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Hoang SH, Tveter KM, Mezhibovsky E, Roopchand DE. Proanthocyanidin B2 derived metabolites may be ligands for bile acid receptors S1PR2, PXR and CAR: an in silico approach. J Biomol Struct Dyn 2024; 42:4249-4262. [PMID: 37340688 PMCID: PMC10730774 DOI: 10.1080/07391102.2023.2224886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023]
Abstract
Bile acids (BAs) act as signaling molecules via their interactions with various nuclear (FXR, VDR, PXR and CAR) and G-protein coupled (TGR5, M3R, S1PR2) BA receptors. Stimulation of these BA receptors influences several processes, including inflammatory responses and glucose and xenobiotic metabolism. BA profiles and BA receptor activity are deregulated in cardiometabolic diseases; however, dietary polyphenols were shown to alter BA profile and signaling in association with improved metabolic phenotypes. We previously reported that supplementing mice with a proanthocyanidin (PAC)-rich grape polyphenol (GP) extract attenuated symptoms of glucose intolerance in association with changes to BA profiles, BA receptor gene expression, and/or downstream markers of BA receptor activity. Exact mechanisms by which polyphenols modulate BA signaling are not known, but some hypotheses include modulation of the BA profile via changes to gut bacteria, or alteration of ligand-availability via BA sequestration. Herein, we used an in silico approach to investigate putative binding affinities of proanthocyanidin B2 (PACB2) and PACB2 metabolites to nuclear and G-protein coupled BA receptors. Molecular docking and dynamics simulations revealed that certain PACB2 metabolites had stable binding affinities to S1PR2, PXR and CAR, comparable to that of known natural and synthetic BA ligands. These findings suggest PACB2 metabolites may be novel ligands of S1PR2, CAR, and PXR receptors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Skyler H. Hoang
- Department of Food Science, New Jersey Institute for Food, Nutrition, and Health (Rutgers Center for Lipid Research and Center for Nutrition, Microbiome, and Health), Rutgers University, 61 Dudley Road, New Brunswick, New Jersey, 08901 USA
- Department of Cell Biology and Neuroscience, Rutgers University, Piscataway, New Jersey, USA
| | - Kevin M. Tveter
- Department of Food Science, New Jersey Institute for Food, Nutrition, and Health (Rutgers Center for Lipid Research and Center for Nutrition, Microbiome, and Health), Rutgers University, 61 Dudley Road, New Brunswick, New Jersey, 08901 USA
| | - Esther Mezhibovsky
- Department of Food Science, New Jersey Institute for Food, Nutrition, and Health (Rutgers Center for Lipid Research and Center for Nutrition, Microbiome, and Health), Rutgers University, 61 Dudley Road, New Brunswick, New Jersey, 08901 USA
- Department of Nutritional Sciences, Rutgers University, New Brunswick, New Jersey, USA
| | - Diana E. Roopchand
- Department of Food Science, New Jersey Institute for Food, Nutrition, and Health (Rutgers Center for Lipid Research and Center for Nutrition, Microbiome, and Health), Rutgers University, 61 Dudley Road, New Brunswick, New Jersey, 08901 USA
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2
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Cato ML, D'Agostino EH, Spurlin RM, Flynn AR, Cornelison JL, Johnson AM, Fujita RA, Abraham SM, Jui NT, Ortlund EA. Comparison of activity, structure, and dynamics of SF-1 and LRH-1 complexed with small molecule modulators. J Biol Chem 2023; 299:104921. [PMID: 37328104 PMCID: PMC10407255 DOI: 10.1016/j.jbc.2023.104921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 05/29/2023] [Accepted: 06/08/2023] [Indexed: 06/18/2023] Open
Abstract
Steroidogenic factor-1 (SF-1) is a phospholipid-sensing nuclear receptor expressed in the adrenal glands, gonads, and hypothalamus which controls steroidogenesis and metabolism. There is significant therapeutic interest in SF-1 because of its oncogenic properties in adrenocortical cancer. Synthetic modulators are attractive for targeting SF-1 for clinical and laboratory purposes due to the poor pharmaceutical properties of its native phospholipid ligands. While small molecule agonists targeting SF-1 have been synthesized, no crystal structures have been reported of SF-1 in complexes with synthetic compounds. This has prevented the establishment of structure-activity relationships that would enable better characterization of ligand-mediated activation and improvement in current chemical scaffolds. Here, we compare the effects of small molecules in SF-1 and its close homolog, liver receptor homolog-1 (LRH-1), and identify several molecules that specifically activate LRH-1. We also report the first crystal structure of SF-1 in complex with a synthetic agonist that displays low nanomolar affinity and potency for SF-1. We use this structure to explore the mechanistic basis for small molecule agonism of SF-1, especially compared to LRH-1, and uncover unique signaling pathways that drive LRH-1 specificity. Molecular dynamics simulations reveal differences in protein dynamics at the pocket mouth as well as ligand-mediated allosteric communication from this region to the coactivator binding interface. Our studies, therefore, shed important insight into the allostery driving SF-1 activity and show potential for modulation of LRH-1 over SF-1.
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Affiliation(s)
- Michael L Cato
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Emma H D'Agostino
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | | | - Autumn R Flynn
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
| | | | - Alyssa M Johnson
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
| | - Rei A Fujita
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Sarah M Abraham
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Nathan T Jui
- Department of Chemistry, Emory University, Atlanta, Georgia, USA
| | - Eric A Ortlund
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA.
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Lagadec F, Carlon-Andres I, Ragues J, Port S, Wodrich H, Kehlenbach RH. CRM1 Promotes Capsid Disassembly and Nuclear Envelope Translocation of Adenovirus Independently of Its Export Function. J Virol 2022; 96:e0127321. [PMID: 34757845 PMCID: PMC8826800 DOI: 10.1128/jvi.01273-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 07/28/2021] [Accepted: 11/01/2021] [Indexed: 11/20/2022] Open
Abstract
After receptor-mediated endocytosis and endosomal escape, adenoviral capsids can travel via microtubule organizing centers to the nuclear envelope. Upon capsid disassembly, viral genome import into nuclei of interphase cells then occurs through nuclear pore complexes, involving the nucleoporins Nup214 and Nup358. Import also requires the activity of the classic nuclear export receptor CRM1, as it is blocked by the selective inhibitor leptomycin B. We have now used artificially enucleated as well as mitotic cells to analyze the role of an intact nucleus in different steps of the viral life cycle. In enucleated U2OS cells, viral capsids traveled to the microtubule organizing center, whereas their removal from this complex was blocked, suggesting that this step required nuclear factors. In mitotic cells, on the other hand, CRM1 promoted capsid disassembly and genome release, suggesting a role of this protein that does not require intact nuclear envelopes or nuclear pore complexes and is distinct from its function as a nuclear export receptor. Similar to enucleation, inhibition of CRM1 by leptomycin B also leads to an arrest of adenoviral capsids at the microtubule organizing center. In a small-scale screen using leptomycin B-resistant versions of CRM1, we identified a mutant, CRM1 W142A P143A, that is compromised with respect to adenoviral capsid disassembly in both interphase and mitotic cells. Strikingly, this mutant is capable of exporting cargo proteins out of the nucleus of living cells or digitonin-permeabilized cells, pointing to a role of the mutated region that is not directly linked to nuclear export. IMPORTANCE A role of nucleoporins and of soluble transport factors in adenoviral genome import into the nucleus of infected cells in interphase has previously been established. The nuclear export receptor CRM1 promotes genome import, but its precise function is not known. Using enucleated and mitotic cells, we showed that CRM1 does not simply function by exporting a crucial factor out of the nucleus that would then trigger capsid disassembly and genome import. Instead, CRM1 has an export-independent role, a notion that is also supported by a mutant, CRM1 W142A P143A, which is export competent but deficient in viral capsid disassembly, in both interphase and mitotic cells.
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Affiliation(s)
- Floriane Lagadec
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center of Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
- CNRS UMR 5234, Fundamental Microbiology and Pathogenicity, Université de Bordeaux, Bordeaux, France
| | - Irene Carlon-Andres
- CNRS UMR 5234, Fundamental Microbiology and Pathogenicity, Université de Bordeaux, Bordeaux, France
| | - Jessica Ragues
- CNRS UMR 5234, Fundamental Microbiology and Pathogenicity, Université de Bordeaux, Bordeaux, France
| | - Sarah Port
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center of Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
| | - Harald Wodrich
- CNRS UMR 5234, Fundamental Microbiology and Pathogenicity, Université de Bordeaux, Bordeaux, France
| | - Ralph H. Kehlenbach
- Department of Molecular Biology, Faculty of Medicine, Göttingen Center of Biosciences (GZMB), Georg-August-University Göttingen, Göttingen, Germany
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Fung HYJ, Chook YM. Crystallization of Nuclear Export Signals or Small-Molecule Inhibitors Bound to Nuclear Exporter CRM1. Methods Mol Biol 2022; 2502:285-297. [PMID: 35412246 DOI: 10.1007/978-1-0716-2337-4_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The Karyopherin protein CRM1 or XPO1 is the major nuclear export receptor that regulates nuclear exit of thousands of macromolecules in the cell. CRM1 recognizes protein cargoes by binding to their 8-15 residue-long nuclear export signals (NESs). A ternary CRM1-Ran-RanBP1 complex engineered to be suitable for crystallization has enabled structure determination by X-ray crystallography of CRM1 bound to many NES peptides and small-molecule inhibitors. Here, we present a protocol for the purification of the individual proteins, formation of the ternary CRM1-Ran-RanBP1 complex and crystallization of this complex for X-ray crystallography.
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Affiliation(s)
- Ho Yee Joyce Fung
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yuh Min Chook
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.
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Abstract
CRM1 recognizes hundreds to thousands of protein cargoes by binding to the eight to fifteen residue-long nuclear export signals (NESs) within their polypeptide chains. Various assays to measure the binding affinity of NESs for CRM1 have been developed. CRM1 binds to NESs with a wide range of binding affinities, with dissociation constants that span from low nanomolar to tens of micromolar. An optimized binding affinity assay with improved throughput was recently developed to measure binding affinities of NES peptides for CRM1 in the presence of excess RanGTP. The assay can measure affinities, with multiple replicates, for up to seven different NES peptides per screening plate. Here, we present a protocol for the purification of the necessary proteins and for measuring CRM1-NES binding affinities.
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Affiliation(s)
- Ho Yee Joyce Fung
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Yuh Min Chook
- Department of Pharmacology, UT Southwestern Medical Center, Dallas, TX, USA.
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Chandra S, Mannino PJ, Thaller DJ, Ader NR, King MC, Melia TJ, Lusk CP. Atg39 selectively captures inner nuclear membrane into lumenal vesicles for delivery to the autophagosome. J Cell Biol 2021; 220:e202103030. [PMID: 34714326 PMCID: PMC8575018 DOI: 10.1083/jcb.202103030] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 08/26/2021] [Accepted: 09/29/2021] [Indexed: 12/26/2022] Open
Abstract
Mechanisms that turn over components of the nucleus and inner nuclear membrane (INM) remain to be fully defined. We explore how components of the INM are selected by a cytosolic autophagy apparatus through a transmembrane nuclear envelope-localized cargo adaptor, Atg39. A split-GFP reporter showed that Atg39 localizes to the outer nuclear membrane (ONM) and thus targets the INM across the nuclear envelope lumen. Consistent with this, sequence elements that confer both nuclear envelope localization and a membrane remodeling activity are mapped to the Atg39 lumenal domain; these lumenal motifs are required for the autophagy-mediated degradation of integral INM proteins. Interestingly, correlative light and electron microscopy shows that the overexpression of Atg39 leads to the expansion of the ONM and the enclosure of a network of INM-derived vesicles in the nuclear envelope lumen. Thus, we propose an outside-in model of nucleophagy where INM is delivered into vesicles in the nuclear envelope lumen, which can be targeted by the autophagosome.
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Affiliation(s)
| | | | | | | | | | - Thomas J. Melia
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
| | - C. Patrick Lusk
- Department of Cell Biology, Yale School of Medicine, New Haven, CT
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Großkopf H, Vogel S, Müller CD, Köhling S, Dürig JN, Möller S, Schnabelrauch M, Rademann J, Hempel U, von Bergen M, Schubert K. Identification of intracellular glycosaminoglycan-interacting proteins by affinity purification mass spectrometry. Biol Chem 2021; 402:1427-1440. [PMID: 34472763 DOI: 10.1515/hsz-2021-0167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 02/25/2021] [Accepted: 07/04/2021] [Indexed: 12/20/2022]
Abstract
Glycosaminoglycans (GAGs) are essential functional components of the extracellular matrix (ECM). Artificial GAGs like sulfated hyaluronan (sHA) exhibit pro-osteogenic properties and boost healing processes. Hence, they are of high interest for supporting bone regeneration and wound healing. Although sulfated GAGs (sGAGs) appear intracellularly, the knowledge about intracellular effects and putative interaction partners is scarce. Here we used an affinity-purification mass spectrometry-based (AP-MS) approach to identify novel and particularly intracellular sGAG-interacting proteins in human bone marrow stromal cells (hBMSC). Overall, 477 proteins were found interacting with at least one of four distinct sGAGs. Enrichment analysis for protein localization showed that mainly intracellular and cell-associated interacting proteins were identified. The interaction of sGAG with α2-macroglobulin receptor-associated protein (LRPAP1), exportin-1 (XPO1), and serine protease HTRA1 (HTRA1) was confirmed in reverse assays. Consecutive pathway and cluster analysis led to the identification of biological processes, namely processes involving binding and processing of nucleic acids, LRP1-dependent endocytosis, and exosome formation. Respecting the preferentially intracellular localization of sGAG in vesicle-like structures, also the interaction data indicate sGAG-specific modulation of vesicle-based transport processes. By identifying many sGAG-specific interacting proteins, our data provide a resource for upcoming studies aimed at molecular mechanisms and understanding of sGAG cellular effects.
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Affiliation(s)
- Henning Großkopf
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig D-04318, Germany
| | - Sarah Vogel
- Institute of Physiological Chemistry, Medical Faculty, Technische Universität Dresden, Dresden D-01307, Germany
| | - Claudia Damaris Müller
- Institute of Physiological Chemistry, Medical Faculty, Technische Universität Dresden, Dresden D-01307, Germany
| | - Sebastian Köhling
- Institute of Pharmacy, Freie Universität Berlin, Berlin D-14195, Germany
| | - Jan-Niklas Dürig
- Institute of Pharmacy, Freie Universität Berlin, Berlin D-14195, Germany
| | - Stephanie Möller
- Biomaterials Department, INNOVENT e.V. Technologieentwicklung Jena, Jena D-07745, Germany
| | - Matthias Schnabelrauch
- Biomaterials Department, INNOVENT e.V. Technologieentwicklung Jena, Jena D-07745, Germany
| | - Jörg Rademann
- Institute of Pharmacy, Freie Universität Berlin, Berlin D-14195, Germany
| | - Ute Hempel
- Institute of Physiological Chemistry, Medical Faculty, Technische Universität Dresden, Dresden D-01307, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig D-04318, Germany
- Institute of Biochemistry, Faculty of Life Sciences, Universität Leipzig, Leipzig D-04103, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research GmbH - UFZ, Leipzig D-04318, Germany
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Abstract
Here, we describe an optimized protocol to identify specific nuclear receptor ligands. First, to rule out any compound interference with luciferase activity per se, we describe an in vitro assay assessing potential inhibition or activation of luciferase enzymatic activity. Second, to comply with EMA and FDA guidelines to mitigate drug-drug interactions, we detail assays assessing constitutive androstane receptor (CAR) and pregnane X receptor (PXR) activation ability. Finally, to minimize off-target detection effects, we describe the use of mammalian one- (or two-) hybrid systems. For complete details on the use and execution of this protocol, please refer to Hering et al. (2018).
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Affiliation(s)
- Alexandre Berthier
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, 59000 Lille, France
| | - Bart Staels
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, 59000 Lille, France
| | - Philippe Lefebvre
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1011-EGID, 59000 Lille, France
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Meng F, Zong W, Wei X, Tao Y, Wang G, Liao Z, Chen M. Dolomiaea souliei ethyl acetate extract protected against α-naphthylisothiocyanate-induced acute intrahepatic cholestasis through regulation of farnesoid x receptor-mediated bile acid metabolism. Phytomedicine 2021; 87:153588. [PMID: 34091148 DOI: 10.1016/j.phymed.2021.153588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/25/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Cholestasis is characterized by accumulation of bile components in liver and systemic circulation. Restoration of bile acid homeostasis via activating farnesoid x receptor (FXR) is a promising strategy for the treatment of cholestasis. FXR-SHP (small heterodimer partner) axis plays an important role in maintaining bile acid homeostasis. PURPOSE To investigate the anti-cholestasis effect of Dolomiaea souliei (Franch.) C.Shih (D. souliei) and clarify its underlying mechanism against α-naphthylisothiocyanate (ANIT) induced acute intrahepatic cholestasis. METHODS ANIT-induced Sprague-Dawley rats were employed to investigate the anti-cholestasis effect of D. souliei ethyl acetate extract (DSE). Ursodeoxycholic acid (UDCA) was used as positive control. Bile flow and blood biochemical parameters were measured. Liver histopathological examination was conducted via hematoxylin-eosin staining. Western blot analysis was carried out to evaluate the protein levels related to bile acids metabolism and inflammation. The interactions between FXR and costunolide or dehydrocostus lactone, were conducted by molecular docking experiments. The effect of costunolide and dehydrocostus lactone on aspartate aminotransferase (AST), alanine aminotransferase (ALT) levels and FXR expression were also evaluated using guggulsterone-induced L02 cells. RESULTS DSE could promote bile excretions and protect against ANIT-induced liver damage in cholestasis rats. Protein levels of FXR, SHP, Na+/taurocholate cotransporter (NTCP), bile salt export pump (BSEP), multidrug resistance-associated protein 2 (MRP2) were increased and the expressions of cholesterol 7α-hydroxylase (CYP7A1) and sterol 27-hydroxylase (CYP27A1) were decreased by DSE. Meanwhile, the anti-inflammatory factors, tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), interleukin-6 (IL-6) were also significantly increased, and the pro-inflammatory factor, interleukin-10 (IL-10), was significantly decreased in rats of DSE groups. Molecular docking revealed that costunolide and dehydrocostus lactone could be well docked into the FXR protein molecule, and hydrophobic interactions played the main function. Costunolide could reverse the increased AST and ALT levels and increase the FXR expression in guggulsterone-induced L02 cells. CONCLUSION DSE had an anti-cholestasis effect by activating FXR-SHP axis, inhibiting synthesis of bile acid, and increasing bile secretion, together with inflammatory response and improving liver injury. Costunolide may be the main active component. This study provided a potential therapeutic mechanism for D. souliei as an anti-cholestasis medicine in the treatment of cholestasis liver diseases.
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Affiliation(s)
- FanCheng Meng
- College of Pharmaceutical Sciences, Key Laboratory of Luminescence Analysis and Molecular Sensing (Ministry of Education), Southwest University, No. 2 Tiansheng Road, Chongqing 400715, P.R. China
| | - Wei Zong
- College of Pharmaceutical Sciences, Key Laboratory of Luminescence Analysis and Molecular Sensing (Ministry of Education), Southwest University, No. 2 Tiansheng Road, Chongqing 400715, P.R. China
| | - XiaoDong Wei
- College of Pharmaceutical Sciences, Key Laboratory of Luminescence Analysis and Molecular Sensing (Ministry of Education), Southwest University, No. 2 Tiansheng Road, Chongqing 400715, P.R. China
| | - YunYi Tao
- College of Pharmaceutical Sciences, Key Laboratory of Luminescence Analysis and Molecular Sensing (Ministry of Education), Southwest University, No. 2 Tiansheng Road, Chongqing 400715, P.R. China
| | - GuoWei Wang
- College of Pharmaceutical Sciences, Key Laboratory of Luminescence Analysis and Molecular Sensing (Ministry of Education), Southwest University, No. 2 Tiansheng Road, Chongqing 400715, P.R. China
| | - ZhiHua Liao
- School of Life Sciences, Southwest University, No. 2 Tiansheng Road, Chongqing 400715, P.R. China
| | - Min Chen
- College of Pharmaceutical Sciences, Key Laboratory of Luminescence Analysis and Molecular Sensing (Ministry of Education), Southwest University, No. 2 Tiansheng Road, Chongqing 400715, P.R. China.
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10
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Zhao T, Wang J, He A, Wang S, Chen Y, Lu J, Lv J, Li S, Wang J, Qian M, Li H, Shen X. Mebhydrolin ameliorates glucose homeostasis in type 2 diabetic mice by functioning as a selective FXR antagonist. Metabolism 2021; 119:154771. [PMID: 33831422 DOI: 10.1016/j.metabol.2021.154771] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 03/01/2021] [Accepted: 03/28/2021] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Type 2 diabetes mellitus (T2DM) is a chronic disease with hallmarks of hyperglycemia and hyperlipidemia. Long-term hyperglycemia damages the functions of multiple tissues and organs leading to a series of complications and disability or even death. Nuclear receptor farnesoid X receptor (FXR) antagonism has been recently discovered to exhibit beneficial effect on glucose metabolism in T2DM mice, although the underlying mechanisms remain unclear. Here, we performed the study on the discovery of new FXR antagonist and investigated the mechanism underlying the amelioration of FXR antagonism on glucose homeostasis in T2DM mice by using the determined FXR antagonist as a probe. METHODS FXR antagonist Mebhydrolin was discovered by screening against the lab in-house FDA approved drug library through surface plasmon resonance (SPR), microscale thermophoresis (MST), AlphaScreen, mammalian one-hybrid and transactivation assays. Activity of Mebhydrolin in improving glucose homeostasis was evaluated in db/db and HFD/STZ-induced T2DM mice, and the mechanisms governing the regulation of Mebhydrolin were investigated by assays of immunostaining, Western blot, ELISA, RT-PCR against liver tissues of both T2DM mice and the T2DM mice with liver-specific FXR knockdown injected via adeno-associated-virus AAV-FXR-RNAi and mouse primary hepatocytes. Finally, molecular docking and molecular dynamics (MD) technology-based study was performed to investigate the structural basis for the antagonistic regulation of Mebhydrolin against FXR at an atomic level. FINDINGS Mebhydrolin ameliorated blood glucose homeostasis in T2DM mice by both suppressing hepatic gluconeogenesis via FXR/miR-22-3p/PI3K/AKT/FoxO1 pathway and promoting glycogen synthesis through FXR/miR-22-3p/PI3K/AKT/GSK3β pathway. Structurally, residues L291, M332 and Y373 of FXR were required for Mebhydrolin binding to FXR-LBD, and Mebhydrolin induced H2 and H6 shifting of FXR potently affecting the regulation of the downstream target genes. CONCLUSIONS Our work has revealed a novel mode for the regulation of FXR against glucose metabolism in T2DM mice and highlighted the potential of Mebhydrolin in the treatment of T2DM.
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MESH Headings
- Animals
- Blood Glucose/drug effects
- Blood Glucose/metabolism
- Carbolines/chemistry
- Carbolines/pharmacokinetics
- Carbolines/therapeutic use
- Cells, Cultured
- Diabetes Mellitus, Experimental/chemically induced
- Diabetes Mellitus, Experimental/drug therapy
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Type 2/chemically induced
- Diabetes Mellitus, Type 2/drug therapy
- Diabetes Mellitus, Type 2/metabolism
- Gluconeogenesis/drug effects
- Gluconeogenesis/genetics
- Glucose/metabolism
- HEK293 Cells
- Homeostasis/drug effects
- Humans
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Transgenic
- Molecular Docking Simulation
- Protein Interaction Domains and Motifs
- Receptors, Cytoplasmic and Nuclear/antagonists & inhibitors
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Streptozocin
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Affiliation(s)
- Tong Zhao
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jie Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Anxu He
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shan Wang
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Yidi Chen
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jian Lu
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Jianlu Lv
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Shiliang Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jiaying Wang
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Minyi Qian
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
| | - Honglin Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Xu Shen
- School of Medicine& Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China.
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Fakih TM, Kurniawan F, Yusuf M, Mudasir M, Tjahjono DH. Molecular Dynamics of Cobalt Protoporphyrin Antagonism of the Cancer Suppressor REV-ERBβ. Molecules 2021; 26:3251. [PMID: 34071361 PMCID: PMC8198987 DOI: 10.3390/molecules26113251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/06/2021] [Revised: 05/15/2021] [Accepted: 05/26/2021] [Indexed: 11/17/2022] Open
Abstract
Nuclear receptor REV-ERBβ is an overexpressed oncoprotein that has been used as a target for cancer treatment. The metal-complex nature of its ligand, iron protoporphyrin IX (Heme), enables the REV-ERBβ to be used for multiple therapeutic modalities as a photonuclease, a photosensitizer, or a fluorescence imaging agent. The replacement of iron with cobalt as the metal center of protoporphyrin IX changes the ligand from an agonist to an antagonist of REV-ERBβ. The mechanism behind that phenomenon is still unclear, despite the availability of crystal structures of REV-ERBβ in complex with Heme and cobalt protoporphyrin IX (CoPP). This study used molecular dynamic simulations to compare the effects of REV-ERBβ binding to Heme and CoPP, respectively. The initial poses of Heme and CoPP in complex with agonist and antagonist forms of REV-ERBβ were predicted using molecular docking. The binding energies of each ligand were calculated using the MM/PBSA method. The computed binding affinity of Heme to REV-ERBβ was stronger than that of CoPP, in agreement with experimental results. CoPP altered the conformation of the ligand-binding site of REV-ERBβ, disrupting the binding site for nuclear receptor corepressor, which is required for REV-ERBβ to regulate the transcription of downstream target genes. Those results suggest that a subtle change in the metal center of porphyrin can change the behavior of porphyrin in cancer cell signaling. Therefore, modification of porphyrin-based agents for cancer therapy should be conducted carefully to avoid triggering unfavorable effects.
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Affiliation(s)
- Taufik Muhammad Fakih
- School of Pharmacy, Bandung Institute of Technology, Jalan Ganesha 10, Bandung 40135, Indonesia; (T.M.F.); (F.K.)
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Islam Bandung, Jalan Rangga Gading 8, Bandung 40116, Indonesia
| | - Fransiska Kurniawan
- School of Pharmacy, Bandung Institute of Technology, Jalan Ganesha 10, Bandung 40135, Indonesia; (T.M.F.); (F.K.)
| | - Muhammad Yusuf
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, Jalan Raya Bandung Sumedang Km 21, Sumedang 45363, Indonesia;
| | - Mudasir Mudasir
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Gadjah Mada, Sekip Utara BLS 21, Yogyakarta 55281, Indonesia;
| | - Daryono Hadi Tjahjono
- School of Pharmacy, Bandung Institute of Technology, Jalan Ganesha 10, Bandung 40135, Indonesia; (T.M.F.); (F.K.)
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12
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Willems S, Gellrich L, Chaikuad A, Kluge S, Werz O, Heering J, Knapp S, Lorkowski S, Schubert-Zsilavecz M, Merk D. Endogenous vitamin E metabolites mediate allosteric PPARγ activation with unprecedented co-regulatory interactions. Cell Chem Biol 2021; 28:1489-1500.e8. [PMID: 33989565 DOI: 10.1016/j.chembiol.2021.04.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 03/29/2021] [Accepted: 04/23/2021] [Indexed: 02/07/2023]
Abstract
Vitamin E exhibits pharmacological effects beyond established antioxidant activity suggesting involvement of unidentified mechanisms. Here, we characterize endogenously formed tocopherol carboxylates and the vitamin E mimetic garcinoic acid (GA) as activators of the peroxisome proliferator-activated receptor gamma (PPARγ). Co-stimulation of PPARγ with GA and the orthosteric agonist pioglitazone resulted in additive transcriptional activity. In line with this, the PPARγ-GA complex adopted a fully active conformation and interestingly contained two bound GA molecules with one at an allosteric site. A co-regulator interaction scan demonstrated an unanticipated co-factor recruitment profile for GA-bound PPARγ compared with canonical PPARγ agonists and gene expression analysis revealed different effects of GA and pioglitazone on PPAR signaling in hepatocytes. These observations reveal allosteric mechanisms of PPARγ modulation as an alternative avenue to PPARγ targeting and suggest contributions of PPARγ activation by α-13-tocopherolcarboxylate to the pharmacological effects of vitamin E.
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Affiliation(s)
- Sabine Willems
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Leonie Gellrich
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438, Germany; Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Stefan Kluge
- Chair of Nutritional Biochemistry and Physiology, Institute of Nutrition, Friedrich-Schiller-University Jena, Jena 07743, Germany; Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, University of Jena, Jena 07743, Germany
| | - Oliver Werz
- Chair of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Jena 07743, Germany
| | - Jan Heering
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt 60596, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438, Germany; Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt 60438, Germany
| | - Stefan Lorkowski
- Chair of Nutritional Biochemistry and Physiology, Institute of Nutrition, Friedrich-Schiller-University Jena, Jena 07743, Germany; Competence Cluster for Nutrition and Cardiovascular Health (nutriCARD) Halle-Jena-Leipzig, University of Jena, Jena 07743, Germany
| | | | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt 60438, Germany.
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13
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Wang M, Liu F, Yao Y, Zhang Q, Lu Z, Zhang R, Liu C, Lin C, Zhu C. Network pharmacology-based mechanism prediction and pharmacological validation of Xiaoyan Lidan formula on attenuating alpha-naphthylisothiocyanate induced cholestatic hepatic injury in rats. J Ethnopharmacol 2021; 270:113816. [PMID: 33444723 DOI: 10.1016/j.jep.2021.113816] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 01/04/2021] [Accepted: 01/06/2021] [Indexed: 06/12/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The well-known Chinese prescription, Xiaoyan Lidan Formula (XYLDF), possesses efficiency of heat-clearing, dampness-eliminating and jaundice-removing. It has long been used clinically for the treatment of hepatobiliary diseases due to intrahepatic cholestasis (IHC). However, the mechanism of XYLDF for its therapeutic effects remains elusive. AIM OF THE STUDY The study aimed to explore the potential targets for liver protective mechanism of XYLDF based on network pharmacology and experimental assays in ANIT-induced cholestatic hepatic injury (CHI) in rats. MATERIALS AND METHODS On the basis of the 29 serum migrant compounds of XYLDF elucidated by UPLC-TOF-MS/MS, a network pharmacology approach was applied for the mechanism prediction. Systematic networks were constructed to identify potential molecular targets, biological processes, and signaling pathways. And the interactions between significantly potential targets and active compounds were simulated by molecular docking. For the mechanism validation, an ANIT-induced rat model was used to evaluate the effects of XYLDF on CHI according to serum biochemistry, bile flow rates, histopathological examination, and the gene and protein expression including enzymes related to synthesis, export, and import of bile acid in liver and ileum, and those of inflammatory cytokines, analyzed by RT-qPCR and WB. RESULTS The results of network pharmacology research indicated TNF (TNF-α), RELA (NF-κB), NR1H4 (FXR), and ICAM1 (ICAM-1) to be the important potential targets of XYLDF for cholestatic liver injury, which are related to bile metabolism and NF-κB-mediated inflammatory signaling. And the molecular docking had pre-validated the prediction of network pharmacology, as the core active compounds of XYLDF had shown strong simulation binding affinity with FXR, followed by NF-κB, TNF-α, and ICAM-1. Meanwhile, the effects of XYLDF after oral administration on ANIT-induced CHI in rats exhibited the decreased levels of transaminases (ALT and AST), TBA, and TBIL in serum, raised bile flow rates, and markedly improved hepatic histopathology. Furthermore, consistent to the above targets prediction and molecular docking, XYLDF significantly up-regulated the expression of FXR, SHP, BSEP, and MRP2, and down-regulated CYP7A1 and NTCP in liver, and promoted expression of IBABP and OSTα/β in ileum, suggesting the activation of FXR-mediated pathway referring to bile acid synthesis, transportation, and reabsorption. Moreover, the lower levels of TNF-α in plasma and liver, as well as the reduced hepatic gene and protein expression of NF-κB, TNF-α, and ICAM-1 after XYLDF treatment revealed the suppression of NF-κB-mediated inflammatory signaling pathway, as evidenced by the inhibition of nuclear translocation of NF-κB. CONCLUSIONS XYLDF exhibited an ameliorative liver protective effect on ANIT-induced cholestatic hepatic injury. The present study has confirmed its mechanism as activating the FXR-regulated bile acid pathway and inhibiting inflammation via the NF-κB signaling pathway.
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MESH Headings
- 1-Naphthylisothiocyanate/toxicity
- Animals
- Bile Acids and Salts/metabolism
- Chemical and Drug Induced Liver Injury/blood
- Chemical and Drug Induced Liver Injury/drug therapy
- Chemical and Drug Induced Liver Injury/pathology
- Cholestasis, Intrahepatic/blood
- Cholestasis, Intrahepatic/chemically induced
- Cholestasis, Intrahepatic/drug therapy
- Cholestasis, Intrahepatic/pathology
- Disease Models, Animal
- Drugs, Chinese Herbal/pharmacology
- Drugs, Chinese Herbal/therapeutic use
- Inflammation/drug therapy
- Inflammation/metabolism
- Male
- Metabolic Networks and Pathways/drug effects
- Molecular Docking Simulation
- NF-kappa B/metabolism
- Protective Agents/pharmacology
- Protective Agents/therapeutic use
- Protein Interaction Maps/drug effects
- Rats, Sprague-Dawley
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/metabolism
- Signal Transduction/drug effects
- Rats
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Affiliation(s)
- Meiqi Wang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No.232 Waihuandong Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Fangle Liu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No.232 Waihuandong Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Yufeng Yao
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No.232 Waihuandong Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Qiuyu Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No.232 Waihuandong Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Zenghui Lu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No.232 Waihuandong Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Runjing Zhang
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No.232 Waihuandong Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Changhui Liu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No.232 Waihuandong Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China
| | - Chaozhan Lin
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No.232 Waihuandong Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China.
| | - Chenchen Zhu
- School of Pharmaceutical Sciences, Guangzhou University of Chinese Medicine, No.232 Waihuandong Rd, Guangzhou Higher Education Mega Center, Guangzhou, 510006, China.
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14
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Sui M, Xiong M, Li Y, Zhou Q, Shen X, Jia D, Gou M, Sun Q. Cancer Therapy with Nanoparticle-Medicated Intracellular Expression of Peptide CRM1-Inhibitor. Int J Nanomedicine 2021; 16:2833-2847. [PMID: 33883894 PMCID: PMC8054660 DOI: 10.2147/ijn.s266398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/29/2020] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION Peptides can be rationally designed as non-covalent inhibitors for molecularly targeted therapy. However, it remains challenging to efficiently deliver the peptides into the targeted cells, which often severely affects their therapeutic efficiency. METHODS Herein, we created a novel non-covalent peptide inhibitor against nuclear export factor CRM1 by a structure-guided drug design method and targetedly delivered the peptide into cancer cells by a nanoparticle-mediated gene expression system for use as a cancer therapy. RESULTS The nuclear export signal (NES)-optimized CRM1 peptide inhibitor colocalized with CRM1 to the nuclear envelope and inhibited nuclear export in cancer cell lines in vitro. The crystal structures of the inhibitors complexed with CRM1 were solved. In contrast to the covalent inhibitors, the peptides were similarly effective against cells harboring the CRM1 C528S mutation. Moreover, a plasmid encoding the peptides was delivered by a iRGD-modified nanoparticle to efficiently target and transfect the cancer cells in vivo after intravenous administration. The peptides could be selectively expressed in the tumor, resulting in the efficient inhibition of subcutaneous melanoma xenografts without obvious systemic toxicity. DISCUSSION This work provides an effective strategy to design peptide-based molecularly targeted therapeutics, which could lead to the development of future targeted therapy.
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Affiliation(s)
- Min Sui
- Department of Pathology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Centre for Biotherapy, Chengdu, 610041, People’s Republic of China
| | - Meimei Xiong
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People’s Republic of China
| | - Yuling Li
- Department of Pathology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Centre for Biotherapy, Chengdu, 610041, People’s Republic of China
| | - Qiao Zhou
- Department of Pathology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Centre for Biotherapy, Chengdu, 610041, People’s Republic of China
| | - Xiaofei Shen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, Division of Neurology, West China Second University Hospital, Sichuan University, Chengdu, 610041, People’s Republic of China
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Pediatrics, Division of Neurology, West China Second University Hospital, Sichuan University, Chengdu, 610041, People’s Republic of China
| | - Maling Gou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, People’s Republic of China
| | - Qingxiang Sun
- Department of Pathology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Centre for Biotherapy, Chengdu, 610041, People’s Republic of China
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15
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Zheng W. Predicting cryptic ligand binding sites based on normal modes guided conformational sampling. Proteins 2021; 89:416-426. [PMID: 33244830 DOI: 10.1002/prot.26027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/26/2020] [Accepted: 11/21/2020] [Indexed: 12/22/2022]
Abstract
To greatly expand the druggable genome, fast and accurate predictions of cryptic sites for small molecules binding in target proteins are in high demand. In this study, we have developed a fast and simple conformational sampling scheme guided by normal modes solved from the coarse-grained elastic models followed by atomistic backbone refinement and side-chain repacking. Despite the observations of complex and diverse conformational changes associated with ligand binding, we found that simply sampling along each of the lowest 30 modes is near optimal for adequately restructuring cryptic sites so they can be detected by existing pocket finding programs like fpocket and concavity. We further trained machine-learning protocols to optimize the combination of the sampling-enhanced pocket scores with other dynamic and conservation scores, which only slightly improved the performance. As assessed based on a training set of 84 known cryptic sites and a test set of 14 proteins, our method achieved high accuracy of prediction (with area under the receiver operating characteristic curve >0.8) comparable to the CryptoSite server. Compared with CryptoSite and other methods based on extensive molecular dynamics simulation, our method is much faster (1-2 hours for an average-size protein) and simpler (using only pocket scores), so it is suitable for high-throughput processing of large datasets of protein structures at the genome scale.
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Affiliation(s)
- Wenjun Zheng
- Department of Physics, University at Buffalo, Buffalo, New York, USA
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16
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Yasukawa T, Tsutsui A, Tomomori-Sato C, Sato S, Saraf A, Washburn MP, Florens L, Terada T, Shimizu K, Conaway RC, Conaway JW, Aso T. NRBP1-Containing CRL2/CRL4A Regulates Amyloid β Production by Targeting BRI2 and BRI3 for Degradation. Cell Rep 2021; 30:3478-3491.e6. [PMID: 32160551 DOI: 10.1016/j.celrep.2020.02.059] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 01/10/2019] [Revised: 12/09/2019] [Accepted: 02/13/2020] [Indexed: 11/18/2022] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disease caused by accumulations of Aβ peptides. Production and fibrillation of Aβ are downregulated by BRI2 and BRI3, which are physiological inhibitors of amyloid precursor protein (APP) processing and Aβ oligomerization. Here, we identify nuclear receptor binding protein 1 (NRBP1) as a substrate receptor of a Cullin-RING ubiquitin ligase (CRL) that targets BRI2 and BRI3 for degradation. Moreover, we demonstrate that (1) dimerized NRBP1 assembles into a functional Cul2- and Cul4A-containing heterodimeric CRL through its BC-box and an overlapping cryptic H-box, (2) both Cul2 and Cul4A contribute to NRBP1 CRL function, and (3) formation of the NRBP1 heterodimeric CRL is strongly enhanced by chaperone-like function of TSC22D3 and TSC22D4. NRBP1 knockdown in neuronal cells results in an increase in the abundance of BRI2 and BRI3 and significantly reduces Aβ production. Thus, disrupting interactions between NRBP1 and its substrates BRI2 and BRI3 may provide a useful therapeutic strategy for AD.
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Affiliation(s)
- Takashi Yasukawa
- Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
| | - Aya Tsutsui
- Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan
| | | | - Shigeo Sato
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Anita Saraf
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Michael P Washburn
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Pathology and Laboratory Medicine, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Laurence Florens
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Tohru Terada
- Interfaculty Initiative in Information Studies, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Kentaro Shimizu
- Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Ronald C Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Joan W Conaway
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA; Department of Biochemistry and Molecular Biology, Kansas University Medical Center, Kansas City, KS 66160, USA
| | - Teijiro Aso
- Department of Functional Genomics, Kochi Medical School, Kohasu, Oko-cho, Nankoku, Kochi 783-8505, Japan.
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17
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Meiners A, Bäcker S, Hadrović I, Heid C, Beuck C, Ruiz-Blanco YB, Mieres-Perez J, Pörschke M, Grad JN, Vallet C, Hoffmann D, Bayer P, Sánchez-García E, Schrader T, Knauer SK. Specific inhibition of the Survivin-CRM1 interaction by peptide-modified molecular tweezers. Nat Commun 2021; 12:1505. [PMID: 33686072 PMCID: PMC7940618 DOI: 10.1038/s41467-021-21753-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 02/02/2021] [Indexed: 01/31/2023] Open
Abstract
Survivin's dual function as apoptosis inhibitor and regulator of cell proliferation is mediated via its interaction with the export receptor CRM1. This protein-protein interaction represents an attractive target in cancer research and therapy. Here, we report a sophisticated strategy addressing Survivin's nuclear export signal (NES), the binding site of CRM1, with advanced supramolecular tweezers for lysine and arginine. These were covalently connected to small peptides resembling the natural, self-complementary dimer interface which largely overlaps with the NES. Several biochemical methods demonstrated sequence-selective NES recognition and interference with the critical receptor interaction. These data were strongly supported by molecular dynamics simulations and multiscale computational studies. Rational design of lysine tweezers equipped with a peptidic recognition element thus allowed to address a previously unapproachable protein surface area. As an experimental proof-of-principle for specific transport signal interference, this concept should be transferable to any protein epitope with a flanking well-accessible lysine.
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Affiliation(s)
- Annika Meiners
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Sandra Bäcker
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Inesa Hadrović
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christian Heid
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany
| | - Christine Beuck
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Yasser B Ruiz-Blanco
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Joel Mieres-Perez
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Marius Pörschke
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Jean-Noël Grad
- Department of Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Cecilia Vallet
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Daniel Hoffmann
- Department of Bioinformatics and Computational Biophysics, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Peter Bayer
- Department of Structural and Medicinal Biology, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany
| | - Elsa Sánchez-García
- Department of Computational Biochemistry, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
| | - Thomas Schrader
- Institute of Organic Chemistry I, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.
| | - Shirley K Knauer
- Department of Molecular Biology II, Centre for Medical Biotechnology (ZMB), University of Duisburg-Essen, Essen, Germany.
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18
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Shaikhqasem A, Schmitt K, Valerius O, Ficner R. Crystal structure of human CRM1, covalently modified by 2-mercaptoethanol on Cys528, in complex with RanGTP. Acta Crystallogr F Struct Biol Commun 2021; 77:70-78. [PMID: 33682791 PMCID: PMC7938638 DOI: 10.1107/s2053230x2100203x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 01/05/2021] [Accepted: 02/21/2021] [Indexed: 11/23/2022] Open
Abstract
CRM1 is a nuclear export receptor that has been intensively targeted over the last decade for the development of antitumor and antiviral drugs. Structural analysis of several inhibitor compounds bound to CRM1 revealed that their mechanism of action relies on the covalent modification of a critical cysteine residue (Cys528 in the human receptor) located in the nuclear export signal-binding cleft. This study presents the crystal structure of human CRM1, covalently modified by 2-mercaptoethanol on Cys528, in complex with RanGTP at 2.58 Å resolution. The results demonstrate that buffer components can interfere with the characterization of cysteine-dependent inhibitor compounds.
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Affiliation(s)
- Alaa Shaikhqasem
- Department for Molecular Structural Biology, Georg-August-Universität Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
| | - Kerstin Schmitt
- Department of Molecular Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstrasse 8, 37077 Göttingen, Germany
| | - Oliver Valerius
- Department of Molecular Microbiology and Genetics, Georg-August-Universität Göttingen, Grisebachstrasse 8, 37077 Göttingen, Germany
| | - Ralf Ficner
- Department for Molecular Structural Biology, Georg-August-Universität Göttingen, Justus-von-Liebig Weg 11, 37077 Göttingen, Germany
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19
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Ekka MK, Meena LS. Essential biochemical, biophysical and computational inputs on efficient functioning of Mycobacterium tuberculosis H 37Rv FtsY. Int J Biol Macromol 2021; 171:59-73. [PMID: 33412199 DOI: 10.1016/j.ijbiomac.2020.12.182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 11/19/2022]
Abstract
Mycobacterium tuberculosis (M. tuberculosis H37Rv) utilizes the signal recognition particle pathway (SRP pathway) system for secretion of various proteins from ribosomes to the extracellular surface which plays an important role in the machinery running inside the bacterium. This system comprises of three major components FtsY, FfH and 4.5S rRNA. This manuscript highlights essential factors responsible for the optimized enzymatic activity of FtsY. Kinetic parameters include Vmax and Km for the hydrolysis of GTP by ftsY which were 20.25±5.16 μM/min/mg and 39.95±7.7 μM respectively. kcat and catalytic efficiency of the reaction were 0.012±0.003 s-1 and 0.00047±0.0001 μM/s-1 respectively. These values were affected upon changing the standard conditions. Cations (Mg2+ and Mn2+) play important role in FtsY enzymatic activity as increasing Mg2+ decrease the activity. Mn2+on the other hand is required at higher concentration around 60 mM for carrying optimum GTPase activity. FtsY is hydrolyzing ATP and GDP as well and GDP acts as an inhibitor of the reaction. MD simulation shows effective binding and stabilization of the FtsY complexed structure with GTP, GDP and ATP. Mutational analysis was done at two important residues of GTP binding motif of FtsY, namely, GXXXXGK (K236) and DXXG (D367) and showed that these mutations significantly decrease FtsY GTPase activity. FtsY is comprised of α helices, but this structural pattern was shown to change with increasing concentrations of GTP and ATP which symbolize that these ligands cause significant conformational change by variating the secondary structure to transduce signals required by downstream effectors. This binding favors the functional stabilization of FtsY by destabilization of α-helix integrity. Revealing the hidden aspects of the functioning of FtsY might be an essential part for the understanding of the SRP pathway which is one of the important contributors of M. tuberculosis virulence.
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Affiliation(s)
- Mary Krishna Ekka
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh 201 002, India
| | - Laxman S Meena
- CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC, Ghaziabad, Uttar Pradesh 201 002, India.
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20
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Wei X, Ma Y, Dong Z, Wang G, Lan X, Liao Z, Chen M. Dehydrodiconiferyl alcohol, a lignan from Herpetospermum pedunculosum, alleviates cholestasis by activating pathways associated with the farnesoid X receptor. Phytomedicine 2021; 80:153378. [PMID: 33113499 DOI: 10.1016/j.phymed.2020.153378] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 09/07/2020] [Accepted: 10/11/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND In our previous study, we demonstrated the hepatoprotective effect of Herpetospermum pedunculosum in cholestatic rats. A bioassay-guided study also led to the identification and isolation of a lignan, dihydrodiconiferyl alcohol (DA) from the seeds of H. pedunculosum. PURPOSE To investigate whether DA could alleviate cholestasis and determine the mechanisms underlying such action. METHODS Male Sprague-Dawley (SD) rats were administered with DA (10, 20 or 40 mg/kg) intragastrically once daily for 7 days prior to treatment with α-naphthylisothiocyanate (ANIT) (60 mg/kg). We then evaluated the levels of a range of serum indicators, determined bile flow, and carried out histopathological analyses. Western blotting was then used to investigate the levels of inflammatory mediators and the Farnesoid X Receptor (FXR), proteins involved in the downstream biosynthesis of bile acids, and a range of transport proteins. Molecular docking was used to simulate the interaction between DA and FXR. Cell viability of human hepatocytes (L-02) cells was determined by MTT. Then, we treated guggulsterone-inhibited L-02 cells, Si-FXR L-02 cells, and FXR-overexpression cells with the FXR agonist GW4064 (6 μM) or DA (25, 50 and 100 μM) for 24 h before detecting gene and protein expression by RT-PCR and western blotting, respectively. RESULTS DA significantly attenuated ANIT-induced cholestasis in SD rats by reducing liver function indicators in the serum, increasing bile flow, improving the recovery of histopathological injuries in the liver, and by alleviating pro-inflammatory cytokines in the liver. DA also increased the expression levels of FXR and altered the levels of downstream proteins in the liver tissues, thus indicating that DA might alleviate cholestasis by regulating the FXR. Molecular docking simulations predicted that DA was as an agonist of FXR. In vitro mechanical studies further showed that DA increased the mRNA and protein expression levels of FXR, Small Heterodimer Partner 1/2, Bile Salt Export Pump, Multidrug Resistance-associated Protein 2, and Na+/taurocholate Co-transporting Polypeptide, in both guggulsterone-inhibited and Si-FXR L-02 cells. Moreover, DA enhanced the mRNA and protein expression of FXR, and its downstream genes and proteins, in L-02 cells containing an FXR-overexpression plasmid. CONCLUSION DA may represent an effective agonist for FXR has significant therapeutic potential for the treatment of cholestatic liver injury.
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MESH Headings
- 1-Naphthylisothiocyanate/toxicity
- ATP Binding Cassette Transporter, Subfamily B, Member 11/metabolism
- Animals
- Bile/metabolism
- Bile Acids and Salts/metabolism
- Cholestasis, Intrahepatic/chemically induced
- Cholestasis, Intrahepatic/drug therapy
- Cholestasis, Intrahepatic/metabolism
- Cholestasis, Intrahepatic/pathology
- Cucurbitaceae/chemistry
- Hepatocytes/drug effects
- Humans
- Isoxazoles/pharmacology
- Liver/drug effects
- Liver/metabolism
- Liver/pathology
- Male
- Molecular Docking Simulation
- Phenols/chemistry
- Phenols/pharmacology
- Rats, Sprague-Dawley
- Receptors, Cytoplasmic and Nuclear/agonists
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Rats
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Affiliation(s)
- Xiaodong Wei
- College of Pharmaceutical Sciences, Southwest University, No.2 Tiansheng Road, Chongqing 400715, PR China
| | - Yingxiong Ma
- College of Pharmaceutical Sciences, Southwest University, No.2 Tiansheng Road, Chongqing 400715, PR China
| | - Zhaoyue Dong
- College of Pharmaceutical Sciences, Southwest University, No.2 Tiansheng Road, Chongqing 400715, PR China
| | - Guowei Wang
- College of Pharmaceutical Sciences, Southwest University, No.2 Tiansheng Road, Chongqing 400715, PR China
| | - Xiaozhong Lan
- TAAHC-SWU Medicinal Plant R&D Center, Xizang Agriculture and Animal Husbandry College, Nyingchi, Tibet, PR China
| | - Zhihua Liao
- School of Life Sciences, Southwest University, Chongqing 400715, PR China
| | - Min Chen
- College of Pharmaceutical Sciences, Southwest University, No.2 Tiansheng Road, Chongqing 400715, PR China.
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21
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Abstract
Chirality is an important consideration in drug development: it can influence recognition of the intended target, pharmacokinetics, and off-target effects. Here, we investigate how chirality affects the activity and mechanism of action of RJW100, a racemic agonist of the nuclear receptors liver receptor homolog-1 (LRH-1) and steroidogenic factor-1 (SF-1). LRH-1 and SF-1 modulators are highly sought as treatments for metabolic and neoplastic diseases, and RJW100 has one of the few scaffolds shown to activate them. However, enantiomer-specific effects on receptor activation are poorly understood. We show that the enantiomers have similar binding affinities, but RR-RJW100 stabilizes both receptors and is 46% more active than SS-RJW100 in LRH-1 luciferase reporter assays. We present an LRH-1 crystal structure that illuminates striking mechanistic differences: SS-RJW100 adopts multiple configurations in the pocket and fails to make an interaction critical for activation by RR-RJW100. In molecular dynamics simulations, SS-RJW100 attenuates intramolecular signalling important for coregulator recruitment, consistent with previous observations that it weakly recruits coregulators in vitro. These studies provide a rationale for pursuing enantiomerically pure RJW100 derivatives: they establish RR-RJW100 as the stronger LRH-1 agonist and identify a potential for optimizing the SS-RJW100 scaffold for antagonist design.
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Affiliation(s)
- Suzanne G Mays
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
- Centre for Genomic Regulation, Carrer Dr. Aiguader, 88, 08003, Barcelona, Spain
| | - Józef Stec
- School of Chemistry, University of Southampton, Southampton, Hants, SO17, United Kingdom
- Department of Pharmaceutical Sciences, College of Pharmacy, Marshall B. Ketchum University, 2575 Yorba Linda Blvd, Fullerton, CA, 82831, USA
| | - Xu Liu
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Emma H D'Agostino
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA
| | - Richard J Whitby
- School of Chemistry, University of Southampton, Southampton, Hants, SO17, United Kingdom
| | - Eric A Ortlund
- Department of Biochemistry, Emory University, Atlanta, GA, 30322, USA.
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22
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Han Y, Lyman KA, Foote KM, Chetkovich DM. The structure and function of TRIP8b, an auxiliary subunit of hyperpolarization-activated cyclic-nucleotide gated channels. Channels (Austin) 2020; 14:110-122. [PMID: 32189562 PMCID: PMC7153792 DOI: 10.1080/19336950.2020.1740501] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 01/21/2020] [Revised: 02/18/2020] [Accepted: 02/21/2020] [Indexed: 02/08/2023] Open
Abstract
Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are expressed throughout the mammalian central nervous system (CNS). These channels have been implicated in a wide range of diseases, including Major Depressive Disorder and multiple subtypes of epilepsy. The diversity of functions that HCN channels perform is in part attributable to differences in their subcellular localization. To facilitate a broad range of subcellular distributions, HCN channels are bound by auxiliary subunits that regulate surface trafficking and channel function. One of the best studied auxiliary subunits is tetratricopeptide-repeat containing, Rab8b-interacting protein (TRIP8b). TRIP8b is an extensively alternatively spliced protein whose only known function is to regulate HCN channels. TRIP8b binds to HCN pore-forming subunits at multiple interaction sites that differentially regulate HCN channel function and subcellular distribution. In this review, we summarize what is currently known about the structure and function of TRIP8b isoforms with an emphasis on the role of this auxiliary subunit in health and disease.
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Affiliation(s)
- Ye Han
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kyle A. Lyman
- Department of Neurology, Stanford University, Palo Alto, CA, USA
| | - Kendall M. Foote
- Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Dane M. Chetkovich
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
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23
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Abstract
The proper segregation of basic elements such as the compartmentalization of the genome and the shuttling of macromolecules between the nucleus and the cytoplasm is a crucial mechanism for homeostasis maintenance in eukaryotic cells. XPO1 (Exportin 1) is the major nuclear export receptor and is required for the export of proteins and RNAs out of the nucleus. STK38 (also known as NDR1) is a Hippo pathway serine/threonine kinase with multifarious functions in normal and cancer cells. In this review, we summarize the history of the discovery of the nucleo/cytoplasmic shuttling of proteins and focus on the major actor of nuclear export: XPO1. After describing the molecular events required for XPO1-mediated nuclear export of proteins, we introduce the Hippo pathway STK38 kinase, synthetize its regulation mechanisms as well as its biological functions in both normal and cancer cells, and finally its intersection with XPO1 biology. We discuss the recently identified mechanism of XPO1 activation by phosphorylation of XPO1_S1055 by STK38 and contextualize this finding according to the biological functions previously reported for both XPO1 and STK38, including the second identity of STK38 as an autophagy regulator. Finally, we phrase this newly identified activation mechanism into the general nuclear export machinery and examine the possible outcomes of nuclear export inhibition in cancer treatment.
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Affiliation(s)
- Alexandre PJ Martin
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, USA
| | - Jacques H Camonis
- Inserm U830, Institut Curie, Centre de Recherche, Paris Sciences et Lettres Research University, Paris, France
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24
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Jaladanki CK, He Y, Zhao LN, Maurer-Stroh S, Loo LH, Song H, Fan H. Virtual screening of potentially endocrine-disrupting chemicals against nuclear receptors and its application to identify PPARγ-bound fatty acids. Arch Toxicol 2020; 95:355-374. [PMID: 32909075 PMCID: PMC7811525 DOI: 10.1007/s00204-020-02897-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 07/02/2020] [Accepted: 08/27/2020] [Indexed: 12/17/2022]
Abstract
Nuclear receptors (NRs) are key regulators of energy homeostasis, body development, and sexual reproduction. Xenobiotics binding to NRs may disrupt natural hormonal systems and induce undesired adverse effects in the body. However, many chemicals of concerns have limited or no experimental data on their potential or lack-of-potential endocrine-disrupting effects. Here, we propose a virtual screening method based on molecular docking for predicting potential endocrine-disrupting chemicals (EDCs) that bind to NRs. For 12 NRs, we systematically analyzed how multiple crystal structures can be used to distinguish actives and inactives found in previous high-throughput experiments. Our method is based on (i) consensus docking scores from multiple structures at a single functional state (agonist-bound or antagonist-bound), (ii) multiple functional states (agonist-bound and antagonist-bound), and (iii) multiple pockets (orthosteric site and alternative sites) of these NRs. We found that the consensus enrichment from multiple structures is better than or comparable to the best enrichment from a single structure. The discriminating power of this consensus strategy was further enhanced by a chemical similarity-weighted scoring scheme, yielding better or comparable enrichment for all studied NRs. Applying this optimized method, we screened 252 fatty acids against peroxisome proliferator-activated receptor gamma (PPARγ) and successfully identified 3 previously unknown fatty acids with Kd = 100-250 μM including two furan fatty acids: furannonanoic acid (FNA) and furanundecanoic acid (FUA), and one cyclopropane fatty acid: phytomonic acid (PTA). These results suggested that the proposed method can be used to rapidly screen and prioritize potential EDCs for further experimental evaluations.
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Affiliation(s)
- Chaitanya K Jaladanki
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore
- Toxicity Mode-of-Action Discovery (ToxMAD) Platform, Innovations in Food and Chemical Safety Programme, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore
| | - Yang He
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Li Na Zhao
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore
- Toxicity Mode-of-Action Discovery (ToxMAD) Platform, Innovations in Food and Chemical Safety Programme, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore
| | - Lit-Hsin Loo
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore
- Toxicity Mode-of-Action Discovery (ToxMAD) Platform, Innovations in Food and Chemical Safety Programme, Agency for Science, Technology, and Research (A*STAR), Singapore, 138671, Singapore
| | - Haiwei Song
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore.
| | - Hao Fan
- Bioinformatics Institute (BII), Agency for Science, Technology, and Research (A*STAR), 30 Biopolis Street, Matrix No. 07-01, Singapore, 138671, Singapore.
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25
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Shaikhqasem A, Dickmanns A, Neumann P, Ficner R. Characterization of Inhibition Reveals Distinctive Properties for Human and Saccharomyces cerevisiae CRM1. J Med Chem 2020; 63:7545-7558. [PMID: 32585100 DOI: 10.1021/acs.jmedchem.0c00143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The receptor CRM1 is responsible for the nuclear export of many tumor-suppressor proteins and viral ribonucleoproteins. This renders CRM1 an interesting target for therapeutic intervention in diverse cancer types and viral diseases. Structural studies of Saccharomyces cerevisiae CRM1 (ScCRM1) complexes with inhibitors defined the molecular basis for CRM1 inhibition. Nevertheless, no structural information is available for inhibitors bound to human CRM1 (HsCRM1). Here, we present the structure of the natural inhibitor Leptomycin B bound to the HsCRM1-RanGTP complex. Despite high sequence conservation and structural similarity in the NES-binding cleft region, ScCRM1 exhibits 16-fold lower binding affinity than HsCRM1 toward PKI-NES and significant differences in affinities toward potential CRM1 inhibitors. In contrast to HsCRM1, competition assays revealed that a human adapted mutant ScCRM1-T539C does not bind all inhibitors tested. Taken together, our data indicate the importance of using HsCRM1 for molecular analysis and development of novel antitumor and antiviral drugs.
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Affiliation(s)
- Alaa Shaikhqasem
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Achim Dickmanns
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Piotr Neumann
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
| | - Ralf Ficner
- Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany
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26
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Matsuzaka Y, Uesawa Y. Molecular Image-Based Prediction Models of Nuclear Receptor Agonists and Antagonists Using the DeepSnap-Deep Learning Approach with the Tox21 10K Library. Molecules 2020; 25:molecules25122764. [PMID: 32549344 PMCID: PMC7356846 DOI: 10.3390/molecules25122764] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/06/2020] [Accepted: 06/12/2020] [Indexed: 02/07/2023] Open
Abstract
The interaction of nuclear receptors (NRs) with chemical compounds can cause dysregulation of endocrine signaling pathways, leading to adverse health outcomes due to the disruption of natural hormones. Thus, identifying possible ligands of NRs is a crucial task for understanding the adverse outcome pathway (AOP) for human toxicity as well as the development of novel drugs. However, the experimental assessment of novel ligands remains expensive and time-consuming. Therefore, an in silico approach with a wide range of applications instead of experimental examination is highly desirable. The recently developed novel molecular image-based deep learning (DL) method, DeepSnap-DL, can produce multiple snapshots from three-dimensional (3D) chemical structures and has achieved high performance in the prediction of chemicals for toxicological evaluation. In this study, we used DeepSnap-DL to construct prediction models of 35 agonist and antagonist allosteric modulators of NRs for chemicals derived from the Tox21 10K library. We demonstrate the high performance of DeepSnap-DL in constructing prediction models. These findings may aid in interpreting the key molecular events of toxicity and support the development of new fields of machine learning to identify environmental chemicals with the potential to interact with NR signaling pathways.
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27
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Lei Y, An Q, Zhang Y, Luo P, Luo Y, Shen X, Jia D, Sun Q. Engineering chromosome region maintenance 1 fragments that bind to nuclear export signals. Protein Sci 2020; 29:1366-1372. [PMID: 31495993 PMCID: PMC7255508 DOI: 10.1002/pro.3724] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 02/05/2023]
Abstract
Chromosome region maintenance 1 (CRM1) exports nuclear export signal (NES) containing cargos from nucleus to cytoplasm and plays critical roles in cancer and viral infections. Biochemical and biophysical studies on this protein were often obstructed by its low purification yield and stability. With the help of PROSS server and NES protection strategy, we successfully designed three small fragments of CRM1, each made of four HEAT repeats and capable of binding to NESs in the absence of RanGTP. One of the fragments, C7, showed dramatically improved purification yield, thermostability, mechanostability, and resistance to protease digestion. We showed by isothermal titration that the protein kinase inhibitor NES binds to C7 at 1.18 μM affinity. Direct binding to C7 by several reported CRM1 inhibitors derived from plants were verified using pull-down assays. These fragments might be useful for the development of CRM1 inhibitors towards treatment of related diseases. The strategy applied here might help to tackle similar problems encountered in different fields.
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Affiliation(s)
- Yuqin Lei
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Center, West China HospitalSichuan University, and Collaborative Innovation Centre of BiotherapyChengduChina
| | - Qi An
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Center, West China HospitalSichuan University, and Collaborative Innovation Centre of BiotherapyChengduChina
| | - Yuqing Zhang
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Center, West China HospitalSichuan University, and Collaborative Innovation Centre of BiotherapyChengduChina
| | - Ping Luo
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Center, West China HospitalSichuan University, and Collaborative Innovation Centre of BiotherapyChengduChina
| | - Youfu Luo
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Center, West China HospitalSichuan University, and Collaborative Innovation Centre of BiotherapyChengduChina
| | - Xiaofei Shen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, Division of NeurologyWest China Second University Hospital, Sichuan UniversityChengduChina
| | - Da Jia
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, Division of NeurologyWest China Second University Hospital, Sichuan UniversityChengduChina
| | - Qingxiang Sun
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Center, West China HospitalSichuan University, and Collaborative Innovation Centre of BiotherapyChengduChina
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28
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Abstract
In eukaryotic cells, about one-third of the synthesized proteins are translocated into the endoplasmic reticulum; they are membrane or lumen resident proteins and proteins direct to the Golgi apparatus. The co-translational translocation takes place through the heterotrimeric protein-conducting channel Sec61 which is associated with the ribosome and many accessory components, such as the heterotetrameric translocon-associated protein (TRAP) complex. Recently, microscopic techniques, such as cryo-electron microscopy and cryo-electron tomography, have enabled the determination of the translocation machinery structure. However, at present, there is a lack of understanding regarding the roles of some of its components; indeed, the TRAP complex function during co-translational translocation needs to be established. In addition, TRAP may play a role during unfolded protein response, endoplasmic-reticulum-associated protein degradation and congenital disorder of glycosylation (ssr4 CDG). In this article, I describe the current understanding of the TRAP complex in the light of its possible function(s).
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Affiliation(s)
- Antonietta Russo
- Medical Biochemistry and Molecular Biology, UKS, University of Saarland, Homburg, Germany
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29
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Abstract
Endocrine-disrupting chemicals have been shown to interfere with the endocrine system function at the level of hormone synthesis, transport, metabolism, binding, action, and elimination. They are associated with several health problems in humans: obesity, diabetes mellitus, infertility, impaired thyroid and neuroendocrine functions, neurodevelopmental problems, and cancer are among them. As drugs are chemicals humans can be frequently exposed to for longer periods of time, special emphasis should be put on their endocrine-disrupting potential. In this study, we conducted a screen of 1046 US-approved and marketed small-molecule drugs (molecular weight between 60 and 600) for estimating their endocrine-disrupting properties. Binding affinity to 12 nuclear receptors was assessed with a molecular-docking program, Endocrine Disruptome. We identified 130 drugs with a high binding affinity to a nuclear receptor that is not their pharmacological target. In a subset of drugs with predicted high binding affinities to a nuclear receptor with Endocrine Disruptome, the positive predictive value was 0.66 when evaluated with in silico results obtained with another molecular docking program, VirtualToxLab, and 0.32 when evaluated with in vitro results from the Tox21 database. Computational screening was proven useful in prioritizing drugs for in vitro testing. We suggest that the novel interactions of drugs with nuclear receptors predicted here are further investigated.
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Affiliation(s)
| | - Marija Sollner Dolenc
- Faculty of Pharmacy; University of Ljubljana, Aškerčeva cesta 7, SI-1000 Ljubljana, Slovenia;
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30
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Pant S, Tajkhorshid E. Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes. J Comput Chem 2020; 41:489-499. [PMID: 31762060 PMCID: PMC7000246 DOI: 10.1002/jcc.26109] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/03/2019] [Accepted: 10/15/2019] [Indexed: 01/17/2023]
Abstract
The pleckstrin homology (PH) domain of general receptor for phosphoionositides 1 (GRP1-PHD) binds specifically to phosphatidylinositol (3,4,5)-triphosphate (PIP3 ), and acts as a second messenger. Using an extensive array of molecular dynamics (MD) simulations employing highly mobile membrane mimetic (HMMM) model as well as complementary full membrane simulations, we capture differentiable binding and dynamics of GRP1-PHD in the presence of membranes containing PC, PS, and PIP3 lipids in varying compositions. While GRP1-PHD forms only transient interactions with pure PC membranes, incorporation of anionic lipids resulted in stable membrane-bound configurations. We report the first observation of two distinct PIP3 binding modes on GRP1-PHD, involving PIP3 interactions at a "canonical" and at an "alternate" site, suggesting the possibility of simultaneous binding of multiple anionic lipids. The full membrane simulations confirmed the stability of the membrane bound pose of GRP1-PHD as captured from our HMMM membrane binding simulations. By performing additional steered membrane unbinding simulations and calculating nonequilibrium work associated with the process, as well as metadynamics simulations, on the protein bound to full membranes, allowing for more quantitative examination of the binding strength of the GRP1-PHD to the membrane, we demonstrate that along with the bound PIP3 , surrounding anionic PS lipids increase the energetic cost of unbinding of GRP1-PHD from the canonical mode, causing them to dissociate more slowly than the alternate mode. Our results demonstrate that concurrent binding of multiple anionic lipids by GRP1-PHD contributes to its membrane affinity, which in turn control its signaling activity. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Shashank Pant
- Center for Biophysics and Quantitative Biology, Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801
| | - Emad Tajkhorshid
- Center for Biophysics and Quantitative Biology, Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801
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Yamamoto E, Domański J, Naughton FB, Best RB, Kalli AC, Stansfeld PJ, Sansom MSP. Multiple lipid binding sites determine the affinity of PH domains for phosphoinositide-containing membranes. Sci Adv 2020; 6:eaay5736. [PMID: 32128410 PMCID: PMC7030919 DOI: 10.1126/sciadv.aay5736] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 12/03/2019] [Indexed: 05/19/2023]
Abstract
Association of peripheral proteins with lipid bilayers regulates membrane signaling and dynamics. Pleckstrin homology (PH) domains bind to phosphatidylinositol phosphate (PIP) molecules in membranes. The effects of local PIP enrichment on the interaction of PH domains with membranes is unclear. Molecular dynamics simulations allow estimation of the binding energy of GRP1 PH domain to PIP3-containing membranes. The free energy of interaction of the PH domain with more than two PIP3 molecules is comparable to experimental values, suggesting that PH domain binding involves local clustering of PIP molecules within membranes. We describe a mechanism of PH binding proceeding via an encounter state to two bound states which differ in the orientation of the protein relative to the membrane, these orientations depending on the local PIP concentration. These results suggest that nanoscale clustering of PIP molecules can control the strength and orientation of PH domain interaction in a concentration-dependent manner.
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Affiliation(s)
- Eiji Yamamoto
- Department of System Design Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Jan Domański
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Fiona B. Naughton
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Antreas C. Kalli
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
- Leeds Institute of Cardiovascular and Metabolic Medicine and Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Phillip J. Stansfeld
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
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Pham B, Arons AB, Vincent JG, Fernandez EJ, Shen T. Regulatory Mechanics of Constitutive Androstane Receptors: Basal and Ligand-Directed Actions. J Chem Inf Model 2019; 59:5174-5182. [PMID: 31714771 DOI: 10.1021/acs.jcim.9b00695] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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] [Indexed: 12/13/2022]
Abstract
Constitutive androstane receptor (CAR) is a nuclear hormone receptor that primarily functions in sensing and metabolizing xenobiotics. The basal activity of this receptor is relatively high, and CAR is deemed active in the absence of ligand. The (over)activation can promote drug toxicity and tumor growth. Thus, therapeutic treatments seek inverse agonists to inhibit or modulate CAR activities. To advance our understanding of the regulatory mechanisms of CAR, we used computational and experimental approaches to elucidate three aspects of CAR activation and inactivation: (1) ligand-dependent actions, (2) ligand-orthologue specificity, and (3) constitutive activity. For ligand-dependent actions, we examined the ligand-bound simulations and identified two sets of ligand-induced contacts promoting CAR activation via coactivator binding (H11-H12 contact) or inactivation via corepressor binding (H4-H11 contact). For orthologue specificity, we addressed a puzzling fact that murine CAR (mCAR) and human CAR (hCAR) respond differently to the same ligand (CITCO), despite their high sequence homology. We found that the helix H7 of hCAR is responsible for a stronger binding of the ligand CITCO compared to mCAR, hence a stronger CITCO-induced activation. For basal activity, we reported computer-generated unliganded CAR structures and critical mutagenesis (mCAR's V209A and N333D) results of a cell-based transcription assay. Our results reveal that the basal conformation of CAR shares prominent features with the agonist-bound form, and helix HX has an important contribution to the constitutive activity. These findings altogether can be useful for the understanding of constitutively active receptors and the design of drug molecules targeting them.
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Affiliation(s)
- Bill Pham
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Avery Bancroft Arons
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Jeremy G Vincent
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Elias J Fernandez
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
| | - Tongye Shen
- Department of Biochemistry & Cellular and Molecular Biology , University of Tennessee , Knoxville , Tennessee 37996 , United States
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Alexander SPH, Kelly E, Mathie A, Peters JA, Veale EL, Armstrong JF, Faccenda E, Harding SD, Pawson AJ, Sharman JL, Southan C, Buneman OP, Cidlowski JA, Christopoulos A, Davenport AP, Fabbro D, Spedding M, Striessnig J, Davies JA. THE CONCISE GUIDE TO PHARMACOLOGY 2019/20: Introduction and Other Protein Targets. Br J Pharmacol 2019; 176 Suppl 1:S1-S20. [PMID: 31710719 PMCID: PMC6844537 DOI: 10.1111/bph.14747] [Citation(s) in RCA: 257] [Impact Index Per Article: 51.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. Although the Concise Guide represents approximately 400 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/10.1111/bph.14747. In addition to this overview, in which are identified Other protein targets which fall outside of the subsequent categorisation, there are six areas of focus: G protein-coupled receptors, ion channels, nuclear hormone receptors, catalytic receptors, enzymes and transporters. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2019, and supersedes data presented in the 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate.
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Affiliation(s)
- Stephen P H Alexander
- School of Life Sciences, University of Nottingham Medical School, Nottingham, NG7 2UH, UK
| | - Eamonn Kelly
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK
| | - Alistair Mathie
- Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Anson Building, Central Avenue, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
| | - John A Peters
- Neuroscience Division, Medical Education Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Emma L Veale
- Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Anson Building, Central Avenue, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
| | - Jane F Armstrong
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Elena Faccenda
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Simon D Harding
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Adam J Pawson
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Joanna L Sharman
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Christopher Southan
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - O Peter Buneman
- Laboratory for Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, EH8 9LE, UK
| | - John A Cidlowski
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Arthur Christopoulos
- Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, Parkville, Victoria, 3052, Australia
| | | | | | | | - Jörg Striessnig
- Pharmacology and Toxicology, Institute of Pharmacy, University of Innsbruck, A-6020, Innsbruck, Austria
| | - Jamie A Davies
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
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Zhu G, Chang Y, Xu X, Tang K, Chen C, Lei M, Zhu JK, Duan CG. EXPORTIN 1A prevents transgene silencing in Arabidopsis by modulating nucleo-cytoplasmic partitioning of HDA6. J Integr Plant Biol 2019; 61:1243-1254. [PMID: 30697937 DOI: 10.1111/jipb.12787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 01/25/2019] [Indexed: 05/28/2023]
Abstract
In eukaryotic cells, transport of macromolecules across the nuclear envelope is an essential process that ensures rapid exchange of cellular components, including protein and RNA molecules. Chromatin regulators involved in epigenetic control are among the molecules exported across the nuclear envelope, but the significance of this nucleo-cytoplasmic trafficking is not well understood. Here, we use a forward screen to isolate XPO1A (a nuclear export receptor in Arabidopsis) as an anti-silencing factor that protects transgenes from transcriptional silencing. Loss-of-function of XPO1A leads to locus-specific DNA hypermethylation at transgene promoters and some endogenous loci. We found that XPO1A directly interacts with histone deacetylase HDA6 in vivo and that the xpo1a mutation causes increased nuclear retention of HDA6 protein and results in reduced histone acetylation and enhanced transgene silencing. Our results reveal a new mechanism of epigenetic regulation through the modulation of XPO1A-dependent nucleo-cytoplasm partitioning of a chromatin regulator.
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Affiliation(s)
- Guohui Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yanan Chang
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 201602, China
- The University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuezhong Xu
- College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Kai Tang
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Chunxiang Chen
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 201602, China
- The University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingguang Lei
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jian-Kang Zhu
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 201602, China
| | - Cheng-Guo Duan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Shanghai Center for Plant Stress Biology and Center of Excellence for Molecular Plant Sciences, the Chinese Academy of Sciences, Shanghai, 201602, China
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Alexander SPH, Kelly E, Mathie A, Peters JA, Veale EL, Armstrong JF, Faccenda E, Harding SD, Pawson AJ, Sharman JL, Southan C, Davies JA. THE CONCISE GUIDE TO PHARMACOLOGY 2019/20: Transporters. Br J Pharmacol 2019; 176 Suppl 1:S397-S493. [PMID: 31710713 PMCID: PMC6844579 DOI: 10.1111/bph.14753] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The Concise Guide to PHARMACOLOGY 2019/20 is the fourth in this series of biennial publications. The Concise Guide provides concise overviews of the key properties of nearly 1800 human drug targets with an emphasis on selective pharmacology (where available), plus links to the open access knowledgebase source of drug targets and their ligands (www.guidetopharmacology.org), which provides more detailed views of target and ligand properties. Although the Concise Guide represents approximately 400 pages, the material presented is substantially reduced compared to information and links presented on the website. It provides a permanent, citable, point-in-time record that will survive database updates. The full contents of this section can be found at http://onlinelibrary.wiley.com/doi/10.1111/bph.14753. Transporters are one of the six major pharmacological targets into which the Guide is divided, with the others being: G protein-coupled receptors, ion channels, nuclear hormone receptors, catalytic receptors and enzymes. These are presented with nomenclature guidance and summary information on the best available pharmacological tools, alongside key references and suggestions for further reading. The landscape format of the Concise Guide is designed to facilitate comparison of related targets from material contemporary to mid-2019, and supersedes data presented in the 2017/18, 2015/16 and 2013/14 Concise Guides and previous Guides to Receptors and Channels. It is produced in close conjunction with the International Union of Basic and Clinical Pharmacology Committee on Receptor Nomenclature and Drug Classification (NC-IUPHAR), therefore, providing official IUPHAR classification and nomenclature for human drug targets, where appropriate.
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Affiliation(s)
- Stephen P H Alexander
- School of Life Sciences, University of Nottingham Medical School, Nottingham, NG7 2UH, UK
| | - Eamonn Kelly
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Bristol, BS8 1TD, UK
| | - Alistair Mathie
- Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Anson Building, Central Avenue, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
| | - John A Peters
- Neuroscience Division, Medical Education Institute, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK
| | - Emma L Veale
- Medway School of Pharmacy, The Universities of Greenwich and Kent at Medway, Anson Building, Central Avenue, Chatham Maritime, Chatham, Kent, ME4 4TB, UK
| | - Jane F Armstrong
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Elena Faccenda
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Simon D Harding
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Adam J Pawson
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Joanna L Sharman
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Christopher Southan
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
| | - Jamie A Davies
- Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, EH8 9XD, UK
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Fujimori K, Iguchi Y, Yamashita Y, Gohda K, Teno N. Synthesis of Novel Farnesoid X Receptor Agonists and Validation of Their Efficacy in Activating Differentiation of Mouse Bone Marrow-Derived Mesenchymal Stem Cells into Osteoblasts. Molecules 2019; 24:molecules24224155. [PMID: 31744088 PMCID: PMC6891315 DOI: 10.3390/molecules24224155] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/08/2019] [Accepted: 11/14/2019] [Indexed: 01/14/2023] Open
Abstract
The modulators of farnesoid X receptor (FXR), a bile acid receptor, regulate various biological processes including bile acid metabolism, and are associated with the control of fatty liver and osteoporosis. Thus, the control of FXR activity and development of FXR modulators are critical not only for research, but also for clinical application. In this study, we synthesized novel FXR agonists 1–4 possessing isoxazole and N-substituted benzimidazole moieties, and compared their effects on osteoblast differentiation with the known FXR agonists, chenodeoxycholic acid and a synthetic compound, GW4064. Two (3 and 4) of the four novel FXR agonists 1–4 showed high specificities for FXR. Computer-assisted modeling suggested that the binding of the FXR agonist 3 with ligand binding domain of FXR was similar to GW4064. FXR was expressed in mouse bone marrow-derived mesenchymal stem cell (MSC)-like ST2 cells (ST-2 MSCs). The FXR agonists activated the BMP-2-induced differentiation of ST-2 MSCs into osteoblasts and enhanced the expression of RUNX2. Moreover, the potency of the FXR agonist 3 was comparable to GW4064 in promoting osteoblast differentiation of ST-2 MSCs. These results indicate that FXR activation enhanced the BMP-2-induced differentiation of MSCs into osteoblasts through activating RUNX2 expression. FXR could be a potential therapeutic target for the treatment of bone diseases such as osteoporosis.
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Affiliation(s)
- Ko Fujimori
- Department of Pathobiochemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
- Correspondence: ; Tel.: +81-72-690-1215
| | - Yusuke Iguchi
- Faculty of Pharmaceutical Sciences, Hiroshima International University, 5-1-1, Hirokoshingai, Kure, Hiroshima 737-0112, Japan; (Y.I.); (Y.Y.)
| | - Yukiko Yamashita
- Faculty of Pharmaceutical Sciences, Hiroshima International University, 5-1-1, Hirokoshingai, Kure, Hiroshima 737-0112, Japan; (Y.I.); (Y.Y.)
| | - Keigo Gohda
- Computer-aided Molecular Modeling Research Center, Kansai (CAMM-Kansai), 3-32-302, Tsuto-Otsuka, Nishinomiya, Hyogo 663-8241, Japan;
| | - Naoki Teno
- Graduate School of Pharmaceutical Sciences, Hiroshima International University, 5-1-1, Hirokoshingai, Kure, Hiroshima 737-0112, Japan;
- Faculty of Clinical Nutrition, Hiroshima International University, 5-1-1, Hirokoshingai, Kure, Hiroshima 737-0112, Japan
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37
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Blus BJ, Koh J, Krolak A, Seo HS, Coutavas E, Blobel G. Allosteric modulation of nucleoporin assemblies by intrinsically disordered regions. Sci Adv 2019; 5:eaax1836. [PMID: 31807700 PMCID: PMC6881172 DOI: 10.1126/sciadv.aax1836] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 09/25/2019] [Indexed: 05/12/2023]
Abstract
Intrinsically disordered regions (IDRs) of proteins are implicated in key macromolecular interactions. However, the molecular forces underlying IDR function within multicomponent assemblies remain elusive. By combining thermodynamic and structural data, we have discovered an allostery-based mechanism regulating the soluble core region of the nuclear pore complex (NPC) composed of nucleoporins Nup53, Nic96, and Nup157. We have identified distinct IDRs in Nup53 that are functionally coupled when binding to partner nucleoporins and karyopherins (Kaps) involved in NPC assembly and nucleocytoplasmic transport. We show that the Nup53·Kap121 complex forms an ensemble of structures that destabilize Nup53 hub interactions. Our study provides a molecular framework for understanding how disordered and folded domains communicate within macromolecular complexes.
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Affiliation(s)
- Bartlomiej Jan Blus
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
- Corresponding author.
| | - Junseock Koh
- School of Biological Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Aleksandra Krolak
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Hyuk-Soo Seo
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Elias Coutavas
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Günter Blobel
- Laboratory of Cell Biology, Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
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Taylor J, Sendino M, Gorelick AN, Pastore A, Chang MT, Penson AV, Gavrila EI, Stewart C, Melnik EM, Herrejon Chavez F, Bitner L, Yoshimi A, Lee SCW, Inoue D, Liu B, Zhang XJ, Mato AR, Dogan A, Kharas MG, Chen Y, Wang D, Soni RK, Hendrickson RC, Prieto G, Rodriguez JA, Taylor BS, Abdel-Wahab O. Altered Nuclear Export Signal Recognition as a Driver of Oncogenesis. Cancer Discov 2019; 9:1452-1467. [PMID: 31285298 PMCID: PMC6774834 DOI: 10.1158/2159-8290.cd-19-0298] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 06/20/2019] [Accepted: 07/01/2019] [Indexed: 12/17/2022]
Abstract
Altered expression of XPO1, the main nuclear export receptor in eukaryotic cells, has been observed in cancer, and XPO1 has been a focus of anticancer drug development. However, mechanistic evidence for cancer-specific alterations in XPO1 function is lacking. Here, genomic analysis of 42,793 cancers identified recurrent and previously unrecognized mutational hotspots in XPO1. XPO1 mutations exhibited striking lineage specificity, with enrichment in a variety of B-cell malignancies, and introduction of single amino acid substitutions in XPO1 initiated clonal, B-cell malignancy in vivo. Proteomic characterization identified that mutant XPO1 altered the nucleocytoplasmic distribution of hundreds of proteins in a sequence-specific manner that promoted oncogenesis. XPO1 mutations preferentially sensitized cells to inhibitors of nuclear export, providing a biomarker of response to this family of drugs. These data reveal a new class of oncogenic alteration based on change-of-function mutations in nuclear export signal recognition and identify therapeutic targets based on altered nucleocytoplasmic trafficking. SIGNIFICANCE: Here, we identify that heterozygous mutations in the main nuclear exporter in eukaryotic cells, XPO1, are positively selected in cancer and promote the initiation of clonal B-cell malignancies. XPO1 mutations alter nuclear export signal recognition in a sequence-specific manner and sensitize cells to compounds in clinical development inhibiting XPO1 function.This article is highlighted in the In This Issue feature, p. 1325.
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MESH Headings
- Active Transport, Cell Nucleus
- Animals
- Cell Proliferation
- Cell Transformation, Neoplastic
- Disease Models, Animal
- Gene Expression
- Genes, bcl-2
- Genes, myc
- Humans
- Karyopherins/chemistry
- Karyopherins/genetics
- Karyopherins/metabolism
- Leukemia, B-Cell/genetics
- Leukemia, B-Cell/metabolism
- Leukemia, B-Cell/mortality
- Leukemia, B-Cell/pathology
- Mice
- Mutation
- Nuclear Export Signals
- Organ Specificity/genetics
- Protein Binding
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Structure-Activity Relationship
- Exportin 1 Protein
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Affiliation(s)
- Justin Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria Sendino
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Barrio Sarriena s/n, Leioa, Spain
| | - Alexander N Gorelick
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alessandro Pastore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Matthew T Chang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alexander V Penson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elena I Gavrila
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Connor Stewart
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ella M Melnik
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Lillian Bitner
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Akihide Yoshimi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Stanley Chun-Wei Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daichi Inoue
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Bo Liu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Xiao J Zhang
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anthony R Mato
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ahmet Dogan
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael G Kharas
- Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yuhong Chen
- Blood Research Institute, Blood Center of Wisconsin, Milwaukee, Wisconsin
| | - Demin Wang
- Blood Research Institute, Blood Center of Wisconsin, Milwaukee, Wisconsin
| | - Rajesh K Soni
- Microchemistry and Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ronald C Hendrickson
- Microchemistry and Proteomics Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gorka Prieto
- Department of Communications Engineering, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Jose A Rodriguez
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country, Barrio Sarriena s/n, Leioa, Spain
| | - Barry S Taylor
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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Matsuzaka Y, Uesawa Y. Prediction Model with High-Performance Constitutive Androstane Receptor (CAR) Using DeepSnap-Deep Learning Approach from the Tox21 10K Compound Library. Int J Mol Sci 2019; 20:ijms20194855. [PMID: 31574921 PMCID: PMC6801383 DOI: 10.3390/ijms20194855] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 09/23/2019] [Accepted: 09/27/2019] [Indexed: 12/30/2022] Open
Abstract
The constitutive androstane receptor (CAR) plays pivotal roles in drug-induced liver injury through the transcriptional regulation of drug-metabolizing enzymes and transporters. Thus, identifying regulatory factors for CAR activation is important for understanding its mechanisms. Numerous studies conducted previously on CAR activation and its toxicity focused on in vivo or in vitro analyses, which are expensive, time consuming, and require many animals. We developed a computational model that predicts agonists for the CAR using the Toxicology in the 21st Century 10k library. Additionally, we evaluate the prediction performance of novel deep learning (DL)-based quantitative structure-activity relationship analysis called the DeepSnap-DL approach, which is a procedure of generating an omnidirectional snapshot portraying three-dimensional (3D) structures of chemical compounds. The CAR prediction model, which applies a 3D structure generator tool, called CORINA-generated and -optimized chemical structures, in the DeepSnap-DL demonstrated better performance than the existing methods using molecular descriptors. These results indicate that high performance in the prediction model using the DeepSnap-DL approach may be important to prepare suitable 3D chemical structures as input data and to enable the identification of modulators of the CAR.
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Affiliation(s)
- Yasunari Matsuzaka
- Department of Medical Molecular Informatics, Meiji Pharmaceutical University, Tokyo 204-8588, Japan.
| | - Yoshihiro Uesawa
- Department of Medical Molecular Informatics, Meiji Pharmaceutical University, Tokyo 204-8588, Japan.
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Zhao XM, Qin ZY, Zhang J, Yang Y, Jia P, Yang Q, Ma EB, Zhang JZ. Nuclear receptor hormone receptor 39 is required for locust moulting by regulating the chitinase and carboxypeptidase genes. Insect Mol Biol 2019; 28:537-549. [PMID: 30719786 DOI: 10.1111/imb.12569] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The nuclear receptor-mediated 20-hydroxyecdysone (20E) signalling pathway plays crucial roles in insects by initiating and regulating moulting and metamorphosis. In the present study, we identified and characterized a cDNA encoding a putative nuclear receptor protein (Locusta migratoria hormone receptor 39, LmHR39) based on L. migratoria transcriptomics data. Reverse-transcription quantitative PCR (RT-qPCR) revealed that LmHR39 shows low-level expression in the early days of fifth-instar nymphs, and peak expression occurs on day 5, which is followed by a decrease before ecdysis. LmHR39 transcription could be induced by 20E in vivo and was significantly suppressed by knocking down the expression of the L. migratoria ecdysone receptor gene and early-late gene LmHR3. After RNA interference of LmHR39 with double-stranded RNA (dsRNA), 85% of the insects showed abnormal morphology, with curly wings after moulting and delayed eclosion time. Haematoxylin and eosin staining indicated that apolysis of the integument and wing pad cuticle in the dsLmHR39-treated insects was delayed compared to that in the dsRNA for green fluorescent protein-injected control. Furthermore, RNA-sequencing and RT-qPCR analysis showed the expression level of carboxypeptidase genes (Carboxypeptidase A (CPA) and Carboxypeptidase M (CPM)) and chitin degrading genes (LmChitinase5 (LmCHT5) and LmChitinase10 (LmCHT10)) dramatically declined in the dsLmHR39-treated insects, implying that the LmHR39-mediated 20E signalling pathway is involved in the regulation of carboxypeptidase genes (CPA and CPM) and chitinase genes (LmCHT5 and LmCHT10), and participated in apolysis of the integument and wing pads during locust moulting.
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Affiliation(s)
- X-M Zhao
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Z-Y Qin
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
- College of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - J Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
- College of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Y Yang
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
- College of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - P Jia
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
- College of Life Science, Shanxi University, Taiyuan, Shanxi, China
| | - Q Yang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - E-B Ma
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
| | - J-Z Zhang
- Research Institute of Applied Biology, Shanxi University, Taiyuan, Shanxi, China
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41
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Moore TW, Frasor J. Editorial for Special Issue on "Alternative nuclear receptor ligands". Mol Cell Endocrinol 2019; 493:110479. [PMID: 31173820 DOI: 10.1016/j.mce.2019.110479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Terry W Moore
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood St., Chicago, Illinois 60612, USA; University of Illinois Cancer Center, 1801 W Taylor St., Chicago, Illinois 60612, USA.
| | - Jonna Frasor
- University of Illinois Cancer Center, 1801 W Taylor St., Chicago, Illinois 60612, USA; Department of Physiology and Biophysics, College of Medicine, University of Illinois at Chicago, 835 S. Wolcott St., Chicago, Illinois 60612, USA
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42
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Jiménez-Panizo A, Pérez P, Rojas AM, Fuentes-Prior P, Estébanez-Perpiñá E. Non-canonical dimerization of the androgen receptor and other nuclear receptors: implications for human disease. Endocr Relat Cancer 2019; 26:R479-R497. [PMID: 31252411 DOI: 10.1530/erc-19-0132] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 06/26/2019] [Indexed: 11/08/2022]
Abstract
Nuclear receptors are transcription factors that play critical roles in development, homeostasis and metabolism in all multicellular organisms. An important family of nuclear receptors comprises those members that respond to steroid hormones, and which is subdivided in turn into estrogen receptor (ER) isoforms α and β (NR3A1 and A2, respectively), and a second subfamily of so-called oxosteroid receptors. The latter includes the androgen receptor (AR/NR3C4), the glucocorticoid receptor (GR/NR3C1), the mineralocorticoid receptor (MR/NR3C2) and the progesterone receptor (PR/NR3C3). Here we review recent advances in our understanding of the structure-and-function relationship of steroid nuclear receptors and discuss their implications for the etiology of human diseases. We focus in particular on the role played by AR dysregulation in both prostate cancer (PCa) and androgen insensitivity syndromes (AIS), but also discuss conditions linked to mutations of the GR gene as well as those in a non-steroidal receptor, the thyroid hormone receptor (TR). Finally, we explore how these recent results might be exploited for the development of novel and selective therapeutic strategies.
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MESH Headings
- Androgen-Insensitivity Syndrome/etiology
- Androgen-Insensitivity Syndrome/metabolism
- Androgen-Insensitivity Syndrome/pathology
- Humans
- Male
- Prostatic Neoplasms/etiology
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Protein Multimerization
- Receptors, Androgen/chemistry
- Receptors, Androgen/genetics
- Receptors, Androgen/metabolism
- Receptors, Cytoplasmic and Nuclear/chemistry
- Receptors, Cytoplasmic and Nuclear/genetics
- Receptors, Cytoplasmic and Nuclear/metabolism
- Receptors, Glucocorticoid/chemistry
- Receptors, Glucocorticoid/genetics
- Receptors, Glucocorticoid/metabolism
- Receptors, Mineralocorticoid/chemistry
- Receptors, Mineralocorticoid/genetics
- Receptors, Mineralocorticoid/metabolism
- Receptors, Progesterone/chemistry
- Receptors, Progesterone/genetics
- Receptors, Progesterone/metabolism
- Receptors, Thyroid Hormone/chemistry
- Receptors, Thyroid Hormone/genetics
- Receptors, Thyroid Hormone/metabolism
- Steroids/metabolism
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Affiliation(s)
- Alba Jiménez-Panizo
- Department of Biochemistry and Molecular Biomedicine, Institute of Biomedicine (IBUB) of the University of Barcelona (UB), Barcelona, Spain
| | - Paloma Pérez
- Instituto de Biomedicina de Valencia (IBV)-CSIC, Valencia, Spain
| | - Ana M Rojas
- Computational Biology and Bioinformatics Group, Andalusian Center for Developmental Biology (CABD-CSIC), Sevilla, Spain
| | - Pablo Fuentes-Prior
- Molecular Bases of Disease, Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain
| | - Eva Estébanez-Perpiñá
- Department of Biochemistry and Molecular Biomedicine, Institute of Biomedicine (IBUB) of the University of Barcelona (UB), Barcelona, Spain
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Abstract
Nuclear receptors comprise a class of intracellular transcription factors whose major role is to act as sensors of various stimuli and to convert the external signal into a transcriptional output. Nuclear receptors (NRs) achieve this by possessing a ligand binding domain, which can bind cell permeable agonists, a DNA-binding domain, which binds the upstream sequences of target genes, and a regulatory domain that recruits the transcriptional machinery. The ligand binding alters the activation state of the NR, either by activating or inactivating its transcriptional output. Given the central role of NRs in signal transduction, many currently approved therapeutics modulate the activity of NRs. Here we discuss how PROTAC degraders afford a novel approach to abrogate the downstream signaling activity of NRs. We highlight six broad functional reasons why PROTAC degraders are preferable to the classical ligand binding pocket antagonists, with specific examples provided for each category. Lastly, as Androgen Receptor and Estrogen Receptor PROTAC degraders are being pursued as treatment for prostate cancer and breast cancer, respectively, a rationale is provided for the translational utility for the degradation of these two NRs.
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Affiliation(s)
| | - Taavi K Neklesa
- Halda Therapeutics, 23 Business Park, Branford, CT, 06405, USA.
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44
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Lee Y, Pei J, Baumhardt JM, Chook YM, Grishin NV. Structural prerequisites for CRM1-dependent nuclear export signaling peptides: accessibility, adapting conformation, and the stability at the binding site. Sci Rep 2019; 9:6627. [PMID: 31036839 PMCID: PMC6488578 DOI: 10.1038/s41598-019-43004-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 02/13/2019] [Accepted: 04/11/2019] [Indexed: 01/08/2023] Open
Abstract
Nuclear export signal (NES) motifs function as essential regulators of the subcellular location of proteins by interacting with the major nuclear exporter protein, CRM1. Prediction of NES is of great interest in many aspects of research including cancer, but currently available methods, which are mostly based on the sequence-based approaches, have been suffered from high false positive rates since the NES consensus patterns are quite commonly observed in protein sequences. Therefore, finding a feature that can distinguish real NES motifs from false positives is desired to improve the prediction power, but it is quite challenging when only using the sequence. Here, we provide a comprehensive table for the validated cargo proteins, containing the location of the NES consensus patterns with the disordered propensity plots, known protein domain information, and the predicted secondary structures. It could be useful for determining the most plausible NES region in the context of the whole protein sequence and suggests possibilities for some non-binders of the annotated regions. In addition, using the currently available crystal structures of CRM1 bound to various classes of NES peptides, we adopted, for the first time, the structure-based prediction of the NES motifs bound to the CRM1's binding groove. Combining sequence-based and structure-based predictions, we suggest a novel and more straight-forward approach to identify CRM1-binding NES sequences by analysis of their structural prerequisites and energetic evaluation of the stability at the CRM1's binding site.
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Affiliation(s)
- Yoonji Lee
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jimin Pei
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jordan M Baumhardt
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yuh Min Chook
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Nick V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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45
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Meijer FA, Leijten-van de Gevel IA, de Vries RMJM, Brunsveld L. Allosteric small molecule modulators of nuclear receptors. Mol Cell Endocrinol 2019; 485:20-34. [PMID: 30703487 DOI: 10.1016/j.mce.2019.01.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 01/23/2019] [Accepted: 01/25/2019] [Indexed: 02/08/2023]
Abstract
Nuclear Receptors (NRs) are multi-domain proteins, whose natural regulation occurs via ligands for a classical, orthosteric, binding pocket and via intra- and inter-domain allosteric mechanisms. Allosteric modulation of NRs via synthetic small molecules has recently emerged as an interesting entry to address the need for small molecules targeting NRs in pathology, via novel modes of action and with beneficial profiles. In this review the general concept of allosteric modulation in drug discovery is first discussed, serving as a background and inspiration for NRs. Subsequently, the review focuses on examples of small molecules that allosterically modulate NRs, with a strong focus on structural information and the ligand binding domain. Recently discovered nanomolar potent allosteric site NR modulators are catapulting allosteric targeting of NRs to the center of attention. The obtained insights serve as a basis for recommendations for the next steps to take in allosteric small molecular targeting of NRs.
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Affiliation(s)
- Femke A Meijer
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Iris A Leijten-van de Gevel
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Rens M J M de Vries
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Den Dolech 2, 5612AZ, Eindhoven, the Netherlands.
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46
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Tian Q, Zhao G, Sun Y, Yuan D, Guo Q, Zhang Y, Liu J, Zhang S. Exportin-1 is required for the maintenance of the planarian epidermal lineage. Int J Biol Macromol 2019; 126:1050-1055. [PMID: 30615964 DOI: 10.1016/j.ijbiomac.2019.01.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 06/27/2018] [Revised: 01/03/2019] [Accepted: 01/03/2019] [Indexed: 01/27/2023]
Abstract
Nucleocytoplasmic transport is essential for normal cellular function that mediates cargo transport from the cytoplasm to the nucleus. However, the mechanisms of nucleocytoplasmic transport that integrate stem cell development remain largely unknown. Since it has a large population of stem cells, the planarian flatworm is an ideal system for the study of adult stem cell lineage development in vivo. Here, we focus on exportin-1, which is the most conserved nuclear export receptor. Homologs of exportin-1 have no currently known role in stem cell biology. RNA interference targeting exportin-1 caused a failure in anterior and posterior regeneration, and resulted in curly and lysis phenotypes in both intact and regenerating flatworms. During the course of exportin-1 RNAi phenotype, cell division was significantly decreased, and the expression of the epidermal cell markers (vimentin and laminB) were lost from the intact body. Additionally, the expression levels of the neoblast marker piwiA decreased. By contrast, the expression levels of the epidermal progenitor markers NB21.11e and AGAT1 increased. These results suggest that exportin-1 is required for the maintenance of the epidermal lineage in planarians. Inhibition of exportin-1 could promote the premature differentiation of neoblasts to the epidermal lineages, disrupting the proper epidermal maturation.
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Affiliation(s)
- Qingnan Tian
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Guixia Zhao
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yujia Sun
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Dandan Yuan
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Qi Guo
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Yizhe Zhang
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiaqian Liu
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China.
| | - Shoutao Zhang
- School of LifeSciences, Zhengzhou University, Zhengzhou, Henan, China; Henan Key Laboratory of Bioactive Macromolecules, Zhengzhou, Henan, China.
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47
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Veras Ribeiro Filho H, Tambones IL, Mariano Gonçalves Dias M, Bernardi Videira N, Bruder M, Amorim Amato A, Migliorini Figueira AC. Modulation of nuclear receptor function: Targeting the protein-DNA interface. Mol Cell Endocrinol 2019; 484:1-14. [PMID: 30703486 DOI: 10.1016/j.mce.2019.01.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 02/02/2023]
Abstract
Nuclear receptors (NRs) are a superfamily of ligand-dependent transcription factors that modulate several biological processes. Traditionally, modulation of NRs has been focused on the development of ligands that recognize and bind to the ligand binding domain (LBD), resulting in activation or repression of transcription through the recruitment of coregulators. However, for more severe diseases, such as breast and prostate cancer, the conventional treatment addressing LBD modulation is not always successful, due to tumor resistance. To overcome these challenges and aiming to modulate NR activity by inhibiting the NR-DNA interaction, new studies focus on the development of molecules targeting alternative sites and domains on NRs. Here, we discuss two different approaches for this alternative NR modulation: one targeting the NR DNA binding domain (DBD); and the other targeting the DNA sites recognized by NRs. Our aim is to present the challenges and perspectives for developing specific inhibitors for each purpose, alongside with already reported examples.
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Affiliation(s)
- Helder Veras Ribeiro Filho
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil; Graduate Program in Biosciences and Technology of Bioactive Products, Institute of Biology, State University of Campinas (Unicamp), Campinas, 13083-970, Brazil
| | - Izabella Luisa Tambones
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil; Graduate Program in Biosciences and Technology of Bioactive Products, Institute of Biology, State University of Campinas (Unicamp), Campinas, 13083-970, Brazil
| | - Marieli Mariano Gonçalves Dias
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil; Graduate Program in Molecular and Functional Biology, Institute of Biology, State University of Campinas (Unicamp), Campinas, SP, 13083-970, Brazil
| | - Natalia Bernardi Videira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil
| | - Marjorie Bruder
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil
| | - Angélica Amorim Amato
- Laboratory of Molecular Pharmacology, Department of Pharmaceutical Science, University of Brasilia (UnB), Brasília, DF, 70910-900, Brazil
| | - Ana Carolina Migliorini Figueira
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, 13083-970, Brazil.
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48
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Piskacek M, Havelka M, Jendruchova K, Knight A. Nuclear hormone receptors: Ancient 9aaTAD and evolutionally gained NCoA activation pathways. J Steroid Biochem Mol Biol 2019; 187:118-123. [PMID: 30468856 DOI: 10.1016/j.jsbmb.2018.11.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/18/2018] [Accepted: 11/18/2018] [Indexed: 12/12/2022]
Abstract
In higher metazoans, the nuclear hormone receptors activate transcription trough their specific adaptors, nuclear hormone receptor adaptors NCoA, which are absent in lower metazoans. The Nine amino acid TransActivation Domain, 9aaTAD, was reported for a large number of the transcription activators that recruit general mediators of transcription. In this study, we demonstrated that the 9aaTAD from NHR-49 receptor of nematode C.elegans activates transcription as a small peptide. We showed that the ancient 9aaTAD domains are conserved in the nuclear hormone receptors including human HNF4, RARa, VDR and PPARg. Also their small 9aaTAD peptides effectively activated transcription in absence of the NCoA adaptors. We also showed that adjacent H11 domains in ancient and modern hormone receptors have an inhibitory effect on their 9aaTAD function.
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Affiliation(s)
- Martin Piskacek
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Czech Republic; Laboratory of Cancer Biology and Genetics, Czech Republic; Gamma Delta T Cell Laboratory, Czech Republic.
| | - Marek Havelka
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Czech Republic; Laboratory of Cancer Biology and Genetics, Czech Republic; Gamma Delta T Cell Laboratory, Czech Republic
| | - Kristina Jendruchova
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Czech Republic; Laboratory of Cancer Biology and Genetics, Czech Republic; Gamma Delta T Cell Laboratory, Czech Republic
| | - Andrea Knight
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Czech Republic; Laboratory of Cancer Biology and Genetics, Czech Republic; Gamma Delta T Cell Laboratory, Czech Republic
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49
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van de Wiel SMW, Bijsmans ITGW, van Mil SWC, van de Graaf SFJ. Identification of FDA-approved drugs targeting the Farnesoid X Receptor. Sci Rep 2019; 9:2193. [PMID: 30778102 PMCID: PMC6379390 DOI: 10.1038/s41598-019-38668-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 12/21/2018] [Indexed: 12/25/2022] Open
Abstract
The farnesoid X receptor (FXR) belongs to the nuclear receptor family and is activated by bile acids. Multiple, chemically rather diverse, FXR agonists have been developed and several of these compounds are currently tested in clinical trials for NAFLD and cholestasis. Here, we investigated possible FXR-agonism or antagonism of existing FDA/EMA-approved drugs. By using our recently developed FRET-sensor, containing the ligand binding domain of FXR (FXR-LBD), 1280 FDA-approved drugs were screened for their ability to activate FXR in living cells using flow cytometry. Fifteen compounds induced the sensor for more than twenty percent above background. Real-time confocal microscopy confirmed that avermectin B1a, gliquidone, nicardipine, bepridil and triclosan activated the FRET sensor within two minutes. These compounds, including fluticasone, increased mRNA expression of FXR target genes OSTα and OSTβ in Huh7 cells, and in most cases also of MRP2, SHP and FGF19. Finally, avermectin B1a, gliquidone, nicardipine and bepridil significantly increased IBABP promoter activity in a luciferase reporter assay in a dose-dependent manner. In conclusion, six FDA/EMA-approved drugs currently used in the clinical practice exhibit moderate agonistic FXR activity. This may on the one hand explain (undesired) side-effects, but on the other hand may form an opportunity for polypharmacology.
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Affiliation(s)
- Sandra M W van de Wiel
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology and Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology and Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ingrid T G W Bijsmans
- Center for Molecular Medicine, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Saskia W C van Mil
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology and Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Center for Molecular Medicine, UMC Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Stan F J van de Graaf
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology and Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
- Department of Gastroenterology and Hepatology, Amsterdam Gastroenterology and Metabolism, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
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50
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Tonnessen BW, Bossa-Castro AM, Mauleon R, Alexandrov N, Leach JE. Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice. Sci Rep 2019; 9:1536. [PMID: 30733489 PMCID: PMC6367480 DOI: 10.1038/s41598-018-38195-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/18/2018] [Indexed: 12/30/2022] Open
Abstract
Plant disease resistance that is durable and effective against diverse pathogens (broad-spectrum) is essential to stabilize crop production. Such resistance is frequently controlled by Quantitative Trait Loci (QTL), and often involves differential regulation of Defense Response (DR) genes. In this study, we sought to understand how expression of DR genes is orchestrated, with the long-term goal of enabling genome-wide breeding for more effective and durable resistance. We identified short sequence motifs in rice promoters that are shared across Broad-Spectrum DR (BS-DR) genes co-expressed after challenge with three major rice pathogens (Magnaporthe oryzae, Rhizoctonia solani, and Xanthomonas oryzae pv. oryzae) and several chemical elicitors. Specific groupings of these BS-DR-associated motifs, called cis-Regulatory Modules (CRMs), are enriched in DR gene promoters, and the CRMs include cis-elements known to be involved in disease resistance. Polymorphisms in CRMs occur in promoters of genes in resistant relative to susceptible BS-DR haplotypes providing evidence that these CRMs have a predictive role in the contribution of other BS-DR genes to resistance. Therefore, we predict that a CRM signature within BS-DR gene promoters can be used as a marker for future breeding practices to enrich for the most responsive and effective BS-DR genes across the genome.
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Affiliation(s)
| | | | - Ramil Mauleon
- International Rice Research Institute, Manila, Philippines
| | | | - Jan E Leach
- Colorado State University, Fort Collins, CO, USA.
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