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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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2
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Reddy KKA, Jayashree M, Govindu PCV, Gowd KH. Ligand-induced transition in conformations of vicinal cysteine disulfides in proteins. Proteins 2020; 89:599-613. [PMID: 33378101 DOI: 10.1002/prot.26039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 11/04/2020] [Accepted: 12/12/2020] [Indexed: 01/02/2023]
Abstract
Vicinal cysteine disulfides are thought to be associated with specific conformations of cysteine disulfides due to the restricted rotation of single bonds in an eight-membered cyclic disulfide loop. Conformations of vicinal cysteine disulfides are analyzed using χ1 , χ2 , χ3 , χ2 ', χ1 ' torsion angles in the crystal structures of proteins retrieved from Protein Data Bank (PDB). 85% of vicinal disulfides have (+, -)LHStaple conformation with trans configuration of the peptide bond and 9% have (-, -)RHStaple conformation with cis configured peptide bond. Conformational analysis of dipeptide Cys-Cys vicinal disulfide by density functional theory (DFT) further supported (+, -)LHStaple, (-, -)RHStaple, and (+, +)RHStaple as the preferred conformations of vicinal disulfides. Interestingly, the rare conformations of vicinal disulfides are observed in the ligand-bound forms of proteins and have higher disulfide strain energy. Conformations of vicinal disulfides in palmitoyl protein thioesterase 1, AChBP, and α7 nicotinic receptor are changed from preferred (+, -)LHStaple to rare (+, -)AntiLHHook/(+, -)AntiRHHook/(+, +)RHStaple conformation due to binding of ligands. Surprisingly, ligands are proximal to the vicinal disulfides in protein complexes that exhibited rare conformations of vicinal disulfides. The report has identified (+, -) LHStaple/(-, -) RHStaple as the hallmark conformations of vicinal disulfides and unraveled ligand-induced transition in conformations of vicinal cysteine disulfides in proteins.
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Affiliation(s)
- K Kasi Amarnath Reddy
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, India
| | - Muddagoni Jayashree
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, India
| | - Panchada Ch V Govindu
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, India
| | - Konkallu Hanumae Gowd
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, India
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3
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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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4
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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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5
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Otvos RA, Still KBM, Somsen GW, Smit AB, Kool J. Drug Discovery on Natural Products: From Ion Channels to nAChRs, from Nature to Libraries, from Analytics to Assays. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2019; 24:362-385. [PMID: 30682257 PMCID: PMC6484542 DOI: 10.1177/2472555218822098] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 11/16/2018] [Accepted: 12/07/2018] [Indexed: 12/21/2022]
Abstract
Natural extracts are complex mixtures that may be rich in useful bioactive compounds and therefore are attractive sources for new leads in drug discovery. This review describes drug discovery from natural products and in explaining this process puts the focus on ion-channel drug discovery. In particular, the identification of bioactives from natural products targeting nicotinic acetylcholine receptors (nAChRs) and serotonin type 3 receptors (5-HT3Rs) is discussed. The review is divided into three parts: "Targets," "Sources," and "Approaches." The "Targets" part will discuss the importance of ion-channel drug targets in general, and the α7-nAChR and 5-HT3Rs in particular. The "Sources" part will discuss the relevance for drug discovery of finding bioactive compounds from various natural sources such as venoms and plant extracts. The "Approaches" part will give an overview of classical and new analytical approaches that are used for the identification of new bioactive compounds with the focus on targeting ion channels. In addition, a selected overview is given of traditional venom-based drug discovery approaches and of diverse hyphenated analytical systems used for screening complex bioactive mixtures including venoms.
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Affiliation(s)
- Reka A. Otvos
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kristina B. M. Still
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Govert W. Somsen
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Jeroen Kool
- The Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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6
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Jones AK. Genomics, cys-loop ligand-gated ion channels and new targets for the control of insect pests and vectors. CURRENT OPINION IN INSECT SCIENCE 2018; 30:1-7. [PMID: 30553480 DOI: 10.1016/j.cois.2018.07.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 07/29/2018] [Accepted: 07/29/2018] [Indexed: 05/27/2023]
Affiliation(s)
- Andrew K Jones
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford OX3 0BP, UK.
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7
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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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8
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Kanin MR, Pontrello JK. Introducing chemical biology applications to introductory organic chemistry students using series of weekly assignments. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 44:168-178. [PMID: 26560414 DOI: 10.1002/bmb.20930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/12/2015] [Accepted: 10/04/2015] [Indexed: 06/05/2023]
Abstract
Calls to bring interdisciplinary content and examples into introductory science courses have increased, yet strategies that involve course restructuring often suffer from the need for a significant faculty commitment to motivate change. Minimizing the need for dramatic course reorganization, the structure, reactivity, and chemical biology applications of classes of biological monomers and polymers have been integrated into introductory organic chemistry courses through three series of semester-long weekly assignments that explored (a) Carbohydrates and Oligosaccharides, (b) Amino Acids, Peptides, and Proteins, and (c) Nucleosides, Nucleotides, and Nucleic Acids. Comparisons of unannounced pre- and post tests revealed improved understanding of a reaction introduced in the assignments, and course examinations evaluated cumulative assignment topics. Course surveys revealed that demonstrating biologically relevant applications consistently throughout the semesters enhanced student interest in the connection between basic organic chemistry content and its application to new and unfamiliar bio-related examples. Covering basic material related to these classes of molecules outside of the classroom opened lecture time to allow the instructor to further build on information developed through the weekly assignments, teaching advanced topics and applications typically not covered in an introductory organic chemistry lecture course. Assignments were implemented as homework, either with or without accompanying discussion, in both laboratory and lecture organic courses within the context of the existing course structures.
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Affiliation(s)
- Maralee R Kanin
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, 02454
| | - Jason K Pontrello
- Department of Chemistry, Brandeis University, Waltham, Massachusetts, 02454
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9
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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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10
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Otvos RA, Mladic M, Arias-Alpizar G, Niessen WMA, Somsen GW, Smit AB, Kool J. At-Line Cellular Screening Methodology for Bioactives in Mixtures Targeting the α7-Nicotinic Acetylcholine Receptor. ACTA ACUST UNITED AC 2016; 21:459-67. [DOI: 10.1177/1087057115625307] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 12/11/2015] [Indexed: 01/03/2023]
Abstract
The α7-nicotinic acetylcholine receptor (α7-nAChR) is a ligand-gated ion channel expressed in different regions of the central nervous system (CNS). The α7-nAChR has been associated with Alzheimer’s disease, epilepsy, and schizophrenia, and therefore is extensively studied as a drug target for the treatment of these diseases. Important sources for new compounds in drug discovery are natural extracts. Since natural extracts are complex mixtures, identification of the bioactives demands the use of analytical techniques to separate a bioactive from inactive compounds. This study describes screening methodology for identifying bioactive compounds in mixtures acting on the α7-nAChR. The methodology developed combines liquid chromatography (LC) coupled via a split with both an at-line calcium (Ca2+)-flux assay and high-resolution mass spectrometry (MS). This allows evaluation of α7-nAChR responses after LC separation, while parallel MS enables compound identification. The methodology was optimized for analysis of agonists and positive allosteric modulators, and was successfully applied to screening of the hallucinogen mushroom Psilocybe Mckennaii. The crude mushroom extract was analyzed using both reversed-phase and hydrophilic interaction liquid chromatography. Matching retention times and peak shapes of bioactives found with data from the parallel MS measurements allowed rapid pinpointing of accurate masses corresponding to the bioactives.
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Affiliation(s)
- Reka A. Otvos
- AIMMS Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Marija Mladic
- AIMMS Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Gabriela Arias-Alpizar
- AIMMS Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Wilfried M. A. Niessen
- AIMMS Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- hyphen MassSpec, Warmond, the Netherlands
| | - Govert W. Somsen
- AIMMS Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Jeroen Kool
- AIMMS Division of BioAnalytical Chemistry, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
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11
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King MD, Phillips P, Turner MW, Katz M, Lew S, Bradburn S, Andersen T, Mcdougal OM. Computational exploration of a protein receptor binding space with student proposed peptide ligands. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 44:63-67. [PMID: 26537635 PMCID: PMC5367464 DOI: 10.1002/bmb.20925] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 09/02/2015] [Accepted: 09/16/2015] [Indexed: 06/05/2023]
Abstract
Computational molecular docking is a fast and effective in silico method for the analysis of binding between a protein receptor model and a ligand. The visualization and manipulation of protein to ligand binding in three-dimensional space represents a powerful tool in the biochemistry curriculum to enhance student learning. The DockoMatic tutorial described herein provides a framework by which instructors can guide students through a drug screening exercise. Using receptor models derived from readily available protein crystal structures, docking programs have the ability to predict ligand binding properties, such as preferential binding orientations and binding affinities. The use of computational studies can significantly enhance complimentary wet chemical experimentation by providing insight into the important molecular interactions within the system of interest, as well as guide the design of new candidate ligands based on observed binding motifs and energetics. In this laboratory tutorial, the graphical user interface, DockoMatic, facilitates docking job submissions to the docking engine, AutoDock 4.2. The purpose of this exercise is to successfully dock a 17-amino acid peptide, α-conotoxin TxIA, to the acetylcholine binding protein from Aplysia californica-AChBP to determine the most stable binding configuration. Each student will then propose two specific amino acid substitutions of α-conotoxin TxIA to enhance peptide binding affinity, create the mutant in DockoMatic, and perform docking calculations to compare their results with the class. Students will also compare intermolecular forces, binding energy, and geometric orientation of their prepared analog to their initial α-conotoxin TxIA docking results.
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Affiliation(s)
- Matthew D. King
- Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725
| | - Paul Phillips
- Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725
| | - Matthew W. Turner
- Biomolecular Sciences PhD Program, Boise State University, Boise, Idaho 83725
| | - Michael Katz
- Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725
| | - Sarah Lew
- Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725
| | - Sarah Bradburn
- Department of Computer Science and Engineering, Boise State University, Boise, Idaho 83725
| | - Tim Andersen
- Department of Computer Science and Engineering, Boise State University, Boise, Idaho 83725
| | - Owen M. Mcdougal
- Department of Chemistry and Biochemistry, Boise State University, Boise, Idaho 83725
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12
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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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13
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Jaikhan P, Boonyarat C, Arunrungvichian K, Taylor P, Vajragupta O. Design and Synthesis of Nicotinic Acetylcholine Receptor Antagonists and their Effect on Cognitive Impairment. Chem Biol Drug Des 2015; 87:39-56. [DOI: 10.1111/cbdd.12627] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 07/03/2015] [Accepted: 07/15/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Pattaporn Jaikhan
- Center of Excellence for Innovation in Drug Design and Discovery; Faculty of Pharmacy; Mahidol University; 447 Sri-Ayudya Road Bangkok 10400 Thailand
| | - Chantana Boonyarat
- Department of Pharmaceutical Chemistry; Faculty of Pharmaceutical Science; KhonKaen University; KhonKaen 4000 Thailand
| | - Kuntarat Arunrungvichian
- Center of Excellence for Innovation in Drug Design and Discovery; Faculty of Pharmacy; Mahidol University; 447 Sri-Ayudya Road Bangkok 10400 Thailand
- Department of Pharmacology; Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California; San Diego 9500 Gilman Drive La Jolla CA 92093-0657 USA
| | - Palmer Taylor
- Department of Pharmacology; Skaggs School of Pharmacy and Pharmaceutical Sciences; University of California; San Diego 9500 Gilman Drive La Jolla CA 92093-0657 USA
| | - Opa Vajragupta
- Center of Excellence for Innovation in Drug Design and Discovery; Faculty of Pharmacy; Mahidol University; 447 Sri-Ayudya Road Bangkok 10400 Thailand
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14
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Ferreira LG, Dos Santos RN, Oliva G, Andricopulo AD. Molecular docking and structure-based drug design strategies. Molecules 2015; 20:13384-421. [PMID: 26205061 PMCID: PMC6332083 DOI: 10.3390/molecules200713384] [Citation(s) in RCA: 991] [Impact Index Per Article: 110.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/14/2015] [Accepted: 07/20/2015] [Indexed: 02/07/2023] Open
Abstract
Pharmaceutical research has successfully incorporated a wealth of molecular modeling methods, within a variety of drug discovery programs, to study complex biological and chemical systems. The integration of computational and experimental strategies has been of great value in the identification and development of novel promising compounds. Broadly used in modern drug design, molecular docking methods explore the ligand conformations adopted within the binding sites of macromolecular targets. This approach also estimates the ligand-receptor binding free energy by evaluating critical phenomena involved in the intermolecular recognition process. Today, as a variety of docking algorithms are available, an understanding of the advantages and limitations of each method is of fundamental importance in the development of effective strategies and the generation of relevant results. The purpose of this review is to examine current molecular docking strategies used in drug discovery and medicinal chemistry, exploring the advances in the field and the role played by the integration of structure- and ligand-based methods.
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Affiliation(s)
- Leonardo G Ferreira
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Av. João Dagnone 1100, São Carlos-SP 13563-120, Brazil.
| | - Ricardo N Dos Santos
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Av. João Dagnone 1100, São Carlos-SP 13563-120, Brazil.
| | - Glaucius Oliva
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Av. João Dagnone 1100, São Carlos-SP 13563-120, Brazil.
| | - Adriano D Andricopulo
- Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo, Av. João Dagnone 1100, São Carlos-SP 13563-120, Brazil.
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15
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Ihara M, Sattelle DB, Matsuda K. Probing new components (loop G and the α-α interface) of neonicotinoid binding sites on nicotinic acetylcholine receptors. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2015; 121:47-52. [PMID: 26047111 DOI: 10.1016/j.pestbp.2015.02.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 02/25/2015] [Accepted: 02/25/2015] [Indexed: 06/04/2023]
Abstract
Neonicotinoid insecticides interact with the orthosteric site on the extracellular ligand binding domain (LBD) of nicotinic acetylcholine receptors (nAChRs), typically activating the cation permeable ion channels. In nAChRs consisting of two α and three non-α subunits, LBDs contain six loops (loops A, B and C on the α subunit and loops D, E and F on the non-α subunit) which make up the orthosteric binding site at the α/non-α subunit interfaces. Recently, an additional site (loop G) on the β1 strand has been identified. Also, when the α/non-α subunit ratio is 3/2, another binding site is generated at the interface of two adjacent α subunits. Roles for loop G and the α-α interface in the interactions with neonicotinoids are discussed with reference to recent structural and physiological data.
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Affiliation(s)
- Makoto Ihara
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan.
| | - David B Sattelle
- The Wolfson Institute for Biomedical Research, Department of Medicine, University College London, Cruciform Building, Gower Street, London, WC1E 6BT, UK
| | - Kazuhiko Matsuda
- Department of Applied Biological Chemistry, Faculty of Agriculture, Kinki University, 3327-204 Nakamachi, Nara 631-8505, Japan.
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16
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Harmicine, a Tetracyclic Tetrahydro-β-Carboline: From the First Synthetic Precedent to Isolation from Natural Sources to Target-Oriented Synthesis (Review)*. Chem Heterocycl Compd (N Y) 2014. [DOI: 10.1007/s10593-014-1602-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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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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18
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Absalom NL, Quek G, Lewis TM, Qudah T, von Arenstorff I, Ambrus JI, Harpsøe K, Karim N, Balle T, McLeod MD, Chebib M. Covalent trapping of methyllycaconitine at the α4-α4 interface of the α4β2 nicotinic acetylcholine receptor: antagonist binding site and mode of receptor inhibition revealed. J Biol Chem 2013; 288:26521-32. [PMID: 23893416 DOI: 10.1074/jbc.m113.475053] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The α4β2 nicotinic acetylcholine receptors (nAChRs) are widely expressed in the brain and are implicated in a variety of physiological processes. There are two stoichiometries of the α4β2 nAChR, (α4)2(β2)3 and (α4)3(β2)2, with different sensitivities to acetylcholine (ACh), but their pharmacological profiles are not fully understood. Methyllycaconitine (MLA) is known to be an antagonist of nAChRs. Using the two-electrode voltage clamp technique and α4β2 nAChRs in the Xenopus oocyte expression system, we demonstrate that inhibition by MLA occurs via two different mechanisms; that is, a direct competitive antagonism and an apparently insurmountable mechanism that only occurs after preincubation with MLA. We hypothesized an additional MLA binding site in the α4-α4 interface that is unique to this stoichiometry. To prove this, we covalently trapped a cysteine-reactive MLA analog at an α4β2 receptor containing an α4(D204C) mutation predicted by homology modeling to be within reach of the reactive probe. We demonstrate that covalent trapping results in irreversible reduction of ACh-elicited currents in the (α4)3(β2)2 stoichiometry, indicating that MLA binds to the α4-α4 interface of the (α4)3(β2)2 and providing direct evidence of ligand binding to the α4-α4 interface. Consistent with other studies, we propose that the α4-α4 interface is a structural target for potential therapeutics that modulate (α4)3(β2)2 nAChRs.
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Affiliation(s)
- Nathan L Absalom
- From the Faculty of Pharmacy, University of Sydney, Sydney, NSW 2006, Australia
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19
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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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20
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Lv Z, Tek A, Da Silva F, Empereur-mot C, Chavent M, Baaden M. Game on, science - how video game technology may help biologists tackle visualization challenges. PLoS One 2013; 8:e57990. [PMID: 23483961 PMCID: PMC3590297 DOI: 10.1371/journal.pone.0057990] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 01/31/2013] [Indexed: 11/21/2022] Open
Abstract
The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists? This approach points to an extension of open computer programs, not only providing access to the source code, but also delivering an easily modifiable and extensible scientific research tool. In this work, we will explore these questions using the Unity3D game engine to develop and prototype a biological network and molecular visualization application for subsequent use in research or education. We have compared several routines to represent spheres and links between them, using either built-in Unity3D features or our own implementation. These developments resulted in a stand-alone viewer capable of displaying molecular structures, surfaces, animated electrostatic field lines and biological networks with powerful, artistic and illustrative rendering methods. We consider this work as a proof of principle demonstrating that the functionalities of classical viewers and more advanced novel features could be implemented in substantially less time and with less development effort. Our prototype is easily modifiable and extensible and may serve others as starting point and platform for their developments. A webserver example, standalone versions for MacOS X, Linux and Windows, source code, screen shots, videos and documentation are available at the address: http://unitymol.sourceforge.net/.
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Affiliation(s)
- Zhihan Lv
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot Sorbonne Paris Cité, Paris, France
- Ocean University of China, QingDao, People’s Republic of China
| | - Alex Tek
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot Sorbonne Paris Cité, Paris, France
- Université Pierre et Marie Curie, UPMC-Sorbonne Universités, Paris, France
| | - Franck Da Silva
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot Sorbonne Paris Cité, Paris, France
| | - Charly Empereur-mot
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot Sorbonne Paris Cité, Paris, France
| | | | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot Sorbonne Paris Cité, Paris, France
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21
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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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22
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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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