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Graur A, Haymond A, Lee KH, Viscarra F, Russo P, Luchini A, Paige M, Bermudez-Diaz I, Kabbani N. Protein Painting Mass Spectrometry in the Discovery of Interaction Sites within the Acetylcholine Binding Protein. ACS Chem Neurosci 2024; 15:2322-2333. [PMID: 38804618 PMCID: PMC11157483 DOI: 10.1021/acschemneuro.4c00149] [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: 03/15/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) are a family of ligand-gated ion channel receptors that contribute to cognition, memory, and motor control in many organisms. The pharmacological targeting of these receptors, using small molecules or peptides, presents an important strategy for the development of drugs that can treat important human diseases, including neurodegenerative disorders. The Aplysia californica acetylcholine binding protein (Ac-AChBP) is a structural surrogate of the nAChR with high homology to the extracellular ligand binding domain of homopentameric nAChRs. In this study, we optimized protein-painting-based mass spectrometry to identify regions of interaction between the Ac-AChBP and several nAChR ligands. Using molecular dyes that adhere to the surface of a solubilized Ac-AChBP complex, we identified amino acid residues that constitute a contact site within the Ac-AChBP for α-bungarotoxin, choline, nicotine, and amyloid-β 1-42. By integrating innovation in protein painting mass spectrometry with computational structural modeling, we present a new experimental tool for analyzing protein interactions of the nAChR.
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Affiliation(s)
- Alexandru Graur
- School
of Systems Biology, George Mason University, Fairfax, Virginia 22030, United States
| | - Amanda Haymond
- Center
for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110, United States
| | - Kyung Hyeon Lee
- Department
of Chemistry and Biochemistry, George Mason
University, Fairfax, Virginia 20110, United States
| | - Franco Viscarra
- Department
of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Headington, Oxford OX3 0BP, United Kingdom
- Structural
Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Paul Russo
- Center
for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110, United States
| | - Alessandra Luchini
- Center
for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110, United States
| | - Mikell Paige
- Department
of Chemistry and Biochemistry, George Mason
University, Fairfax, Virginia 20110, United States
| | - Isabel Bermudez-Diaz
- Department
of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Headington, Oxford OX3 0BP, United Kingdom
| | - Nadine Kabbani
- School
of Systems Biology, George Mason University, Fairfax, Virginia 22030, United States
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2
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Barrantes FJ. Structure and function meet at the nicotinic acetylcholine receptor-lipid interface. Pharmacol Res 2023; 190:106729. [PMID: 36931540 DOI: 10.1016/j.phrs.2023.106729] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/17/2023]
Abstract
The nicotinic acetylcholine receptor (nAChR) is a transmembrane protein that mediates fast intercellular communication in response to the endogenous neurotransmitter acetylcholine. It is the best characterized and archetypal molecule in the superfamily of pentameric ligand-gated ion channels (pLGICs). As a typical transmembrane macromolecule, it interacts extensively with its vicinal lipid microenvironment. Experimental evidence provides a wealth of information on receptor-lipid crosstalk: the nAChR exerts influence on its immediate membrane environment and conversely, the lipid moiety modulates ligand binding, affinity state transitions and gating of ion translocation functions of the receptor protein. Recent cryogenic electron microscopy (cryo-EM) studies have unveiled the occurrence of sites for phospholipids and cholesterol on the lipid-exposed regions of neuronal and electroplax nAChRs, confirming early spectroscopic and affinity labeling studies demonstrating the close contact of lipid molecules with the receptor transmembrane segments. This new data provides structural support to the postulated "lipid sensor" ability displayed by the outer ring of M4 transmembrane domains and their modulatory role on nAChR function, as we postulated a decade ago. Borrowing from the best characterized nAChR, the electroplax (muscle-type) receptor, and exploiting new structural information on the neuronal nAChR, it is now possible to achieve an improved depiction of these sites. In combination with site-directed mutagenesis, single-channel electrophysiology, and molecular dynamics studies, the new structural information delivers a more comprehensive portrayal of these lipid-sensitive loci, providing mechanistic explanations for their ability to modulate nAChR properties and raising the possibility of targetting them in disease.
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Affiliation(s)
- Francisco J Barrantes
- Laboratory of Molecular Neurobiology, Biomedical Research Institute, Faculty of Medical Sciences, Pontifical Catholic University of Argentina (UCA) - Argentine Scientific & Technol. Research Council (CONICET), Av. Alicia Moreau de Justo 1600, C1107AAZ Buenos Aires, Argentina.
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3
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Speculation on How RIC-3 and Other Chaperones Facilitate α7 Nicotinic Receptor Folding and Assembly. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27144527. [PMID: 35889400 PMCID: PMC9318448 DOI: 10.3390/molecules27144527] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/07/2022] [Accepted: 07/09/2022] [Indexed: 11/17/2022]
Abstract
The process of how multimeric transmembrane proteins fold and assemble in the endoplasmic reticulum is not well understood. The alpha7 nicotinic receptor (α7 nAChR) is a good model for multimeric protein assembly since it has at least two independent and specialized chaperones: Resistance to Inhibitors of Cholinesterase 3 (RIC-3) and Nicotinic Acetylcholine Receptor Regulator (NACHO). Recent cryo-EM and NMR data revealed structural features of α7 nAChRs. A ser-ala-pro (SAP) motif precedes a structurally important but unique "latch" helix in α7 nAChRs. A sampling of α7 sequences suggests the SAP motif is conserved from C. elegans to humans, but the latch sequence is only conserved in vertebrates. How RIC-3 and NACHO facilitate receptor subunits folding into their final pentameric configuration is not known. The artificial intelligence program AlphaFold2 recently predicted structures for NACHO and RIC-3. NACHO is highly conserved in sequence and structure across species, but RIC-3 is not. This review ponders how different intrinsically disordered RIC-3 isoforms from C. elegans to humans interact with α7 nAChR subunits despite having little sequence homology across RIC-3 species. Two models from the literature about how RIC-3 assists α7 nAChR assembly are evaluated considering recent structural information about the receptor and its chaperones.
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4
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Cartereau A, Taillebois E, Le Questel JY, Thany SH. Mode of Action of Neonicotinoid Insecticides Imidacloprid and Thiacloprid to the Cockroach Pameα7 Nicotinic Acetylcholine Receptor. Int J Mol Sci 2021; 22:9880. [PMID: 34576043 PMCID: PMC8471617 DOI: 10.3390/ijms22189880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 12/28/2022] Open
Abstract
The functional expression of the cockroach Pameα7 nicotinic acetylcholine receptor subunit has been previously studied, and was found to be able to form a homomeric receptor when expressed in Xenopus laevis oocytes. In this study, we found that the neonicotinoid insecticide imidacloprid is unable to activate the cockroach Pameα7 receptor, although thiacloprid induces low inward currents, suggesting that it is a partial agonist. In addition, the co-application or 5 min pretreatment with 10 µM imidacloprid increased nicotine current amplitudes, while the co-application or 5 min pretreatment with 10 µM thiacloprid decreased nicotine-evoked current amplitudes by 54% and 28%, respectively. This suggesting that these two representatives of neonicotinoid insecticides bind differently to the cockroach Pameα7 receptor. Interestingly, the docking models demonstrate that the orientation and interactions of the two insecticides in the cockroach Pameα7 nAChR binding pocket are very similar. Electrophysiological results have provided evidence to suggest that imidacloprid and thiacloprid could act as modulators of the cockroach Pameα7 receptors.
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Affiliation(s)
- Alison Cartereau
- Université d’Orléans, LBLGC USC INRAE 1328, 45067 Orléans, France; (A.C.); (E.T.)
| | - Emiliane Taillebois
- Université d’Orléans, LBLGC USC INRAE 1328, 45067 Orléans, France; (A.C.); (E.T.)
| | | | - Steeve H. Thany
- Université d’Orléans, LBLGC USC INRAE 1328, 45067 Orléans, France; (A.C.); (E.T.)
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5
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FitzGerald EA, Butko MT, Boronat P, Cederfelt D, Abramsson M, Ludviksdottir H, van Muijlwijk-Koezen JE, de Esch IJP, Dobritzsch D, Young T, Danielson UH. Discovery of fragments inducing conformational effects in dynamic proteins using a second-harmonic generation biosensor. RSC Adv 2021; 11:7527-7537. [PMID: 35423271 PMCID: PMC8694943 DOI: 10.1039/d0ra09844b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/28/2021] [Indexed: 01/13/2023] Open
Abstract
Biophysical screening of compound libraries for the identification of ligands that interact with a protein is efficient, but does typically not reveal if (or how) ligands may interfere with its functional properties. For this a biochemical/functional assay is required. But for proteins whose function is dependent on a conformational change, such assays are typically complex or have low throughput. Here we have explored a high-throughput second-harmonic generation (SHG) biosensor to detect fragments that induce conformational changes upon binding to a protein in real time and identify dynamic regions. Multiwell plate format SHG assays were developed for wild-type and six engineered single-cysteine mutants of acetyl choline binding protein (AChBP), a homologue to ligand gated ion channels (LGICs). They were conjugated with second harmonic-active labels via amine or maleimide coupling. To validate the assay, it was confirmed that the conformational changes induced in AChBP by nicotinic acetyl choline receptor (nAChR) agonists and antagonists were qualitatively different. A 1056 fragment library was subsequently screened against all variants and conformational modulators of AChBP were successfully identified, with hit rates from 9-22%, depending on the AChBP variant. A subset of four hits was selected for orthogonal validation and structural analysis. A time-resolved grating-coupled interferometry-based biosensor assay confirmed the interaction to be a reversible 1-step 1 : 1 interaction, and provided estimates of affinities and interaction kinetic rate constants (K D = 0.28-63 μM, k a = 0.1-6 μM-1 s-1, k d = 1 s-1). X-ray crystallography of two of the fragments confirmed their binding at a previously described conformationally dynamic site, corresponding to the regulatory site of LGICs. These results reveal that SHG has the sensitivity to identify fragments that induce conformational changes in a protein. A selection of fragment hits with a response profile different to known LGIC regulators was characterized and confirmed to bind to dynamic regions of the protein.
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Affiliation(s)
- Edward A FitzGerald
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
- Beactica Therapeutics Virdings allé 2 Uppsala 754 40 Sweden
| | | | - Pierre Boronat
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Daniela Cederfelt
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | - Mia Abramsson
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | | | - Jacqueline E van Muijlwijk-Koezen
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Iwan J P de Esch
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Doreen Dobritzsch
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | - Tracy Young
- Biodesy, Inc. 170 Harbor Way South San Francisco 94080 CA USA
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
- Science for Life Laboratory, Uppsala University Sweden
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6
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Camacho-Hernandez GA, Taylor P. Lessons from nature: Structural studies and drug design driven by a homologous surrogate from invertebrates, AChBP. Neuropharmacology 2020; 179:108108. [DOI: 10.1016/j.neuropharm.2020.108108] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/08/2020] [Accepted: 04/12/2020] [Indexed: 02/07/2023]
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7
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Gulsevin A, Meiler J, Horenstein NA. A Computational Analysis of the Factors Governing the Dynamics of α7 nAChR and Its Homologs. Biophys J 2020; 119:1656-1669. [PMID: 33010233 PMCID: PMC7642335 DOI: 10.1016/j.bpj.2020.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 09/10/2020] [Accepted: 09/10/2020] [Indexed: 12/18/2022] Open
Abstract
The α7 nicotinic acetylcholine receptor is a homopentameric ion channel from the Cys-loop receptor superfamily targeted for psychiatric indications and inflammatory pain. Molecular dynamics studies of the receptor have focused on residue mobility and global conformational changes to address receptor function. However, a comparative analysis of α7 with its homologs that cannot trigger channel opening has not been made so far. To identify the residues involved in α7 activation, we ran triplicate 500-ns molecular dynamics simulations with an α7 extracellular domain homology model and two acetylcholine-binding protein homologs. We tested the effect of ligand binding and amino acid sequence on the structure and dynamics of the three proteins. We found that mobile regions identified based on root mean-square deviation and root mean-square fluctuation values are not always consistent among the individual α7 extracellular domain simulations. Comparison of the replica-average properties of the three proteins based on dynamic cross-correlation maps showed that ligand binding affects the coupling between the C-loop and the Cys-loop, vestibular loop, and β1-β2 loops. In addition, the main-immunogenic-region-like domain of α7 went through correlated motions with multiple domains of the receptor. These correlated motions were absent or diminished in α7 homologs, suggesting a unique role in α7 activation.
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Affiliation(s)
- Alican Gulsevin
- Department of Chemistry, Biochemistry Division, University of Florida, Gainesville, Florida; Department of Chemistry, Vanderbilt University, Nashville, Tennessee.
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee; Leipzig University Medical School, Institute for Drug Discovery, Leipzig, Germany
| | - Nicole A Horenstein
- Department of Chemistry, Biochemistry Division, University of Florida, Gainesville, Florida
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8
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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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9
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Oliveira ASF, Shoemark DK, Campello HR, Wonnacott S, Gallagher T, Sessions RB, Mulholland AJ. Identification of the Initial Steps in Signal Transduction in the α4β2 Nicotinic Receptor: Insights from Equilibrium and Nonequilibrium Simulations. Structure 2019; 27:1171-1183.e3. [PMID: 31130483 DOI: 10.1016/j.str.2019.04.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/28/2019] [Accepted: 04/10/2019] [Indexed: 02/02/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) modulate synaptic transmission in the nervous system. These receptors have emerged as therapeutic targets in drug discovery for treating several conditions, including Alzheimer's disease, pain, and nicotine addiction. In this in silico study, we use a combination of equilibrium and nonequilibrium molecular dynamics simulations to map dynamic and structural changes induced by nicotine in the human α4β2 nAChR. They reveal a striking pattern of communication between the extracellular binding pockets and the transmembrane domains (TMDs) and show the sequence of conformational changes associated with the initial steps in this process. We propose a general mechanism for signal transduction for Cys-loop receptors: the mechanistic steps for communication proceed firstly through loop C in the principal subunit, and are subsequently transmitted, gradually and cumulatively, to loop F of the complementary subunit, and then to the TMDs through the M2-M3 linker.
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Affiliation(s)
- A Sofia F Oliveira
- School of Biochemistry, University of Bristol, Bristol BS8 1DT, UK; Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | | | - Hugo Rego Campello
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | - Susan Wonnacott
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Timothy Gallagher
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK
| | | | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, UK.
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10
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Brissonnet Y, Araoz R, Sousa R, Percevault L, Brument S, Deniaud D, Servent D, Le Questel JY, Lebreton J, Gouin SG. Di- and heptavalent nicotinic analogues to interfere with α7 nicotinic acetylcholine receptors. Bioorg Med Chem 2019; 27:700-707. [PMID: 30692022 DOI: 10.1016/j.bmc.2019.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/07/2019] [Accepted: 01/13/2019] [Indexed: 12/11/2022]
Abstract
In the field of nicotinic acetylcholine receptors (nAChRs), recognized as important therapeutic targets, much effort has been dedicated to the development of nicotinic analogues to agonize or antagonize distinct homo- and heteropentamers nAChR subtypes, selectively. In this work we developed di- and heptavalent nicotinic derivatives based on ethylene glycol (EG) and cyclodextrin cores, respectively. The compounds showed a concentration dependent inhibition of acetylcholine-induced currents on α7 nAChR expressed by Xenopus oocytes. Interesting features were observed with the divalent nicotinic derivatives, acting as antagonists with varied inhibitory concentrations (IC50) in function of the spacer arm length. The best divalent compounds showed a 16-fold lowered IC50 compared to the monovalent reference (12 vs 195 µM). Docking investigations provide guidelines to rationalize these experimental findings.
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Affiliation(s)
- Yoan Brissonnet
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Romulo Araoz
- CNRS, Neuro-PSI, UMR9197, 91191 Gif-Sur-Yvette, France; CEA/DRF/JOLIOT/SIMOPRO/Toxines Récepteur et Canaux Ioniques, F-91191 Gif-Sur-Yvette, France.
| | - Rui Sousa
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Lucie Percevault
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Sami Brument
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - David Deniaud
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Denis Servent
- CEA/DRF/JOLIOT/SIMOPRO/Toxines Récepteur et Canaux Ioniques, F-91191 Gif-Sur-Yvette, France
| | - Jean-Yves Le Questel
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France.
| | - Jacques Lebreton
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France
| | - Sébastien G Gouin
- Université de Nantes, CEISAM, Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation, UMR CNRS 6230, UFR des Sciences et des Techniques, 2, rue de la Houssinière, BP 92208, 44322 Nantes Cedex 3, France.
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11
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Smelt CLC, Sanders VR, Newcombe J, Burt RP, Sheppard TD, Topf M, Millar NS. Identification by virtual screening and functional characterisation of novel positive and negative allosteric modulators of the α7 nicotinic acetylcholine receptor. Neuropharmacology 2018; 139:194-204. [PMID: 30009834 PMCID: PMC6078708 DOI: 10.1016/j.neuropharm.2018.07.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/19/2018] [Accepted: 07/08/2018] [Indexed: 01/01/2023]
Abstract
Several previous studies have demonstrated that the activity of neurotransmitters acting on ligand-gated ion channels such as the nicotinic acetylcholine receptor (nAChR) can be altered by compounds binding to allosteric modulatory sites. In the case of α7 nAChRs, both positive and negative allosteric modulators (PAMs and NAMs) have been identified and have attracted considerable interest. A recent study, employing revised structural models of the transmembrane domain of the α7 nAChR in closed and open conformations, has provided support for an inter-subunit transmembrane allosteric binding site (Newcombe et al 2017). In the present study, we have performed virtual screening of the DrugBank database using pharmacophore queries that were based on the predicted binding mode of PAMs to α7 nAChR structural models. A total of 81 compounds were identified in the DrugBank database, of which the 25 highest-ranked hits corresponded to one of four previously-identified therapeutic compound groups (carbonic anhydrase inhibitors, cyclin-dependent kinase inhibitors, diuretics targeting the Na+-K+-Cl- cotransporter, and fluoroquinolone antibiotics targeting DNA gyrase). The top-ranked compound from each of these four groups (DB04763, DB08122, furosemide and pefloxacin, respectively) was tested for its effects on human α7 nAChR expressed in Xenopus oocytes using two-electrode voltage-clamp electrophysiology. These studies, conducted with wild-type, mutant and chimeric receptors, resulted in all four compounds exerting allosteric modulatory effects. While DB04763, DB08122 and pefloxacin were antagonists, furosemide potentiated ACh responses. Our findings, supported by docking studies, are consistent with these compounds acting as PAMs and NAMs of the α7 nAChR via interaction with a transmembrane site. Identification of α7 nAChR positive and negative allosteric modulators. Furosemide is a positive allosteric modulator of α7 nAChRs. DB04763, DB08122 and pefloxacin are negative allosteric modulators of α7 nAChRs. Modulation of α7 nAChRs by an allosteric transmembrane site.
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Affiliation(s)
| | | | - Joseph Newcombe
- Department of Chemistry, University College London, London, UK; Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | - Richard P Burt
- Division of Biosciences, University College London, London, UK
| | - Tom D Sheppard
- Department of Chemistry, University College London, London, UK
| | - Maya Topf
- Institute of Structural and Molecular Biology, Birkbeck College, London, UK
| | - Neil S Millar
- Division of Biosciences, University College London, London, UK.
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12
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Designing selective modulators for the nicotinic receptor subtypes: challenges and opportunities. Future Med Chem 2018; 10:433-459. [PMID: 29451400 DOI: 10.4155/fmc-2017-0169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nicotinic receptors are membrane proteins involved in several physiological processes. They are considered suitable drug targets for various CNS disorders or conditions, as shown by the large number of compounds which have entered clinical trials. In recent years, nonconventional agonists have been discovered: positive allosteric modulators, allosteric agonists, site-specific agonists and silent desensitizers are compounds able to modulate the receptor interacting at sites different from the orthodox one, or to desensitize the receptor without prior opening. While these new findings can further complicate the pharmacology of these proteins and the design and optimization of ligands, they undoubtedly offer new opportunities to find drugs for the many therapeutic indications involving nicotinic receptors.
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13
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Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models. Proc Natl Acad Sci U S A 2017; 114:E8100-E8109. [PMID: 28874590 DOI: 10.1073/pnas.1703952114] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Venom peptide toxins such as conotoxins play a critical role in the characterization of nicotinic acetylcholine receptor (nAChR) structure and function and have potential as nervous system therapeutics as well. However, the lack of solved structures of conotoxins bound to nAChRs and the large size of these peptides are barriers to their computational docking and design. We addressed these challenges in the context of the α4β2 nAChR, a widespread ligand-gated ion channel in the brain and a target for nicotine addiction therapy, and the 19-residue conotoxin α-GID that antagonizes it. We developed a docking algorithm, ToxDock, which used ensemble-docking and extensive conformational sampling to dock α-GID and its analogs to an α4β2 nAChR homology model. Experimental testing demonstrated that a virtual screen with ToxDock correctly identified three bioactive α-GID mutants (α-GID[A10V], α-GID[V13I], and α-GID[V13Y]) and one inactive variant (α-GID[A10Q]). Two mutants, α-GID[A10V] and α-GID[V13Y], had substantially reduced potency at the human α7 nAChR relative to α-GID, a desirable feature for α-GID analogs. The general usefulness of the docking algorithm was highlighted by redocking of peptide toxins to two ion channels and a binding protein in which the peptide toxins successfully reverted back to near-native crystallographic poses after being perturbed. Our results demonstrate that ToxDock can overcome two fundamental challenges of docking large toxin peptides to ion channel homology models, as exemplified by the α-GID:α4β2 nAChR complex, and is extendable to other toxin peptides and ion channels. ToxDock is freely available at rosie.rosettacommons.org/tox_dock.
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Ma Q, Tae HS, Wu G, Jiang T, Yu R. Exploring the Relationship between Nicotinic Acetylcholine Receptor Ligand Size, Efficiency, Efficacy, and C-Loop Opening. J Chem Inf Model 2017; 57:1947-1956. [PMID: 28718646 DOI: 10.1021/acs.jcim.7b00152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels mediating fundamental physiological activities in the nervous system and have become important targets for drug design. For a long time, the acetylcholine binding protein (AChBP) has been used as a surrogate to study the nAChR structure-function. Taking advantage of more than 100 AChBP crystal structures in the Protein DataBank (PDB), we explored the relationship between the size, efficiency, and efficacy of nAChR ligands and the C-loop movement. We found that the size of the ligand is correlated with the opening of the C-loop, which can be used in selecting AChBP crystal structures with appropriate C-loop opening to be used for nAChR ligand docking. Ligand size and C-loop opening are reversely correlated with the ligand efficiency rather than the binding affinity. Ligand efficiency could be accurately predicted using simple computational docking, giving a correlation coefficients (R2) up to 0.73. The efficacy of nAChR ligands might be related to ligand size, C-loop opening, and ligand efficiency. Results from this study are useful for engineering the binding affinity and efficacy of nAChR ligands.
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Affiliation(s)
- Qianyun Ma
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology , Qingdao 266003, China
| | - Han-Shen Tae
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong , Wollongong, New South Wales 2522, Australia
| | - Guanzhao Wu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology , Qingdao 266003, China
| | - Tao Jiang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology , Qingdao 266003, China
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China , Qingdao 266003, China.,Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology , Qingdao 266003, China
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15
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Ruepp MD, Wei H, Leuenberger M, Lochner M, Thompson AJ. The binding orientations of structurally-related ligands can differ; A cautionary note. Neuropharmacology 2017; 119:48-61. [PMID: 28137449 PMCID: PMC5464333 DOI: 10.1016/j.neuropharm.2017.01.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 01/13/2017] [Accepted: 01/24/2017] [Indexed: 11/19/2022]
Abstract
Crystal structures can identify ligand-receptor interactions and assist the development of novel therapeutics, but experimental challenges sometimes necessitate the use of homologous proteins. Tropisetron is an orthosteric ligand at both 5-HT3 and α7 nACh receptors and its binding orientation has been determined in the structural homologue AChBP (pdbid: 2WNC). Co-crystallisation with a structurally-related ligand, granisetron, reveals an almost identical orientation (pdbid; 2YME). However, there is a >1000-fold difference in the affinity of tropisetron at 5-HT3 versus α7 nACh receptors, and α7 nACh receptors do not bind granisetron. These striking pharmacological differences prompt questions about which receptor the crystal structures most closely represent and whether the ligand orientations are correct. Here we probe the binding orientation of tropisetron and granisetron at 5-HT3 receptors by in silico modelling and docking, radioligand binding on cysteine-substituted 5-HT3 receptor mutants transiently expressed in HEK 293 cells, and synthetic modification of the ligands. For 15 of the 23 cysteine substitutions, the effects on tropisetron and granisetron were different. Structure-activity relationships on synthesised derivatives of both ligands were also consistent with different orientations, revealing that contrary to the crystallographic evidence from AChBP, the two ligands adopt different orientations in the 5-HT3 receptor binding site. Our results show that even quite structurally similar molecules can adopt different orientations in the same binding site, and that caution may be needed when using homologous proteins to predict ligand binding. The drugs granisetron and tropisetron are structurally similar. Crystals of them bound to AChBP suggest they have similar binding orientations. At 5-HT3R, the effects of mutagenesis indicate that their orientations differ. SAR on both of these drugs also supports different orientations.
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Affiliation(s)
- Marc-David Ruepp
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Hao Wei
- Department of Pharmacology, University of Cambridge, Cambridge, UK
| | - Michele Leuenberger
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Martin Lochner
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland; Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.
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16
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Shahsavar A, Gajhede M, Kastrup JS, Balle T. Structural Studies of Nicotinic Acetylcholine Receptors: Using Acetylcholine-Binding Protein as a Structural Surrogate. Basic Clin Pharmacol Toxicol 2016; 118:399-407. [DOI: 10.1111/bcpt.12528] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/02/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Azadeh Shahsavar
- Department of Molecular Biology and Genetics; Danish Research Institute of Translational Neuroscience - DANDRITE; Aarhus University; Aarhus Denmark
- Department of Drug Design and Pharmacology; Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
| | - Michael Gajhede
- Department of Drug Design and Pharmacology; Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
| | - Jette S. Kastrup
- Department of Drug Design and Pharmacology; Faculty of Health and Medical Sciences; University of Copenhagen; Copenhagen Denmark
| | - Thomas Balle
- Faculty of Pharmacy; The University of Sydney; Sydney NSW Australia
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17
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Bertrand D, Lee CHL, Flood D, Marger F, Donnelly-Roberts D. Therapeutic Potential of α7 Nicotinic Acetylcholine Receptors. Pharmacol Rev 2015; 67:1025-73. [DOI: 10.1124/pr.113.008581] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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18
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Beck ME, Gutbrod O, Matthiesen S. Insight into the Binding Mode of Agonists of the Nicotinic Acetylcholine Receptor from Calculated Electron Densities. Chemphyschem 2015; 16:2760-2767. [PMID: 26175091 PMCID: PMC4576818 DOI: 10.1002/cphc.201500341] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Indexed: 01/22/2023]
Abstract
Insect nicotinic acetylcholine receptors (nAChRs) are among the most prominent and most economically important insecticide targets. Thus, an understanding of the modes of binding of respective agonists is important for the design of specific compounds with favorable vertebrate profiles. In the case of nAChRs, the lack of available high-resolution X-ray structures leaves theoretical considerations as the only viable option. Starting from classical homology and docking approaches, binding mode hypotheses are created for five agonists of the nAChR, covering insecticides in the main group 4 of the Insecticide Resistance Action Committee (IRAC) mode of action (MoA) classification, namely, neonicotinoids, nicotine, sulfoxaflor, and butenolides. To better understand these binding modes, the topologies of calculated electron densities of small-model systems are analyzed in the framework of the quantum theory of atoms in molecules. The theoretically obtained modes of binding are very much in line with the biology-driven IRAC MoA classification of the investigated ligands.
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Affiliation(s)
- Michael E Beck
- Head of Computational Science, Bayer CropScience AG, R&D-SMR-RT-Computational Science, Alfred-Nobel-Strasse 5040789 Monheim am Rhein (Germany)
| | - Oliver Gutbrod
- Molecular Modelling, Bayer CropScience AG, R&D-SMR-RT-Computational Science, Alfred-Nobel-Strasse 5040789 Monheim am Rhein (Germany)
| | - Svend Matthiesen
- Molecular Modelling, Bayer CropScience AG, R&D-SMR-RT-Computational Science, Alfred-Nobel-Strasse 5040789 Monheim am Rhein (Germany)
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19
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Chiodo L, Malliavin TE, Maragliano L, Cottone G, Ciccotti G. A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation. PLoS One 2015; 10:e0133011. [PMID: 26208301 PMCID: PMC4514475 DOI: 10.1371/journal.pone.0133011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 06/22/2015] [Indexed: 11/20/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAchRs) are ligand-gated ion channels that regulate chemical transmission at the neuromuscular junction. Structural information is available at low resolution from open and closed forms of an eukaryotic receptor, and at high resolution from other members of the same structural family, two prokaryotic orthologs and an eukaryotic GluCl channel. Structures of human channels however are still lacking. Homology modeling and Molecular Dynamics simulations are valuable tools to predict structures of unknown proteins, however, for the case of human nAchRs, they have been unsuccessful in providing a stable open structure so far. This is due to different problems with the template structures: on one side the homology with prokaryotic species is too low, while on the other the open eukaryotic GluCl proved itself unstable in several MD studies and collapsed to a dehydrated, non-conductive conformation, even when bound to an agonist. Aim of this work is to obtain, by a mixing of state-of-the-art homology and simulation techniques, a plausible prediction of the structure (still unknown) of the open state of human α7 nAChR complexed with epibatidine, from which it is possible to start structural and functional test studies. To prevent channel closure we employ a restraint that keeps the transmembrane pore open, and obtain in this way a stable, hydrated conformation. To further validate this conformation, we run four long, unbiased simulations starting from configurations chosen at random along the restrained trajectory. The channel remains stable and hydrated over the whole runs. This allows to assess the stability of the putative open conformation over a cumulative time of 1 μs, 800 ns of which are of unbiased simulation. Mostly based on the analysis of pore hydration and size, we suggest that the obtained structure has reasonable chances to be (at least one of the possible) structures of the channel in the open conformation.
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Affiliation(s)
- Letizia Chiodo
- Center for Life Nano Science @Sapienza, Istituto Italiano di Tecnologia, Rome, Italy
| | - Thérèse E. Malliavin
- Institut Pasteur and CNRS UMR 3528, Unité de Bioinformatique Structurale, Paris, France
| | - Luca Maragliano
- Center for Synaptic Neuroscience, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Grazia Cottone
- Department of Physics and Chemistry, University of Palermo, Palermo, Italy
- School of Physics, University College Dublin, Dublin, Ireland
| | - Giovanni Ciccotti
- School of Physics, University College Dublin, Dublin, Ireland
- Department of Physics, University of Roma “La Sapienza”, Rome, Italy
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20
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Virtual screening studies of Chinese medicine Coptidis Rhizoma as alpha7 nicotinic acetylcholine receptor agonists for treatment of Alzheimer’s disease. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.01.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Selvam B, Graton J, Laurent AD, Alamiddine Z, Mathé-Allainmat M, Lebreton J, Coqueret O, Olivier C, Thany SH, Le Questel JY. Imidacloprid and thiacloprid neonicotinoids bind more favourably to cockroach than to honeybee α6 nicotinic acetylcholine receptor: Insights from computational studies. J Mol Graph Model 2015; 55:1-12. [DOI: 10.1016/j.jmgm.2014.10.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Revised: 10/30/2014] [Accepted: 10/31/2014] [Indexed: 11/26/2022]
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22
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Structural basis for cooperative interactions of substituted 2-aminopyrimidines with the acetylcholine binding protein. Proc Natl Acad Sci U S A 2014; 111:10749-54. [PMID: 25006260 DOI: 10.1073/pnas.1410992111] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The nicotinic acetylcholine receptor (nAChR) and the acetylcholine binding protein (AChBP) are pentameric oligomers in which binding sites for nicotinic agonists and competitive antagonists are found at selected subunit interfaces. The nAChR spontaneously exists in multiple conformations associated with its activation and desensitization steps, and conformations are selectively stabilized by binding of agonists and antagonists. In the nAChR, agonist binding and the associated conformational changes accompanying activation and desensitization are cooperative. AChBP, which lacks the transmembrane spanning and cytoplasmic domains, serves as a homology model of the extracellular domain of the nAChRs. We identified unique cooperative binding behavior of a number of 4,6-disubstituted 2-aminopyrimidines to Lymnaea AChBP, with different molecular variants exhibiting positive, nH > 1.0, and negative cooperativity, nH < 1.0. Therefore, for a distinctive set of ligands, the extracellular domain of a nAChR surrogate suffices to accommodate cooperative interactions. X-ray crystal structures of AChBP complexes with examples of each allowed the identification of structural features in the ligands that confer differences in cooperative behavior. Both sets of molecules bind at the agonist-antagonist site, as expected from their competition with epibatidine. An analysis of AChBP quaternary structure shows that cooperative ligand binding is associated with a blooming or flare conformation, a structural change not observed with the classical, noncooperative, nicotinic ligands. Positively and negatively cooperative ligands exhibited unique features in the detailed binding determinants and poses of the complexes.
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23
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Atkinson A, Graton J, Le Questel JY. Insights into a highly conserved network of hydrogen bonds in the agonist binding site of nicotinic acetylcholine receptors: a structural and theoretical study. Proteins 2014; 82:2303-17. [PMID: 24752960 DOI: 10.1002/prot.24589] [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: 01/13/2014] [Revised: 04/02/2014] [Accepted: 04/15/2014] [Indexed: 11/07/2022]
Abstract
Structural and theoretical studies on the geometrical features of a hydrogen-bond network occurring in the binding site of nicotinic acetylcholine receptors (nAChRs) and composed of interconnected WxPD (Trp-x-Pro-Asp) and SWyz (Ser-Trp-yz) sequences from loops A and B, respectively, have been carried out. Multiple sequence alignments using as template the sequence of the apoform of Aplysia californica acetylcholine binding protein (Ac-AChBP) show the strict conservation of serine and tryptophan residues of the loop B SWyz sequence. Considering a sample of 19 high resolution AChBP structures, the strong conformational preferences of the key tryptophan residue has been pointing out, whatever the form, free or bounded, of AChBP. The geometry of the motif hydrogen-bond network has been characterized through the analyses of seven distances. The robustness of the various hydrogen-bond interactions is pointed out, the one involving the aspartate carboxylate group and the serine residue being the shortest of the network. The role of a cooperative effect involving a NH(His145)…OH (Ser142) hydrogen bond is highlighted. Density functional theory calculations on several simplified models based on the motif hydrogen-bond network allow probing the importance of the various hydrogen-bond interactions. The removal of the Ser142 hydroxyl group induces strong structural rearrangements, in agreement with the structural observations. Molecular electrostatic potential calculations on model systems highlight the importance of a cooperative effect in the whole hydrogen-bond network. More precisely, the key role of the Ser142 hydroxyl group, involved in several hydrogen bonds, is underlined.
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Affiliation(s)
- Alexandre Atkinson
- Université de Nantes, CEISAM UMR 6230, UFR des Sciences et des Techniques, 2 rue de la Houssinière, BP 92208, Nantes, F-44322, France
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24
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Kudryavtsev D, Makarieva T, Utkina N, Santalova E, Kryukova E, Methfessel C, Tsetlin V, Stonik V, Kasheverov I. Marine natural products acting on the acetylcholine-binding protein and nicotinic receptors: from computer modeling to binding studies and electrophysiology. Mar Drugs 2014; 12:1859-75. [PMID: 24686559 PMCID: PMC4012456 DOI: 10.3390/md12041859] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 02/20/2014] [Accepted: 03/11/2014] [Indexed: 12/29/2022] Open
Abstract
For a small library of natural products from marine sponges and ascidians, in silico docking to the Lymnaea stagnalis acetylcholine-binding protein (AChBP), a model for the ligand-binding domains of nicotinic acetylcholine receptors (nAChRs), was carried out and the possibility of complex formation was revealed. It was further experimentally confirmed via competition with radioiodinated α-bungarotoxin ([¹²⁵I]-αBgt) for binding to AChBP of the majority of analyzed compounds. Alkaloids pibocin, varacin and makaluvamines С and G had relatively high affinities (K(i) 0.5-1.3 μM). With the muscle-type nAChR from Torpedo californica ray and human neuronal α7 nAChR, heterologously expressed in the GH4C1 cell line, no competition with [¹²⁵I]-αBgt was detected in four compounds, while the rest showed an inhibition. Makaluvamines (K(i) ~ 1.5 μM) were the most active compounds, but only makaluvamine G and crambescidine 359 revealed a weak selectivity towards muscle-type nAChR. Rhizochalin, aglycone of rhizochalin, pibocin, makaluvamine G, monanchocidin, crambescidine 359 and aaptamine showed inhibitory activities in electrophysiology experiments on the mouse muscle and human α7 nAChRs, expressed in Xenopus laevis oocytes. Thus, our results confirm the utility of the modeling studies on AChBPs in a search for natural compounds with cholinergic activity and demonstrate the presence of the latter in the analyzed marine biological sources.
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Affiliation(s)
- Denis Kudryavtsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, Moscow 117997, Russia.
| | - Tatyana Makarieva
- Elyakov Pacific Institute of Bioorganic Chemistry (PIBOC), Russian Academy of Sciences, Prospect 100 let Vladivostoku, 159, Vladivostok 690022, Russia.
| | - Natalia Utkina
- Elyakov Pacific Institute of Bioorganic Chemistry (PIBOC), Russian Academy of Sciences, Prospect 100 let Vladivostoku, 159, Vladivostok 690022, Russia.
| | - Elena Santalova
- Elyakov Pacific Institute of Bioorganic Chemistry (PIBOC), Russian Academy of Sciences, Prospect 100 let Vladivostoku, 159, Vladivostok 690022, Russia.
| | - Elena Kryukova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, Moscow 117997, Russia.
| | | | - Victor Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, Moscow 117997, Russia.
| | - Valentin Stonik
- Elyakov Pacific Institute of Bioorganic Chemistry (PIBOC), Russian Academy of Sciences, Prospect 100 let Vladivostoku, 159, Vladivostok 690022, Russia.
| | - Igor Kasheverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, Moscow 117997, Russia.
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Miniaturized bioaffinity assessment coupled to mass spectrometry for guided purification of bioactives from toad and cone snail. BIOLOGY 2014; 3:139-56. [PMID: 24833338 PMCID: PMC4009767 DOI: 10.3390/biology3010139] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 01/23/2014] [Accepted: 01/26/2014] [Indexed: 11/17/2022]
Abstract
A nano-flow high-resolution screening platform, featuring a parallel chip-based microfluidic bioassay and mass spectrometry coupled to nano-liquid chromatography, was applied to screen animal venoms for nicotinic acetylcholine receptor like (nAChR) affinity by using the acetylcholine binding protein, a mimic of the nAChR. The potential of this microfluidic platform is demonstrated by profiling the Conus textile venom proteome, consisting of over 1,000 peptides. Within one analysis (<90 min, 500 ng venom injected), ligands are detected and identified. To show applicability for non-peptides, small molecular ligands such as steroidal ligands were identified in skin secretions from two toad species (Bufo alvarius and Bufo marinus). Bioactives from the toad samples were subsequently isolated by MS-guided fractionation. The fractions analyzed by NMR and a radioligand binding assay with α7-nAChR confirmed the identity and bioactivity of several new ligands.
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26
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Mohammad Hosseini Naveh Z, Malliavin TE, Maragliano L, Cottone G, Ciccotti G. Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics. PLoS One 2014; 9:e88555. [PMID: 24551117 PMCID: PMC3923797 DOI: 10.1371/journal.pone.0088555] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 01/07/2014] [Indexed: 11/19/2022] Open
Abstract
Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP), a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD) and Temperature Accelerated Molecular Dynamics (TAMD) simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both conformations of the native protein are stable, while the agonist-bound structure evolves toward the apo one if the orientation of few key sidechains in the orthosteric cavity is modified. Conversely, TAMD simulations initiated from the native conformations are able to produce the spontaneous transition. With respect to the modified conformations, TAMD accelerates the transition by at least a factor 10. The analysis of some specific residue-residue interactions points out that the transition mechanism is based on the disruption/formation of few key hydrogen bonds. Finally, while early events of ligand dissociation are observed already in standard MD, TAMD accelerates the ligand detachment and, at the highest TAMD effective temperature, it is able to produce a complete dissociation path in one AChBP subunit.
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Affiliation(s)
| | - Therese E. Malliavin
- Institut Pasteur and CNRS UMR 3528, Unité de Bioinformatique Structurale, Paris, France
| | - Luca Maragliano
- Department of Neuroscience and Brain Technologies, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Grazia Cottone
- School of Physics, University College Dublin, Dublin, Ireland
- Department of Physics and Chemistry, University of Palermo, Palermo, Italy
- * E-mail:
| | - Giovanni Ciccotti
- School of Physics, University College Dublin, Dublin, Ireland
- Department of Physics, University of Roma “La Sapienza”, Rome, Italy
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Comitani F, Cohen N, Ashby J, Botten D, Lummis SCR, Molteni C. Insights into the binding of GABA to the insect RDL receptor from atomistic simulations: a comparison of models. J Comput Aided Mol Des 2014; 28:35-48. [PMID: 24442887 PMCID: PMC3927061 DOI: 10.1007/s10822-013-9704-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 12/26/2013] [Indexed: 01/19/2023]
Abstract
The resistance to dieldrin (RDL) receptor is an insect pentameric ligand-gated ion channel (pLGIC). It is activated by the neurotransmitter γ-aminobutyric acid (GABA) binding to its extracellular domain; hence elucidating the atomistic details of this interaction is important for understanding how the RDL receptor functions. As no high resolution structures are currently available, we built homology models of the extracellular domain of the RDL receptor using different templates, including the widely used acetylcholine binding protein and two pLGICs, the Erwinia Chrysanthemi ligand-gated ion channel (ELIC) and the more recently resolved GluCl. We then docked GABA into the selected three dimensional structures, which we used as starting points for classical molecular dynamics simulations. This allowed us to analyze in detail the behavior of GABA in the binding sites, including the hydrogen bond and cation-π interaction networks it formed, the conformers it visited and the possible role of water molecules in mediating the interactions; we also estimated the binding free energies. The models were all stable and showed common features, including interactions consistent with experimental data and similar to other pLGICs; differences could be attributed to the quality of the models, which increases with increasing sequence identity, and the use of a pLGIC template. We supplemented the molecular dynamics information with metadynamics, a rare event method, by exploring the free energy landscape of GABA binding to the RDL receptor. Overall, we show that the GluCl template provided the best models. GABA forming direct salt-bridges with Arg211 and Glu204, and cation-π interactions with an aromatic cage including Tyr109, Phe206 and Tyr254, represents a favorable binding arrangement, and the interaction with Glu204 can also be mediated by a water molecule.
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Affiliation(s)
- Federico Comitani
- Physics Department, King's College London, Strand, London, WC2R 2LS, UK
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28
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Kombo DC, Bencherif M. Comparative study on the use of docking and Bayesian categorization to predict ligand binding to nicotinic acetylcholine receptors (nAChRs) subtypes. J Chem Inf Model 2013; 53:3212-22. [PMID: 24328365 DOI: 10.1021/ci400493a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We have carried out a comparative study between docking into homology models and Bayesian categorization, as applied to virtual screening of nicotinic ligands for binding at various nAChRs subtypes (human and rat α4β2, α7, α3β4, and α6β2β3). We found that although results vary with receptor subtype, Bayesian categorization exhibits higher accuracy and enrichment than unconstrained docking into homology models. However, docking accuracy is improved when one sets up a hydrogen-bond (HB) constraint between the cationic center of the ligand and the main-chain carbonyl group of the conserved Trp-149 or its homologue (a residue involved in cation-π interactions with the ligand basic nitrogen atom). This finding suggests that this HB is a hallmark of nicotinic ligands binding to nAChRs. Best predictions using either docking or Bayesian were obtained with the human α7 nAChR, when 100 nM was used as cutoff for biological activity. We also found that ligand-based Bayesian-derived enrichment factors and structure-based docking-derived enrichment factors highly correlate to each other. Moreover, they correlate with the mean molecular fractional polar surface area of actives ligands and the fractional hydrophobic/hydrophilic surface area of the binding site, respectively. This result is in agreement with the fact that hydrophobicity strongly contributes in promoting nicotinic ligands binding to their cognate nAChRs.
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Affiliation(s)
- David C Kombo
- Targacept, Inc., 100 North Main Street, Winston-Salem, North Carolina 27101, United States
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Nys M, Kesters D, Ulens C. Structural insights into Cys-loop receptor function and ligand recognition. Biochem Pharmacol 2013; 86:1042-53. [DOI: 10.1016/j.bcp.2013.07.001] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 07/03/2013] [Accepted: 07/03/2013] [Indexed: 11/28/2022]
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Computational studies of novel carbonyl-containing diazabicyclic ligands interacting with α4β2 nicotinic acetylcholine receptor (nAChR) reveal alternative binding modes. Bioorg Med Chem Lett 2013; 23:5105-13. [DOI: 10.1016/j.bmcl.2013.07.028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Revised: 07/05/2013] [Accepted: 07/16/2013] [Indexed: 11/22/2022]
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Jeschke P, Nauen R, Beck ME. Nicotinic acetylcholine receptor agonists: a milestone for modern crop protection. Angew Chem Int Ed Engl 2013; 52:9464-85. [PMID: 23934864 DOI: 10.1002/anie.201302550] [Citation(s) in RCA: 181] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Indexed: 11/08/2022]
Abstract
The destruction of crops by invertebrate pests is a major threat against a background of a continuously rising demand in food supply for a growing world population. Therefore, efficient crop protection measures in a vast range of agricultural settings are of utmost importance to guarantee sustainable yields. The discovery of synthetic agonists selectively addressing the nicotinic acetylcholine receptors (nAChRs), located in the central nervous system of insects, for use as insecticides was a major milestone in applied crop protection research. These compounds, as a result of their high target specificity and versatility in application methods, opened a new innovative era in the control of some of the world's most devastating insect pests. These insecticides also contributed massively to extending our knowledge of the biochemistry of insect nicotinic acetylcholine receptors. The global economic success of synthetic nAChR agonists as insecticides renders the nicotinic acetylcholine receptor still one of the most attractive target sites for exploration in insecticide discovery.
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Affiliation(s)
- Peter Jeschke
- Bayer CropScience AG, BCS AG R&D-SMR-PC-PCC C2, Alfred-Nobel-Strasse 50, Building 6510, 40789 Monheim am Rhein, Germany.
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Jeschke P, Nauen R, Beck ME. Nicotinische Acetylcholinrezeptor-Agonisten: ein Meilenstein für den modernen Pflanzenschutz. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302550] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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33
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Molgó J, Aráoz R, Benoit E, Iorga BI. Physical and virtual screening methods for marine toxins and drug discovery targeting nicotinic acetylcholine receptors. Expert Opin Drug Discov 2013; 8:1203-23. [DOI: 10.1517/17460441.2013.822365] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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34
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Dederer H, Berger M, Meyer T, Werr M, Ilg T. Structure-activity relationships of acetylcholine derivatives with Lucilia cuprina nicotinic acetylcholine receptor α1 and α2 subunits in chicken β2 subunit hybrid receptors in comparison with chicken nicotinic acetylcholine receptor α4/β2. INSECT MOLECULAR BIOLOGY 2013; 22:183-198. [PMID: 23331538 DOI: 10.1111/imb.12014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Insect nicotinic acetylcholine (ACh) receptors (nAChRs) are the targets of several insecticide classes. In the present study, we report the gene identification and cloning of nAChR α1 and α2 subunits (Lcα1 and Lcα2) from the sheep blowfly Lucilia cuprina. Xenopus oocytes voltage clamp experiments as hybrids with the chicken β2 nAChR (Ggβ2) subunit resulted in ACh-gated ion channels with distinct dose-response curves for Lcα1/Ggβ2 (effective concentration 50% [EC50 ] = 80 nM; nH = 1.05), and Lcα2/Ggβ2 (EC50 = 5.37 μM, nH = 1.46). The neonicotinoid imidacloprid was a potent agonist for the α-bungarotoxin-sensitive Lcα1/Ggβ2 (EC50 ∼ 20 nM), while the α-bungarotoxin-resistant Lcα2/Ggβ2 showed a 30-fold lower sensitivity to this insecticide (EC50 = 0.62 μM). Thirteen close derivatives of ACh were analysed in EC50 , Hill coefficient and maximum current (relative to ACh) determinations for Lcα1/Ggβ2 and Lcα2/Ggβ2 and the chicken Ggα4/Ggβ2 nAChRs, and comparisons relative to ACh allowed the definition of novel structure-activity and structure-selectivity relationships. In the case of N-ethyl-acetylcholine, the EC50 of the chicken Ggα4/Ggβ2 rose by a factor of 1000, while for both Lcα1/Ggβ2 and Lcα2/Ggβ2, potency remained unchanged. Further derivatives with insect nAChR selectivity potential were acetyl-α-methylcholine and trimethyl-(3-methoxy-3-oxopropyl)ammonium, followed by acetylhomocholine and trimethyl-(4-oxopentyl) ammonium. Our results may provide guidance for the identification or design of insect-specific nAChR agonists using structure-based or in silico methods.
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Affiliation(s)
- H Dederer
- MSD Animal Health Innovation GmbH, Schwabenheim, Germany
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Rodríguez LP, Vilariño N, Molgó J, Aráoz R, Louzao MC, Taylor P, Talley T, Botana LM. Development of a solid-phase receptor-based assay for the detection of cyclic imines using a microsphere-flow cytometry system. Anal Chem 2013; 85:2340-7. [PMID: 23343192 PMCID: PMC3597463 DOI: 10.1021/ac3033432] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biologically active macrocycles containing a cyclic imine were isolated for the first time from aquaculture sites in Nova Scotia, Canada, during the 1990s. These compounds display a "fast-acting" toxicity in the traditional mouse bioassay for lipophilic marine toxins. Our work aimed at developing a receptor-based detection method for spirolides using a microsphere/flow cytometry Luminex system. For the assay, two alternatives were considered as binding proteins, the Torpedo marmorata nicotinic acetylcholine receptor (nAChR) and the Lymnaea stagnalis acetylcholine binding protein (Ls-AChBP). A receptor-based inhibition assay was developed using the immobilization of nAChR or Ls-AChBP on the surface of carboxylated microspheres and the competition of cyclic imines with biotin-α-bungarotoxin (α-BTX) for binding to these proteins. The amount of biotin-α-BTX bound to the surface of the microspheres was quantified using phycoerythrin (PE)-labeled streptavidin, and the fluorescence was analyzed in a Luminex 200 system. AChBP and nAChR bound to 13-desmethyl spirolide C efficiently; however, the cross-reactivity profile of the nAChR for spirolides and gymnodimine more closely matched the relative toxic potencies reported for these toxins. The nAChR was selected for further assay development. A simple sample preparation protocol consisting of an extraction with acetone yielded a final extract with no matrix interference on the nAChR/microsphere-based assay for mussels, scallops, and clams. This cyclic imine detection method allowed the detection of 13-desmethyl spirolide C in the range of 10-6000 μg/kg of shellfish meat, displaying a higher sensitivity and wider dynamic range than other receptor-based assays previously published. This microsphere-based assay provides a rapid, sensitive, and easily performed screening method that could be multiplexed for the simultaneous detection of several marine toxins.
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Affiliation(s)
- Laura P. Rodríguez
- Universidad de Santiago de Compostela, Departamento de Farmacología, Facultad de Veterinaria, 27002 Lugo, Spain
| | - Natalia Vilariño
- Universidad de Santiago de Compostela, Departamento de Farmacología, Facultad de Veterinaria, 27002 Lugo, Spain
| | - Jordi Molgó
- CNRS, Institut de Neurobiologie Alfred Fessard FRC2118, Laboratoire de Neurobiologie et Développement UPR3294, 91198 Gif-sur-Yvette Cedex, France
| | - Rómulo Aráoz
- CNRS, Institut de Neurobiologie Alfred Fessard FRC2118, Laboratoire de Neurobiologie et Développement UPR3294, 91198 Gif-sur-Yvette Cedex, France
| | - M. Carmen Louzao
- Universidad de Santiago de Compostela, Departamento de Farmacología, Facultad de Veterinaria, 27002 Lugo, Spain
| | - Palmer Taylor
- Department of Pharmacology, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA
| | - Todd Talley
- Department of Pharmacology, Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California at San Diego, La Jolla, CA, USA
| | - Luis M. Botana
- Universidad de Santiago de Compostela, Departamento de Farmacología, Facultad de Veterinaria, 27002 Lugo, Spain
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36
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Virtual screening for alpha7 nicotinic acetylcholine receptor for treatment of Alzheimer's disease. J Mol Graph Model 2013; 39:98-107. [DOI: 10.1016/j.jmgm.2012.11.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 11/19/2012] [Accepted: 11/20/2012] [Indexed: 11/18/2022]
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37
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Nicotinic acetylcholine receptors: From basic science to therapeutics. Pharmacol Ther 2013; 137:22-54. [DOI: 10.1016/j.pharmthera.2012.08.012] [Citation(s) in RCA: 382] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 08/20/2012] [Indexed: 12/14/2022]
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38
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Xiao Y, Hammond PS, Mazurov AA, Yohannes D. Multiple Interaction Regions in the Orthosteric Ligand Binding Domain of the α7 Neuronal Nicotinic Acetylcholine Receptor. J Chem Inf Model 2012; 52:3064-73. [DOI: 10.1021/ci3001953] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yunde Xiao
- Targacept, Inc., 200 East
First Street, Suite 300, Winston-Salem, North Carolina 27101, United
States
| | - Philip S. Hammond
- Targacept, Inc., 200 East
First Street, Suite 300, Winston-Salem, North Carolina 27101, United
States
| | - Anatoly A. Mazurov
- Targacept, Inc., 200 East
First Street, Suite 300, Winston-Salem, North Carolina 27101, United
States
| | - Daniel Yohannes
- Targacept, Inc., 200 East
First Street, Suite 300, Winston-Salem, North Carolina 27101, United
States
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Jadey S, Auerbach A. An integrated catch-and-hold mechanism activates nicotinic acetylcholine receptors. ACTA ACUST UNITED AC 2012; 140:17-28. [PMID: 22732309 PMCID: PMC3382718 DOI: 10.1085/jgp.201210801] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In neuromuscular acetylcholine (ACh) receptor channels (AChRs), agonist molecules bind with a low affinity (LA) to two sites that can switch to high affinity (HA) and increase the probability of channel opening. We measured (by using single-channel kinetic analysis) the rate and equilibrium constants for LA binding and channel gating for several different agonists of adult-type mouse AChRs. Almost all of the variation in the equilibrium constants for LA binding was from differences in the association rate constants. These were consistently below the limit set by diffusion and were substantially different even though the agonists had similar sizes and the same charge. This suggests that binding to resting receptors is not by diffusion alone and, hence, that each binding site can undergo two conformational changes ("catch" and "hold") that connect three different structures (apo-, LA-bound, and HA-bound). Analyses of ACh-binding protein structures suggest that this binding site, too, may adopt three discrete structures having different degrees of loop C displacement ("capping"). For the agonists we tested, the logarithms of the equilibrium constants for LA binding and LA↔HA gating were correlated. Although agonist binding and channel gating have long been considered to be separate processes in the activation of ligand-gated ion channels, this correlation implies that the catch-and-hold conformational changes are energetically linked and together comprise an integrated process having a common structural basis. We propose that loop C capping mainly reflects agonist binding, with its two stages corresponding to the formation of the LA and HA complexes. The catch-and-hold reaction coordinate is discussed in terms of preopening states and thermodynamic cycles of activation.
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Affiliation(s)
- Snehal Jadey
- Department of Physiology and Biophysics, State University of New York, Buffalo, NY 14214, USA
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40
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Reymond JL, Awale M. Exploring chemical space for drug discovery using the chemical universe database. ACS Chem Neurosci 2012; 3:649-57. [PMID: 23019491 DOI: 10.1021/cn3000422] [Citation(s) in RCA: 171] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 04/25/2012] [Indexed: 01/20/2023] Open
Abstract
Herein we review our recent efforts in searching for bioactive ligands by enumeration and virtual screening of the unknown chemical space of small molecules. Enumeration from first principles shows that almost all small molecules (>99.9%) have never been synthesized and are still available to be prepared and tested. We discuss open access sources of molecules, the classification and representation of chemical space using molecular quantum numbers (MQN), its exhaustive enumeration in form of the chemical universe generated databases (GDB), and examples of using these databases for prospective drug discovery. MQN-searchable GDB, PubChem, and DrugBank are freely accessible at www.gdb.unibe.ch.
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Affiliation(s)
- Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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41
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Du J, Dong H, Zhou HX. Size matters in activation/inhibition of ligand-gated ion channels. Trends Pharmacol Sci 2012; 33:482-93. [PMID: 22789930 DOI: 10.1016/j.tips.2012.06.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 06/07/2012] [Accepted: 06/13/2012] [Indexed: 11/18/2022]
Abstract
Cys loop, glutamate, and P2X receptors are ligand-gated ion channels (LGICs) with 5, 4, and 3 protomers, respectively. There is now growing atomic level understanding of their gating mechanisms. Although each family is unique in the architecture of the ligand-binding pocket, the pathway for motions to propagate from ligand-binding domain to transmembrane domain, and the gating motions of the transmembrane domain, there are common features among the LGICs, which are the focus of the present review. In particular, agonists and competitive antagonists apparently induce opposite motions of the binding pocket. A simple way to control the motional direction is ligand size. Agonists, usually small, induce closure of the binding pocket, leading to opening of the channel pore, whereas antagonists, usually large, induce opening of the binding pocket, thereby stabilizing the closed pore. A cross-family comparison of the gating mechanisms of the LGICs, focusing in particular on the role played by ligand size, provides new insight on channel activation/inhibition and design of pharmacological compounds.
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Affiliation(s)
- Juan Du
- Department of Physics and Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA
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42
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Akdemir A, Edink E, Thompson AJ, Lummis SCR, Kooistra AJ, de Graaf C, de Esch IJP. Identification of novel α7 nicotinic receptor ligands by in silico screening against the crystal structure of a chimeric α7 receptor ligand binding domain. Bioorg Med Chem 2012; 20:5992-6002. [PMID: 22959526 PMCID: PMC3460237 DOI: 10.1016/j.bmc.2012.06.054] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2012] [Revised: 06/28/2012] [Accepted: 06/29/2012] [Indexed: 11/24/2022]
Abstract
A hierarchical in silico screening procedure using the crystal structure of an agonist bound chimeric α7/Ls-AChBP protein was successfully applied to both proprietary and commercial databases containing drug-like molecules. An overall hit rate of 26% (pKi ⩾5.0) was obtained, with an even better hit rate of 35% for the commercial compound collection. Structurally novel and diverse ligands were identified. Binding studies with [3H]epibatidine on chimeric α7/5-HT3 receptors yielded submicromolar inhibition constants for identified hits. Compared to a previous screening procedure that utilized the wild type Ls-AChBP crystal structure, the current study shows that the recently obtained α7/Ls-AChBP chimeric protein crystal structure is a better template for the identification of novel α7 receptor ligands.
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Affiliation(s)
- Atilla Akdemir
- Division of Pharmacology, Faculty of Pharmacy, Bezmialem Vakif University, Istanbul, Turkey
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Rojsanga P, Boonyarat C, Utsintong M, Nemecz Á, Yamauchi JG, Talley TT, Olson AJ, Matsumoto K, Vajragupta O. The effect of crebanine on memory and cognition impairment via the alpha-7 nicotinic acetylcholine receptor. Life Sci 2012; 91:107-14. [PMID: 22749860 DOI: 10.1016/j.lfs.2012.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2012] [Revised: 06/08/2012] [Accepted: 06/15/2012] [Indexed: 12/11/2022]
Abstract
AIMS The aims of the present study were to investigate the effect of crebanine on memory and cognition impairment in mice and to elucidate the underlying molecular mechanisms. MAIN METHODS The memory-enhancing effects of crebanine were assessed with a water maze test using scopolamine-induced amnesic mice. The molecular mechanism was explored in silico by docking crebanine against acetylcholine binding proteins (AChBPs) and in vitro with a radioligand competition assay using (±)-[(3)H]-epibatidine. The pharmacological behavior was assessed by observing changes to the functional activity of α7-nAChRs expressed in Xenopus oocytes and by fluorescent assays on recombinant ligand gated ion channel (LGIC) receptors expressed in mammalian cells. KEY FINDINGS The administration of crebanine significantly improved the cognitive deficits induced by scopolamine, as measured by the water maze test. The docking results demonstrated that crebanine bound to the active binding site of the AChBP template with a good docking energy. Crebanine significantly inhibited the binding of (±)-[(3)H]-epibatidine to AChBPs with K(i) values of 179 nM and 538 nM for Ls and Ac, respectively. Further functional assays performed using two separate protocols indicated that crebanine is an antagonist of the α7-nAChR with an IC(50) of 19.1μM. SIGNIFICANCE The observed actions of crebanine against amnesia and its effect on α7-nAChRs will be beneficial for target-based drug design; crebanine or its scaffold can be used as the starting point to develop a drug for Alzheimer's disease. The cognition-enhancing effects of crebanine and the underlying mechanism based on α7-nAChRs are consistent with its traditional use. These findings demonstrate the potential utility of crebanine in the development of neurodegenerative therapy.
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Affiliation(s)
- Piyanuch Rojsanga
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
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44
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Hritcu L, Stefan M, Brandsch R, Mihasan M. 6-hydroxy-l-nicotine from Arthrobacter nicotinovorans sustain spatial memory formation by decreasing brain oxidative stress in rats. J Physiol Biochem 2012; 69:25-34. [DOI: 10.1007/s13105-012-0184-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 06/05/2012] [Indexed: 12/31/2022]
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Stober ST, Abrams CF. Enhanced meta-analysis of acetylcholine binding protein structures reveals conformational signatures of agonism in nicotinic receptors. Protein Sci 2012; 21:307-17. [PMID: 22170867 DOI: 10.1002/pro.2016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The soluble acetylcholine binding protein (AChBP) is the default structural proxy for pentameric ligand-gated ion channels (LGICs). Unfortunately, it is difficult to recognize conformational signatures of LGIC agonism and antagonism within the large set of AChBP crystal structures in both apo and ligand-bound states, primarily because AChBP conformations in this set are nearly superimposable (root mean square deviation < 1.5 Å). We have undertaken a systematic, alignment-free approach to elucidate conformational differences displayed by AChBP that cleanly differentiate apo/antagonist-bound from agonist-bound states. Our approach uses statistical inference based on both crystallographic states and conformations sampled during long molecular dynamics simulations to select important inter-C(α) distances and map their collective values onto functional states. We observe that binding of (nAChR) agonists to AChBP elicits clockwise rotation of the inner β-sheet with respect to the outer β-sheet, causing tilting of the cys-loop away from the five-fold axis, in a manner quite similar to that speculated for α-subunits of the heteromeric nAChR structure (Unwin, J Mol Biol 2005;346:967), making this motion potentially important in transmission of the gating signal to the transmembrane domain of a LGIC. The method is also successful at discriminating partial from full agonists and supports the hypothesis that a particularly controversial ligand, lobeline, is in fact an LGIC antagonist.
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Affiliation(s)
- Spencer T Stober
- Department of Chemical and Biological Engineering, Drexel University, Philadelphia, Pennsylvania 19104, USA
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46
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Bréthous L, Garcia-Delgado N, Schwartz J, Bertrand S, Bertrand D, Reymond JL. Synthesis and Nicotinic Receptor Activity of Chemical Space Analogues of N-(3R)-1-Azabicyclo[2.2.2]oct-3-yl-4-chlorobenzamide (PNU-282,987) and 1,4-Diazabicyclo[3.2.2]nonane-4-carboxylic Acid 4-Bromophenyl Ester (SSR180711). J Med Chem 2012; 55:4605-18. [DOI: 10.1021/jm300030r] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lise Bréthous
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Noemi Garcia-Delgado
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Julian Schwartz
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
| | - Sonia Bertrand
- HiQScreen, 15 rue de l'Athénée, 1206 Geneva, Switzerland
| | | | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Berne, Freiestrasse 3, 3012 Berne, Switzerland
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47
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Kombo DC, Mazurov AA, Chewning J, Hammond PS, Tallapragada K, Hauser TA, Speake J, Yohannes D, Caldwell WS. Discovery of novel α7 nicotinic acetylcholine receptor ligands via pharmacophoric and docking studies of benzylidene anabaseine analogs. Bioorg Med Chem Lett 2012; 22:1179-86. [DOI: 10.1016/j.bmcl.2011.11.090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Revised: 11/18/2011] [Accepted: 11/21/2011] [Indexed: 11/25/2022]
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Rohde LAH, Ahring PK, Jensen ML, Nielsen EØ, Peters D, Helgstrand C, Krintel C, Harpsøe K, Gajhede M, Kastrup JS, Balle T. Intersubunit bridge formation governs agonist efficacy at nicotinic acetylcholine α4β2 receptors: unique role of halogen bonding revealed. J Biol Chem 2011; 287:4248-59. [PMID: 22170047 DOI: 10.1074/jbc.m111.292243] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The α4β2 subtype of the nicotinic acetylcholine receptor has been pursued as a drug target for treatment of psychiatric and neurodegenerative disorders and smoking cessation aids for decades. Still, a thorough understanding of structure-function relationships of α4β2 agonists is lacking. Using binding experiments, electrophysiology and x-ray crystallography we have investigated a consecutive series of five prototypical pyridine-containing agonists derived from 1-(pyridin-3-yl)-1,4-diazepane. A correlation between binding affinities at α4β2 and the acetylcholine-binding protein from Lymnaea stagnalis (Ls-AChBP) confirms Ls-AChBP as structural surrogate for α4β2 receptors. Crystal structures of five agonists with efficacies at α4β2 from 21-76% were determined in complex with Ls-AChBP. No variation in closure of loop C is observed despite large efficacy variations. Instead, the efficacy of a compound appears tightly coupled to its ability to form a strong intersubunit bridge linking the primary and complementary binding interfaces. For the tested agonists, a specific halogen bond was observed to play a large role in establishing such strong intersubunit anchoring.
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Affiliation(s)
- Line Aagot Hede Rohde
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Copenhagen 2100, Denmark
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Edink E, Akdemir A, Jansen C, van Elk R, Zuiderveld O, de Kanter FJJ, van Muijlwijk-Koezen JE, Smit AB, Leurs R, de Esch IJP. Structure-based design, synthesis and structure-activity relationships of dibenzosuberyl- and benzoate-substituted tropines as ligands for acetylcholine-binding protein. Bioorg Med Chem Lett 2011; 22:1448-54. [PMID: 22243960 DOI: 10.1016/j.bmcl.2011.12.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Revised: 11/30/2011] [Accepted: 12/01/2011] [Indexed: 12/26/2022]
Abstract
Using structure-based optimization procedures on in silico hits, dibenzosuberyl- and benzoate substituted tropines were designed as ligands for acetylcholine-binding protein (AChBP). This protein is a homolog to the ligand binding domain of the nicotinic acetylcholine receptor (nAChR). Distinct SAR is observed between two AChBP species variants and between the α7 and α4β2 nAChR subtype. The AChBP species differences are indicative of a difference in accessibility of a ligand-inducible subpocket. Hereby, we have identified a region that can be scrutinized to achieve selectivity for nicotinic receptor subtypes.
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Affiliation(s)
- Ewald Edink
- Leiden/Amsterdam Center of Drug Research, Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems, VU University Amsterdam, The Netherlands
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Reymond JL, van Deursen R, Bertrand D. What we have learned from crystal structures of proteins to receptor function. Biochem Pharmacol 2011; 82:1521-7. [DOI: 10.1016/j.bcp.2011.07.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/04/2011] [Accepted: 07/06/2011] [Indexed: 12/13/2022]
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