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The Retinoid and Non-Retinoid Ligands of the Rod Visual G Protein-Coupled Receptor. Int J Mol Sci 2019; 20:ijms20246218. [PMID: 31835521 PMCID: PMC6941084 DOI: 10.3390/ijms20246218] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 11/27/2019] [Accepted: 12/06/2019] [Indexed: 02/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs) play a predominant role in the drug discovery effort. These cell surface receptors are activated by a variety of specific ligands that bind to the orthosteric binding pocket located in the extracellular part of the receptor. In addition, the potential binding sites located on the surface of the receptor enable their allosteric modulation with critical consequences for their function and pharmacology. For decades, drug discovery focused on targeting the GPCR orthosteric binding sites. However, finding that GPCRs can be modulated allosterically opened a new venue for developing novel pharmacological modulators with higher specificity. Alternatively, focus on discovering of non-retinoid small molecules beneficial in retinopathies associated with mutations in rhodopsin is currently a fast-growing pharmacological field. In this review, we summarize the accumulated knowledge on retinoid ligands and non-retinoid modulators of the light-sensing GPCR, rhodopsin and their potential in combating the specific vision-related pathologies. Also, recent findings reporting the potential of biologically active compounds derived from natural products as potent rod opsin modulators with beneficial effects against degenerative diseases related to this receptor are highlighted here.
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2
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Mitchell J, Yanamala N, Tan YL, Gardner EE, Tirupula KC, Balem F, Sheves M, Nietlispach D, Klein‐Seetharaman J. Structural and Functional Consequences of the Weak Binding of Chlorin e6 to Bovine Rhodopsin. Photochem Photobiol 2019; 95:787-802. [DOI: 10.1111/php.13074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 12/07/2018] [Indexed: 12/14/2022]
Affiliation(s)
- James Mitchell
- Biomedical Sciences Division Warwick Medical School University of Warwick Coventry UK
| | - Naveena Yanamala
- Department of Structural Biology School of Medicine University of Pittsburgh Pittsburgh PA
| | - Yi Lei Tan
- Department of Biochemistry University of Cambridge Cambridge UK
| | - Eric E. Gardner
- Department of Structural Biology School of Medicine University of Pittsburgh Pittsburgh PA
| | - Kalyan C. Tirupula
- Department of Structural Biology School of Medicine University of Pittsburgh Pittsburgh PA
| | - Fernanda Balem
- Department of Structural Biology School of Medicine University of Pittsburgh Pittsburgh PA
| | - Mordechai Sheves
- Organic Chemistry Department Weizmann Institute of Science Rehovot Israel
| | | | - Judith Klein‐Seetharaman
- Biomedical Sciences Division Warwick Medical School University of Warwick Coventry UK
- Department of Structural Biology School of Medicine University of Pittsburgh Pittsburgh PA
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3
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Lobysheva E, Taylor CM, Marshall GR, Kisselev OG. Tauroursodeoxycholic acid binds to the G-protein site on light activated rhodopsin. Exp Eye Res 2018; 170:51-57. [PMID: 29454859 PMCID: PMC5983371 DOI: 10.1016/j.exer.2018.02.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 02/14/2018] [Accepted: 02/14/2018] [Indexed: 12/18/2022]
Abstract
The heterotrimeric G-protein binding site on G-protein coupled receptors remains relatively unexplored regarding its potential as a new target of therapeutic intervention or as a secondary site of action by the existing drugs. Tauroursodeoxycholic acid bears structural resemblance to several compounds that were previously identified to specifically bind to the light-activated form of the visual receptor rhodopsin and to inhibit its activation of transducin. We show that TUDCA stabilizes the active form of rhodopsin, metarhodopsin II, and does not display the detergent-like effects of common amphiphilic compounds that share the cholesterol scaffold structure, such as deoxycholic acid. Computer docking of TUDCA to the model of light-activated rhodopsin revealed that it interacts using similar mode of binding to the C-terminal domain of transducin alpha subunit. The ring regions of TUDCA made hydrophobic contacts with loop 3 region of rhodopsin, while the tail of TUDCA is exposed to solvent. The results show that TUDCA interacts specifically with rhodopsin, which may contribute to its wide-ranging effects on retina physiology and as a potential therapeutic compound for retina degenerative diseases.
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Affiliation(s)
- E Lobysheva
- Department of Ophthalmology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - C M Taylor
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - G R Marshall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - O G Kisselev
- Department of Ophthalmology, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA.
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4
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Ortiz Zacarías NV, Lenselink EB, IJzerman AP, Handel TM, Heitman LH. Intracellular Receptor Modulation: Novel Approach to Target GPCRs. Trends Pharmacol Sci 2018; 39:547-559. [PMID: 29653834 DOI: 10.1016/j.tips.2018.03.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 03/07/2018] [Accepted: 03/08/2018] [Indexed: 12/23/2022]
Abstract
Recent crystal structures of multiple G protein-coupled receptors (GPCRs) have revealed a highly conserved intracellular pocket that can be used to modulate these receptors from the inside. This novel intracellular site partially overlaps with the G protein and β-arrestin binding site, providing a new manner of pharmacological intervention. Here we provide an update of the architecture and function of the intracellular region of GPCRs, until now portrayed as the signaling domain. We review the available evidence on the presence of intracellular binding sites among chemokine receptors and other class A GPCRs, as well as different strategies to target it, including small molecules, pepducins, and nanobodies. Finally, the potential advantages of intracellular (allosteric) ligands over orthosteric ligands are also discussed.
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Affiliation(s)
- Natalia V Ortiz Zacarías
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Eelke B Lenselink
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Tracy M Handel
- University of California, San Diego, Skaggs School of Pharmacy and Pharmaceutical Sciences, La Jolla, CA 92093, USA
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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5
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Cross JB. Methods for Virtual Screening of GPCR Targets: Approaches and Challenges. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017; 1705:233-264. [PMID: 29188566 DOI: 10.1007/978-1-4939-7465-8_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Virtual screening (VS) has become an integral part of the drug discovery process and is a valuable tool for finding novel chemical starting points for GPCR targets. Ligand-based VS makes use of biochemical data for known, active compounds and has been applied successfully to many diverse GPCRs. Recent progress in GPCR X-ray crystallography has made it possible to incorporate detailed structural information into the VS process. This chapter outlines the latest VS techniques along with examples that highlight successful applications of these methods. Best practices for increasing the likelihood of VS success, as well as ongoing challenges, are also discussed.
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Affiliation(s)
- Jason B Cross
- University of Texas MD Anderson Cancer Center, Houston, TX, 77054, USA.
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6
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Kim S, Han L, Yu B, Hähnke VD, Bolton EE, Bryant SH. PubChem structure-activity relationship (SAR) clusters. J Cheminform 2015; 7:33. [PMID: 26150895 PMCID: PMC4492103 DOI: 10.1186/s13321-015-0070-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/21/2015] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Developing structure-activity relationships (SARs) of molecules is an important approach in facilitating hit exploration in the early stage of drug discovery. Although information on millions of compounds and their bioactivities is freely available to the public, it is very challenging to infer a meaningful and novel SAR from that information. RESULTS Research discussed in the present paper employed a bioactivity-centered clustering approach to group 843,845 non-inactive compounds stored in PubChem according to both structural similarity and bioactivity similarity, with the aim of mining bioactivity data in PubChem for useful SAR information. The compounds were clustered in three bioactivity similarity contexts: (1) non-inactive in a given bioassay, (2) non-inactive against a given protein, and (3) non-inactive against proteins involved in a given pathway. In each context, these small molecules were clustered according to their two-dimensional (2-D) and three-dimensional (3-D) structural similarities. The resulting 18 million clusters, named "PubChem SAR clusters", were delivered in such a way that each cluster contains a group of small molecules similar to each other in both structure and bioactivity. CONCLUSIONS The PubChem SAR clusters, pre-computed using publicly available bioactivity information, make it possible to quickly navigate and narrow down the compounds of interest. Each SAR cluster can be a useful resource in developing a meaningful SAR or enable one to design or expand compound libraries from the cluster. It can also help to predict the potential therapeutic effects and pharmacological actions of less-known compounds from those of well-known compounds (i.e., drugs) in the same cluster.
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Affiliation(s)
- Sunghwan Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Lianyi Han
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Bo Yu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Volker D Hähnke
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Evan E Bolton
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894 USA
| | - Stephen H Bryant
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, 8600 Rockville Pike, Bethesda, MD 20894 USA
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Kooistra AJ, de Graaf C, Timmerman H. The receptor concept in 3D: from hypothesis and metaphor to GPCR-ligand structures. Neurochem Res 2014; 39:1850-61. [PMID: 25103230 DOI: 10.1007/s11064-014-1398-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 07/21/2014] [Accepted: 07/22/2014] [Indexed: 12/17/2022]
Abstract
The first mentioning of the word "receptor" for the structure with which a bioactive compound should react for obtaining its specific influence on a physiological system goes back to the years around 1900. The receptor concept was adapted from the lock and key theory for the enzyme substrate and blockers interactions. Through the years the concept, in the beginning rather being a metaphor, not a model, was refined and became reality in recent years. Not only the structures of receptors were elucidated, also the receptor machineries were unraveled. Following a brief historical review we will describe how the recent breakthroughs in the experimental determination of G protein-coupled receptor (GPCR) crystal structures can be complemented by computational modeling, medicinal chemistry, biochemical, and molecular pharmacological studies to obtain new insights into the molecular determinants of GPCR-ligand binding and activation. We will furthermore discuss how this information can be used for structure-based discovery of novel GPCR ligands that bind specific (allosteric) binding sites with desired effects on GPCR functional activity.
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Affiliation(s)
- Albert J Kooistra
- Division of Medicinal Chemistry, Faculty of Sciences, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS), VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
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Stulov SV, Misharin AY. Synthesis of steroids with nitrogen-containing substituents in ring D (Review). Chem Heterocycl Compd (N Y) 2013. [DOI: 10.1007/s10593-013-1158-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Kooistra AJ, Roumen L, Leurs R, de Esch IJ, de Graaf C. From Heptahelical Bundle to Hits from the Haystack. Methods Enzymol 2013; 522:279-336. [DOI: 10.1016/b978-0-12-407865-9.00015-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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10
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Tang YT, Gao R, Havranek JJ, Groisman EA, Stock AM, Marshall GR. Inhibition of bacterial virulence: drug-like molecules targeting the Salmonella enterica PhoP response regulator. Chem Biol Drug Des 2012; 79:1007-17. [PMID: 22339993 PMCID: PMC3445336 DOI: 10.1111/j.1747-0285.2012.01362.x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Two-component signal transduction (TCST) is the predominant signaling scheme used in bacteria to sense and respond to environmental changes in order to survive and thrive. A typical TCST system consists of a sensor histidine kinase to detect external signals and an effector response regulator to respond to external changes. In the signaling scheme, the histidine kinase phosphorylates and activates the response regulator, which functions as a transcription factor to modulate gene expression. One promising strategy toward antibacterial development is to target TCST regulatory systems, specifically the response regulators to disrupt the expression of genes important for virulence. In Salmonella enterica, the PhoQ/PhoP signal transduction system is used to sense and respond to low magnesium levels and regulates the expression for over 40 genes necessary for growth under these conditions, and more interestingly, genes that are important for virulence. In this study, a hybrid approach coupling computational and experimental methods was applied to identify drug-like compounds to target the PhoP response regulator. A computational approach of structure-based virtual screening combined with a series of biochemical and biophysical assays was used to test the predictability of the computational strategy and to characterize the mode of action of the compounds. Eight compounds from virtual screening inhibit the formation of the PhoP-DNA complex necessary for virulence gene regulation. This investigation served as an initial case study for targeting TCST response regulators to modulate the gene expression of a signal transduction pathway important for bacterial virulence. With the increasing resistance of pathogenic bacteria to current antibiotics, targeting TCST response regulators that control virulence is a viable strategy for the development of antimicrobial therapeutics with novel modes of action.
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Affiliation(s)
- Yat T Tang
- Center for Computational Biology, Department of Biochemistry and Molecular Biophysics, Washington University School of MedicineSt. Louis, MO 63110, USA
| | - Rong Gao
- Howard Hughes Medical Institute, Center for Advanced Biotechnology and Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical SchoolPiscataway, NJ 08854, USA
| | - James J Havranek
- Department of Genetics, Washington University School of MedicineSt. Louis, MO 63110, USA
| | - Eduardo A Groisman
- Howard Hughes Medical Institute, Department of Molecular Microbiology, Washington University School of MedicineSt. Louis, MO 63110, USA
| | - Ann M Stock
- Howard Hughes Medical Institute, Center for Advanced Biotechnology and Medicine, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical SchoolPiscataway, NJ 08854, USA
| | - Garland R Marshall
- Center for Computational Biology, Department of Biochemistry and Molecular Biophysics, Washington University School of MedicineSt. Louis, MO 63110, USA
- *Corresponding author: Garland R. Marshall,
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11
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Yanamala N, Gardner E, Riciutti A, Klein-Seetharaman J. The cytoplasmic rhodopsin-protein interface: potential for drug discovery. Curr Drug Targets 2012; 13:3-14. [PMID: 21777183 PMCID: PMC3275648 DOI: 10.2174/138945012798868461] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2010] [Revised: 02/08/2011] [Accepted: 02/10/2011] [Indexed: 01/20/2023]
Abstract
The mammalian dim-light photoreceptor rhodopsin is a prototypic G protein coupled receptor (GPCR), interacting with the G protein, transducin, rhodopsin kinase, and arrestin. All of these proteins interact with rhodopsin at its cytoplasmic surface. Structural and modeling studies have provided in-depth descriptions of the respective interfaces. Overlap and thus competition for binding surfaces is a major regulatory mechanism for signal processing. Recently, it was found that the same surface is also targeted by small molecules. These ligands can directly interfere with the binding and activation of the proteins of the signal transduction cascade, but they can also allosterically modulate the retinal ligand binding pocket. Because the pocket that is targeted contains residues that are highly conserved across Class A GPCRs, these findings imply that it may be possible to target multiple GPCRs with the same ligand(s). This is desirable for example in complex diseases such as cancer where multiple GPCRs participate in the disease networks.
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Affiliation(s)
- Naveena Yanamala
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Eric Gardner
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Alec Riciutti
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Judith Klein-Seetharaman
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
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12
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Wildman SA, Zheng X, Sept D, Auletta JT, Rosenberry TL, Marshall GR. Drug-like Leads for Steric Discrimination between Substrate and Inhibitors of Human Acetylcholinesterase. Chem Biol Drug Des 2011; 78:495-504. [DOI: 10.1111/j.1747-0285.2011.01157.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Yanamala N, Klein-Seetharaman J. Allosteric Modulation of G Protein Coupled Receptors by Cytoplasmic, Transmembrane and Extracellular Ligands. Pharmaceuticals (Basel) 2010; 3:3324-3342. [PMID: 24009470 PMCID: PMC3760430 DOI: 10.3390/ph3103324] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
G protein coupled receptors (GPCRs) bind diverse classes of ligands, and depending on the receptor, these may bind in their transmembrane or the extracellular domains, demonstrating the principal ability of GPCRs to bind ligand in either domains. Most recently, it was also observed that small molecule ligands can bind in the cytoplasmic domain, and modulate binding and response to extracellular or transmembrane ligands. Thus, all three domains in GPCRs are potential sites for allosteric ligands, and whether a ligand is allosteric or orthosteric depends on the receptor. Here, we will review the evidence supporting the presence of putative binding pockets in all three domains of GPCRs and discuss possible pathways of communication between these pockets.
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Affiliation(s)
| | - Judith Klein-Seetharaman
- To whom correspondence should be addressed; E-Mail: ; Tel.: +1 412 383 7325; Fax: +1 412 648 8998
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14
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Musmuca I, Caroli A, Mai A, Kaushik-Basu N, Arora P, Ragno R. Combining 3-D quantitative structure-activity relationship with ligand based and structure based alignment procedures for in silico screening of new hepatitis C virus NS5B polymerase inhibitors. J Chem Inf Model 2010; 50:662-76. [PMID: 20225870 DOI: 10.1021/ci9004749] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The viral NS5B RNA-dependent RNA-polymerase (RdRp) is one of the best-studied and promising targets for the development of novel therapeutics against hepatitis C virus (HCV). Allosteric inhibition of this enzyme has emerged as a viable strategy toward blocking replication of viral RNA in cell based systems. Herein, we describe how the combination of a complete computational procedure together with biological studies led to the identification of novel molecular scaffolds, hitherto untested toward NS5B polymerase. Structure based 3-D quantitative structure-activity relationship (QSAR) models were generated employing NS5B non-nucleoside inhibitors (NNIs), whose bound conformations were readily available from the protein database (PDB). These were grouped into two training sets of structurally diverse NS5B NNIs, based on their binding to the enzyme thumb (15 NNIs) or palm (10 NNIs) domains. Ligand based (LB) and structure based (SB) alignments were rigorously investigated to assess the reliability on the correct molecular alignment for unknown binding mode modeled compounds. Both Surflex and Autodock programs were able to reproduce with minimal errors the experimental binding conformations of 24 experimental NS5B allosteric inhibitors. Eighty-one (thumb) and 223 (palm) modeled compounds taken from literature were LB and SB aligned and used as external validation sets for the development of 3-D QSAR models. Low error of prediction proved the 3-D QSARs to be useful scoring functions for the in silico screening procedure. Finally, the virtual screening of the NCI Diversity Set led to the selection for enzymatic assays of 20 top-scoring molecules for each final model. Among the 40 selected molecules, preliminary data yielded four derivatives exhibiting IC(50) values ranging between 45 and 75 microM. Binding mode analysis of hit compounds within the NS5B polymerase thumb domain showed that one of them, NSC 123526, exhibited a docked conformation which was in good agreement with the thumb training set most active compound (6).
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Affiliation(s)
- Ira Musmuca
- Dipartimento di Chimica e Tecnologie del Farmaco, Istituto Pasteur-Fondazione Cenci Bolognetti, Sapienza Universita di Roma, P le A Moro 5, 00185 Rome, Italy
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15
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Sgourakis NG, Garcia AE. The membrane complex between transducin and dark-state rhodopsin exhibits large-amplitude interface dynamics on the sub-microsecond timescale: insights from all-atom MD simulations. J Mol Biol 2010; 398:161-73. [PMID: 20184892 DOI: 10.1016/j.jmb.2010.02.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2010] [Revised: 02/16/2010] [Accepted: 02/17/2010] [Indexed: 11/16/2022]
Abstract
Rhodopsin, the prototype class A G-protein-coupled receptor, is a very important model system for all seven-transmembrane domain proteins. Characterization of the interactions between rhodopsin and transducin, its intracellular G-protein counterpart, and the fluctuations in these interactions due to thermal motions is required for an understanding of early events in the mechanism of signal transduction. In this study, we used all-atom molecular dynamics simulations of a transmembrane protein complex between rhodopsin and the heterotrimeric transducin (G alpha beta gamma) in an all-atom DOPC (1,2-dioleoylsn-glycero-3-phosphocholine) membrane-water environment. Based on the analysis of a microsecond-timescale simulation trajectory, we characterized the dynamics of the system and its effects in the structural features of the protein subunits. Our simulations describe a highly dynamic interaction interface where the system is alternating between distinct domain orientations at the 10- to 100-ns timescale that can be further classified into interaction modes involving contacts between distinct structural features on the protein subunits. We related our results with experimental measurements from a variety of studies and high-resolution models of activated rhodopsin. Monitoring key structural features that are involved in the activation process along our simulation trajectory indicates the presence of extensive dynamics in the dark-adapted state, including a motion of Y223 from helix 3 toward the "ionic-lock" interactions of the conserved ERY motif. The dynamic picture shown here is consistent with a framework in which the dark-state fluctuations sample conformations consistent with the activated state. These results provide an atomic-level description of the dynamics of the full complex and further suggest novel mutagenesis experiments that can be used to investigate the stability and dynamics of this model membrane protein receptor system.
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Affiliation(s)
- Nikolaos G Sgourakis
- Department of Biology, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180, USA
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16
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Taylor CM, Rockweiler NB, Liu C, Rikimaru L, Tunemalm AK, Kisselev OG, Marshall GR. Using ligand-based virtual screening to allosterically stabilize the activated state of a GPCR. Chem Biol Drug Des 2010; 75:325-32. [PMID: 20659113 DOI: 10.1111/j.1747-0285.2009.00944.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
G-protein coupled receptors play an essential role in many biological processes. Despite an increase in the number of solved X-ray crystal structures of G-protein coupled receptors, capturing a G-protein coupled receptor in its activated state for structural analysis has proven to be difficult. An unexplored paradigm is stabilization of one or more conformational states of a G-protein coupled receptor via binding a small molecule to the intracellular loops. A short tetrazole peptidomimetic based on the photoactivated state of rhodopsin-bound structure of Gt(alpha)(340-350) was previously designed and shown to stabilize the photoactivated state of rhodopsin, the G-protein coupled receptor involved in vision. A pharmacophore model derived from the designed tetrazole tetrapeptide was used for ligand-based virtual screening to enhance the possible discovery of novel scaffolds. Maybridge Hitfinder and National Cancer Institute diversity libraries were screened for compounds containing the pharmacophore. Forty-seven compounds resulted from virtually screening the Maybridge library, whereas no hits resulted with the National Cancer Institute library. Three of the 47 Maybridge compounds were found to stabilize the MII state. As these compounds did not inhibit binding of transducin to photoactivated state of rhodopsin, they were assumed to be allosteric ligands. These compounds are potentially useful for crystallographic studies where complexes with these compounds might capture rhodopsin in its activated conformational state.
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Affiliation(s)
- Christina M Taylor
- Department of Biochemistry and Molecular Biophysics, Washington University, St. Louis, MO 63110, USA
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17
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Ananthan S, Zhang W, Hobrath JV. Recent advances in structure-based virtual screening of G-protein coupled receptors. AAPS JOURNAL 2009; 11:178-85. [PMID: 19291412 DOI: 10.1208/s12248-009-9094-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2008] [Accepted: 02/09/2009] [Indexed: 11/30/2022]
Abstract
In addition to the rhodopsin crystal structure, high-resolution crystal structures of ligand-mediated G-protein-coupled receptors (GPCRs) have recently become available, and these have become attractive templates for developing homology models of several GPCRs of therapeutic interest. These crystal structures and the homology models derived from them have provided significant insights into ligand-receptor interactions. Moreover, several studies have demonstrated that the structural models are indeed suitable for virtual screening of compound databases to identify new ligands for various GPCRs. Recent examples of such virtual screening against GPCRs are discussed in this review.
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Affiliation(s)
- Subramaniam Ananthan
- Drug Discovery Division, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205, USA.
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