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Habermann S, Gerken LRH, Kociak M, Monachon C, Kissling VM, Gogos A, Herrmann IK. Cathodoluminescent and Characteristic X-Ray-Emissive Rare-Earth-Doped Core/Shell Protein Labels for Spectromicroscopic Analysis of Cell Surface Receptors. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404309. [PMID: 39246186 DOI: 10.1002/smll.202404309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/20/2024] [Indexed: 09/10/2024]
Abstract
Understanding the localization and the interactions of biomolecules at the nanoscale and in the cellular context remains challenging. Electron microscopy (EM), unlike light-based microscopy, gives access to the cellular ultrastructure yet results in grey-scale images and averts unambiguous (co-)localization of biomolecules. Multimodal nanoparticle-based protein labels for correlative cathodoluminescence electron microscopy (CCLEM) and energy-dispersive X-ray spectromicroscopy (EDX-SM) are presented. The single-particle STEM-cathodoluminescence (CL) and characteristic X-ray emissivity of sub-20 nm lanthanide-doped nanoparticles are exploited as unique spectral fingerprints for precise label localization and identification. To maximize the nanoparticle brightness, lanthanides are incorporated in a low-phonon host lattice and separated from the environment using a passivating shell. The core/shell nanoparticles are then functionalized with either folic (terbium-doped) or caffeic acid (europium-doped). Their potential for (protein-)labeling is successfully demonstrated using HeLa cells expressing different surface receptors that bind to folic or caffeic acid, respectively. Both particle populations show single-particle CL emission along with a distinctive energy-dispersive X-ray signal, with the latter enabling color-based localization of receptors within swift imaging times well below 2 min perμ m $\umu\text{m}$ 2 while offering high resolution with a pixel size of 2.78 nm. Taken together, these results open a route to multi-color labeling based on electron spectromicroscopy.
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Affiliation(s)
- Sebastian Habermann
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092, Zurich, Switzerland
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland
| | - Lukas R H Gerken
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092, Zurich, Switzerland
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland
| | - Mathieu Kociak
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, Orsay, 91405, France
| | | | - Vera M Kissling
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland
| | - Alexander Gogos
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092, Zurich, Switzerland
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland
| | - Inge K Herrmann
- Nanoparticle Systems Engineering Laboratory, Institute of Energy and Process Engineering, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, 8092, Zurich, Switzerland
- Laboratory for Particles Biology Interactions, Department Materials Meet Life, Swiss Federal Laboratories for Materials Science and Technology (Empa), Lerchenfeldstrasse 5, 9014, St. Gallen, Switzerland
- The Ingenuity Lab, University Hospital Balgrist, Balgrist Campus, Forchstrasse 340, 8008, Zurich, Switzerland
- Faculty of Medicine, University of Zurich, Rämistrasse 74, 8006, Zurich, Switzerland
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2
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Lee KH, Shi L. Unraveling Activation-Related Rearrangements and Intrinsic Divergence from Ligand-Specific Conformational Changes of the Dopamine D3 and D2 Receptors. J Chem Inf Model 2024; 64:1778-1793. [PMID: 38454785 DOI: 10.1021/acs.jcim.3c01956] [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: 03/09/2024]
Abstract
Effective rational drug discovery hinges on understanding the functional states of the target protein and distinguishing it from homologues. However, for the G protein coupled receptors, both activation-related conformational changes (ACCs) and intrinsic divergence among receptors can be misled or obscured by ligand-specific conformational changes (LCCs). Here, we unraveled ACCs and intrinsic divergence from LCCs of the dopamine D3 and D2 receptors (D3R and D2R), by analyzing their experimentally determined structures and the molecular dynamics (MD) simulation results of the receptors bound with various ligands. In addition to the ACCs common to other aminergic receptors, we revealed unique ACCs for these two receptors, including the extracellular portion of TM5 (TM5e) and TM6e shifting away from TM2e and TM3e, with a subtle rotation of TM5e. In identifying intrinsic divergence, we found more outward tilting of TM6e in the D2R compared to the D3R in both the experimental structures and simulations bound with ligands in different scaffolds. However, this difference was drastically reduced in the simulations bound with nonselective agonist quinpirole, suggesting a misleading effect of LCCs. Further, in the quinpirole-bound simulations, TM1 showed a greater disparity between these receptors, indicating that LCCs may also obscure intrinsic divergence. Importantly, our MD simulations revealed divergence in the dynamics of these receptors. Specifically, the D2R exhibited heightened flexibility compared to the D3R in the extracellular loops and TMs 5e, 6e, and 7e, associated with its greater ligand binding site plasticity. Our results lay the groundwork for crafting ligands specifically targeting the D2R and D3R with more precise pharmacological profiles.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
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3
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Xu Y, Wang J, He Z, Rao Z, Zhang Z, Zhou J, Zhou T, Wang H. A review on the effect of COX-2-mediated mechanisms on development and progression of gastric cancer induced by nicotine. Biochem Pharmacol 2024; 220:115980. [PMID: 38081368 DOI: 10.1016/j.bcp.2023.115980] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023]
Abstract
Smoking is a documented risk factor for cancer, e.g., gastric cancer. Nicotine, the principal tobacco alkaloid, would exert its role of contribution to gastric cancer development and progression through nicotinic acetylcholine receptors (nAChRs) and β-adrenergic receptors (β-ARs), which then promote cancer cell proliferation, migration and invasion. As a key isoenzyme in conversion of arachidonic acid to prostaglandins, cyclooxygenase-2 (COX-2) has been demonstrated to have a wide range of effects in carcinogenesis and tumor development. At present, many studies have reported the effect of nicotine on gastric cancer by binding to nAChR, as well as indirectly stimulating β-AR to mediate COX-2-related pathways. This review summarizes these studies, and also proposes more potential COX-2-mediated mechanisms. These events might contribute to the growth and progression of gastric cancer exposed to nicotine through tobacco smoke or cigarette substitutes. Also, this review article has therefore the potential not only to make a significant contribution to the treatment and prognosis of gastric cancer for smokers but also to the clinical application of COX-2 antagonists. In addition, this work also discusses the considerable challenges of this field with special reference to the future perspective of COX-2-mediated mechanisms in development and progression of gastric cancer induced by nicotine.
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Affiliation(s)
- Yuqin Xu
- School of Public Health, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Chongqing Research Institute of Nanchang University, Tai Bai Road, Tongnan, Chongqing 402679, PR China
| | - Juan Wang
- School of Public Health, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China
| | - Zihan He
- School of Public Health, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Chongqing Research Institute of Nanchang University, Tai Bai Road, Tongnan, Chongqing 402679, PR China
| | - Zihan Rao
- School of Public Health, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Chongqing Research Institute of Nanchang University, Tai Bai Road, Tongnan, Chongqing 402679, PR China
| | - Zhongwei Zhang
- School of Public Health, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Chongqing Research Institute of Nanchang University, Tai Bai Road, Tongnan, Chongqing 402679, PR China
| | - Jianming Zhou
- School of Public Health, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Chongqing Research Institute of Nanchang University, Tai Bai Road, Tongnan, Chongqing 402679, PR China
| | - Tong Zhou
- School of Public Health, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Chongqing Research Institute of Nanchang University, Tai Bai Road, Tongnan, Chongqing 402679, PR China
| | - Huai Wang
- School of Public Health, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Jiangxi Medical College, Nanchang University, No. 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Chongqing Research Institute of Nanchang University, Tai Bai Road, Tongnan, Chongqing 402679, PR China.
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4
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Pasha A, Tondo A, Favre C, Calvani M. Inside the Biology of the β3-Adrenoceptor. Biomolecules 2024; 14:159. [PMID: 38397396 PMCID: PMC10887351 DOI: 10.3390/biom14020159] [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: 12/31/2023] [Revised: 01/24/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Since the first discovery in 1989, the β3-adrenoceptor (β3-AR) has gained great attention because it showed the ability to regulate many physiologic and metabolic activities, such as thermogenesis and lipolysis in brown and white adipose tissue, respectively (BAT, WAT), negative inotropic effects in cardiomyocytes, and relaxation of the blood vessels and the urinary bladder. The β3-AR has been suggested as a potential target for cancer treatment, both in adult and pediatric tumors, since under hypoxia its upregulation in the tumor microenvironment (TME) regulates stromal cell differentiation, tumor growth and metastases, signifying that its agonism/antagonism could be useful for clinical benefits. Promising results in cancer research have proposed the β3-AR being targeted for the treatment of many conditions, with some drugs, at present, undergoing phase II and III clinical trials. In this review, we report the scientific journey followed by the research from the β3-Ars' discovery, with focus on the β3-Ars' role in cancer initiation and progression that elects it an intriguing target for novel antineoplastic approaches. The overview highlights the great potential of the β3-AR, both in physiologic and pathologic conditions, with the intention to display the possible benefits of β3-AR modulation in cancer reality.
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Affiliation(s)
- Amada Pasha
- Department of Pediatric Hematology–Oncology, Meyer Children’s Hospital IRCCS, 50139 Florence, Italy; (A.P.); (A.T.); (C.F.)
- Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50139 Florence, Italy
| | - Annalisa Tondo
- Department of Pediatric Hematology–Oncology, Meyer Children’s Hospital IRCCS, 50139 Florence, Italy; (A.P.); (A.T.); (C.F.)
| | - Claudio Favre
- Department of Pediatric Hematology–Oncology, Meyer Children’s Hospital IRCCS, 50139 Florence, Italy; (A.P.); (A.T.); (C.F.)
| | - Maura Calvani
- Department of Pediatric Hematology–Oncology, Meyer Children’s Hospital IRCCS, 50139 Florence, Italy; (A.P.); (A.T.); (C.F.)
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5
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Chiesa L, Sick E, Kellenberger E. Predicting the duration of action of β2-adrenergic receptor agonists: Ligand and structure-based approaches. Mol Inform 2023; 42:e202300141. [PMID: 37872120 DOI: 10.1002/minf.202300141] [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: 06/11/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 10/25/2023]
Abstract
Agonists of the β2 adrenergic receptor (ADRB2) are an important class of medications used for the treatment of respiratory diseases. They can be classified as short acting (SABA) or long acting (LABA), with each class playing a different role in patient management. In this work we explored both ligand-based and structure-based high-throughput approaches to classify β2-agonists based on their duration of action. A completely in-silico prediction pipeline using an AlphaFold generated structure was used for structure-based modelling. Our analysis identified the ligands' 3D structure and lipophilicity as the most relevant features for the prediction of the duration of action. Interaction-based methods were also able to select ligands with the desired duration of action, incorporating the bias directly in the structure-based drug discovery pipeline without the need for further processing.
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Affiliation(s)
- Luca Chiesa
- Laboratoire d'Innovation Thérapeutique, Faculté de Pharmacie, UMR7200 CNRS Université de Strasbourg, 67400, Illkirch, France
| | - Emilie Sick
- Laboratoire de Conception et Application de Molécules Bioactives, Faculté de Pharmacie, UMR7199 CNRS Université de Strasbourg, 67400, Illkirch, France
| | - Esther Kellenberger
- Laboratoire d'Innovation Thérapeutique, Faculté de Pharmacie, UMR7200 CNRS Université de Strasbourg, 67400, Illkirch, France
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6
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Lee KH, Shi L. Unraveling activation-related rearrangements and intrinsic divergence from ligand-induced conformational changes of the dopamine D3 and D2 receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.11.566699. [PMID: 38014309 PMCID: PMC10680602 DOI: 10.1101/2023.11.11.566699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Effective rational drug discovery targeting a specific protein hinges on understanding their functional states and distinguishing it from homologs. However, for the G protein coupled receptors, both the activation-related conformational changes (ACCs) and the intrinsic divergence among receptors can be misled or obscured by ligand-induced conformational changes (LCCs). Here, we unraveled ACCs and intrinsic divergence from LCCs of the dopamine D3 and D2 receptors (D3R and D2R), by analyzing their experimentally determined structures and the molecular dynamics simulation results of the receptors bound with different ligands. In addition to the ACCs common to other aminergic receptors, we revealed unique ACCs for these two receptors including TM5e and TM6e shifting away from TM2e and TM3e, with a subtle rotation of TM5e. In identifying intrinsic divergence, we found pronounced outward tilting of TM6e in the D2R compared to the D3R in both experimental structures and simulations with ligands in different scaffolds. This tilting was drastically reduced in the simulations of the receptors bound with nonselective full agonist quinpirole, suggesting a misleading impact of LCCs. Further, in the quinpirole-bound simulations, TM1 showed a greater disparity between these receptors, indicating that LCCs may obscure intrinsic divergence. In addition, our analysis showed that the impact of the nonconserved TM1 propagated to conserved Trp7.40 and Glu2.65, both are ligand binding residues. We also found that the D2R exhibited heightened flexibility compared to the D3R in the extracellular portions of TMs 5, 6, and 7, potentially associated with its greater ligand binding site plasticity. Our results lay the groundwork for crafting ligands specifically targeting D2R or D3R with more precise pharmacological profiles.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA
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7
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Calderón JC, Ibrahim P, Gobbo D, Gervasio FL, Clark T. Activation/Deactivation Free-Energy Profiles for the β 2-Adrenergic Receptor: Ligand Modes of Action. J Chem Inf Model 2023; 63:6332-6343. [PMID: 37824365 DOI: 10.1021/acs.jcim.3c00805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023]
Abstract
We use enhanced-sampling simulations with an effective collective variable to study the activation of the β2-adrenergic receptor in the presence of ligands with different efficacy. The free-energy profiles are computed for the ligand-free (apo) receptor and binary (apo-receptor + G-protein α-subunit and receptor + ligand) and ternary complexes. The results are not only compatible with available experiments but also allow unprecedented structural insight into the nature of GPCR conformations along the activation pathway and their role in the activation mechanism. In particular, the simulations reveal an unexpected mode of action of partial agonists such as salmeterol and salbutamol that arises already in the binary complex without the G-protein. Specific differences in the polar interactions with residues in TM5, which are required to stabilize an optimal TM6 conformation that facilitates G-protein binding and receptor activation, play a major role in differentiating them from full agonists.
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Affiliation(s)
- Jacqueline C Calderón
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstraße 25, 91052 Erlangen, Germany
| | - Passainte Ibrahim
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, 04109 Leipzig, Germany
| | - Dorothea Gobbo
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
| | - Francesco Luigi Gervasio
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
- Chemistry Department, University College London, WC1H 0AJ London, United Kingdom
- Swiss Bioinformatics Institute, CH1206 Geneva, Switzerland
| | - Timothy Clark
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstraße 25, 91052 Erlangen, Germany
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8
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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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9
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Calderón JC, Ibrahim P, Gobbo D, Gervasio FL, Clark T. General Metadynamics Protocol To Simulate Activation/Deactivation of Class A GPCRs: Proof of Principle for the Serotonin Receptor. J Chem Inf Model 2023; 63:3105-3117. [PMID: 37161278 DOI: 10.1021/acs.jcim.3c00208] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We present a generally applicable metadynamics protocol for characterizing the activation free-energy profiles of class A G-protein coupled receptors and a proof-of-principle study for the 5HT1A-receptor. The almost universal A100 activation index, which depends on five inter-helix distances, is used as the single collective variable in well-tempered multiple-walker metadynamics simulations. Here, we show free-energy profiles for the serotonin receptor as binary (apo-receptor + G-protein-α-subunit and receptor + ligand) and ternary complexes with two prototypical orthosteric ligands: the full agonist serotonin and the partial agonist aripiprazole. Our results are not only compatible with previously reported experimental and computational data, but they also allow differences between active and inactive conformations to be determined in unprecedented atomic detail, and with respect to the so-called microswitches that have been suggested as determinants of activation, giving insight into their role in the activation mechanism.
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Affiliation(s)
- Jacqueline C Calderón
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, 91052 Erlangen, Germany
| | - Passainte Ibrahim
- Institute of Medical Physics and Biophysics, Faculty of Medicine, University of Leipzig, Leipzig 04107, Germany
| | - Dorothea Gobbo
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
| | - Francesco Luigi Gervasio
- Pharmaceutical Sciences, University of Geneva, CH1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, CH1206 Geneva, Switzerland
- Chemistry Department, University College London, WC1H 0AJ London, U.K
| | - Timothy Clark
- Computer-Chemistry-Center, Department of Chemistry and Pharmacy, Friedrich-Alexander-University Erlangen-Nuernberg, Naegelsbachstr. 25, 91052 Erlangen, Germany
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10
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Benítez-Angeles M, Juárez-González E, Vergara-Jaque A, Llorente I, Rangel-Yescas G, Thébault SC, Hiriart M, Islas LD, Rosenbaum T. Unconventional interactions of the TRPV4 ion channel with beta-adrenergic receptor ligands. Life Sci Alliance 2023; 6:6/3/e202201704. [PMID: 36549871 PMCID: PMC9780703 DOI: 10.26508/lsa.202201704] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/05/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
The transient receptor potential vanilloid 4 (TRPV4) ion channel is present in different tissues including those of the airways. This channel is activated in response to stimuli such as changes in temperature, hypoosmotic conditions, mechanical stress, and chemicals from plants, lipids, and others. TRPV4's overactivity and/or dysfunction has been associated with several diseases, such as skeletal dysplasias, neuromuscular disorders, and lung pathologies such as asthma and cardiogenic lung edema and COVID-19-related respiratory malfunction. TRPV4 antagonists and blockers have been described; nonetheless, the mechanisms involved in achieving inhibition of the channel remain scarce, and the search for safe use of these molecules in humans continues. Here, we show that the widely used bronchodilator salbutamol and other ligands of β-adrenergic receptors inhibit TRPV4's activation. We also demonstrate that inhibition of TRPV4 by salbutamol is achieved through interaction with two residues located in the outer region of the pore and that salbutamol leads to channel closing, consistent with an allosteric mechanism. Our study provides molecular insights into the mechanisms that regulate the activity of this physiopathologically important ion channel.
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Affiliation(s)
- Miguel Benítez-Angeles
- Departamento de Neurociencia Cognitiva, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), México, México
| | - Emmanuel Juárez-González
- Departamento de Neurociencia Cognitiva, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), México, México
| | - Ariela Vergara-Jaque
- Center for Bioinformatics, Simulation and Modeling, Faculty of Engineering, Universidad de Talca, Talca, Chile.,Millennium Nucleus of Ion Channel-Associated Diseases, Santiago, Chile
| | - Itzel Llorente
- Departamento de Neurociencia Cognitiva, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), México, México
| | | | | | - Marcia Hiriart
- Departamento de Neurociencia Cognitiva, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), México, México
| | - León D Islas
- Departamento de Fisiología, Facultad de Medicina, UNAM, México, México
| | - Tamara Rosenbaum
- Departamento de Neurociencia Cognitiva, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México (UNAM), México, México
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11
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L-DOPA and Droxidopa: From Force Field Development to Molecular Docking into Human β2-Adrenergic Receptor. Life (Basel) 2022; 12:life12091393. [PMID: 36143429 PMCID: PMC9501711 DOI: 10.3390/life12091393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/10/2022] [Accepted: 09/01/2022] [Indexed: 11/30/2022] Open
Abstract
The increasing interest in the molecular mechanism of the binding of different agonists and antagonists to β2-adrenergic receptor (β2AR) inactive and active states has led us to investigate protein–ligand interactions using molecular docking calculations. To perform this study, the 3.2 Å X-ray crystal structure of the active conformation of human β2AR in the complex with the endogenous agonist adrenaline has been used as a template for investigating the binding of two exogenous catecholamines to this adrenergic receptor. Here, we show the derivation of L-DOPA and Droxidopa OPLS all atom (AA) force field (FF) parameters via quantum mechanical (QM) calculations, molecular dynamics (MD) simulations in aqueous solutions of the two catecholamines and the molecular docking of both ligands into rigid and flexible β2AR models. We observe that both ligands share with adrenaline similar experimentally observed binding anchor sites, which are constituted by Asp113/Asn312 and Ser203/Ser204/Ser207 side chains. Moreover, both L-DOPA and Droxidopa molecules exhibit binding affinities comparable to that predicted for adrenaline, which is in good agreement with previous experimental and computational results. L-DOPA and Droxidopa OPLS AA FFs have also been tested by performing MD simulations of these ligands docked into β2AR proteins embedded in lipid membranes. Both hydrogen bonds and hydrophobic interaction networks observed over the 1 μs MD simulation are comparable with those derived from molecular docking calculations and MD simulations performed with the CHARMM FF.
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12
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Tosso RD, Zarycz MNC, Schiel A, Goicoechea Moro L, Baldoni HA, Angelina E, Enriz RD. Evaluating the conformational space of the active site of D 2 dopamine receptor. Scope and limitations of the standard docking methods. J Comput Chem 2022; 43:1298-1312. [PMID: 35638694 DOI: 10.1002/jcc.26938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/11/2022] [Accepted: 05/08/2022] [Indexed: 11/05/2022]
Abstract
We report here for the first time the potential energy surfaces (PES) of phenyletilamine (PEA) and meta-tyramine (m-OH-PEA) at the D2 dopamine receptor (D2DR) binding site. PESs not only allow us to observe all the critical points of the surface (minimums, maximums, and transition states), but also to note the ease or difficulty that each local minima have for their conformational inter-conversions and therefore know the conformational flexibility that these ligands have in their active sites. Taking advantage of possessing this valuable information, we analyze how accurate a standard docking study is in these cases. Our results indicate that although we have to be careful in how to carry out this type of study and to consider performing some extra-simulations, docking calculations can be satisfactory. In order to analyze in detail the different molecular interactions that are stabilizing the different ligand-receptor (L-R) complexes, we carried out quantum theory of atoms in molecules (QTAIM) computations and NMR shielding calculations. Although some of these techniques are a bit tedious and require more computational time, our results demonstrate the importance of performing computational simulations using different types of combined techniques (docking/MD/hybrid QM-MM/QTAIM and NMR shielding calculations) in order to obtain more accurate results. Our results allow us to understand in details the molecular interactions stabilizing and destabilizing the different L-R complexes reported here. Thus, the different activities observed for dopamine (DA), m-OH-PEA, and PEA can be clearly explained at molecular level.
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Affiliation(s)
- Rodrigo D Tosso
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas, San Luis, Argentina
| | - M Natalia C Zarycz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas, San Luis, Argentina
| | - Ayelén Schiel
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas, San Luis, Argentina
| | - Luisa Goicoechea Moro
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas, San Luis, Argentina
| | - Héctor A Baldoni
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis; Instituto de Matemáticas, San Luis, Argentina
| | - Emilio Angelina
- Laboratorio de Estructura Molecular y Propiedades, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Instituto de Química Básica y Aplicada, Corrientes, Argentina
| | - Ricardo D Enriz
- Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Instituto Multidisciplinario de Investigaciones Biológicas, San Luis, Argentina
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13
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Biswas AD, Catte A, Mancini G, Barone V. Analysis of L-DOPA and droxidopa binding to human β 2-adrenergic receptor. Biophys J 2021; 120:5631-5643. [PMID: 34767786 PMCID: PMC8715240 DOI: 10.1016/j.bpj.2021.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 12/29/2022] Open
Abstract
Over the last two decades, an increasing number of studies has been devoted to a deeper understanding of the molecular process involved in the binding of various agonists and antagonists to active and inactive conformations of β2-adrenergic receptor (β2AR). The 3.2 Å x-ray crystal structure of human β2AR active state in combination with the endogenous low affinity agonist adrenaline offers an ideal starting structure for studying the binding of various catecholamines to adrenergic receptors. We show that molecular docking of levodopa (L-DOPA) and droxidopa into rigid and flexible β2AR models leads for both ligands to binding anchor sites comparable to those experimentally reported for adrenaline, namely D113/N312 and S203/S204/S207 side chains. Both ligands have a hydrogen bond network that is extremely similar to those of noradrenaline and dopamine. Interestingly, redocking neutral and protonated versions of adrenaline to rigid and flexible β2AR models results in binding poses that are more energetically stable and distinct from the x-ray crystal structure. Similarly, lowest energy conformations of noradrenaline and dopamine generated by docking into flexible β2AR models had binding free energies lower than those of best poses in rigid receptor models. Furthermore, our findings show that L-DOPA and droxidopa molecules have binding affinities comparable to those predicted for adrenaline, noradrenaline, and dopamine, which are consistent with previous experimental and computational findings and supported by the molecular dynamics simulations of β2AR-ligand complexes performed here.
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14
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Liu T, Zhan X, Yu Y, Wang S, Lu C, Lin G, Zhu X, He W, You M, You S. Molecular and pharmacological characterization of biogenic amine receptors from the diamondback moth, Plutella xylostella. PEST MANAGEMENT SCIENCE 2021; 77:4462-4475. [PMID: 34004073 DOI: 10.1002/ps.6481] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/12/2021] [Accepted: 05/18/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUD Insect biogenic amines play important roles in mediating behavioral and physiological processes. They exert their effects by binding to biogenic amine receptors (BARs), which are specific receptor proteins in the G-protein-coupled receptor superfamily. BAR genes have been cloned and characterized from multiple model insects, including Drosophila melanogaster, Anopheles gambiae, Bombyx mori, Apis mellifera and Tribolium castaneum. However, relatively little work has addressed the molecular properties, expression profiles, and pharmacological characterization of BARs from other insects, including important pests. RESULTS In this study, we cloned 17 genes encoding putative biogenic amine receptor proteins from Plutella xylostella, a global pest of Brassica crops. These PxBAR genes were five octopamine receptors (PxOA1, PxOA2B1, PxOA2B2, PxOA2B3, and PxOA3), three tyramine receptors (PxTAR1A, PxTAR1B, and PxTAR2), four dopamine receptors (PxDOP1, PxDOP2, PxDOP3, and PxDopEcR), and five serotonin receptors (Px5-HT1A , Px5-HT1B , Px5-HT2A , Px5-HT2B , and Px5-HT7 ). All PxBARs showed considerable sequence identity with orthologous BARs, and phylogenetic analysis clustered the receptors within their respective groups while preserving organismal evolutionary relationships. We investigated their molecular properties and expression profiles, and pharmacologically characterized the dopamine receptor, PxDOP2. CONCLUSIONS Our study provides important information and resources on biogenic amine receptors from P. xylostella, which suggests potential target sites for controlling this pest species. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Tiansheng Liu
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Xue Zhan
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Yuan Yu
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Shaozhen Wang
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Cong Lu
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Guifang Lin
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Xiangyu Zhu
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Weiyi He
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
| | - Shijun You
- State Key Laboratory of Ecological Pest Control for Fujian-Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China
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15
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Belkacemi L, Darmani NA. Dopamine receptors in emesis: Molecular mechanisms and potential therapeutic function. Pharmacol Res 2020; 161:105124. [PMID: 32814171 DOI: 10.1016/j.phrs.2020.105124] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/20/2020] [Accepted: 08/05/2020] [Indexed: 12/19/2022]
Abstract
Dopamine is a member of the catecholamine family and is associated with multiple physiological functions. Together with its five receptor subtypes, dopamine is closely linked to neurological disorders such as schizophrenia, Parkinson's disease, depression, attention deficit-hyperactivity, and restless leg syndrome. Unfortunately, several dopamine receptor-based agonists used to treat some of these diseases cause nausea and vomiting as impending side-effects. The high degree of cross interactions of dopamine receptor ligands with many other targets including G-protein coupled receptors, transporters, enzymes, and ion-channels, add to the complexity of discovering new targets for the treatment of nausea and vomiting. Using activation status of signaling cascades as mechanism-based biomarkers to foresee drug sensitivity combined with the development of dopamine receptor-based biased agonists may hold great promise and seems as the next step in drug development for the treatment of such multifactorial diseases. In this review, we update the present knowledge on dopamine and dopamine receptors and their potential roles in nausea and vomiting. The pre- and clinical evidence provided in this review supports the implication of both dopamine and dopamine receptor agonists in the incidence of emesis. Besides the conventional dopaminergic antiemetic drugs, potential novel antiemetic targeting emetic protein signaling cascades may offer superior selectivity profile and potency.
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Affiliation(s)
- Louiza Belkacemi
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, 91766, USA
| | - Nissar A Darmani
- Department of Basic Medical Sciences, College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, 91766, USA.
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16
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Schneider J, Korshunova K, Si Chaib Z, Giorgetti A, Alfonso-Prieto M, Carloni P. Ligand Pose Predictions for Human G Protein-Coupled Receptors: Insights from the Amber-Based Hybrid Molecular Mechanics/Coarse-Grained Approach. J Chem Inf Model 2020; 60:5103-5116. [PMID: 32786708 DOI: 10.1021/acs.jcim.0c00661] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Human G protein-coupled receptors (hGPCRs) are the most frequent targets of Food and Drug Administration (FDA)-approved drugs. Structural bioinformatics, along with molecular simulation, can support structure-based drug design targeting hGPCRs. In this context, several years ago, we developed a hybrid molecular mechanics (MM)/coarse-grained (CG) approach to predict ligand poses in low-resolution hGPCR models. The approach was based on the GROMOS96 43A1 and PRODRG united-atom force fields for the MM part. Here, we present a new MM/CG implementation using, instead, the Amber 14SB and GAFF all-atom potentials for proteins and ligands, respectively. The new implementation outperforms the previous one, as shown by a variety of applications on models of hGPCR/ligand complexes at different resolutions, and it is also more user-friendly. Thus, it emerges as a useful tool to predict poses in low-resolution models and provides insights into ligand binding similarly to all-atom molecular dynamics, albeit at a lower computational cost.
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Affiliation(s)
- Jakob Schneider
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany.,JARA-Institute: Molecular Neuroscience and Neuroimaging, Institute for Neuroscience and Medicine INM-11/JARA-BRAIN Institute JBI-2, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Ksenia Korshunova
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany
| | - Zeineb Si Chaib
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,RWTH Aachen University, 52062 Aachen, Germany
| | - Alejandro Giorgetti
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Biotechnology, University of Verona, 37314 Verona, Italy.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Mercedes Alfonso-Prieto
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Cecile and Oskar Vogt Institute for Brain Research, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Paolo Carloni
- Computational Biomedicine, Institute for Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Department of Physics, RWTH Aachen University, 52074 Aachen, Germany.,JARA-Institute: Molecular Neuroscience and Neuroimaging, Institute for Neuroscience and Medicine INM-11/JARA-BRAIN Institute JBI-2, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,JARA-HPC, IAS-5/INM-9 Computational Biomedicine, Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
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17
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Activation of the α 2B adrenoceptor by the sedative sympatholytic dexmedetomidine. Nat Chem Biol 2020; 16:507-512. [PMID: 32152538 DOI: 10.1038/s41589-020-0492-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 12/31/2019] [Accepted: 02/04/2020] [Indexed: 12/20/2022]
Abstract
The α2 adrenergic receptors (α2ARs) are G protein-coupled receptors (GPCRs) that respond to adrenaline and noradrenaline and couple to the Gi/o family of G proteins. α2ARs play important roles in regulating the sympathetic nervous system. Dexmedetomidine is a highly selective α2AR agonist used in post-operative patients as an anxiety-reducing, sedative medicine that decreases the requirement for opioids. As is typical for selective αAR agonists, dexmedetomidine consists of an imidazole ring and a substituted benzene moiety lacking polar groups, which is in contrast to βAR-selective agonists, which share an ethanolamine group and an aromatic system with polar, hydrogen-bonding substituents. To better understand the structural basis for the selectivity and efficacy of adrenergic agonists, we determined the structure of the α2BAR in complex with dexmedetomidine and Go at a resolution of 2.9 Å by single-particle cryo-EM. The structure reveals the mechanism of α2AR-selective activation and provides insights into Gi/o coupling specificity.
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18
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Zhou Y, Cao C, He L, Wang X, Zhang XC. Crystal structure of dopamine receptor D4 bound to the subtype selective ligand, L745870. eLife 2019; 8:e48822. [PMID: 31750832 PMCID: PMC6872212 DOI: 10.7554/elife.48822] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Accepted: 11/06/2019] [Indexed: 12/12/2022] Open
Abstract
Multiple subtypes of dopamine receptors within the GPCR superfamily regulate neurological processes through various downstream signaling pathways. A crucial question about the dopamine receptor family is what structural features determine the subtype-selectivity of potential drugs. Here, we report the 3.5-angstrom crystal structure of mouse dopamine receptor D4 (DRD4) complexed with a subtype-selective antagonist, L745870. Our structure reveals a secondary binding pocket extended from the orthosteric ligand-binding pocket to a DRD4-specific crevice located between transmembrane helices 2 and 3. Additional mutagenesis studies suggest that the antagonist L745870 prevents DRD4 activation by blocking the relative movement between transmembrane helices 2 and 3. These results expand our knowledge of the molecular basis for the physiological functions of DRD4 and assist new drug design.
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Affiliation(s)
- Ye Zhou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Can Cao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
| | - Lingli He
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
| | - Xianping Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
| | - Xuejun Cai Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in BiomacromoleculesInstitute of Biophysics, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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19
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Shen A, Chen D, Kaur M, Bartels P, Xu B, Shi Q, Martinez JM, Man KNM, Nieves-Cintron M, Hell JW, Navedo MF, Yu XY, Xiang YK. β-blockers augment L-type Ca 2+ channel activity by targeting spatially restricted β 2AR signaling in neurons. eLife 2019; 8:49464. [PMID: 31609201 PMCID: PMC6813027 DOI: 10.7554/elife.49464] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/13/2019] [Indexed: 01/02/2023] Open
Abstract
G protein-coupled receptors (GPCRs) transduce pleiotropic intracellular signals in mammalian cells. Here, we report neuronal excitability of β-blockers carvedilol and alprenolol at clinically relevant nanomolar concentrations. Carvedilol and alprenolol activate β2AR, which promote G protein signaling and cAMP/PKA activities without action of G protein receptor kinases (GRKs). The cAMP/PKA activities are restricted within the immediate vicinity of activated β2AR, leading to selectively enhance PKA-dependent phosphorylation and stimulation of endogenous L-type calcium channel (LTCC) but not AMPA receptor in rat hippocampal neurons. Moreover, we have engineered a mutant β2AR that lacks the catecholamine binding pocket. This mutant is preferentially activated by carvedilol but not the orthosteric agonist isoproterenol. Carvedilol activates the mutant β2AR in mouse hippocampal neurons augmenting LTCC activity through cAMP/PKA signaling. Together, our study identifies a mechanism by which β-blocker-dependent activation of GPCRs promotes spatially restricted cAMP/PKA signaling to selectively target membrane downstream effectors such as LTCC in neurons.
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Affiliation(s)
- Ao Shen
- Key Laboratory of Molecular Target and Clinical Pharmacology, State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.,Department of Pharmacology, University of California Davis, Davis, United States
| | - Dana Chen
- Department of Pharmacology, University of California Davis, Davis, United States
| | - Manpreet Kaur
- Department of Pharmacology, University of California Davis, Davis, United States
| | - Peter Bartels
- Department of Pharmacology, University of California Davis, Davis, United States
| | - Bing Xu
- Department of Pharmacology, University of California Davis, Davis, United States.,VA Northern California Health Care System, Mather, United States
| | - Qian Shi
- Department of Pharmacology, University of California Davis, Davis, United States
| | - Joseph M Martinez
- Department of Pharmacology, University of California Davis, Davis, United States
| | - Kwun-Nok Mimi Man
- Department of Pharmacology, University of California Davis, Davis, United States
| | | | - Johannes W Hell
- Department of Pharmacology, University of California Davis, Davis, United States
| | - Manuel F Navedo
- Department of Pharmacology, University of California Davis, Davis, United States
| | - Xi-Yong Yu
- Key Laboratory of Molecular Target and Clinical Pharmacology, State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yang K Xiang
- Department of Pharmacology, University of California Davis, Davis, United States.,VA Northern California Health Care System, Mather, United States
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20
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Dilcan G, Doruker P, Akten ED. Ligand-binding affinity of alternative conformers of human β 2 -adrenergic receptor in the presence of intracellular loop 3 (ICL3) and their potential use in virtual screening studies. Chem Biol Drug Des 2019; 93:883-899. [PMID: 30637937 DOI: 10.1111/cbdd.13478] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/14/2018] [Accepted: 11/24/2018] [Indexed: 12/25/2022]
Abstract
This study investigates the structural distinctiveness of orthosteric ligand-binding sites of several human β2 adrenergic receptor (β2 -AR) conformations that have been obtained from a set of independent molecular dynamics (MD) simulations in the presence of intracellular loop 3 (ICL3). A docking protocol was established in order to classify each receptor conformation via its binding affinity to selected ligands with known efficacy. This work's main goal was to reveal many subtle features of the ligand-binding site, presenting alternative conformations, which might be considered as either active- or inactive-like but mostly specific for that ligand. Agonists, inverse agonists, and antagonists were docked to each MD conformer with distinct binding pockets, using different docking tools and scoring functions. Mostly favored receptor conformation persistently observed in all docking/scoring evaluations was classified as active or inactive based on the type of ligand's biological effect. Classified MD conformers were further tested for their ability to discriminate agonists from inverse agonists/antagonists, and several conformers were proposed as important targets to be used in virtual screening experiments that were often limited to a single X-ray structure.
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Affiliation(s)
- Gonca Dilcan
- Graduate School of Computational Biology and Bioinformatics, Kadir Has University, Istanbul, Turkey
| | - Pemra Doruker
- Department of Chemical Engineering and Polymer Research Center, Bogazici University, Istanbul, Turkey
| | - Ebru Demet Akten
- Department of Bioinformatics and Genetics, Faculty of Natural Sciences and Engineering, Kadir Has University, Istanbul, Turkey
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21
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Gassias E, Durand N, Demondion E, Bourgeois T, Aguilar P, Bozzolan F, Debernard S. A critical role for Dop1-mediated dopaminergic signaling in the plasticity of behavioral and neuronal responses to sex pheromone in a moth. J Exp Biol 2019; 222:jeb.211979. [DOI: 10.1242/jeb.211979] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/25/2019] [Indexed: 12/22/2022]
Abstract
Most animal species, including insects, are able to modulate their responses to sexual chemosignals and this flexibility originates from the remodeling of olfactory areas under the influence of dopaminergic system. In the moth Agrotis ipsilon, the behavioral response of males to the female-emitted sex pheromone increases throughout adult life and after a prior exposure to pheromone signal and this change is accompanied by an increase in neuronal sensitivity within the primary olfactory centers, the antennal lobes (ALs). To identify the underlying neuromodulatory mechanisms, we examined whether this age- and experience-dependent olfactory plasticity is mediated by dopamine (DA) through the Dop1 receptor, an ortholog of the vertebrate D1-type dopamine receptors, which is positively coupled to adenylyl cyclase. We cloned A. ipsilon Dop1 (AiDop1) which is expressed predominantly in brain and especially in ALs and its knockdown induced decreased AL cAMP amounts and altered sex pheromone-orientated flight. The levels of DA, AiDop1 expression and cAMP in ALs increased from the third day of adult life and at 24h and 48h following pre-exposure to sex pheromone and the dynamic of these changes correlated with the increased responsiveness to sex pheromone. These results demonstrate that Dop1 is required for the display of male sexual behavior and that age- and experience-related neuronal and behavioral changes are sustained by DA-Dop1 signaling that operates within ALs probably through cAMP-dependent mechanisms in A. ipsilon. Thus, this study expands our understanding of the neuromodulatory mechanisms underlying olfactory plasticity, mechanisms that appear to be highly conserved between insects and mammals.
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Affiliation(s)
- Edmundo Gassias
- Institute of Biology, Complutense University of Madrid, Pozuelo de Alarcon, 28223 Madrid, Spain
| | - Nicolas Durand
- FRE CNRS 3498, Ecologie et Dynamique des Systèmes Anthropisés, Université de Picardie, Jules Verne, 80039 Amiens, France
| | - Elodie Demondion
- Sorbonne Université, INRA, CNRS, UPEC, IRD, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, 78026 Versailles, France
| | - Thomas Bourgeois
- Sorbonne Université, INRA, CNRS, UPEC, IRD, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, 78026 Versailles, France
| | - Paleo Aguilar
- Institute of Biology, Complutense University of Madrid, Pozuelo de Alarcon, 28223 Madrid, Spain
| | - Françoise Bozzolan
- Sorbonne Université, INRA, CNRS, UPEC, IRD, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, 75005 Paris, France
| | - Stéphane Debernard
- Sorbonne Université, INRA, CNRS, UPEC, IRD, Univ. P7, Institute of Ecology and Environmental Sciences of Paris, 75005 Paris, France
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22
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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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23
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Oncotoxic Properties of Serotonin Transporter Inhibitors and 5-HT 1A Receptor Ligands. Int J Mol Sci 2018; 19:ijms19103260. [PMID: 30347827 PMCID: PMC6214143 DOI: 10.3390/ijms19103260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/15/2018] [Accepted: 10/18/2018] [Indexed: 11/16/2022] Open
Abstract
The cytotoxic activity of several serotonin transporter (SERT) inhibitors and subtype of serotonin receptor 1A (5-HT1A receptor) ligands have been examined in androgen-insensitive human PC-3 prostate and neuroblastoma SH-SY5Y cancer cells. Almost all of the studied compounds (except 5-HT1A receptor agonist (2R)-(+)-8-Hydroxy-2-(di-n-propylamino)tetralin hydrobromide (8-OH-DPAT)) exhibited absolute cytotoxic activity against the examined cancer cells. The compound 4-Fluoro-N-[2-[4-(7-methoxy-1-naphthalenyl)-1-piperazinyl]ethyl]benzamide hydrochloride (S14506) that showed highest activity against neuroblastoma tumors was the 5-HT1A receptor agonist (although not alike other 5-HT1A receptor agonists). On the other hand, the compound 6-nitro-2-(4-undecylpiperazin-1-yl)quinoline hydrochloride (AZ07) that had the highest activity against PC-3 prostate cancer cells was a compound exhibiting antagonistic activity against the 5-HT1A receptor. Thus, compounds of oncotoxic properties S14506 and AZ07 should be evaluated further for their potential use in the prevention and treatment of cancer. Most of the 15 compounds tested exhibited either agonistic or antagonistic activity for both the cyclic adenosine monophosphate (cAMP) and extracellular signal-regulated kinase 1 and 2 (ERK1/2) pathways in human embryonic kidney 293 (HEK293) cells that overexpress the 5HT1AR gene. However, compounds paroxetine, N-Ac-paroxetine and 2-[4-(cyclobutylmethyl)piperazin-1-yl]-6-nitroquinoline hydrochloride (AB22) simultaneously exhibited antagonistic activity on the cAMP pathway and agonistic activity on the ERK1/2 pathway. Fluoxetine relative to compound AZ07 had almost three times lower cytotoxic activity against PC-3 prostate cancer cells. However, the proapoptotic activity of fluoxetine compared to compound AZ07 is almost two times higher which would suggest that the cytotoxic activity of both compounds may be dependent on different cell death mechanisms. Compound S14506 was found to be an antagonist of the serine-threonine protein kinase B (Akt) pathway. Prosurvival Akt activity may be reversed by Akt antagonists. Therefore, the antagonistic activity of S14506 on the Akt pathway may evoke caspase-3 expression and cytotoxicity. It appears that one should not expect a straightforward relationship between the activation of particular serotonergic pathways by selective serotonin reuptake inhibitors (SSRIs) and 5-HT1A receptor ligands and their cytotoxic or cytoprotective activity. Additionally, nuclear transcription factor κB (NF-κB), which may be involved in 5-HT-dependent biochemical pathways by coordinating different subunits in the formation of a dimer, may regulate the transcription of different transduction pathways. Therefore, it can be suggested that the mechanism of the cytotoxic activity of certain compounds (serotonergic against nonserotonergic) may depend on the compound and cancer type being examined. Docking studies showed that S14506, buspirone and spiperone bind in similar ways in the 5-HT1A receptor model and interacted with similar 5-HT1A receptor residues. S14506 and spiperone were found to be located closer to both phenylalanines in TM6 than buspirone, thus exhibiting more antagonist binding modes.
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Xu G, Wu SF, Gu GX, Teng ZW, Ye GY, Huang J. Pharmacological characterization of dopamine receptors in the rice striped stem borer, Chilo suppressalis. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2017; 83:80-93. [PMID: 28302436 DOI: 10.1016/j.ibmb.2017.03.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/10/2017] [Accepted: 03/12/2017] [Indexed: 06/06/2023]
Abstract
Dopamine is an important neurotransmitter and neuromodulator in both vertebrates and invertebrates and is the most abundant monoamine present in the central nervous system of insects. A complement of functionally distinct dopamine receptors mediate the signal transduction of dopamine by modifying intracellular Ca2+ and cAMP levels. In the present study, we pharmacologically characterized three types of dopamine receptors, CsDOP1, CsDOP2 and CsDOP3, from the rice striped stem borer, Chilo suppressalis. All three receptors show considerable sequence identity with orthologous dopamine receptors. The phylogenetic analysis also clusters the receptors within their respective groups. Transcript levels of CsDOP1, CsDOP2 and CsDOP3 were all expressed at high levels in the central nervous system, indicating their important roles in neural processes. After heterologous expression in HEK 293 cells, CsDOP1, CsDOP2 and CsDOP3 were dose-dependently activated by dopamine and synthetic dopamine receptor agonists. They can also be blocked by different series of antagonists. This study offers important information on three dopamine receptors from C. suppressalis that will provide the basis for forthcoming studies investigating their roles in behaviors and physiology, and facilitate the development of new insecticides for pest control.
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Affiliation(s)
- Gang Xu
- State Key Laboratory of Rice Biology & Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Shun-Fan Wu
- State Key Laboratory of Rice Biology & Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China; College of Plant Protection, Nanjing Agricultural University, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China.
| | - Gui-Xiang Gu
- State Key Laboratory of Rice Biology & Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Zi-Wen Teng
- State Key Laboratory of Rice Biology & Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Gong-Yin Ye
- State Key Laboratory of Rice Biology & Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
| | - Jia Huang
- State Key Laboratory of Rice Biology & Ministry of Agriculture, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China.
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25
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Hugo EA, Cassels BK, Fierro A. Functional roles of T3.37 and S5.46 in the activation mechanism of the dopamine D1 receptor. J Mol Model 2017; 23:142. [PMID: 28361444 DOI: 10.1007/s00894-017-3313-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 03/13/2017] [Indexed: 12/25/2022]
Abstract
The activation mechanism of dopamine receptors is unknown. The amino acids S5.42, S5.43, and S5.46 located in helix 5 appear to be crucial, but their specific roles in receptor activation have not been studied. We modeled the D1 dopamine receptor using the crystal structures of the D3 dopamine and β2 adrenergic receptors. Molecular dynamics simulations show that the interaction of dopamine with the D1 receptor leads to the formation of a hydrogen-bond network with its catechol group and helices 3, 5, and 6, including water molecules. The para hydroxyl group of dopamine binds directly to S5.42 and N6.55, the latter also interacting with S5.43. Unexpectedly, S5.46 does not interact directly with the catechol; instead, it interacts through a water molecule with S5.42 and directly with T3.37. The formation of this hydrogen-bond network, part of which was previously observed in docking studies with dopamine agonists, triggers the opening of the E6.30-R3.60 ionic lock associated with the activation of GPCRs. These changes do not occur in the unbonded (apo) receptor or when it is in a complex with the antagonist 3-methoxy-5,6,7,8,9,14-hexahydrodibenz[d,g]azecine. Our results provide valuable insight into the T3.37-S5.46-water-S5.43-ligand interaction, which may be crucial to the activation of the D1 dopamine receptor and should be considered during the design of novel agonists. Graphical Abstract General representation of the relationship between the formation of the HBN and the opening of the R3.50-E6.30 ionic lock.
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Affiliation(s)
- Estefanía A Hugo
- Department of Chemistry, Faculty of Sciences, University of Chile, Ñuñoa, 7750000, Santiago, Chile.
| | - Bruce K Cassels
- Department of Chemistry, Faculty of Sciences, University of Chile, Ñuñoa, 7750000, Santiago, Chile
| | - Angélica Fierro
- Departamento de Química Orgánica, Facultad de Química, Pontificia Universidad Católica de Chile, Macul, 7810003, Santiago, Chile.
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26
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Liu G, Wang P, Li C, Wang J, Sun Z, Zhao X, Zheng X. Confirming therapeutic target of protopine using immobilized β 2 -adrenoceptor coupled with site-directed molecular docking and the target-drug interaction by frontal analysis and injection amount-dependent method. J Mol Recognit 2017; 30. [PMID: 28124461 DOI: 10.1002/jmr.2613] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2016] [Revised: 12/17/2016] [Accepted: 01/03/2017] [Indexed: 11/09/2022]
Abstract
Drug-protein interaction analysis is pregnant in designing new leads during drug discovery. We prepared the stationary phase containing immobilized β2 -adrenoceptor (β2 -AR) by linkage of the receptor on macroporous silica gel surface through N,N'-carbonyldiimidazole method. The stationary phase was applied in identifying antiasthmatic target of protopine guided by the prediction of site-directed molecular docking. Subsequent application of immobilized β2 -AR in exploring the binding of protopine to the receptor was realized by frontal analysis and injection amount-dependent method. The association constants of protopine to β2 -AR by the 2 methods were (1.00 ± 0.06) × 105 M-1 and (1.52 ± 0.14) × 104 M-1 . The numbers of binding sites were (1.23 ± 0.07) × 10-7 M and (9.09 ± 0.06) × 10-7 M, respectively. These results indicated that β2 -AR is the specific target for therapeutic action of protopine in vivo. The target-drug binding occurred on Ser169 in crystal structure of the receptor. Compared with frontal analysis, injection amount-dependent method is advantageous to drug saving, improvement of sampling efficiency, and performing speed. It has grave potential in high-throughput drug-receptor interaction analysis.
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Affiliation(s)
- Guangxin Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Pei Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Chan Li
- Drug Certificate Center, Shaanxi Food and Drug Administration, Xi'an, China
| | - Jing Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Zhenyu Sun
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Xinfeng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Xiaohui Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
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27
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Bhattacharya S, Salomon-Ferrer R, Lee S, Vaidehi N. Conserved Mechanism of Conformational Stability and Dynamics in G-Protein-Coupled Receptors. J Chem Theory Comput 2016; 12:5575-5584. [PMID: 27709935 DOI: 10.1021/acs.jctc.6b00618] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
G-protein-coupled receptors (GPCRs) are transmembrane receptors involved in diverse biological functions. Despite the diversity in their amino acid sequences, class A GPCRs exhibit a conserved structural topology and possibly a common mechanism of receptor activation. To understand how this high sequence diversity translates to a conserved functional mechanism, we have compared the dynamic behavior of eight class A GPCRs comprised of six biogenic amine receptors, adenosine A2A, and the peptide receptor protease-activated receptor 1. Starting from the crystal structures of the inactive state of these receptors bound to inverse agonists or antagonists, we have performed multiple all-atom MD simulations adding up to several microseconds of simulation. We elucidated the similarities and differences in the dynamic behavior and the conformational ensembles sampled by these eight class A GPCRs. Among the six biogenic amine receptors studied here, β2-adrenergic receptor shows the highest level of fluctuation in the sixth and seventh transmembrane helices, possibly explaining its high basal activity. In contrast, the muscarinic acetylcholine receptors show the lowest fluctuations as well as tight packing and low hydration of the transmembrane domain. All eight GPCRs show several conserved allosteric communication pipelines from the residues in the agonist binding site with the G-protein interface. Positions of the residues along these pipelines that serve as major hubs of allosteric communication are conserved in their respective structures. These findings have important implications in understanding the dynamics and allosteric mechanism of communication in class A GPCRs and hence are useful for designing conformation-specific drugs.
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Affiliation(s)
- Supriyo Bhattacharya
- Beckman Research Institute, City of Hope National Medical Center , 1500 Duarte Road, Duarte, California 91010, United States
| | - Romelia Salomon-Ferrer
- Beckman Research Institute, City of Hope National Medical Center , 1500 Duarte Road, Duarte, California 91010, United States
| | - Sangbae Lee
- Beckman Research Institute, City of Hope National Medical Center , 1500 Duarte Road, Duarte, California 91010, United States
| | - Nagarajan Vaidehi
- Beckman Research Institute, City of Hope National Medical Center , 1500 Duarte Road, Duarte, California 91010, United States
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28
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Manna M, Kulig W, Javanainen M, Tynkkynen J, Hensen U, Müller DJ, Rog T, Vattulainen I. How To Minimize Artifacts in Atomistic Simulations of Membrane Proteins, Whose Crystal Structure Is Heavily Engineered: β₂-Adrenergic Receptor in the Spotlight. J Chem Theory Comput 2016; 11:3432-45. [PMID: 26575777 DOI: 10.1021/acs.jctc.5b00070] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Atomistic molecular dynamics (MD) simulations are used extensively to elucidate membrane protein properties. These simulations are based on three-dimensional protein structures that in turn are often based on crystallography. The protein structures resolved in crystallographic studies typically do not correspond to pristine proteins, however. Instead the crystallized proteins are commonly engineered, including structural modifications (mutations, replacement of protein sequences by antibodies, bound ligands, etc.) whose impact on protein structure and dynamics is largely unknown. Here we explore this issue through atomistic MD simulations (∼5 μs in total), focusing on the β2-adrenergic receptor (β2AR) that is one of the most studied members of the G-protein coupled receptor superfamily. Starting from an inactive-state crystal structure of β2AR, we remove the many modifications in β2AR systematically one at a time, in six consecutive steps. After each step, we equilibrate the system and simulate it quite extensively. The results of this step-by-step approach highlight that the structural modifications used in crystallization can affect ligand and G-protein binding sites, packing at the transmembrane-helix interface region, and the dynamics of connecting loops in β2AR. When the results of the systematic step-by-step approach are compared to an all-at-once technique where all modifications done on β2AR are removed instantaneously at the same time, it turns out that the step-by-step method provides results that are superior in terms of maintaining protein structural stability. The results provide compelling evidence that for membrane proteins whose 3D structure is based on structural engineering, the preparation of protein structure for atomistic MD simulations is a delicate and sensitive process. The results show that most valid results are found when the structural modifications are reverted slowly, one at a time.
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Affiliation(s)
- Moutusi Manna
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Waldemar Kulig
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Matti Javanainen
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Joona Tynkkynen
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Ulf Hensen
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich , 4058 Basel, Switzerland
| | - Daniel J Müller
- Department of Biosystems Science and Engineering (D-BSSE), ETH-Zürich , 4058 Basel, Switzerland
| | - Tomasz Rog
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland
| | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology , P.O. Box 692, FI-33101 Tampere, Finland.,MEMPHYS-Center for Biomembrane Physics, University of Southern Denmark , Odense, Denmark
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29
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Eyun SI, Moriyama H, Hoffmann FG, Moriyama EN. Molecular Evolution and Functional Divergence of Trace Amine-Associated Receptors. PLoS One 2016; 11:e0151023. [PMID: 26963722 PMCID: PMC4786312 DOI: 10.1371/journal.pone.0151023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 02/09/2016] [Indexed: 12/31/2022] Open
Abstract
Trace amine-associated receptors (TAARs) are a member of the G-protein-coupled receptor superfamily and are known to be expressed in olfactory sensory neurons. A limited number of molecular evolutionary studies have been done for TAARs so far. To elucidate how lineage-specific evolution contributed to their functional divergence, we examined 30 metazoan genomes. In total, 493 TAAR gene candidates (including 84 pseudogenes) were identified from 26 vertebrate genomes. TAARs were not identified from non-vertebrate genomes. An ancestral-type TAAR-like gene appeared to have emerged in lamprey. We found four therian-specific TAAR subfamilies (one eutherian-specific and three metatherian-specific) in addition to previously known nine subfamilies. Many species-specific TAAR gene duplications and losses contributed to a large variation of TAAR gene numbers among mammals, ranging from 0 in dolphin to 26 in flying fox. TAARs are classified into two groups based on binding preferences for primary or tertiary amines as well as their sequence similarities. Primary amine-detecting TAARs (TAAR1-4) have emerged earlier, generally have single-copy orthologs (very few duplication or loss), and have evolved under strong functional constraints. In contrast, tertiary amine-detecting TAARs (TAAR5-9) have emerged more recently and the majority of them experienced higher rates of gene duplications. Protein members that belong to the tertiary amine-detecting TAAR group also showed the patterns of positive selection especially in the area surrounding the ligand-binding pocket, which could have affected ligand-binding activities and specificities. Expansions of the tertiary amine-detecting TAAR gene family may have played important roles in terrestrial adaptations of therian mammals. Molecular evolution of the TAAR gene family appears to be governed by a complex, species-specific, interplay between environmental and evolutionary factors.
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Affiliation(s)
- Seong-il Eyun
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States of America
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States of America
| | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States of America
| | - Federico G. Hoffmann
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology and Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS, 39762, United States of America
| | - Etsuko N. Moriyama
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States of America
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, 68588, United States of America
- * E-mail:
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30
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Sato T, Baker J, Warne T, Brown GA, Leslie AGW, Congreve M, Tate CG. Pharmacological Analysis and Structure Determination of 7-Methylcyanopindolol-Bound β1-Adrenergic Receptor. Mol Pharmacol 2015; 88:1024-34. [PMID: 26385885 DOI: 10.1124/mol.115.101030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 09/17/2015] [Indexed: 11/22/2022] Open
Abstract
Comparisons between structures of the β1-adrenergic receptor (AR) bound to either agonists, partial agonists, or weak partial agonists led to the proposal that rotamer changes of Ser(5.46), coupled to a contraction of the binding pocket, are sufficient to increase the probability of receptor activation. (RS)-4-[3-(tert-butylamino)-2-hydroxypropoxy]-1H-indole-2-carbonitrile (cyanopindolol) is a weak partial agonist of β1AR and, based on the hypothesis above, we predicted that the addition of a methyl group to form 4-[(2S)-3-(tert-butylamino)-2-hydroxypropoxy]-7-methyl-1H-indole-2-carbonitrile (7-methylcyanopindolol) would dramatically reduce its efficacy. An eight-step synthesis of 7-methylcyanopindolol was developed and its pharmacology was analyzed. 7-Methylcyanopindolol bound with similar affinity to cyanopindolol to both β1AR and β2AR. As predicted, the efficacy of 7-methylcyanopindolol was reduced significantly compared with cyanopindolol, acting as a very weak partial agonist of turkey β1AR and an inverse agonist of human β2AR. The structure of 7-methylcyanopindolol-bound β1AR was determined to 2.4-Å resolution and found to be virtually identical to the structure of cyanopindolol-bound β1AR. The major differences in the orthosteric binding pocket are that it has expanded by 0.3 Å in 7-methylcyanopindolol-bound β1AR and the hydroxyl group of Ser(5.46) is positioned 0.8 Å further from the ligand, with respect to the position of the Ser(5.46) side chain in cyanopindolol-bound β1AR. Thus, the molecular basis for the reduction in efficacy of 7-methylcyanopindolol compared with cyanopindolol may be regarded as the opposite of the mechanism proposed for the increase in efficacy of agonists compared with antagonists.
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Affiliation(s)
- Tomomi Sato
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.)
| | - Jillian Baker
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.)
| | - Tony Warne
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.)
| | - Giles A Brown
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.)
| | - Andrew G W Leslie
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.)
| | - Miles Congreve
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.)
| | - Christopher G Tate
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom (T.S., T.W., A.G.W.L., C.G.T.); Heptares Therapeutics Ltd, Welwyn Garden City, United Kingdom (G.A.B., M.C.); School of Life Sciences, University of Nottingham, Medical School, Queen's Medical Centre, Nottingham, United Kingdom (J.B.); KEK High Energy Accelerator Research Organization, Institute of Materials Structure Science, Structural Biology Research Center, Tsukuba, Japan (T.S.)
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Comparison of zonal elution and nonlinear chromatography in determination of the interaction between seven drugs and immobilised β2-adrenoceptor. J Chromatogr A 2015; 1401:75-83. [DOI: 10.1016/j.chroma.2015.05.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 05/05/2015] [Indexed: 12/17/2022]
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Kooistra AJ, Leurs R, de Esch IJP, de Graaf C. Structure-Based Prediction of G-Protein-Coupled Receptor Ligand Function: A β-Adrenoceptor Case Study. J Chem Inf Model 2015; 55:1045-61. [DOI: 10.1021/acs.jcim.5b00066] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Albert J. Kooistra
- Amsterdam Institute for Molecules,
Medicines and Systems (AIMMS), Division of Medicinal Chemistry, Faculty
of Science, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Rob Leurs
- Amsterdam Institute for Molecules,
Medicines and Systems (AIMMS), Division of Medicinal Chemistry, Faculty
of Science, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Iwan J. P. de Esch
- Amsterdam Institute for Molecules,
Medicines and Systems (AIMMS), Division of Medicinal Chemistry, Faculty
of Science, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Chris de Graaf
- Amsterdam Institute for Molecules,
Medicines and Systems (AIMMS), Division of Medicinal Chemistry, Faculty
of Science, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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33
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McCorvy JD, Roth BL. Structure and function of serotonin G protein-coupled receptors. Pharmacol Ther 2015; 150:129-42. [PMID: 25601315 DOI: 10.1016/j.pharmthera.2015.01.009] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 12/12/2014] [Indexed: 12/18/2022]
Abstract
Serotonin receptors are prevalent throughout the nervous system and the periphery, and remain one of the most lucrative and promising drug discovery targets for disorders ranging from migraine headaches to neuropsychiatric disorders such as schizophrenia and depression. There are 14 distinct serotonin receptors, of which 13 are G protein-coupled receptors (GPCRs), which are targets for approximately 40% of the approved medicines. Recent crystallographic and biochemical evidence has provided a converging understanding of the basic structure and functional mechanics of GPCR activation. Currently, two GPCR crystal structures exist for the serotonin family, the 5-HT1B and 5-HT2B receptor, with the antimigraine and valvulopathic drug ergotamine bound. The first serotonin crystal structures not only provide the first evidence of serotonin receptor topography but also provide mechanistic explanations into functional selectivity or biased agonism. This review will detail the findings of these crystal structures from a molecular and mutagenesis perspective for driving rational drug design for novel therapeutics incorporating biased signaling.
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MESH Headings
- Allosteric Site
- Animals
- Ergotamine/pharmacology
- Ergotamine/therapeutic use
- GTP-Binding Proteins/physiology
- Heart Valve Diseases/drug therapy
- Heart Valve Diseases/metabolism
- Humans
- Migraine Disorders/drug therapy
- Migraine Disorders/metabolism
- Models, Molecular
- Protein Conformation
- Receptor, Serotonin, 5-HT1B/chemistry
- Receptor, Serotonin, 5-HT1B/metabolism
- Receptor, Serotonin, 5-HT2B/chemistry
- Receptor, Serotonin, 5-HT2B/metabolism
- Receptors, Serotonin/chemistry
- Receptors, Serotonin/metabolism
- Serotonin Receptor Agonists/pharmacology
- Serotonin Receptor Agonists/therapeutic use
- Signal Transduction
- Vasoconstrictor Agents/pharmacology
- Vasoconstrictor Agents/therapeutic use
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Affiliation(s)
- John D McCorvy
- Department of Pharmacology and Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Chapel Hill Medical School, Chapel Hill, NC 27514, USA
| | - Bryan L Roth
- Department of Pharmacology and Division of Chemical Biology and Medicinal Chemistry, University of North Carolina Chapel Hill Medical School, Chapel Hill, NC 27514, USA
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34
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Verlinden H, Vleugels R, Verdonck R, Urlacher E, Vanden Broeck J, Mercer A. Pharmacological and signalling properties of a D2-like dopamine receptor (Dop3) in Tribolium castaneum. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 56:9-20. [PMID: 25449128 DOI: 10.1016/j.ibmb.2014.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 11/05/2014] [Accepted: 11/06/2014] [Indexed: 06/04/2023]
Abstract
Dopamine is an important neurotransmitter in the central nervous system of vertebrates and invertebrates. Despite their evolutionary distance, striking parallels exist between deuterostomian and protostomian dopaminergic systems. In both, signalling is achieved via a complement of functionally distinct dopamine receptors. In this study, we investigated the sequence, pharmacology and tissue distribution of a D2-like dopamine receptor from the red flour beetle Tribolium castaneum (TricaDop3) and compared it with related G protein-coupled receptors in other invertebrate species. The TricaDop3 receptor-encoding cDNA shows considerable sequence similarity with members of the Dop3 receptor class. Real time qRT-PCR showed high expression in both the central brain and the optic lobes, consistent with the role of dopamine as neurotransmitter. Activation of TricaDop3 expressed in mammalian cells increased intracellular Ca(2+) signalling and decreased NKH-477 (a forskolin analogue)-stimulated cyclic AMP levels in a dose-dependent manner. We studied the pharmacological profile of the TricaDop3 receptor and demonstrated that the synthetic vertebrate dopamine receptor agonists, 2 - amino- 6,7 - dihydroxy - 1,2,3,4 - tetrahydronaphthalene hydrobromide (6,7-ADTN) and bromocriptine acted as agonists. Methysergide was the most potent of the antagonists tested and showed competitive inhibition in the presence of dopamine. This study offers important information on the Dop3 receptor from Tribolium castaneum that will facilitate functional analyses of dopamine receptors in insects and other invertebrates.
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Affiliation(s)
- Heleen Verlinden
- Department of Animal Physiology and Neurobiology, Zoological Institute, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium; Department of Zoology, University of Otago, 340 Great King Street, Dunedin, New Zealand.
| | - Rut Vleugels
- Department of Animal Physiology and Neurobiology, Zoological Institute, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium
| | - Rik Verdonck
- Department of Animal Physiology and Neurobiology, Zoological Institute, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium
| | - Elodie Urlacher
- Department of Zoology, University of Otago, 340 Great King Street, Dunedin, New Zealand
| | - Jozef Vanden Broeck
- Department of Animal Physiology and Neurobiology, Zoological Institute, KU Leuven, Naamsestraat 59, 3000 Leuven, Belgium
| | - Alison Mercer
- Department of Zoology, University of Otago, 340 Great King Street, Dunedin, New Zealand
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35
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Kastner KW, Shoue DA, Estiu GL, Wolford J, Fuerst MF, Markley LD, Izaguirre JA, McDowell MA. Characterization of the Anopheles gambiae octopamine receptor and discovery of potential agonists and antagonists using a combined computational-experimental approach. Malar J 2014; 13:434. [PMID: 25407998 PMCID: PMC4253978 DOI: 10.1186/1475-2875-13-434] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/03/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Octopamine receptors (OARs) perform key functions in the biological pathways of primarily invertebrates, making this class of G-protein coupled receptors (GPCRs) a potentially good target for insecticides. However, the lack of structural and experimental data for this insect-essential GPCR family has promoted the development of homology models that are good representations of their biological equivalents for in silico screening of small molecules. METHODS Two Anopheles gambiae OARs were cloned, analysed and functionally characterized using a heterologous cell reporter system. Four antagonist- and four agonist-binding homology models were generated and virtually screened by docking against compounds obtained from the ZINC database. Resulting compounds from the virtual screen were tested experimentally using an in vitro reporter assay and in a mosquito larvicide bioassay. RESULTS Six An. gambiae OAR/tyramine receptor genes were identified. Phylogenetic analysis revealed that the OAR (AGAP000045) that encodes two open reading frames is an α-adrenergic-like receptor. Both splice variants signal through cAMP and calcium. Mutagenesis analysis revealed that D100 in the TM3 region and S206 and S210 in the TM5 region are important to the activation of the GPCR. Some 2,150 compounds from the virtual screen were structurally analysed and 70 compounds were experimentally tested against AgOAR45B expressed in the GloResponse™CRE-luc2P HEK293 reporter cell line, revealing 21 antagonists, 17 weak antagonists, 2 agonists, and 5 weak agonists. CONCLUSION Reported here is the functional characterization of two An. gambiae OARs and the discovery of new OAR agonists and antagonists based on virtual screening and molecular dynamics simulations. Four compounds were identified that had activity in a mosquito larva bioassay, three of which are imidazole derivatives. This combined computational and experimental approach is appropriate for the discovery of new and effective insecticides.
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Affiliation(s)
| | | | | | | | | | | | | | - Mary Ann McDowell
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, USA.
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Rodríguez D, Ranganathan A, Carlsson J. Strategies for improved modeling of GPCR-drug complexes: blind predictions of serotonin receptors bound to ergotamine. J Chem Inf Model 2014; 54:2004-21. [PMID: 25030302 DOI: 10.1021/ci5002235] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The recent increase in the number of atomic-resolution structures of G protein-coupled receptors (GPCRs) has contributed to a deeper understanding of ligand binding to several important drug targets. However, reliable modeling of GPCR-ligand complexes for the vast majority of receptors with unknown structure remains to be one of the most challenging goals for computer-aided drug design. The GPCR Dock 2013 assessment, in which researchers were challenged to predict the crystallographic structures of serotonin 5-HT(1B) and 5-HT(2B) receptors bound to ergotamine, provided an excellent opportunity to benchmark the current state of this field. Our contributions to GPCR Dock 2013 accurately predicted the binding mode of ergotamine with RMSDs below 1.8 Å for both receptors, which included the best submissions for the 5-HT(1B) complex. Our models also had the most accurate description of the binding sites and receptor-ligand contacts. These results were obtained using a ligand-guided homology modeling approach, which combines extensive molecular docking screening with incorporation of information from multiple crystal structures and experimentally derived restraints. In this work, we retrospectively analyzed thousands of structures that were generated during the assessment to evaluate our modeling strategies. Major contributors to accuracy were found to be improved modeling of extracellular loop two in combination with the use of molecular docking to optimize the binding site for ligand recognition. Our results suggest that modeling of GPCR-drug complexes has reached a level of accuracy at which structure-based drug design could be applied to a large number of pharmaceutically relevant targets.
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Affiliation(s)
- David Rodríguez
- Science for Life Laboratory, Stockholm University , Box 1031, SE-171 21 Solna, Sweden
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37
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Shonberg J, Lopez L, Scammells PJ, Christopoulos A, Capuano B, Lane JR. Biased Agonism at G Protein-Coupled Receptors: The Promise and the Challenges-A Medicinal Chemistry Perspective. Med Res Rev 2014; 34:1286-330. [DOI: 10.1002/med.21318] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Jeremy Shonberg
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University (Parkville Campus); Parkville Victoria Australia
| | - Laura Lopez
- Drug Discovery Biology; Monash Institute of Pharmaceutical Sciences; Monash University (Parkville Campus); Parkville Victoria Australia
| | - Peter J. Scammells
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University (Parkville Campus); Parkville Victoria Australia
| | - Arthur Christopoulos
- Drug Discovery Biology; Monash Institute of Pharmaceutical Sciences; Monash University (Parkville Campus); Parkville Victoria Australia
| | - Ben Capuano
- Medicinal Chemistry; Monash Institute of Pharmaceutical Sciences; Monash University (Parkville Campus); Parkville Victoria Australia
| | - J. Robert Lane
- Drug Discovery Biology; Monash Institute of Pharmaceutical Sciences; Monash University (Parkville Campus); Parkville Victoria Australia
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38
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Li Q, Bian L, Zhao X, Gao X, Zheng J, Li Z, Zhang Y, Jiang R, Zheng X. Immobilised histidine tagged β2-adrenoceptor oriented by a diazonium salt reaction and its application in exploring drug-protein interaction using ephedrine and pseudoephedrine as probes. PLoS One 2014; 9:e94955. [PMID: 24747442 PMCID: PMC3991622 DOI: 10.1371/journal.pone.0094955] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2013] [Accepted: 03/21/2014] [Indexed: 02/06/2023] Open
Abstract
A new oriented method using a diazonium salt reaction was developed for linking β2-adrenoceptor (β2-AR) on the surface of macroporous silica gel. Stationary phase containing the immobilised receptor was used to investigate the interaction between β2-AR and ephedrine plus pseudoephedrine by zonal elution. The isotherms of the two drugs best fit the Langmuir model. Only one type of binding site was found for ephedrine and pseudoephedrine targeting β2-AR. At 37 °C, the association constants during the binding were (5.94±0.05)×103/M for ephedrine and (3.80±0.02) ×103/M for pseudoephedrine, with the binding sites of (8.92±0.06) ×10−4 M. Thermodynamic studies showed that the binding of the two compounds to β2-AR was a spontaneous reaction with exothermal processes. The ΔGθ, ΔHθ and ΔSθ for the interaction between ephedrine and β2-AR were −(22.33±0.04) kJ/mol, −(6.51±0.69) kJ/mol and 50.94±0.31 J/mol·K, respectively. For the binding of pseudoephedrine to the receptor, these values were −(21.17±0.02) kJ/mol, −(7.48±0.56) kJ/mol and 44.13±0.01 J/mol·K. Electrostatic interaction proved to be the driving force during the binding of the two drugs to β2-AR. The proposed immobilised method will have great potential for attaching protein to solid substrates and realizing the interactions between proteins and drugs.
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Affiliation(s)
- Qian Li
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Liujiao Bian
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Xinfeng Zhao
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Xiaokang Gao
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Jianbin Zheng
- Institute of Analytical Science, Northwest University, Xi'an, Shaanxi, China
| | - Zijian Li
- Institute of Vascular Medicine, Peking University; Third Hospital and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Beijing, China
| | - Youyi Zhang
- Institute of Vascular Medicine, Peking University; Third Hospital and Key Laboratory of Molecular Cardiovascular Sciences, Ministry of Education, Beijing, China
- * E-mail: (YZ); (XZ)
| | - Ru Jiang
- School of Pharmacy, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
- * E-mail: (YZ); (XZ)
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39
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Zhao X, Li Q, Xiao C, Zhang Y, Bian L, Zheng J, Zheng X, Li Z, Zhang Y, Fan T. Oriented immobilisation of histidine-tagged protein and its application in exploring interactions between ligands and proteins. Anal Bioanal Chem 2014; 406:2975-85. [DOI: 10.1007/s00216-014-7723-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 02/17/2014] [Accepted: 02/24/2014] [Indexed: 11/28/2022]
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40
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Johnston JM, Filizola M. Beyond standard molecular dynamics: investigating the molecular mechanisms of G protein-coupled receptors with enhanced molecular dynamics methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 796:95-125. [PMID: 24158803 PMCID: PMC4074508 DOI: 10.1007/978-94-007-7423-0_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The majority of biological processes mediated by G Protein-Coupled Receptors (GPCRs) take place on timescales that are not conveniently accessible to standard molecular dynamics (MD) approaches, notwithstanding the current availability of specialized parallel computer architectures, and efficient simulation algorithms. Enhanced MD-based methods have started to assume an important role in the study of the rugged energy landscape of GPCRs by providing mechanistic details of complex receptor processes such as ligand recognition, activation, and oligomerization. We provide here an overview of these methods in their most recent application to the field.
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Affiliation(s)
- Jennifer M. Johnston
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
| | - Marta Filizola
- Department of Structural and Chemical Biology, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029, USA
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Canal CE, Cordova-Sintjago T, Liu Y, Kim MS, Morgan D, Booth RG. Molecular pharmacology and ligand docking studies reveal a single amino acid difference between mouse and human serotonin 5-HT2A receptors that impacts behavioral translation of novel 4-phenyl-2-dimethylaminotetralin ligands. J Pharmacol Exp Ther 2013; 347:705-16. [PMID: 24080681 DOI: 10.1124/jpet.113.208637] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
During translational studies to develop 4-phenyl-2-dimethylaminotetralin (PAT) compounds for neuropsychiatric disorders, the (2R,4S)-trans-(+)- and (2S,4R)-trans-(-)-enantiomers of the analog 6-hydroxy-7-chloro-PAT (6-OH-7-Cl-PAT) demonstrated unusual pharmacology at serotonin (5-HT) 5-HT2 G protein-coupled receptors (GPCRs). The enantiomers had similar affinities (Ki) at human (h) 5-HT2A receptors (≈ 70 nM). In an in vivo mouse model of 5-HT2A receptor activation [(±)-(2,5)-dimethoxy-4-iodoamphetamine (DOI)-elicited head twitch], however, (-)-6-OH-7-Cl-PAT was about 5-fold more potent than the (+)-enantiomer at attenuating the DOI-elicited response. It was discovered that (+)-6-OH-7-Cl-PAT (only) had ≈ 40-fold-lower affinity at mouse (m) compared with h5-HT2A receptors. Molecular modeling and computational ligand docking studies indicated that the 6-OH moiety of (+)- but not (-)-6-OH-7-Cl-PAT could form a hydrogen bond with serine residue 5.46 of the h5-HT2A receptor. The m5-HT2A as well as m5-HT2B, h5-HT2B, m5-HT2C, and h5-HT2C receptors have alanine at position 5.46, obviating this interaction; (+)-6-OH-7-Cl-PAT also showed ≈ 50-fold lower affinity than (-)-6-OH-7-Cl-PAT at m5-HT2C and h5-HT2C receptors. Mutagenesis studies confirmed that 5-HT2A S5.46 is critical for (+)- but not (-)-6-OH-7-Cl-PAT binding, as well as function. The (+)-6-OH-7-Cl-PAT enantiomer showed partial agonist effects at h5-HT2A wild-type (WT) and m5-HT2A A5.46S point-mutated receptors but did not activate m5-HT2A WT and h5-HT2A S5.46A point-mutated receptors, or h5-HT2B, h5-HT2C, and m5-HT2C receptors; (-)-6-OH-7-Cl-PAT did not activate any of the 5-HT2 receptors. Experiments also included the (2R,4S)-trans-(+)- and (2S,4R)-trans-(-)-enantiomers of 6-methoxy-7-chloro-PAT to validate hydrogen bonding interactions proposed for the corresponding 6-OH analogs. Results indicate that PAT ligand three-dimensional structure impacts target receptor binding and translational outcomes, supporting the hypothesis that GPCR ligand structure governs orthosteric binding pocket molecular determinants and resulting pharmacology.
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Affiliation(s)
- Clinton E Canal
- Center for Drug Discovery (C.E.C., T.C.-S., Y.L., R.G.B.), Department of Pharmaceutical Sciences (C.E.C., T.C.-S., Y.L., R.G.B.), and Department of Chemistry and Chemical Biology (R.G.B.), Northeastern University, Boston, Massachusetts; and Department of Medicinal Chemistry (M.S.K., T.C.-S.) and Department of Psychiatry (D.M.), University of Florida, Gainesville, Florida
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Adrenaline-activated structure of β2-adrenoceptor stabilized by an engineered nanobody. Nature 2013; 502:575-579. [PMID: 24056936 PMCID: PMC3822040 DOI: 10.1038/nature12572] [Citation(s) in RCA: 387] [Impact Index Per Article: 35.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 08/13/2013] [Indexed: 12/18/2022]
Abstract
G protein-coupled receptors (GPCRs) are integral membrane proteins that play an essential role in human physiology, yet the molecular processes through which they bind to their endogenous agonists and activate effector proteins remain poorly understood. Thus far, it has not been possible to capture an active-state GPCR bound to its native neurotransmitter. Crystal structures of agonist-bound GPCRs have relied on the use of either exceptionally high-affinity agonists1,2 or receptor stabilization by mutagenesis3-5. Many natural agonists such as adrenaline, which activates the β2-adrenoceptor (β2AR), bind with relatively low affinity, and they are often chemically unstable. Using directed evolution, we engineered a high-affinity camelid antibody fragment that stabilizes the active state of the β2AR, and used this to obtain crystal structures of the activated receptor bound to multiple ligands. Here, we present structures of active-state β2AR bound to three chemically distinct agonists: the ultra high-affinity agonist BI167107, the high-affinity catecholamine agonist hydroxybenzyl isoproterenol, and the low-affinity endogenous agonist adrenaline. The crystal structures reveal a highly conserved overall ligand recognition and activation mode despite diverse ligand chemical structures and affinities that range from 100 nM to ~80 pM. The adrenaline-bound receptor structure is overall similar to the others, but shows substantial rearrangements in extracellular loop three and the extracellular tip of transmembrane helix 6. These structures also reveal a water-mediated hydrogen bond between two conserved tyrosines, which appears to stabilize the active state of the β2AR and related GPCRs.
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Plazinska A, Kolinski M, Wainer IW, Jozwiak K. Molecular interactions between fenoterol stereoisomers and derivatives and the β₂-adrenergic receptor binding site studied by docking and molecular dynamics simulations. J Mol Model 2013; 19:4919-30. [PMID: 24043542 PMCID: PMC3825559 DOI: 10.1007/s00894-013-1981-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 08/21/2013] [Indexed: 11/26/2022]
Abstract
The β2 adrenergic receptor (β2-AR) has become a model system for studying the ligand recognition process and mechanism of the G protein coupled receptors activation. In the present study stereoisomers of fenoterol and some of its derivatives (N = 94 molecules) were used as molecular probes to identify differences in stereo-recognition interactions between β2-AR and structurally similar agonists. The present study aimed at determining the 3D molecular models of the fenoterol derivative-β2-AR complexes. Molecular models of β2-AR have been developed by using the crystal structure of the human β2-AR T4 lysozyme fusion protein with bound (S)-carazolol (PDB ID: 2RH1) and more recently reported structure of a nanobody-stabilized active state of the β2-AR with the bound full agonist BI-167107 (PDB ID: 3P0G). The docking procedure allowed us to study the similarities and differences in the recognition binding site(s) for tested ligands. The agonist molecules occupied the same binding region, between TM III, TM V, TM VI and TM VII. The residues identified by us during docking procedure (Ser203, Ser207, Asp113, Lys305, Asn312, Tyr308, Asp192) were experimentally indicated in functional and biophysical studies as being very important for the agonist-receptor interactions. Moreover, the additional space, an extension of the orthosteric pocket, was identified and described. Furthermore, the molecular dynamics simulations were used to study the molecular mechanism of interaction between ligands ((R,R')- and (S,S')-fenoterol) and β2-AR. Our research offers new insights into the ligand stereoselective interaction with one of the most important GPCR member. This study may also facilitate the design of improved selective medications, which can be used to treat, prevent and control heart failure symptoms.
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Affiliation(s)
- Anita Plazinska
- Laboratory of Medicinal Chemistry and Neuroengineering, Medical University of Lublin, ul. Chodzki 4a, 20-093 Lublin, Poland
| | - Michal Kolinski
- Laboratory of Medicinal Chemistry and Neuroengineering, Medical University of Lublin, ul. Chodzki 4a, 20-093 Lublin, Poland
- Bioinformatics Laboratory, Mossakowski Medical Research Centre Polish Academy of Sciences, 5 Pawinskiego Str., 02-106 Warsaw, Poland
| | - Irving W. Wainer
- Laboratory of Clinical Investigations, National Institute on Aging, Baltimore, MD USA
| | - Krzysztof Jozwiak
- Laboratory of Medicinal Chemistry and Neuroengineering, Medical University of Lublin, ul. Chodzki 4a, 20-093 Lublin, Poland
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Stäubert C, Bohnekamp J, Schöneberg T. Determinants involved in subtype-specific functions of rat trace amine-associated receptors 1 and 4. Br J Pharmacol 2013; 168:1266-78. [PMID: 23072560 DOI: 10.1111/bph.12020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Revised: 09/26/2012] [Accepted: 10/07/2012] [Indexed: 01/14/2023] Open
Abstract
AIMS The trace amine-associated receptor (Taar) family displays high species- and subtype-specific pharmacology. Several trace amines such as β-phenylethylamine (β-PEA), p-tyramine and tryptamine are agonists at TA(1) but poorly activate rat and mouse Taar4. PRINCIPAL RESULTS Using rat TA(1) and Taar4 chimera, we identified determinants in transmembrane helices 3 and 6, which, when replaced by the corresponding portion of rat TA(1) , can rescue cell surface expression of rat Taar4. When expressed at the cell surface, rat Taar4 pharmacology was very similar to that of TA(1) and coupled to the Gα(s) -protein/AC pathway. Our data suggest that binding pockets of Taar for surrogate agonists overlap between paralogs. CONCLUSIONS This implicates that the repertoire of Taar ensures functional redundancy, tissue- and cell-specific expression and/or different downstream signalling rather than different agonist specificity.
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Affiliation(s)
- C Stäubert
- Institute of Biochemistry, Medical Faculty, University Leipzig, Leipzig, Germany
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The importance of interactions with helix 5 in determining the efficacy of β-adrenoceptor ligands. Biochem Soc Trans 2013; 41:159-65. [PMID: 23356277 DOI: 10.1042/bst20120228] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Structures of the inactive state of the thermostabilized β1-adrenoceptor have been determined bound to eight different ligands, including full agonists, partial agonists, inverse agonists and biased agonists. Comparison of the structures shows distinct differences within the binding pocket that correlate with the pharmacological properties of the ligands. These data suggest that full agonists stabilize a structure with a contracted binding pocket and a rotamer change of serine (5.46) compared with when antagonists are bound. Inverse agonists may prevent both of these occurrences, whereas partial agonists stabilize a contraction of the binding pocket but not the rotamer change of serine (5.46). It is likely that subtle changes in the interactions between transmembrane helix 5 (H5) and H3/H4 on agonist binding promote the formation of the activated state.
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Weiss DR, Ahn S, Sassano MF, Kleist A, Zhu X, Strachan R, Roth BL, Lefkowitz RJ, Shoichet BK. Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor. ACS Chem Biol 2013; 8:1018-26. [PMID: 23485065 PMCID: PMC3658555 DOI: 10.1021/cb400103f] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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A prospective,
large library virtual screen against an activated
β2-adrenergic receptor (β2AR) structure returned potent
agonists to the exclusion of inverse-agonists, providing the first
complement to the previous virtual screening campaigns against inverse-agonist-bound
G protein coupled receptor (GPCR) structures, which predicted only
inverse-agonists. In addition, two hits recapitulated the signaling
profile of the co-crystal ligand with respect to the G protein and
arrestin mediated signaling. This functional fidelity has important
implications in drug design, as the ability to predict ligands with
predefined signaling properties is highly desirable. However, the
agonist-bound state provides an uncertain template for modeling the
activated conformation of other GPCRs, as a dopamine D2 receptor (DRD2)
activated model templated on the activated β2AR structure returned
few hits of only marginal potency.
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Affiliation(s)
- Dahlia R. Weiss
- Department of Pharmaceutical
Chemistry, University of California San Francisco, San Francisco, California 94158-2550, United States
| | | | - Maria F. Sassano
- Department of Pharmacology
and
National Institute of Mental Health Psychoactive Drug Screening Program
School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | | | | | | | - Bryan L. Roth
- Department of Pharmacology
and
National Institute of Mental Health Psychoactive Drug Screening Program
School of Medicine, University of North Carolina, Chapel Hill, North Carolina 27599, United States
| | | | - Brian K. Shoichet
- Department of Pharmaceutical
Chemistry, University of California San Francisco, San Francisco, California 94158-2550, United States
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Brueckner F, Piscitelli CL, Tsai CJ, Standfuss J, Deupi X, Schertler GFX. Structure of β-adrenergic receptors. Methods Enzymol 2013; 520:117-51. [PMID: 23332698 DOI: 10.1016/b978-0-12-391861-1.00006-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
β-Adrenergic receptors (βARs) control key physiological functions by transducing signals encoded in catecholamine hormones and neurotransmitters to activate intracellular signaling pathways. As members of the large family of G protein-coupled receptors (GPCRs), βARs have a seven-transmembrane helix topology and signal via G protein- and arrestin-dependent pathways. Until 2007, three-dimensional structural information of GPCRs activated by diffusible ligands, including βARs, was limited to homology models that used the related photoreceptor rhodopsin as a template. Over many years, several labs have developed strategies that have finally allowed the structures of the turkey β(1)AR and the human β(2)AR to be determined experimentally. The challenges to overcome included heterologous receptor overexpression, design of stabilized and crystallizable modified receptor constructs, ligand-affinity purification of active receptor and the development of novel techniques in crystallization and microcrystallography. The structures of βARs in complex with inverse agonists, antagonists, and agonists have revealed the binding mode of ligands with different efficacies, have allowed to obtain insights into ligand selectivity, and have provided better templates for drug design. Also, the structures of β(2)AR in complex with a G protein and a G protein-mimicking nanobody have provided important insights into the mechanism of receptor activation and G protein coupling. This chapter summarizes the strategies and methods that have been successfully applied to the structural studies of βARs. These are exemplified with detailed protocols toward the structure determination of stabilized turkey β(1)AR-ligand complexes. We also discuss the spectacular insights into adrenergic receptor function that were obtained from the structures.
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Affiliation(s)
- Florian Brueckner
- Laboratory of Biomolecular Research, Paul Scherrer Institut, Villigen PSI, Switzerland
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Isin B, Estiu G, Wiest O, Oltvai ZN. Identifying ligand binding conformations of the β2-adrenergic receptor by using its agonists as computational probes. PLoS One 2012; 7:e50186. [PMID: 23300522 PMCID: PMC3534076 DOI: 10.1371/journal.pone.0050186] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Accepted: 10/22/2012] [Indexed: 11/19/2022] Open
Abstract
Recently available G-protein coupled receptor (GPCR) structures and biophysical studies suggest that the difference between the effects of various agonists and antagonists cannot be explained by single structures alone, but rather that the conformational ensembles of the proteins need to be considered. Here we use an elastic network model-guided molecular dynamics simulation protocol to generate an ensemble of conformers of a prototypical GPCR, β(2)-adrenergic receptor (β(2)AR). The resulting conformers are clustered into groups based on the conformations of the ligand binding site, and distinct conformers from each group are assessed for their binding to known agonists of β(2)AR. We show that the select ligands bind preferentially to different predicted conformers of β(2)AR, and identify a role of β(2)AR extracellular region as an allosteric binding site for larger drugs such as salmeterol. Thus, drugs and ligands can be used as "computational probes" to systematically identify protein conformers with likely biological significance.
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Affiliation(s)
- Basak Isin
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Guillermina Estiu
- Department of Chemistry and Biochemistry and Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Olaf Wiest
- Department of Chemistry and Biochemistry and Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana, United States of America
- Laboratory of Computational Chemistry and Drug Design, Laboratory of Chemical Genomics, Peking University, Shenzhen Graduate School, Shenzhen, China
| | - Zoltán N. Oltvai
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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50
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The essential role for aromatic cluster in the β3 adrenergic receptor. Acta Pharmacol Sin 2012; 33:1062-8. [PMID: 22728712 DOI: 10.1038/aps.2012.55] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
AIM To explore the function of the conserved aromatic cluster F213(5.47), F308(6.51), and F309(6.52) in human β3 adrenergic receptor (hβ3AR). METHODS Point mutation technology was used to produce plasmid mutations of hβ3AR. HEK-293 cells were transiently co-transfected with the hβ3AR (wild-type or mutant) plasmids and luciferase reporter vector pCRE-luc. The expression levels of hβ3AR in the cells were determined by Western blot analysis. The constitutive signalling and the signalling induced by the β3AR selective agonist, BRL (BRL37344), were then evaluated. To further explore the interaction mechanism between BRL and β3AR, a three-dimensional complex model of β3AR and BRL was constructed by homology modelling and molecular docking. RESULTS For F308(6.51), Ala and Leu substitution significantly decreased the constitutive activities of β3AR to approximately 10% of that for the wild-type receptor. However, both the potency and maximal efficacy were unchanged by Ala substitution. In the F308(6.51)L construct, the EC(50) value manifested as a "right shift" of approximately two orders of magnitude with an increased E(max). Impressively, the molecular pharmacological phenotype was similar to the wild-type receptor for the introduction of Tyr at position 308(6.51), though the EC(50) value increased by approximately five-fold for the mutant. For F309(6.52), the constitutive signalling for both F309(6.52)A and F309(6.52)L constructs were strongly impaired. In the F309(6.52)A construct, BRL-stimulated signalling showed a normal E(max) but reduced potency. Leu substitution of F309(6.52) reduced both the E(max) and potency. When F309(6.52) was mutated to Tyr, the constitutive activity was decreased approximately three-fold, and BRL-stimulated signalling was significantly impaired. Furthermore, the double mutant (F308(6.51)A_F309(6.52)A) caused the total loss of β3AR function. The predicted binding mode between β3AR and BRL revealed that both F308(6.51) and F309(6.52) were in the BRL binding pocket of β3AR, while F213(5.47) and W305(6.48) were distant from the binding site. CONCLUSION These results revealed that aromatic residues, especially F308(6.51) and F309(6.52), play essential roles in the function of β3AR. Aromatic residues maintained the receptor in a partially activated state and significantly contributed to ligand binding. The results supported the common hypothesis that the aromatic cluster F[Y]5.47/F[Y]6.52/F[Y]6.51 conserved in class A G protein-coupled receptor (GPCR) plays an important role in the structural stability and activation of GPCRs.
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