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Abstract
This chapter details methods to express and modify ATP-gated P2X receptor channels so that they can be controlled using light. Following expression in cells, a photoswitchable tool compound can be used to covalently modify mutant P2X receptors, as previously demonstrated for homomeric P2X2 and P2X3 receptors, and heteromeric P2X2/3 receptors. Engineered P2X receptors can be rapidly and reversibly opened and closed by different wavelengths of light. Light-activated P2X receptors can be mutated further to impart ATP-insensitivity if required. This method offers control of specific P2X receptor channels with high spatiotemporal precision to study their roles in physiology and pathophysiology.
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Affiliation(s)
- Benjamin N Atkinson
- Department of Chemistry, University College London, London, UK
- Wolfson Institute for Biomedical Research, University College London, London, UK
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Vijay Chudasama
- Department of Chemistry, University College London, London, UK
| | - Liam E Browne
- Wolfson Institute for Biomedical Research, University College London, London, UK.
- Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK.
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2
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Scheurer M, Rodenkirch P, Siggel M, Bernardi RC, Schulten K, Tajkhorshid E, Rudack T. PyContact: Rapid, Customizable, and Visual Analysis of Noncovalent Interactions in MD Simulations. Biophys J 2018; 114:577-583. [PMID: 29414703 PMCID: PMC5985026 DOI: 10.1016/j.bpj.2017.12.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/27/2017] [Accepted: 12/04/2017] [Indexed: 12/18/2022] Open
Abstract
Molecular dynamics (MD) simulations have become ubiquitous in all areas of life sciences. The size and model complexity of MD simulations are rapidly growing along with increasing computing power and improved algorithms. This growth has led to the production of a large amount of simulation data that need to be filtered for relevant information to address specific biomedical and biochemical questions. One of the most relevant molecular properties that can be investigated by all-atom MD simulations is the time-dependent evolution of the complex noncovalent interaction networks governing such fundamental aspects as molecular recognition, binding strength, and mechanical and structural stability. Extracting, evaluating, and visualizing noncovalent interactions is a key task in the daily work of structural biologists. We have developed PyContact, an easy-to-use, highly flexible, and intuitive graphical user interface-based application, designed to provide a toolkit to investigate biomolecular interactions in MD trajectories. PyContact is designed to facilitate this task by enabling identification of relevant noncovalent interactions in a comprehensible manner. The implementation of PyContact as a standalone application enables rapid analysis and data visualization without any additional programming requirements, and also preserves full in-program customization and extension capabilities for advanced users. The statistical analysis representation is interactively combined with full mapping of the results on the molecular system through the synergistic connection between PyContact and VMD. We showcase the capabilities and scientific significance of PyContact by analyzing and visualizing in great detail the noncovalent interactions underlying the ion permeation pathway of the human P2X3 receptor. As a second application, we examine the protein-protein interaction network of the mechanically ultrastable cohesin-dockering complex.
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Affiliation(s)
- Maximilian Scheurer
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Biochemistry Center, Heidelberg University, Heidelberg, Germany; Interdisciplinary Center for Scientific Computing, Heidelberg, Germany
| | | | - Marc Siggel
- Biochemistry Center, Heidelberg University, Heidelberg, Germany
| | - Rafael C Bernardi
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Klaus Schulten
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois.
| | - Till Rudack
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Biophysics, Ruhr University Bochum, Bochum, Germany.
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3
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Caseley EA, Muench SP, Fishwick CW, Jiang LH. Structure-based identification and characterisation of structurally novel human P2X7 receptor antagonists. Biochem Pharmacol 2016; 116:130-9. [PMID: 27481062 PMCID: PMC5012888 DOI: 10.1016/j.bcp.2016.07.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 07/28/2016] [Indexed: 12/13/2022]
Abstract
The P2X7 receptor (P2X7R) plays an important role in diverse conditions associated with tissue damage and inflammation, meaning that the human P2X7R (hP2X7R) is an attractive therapeutic target. The crystal structures of the zebrafish P2X4R in the closed and ATP-bound open states provide an unprecedented opportunity for structure-guided identification of new ligands. The present study performed virtual screening of ∼100,000 structurally diverse compounds against the ATP-binding pocket in the hP2X7R. This identified three compounds (C23, C40 and C60) out of 73 top-ranked compounds by testing against hP2X7R-mediated Ca(2+) responses. These compounds were further characterised using Ca(2+) imaging, patch-clamp current recording, YO-PRO-1 uptake and propidium iodide cell death assays. All three compounds inhibited BzATP-induced Ca(2+) responses concentration-dependently with IC50s of 5.1±0.3μM, 4.8±0.8μM and 3.2±0.2μM, respectively. C23 and C40 inhibited BzATP-induced currents in a reversible and concentration-dependent manner, with IC50s of 0.35±0.3μM and 1.2±0.1μM, respectively, but surprisingly C60 did not affect BzATP-induced currents up to 100μM. They suppressed BzATP-induced YO-PRO-1 uptake with IC50s of 1.8±0.9μM, 1.0±0.1μM and 0.8±0.2μM, respectively. Furthermore, these three compounds strongly protected against ATP-induced cell death. Among them, C40 and C60 exhibited strong specificity towards the hP2X7R over the hP2X4R and rP2X3R. In conclusion, our study reports the identification of three novel hP2X7R antagonists with micromolar potency for the first time using a structure-based approach, including the first P2X7R antagonist with preferential inhibition of large pore formation.
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MESH Headings
- Adenosine Triphosphate/analogs & derivatives
- Adenosine Triphosphate/chemistry
- Adenosine Triphosphate/metabolism
- Adenosine Triphosphate/pharmacology
- Amides/chemistry
- Amides/metabolism
- Amides/pharmacology
- Animals
- Anti-Inflammatory Agents, Non-Steroidal/chemistry
- Anti-Inflammatory Agents, Non-Steroidal/metabolism
- Anti-Inflammatory Agents, Non-Steroidal/pharmacology
- Binding Sites
- Calcium Signaling/drug effects
- HEK293 Cells
- Hepatocytes/cytology
- Hepatocytes/drug effects
- Hepatocytes/metabolism
- Humans
- Image Processing, Computer-Assisted
- Indoles/chemistry
- Indoles/metabolism
- Indoles/pharmacology
- Ligands
- Microscopy, Fluorescence
- Models, Molecular
- Patch-Clamp Techniques
- Purinergic P2X Receptor Antagonists/chemistry
- Purinergic P2X Receptor Antagonists/metabolism
- Purinergic P2X Receptor Antagonists/pharmacology
- Rats
- Receptors, Purinergic P2X3/chemistry
- Receptors, Purinergic P2X3/genetics
- Receptors, Purinergic P2X3/metabolism
- Receptors, Purinergic P2X4/chemistry
- Receptors, Purinergic P2X4/genetics
- Receptors, Purinergic P2X4/metabolism
- Receptors, Purinergic P2X7/chemistry
- Receptors, Purinergic P2X7/genetics
- Receptors, Purinergic P2X7/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/metabolism
- Single-Cell Analysis
- Small Molecule Libraries
- Structure-Activity Relationship
- Thiophenes/chemistry
- Thiophenes/metabolism
- Thiophenes/pharmacology
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Affiliation(s)
- Emily A Caseley
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, UK
| | - Stephen P Muench
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, UK
| | | | - Lin-Hua Jiang
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, UK.
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Szántó G, Makó A, Bata I, Farkas B, Kolok S, Vastag M, Cselenyák A. New P2X3 receptor antagonists. Part 1: Discovery and optimization of tricyclic compounds. Bioorg Med Chem Lett 2016; 26:3896-904. [PMID: 27423478 DOI: 10.1016/j.bmcl.2016.07.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/01/2016] [Accepted: 07/03/2016] [Indexed: 01/12/2023]
Abstract
Purinergic P2X3 receptors are trimeric ligand-gated ion channels whose antagonism is an appealing yet challenging and not fully validated drug development idea. With the aim of identification of an orally active, potent human P2X3 receptor antagonist compound that can penetrate the central nervous system, the compound collection of Gedeon Richter was screened. A hit series of tricyclic compounds was subjected to a rapid, two-step optimization process focusing on increasing potency, improving metabolic stability and CNS penetrability. Attempts resulted in compound 65, a potential tool compound for testing P2X3 inhibitory effects in vivo.
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Affiliation(s)
- Gábor Szántó
- Gedeon Richter Plc, Budapest 10, PO Box 27, H-1475, Hungary
| | - Attila Makó
- Gedeon Richter Plc, Budapest 10, PO Box 27, H-1475, Hungary
| | - Imre Bata
- Gedeon Richter Plc, Budapest 10, PO Box 27, H-1475, Hungary
| | - Bence Farkas
- Gedeon Richter Plc, Budapest 10, PO Box 27, H-1475, Hungary
| | - Sándor Kolok
- Gedeon Richter Plc, Budapest 10, PO Box 27, H-1475, Hungary
| | - Mónika Vastag
- Gedeon Richter Plc, Budapest 10, PO Box 27, H-1475, Hungary
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Stephan G, Kowalski-Jahn M, Zens C, Schmalzing G, Illes P, Hausmann R. Inter-subunit disulfide locking of the human P2X3 receptor elucidates ectodomain movements associated with channel gating. Purinergic Signal 2016; 12:221-33. [PMID: 26825305 DOI: 10.1007/s11302-016-9496-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 01/19/2016] [Indexed: 11/27/2022] Open
Abstract
P2X3 receptors (P2X3R) are trimeric ATP-gated cation channels involved in sensory neurotransmission and inflammatory pain. We used homology modeling and molecular dynamic simulations of the hP2X3R to identify inter-subunit interactions of residues that are instrumental to elucidate conformational changes associated with gating of the hPX3R. We identified an ionic interaction between E112 and R198 of the head domain and dorsal fin domain, respectively, and E57 and T263 of the lower body domains of adjacent subunits and detected a marked rearrangement of these domains during gating of the hP3X3R. Double-mutant cycle analysis of the inter-subunit residue pairs E112/R198 and E57/T263 revealed significant interaction-free energies. Disulfide locking of the hP2X3R E112C/R198C or the E57C/T263C double cysteine mutants markedly reduced the ATP-induced current responses. The decreased current amplitude following inter-subunit disulfide cross-linking indicates that disulfide locking of the head and dorsal fin domains or at the level of the lower body domains of the hP2X3R prevents the gating-induced conformational rearrangement of the subunits with respect to each other. The distinct reorganization of the subunit interfaces during gating of the hP2X3R is generally consistent with the gating mechanism of other P2XRs. Charge-reversal mutagenesis and methanethiosulfonate (MTS)-modification of substituted cysteines demonstrated that E112 and R198 interact electrostatically. Both disulfide locking and salt bridge breaking of the E112/R198 interaction reduced the hP2X3R function. We conclude that the inter-subunit salt bridge between E112 and R198 of the head and dorsal fin domains, respectively, serves to control the mobility of these domains during agonist-activation of the hP2X3R.
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Affiliation(s)
- Gabriele Stephan
- Rudolf Boehm Institute of Pharmacology and Toxicology, University of Leipzig, Haertelstrasse 16-18, 04107, Leipzig, Germany
| | - Maria Kowalski-Jahn
- Rudolf Boehm Institute of Pharmacology and Toxicology, University of Leipzig, Haertelstrasse 16-18, 04107, Leipzig, Germany
| | - Christopher Zens
- Rudolf Boehm Institute of Pharmacology and Toxicology, University of Leipzig, Haertelstrasse 16-18, 04107, Leipzig, Germany
| | - Günther Schmalzing
- Department of Molecular Pharmacology, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany
| | - Peter Illes
- Rudolf Boehm Institute of Pharmacology and Toxicology, University of Leipzig, Haertelstrasse 16-18, 04107, Leipzig, Germany.
| | - Ralf Hausmann
- Department of Molecular Pharmacology, RWTH Aachen University, Wendlingweg 2, 52074, Aachen, Germany.
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Zhang HH, Hu J, Zhou YL, Qin X, Song ZY, Yang PP, Hu S, Jiang X, Xu GY. Promoted Interaction of Nuclear Factor-κB With Demethylated Purinergic P2X3 Receptor Gene Contributes to Neuropathic Pain in Rats With Diabetes. Diabetes 2015; 64:4272-84. [PMID: 26130762 DOI: 10.2337/db15-0138] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 06/24/2015] [Indexed: 11/13/2022]
Abstract
Painful diabetic neuropathy is a common complication of diabetes produced by mechanisms that as yet are incompletely defined. The aim of this study was to investigate the roles of nuclear factor-κB (NF-κB) in the regulation of purinergic receptor P2X ligand-gated ion channel 3 (P2X3R) plasticity in dorsal root ganglion (DRG) neurons of rats with painful diabetes. Here, we showed that hindpaw pain hypersensitivity in streptozocin-induced diabetic rats was attenuated by treatment with purinergic receptor antagonist suramin or A-317491. The expression and function of P2X3Rs was markedly enhanced in hindpaw-innervated DRG neurons in diabetic rats. The CpG (cytosine guanine dinucleotide) island in the p2x3r gene promoter region was significantly demethylated, and the expression of DNA methyltransferase 3b was remarkably downregulated in DRGs in diabetic rats. The binding ability of p65 (an active form of NF-κB) with the p2x3r gene promoter region and p65 expression were enhanced significantly in diabetes. The inhibition of p65 signaling using the NF-κB inhibitor pyrrolidine dithiocarbamate or recombinant lentiviral vectors designated as lentiviral vector-p65 small interfering RNA remarkably suppressed P2X3R activities and attenuated diabetic pain hypersensitivity. Insulin treatment significantly attenuated pain hypersensitivity and suppressed the expression of p65 and P2X3Rs. Our findings suggest that the p2x3r gene promoter DNA demethylation and enhanced interaction with p65 contributes to P2X3R sensitization and diabetic pain hypersensitivity.
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MESH Headings
- Animals
- CpG Islands/drug effects
- DNA (Cytosine-5-)-Methyltransferases/antagonists & inhibitors
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA (Cytosine-5-)-Methyltransferases/metabolism
- DNA Methylation/drug effects
- Diabetes Mellitus, Experimental/complications
- Diabetes Mellitus, Experimental/drug therapy
- Diabetic Neuropathies/enzymology
- Diabetic Neuropathies/metabolism
- Diabetic Neuropathies/prevention & control
- Epigenesis, Genetic/drug effects
- Female
- Ganglia, Spinal/drug effects
- Ganglia, Spinal/enzymology
- Ganglia, Spinal/metabolism
- Gene Expression Regulation/drug effects
- Hindlimb
- Hypoglycemic Agents/therapeutic use
- Insulin/therapeutic use
- Nerve Tissue Proteins/antagonists & inhibitors
- Nerve Tissue Proteins/genetics
- Nerve Tissue Proteins/metabolism
- Neuralgia/complications
- Neuralgia/metabolism
- Neuralgia/prevention & control
- Neurons/drug effects
- Neurons/enzymology
- Neurons/metabolism
- Promoter Regions, Genetic/drug effects
- Purinergic P2X Receptor Antagonists/therapeutic use
- RNA Interference
- Rats, Sprague-Dawley
- Receptors, Purinergic P2X3/chemistry
- Receptors, Purinergic P2X3/genetics
- Receptors, Purinergic P2X3/metabolism
- Transcription Factor RelA/agonists
- Transcription Factor RelA/antagonists & inhibitors
- Transcription Factor RelA/genetics
- Transcription Factor RelA/metabolism
- DNA Methyltransferase 3B
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Affiliation(s)
- Hong-Hong Zhang
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Institute of Neuroscience, The Second Affiliated Hospital, Soochow University, Suzhou, People's Republic of China
| | - Ji Hu
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Institute of Neuroscience, The Second Affiliated Hospital, Soochow University, Suzhou, People's Republic of China
| | - You-Lang Zhou
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Institute of Neuroscience, The Second Affiliated Hospital, Soochow University, Suzhou, People's Republic of China
| | - Xin Qin
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Institute of Neuroscience, The Second Affiliated Hospital, Soochow University, Suzhou, People's Republic of China
| | - Zhen-Yuan Song
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Institute of Neuroscience, The Second Affiliated Hospital, Soochow University, Suzhou, People's Republic of China
| | - Pan-Pan Yang
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Institute of Neuroscience, The Second Affiliated Hospital, Soochow University, Suzhou, People's Republic of China
| | - Shufen Hu
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Institute of Neuroscience, The Second Affiliated Hospital, Soochow University, Suzhou, People's Republic of China
| | - Xinghong Jiang
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Institute of Neuroscience, The Second Affiliated Hospital, Soochow University, Suzhou, People's Republic of China
| | - Guang-Yin Xu
- Jiangsu Key Laboratory of Translational Research and Therapy for Neuro-Psycho-Diseases, Institute of Neuroscience, The Second Affiliated Hospital, Soochow University, Suzhou, People's Republic of China
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