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Arumugam M, Manikandan DB, Marimuthu SK, Muthusamy G, Kari ZA, Téllez-Isaías G, Ramasamy T. Evaluating Biofilm Inhibitory Potential in Fish Pathogen, Aeromonas hydrophila by Agricultural Waste Extracts and Assessment of Aerolysin Inhibitors Using In Silico Approach. Antibiotics (Basel) 2023; 12:antibiotics12050891. [PMID: 37237796 DOI: 10.3390/antibiotics12050891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/27/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Aeromonas hydrophila, an opportunistic bacteria, causes several devastating diseases in humans and animals, particularly aquatic species. Antibiotics have been constrained by the rise of antibiotic resistance caused by drug overuse. Therefore, new strategies are required to prevent appropriate antibiotic inability from antibiotic-resistant strains. Aerolysin is essential for A. hydrophila pathogenesis and has been proposed as a potential target for inventing drugs with anti-virulence properties. It is a unique method of disease prevention in fish to block the quorum-sensing mechanism of A. hydrophila. In SEM analysis, the crude solvent extracts of both groundnut shells and black gram pods exhibited a reduction of aerolysin formation and biofilm matrix formation by blocking the QS in A. hydrophila. Morphological changes were identified in the extracts treated bacterial cells. Furthermore, in previous studies, 34 ligands were identified with potential antibacterial metabolites from agricultural wastes, groundnut shells, and black gram pods using a literature survey. Twelve potent metabolites showed interactions between aerolysin and metabolites during molecular docking analysis, in that H-Pyran-4-one-2,3 dihydro-3,5 dihydroxy-6-methyl (-5.3 kcal/mol) and 2-Hexyldecanoic acid (-5.2 kcal/mol) showed promising results with potential hydrogen bond interactions with aerolysin. These metabolites showed a better binding affinity with aerolysin for 100 ns in molecular simulation dynamics. These findings point to a novel strategy for developing drugs using metabolites from agricultural wastes that may be feasible pharmacological solutions for treating A. hydrophila infections for the betterment of aquaculture.
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Affiliation(s)
- Manikandan Arumugam
- Laboratory of Aquabiotics/Nanoscience, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, India
| | - Dinesh Babu Manikandan
- Laboratory of Aquabiotics/Nanoscience, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, India
| | - Sathish Kumar Marimuthu
- Department of Pharmaceutical Technology, University College of Engineering, Bharathidasan Institute of Technology (BIT) Campus, Anna University, Tiruchirappalli 620024, India
| | - Govarthanan Muthusamy
- Department of Environmental Engineering, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Zulhisyam Abdul Kari
- Department of Agricultural Sciences, Faculty of Agro-Based Industry, Jeli Campus, Universiti Malaysia Kelantan, Jeli 17600, Malaysia
- Advanced Livestock and Aquaculture Research Group, Faculty of Agro-Based Industry, Jeli Campus, Universiti Malaysia Kelantan, Jeli 17600, Malaysia
| | | | - Thirumurugan Ramasamy
- Laboratory of Aquabiotics/Nanoscience, Department of Animal Science, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620024, India
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Arzani H, Rafii-Tabar H, Ramezani F. The investigation into the effect of the length of RGD peptides and temperature on the interaction with the αIIbβ3 integrin: a molecular dynamic study. J Biomol Struct Dyn 2022; 40:9701-9712. [PMID: 34060983 DOI: 10.1080/07391102.2021.1932602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The tripeptide Arg-Gly-Asp acid (RGD) is a protein sequence in the binding of proteins to cell surfaces, and is involved in various biological processes such as cell adhesion to the extracellular matrix, platelet activation, hemostasis, etc. The C2 domain of the Von Willebrand Factor (VWF), containing the RGD motif, plays an important role in the initial homeostasis process. It binds to the αIIbβ3 integrin and stimulates platelet aggregation. We have investigated, using the molecular Dynamic (MD) simulation method, the effect of the RGD-peptide length, and temperature variation, on the binding to the αIIbβ3 integrin receptor. We examined 10 different structural modes of the αIIbβ3 at three different temperatures; 237 K, 310 K and 318 K. Our findings show that the amino acids that form a binding pocket include Asp224, Tyr234, Ser226, Tyr190, Tyr189, Trp260, Trp262, Asp259, Lys253, Arg214, Asp217, Ser161 and Ala218 and that the ligand-receptor interaction was increased at higher temperatures. It was also found that the increase in the number of ligands' amino acids and their types (% glycine) plays an important role in the stability, conformation, and ligand-receptor interaction.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hossein Arzani
- Department of Medical Physics and Biomedical Engineering, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hashem Rafii-Tabar
- Department of Medical Physics and Biomedical Engineering, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,The Physics Branch of Iran Academy of Sciences, Tehran, Iran
| | - Fatemeh Ramezani
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
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Imperatorin Interferes with LPS Binding to the TLR4 Co-Receptor and Activates the Nrf2 Antioxidative Pathway in RAW264.7 Murine Macrophage Cells. Antioxidants (Basel) 2021; 10:antiox10030362. [PMID: 33673673 PMCID: PMC7997471 DOI: 10.3390/antiox10030362] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/12/2021] [Accepted: 02/22/2021] [Indexed: 12/15/2022] Open
Abstract
Imperatorin (IMP) could downregulate several inflammatory transcription factor signaling pathways. Some studies have pointed out that IMP could interfere with toll-like receptor 4 (TLR4) signaling. This study evaluates how IMP interferes with the TLR4 co-receptors signaling through the protein-ligand docking model, Western blotting, immunofluorescence (IF), and atomic force microscopy (AFM) assays in lipopolysaccharide (LPS) stimulated macrophage-like RAW264.7 cells in vitro. The results of the protein-ligand docking demonstrate that IMP interferes with LPS binding to the LPS-binding protein (LBP), the cluster of differentiation 14 (CD14), and the toll-like receptor 4/myeloid differentiation factor 2 (TLR4/MD-2) co-receptors in LPS-stimulated RAW264.7 cells. Compared with TLR4 antagonist CLI-095 or dexamethasone, IMP could suppress the protein expressions of LBP, CD14, and TLR4/MD-2 in LPS-stimulated cells. Furthermore, the three-dimensional (3D) image assay of the AFM showed IMP could prevent the LPS-induced morphological change in RAW264.7 cells. Additionally, IMP could activate the nuclear factor erythroid 2-related factor 2 (Nrf2) signaling pathway, and it increased the antioxidative protein expression of heme oxygenase-1 (HO-1), superoxidase dismutase (SOD), and catalase (CAT). Our results are the first to reveal that the anti-inflammatory effect of IMP interferes with LPS binding to TLR4 co-receptor signaling and activates the antioxidative Nrf2 signaling pathway.
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Basak S, Kumar A, Ramsey S, Gibbs E, Kapoor A, Filizola M, Chakrapani S. High-resolution structures of multiple 5-HT 3AR-setron complexes reveal a novel mechanism of competitive inhibition. eLife 2020; 9:e57870. [PMID: 33063666 PMCID: PMC7655109 DOI: 10.7554/elife.57870] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 10/15/2020] [Indexed: 12/13/2022] Open
Abstract
Serotonin receptors (5-HT3AR) play a crucial role in regulating gut movement, and are the principal target of setrons, a class of high-affinity competitive antagonists, used in the management of nausea and vomiting associated with radiation and chemotherapies. Structural insights into setron-binding poses and their inhibitory mechanisms are just beginning to emerge. Here, we present high-resolution cryo-EM structures of full-length 5-HT3AR in complex with palonosetron, ondansetron, and alosetron. Molecular dynamic simulations of these structures embedded in a fully-hydrated lipid environment assessed the stability of ligand-binding poses and drug-target interactions over time. Together with simulation results of apo- and serotonin-bound 5-HT3AR, the study reveals a distinct interaction fingerprint between the various setrons and binding-pocket residues that may underlie their diverse affinities. In addition, varying degrees of conformational change in the setron-5-HT3AR structures, throughout the channel and particularly along the channel activation pathway, suggests a novel mechanism of competitive inhibition.
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Affiliation(s)
- Sandip Basak
- Department of Physiology and Biophysics, Case Western Reserve UniversityClevelandUnited States
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve UniversityClevelandUnited States
| | - Arvind Kumar
- Department of Physiology and Biophysics, Case Western Reserve UniversityClevelandUnited States
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve UniversityClevelandUnited States
| | - Steven Ramsey
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Eric Gibbs
- Department of Physiology and Biophysics, Case Western Reserve UniversityClevelandUnited States
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve UniversityClevelandUnited States
| | - Abhijeet Kapoor
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Sudha Chakrapani
- Department of Physiology and Biophysics, Case Western Reserve UniversityClevelandUnited States
- Cleveland Center for Membrane and Structural Biology, Case Western Reserve UniversityClevelandUnited States
- Department of Neuroscience, School of Medicine, Case Western Reserve UniversityClevelandUnited States
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Zarkadas E, Zhang H, Cai W, Effantin G, Perot J, Neyton J, Chipot C, Schoehn G, Dehez F, Nury H. The Binding of Palonosetron and Other Antiemetic Drugs to the Serotonin 5-HT3 Receptor. Structure 2020; 28:1131-1140.e4. [DOI: 10.1016/j.str.2020.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/18/2020] [Accepted: 07/08/2020] [Indexed: 12/19/2022]
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Gulsevin A, Papke RL, Horenstein N. In Silico Modeling of the α7 Nicotinic Acetylcholine Receptor: New Pharmacological Challenges Associated with Multiple Modes of Signaling. Mini Rev Med Chem 2020; 20:841-864. [PMID: 32000651 PMCID: PMC8719523 DOI: 10.2174/1389557520666200130105256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022]
Abstract
The α7 nicotinic acetylcholine receptor is a homopentameric ion-channel of the Cys-loop superfamily characterized by its low probability of opening, high calcium permeability, and rapid desensitization. The α7 receptor has been targeted for the treatment of the cognitive symptoms of schizophrenia, depression, and Alzheimer's disease, but it is also involved in inflammatory modulation as a part of the cholinergic anti-inflammatory pathway. Despite its functional importance, in silico studies of the α7 receptor cannot produce a general model explaining the structural features of receptor activation, nor predict the mode of action for various ligand classes. Two particular problems in modeling the α7 nAChR are the absence of a high-resolution structure and the presence of five potentially nonequivalent orthosteric ligand binding sites. There is wide variability regarding the templates used for homology modeling, types of ligands investigated, simulation methods, and simulation times. However, a systematic survey focusing on the methodological similarities and differences in modeling α7 has not been done. In this work, we make a critical analysis of the modeling literature of α7 nAChR by comparing the findings of computational studies with each other and with experimental studies under the main topics of structural studies, ligand binding studies, and comparisons with other nAChR. In light of our findings, we also summarize current problems in the field and make suggestions for future studies concerning modeling of the α7 receptor.
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Affiliation(s)
- Alican Gulsevin
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, United States
| | - Roger L Papke
- Department of Pharmacology and Therapeutics, University of Florida, P.O. Box 100267, Gainesville, FL 32610, United States
| | - Nicole Horenstein
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, United States
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Chen X, Lu F, Luo G, Ren Y, Ma J, Zhang Y. Discovery of selective farnesoid X receptor agonists for the treatment of hyperlipidemia from traditional Chinese medicine based on virtual screening and in vitro validation. J Biomol Struct Dyn 2019; 38:4461-4470. [PMID: 31842697 DOI: 10.1080/07391102.2019.1695665] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Farnesoid X receptor (FXR), a bile acid receptor, has important roles in maintaining bile acid and cholesterol homeostasis, which is an attractive target for hyperlipidemia. Present study aimed to discover potential selective FXR agonists over G-protein coupled bile acid receptor 1 (GPBAR1, TGR5) from traditional Chinese medicine (TCM) by using virtual screening, in vitro studies and molecular dynamics simulation (MD). Ligand-based pharmacophore model for FXR was firstly built to screen FXR agonists from the Traditional Chinese Medicine Database (TCMD). Then, 21 FXR crystal structures were clustered in two types and two representative structures (PDB ID: 3OMM and 3P89) were, respectively, used to carry out molecular docking to refine the screened result. Moreover, the pharmacophore model for GPBAR1 was built to screen selective FXR agonists with no activity on GPBAR1. A set of 24 candidate selective FXR agonists which fitvalue of FXR pharmacophore model and docking score of 3OMM and 3P89 were in the top 100 and cannot match the pharmacophore model for GPBAR1 were obtained. By the lipid-lowering activity test in HepG2 cell lines, Arctigenin was identified to be potential selective FXR agonist with the activity of 20 μmol·L-1. After down-regulating FXR, Arctigenin could increase the mRNA of FXR while exerted no effect on the mRNA of GPBAR1. MD was further used to interpret the mechanism of Arctigenin with the representative structures. This research provided a new screening procedure for finding selective candidate compounds and appropriate docking models of a target by considering the structure diversity of PDB structures, which was applied to discovery novel selective FXR agonists to treat hyperlipidemia.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xi Chen
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Fang Lu
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Ganggang Luo
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Yue Ren
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Jing Ma
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
| | - Yanling Zhang
- School of Chinese Material Medica, State Administration of Traditional Chinese Medicine, Research Center of TCM-Information Engineering, Beijing University of Chinese Medicine, Beijing, China
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8
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Investigation of Molecular Details of Keap1-Nrf2 Inhibitors Using Molecular Dynamics and Umbrella Sampling Techniques. Molecules 2019; 24:molecules24224085. [PMID: 31726716 PMCID: PMC6891428 DOI: 10.3390/molecules24224085] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 10/31/2019] [Accepted: 11/09/2019] [Indexed: 11/17/2022] Open
Abstract
In this study, we investigate the atomistic details of Keap1-Nrf2 inhibitors by in-depth modeling techniques, including molecular dynamics (MD) simulations, and the path-based free energy method of umbrella sampling (US). The protein–protein interaction (PPI) of Keap1-Nrf2 is implicated in several neurodegenerative diseases like cancer, diabetes, and cardiomyopathy. A better understanding of the five sub-pocket binding sites for Nrf2 (ETGE and DLG motifs) inside the Kelch domain would expedite the inhibitor design process. We selected four protein–ligand complexes with distinct co-crystal ligands and binding occupancies inside the Nrf2 binding site. We performed 100 ns of MD simulation for each complex and analyzed the trajectories. From the results, it is evident that one ligand (1VV) has flipped inside the binding pocket, whereas the remaining three were stable. We found that Coulombic (Arg483, Arg415, Ser363, Ser508, and Ser602) and Lennard–Jones (Tyr525, Tyr334, and Tyr572) interactions played a significant role in complex stability. The obtained binding free energy values from US simulations were consistent with the potencies of simulated ligands. US simulation highlight the importance of basic and aromatic residues in the binding pocket. A detailed description of the dissociation process brings valuable insight into the interaction of the four selected protein–ligand complexes, which could help in the future to design more potent PPI inhibitors.
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Dawson A, Trumper P, de Souza JO, Parker H, Jones MJ, Hales TG, Hunter WN. Engineering a surrogate human heteromeric α/β glycine receptor orthosteric site exploiting the structural homology and stability of acetylcholine-binding protein. IUCRJ 2019; 6:1014-1023. [PMID: 31709057 PMCID: PMC6830221 DOI: 10.1107/s205225251901114x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/09/2019] [Indexed: 06/10/2023]
Abstract
Protein-engineering methods have been exploited to produce a surrogate system for the extracellular neurotransmitter-binding site of a heteromeric human ligand-gated ion channel, the glycine receptor. This approach circumvents two major issues: the inherent experimental difficulties in working with a membrane-bound ion channel and the complication that a heteromeric assembly is necessary to create a key, physiologically relevant binding site. Residues that form the orthosteric site in a highly stable ortholog, acetylcholine-binding protein, were selected for substitution. Recombinant proteins were prepared and characterized in stepwise fashion exploiting a range of biophysical techniques, including X-ray crystallography, married to the use of selected chemical probes. The decision making and development of the surrogate, which is termed a glycine-binding protein, are described, and comparisons are provided with wild-type and homomeric systems that establish features of molecular recognition in the binding site and the confidence that the system is suited for use in early-stage drug discovery targeting a heteromeric α/β glycine receptor.
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Affiliation(s)
- Alice Dawson
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Paul Trumper
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Juliana Oliveira de Souza
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Holly Parker
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Mathew J. Jones
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
| | - Tim G. Hales
- Division of Systems Medicine, School of Medicine, Ninewells Hospital, University of Dundee, Dundee DD1 9SY, Scotland
| | - William N. Hunter
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland
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Basak S, Gicheru Y, Kapoor A, Mayer ML, Filizola M, Chakrapani S. Molecular mechanism of setron-mediated inhibition of full-length 5-HT 3A receptor. Nat Commun 2019; 10:3225. [PMID: 31324772 PMCID: PMC6642186 DOI: 10.1038/s41467-019-11142-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 06/23/2019] [Indexed: 12/27/2022] Open
Abstract
Serotonin receptor (5-HT3AR) is the most common therapeutic target to manage the nausea and vomiting during cancer therapies and in the treatment of irritable bowel syndrome. Setrons, a class of competitive antagonists, cause functional inhibition of 5-HT3AR in the gastrointestinal tract and brainstem, acting as effective anti-emetic agents. Despite their prevalent use, the molecular mechanisms underlying setron binding and inhibition of 5-HT3AR are not fully understood. Here, we present the structure of granisetron-bound full-length 5-HT3AR solved by single-particle cryo-electron microscopy to 2.92 Å resolution. The reconstruction reveals the orientation of granisetron in the orthosteric site with unambiguous density for interacting sidechains. Molecular dynamics simulations and electrophysiology confirm the granisetron binding orientation and the residues central for ligand recognition. Comparison of granisetron-bound 5-HT3AR with the apo and serotonin-bound structures, reveals key insights into the mechanism underlying 5-HT3AR inhibition.
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Affiliation(s)
- Sandip Basak
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Yvonne Gicheru
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA
| | - Abhijeet Kapoor
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Megan L Mayer
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Marta Filizola
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sudha Chakrapani
- Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.
- Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106-4970, USA.
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Jack T, Leuenberger M, Ruepp MD, Vernekar SKV, Thompson AJ, Braga-Lagache S, Heller M, Lochner M. Mapping the Orthosteric Binding Site of the Human 5-HT 3 Receptor Using Photo-cross-linking Antagonists. ACS Chem Neurosci 2019; 10:438-450. [PMID: 30149702 DOI: 10.1021/acschemneuro.8b00327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The serotonin-gated 5-HT3 receptor is a ligand-gated ion channel. Its location at the synapse in the central and peripheral nervous system has rendered it a prime pharmacological target, for example, for antiemetic drugs that bind with high affinity to the neurotransmitter binding site and prevent the opening of the channel. Advances in structural biology techniques have led to a surge of disclosed three-dimensional receptor structures; however, solving ligand-bound high-resolution 5-HT3 receptor structures has not been achieved to date. Ligand binding poses in the orthosteric binding site have been largely predicted from mutagenesis and docking studies. We report the synthesis of a series of photo-cross-linking compounds whose structures are based on the clinically used antiemetic drug granisetron (Kytril). These displaced [3H]granisetron from the orthosteric binding site with low nanomolar affinities and showed specific photo-cross-linking with the human 5-HT3 receptor. Detailed analysis by protein-MS/MS identified a residue (Met-228) near the tip of binding loop C as the covalent modification site.
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Affiliation(s)
- Thomas Jack
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Michele Leuenberger
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | | | - Andrew J. Thompson
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, U.K
| | - Sophie Braga-Lagache
- Department of BioMedical Research, Mass Spectrometry and Proteomics Laboratory, University of Bern, Inselspital, 3010 Bern, Switzerland
| | - Manfred Heller
- Department of BioMedical Research, Mass Spectrometry and Proteomics Laboratory, University of Bern, Inselspital, 3010 Bern, Switzerland
| | - Martin Lochner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
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12
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Budelier MM, Cheng WWL, Chen ZW, Bracamontes JR, Sugasawa Y, Krishnan K, Mydock-McGrane L, Covey DF, Evers AS. Common binding sites for cholesterol and neurosteroids on a pentameric ligand-gated ion channel. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1864:128-136. [PMID: 30471426 DOI: 10.1016/j.bbalip.2018.11.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/20/2018] [Accepted: 11/16/2018] [Indexed: 11/16/2022]
Abstract
Cholesterol is an essential component of cell membranes, and is required for mammalian pentameric ligand-gated ion channel (pLGIC) function. Computational studies suggest direct interactions between cholesterol and pLGICs but experimental evidence identifying specific binding sites is limited. In this study, we mapped cholesterol binding to Gloeobacter ligand-gated ion channel (GLIC), a model pLGIC chosen for its high level of expression, existing crystal structure, and previous use as a prototypic pLGIC. Using two cholesterol analogue photolabeling reagents with the photoreactive moiety on opposite ends of the sterol, we identified two cholesterol binding sites: an intersubunit site between TM3 and TM1 of adjacent subunits and an intrasubunit site between TM1 and TM4. In both the inter- and intrasubunit sites, cholesterol is oriented such that the 3‑OH group points toward the center of the transmembrane domains rather than toward either the cytosolic or extracellular surfaces. We then compared this binding to that of the cholesterol metabolite, allopregnanolone, a neurosteroid that allosterically modulates pLGICs. The same binding pockets were identified for allopregnanolone and cholesterol, but the binding orientation of the two ligands was markedly different, with the 3‑OH group of allopregnanolone pointing to the intra- and extracellular termini of the transmembrane domains rather than to their centers. We also found that cholesterol increases, whereas allopregnanolone decreases the thermal stability of GLIC. These data indicate that cholesterol and neurosteroids bind to common hydrophobic pockets in the model pLGIC, GLIC, but that their effects depend on the orientation and specific molecular interactions unique to each sterol.
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Affiliation(s)
- Melissa M Budelier
- Department of Anesthesiology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - Wayland W L Cheng
- Department of Anesthesiology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - Zi-Wei Chen
- Department of Anesthesiology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA; Taylor Family Institute for Innovative Psychiatric Research, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - John R Bracamontes
- Department of Anesthesiology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - Yusuke Sugasawa
- Department of Anesthesiology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - Kathiresan Krishnan
- Department of Developmental Biology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - Laurel Mydock-McGrane
- Department of Developmental Biology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - Douglas F Covey
- Department of Anesthesiology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA; Taylor Family Institute for Innovative Psychiatric Research, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA; Department of Developmental Biology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA; Department of Psychiatry, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA
| | - Alex S Evers
- Department of Anesthesiology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA; Taylor Family Institute for Innovative Psychiatric Research, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA; Department of Developmental Biology, Washington University in St Louis, 660 S Euclid Ave, St Louis, MO 63110, USA.
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Polovinkin L, Hassaine G, Perot J, Neumann E, Jensen AA, Lefebvre SN, Corringer PJ, Neyton J, Chipot C, Dehez F, Schoehn G, Nury H. Conformational transitions of the serotonin 5-HT 3 receptor. Nature 2018; 563:275-279. [PMID: 30401839 DOI: 10.1038/s41586-018-0672-3] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 09/07/2018] [Indexed: 01/03/2023]
Abstract
The serotonin 5-HT3 receptor is a pentameric ligand-gated ion channel (pLGIC). It belongs to a large family of receptors that function as allosteric signal transducers across the plasma membrane1,2; upon binding of neurotransmitter molecules to extracellular sites, the receptors undergo complex conformational transitions that result in transient opening of a pore permeable to ions. 5-HT3 receptors are therapeutic targets for emesis and nausea, irritable bowel syndrome and depression3. In spite of several reported pLGIC structures4-8, no clear unifying view has emerged on the conformational transitions involved in channel gating. Here we report four cryo-electron microscopy structures of the full-length mouse 5-HT3 receptor in complex with the anti-emetic drug tropisetron, with serotonin, and with serotonin and a positive allosteric modulator, at resolutions ranging from 3.2 Å to 4.5 Å. The tropisetron-bound structure resembles those obtained with an inhibitory nanobody5 or without ligand9. The other structures include an 'open' state and two ligand-bound states. We present computational insights into the dynamics of the structures, their pore hydration and free-energy profiles, and characterize movements at the gate level and cation accessibility in the pore. Together, these data deepen our understanding of the gating mechanism of pLGICs and capture ligand binding in unprecedented detail.
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Affiliation(s)
| | | | - Jonathan Perot
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France
| | | | - Anders A Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Solène N Lefebvre
- Channel Receptors Unit, CNRS UMR 3571, Institut Pasteur, Paris, France
| | | | - Jacques Neyton
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France.
| | - Christophe Chipot
- Université de Lorraine, CNRS, LPCT, Nancy, France.,Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Francois Dehez
- Université de Lorraine, CNRS, LPCT, Nancy, France.,Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France
| | - Guy Schoehn
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France
| | - Hugues Nury
- CNRS, Université Grenoble Alpes, CEA, IBS, Grenoble, France.
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14
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Ladefoged LK, Munro L, Pedersen AJ, Lummis SCR, Bang-Andersen B, Balle T, Schiøtt B, Kristensen AS. Modeling and Mutational Analysis of the Binding Mode for the Multimodal Antidepressant Drug Vortioxetine to the Human 5-HT3A Receptor. Mol Pharmacol 2018; 94:1421-1434. [DOI: 10.1124/mol.118.113530] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/19/2018] [Indexed: 12/23/2022] Open
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