBP is a requirement for allosteric pharmacology, but that both competitive and allosteric derivatives of SB269652 can display sensitivity to the mutation of a glutamate residue (E952.65) within the SBP. Our findings provide the molecular basis for the differences in affinity between SB269652 derivatives, and reveal how changes to interactions made by the primary pharmacophore of SB269652 in the orthosteric pocket can confer changes in the interactions made by the secondary pharmacophore in the SBP. Our insights provide a structure-activity framework towards rational optimization of bitopic ligands for D2R with tailored competitive versus allosteric properties.
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Affiliation(s)
- Christopher J Draper-Joyce
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Mayako Michino
- Computational Chemistry and Molecular Biophysics Unit, National Institute on Drug Abuse Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, United States
| | - 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, MD 21224, United States
| | - Carmen Klein Herenbrink
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Jeremy Shonberg
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Anitha Kopinathan
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Peter J Scammells
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Ben Capuano
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - David M Thal
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia
| | - Jonathan A Javitch
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York State Psychiatric Institute, New York, NY 10032, United States; Department of Pharmacology, College of Physicians and Surgeons, Columbia University, New York State Psychiatric Institute, New York, NY 10032, United States; Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, NY 10032, United States
| | - Arthur Christopoulos
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 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, MD 21224, United States.
| | - J Robert Lane
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville campus), 399 Royal Parade, Parkville, VIC 3052, Australia.
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Iglesias A, Cimadevila M, la Fuente RAD, Martí-Solano M, Cadavid MI, Castro M, Selent J, Loza MI, Brea J. Serotonin 2A receptor disulfide bridge integrity is crucial for ligand binding to different signalling states but not for its homodimerization. Eur J Pharmacol 2017; 815:138-146. [PMID: 28899696 DOI: 10.1016/j.ejphar.2017.09.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/28/2017] [Accepted: 09/08/2017] [Indexed: 02/06/2023]
Abstract
The serotonin 2A (5-HT2A) receptor is a G-protein coupled receptor (GPCR) with a conserved disulfide bridge formed by Cys148 (transmembrane helix 3, TM3) and Cys227 (extracellular loop 2, ECL-2). We hypothesized that disulfide bridges may determine serotonin 5-HT2A receptor functions such as receptor activation, functional selectivity and ligand recognition. We used the reducing agent dithiothreitol (DTT) to determine how the reduction of disulfide bridges affects radioligand binding, second messenger mobilization and receptor dimerization. A DTT-induced decrease in the number of binding sites (1190 ± 63.55 fmol/mg protein for control cells compared with 921.2 ± 60.84 fmol/mg protein for DTT-treated cells) as well as in the efficacy of both signalling pathways characterized was observed, although the affinity and potency were unchanged. Bioluminiscence resonance energy transfer (BRET) assays revealed the DTT treatment did not modify the homodimeric nature of serotonin 5-HT2A receptors. In molecular dynamic simulations, the ECL-2 of the receptor with a broken cysteine bond adopts a wider variety of conformations, some of which protrude deeper into the receptor orthosteric binding pocket leading to collapse of the pocket. A shrunken binding pocket would be incapable of accommodating lysergic acid diethylamide (LSD). Our findings suggest that the decrease of efficacy may be due to disruption of disulfide bridge between TM3 and ECL-2. This reveals the integrity of the ECL-2 epitope, which should be explored in the development of novel ligands acting as allosteric modulators of serotonin 5-HT2A receptors.
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Affiliation(s)
- Alba Iglesias
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain
| | - Marta Cimadevila
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain
| | - Rocío Ailim de la Fuente
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain; Molecular Pharmacology of G Protein-coupled Receptors Laboratory, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain
| | - María Martí-Solano
- GPCR Drug Discovery Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM) - Department of Experimental and Health Sciences of Pompeu Fabra University (UPF), Barcelona, Spain
| | - María Isabel Cadavid
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain
| | - Marián Castro
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain; Molecular Pharmacology of G Protein-coupled Receptors Laboratory, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain
| | - Jana Selent
- GPCR Drug Discovery Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM) - Department of Experimental and Health Sciences of Pompeu Fabra University (UPF), Barcelona, Spain
| | - María Isabel Loza
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain.
| | - José Brea
- BioFarma Research Group, Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Avenida de Barcelona 22, 15782 Santiago de Compostela, Spain.
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24
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Lu HM, Lu XL, Zhai JH, Zhou RB, Qin YL, Li JD, Zhang CY, Shi JY. Ligand-binding characterization of simulated β-adrenergic-like octopamine receptor in Schistocerca gregaria via progressive structure simulation. J Mol Graph Model 2017; 77:25-32. [PMID: 28822273 DOI: 10.1016/j.jmgm.2017.07.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/21/2017] [Accepted: 07/25/2017] [Indexed: 11/15/2022]
Abstract
It is important to design insecticides having both low drug resistance and less undesirable toxicity for desert locust control. Specific GPCRs of Schistocerca gregaria, especially β-adrenergic-like octopamine receptor (SgOctβR), can be considered as its potential effective insecticide targets. However, either the unavailability of SgOctβR's structure or the inadequate capability of its sequence lead the development of insecticide for Schistocerca gregaria meets its plateau. To relax this difficulty, this paper develops a promising progressive structure simulation from SgOctβR's sequence, to its predicted structure of SgOctβR in vacuum, to its conformation as well as its complex with endogenous ligand octopamine in a solvent-membrane system. The combined approach of multiple sequence alignment, static structural characterization, and dynamic process of conformational change during binding octopamine reveal three important aspects. The first one is the characterization of SgOctβR's active pocket, including the attending secondary structure elements, its hydrophobic residues and nonpolar surface. The second one is the interaction with octopamine, especially the involved hydrogen bonds and an aromatic stacking of pi-pi interactions. The third one is the potential binding sites, including six highly conserved residues and one highly variable residue for locust insecticide design. This work is definitely helpful for the further structure-based drug design for efficient and eco-friendly insecticides, as well as site-directed mutagenesis biochemical research of SgOctβR.
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Affiliation(s)
- Hui-Meng Lu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
| | - Xiao-Li Lu
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
| | - Jia-Hui Zhai
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
| | - Ren-Bin Zhou
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
| | - Yan-Li Qin
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
| | - Jing-Di Li
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
| | - Chen-Yan Zhang
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
| | - Jian-Yu Shi
- Institute for Special Environmental Biophysics, Key Laboratory for Space Bioscience and Biotechnology, School of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, Shaanxi, PR China.
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25
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Heo S, Lee J, Joo K, Shin HC, Lee J. Protein Loop Structure Prediction Using Conformational Space Annealing. J Chem Inf Model 2017; 57:1068-1078. [DOI: 10.1021/acs.jcim.6b00742] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Seungryong Heo
- School
of Systems Biomedical Science, Soongsil University, Seoul 06978, Korea
| | - Juyong Lee
- Laboratory
of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | | | - Hang-Cheol Shin
- School
of Systems Biomedical Science, Soongsil University, Seoul 06978, Korea
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26
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Marina Robles L, Millán-Pacheco C, Pastor N, Del Río G. STRUCTURE-FUNCTION STUDIES OF THE ALPHA PHEROMONE RECEPTOR FROM YEAST. TIP REVISTA ESPECIALIZADA EN CIENCIAS QUÍMICO-BIOLÓGICAS 2017. [DOI: 10.1016/j.recqb.2016.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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27
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Błasiak E, Łukasiewicz S, Szafran-Pilch K, Dziedzicka-Wasylewska M. Genetic variants of dopamine D2 receptor impact heterodimerization with dopamine D1 receptor. Pharmacol Rep 2016; 69:235-241. [PMID: 28119185 DOI: 10.1016/j.pharep.2016.10.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 10/25/2016] [Accepted: 10/26/2016] [Indexed: 01/14/2023]
Abstract
BACKGROUND The human dopamine D2 receptor gene has three polymorphic variants that alter its amino acid sequence: alanine substitution by valine in position 96 (V96A), proline substitution by serine in position 310 (P310S) and serine substitution by cysteine in position 311 (S311C). Their functional role has never been the object of extensive studies, even though there is some evidence that their occurrence correlates with schizophrenia. METHODS The HEK293 cell line was transfected with dopamine D1 and D2 receptors (or genetic variants of the D2 receptor), coupled to fluorescent proteins which allowed us to measure the extent of dimerization of these receptors, using a highly advanced biophysical approach (FLIM-FRET). Additionally, Fluoro-4 AM was used to examine changes in the level of calcium release after ligand stimulation of cells expressing different combinations of dopamine receptors. RESULTS Using FLIM-FRET experiments we have shown that in HEK 293 expressing dopamine receptors, polymorphic mutations in the D2 receptor play a role in dimmer formation with the dopamine D1 receptor. The association level of dopamine receptors is affected by ligand administration, with variable effects depending on polymorphic variant of the D2 dopamine receptor. We have found that the level of heteromer formation is reflected by calcium ion release after ligand stimulation and have observed variations of this effect dependent on the polymorphic variant and the ligand. CONCLUSION The data presented in this paper support the hypothesis on the role of calcium signaling regulated by the D1-D2 heteromer which may be of relevance for schizophrenia etiology.
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Affiliation(s)
- Ewa Błasiak
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
| | - Sylwia Łukasiewicz
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
| | | | - Marta Dziedzicka-Wasylewska
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland; Institute of Pharmacology, Polish Academy of Sciences, Kraków, Poland.
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28
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Nguyen ATN, Baltos JA, Thomas T, Nguyen TD, Muñoz LL, Gregory KJ, White PJ, Sexton PM, Christopoulos A, May LT. Extracellular Loop 2 of the Adenosine A1 Receptor Has a Key Role in Orthosteric Ligand Affinity and Agonist Efficacy. Mol Pharmacol 2016; 90:703-714. [PMID: 27683014 DOI: 10.1124/mol.116.105007] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/27/2016] [Indexed: 12/14/2022] Open
Abstract
The adenosine A1 G protein-coupled receptor (A1AR) is an important therapeutic target implicated in a wide range of cardiovascular and neuronal disorders. Although it is well established that the A1AR orthosteric site is located within the receptor's transmembrane (TM) bundle, prior studies have implicated extracellular loop 2 (ECL2) as having a significant role in contributing to orthosteric ligand affinity and signaling for various G protein-coupled receptors (GPCRs). We thus performed extensive alanine scanning mutagenesis of A1AR-ECL2 to explore the role of this domain on A1AR orthosteric ligand pharmacology. Using quantitative analytical approaches and molecular modeling, we identified ECL2 residues that interact either directly or indirectly with orthosteric agonists and antagonists. Discrete mutations proximal to a conserved ECL2-TM3 disulfide bond selectively affected orthosteric ligand affinity, whereas a cluster of five residues near the TM4-ECL2 juncture influenced orthosteric agonist efficacy. A combination of ligand docking, molecular dynamics simulations, and mutagenesis results suggested that the orthosteric agonist 5'-N-ethylcarboxamidoadenosine binds transiently to an extracellular vestibule formed by ECL2 and the top of TM5 and TM7, prior to entry into the canonical TM bundle orthosteric site. Collectively, this study highlights a key role for ECL2 in A1AR orthosteric ligand binding and receptor activation.
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Affiliation(s)
- Anh T N Nguyen
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., J.-A.B., T.T., L.L.M, K.J.G, P.J.W, P.M.S, A.C., L.T.M), Monash e-Research Centre (T.D.N), and Department of Pharmacology (A.T.N.N, J.-A.B., K.J.G., P.M.S., A.C., L.T.M), Monash University, Parkville, Victoria, Australia
| | - Jo-Anne Baltos
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., J.-A.B., T.T., L.L.M, K.J.G, P.J.W, P.M.S, A.C., L.T.M), Monash e-Research Centre (T.D.N), and Department of Pharmacology (A.T.N.N, J.-A.B., K.J.G., P.M.S., A.C., L.T.M), Monash University, Parkville, Victoria, Australia
| | - Trayder Thomas
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., J.-A.B., T.T., L.L.M, K.J.G, P.J.W, P.M.S, A.C., L.T.M), Monash e-Research Centre (T.D.N), and Department of Pharmacology (A.T.N.N, J.-A.B., K.J.G., P.M.S., A.C., L.T.M), Monash University, Parkville, Victoria, Australia
| | - Toan D Nguyen
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., J.-A.B., T.T., L.L.M, K.J.G, P.J.W, P.M.S, A.C., L.T.M), Monash e-Research Centre (T.D.N), and Department of Pharmacology (A.T.N.N, J.-A.B., K.J.G., P.M.S., A.C., L.T.M), Monash University, Parkville, Victoria, Australia
| | - Laura López Muñoz
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., J.-A.B., T.T., L.L.M, K.J.G, P.J.W, P.M.S, A.C., L.T.M), Monash e-Research Centre (T.D.N), and Department of Pharmacology (A.T.N.N, J.-A.B., K.J.G., P.M.S., A.C., L.T.M), Monash University, Parkville, Victoria, Australia
| | - Karen J Gregory
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., J.-A.B., T.T., L.L.M, K.J.G, P.J.W, P.M.S, A.C., L.T.M), Monash e-Research Centre (T.D.N), and Department of Pharmacology (A.T.N.N, J.-A.B., K.J.G., P.M.S., A.C., L.T.M), Monash University, Parkville, Victoria, Australia
| | - Paul J White
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., J.-A.B., T.T., L.L.M, K.J.G, P.J.W, P.M.S, A.C., L.T.M), Monash e-Research Centre (T.D.N), and Department of Pharmacology (A.T.N.N, J.-A.B., K.J.G., P.M.S., A.C., L.T.M), Monash University, Parkville, Victoria, Australia
| | - Patrick M Sexton
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., J.-A.B., T.T., L.L.M, K.J.G, P.J.W, P.M.S, A.C., L.T.M), Monash e-Research Centre (T.D.N), and Department of Pharmacology (A.T.N.N, J.-A.B., K.J.G., P.M.S., A.C., L.T.M), Monash University, Parkville, Victoria, Australia
| | - Arthur Christopoulos
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., J.-A.B., T.T., L.L.M, K.J.G, P.J.W, P.M.S, A.C., L.T.M), Monash e-Research Centre (T.D.N), and Department of Pharmacology (A.T.N.N, J.-A.B., K.J.G., P.M.S., A.C., L.T.M), Monash University, Parkville, Victoria, Australia
| | - Lauren T May
- Monash Institute of Pharmaceutical Sciences (A.T.N.N., J.-A.B., T.T., L.L.M, K.J.G, P.J.W, P.M.S, A.C., L.T.M), Monash e-Research Centre (T.D.N), and Department of Pharmacology (A.T.N.N, J.-A.B., K.J.G., P.M.S., A.C., L.T.M), Monash University, Parkville, Victoria, Australia
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Busato M, Giorgetti A. Structural modeling of G-protein coupled receptors: An overview on automatic web-servers. Int J Biochem Cell Biol 2016; 77:264-74. [PMID: 27102413 DOI: 10.1016/j.biocel.2016.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 04/09/2016] [Accepted: 04/15/2016] [Indexed: 12/27/2022]
Abstract
Despite the significant efforts and discoveries during the last few years in G protein-coupled receptor (GPCR) expression and crystallization, the receptors with known structures to date are limited only to a small fraction of human GPCRs. The lack of experimental three-dimensional structures of the receptors represents a strong limitation that hampers a deep understanding of their function. Computational techniques are thus a valid alternative strategy to model three-dimensional structures. Indeed, recent advances in the field, together with extraordinary developments in crystallography, in particular due to its ability to capture GPCRs in different activation states, have led to encouraging results in the generation of accurate models. This, prompted the community of modelers to render their methods publicly available through dedicated databases and web-servers. Here, we present an extensive overview on these services, focusing on their advantages, drawbacks and their role in successful applications. Future challenges in the field of GPCR modeling, such as the predictions of long loop regions and the modeling of receptor activation states are presented as well.
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Affiliation(s)
- Mirko Busato
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - Alejandro Giorgetti
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy; Computational Biomedicine, Institute for Advanced Simulation IAS-5 and Computational Biomedicine, Institute of Neuroscience and Medicine INM-9, Forschungszentrum Jülich, Germany.
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30
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Kleist AB, Getschman AE, Ziarek JJ, Nevins AM, Gauthier PA, Chevigné A, Szpakowska M, Volkman BF. New paradigms in chemokine receptor signal transduction: Moving beyond the two-site model. Biochem Pharmacol 2016; 114:53-68. [PMID: 27106080 DOI: 10.1016/j.bcp.2016.04.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 04/13/2016] [Indexed: 10/21/2022]
Abstract
Chemokine receptor (CKR) signaling forms the basis of essential immune cellular functions, and dysregulated CKR signaling underpins numerous disease processes of the immune system and beyond. CKRs, which belong to the seven transmembrane domain receptor (7TMR) superfamily, initiate signaling upon binding of endogenous, secreted chemokine ligands. Chemokine-CKR interactions are traditionally described by a two-step/two-site mechanism, in which the CKR N-terminus recognizes the chemokine globular core (i.e. site 1 interaction), followed by activation when the unstructured chemokine N-terminus is inserted into the receptor TM bundle (i.e. site 2 interaction). Several recent studies challenge the structural independence of sites 1 and 2 by demonstrating physical and allosteric links between these supposedly separate sites. Others contest the functional independence of these sites, identifying nuanced roles for site 1 and other interactions in CKR activation. These developments emerge within a rapidly changing landscape in which CKR signaling is influenced by receptor PTMs, chemokine and CKR dimerization, and endogenous non-chemokine ligands. Simultaneous advances in the structural and functional characterization of 7TMR biased signaling have altered how we understand promiscuous chemokine-CKR interactions. In this review, we explore new paradigms in CKR signal transduction by considering studies that depict a more intricate architecture governing the consequences of chemokine-CKR interactions.
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Affiliation(s)
- Andrew B Kleist
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Anthony E Getschman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Joshua J Ziarek
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Ave, Boston, MA 02115, USA.
| | - Amanda M Nevins
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Pierre-Arnaud Gauthier
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Andy Chevigné
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Martyna Szpakowska
- Department of Infection and Immunity, Luxembourg Institute of Health, L-4354 Esch-sur-Alzette, Luxembourg.
| | - Brian F Volkman
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
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Mutation-Guided Unbiased Modeling of the Fat Sensor GPR119 for High-Yield Agonist Screening. Structure 2015; 23:2377-2386. [PMID: 26526849 DOI: 10.1016/j.str.2015.09.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 09/14/2015] [Accepted: 09/15/2015] [Indexed: 12/14/2022]
Abstract
Recent benchmark studies have demonstrated the difficulties in obtaining accurate predictions of ligand binding conformations to comparative models of G-protein-coupled receptors. We have developed a data-driven optimization protocol, which integrates mutational data and structural information from multiple X-ray receptor structures in combination with a fully flexible ligand docking protocol to determine the binding conformation of AR231453, a small-molecule agonist, in the GPR119 receptor. Resulting models converge to one conformation that explains the majority of data from mutation studies and is consistent with the structure-activity relationship for a large number of AR231453 analogs. Another key property of the refined models is their success in separating active ligands from decoys in a large-scale virtual screening. These results demonstrate that mutation-guided receptor modeling can provide predictions of practical value for describing receptor-ligand interactions and drug discovery.
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32
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Takezako T, Unal H, Karnik SS, Node K. Structure-Function Basis of Attenuated Inverse Agonism of Angiotensin II Type 1 Receptor Blockers for Active-State Angiotensin II Type 1 Receptor. Mol Pharmacol 2015; 88:488-501. [PMID: 26121982 DOI: 10.1124/mol.115.099176] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/29/2015] [Indexed: 01/05/2023] Open
Abstract
Ligand-independent signaling by the angiotensin II type 1 receptor (AT1R) can be activated in clinical settings by mechanical stretch and autoantibodies as well as receptor mutations. Transition of the AT1R to the activated state is known to lower inverse agonistic efficacy of clinically used AT1R blockers (ARBs). The structure-function basis for reduced efficacy of inverse agonists is a fundamental aspect that has been understudied not only in relation to the AT1R but also regarding other homologous receptors. Here, we demonstrate that the active-state transition in the AT1R indeed attenuates an inverse agonistic effect of four biphenyl-tetrazole ARBs through changes in specific ligand-receptor interactions. In the ground state, tight interactions of four ARBs with a set of residues (Ser109(TM3), Phe182(ECL2), Gln257(TM6), Tyr292(TM7), and Asn295(TM7)) results in potent inverse agonism. In the activated state, the ARB-AT1R interactions shift to a different set of residues (Val108(TM3), Ser109(TM3), Ala163(TM4), Phe182(ECL2), Lys199(TM5), Tyr292(TM7), and Asn295(TM7)), resulting in attenuated inverse agonism. Interestingly, V108I, A163T, N295A, and F182A mutations in the activated state of the AT1R shift the functional response to the ARB binding toward agonism, but in the ground state the same mutations cause inverse agonism. Our data show that the second extracellular loop is an important regulator of the functional states of the AT1R. Our findings suggest that the quest for discovering novel ARBs, and improving current ARBs, fundamentally depends on the knowledge of the unique sets of residues that mediate inverse agonistic potency in the two states of the AT1R.
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Affiliation(s)
- Takanobu Takezako
- Department of Advanced Heart Research, Saga University, Saga, Japan (T.T.); Department of Cardiovascular Medicine, Saga University, Saga, Japan (K.N.); Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio (H.U., S.S.K.); Department of Biosignal Pathophysiology, Kobe University Graduate School of Medicine, Kobe, Japan (T.T.); and Department of Basic Sciences, Faculty of Pharmacy and Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey (H.U.)
| | - Hamiyet Unal
- Department of Advanced Heart Research, Saga University, Saga, Japan (T.T.); Department of Cardiovascular Medicine, Saga University, Saga, Japan (K.N.); Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio (H.U., S.S.K.); Department of Biosignal Pathophysiology, Kobe University Graduate School of Medicine, Kobe, Japan (T.T.); and Department of Basic Sciences, Faculty of Pharmacy and Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey (H.U.)
| | - Sadashiva S Karnik
- Department of Advanced Heart Research, Saga University, Saga, Japan (T.T.); Department of Cardiovascular Medicine, Saga University, Saga, Japan (K.N.); Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio (H.U., S.S.K.); Department of Biosignal Pathophysiology, Kobe University Graduate School of Medicine, Kobe, Japan (T.T.); and Department of Basic Sciences, Faculty of Pharmacy and Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey (H.U.)
| | - Koichi Node
- Department of Advanced Heart Research, Saga University, Saga, Japan (T.T.); Department of Cardiovascular Medicine, Saga University, Saga, Japan (K.N.); Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio (H.U., S.S.K.); Department of Biosignal Pathophysiology, Kobe University Graduate School of Medicine, Kobe, Japan (T.T.); and Department of Basic Sciences, Faculty of Pharmacy and Betul Ziya Eren Genome and Stem Cell Center, Erciyes University, Kayseri, Turkey (H.U.)
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Michino M, Beuming T, Donthamsetti P, Newman AH, Javitch JA, Shi L. What can crystal structures of aminergic receptors tell us about designing subtype-selective ligands? Pharmacol Rev 2015; 67:198-213. [PMID: 25527701 DOI: 10.1124/pr.114.009944] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
G protein-coupled receptors (GPCRs) are integral membrane proteins that represent an important class of drug targets. In particular, aminergic GPCRs interact with a significant portion of drugs currently on the market. However, most drugs that target these receptors are associated with undesirable side effects, which are due in part to promiscuous interactions with close homologs of the intended target receptors. Here, based on a systematic analysis of all 37 of the currently available high-resolution crystal structures of aminergic GPCRs, we review structural elements that contribute to and can be exploited for designing subtype-selective compounds. We describe the roles of secondary binding pockets (SBPs), as well as differences in ligand entry pathways to the orthosteric binding site, in determining selectivity. In addition, using the available crystal structures, we have identified conformational changes in the SBPs that are associated with receptor activation and explore the implications of these changes for the rational development of selective ligands with tailored efficacy.
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Affiliation(s)
- Mayako Michino
- Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York (M.M., L.S.); Schrödinger Inc., New York, New York (T.B.); Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York (P.D., J.A.J.); and Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland (A.H.N.)
| | - Thijs Beuming
- Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York (M.M., L.S.); Schrödinger Inc., New York, New York (T.B.); Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York (P.D., J.A.J.); and Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland (A.H.N.)
| | - Prashant Donthamsetti
- Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York (M.M., L.S.); Schrödinger Inc., New York, New York (T.B.); Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York (P.D., J.A.J.); and Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland (A.H.N.)
| | - Amy Hauck Newman
- Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York (M.M., L.S.); Schrödinger Inc., New York, New York (T.B.); Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York (P.D., J.A.J.); and Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland (A.H.N.)
| | - Jonathan A Javitch
- Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York (M.M., L.S.); Schrödinger Inc., New York, New York (T.B.); Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York (P.D., J.A.J.); and Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland (A.H.N.)
| | - Lei Shi
- Department of Physiology and Biophysics and Institute for Computational Biomedicine, Weill Medical College of Cornell University, New York, New York (M.M., L.S.); Schrödinger Inc., New York, New York (T.B.); Departments of Psychiatry and Pharmacology, Columbia University College of Physicians and Surgeons, and Division of Molecular Therapeutics, New York State Psychiatric Institute, New York, New York (P.D., J.A.J.); and Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, Baltimore, Maryland (A.H.N.)
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Banerjee AA, Dupakuntla M, Pathak BR, Mahale SD. FSH receptor-specific residues L501 and I505 in extracellular loop 2 are essential for its function. J Mol Endocrinol 2015; 54:193-204. [PMID: 25791375 DOI: 10.1530/jme-14-0275] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/18/2015] [Indexed: 12/11/2022]
Abstract
The extracellular loop 2 (EL2) of FSH receptor (FSHR) plays a pivotal role in various events downstream of FSH stimulation. Because swapping the six FSHR-specific residues in EL2 (chimeric EL2M) with those from LH/choriogonadotropin receptor resulted in impaired internalization of FSH-FSHR complex and low FSH-induced cAMP production, six substitution mutants of EL2 were generated to ascertain the contribution of individual amino acids to the effects shown by chimeric EL2M. Results revealed that L(501)F mainly and I(505)V to a lesser extent contribute to the diminished receptor function in chimeric EL2M. HEK293 cells stably expressing WT and chimeric EL2M FSHR were generated to track the fate of the receptors post FSH induction. The chimeric EL2M FSHR stable clone showed weak internalization and cAMP response similar to transiently transfected cells. Furthermore, reduced FSH-induced ERK phosphorylation was also observed. The interaction of activated chimeric EL2M and L(501)F FSHR with β-arrestins was weak compared with WT FSHR, thus explaining the impaired internalization of chimeric EL2M and corroborating the indispensable role of EL2 in receptor function.
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Affiliation(s)
- Antara A Banerjee
- Division of Structural BiologyNational Institute for Research in Reproductive Health (Indian Council of Medical Research), Jehangir Merwanji Street, Parel, Mumbai 400 012, IndiaNational Institute for Research in Reproductive Health (Indian Council of Medical Research)ICMR Biomedical Informatics Centre, Jehangir Merwanji Street, Parel, Mumbai 400 012, India
| | - Madhavi Dupakuntla
- Division of Structural BiologyNational Institute for Research in Reproductive Health (Indian Council of Medical Research), Jehangir Merwanji Street, Parel, Mumbai 400 012, IndiaNational Institute for Research in Reproductive Health (Indian Council of Medical Research)ICMR Biomedical Informatics Centre, Jehangir Merwanji Street, Parel, Mumbai 400 012, India
| | - Bhakti R Pathak
- Division of Structural BiologyNational Institute for Research in Reproductive Health (Indian Council of Medical Research), Jehangir Merwanji Street, Parel, Mumbai 400 012, IndiaNational Institute for Research in Reproductive Health (Indian Council of Medical Research)ICMR Biomedical Informatics Centre, Jehangir Merwanji Street, Parel, Mumbai 400 012, India
| | - Smita D Mahale
- Division of Structural BiologyNational Institute for Research in Reproductive Health (Indian Council of Medical Research), Jehangir Merwanji Street, Parel, Mumbai 400 012, IndiaNational Institute for Research in Reproductive Health (Indian Council of Medical Research)ICMR Biomedical Informatics Centre, Jehangir Merwanji Street, Parel, Mumbai 400 012, India Division of Structural BiologyNational Institute for Research in Reproductive Health (Indian Council of Medical Research), Jehangir Merwanji Street, Parel, Mumbai 400 012, IndiaNational Institute for Research in Reproductive Health (Indian Council of Medical Research)ICMR Biomedical Informatics Centre, Jehangir Merwanji Street, Parel, Mumbai 400 012, India
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Duan X, Zhang M, Zhang X, Wang F, Lei M. Molecular modeling and docking study on dopamine D2-like and serotonin 5-HT2A receptors. J Mol Graph Model 2015; 57:143-55. [DOI: 10.1016/j.jmgm.2015.01.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 01/23/2015] [Accepted: 01/29/2015] [Indexed: 01/22/2023]
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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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Wifling D, Bernhardt G, Dove S, Buschauer A. The extracellular loop 2 (ECL2) of the human histamine H4 receptor substantially contributes to ligand binding and constitutive activity. PLoS One 2015; 10:e0117185. [PMID: 25629160 PMCID: PMC4309601 DOI: 10.1371/journal.pone.0117185] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/21/2014] [Indexed: 11/25/2022] Open
Abstract
In contrast to the corresponding mouse and rat orthologs, the human histamine H4 receptor (hH4R) shows extraordinarily high constitutive activity. In the extracellular loop (ECL), replacement of F169 by V as in the mouse H4R significantly reduced constitutive activity. Stabilization of the inactive state was even more pronounced for a double mutant, in which, in addition to F169V, S179 in the ligand binding site was replaced by M. To study the role of the FF motif in ECL2, we generated the hH4R-F168A mutant. The receptor was co-expressed in Sf9 insect cells with the G-protein subunits Gαi2 and Gβ1γ2, and the membranes were studied in [3H]histamine binding and functional [35S]GTPγS assays. The potency of various ligands at the hH4R-F168A mutant decreased compared to the wild-type hH4R, for example by 30- and more than 100-fold in case of the H4R agonist UR-PI376 and histamine, respectively. The high constitutive activity of the hH4R was completely lost in the hH4R-F168A mutant, as reflected by neutral antagonism of thioperamide, a full inverse agonist at the wild-type hH4R. By analogy, JNJ7777120 was a partial inverse agonist at the hH4R, but a partial agonist at the hH4R-F168A mutant, again demonstrating the decrease in constitutive activity due to F168A mutation. Thus, F168 was proven to play a key role not only in ligand binding and potency, but also in the high constitutive activity of the hH4R.
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Affiliation(s)
- David Wifling
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry II, University of Regensburg, Regensburg, Germany
| | - Günther Bernhardt
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry II, University of Regensburg, Regensburg, Germany
| | - Stefan Dove
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry II, University of Regensburg, Regensburg, Germany
| | - Armin Buschauer
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry II, University of Regensburg, Regensburg, Germany
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Gadhe CG, Balupuri A, Cho SJ. In silico characterization of binding mode of CCR8 inhibitor: homology modeling, docking and membrane based MD simulation study. J Biomol Struct Dyn 2015; 33:2491-510. [PMID: 25617117 DOI: 10.1080/07391102.2014.1002006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Human CC-chemokine receptor 8 (CCR8) is a crucial drug target in asthma that belongs to G-protein-coupled receptor superfamily, which is characterized by seven transmembrane helices. To date, there is no X-ray crystal structure available for CCR8; this hampers active research on the target. Molecular basis of interaction mechanism of antagonist with CCR8 remains unclear. In order to provide binding site information and stable binding mode, we performed modeling, docking and molecular dynamics (MD) simulation of CCR8. Docking study of biaryl-ether-piperidine derivative (13C) was performed inside predefined CCR8 binding site to get the representative conformation of 13C. Further, MD simulations of receptor and complex (13C-CCR8) inside dipalmitoylphosphatidylcholine lipid bilayers were performed to explore the effect of lipids. Results analyses showed that the Gln91, Tyr94, Cys106, Val109, Tyr113, Cys183, Tyr184, Ser185, Lys195, Thr198, Asn199, Met202, Phe254, and Glu286 were conserved in both docking and MD simulations. This indicated possible role of these residues in CCR8 antagonism. However, experimental mutational studies on these identified residues could be effective to confirm their importance in CCR8 antagonism. Furthermore, calculated Coulombic interactions represented the crucial roles of Glu286, Lys195, and Tyr113 in CCR8 antagonism. Important residues identified in this study overlap with the previous non-peptide agonist (LMD-009) binding site. Though, the non-peptide agonist and currently studied inhibitor (13C) share common substructure, but they differ in their effects on CCR8. So, to get more insight into their agonist and antagonist effects, further side-by-side experimental studies on both agonist (LMD-009) and antagonist (13C) are suggested.
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Affiliation(s)
- Changdev G Gadhe
- a Department of Life Sciences, College of BioNano Technology , Gachon University , 1342 Seongnamdaero, Sujeong-gu, Seongnam-si , Gyeonggi-do 461-701 , Republic of Korea
| | - Anand Balupuri
- b Department of Bio-New Drug Development, College of Medicine , Chosun University , Gwangju 501-759 , Republic of Korea
| | - Seung Joo Cho
- b Department of Bio-New Drug Development, College of Medicine , Chosun University , Gwangju 501-759 , Republic of Korea.,c Department of Cellular Molecular Medicine, College of Medicine , Chosun University , Gwangju 501-759 , Republic of Korea
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Sensoy O, Weinstein H. A mechanistic role of Helix 8 in GPCRs: Computational modeling of the dopamine D2 receptor interaction with the GIPC1-PDZ-domain. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2015; 1848:976-83. [PMID: 25592838 DOI: 10.1016/j.bbamem.2014.12.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 11/15/2014] [Accepted: 12/02/2014] [Indexed: 01/18/2023]
Abstract
Helix-8 (Hx8) is a structurally conserved amphipathic helical motif in class-A GPCRs, adjacent to the C-terminal sequence that is responsible for PDZ-domain-recognition. The Hx8 segment in the dopamine D2 receptor (D2R) constitutes the C-terminal segment and we investigate its role in the function of D2R by studying the interaction with the PDZ-containing GIPC1 using homology models based on the X-ray structures of very closely related analogs: the D3R for the D2R model, and the PDZ domain of GIPC2 for GIPC1-PDZ. The mechanism of this interaction was investigated with all-atom unbiased molecular dynamics (MD) simulations that reveal the role of the membrane in maintaining the helical fold of Hx8, and with biased MD simulations to elucidate the energy drive for the interaction with the GIPC1-PDZ. We found that it becomes more favorable energetically for Hx8 to adopt the extended conformation observed in all PDZ-ligand complexes when it moves away from the membrane, and that C-terminus palmitoylation of D2R enhanced membrane penetration by the Hx8 backbone. De-palmitoylation enables Hx8 to move out into the aqueous environment for interaction with the PDZ domain. All-atom unbiased MD simulations of the full D2R-GIPC1-PDZ complex in sphingolipid/cholesterol membranes show that the D2R carboxyl C-terminus samples the region of the conserved GFGL motif located on the carboxylate-binding loop of the GIPC1-PDZ, and the entire complex distances itself from the membrane interface. Together, these results outline a likely mechanism of Hx8 involvement in the interaction of the GPCR with PDZ-domains in the course of signaling.
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Affiliation(s)
- Ozge Sensoy
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, USA
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Medical College of Cornell University, New York, NY, USA.
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Beuming T, Lenselink B, Pala D, McRobb F, Repasky M, Sherman W. Docking and Virtual Screening Strategies for GPCR Drug Discovery. Methods Mol Biol 2015; 1335:251-76. [PMID: 26260606 DOI: 10.1007/978-1-4939-2914-6_17] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Progress in structure determination of G protein-coupled receptors (GPCRs) has made it possible to apply structure-based drug design (SBDD) methods to this pharmaceutically important target class. The quality of GPCR structures available for SBDD projects fall on a spectrum ranging from high resolution crystal structures (<2 Å), where all water molecules in the binding pocket are resolved, to lower resolution (>3 Å) where some protein residues are not resolved, and finally to homology models that are built using distantly related templates. Each GPCR project involves a distinct set of opportunities and challenges, and requires different approaches to model the interaction between the receptor and the ligands. In this review we will discuss docking and virtual screening to GPCRs, and highlight several refinement and post-processing steps that can be used to improve the accuracy of these calculations. Several examples are discussed that illustrate specific steps that can be taken to improve upon the docking and virtual screening accuracy. While GPCRs are a unique target class, many of the methods and strategies outlined in this review are general and therefore applicable to other protein families.
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Affiliation(s)
- Thijs Beuming
- Schrödinger, Inc., 120 West 45th Street, New York, NY, 10036, USA,
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Kaiya H, Konno N, Kangawa K, Uchiyama M, Miyazato M. Identification, tissue distribution and functional characterization of the ghrelin receptor in West African lungfish, Protopterus annectens. Gen Comp Endocrinol 2014; 209:106-17. [PMID: 25093625 DOI: 10.1016/j.ygcen.2014.07.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 07/16/2014] [Accepted: 07/26/2014] [Indexed: 12/29/2022]
Abstract
We identified two ghrelin receptor isoforms, the ghrelin receptor type-1a (GHS-R1a) and its alternative splice form (GHS-R1b) for West African lungfish, Protopterus annectens. Lungfish GHS-R1a and 1b comprised 361 and 281 amino acids, respectively. Lungfish GHS-R1a showed the highest identity to coelacanth GHS-R1a (80.4%). The highest expression of GHS-R1a mRNAs was seen in the brain, liver, ovary, heart, intestine, and gills. GHS-R1b mRNAs were also detected in the same tissues with GHS-R1a, but their expression level was 1/20 that of GHS-R1a. In human embryonic kidney 293 cells transiently expressing lungfish GHS-R1a, rat and bullfrog ghrelin, and two GHS-R1a agonists, GHRP-6 and hexarelin, increased intracellular Ca(2+) concentrations. The intensity of the Ca(2+) increases induced by GHS-R1a agonists was twice when compared to that induced by ghrelin, although the median effective doses (ED50) were similar, suggesting a long-lasting effect of GHS-R1a agonists with similar affinity. We also examined changes in the GHS-R gene expression during an eight-week estivation. Body weight was slightly lowered, but plasma sodium and glucose concentrations decreased; plasma urea concentration increased significantly 4weeks after the start of estivation. Overall, expression of GHS-R1a mRNA decreased, but changes in GHS-R1b mRNA expression were inconsistent with those of GHS-R1a during estivation, suggesting an involvement of GHS-R in energy homeostasis, as seen in mammals. Our results suggest that the ghrelin-GHS-R1a system is present in this lungfish although ghrelin has not yet been found. The structure of GHS-R1a is closer to that of tetrapods than Actinopterygian fish, indicating a process of evolution that follows the Crossopterygii such as coelacanth.
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Affiliation(s)
- Hiroyuki Kaiya
- Department of Biochemistry, National Cardiovascular Center Research Institute, 5-7-1 Fujishirodai, Suita, Osaka 565-8565, Japan.
| | - Norifumi Konno
- Laboratory of Regulatory Biology, Graduate School of Science and Engineering, University of Toyama, 3190-Gofuku, Toyama 930-8555, Japan
| | - Kenji Kangawa
- Department of Biochemistry, National Cardiovascular Center Research Institute, 5-7-1 Fujishirodai, Suita, Osaka 565-8565, Japan
| | - Minoru Uchiyama
- Laboratory of Regulatory Biology, Graduate School of Science and Engineering, University of Toyama, 3190-Gofuku, Toyama 930-8555, Japan
| | - Mikiya Miyazato
- Department of Biochemistry, National Cardiovascular Center Research Institute, 5-7-1 Fujishirodai, Suita, Osaka 565-8565, Japan
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Wang F, Chen W, Lin H, Li W. Cloning, expression, and ligand-binding characterization of two neuropeptide Y receptor subtypes in orange-spotted grouper, Epinephelus coioides. FISH PHYSIOLOGY AND BIOCHEMISTRY 2014; 40:1693-1707. [PMID: 25007879 DOI: 10.1007/s10695-014-9960-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Accepted: 06/24/2014] [Indexed: 06/03/2023]
Abstract
As one of the most important multifunctional peptides, neuropeptide Y (NPY) performs its physiological functions through different subtype receptors. In this study, full-length cDNAs of two NPY receptors (YRs) in orange-spotted grouper (Epinephelus coioides) were cloned and named npy8br (y8b) and npy2r (y2). Phylogenetic analysis indicated that the Y8b receptor is an ortholog of the teleostean Y8b receptor, which belongs to the Y1 subfamily, and the Y2 receptor is an ortholog of the teleostean Y2 receptor, which belongs to the Y2 subfamily. Both of the YRs have G protein-coupled receptor family profiles. Multiple alignments demonstrate that the extracellular loop regions of YRs have distinctive residues of each species. Expression profile analysis revealed that the grouper Y8b receptor mRNA is primarily expressed in the brain, stomach and intestine, while the grouper Y2 receptor mRNA is primarily expressed in the brain, ovary, liver and heart. Double immunofluorescence analysis determined that the grouper YRs interact with the grouper NPY around the human embryonic kidney 293T cell surface. Furthermore, site-directed mutagenesis in a phage display system revealed that Asp(6.59) might be a common NPY-binding site, while Asp(2.68) of the Y8b receptor and Glu(5.24) of the Y2 receptor could be likely involved in subtype-specific binding. Combining the expression profile and ligand-binding feature, the grouper Y8b receptor could be involved in regulating food intake via the brain-gut axis and the grouper Y2 receptor might play a role in balancing the regulatory activity of the Y8b receptor and participate in metabolism in the liver and ovary.
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Affiliation(s)
- Fei Wang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, Guangdong Provincial Key Laboratory for Aquatic Economic Animals, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, People's Republic of China
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Gerbier R, Leroux V, Couvineau P, Alvear-Perez R, Maigret B, Llorens-Cortes C, Iturrioz X. New structural insights into the apelin receptor: identification of key residues for apelin binding. FASEB J 2014; 29:314-22. [PMID: 25359495 DOI: 10.1096/fj.14-256339] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Apelin is the endogenous ligand of the orphan 7-transmembrane domain GPCR APJ, now named the apelin receptor (ApelinR). Apelin plays a prominent role in body fluid and cardiovascular homeostasis. To better understand the structural organization of the ApelinR, we built 3 homology 3-dimensional (3D) models of the human ApelinR using the validated cholecystokinin receptor-1 3D model or the X-ray structures of the β2-adrenergic and CXCR4 receptors as templates. Docking of the pyroglutamyl form of apelin 13 (pE13F) into these models revealed the conservation at the bottom of the binding site of a hydrophobic cavity in which the C-terminal Phe of pE13F was embedded. In contrast, at the top of the binding site, depending on the model, different interactions were visualized between acidic residues of the ApelinR and the basic residues of pE13F. Using site-directed mutagenesis, we showed that Asp 92, Glu 172, and Asp 282 of rat ApelinR are key residues in apelin binding by interacting with Lys 8, Arg 2, and Arg 4 of pE13F, respectively. These residues are only seen in the CXCR4-based ApelinR 3D model, further validating this model. These findings bring new insights into the structural organization of the ApelinR and the mode of apelin binding.
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Affiliation(s)
- Romain Gerbier
- College de France, Laboratory of Central Neuropeptides in the Regulation of Body Fluid Homeostasis and Cardiovascular Functions, Center for Interdisciplinary Research in Biology (CIRB), Paris, France; CNRS, UMR 7241, Paris, France; and INSERM, U1050, Paris, France
| | - Vincent Leroux
- College de France, Laboratory of Central Neuropeptides in the Regulation of Body Fluid Homeostasis and Cardiovascular Functions, Center for Interdisciplinary Research in Biology (CIRB), Paris, France; CNRS, UMR 7241, Paris, France; and INSERM, U1050, Paris, France
| | - Pierre Couvineau
- College de France, Laboratory of Central Neuropeptides in the Regulation of Body Fluid Homeostasis and Cardiovascular Functions, Center for Interdisciplinary Research in Biology (CIRB), Paris, France; CNRS, UMR 7241, Paris, France; and INSERM, U1050, Paris, France
| | - Rodrigo Alvear-Perez
- College de France, Laboratory of Central Neuropeptides in the Regulation of Body Fluid Homeostasis and Cardiovascular Functions, Center for Interdisciplinary Research in Biology (CIRB), Paris, France; CNRS, UMR 7241, Paris, France; and INSERM, U1050, Paris, France
| | - Bernard Maigret
- College de France, Laboratory of Central Neuropeptides in the Regulation of Body Fluid Homeostasis and Cardiovascular Functions, Center for Interdisciplinary Research in Biology (CIRB), Paris, France; CNRS, UMR 7241, Paris, France; and INSERM, U1050, Paris, France
| | - Catherine Llorens-Cortes
- College de France, Laboratory of Central Neuropeptides in the Regulation of Body Fluid Homeostasis and Cardiovascular Functions, Center for Interdisciplinary Research in Biology (CIRB), Paris, France; CNRS, UMR 7241, Paris, France; and INSERM, U1050, Paris, France
| | - Xavier Iturrioz
- College de France, Laboratory of Central Neuropeptides in the Regulation of Body Fluid Homeostasis and Cardiovascular Functions, Center for Interdisciplinary Research in Biology (CIRB), Paris, France; CNRS, UMR 7241, Paris, France; and INSERM, U1050, Paris, France
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Ragnarsson L, Andersson Å, Thomas WG, Lewis RJ. Extracellular Surface Residues of the α1B-Adrenoceptor Critical for G Protein–Coupled Receptor Function. Mol Pharmacol 2014; 87:121-9. [DOI: 10.1124/mol.114.094557] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Daga PR, Polgar WE, Zaveri NT. Structure-based virtual screening of the nociceptin receptor: hybrid docking and shape-based approaches for improved hit identification. J Chem Inf Model 2014; 54:2732-43. [PMID: 25148595 PMCID: PMC4210177 DOI: 10.1021/ci500291a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
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The
antagonist-bound crystal structure of the nociceptin receptor
(NOP), from the opioid receptor family, was recently reported along
with those of the other opioid receptors bound to opioid antagonists.
We recently reported the first homology model of the ‘active-state’
of the NOP receptor, which when docked with ‘agonist’
ligands showed differences in the TM helices and residues, consistent
with GPCR activation after agonist binding. In this study, we explored
the use of the active-state NOP homology model for structure-based
virtual screening to discover NOP ligands containing new chemical
scaffolds. Several NOP agonist and antagonist ligands previously reported
are based on a common piperidine scaffold. Given the structure–activity
relationships for known NOP ligands, we developed a hybrid method
that combines a structure-based and ligand-based approach, utilizing
the active-state NOP receptor as well as the pharmacophoric features
of known NOP ligands, to identify novel NOP binding scaffolds by virtual
screening. Multiple conformations of the NOP active site including
the flexible second extracellular loop (EL2) loop were generated by
simulated annealing and ranked using enrichment factor (EF) analysis
and a ligand–decoy dataset containing known NOP agonist ligands.
The enrichment factors were further improved by combining shape-based
screening of this ligand–decoy dataset and calculation of consensus
scores. This combined structure-based and ligand-based EF analysis
yielded higher enrichment factors than the individual methods, suggesting
the effectiveness of the hybrid approach. Virtual screening of the
CNS Permeable subset of the ZINC database was carried out using the
above-mentioned hybrid approach in a tiered fashion utilizing a ligand
pharmacophore-based filtering step, followed by structure-based virtual
screening using the refined NOP active-state models from the enrichment
analysis. Determination of the NOP receptor binding affinity of a
selected set of top-scoring hits resulted in identification of several
compounds with measurable binding affinity at the NOP receptor, one
of which had a new chemotype for NOP receptor binding. The hybrid
ligand-based and structure-based methodology demonstrates an effective
approach for virtual screening that leverages existing SAR and receptor
structure information for identifying novel hits for NOP receptor
binding. The refined active-state NOP homology models obtained from
the enrichment studies can be further used for structure-based optimization
of these new chemotypes to obtain potent and selective NOP receptor
ligands for therapeutic development.
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Affiliation(s)
- Pankaj R Daga
- Astraea Therapeutics, LLC. , 320 Logue Avenue, Mountain View, California 94043, United States
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Kooistra AJ, Kuhne S, de Esch IJP, Leurs R, de Graaf C. A structural chemogenomics analysis of aminergic GPCRs: lessons for histamine receptor ligand design. Br J Pharmacol 2014; 170:101-26. [PMID: 23713847 DOI: 10.1111/bph.12248] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 04/26/2013] [Accepted: 05/03/2013] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND AND PURPOSE Chemogenomics focuses on the discovery of new connections between chemical and biological space leading to the discovery of new protein targets and biologically active molecules. G-protein coupled receptors (GPCRs) are a particularly interesting protein family for chemogenomics studies because there is an overwhelming amount of ligand binding affinity data available. The increasing number of aminergic GPCR crystal structures now for the first time allows the integration of chemogenomics studies with high-resolution structural analyses of GPCR-ligand complexes. EXPERIMENTAL APPROACH In this study, we have combined ligand affinity data, receptor mutagenesis studies, and amino acid sequence analyses to high-resolution structural analyses of (hist)aminergic GPCR-ligand interactions. This integrated structural chemogenomics analysis is used to more accurately describe the molecular and structural determinants of ligand affinity and selectivity in different key binding regions of the crystallized aminergic GPCRs, and histamine receptors in particular. KEY RESULTS Our investigations highlight interesting correlations and differences between ligand similarity and ligand binding site similarity of different aminergic receptors. Apparent discrepancies can be explained by combining detailed analysis of crystallized or predicted protein-ligand binding modes, receptor mutation studies, and ligand structure-selectivity relationships that identify local differences in essential pharmacophore features in the ligand binding sites of different receptors. CONCLUSIONS AND IMPLICATIONS We have performed structural chemogenomics studies that identify links between (hist)aminergic receptor ligands and their binding sites and binding modes. This knowledge can be used to identify structure-selectivity relationships that increase our understanding of ligand binding to (hist)aminergic receptors and hence can be used in future GPCR ligand discovery and design.
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Affiliation(s)
- A J Kooistra
- Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands
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Khoury E, Clément S, Laporte SA. Allosteric and biased g protein-coupled receptor signaling regulation: potentials for new therapeutics. Front Endocrinol (Lausanne) 2014; 5:68. [PMID: 24847311 PMCID: PMC4021147 DOI: 10.3389/fendo.2014.00068] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Accepted: 04/22/2014] [Indexed: 01/14/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are seven-transmembrane proteins that participate in many aspects of the endocrine function and are important targets for drug development. They transduce signals mainly, but not exclusively, via hetero-trimeric G proteins, leading to a diversity of intracellular signaling cascades. Ligands binding at the hormone orthosteric sites of receptors have been classified as agonists, antagonists, and/or inverse agonists based on their ability to mainly modulate G protein signaling. Accumulating evidence also indicates that such ligands, alone or in combination with other ones such as those acting outside the orthosteric hormone binding sites (e.g., allosteric modulators), have the ability to selectively engage subsets of signaling responses as compared to the natural endogenous ligands. Such modes of functioning have been variously referred to as "functional selectivity" or "ligand-biased signaling." In this review, we provide an overview of the current knowledge regarding GPCR-biased signaling and their functional regulation with a focus on the evolving concept that receptor domains can also be targeted to allosterically bias signaling, and discuss the usefulness of such modes of regulation for the design of more efficient therapeutics.
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Affiliation(s)
- Etienne Khoury
- Department of Medicine, McGill University Health Center Research Institute, McGill University, Montreal, QC, Canada
| | - Stéphanie Clément
- Department of Pharmacology and Therapeutics, McGill University Health Center Research Institute, McGill University, Montreal, QC, Canada
| | - Stéphane A. Laporte
- Department of Medicine, McGill University Health Center Research Institute, McGill University, Montreal, QC, Canada
- Department of Pharmacology and Therapeutics, McGill University Health Center Research Institute, McGill University, Montreal, QC, Canada
- Department of Anatomy and Cell Biology, McGill University Health Center Research Institute, McGill University, Montreal, QC, Canada
- *Correspondence: Stéphane A. Laporte, Department of Medicine, Polypeptide Lab, McGill University, Strathcona Anatomy and Dentistry Building, 3640 University Street, Room W315, Montreal, QC H3A 2B2, Canada e-mail:
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Mondal S, Khelashvili G, Johner N, Weinstein H. How the dynamic properties and functional mechanisms of GPCRs are modulated by their coupling to the membrane environment. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:55-74. [PMID: 24158801 DOI: 10.1007/978-94-007-7423-0_4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Experimental observations of the dependence of function and organization of G protein-coupled receptors (GPCRs) on their lipid environment have stimulated new quantitative studies of the coupling between the proteins and the membrane. It is important to develop such a quantitative understanding at the molecular level because the effects of the coupling are seen to be physiologically and clinically significant. Here we review findings that offer insight into how membrane-GPCR coupling is connected to the structural characteristics of the GPCR, from sequence to 3D structural detail, and how this coupling is involved in the actions of ligands on the receptor. The application of a recently developed computational approach designed for quantitative evaluation of membrane remodeling and the energetics of membrane-protein interactions brings to light the importance of the radial asymmetry of the membrane-facing surface of GPCRs in their interaction with the surrounding membrane. As the radial asymmetry creates adjacencies of hydrophobic and polar residues at specific sites of the GPCR, the ability of membrane remodeling to achieve complete hydrophobic matching is limited, and the residual mismatch carries a significant energy cost. The adjacencies are shown to be affected by ligand-induced conformational changes. Thus, functionally important organization of GPCRs in the cell membrane can depend both on ligand-determined properties and on the lipid composition of various membrane regions with different remodeling capacities. That this functionally important reorganization can be driven by oligomerization patterns that reduce the energy cost of the residual mismatch, suggests a new perspective on GPCR dimerization and ligand-GPCR interactions. The relation between the modulatory effects on GPCRs from the binding of specific cell-membrane components, e.g., cholesterol, and those produced by the non-local energetics of hydrophobic mismatch are discussed in this context.
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Affiliation(s)
- Sayan Mondal
- Department of Physiology and Biophysics, Weill Cornell Medical College, Cornell University, Room E-509, 1300 York Avenue, 10065, New York City, NY, USA
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Soriano-Ursúa MA, Trujillo-Ferrara JG, Correa-Basurto J, Vilar S. Recent structural advances of β1 and β2 adrenoceptors yield keys for ligand recognition and drug design. J Med Chem 2013; 56:8207-23. [PMID: 23862978 DOI: 10.1021/jm400471z] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Because they represent attractive drug targets, adrenoceptors have been widely studied. Recent progress in structural data of β-adrenoceptors allows us to understand and predict key interactions in ligand recognition and receptor activation. Nevertheless, an important aspect of this process has only begun to be explored: the stabilization of a conformational state of these receptors upon contact with a ligand and the capacity of a ligand to influence receptor conformation through allosteric modulation, biased signaling, and selectivity. The aim of the present Perspective is to identify the well-defined orthosteric binding site and possible allosteric sites and to analyze the importance of the ligand-receptor interaction in the stabilization of certain receptor conformations. For this purpose, we have reviewed recent advances made through the use of X-ray data from ligand-β-adrenoceptor (including ADRB1 and ADRB2) crystal structures. Most importantly, implications in the medicinal chemistry field are explored in relation to drug design.
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Affiliation(s)
- Marvin A Soriano-Ursúa
- Departments of Biochemistry and Physiology, Laboratory of Molecular Modeling and Bioinformatics, Postgraduate Research Section, Escuela Superior de Medicina, Instituto Politécnico Nacional , Plan de San Luis y Dı́az Mirón s/n, Mexico City, 11340, Mexico
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Kimura T, Vukoti K, Lynch DL, Hurst DP, Grossfield A, Pitman MC, Reggio PH, Yeliseev AA, Gawrisch K. Global fold of human cannabinoid type 2 receptor probed by solid-state 13C-, 15N-MAS NMR and molecular dynamics simulations. Proteins 2013; 82:452-65. [PMID: 23999926 DOI: 10.1002/prot.24411] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 08/12/2013] [Accepted: 08/21/2013] [Indexed: 12/12/2022]
Abstract
The global fold of human cannabinoid type 2 (CB2 ) receptor in the agonist-bound active state in lipid bilayers was investigated by solid-state (13)C- and (15)N magic-angle spinning (MAS) NMR, in combination with chemical-shift prediction from a structural model of the receptor obtained by microsecond-long molecular dynamics (MD) simulations. Uniformly (13)C- and (15)N-labeled CB2 receptor was expressed in milligram quantities by bacterial fermentation, purified, and functionally reconstituted into liposomes. (13)C MAS NMR spectra were recorded without sensitivity enhancement for direct comparison of Cα, Cβ, and C=O bands of superimposed resonances with predictions from protein structures generated by MD. The experimental NMR spectra matched the calculated spectra reasonably well indicating agreement of the global fold of the protein between experiment and simulations. In particular, the (13) C chemical shift distribution of Cα resonances was shown to be very sensitive to both the primary amino acid sequence and the secondary structure of CB2. Thus the shape of the Cα band can be used as an indicator of CB2 global fold. The prediction from MD simulations indicated that upon receptor activation a rather limited number of amino acid residues, mainly located in the extracellular Loop 2 and the second half of intracellular Loop 3, change their chemical shifts significantly (≥ 1.5 ppm for carbons and ≥ 5.0 ppm for nitrogens). Simulated two-dimensional (13) Cα(i)-(13)C=O(i) and (13)C=O(i)-(15)NH(i + 1) dipolar-interaction correlation spectra provide guidance for selective amino acid labeling and signal assignment schemes to study the molecular mechanism of activation of CB2 by solid-state MAS NMR.
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Affiliation(s)
- Tomohiro Kimura
- Laboratory of Membrane Biochemistry and Biophysics, NIAAA, NIH, Bethesda, Maryland, 20892
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