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Xia Q, Liu F, Zhou Y, Yang G, Li F, Liang T, Liu J, Li W, Huang Y, Zhu C. CD47-SIRPα signaling-inspired engineered monocytes for preventing the progression of atherosclerotic plaques. Mater Today Bio 2024; 28:101178. [PMID: 39211288 PMCID: PMC11357865 DOI: 10.1016/j.mtbio.2024.101178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 07/14/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024] Open
Abstract
The accumulation of foam cells in the subendothelial space of the vascular wall to form plaques is the real cause of atherosclerotic lesions. Conventional interventions, such as statins and anti-cytokine or anti-inflammatory therapies, suffer problems in terms of their short therapeutic outcomes and potential disruption of the immune system. The development of more efficient therapeutics to restrict the initial progression of plaques appears to be crucial for treating and preventing atherosclerosis. Decreasing foam cell formation by reversing the excessive phagocytosis of modified low-density lipoprotein (LDL) in macrophages is highly desirable. Here, we developed a strategy based on engineered monocytes to dynamically regulate lipid uptake by macrophages inspired by a CD47-SIRPα signaling-induced defect in the phagocytosis of lesional macrophages at the advanced stage of AS. Briefly, a complex called CD47p-GQDs-miR223, which is designed to interact with SIRPα, was synthesized to remodel monocytes by decreasing the uptake of oxidized LDL through the activation of CD47-SIRPα signaling. After injection, these monocytes compete for recruitment to atherosclerotic plaques, release gene drugs and mediate anti-inflammatory phenotypic remodeling of the aboriginal macrophages, effectively inhibiting the development of foam cells. Our strategy provides a new therapeutic for preventing the progression of atherosclerosis.
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Affiliation(s)
- Qing Xia
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Feila Liu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Yue Zhou
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Guanyuan Yang
- Department of Anatomy, State Key Laboratory of Trauma, Burn and Combined Injury, National and Regional Engineering Laboratory of Tissue Engineering, Third Military Medical University, Chongqing, 400038, China
| | - Fangzhou Li
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, 300192, China
| | - Tingting Liang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Jun Liu
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Wanling Li
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Yaqing Huang
- School of Pharmacy and Bioengineering, Chongqing University of Technology, Chongqing, 400054, China
| | - Chuhong Zhu
- Department of Anatomy, State Key Laboratory of Trauma, Burn and Combined Injury, National and Regional Engineering Laboratory of Tissue Engineering, Third Military Medical University, Chongqing, 400038, China
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Wu K, Huang S, Zhao Y, Umar A, Chen H, Yu Z, Huang J. Hepatocyte nuclear factor 4 located in different developmental stages in Schistosoma japonicum and involved in important metabolic pathways. Biomed J 2024:100726. [PMID: 38621646 DOI: 10.1016/j.bj.2024.100726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 04/01/2024] [Accepted: 04/08/2024] [Indexed: 04/17/2024] Open
Abstract
BACKGROUND Nuclear receptors (NRs) are vital for regulating gene expression un organisms. Hepatocyte nuclear factor 4 (HNF4), a class of NRs, participates in blood feeding and intestinal maintenance in schistosomes. However, there is limited research on the molecular and functional characterization of HNF4 in Schistosoma japonicum (S. japonicum). METHODS Highly specific polyclonal antibodies were generated to analyze the expression and tissue localization of S. japonicum HNF4 (SjHNF4). The potential biological functions of SjHNF4 were characterized by transcriptome and pull-down analysis. Subsequently, enrichment analysis was performed to identify the specific signaling pathways linked to SjHNF4. RESULTS The SjHNF4 protein was expressed heterologously and purified successfully. High purity and high potency polyclonal antibodies were further prepared. The expression of SjHNF4 was higher in female compared to male worms at both transcriptional and protein levels. Female worms expressed SjHNF4 in their perithecium, reproductive system, and certain parts of the intestinal tissues. SjHNF4 was also detected in the perithecium of male worms, as well as in the head, body of cercaria, and eggs. Furthermore, our findings highlighted the potential role of SjHNF4 in blood feeding and its interaction with crucial pathways such as glucose metabolism, lipid metabolism, and nucleotide metabolism. CONCLUSIONS This study shed light on the location of SjHNF4 in different life stages of S. japonicum, particularly associated with the female schistosomes. A strong correlation was observed between SjHNF4 and essential metabolic pathways. These findings laid a solid groundwork for the research on the relationship between NRs and schistosomes.
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Affiliation(s)
- Kaijuan Wu
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China. 410013; China-Africa Research Center of Infectious Diseases, Central South University, Changsha Hunan, China. 410013
| | - Shuaiqin Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China. 410013; China-Africa Research Center of Infectious Diseases, Central South University, Changsha Hunan, China. 410013
| | - Yiming Zhao
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China. 410013; China-Africa Research Center of Infectious Diseases, Central South University, Changsha Hunan, China. 410013
| | - Abdulrahim Umar
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China. 410013
| | - Hao Chen
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China. 410013; China-Africa Research Center of Infectious Diseases, Central South University, Changsha Hunan, China. 410013
| | - Zheng Yu
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, Hunan, China. 410013; China-Africa Research Center of Infectious Diseases, Central South University, Changsha Hunan, China. 410013
| | - Jing Huang
- Department of Parasitology, School of Basic Medical Science, Central South University, Changsha, Hunan, China. 410013; China-Africa Research Center of Infectious Diseases, Central South University, Changsha Hunan, China. 410013.
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Rahman MH, Hegazy L. Mechanism of antagonist ligand binding to REV-ERBα. Sci Rep 2024; 14:8401. [PMID: 38600172 PMCID: PMC11006950 DOI: 10.1038/s41598-024-58945-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/04/2024] [Indexed: 04/12/2024] Open
Abstract
REV-ERBα, a therapeutically promising nuclear hormone receptor, plays a crucial role in regulating various physiological processes such as the circadian clock, inflammation, and metabolism. However, the availability of chemical probes to investigate the pharmacology of this receptor is limited, with SR8278 being the only identified synthetic antagonist. Moreover, no X-ray crystal structures are currently available that demonstrate the binding of REV-ERBα to antagonist ligands. This lack of structural information impedes the development of targeted therapeutics. To address this issue, we employed Gaussian accelerated molecular dynamics (GaMD) simulations to investigate the binding pathway of SR8278 to REV-ERBα. For comparison, we also used GaMD to observe the ligand binding process of STL1267, for which an X-ray structure is available. GaMD simulations successfully captured the binding of both ligands to the receptor's orthosteric site and predicted the ligand binding pathway and important amino acid residues involved in the antagonist SR8278 binding. This study highlights the effectiveness of GaMD in investigating protein-ligand interactions, particularly in the context of drug recognition for nuclear hormone receptors.
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Affiliation(s)
- Mohammad Homaidur Rahman
- Center for Clinical Pharmacology, Washington University School of Medicine, University of Health Sciences and Pharmacy, St. Louis, MO, USA
- Department of Pharmaceutical and Administrative Sciences, University of Health Sciences and Pharmacy, St. Louis, MO, USA
| | - Lamees Hegazy
- Center for Clinical Pharmacology, Washington University School of Medicine, University of Health Sciences and Pharmacy, St. Louis, MO, USA.
- Department of Pharmaceutical and Administrative Sciences, University of Health Sciences and Pharmacy, St. Louis, MO, USA.
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4
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Piir G, Sild S, Maran U. Interpretable machine learning for the identification of estrogen receptor agonists, antagonists, and binders. CHEMOSPHERE 2024; 347:140671. [PMID: 37951393 DOI: 10.1016/j.chemosphere.2023.140671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 10/25/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
An abnormal hormonal activity or exposure to endocrine-disrupting chemicals (EDCs) can cause endocrine system malfunction. Among the many interactions EDCs can affect is the disruption of estrogen signalling, which can lead to adverse health effects such as cancer, osteoporosis, neurodegenerative diseases, cardiovascular disease, insulin resistance, and obesity. Knowing which chemical can act as an EDC is a significant advantage and a practical necessity. New Approach Methodologies (NAM) computational models offer a quick and cost-effective solution for preliminary hazard assessment of chemicals without animal testing. Therefore, a machine learning approach was used to investigate the relationships between estrogen receptor (ER) activity and chemical structure to identify chemicals that can interact with ER. For this purpose, the consolidated in vitro assay data from ToxCast/Tox21 projects was used for developing Random Forest classification models for ER binding, agonists, and antagonists. The overall classification prediction accuracy reaches up to 82%, depending on whether the model predicted agonists, antagonists, or compounds that bind to the active site. Given the imbalance in endocrine disruption data, the derived models are good candidates for deprioritising chemicals and reducing animal testing. The interpretation of theoretical molecular descriptors of the models was consistent with the molecular interactions known in the ligand binding pocket. The estimated class probabilities enabled the analysis of the applicability domain of the developed models and the assessment of the predictions' reliability, followed by the guidelines for interpreting prediction results. The models are openly accessible and useable at QsarDB.org (http://dx.doi.org/10.15152/QDB.259) according to the FAIR (Findable, Accessible, Interoperable, Reusable) principles.
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Affiliation(s)
- Geven Piir
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu, 50411, Estonia
| | - Sulev Sild
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu, 50411, Estonia
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu, 50411, Estonia.
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5
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Khan AF, Karami S, Peidl AS, Waiters KD, Babajide MF, Bawa-Khalfe T. Androgen Receptor in Hormone Receptor-Positive Breast Cancer. Int J Mol Sci 2023; 25:476. [PMID: 38203649 PMCID: PMC10779387 DOI: 10.3390/ijms25010476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/28/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Breast cancer subtypes expressing hormone receptors (HR+ BCa) have a good prognosis and respond to first-line endocrine therapy (ET). However, the majority of HR+ BCa patients exhibit intrinsic or acquired ET resistance (ET-R) and rapid onset of incurable metastatic BCa. With the failure of conventional ET, limited targeted therapy exists for ET-R HR+ BCa patients. The androgen receptor (AR) in HR-negative BCa subtypes is emerging as an attractive alternative target for therapy. The AR drives Luminal AR (LAR) triple-negative breast cancer progression, and LAR patients consistently exhibit positive clinical benefits with AR antagonists in clinical trials. In contrast, the function of the AR in HR+ BCa is more conflicting. AR in HR+ BCa correlates with a favorable prognosis, and yet, the AR supports the development of ET-R BCa. While AR antagonists were ineffective, ongoing clinical trials with a selective AR modulator have shown promise for HR+ BCa patients. To understand the incongruent actions of ARs in HR+ BCa, the current review discusses how the structure and post-translational modification impact AR function. Additionally, completed and ongoing clinical trials with FDA-approved AR-targeting agents for BCa are presented. Finally, we identify promising investigational small molecules and chimera drugs for future HR+ BCa therapy.
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Affiliation(s)
| | | | | | | | | | - Tasneem Bawa-Khalfe
- Center for Nuclear Receptors & Cell Signaling, Department of Biology & Biochemistry, University of Houston, 3517 Cullen Blvd, SERC Bldg., Rm 3010, Houston, TX 77204-5056, USA (K.D.W.)
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6
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Thakur K, Khan H, Grewal AK, Singh TG. Nuclear orphan receptors: A novel therapeutic agent in neuroinflammation. Int Immunopharmacol 2023; 124:110845. [PMID: 37690241 DOI: 10.1016/j.intimp.2023.110845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 08/14/2023] [Accepted: 08/20/2023] [Indexed: 09/12/2023]
Abstract
Orphan receptors constitute a historically varied subsection of a superfamily of nuclear receptors. Nuclear receptors regulate gene expression in response to ligand signals and are particularly alluring therapeutic targets for chronic illnesses. Neuroinflammation and neurodegenerative diseases have been linked to these orphan nuclear receptors. Preclinical and clinical evidence suggests that orphan receptors could serve as future targets in neuroinflammation, such as Parkinson's disease (PD), Alzheimer's Disease (AD), Huntington's Disease (HD), Multiple Sclerosis (MS), and Cerebral Ischemia. Given the therapeutic relevance of certain orphan receptors in a variety of disorders, their potential in neuroinflammation remains unproven. There is substantial evidence that ligand-activated transcription factors have great promise for preventing neurodegenerative and neurological disorders, with certain orphan nuclear receptors i.e., PPARγ, NR4As, and orphan GPCRs holding particularly high potential. Based on previous findings, we attempted to determine the contribution of PPAR, NR4As, and orphan GPCRs-regulated neuroinflammation to the pathogenesis of these disorders and their potential to become novel therapeutic targets.
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Affiliation(s)
- Kiran Thakur
- Chitkara College of Pharmacy, Chitkara University, 140401 Punjab, India
| | - Heena Khan
- Chitkara College of Pharmacy, Chitkara University, 140401 Punjab, India
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7
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Tsai JM, Aguirre JD, Li YD, Brown J, Focht V, Kater L, Kempf G, Sandoval B, Schmitt S, Rutter JC, Galli P, Sandate CR, Cutler JA, Zou C, Donovan KA, Lumpkin RJ, Cavadini S, Park PMC, Sievers Q, Hatton C, Ener E, Regalado BD, Sperling MT, Słabicki M, Kim J, Zon R, Zhang Z, Miller PG, Belizaire R, Sperling AS, Fischer ES, Irizarry R, Armstrong SA, Thomä NH, Ebert BL. UBR5 forms ligand-dependent complexes on chromatin to regulate nuclear hormone receptor stability. Mol Cell 2023; 83:2753-2767.e10. [PMID: 37478846 PMCID: PMC11134608 DOI: 10.1016/j.molcel.2023.06.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 07/23/2023]
Abstract
Nuclear hormone receptors (NRs) are ligand-binding transcription factors that are widely targeted therapeutically. Agonist binding triggers NR activation and subsequent degradation by unknown ligand-dependent ubiquitin ligase machinery. NR degradation is critical for therapeutic efficacy in malignancies that are driven by retinoic acid and estrogen receptors. Here, we demonstrate the ubiquitin ligase UBR5 drives degradation of multiple agonist-bound NRs, including the retinoic acid receptor alpha (RARA), retinoid x receptor alpha (RXRA), glucocorticoid, estrogen, liver-X, progesterone, and vitamin D receptors. We present the high-resolution cryo-EMstructure of full-length human UBR5 and a negative stain model representing its interaction with RARA/RXRA. Agonist ligands induce sequential, mutually exclusive recruitment of nuclear coactivators (NCOAs) and UBR5 to chromatin to regulate transcriptional networks. Other pharmacological ligands such as selective estrogen receptor degraders (SERDs) degrade their receptors through differential recruitment of UBR5 or RNF111. We establish the UBR5 transcriptional regulatory hub as a common mediator and regulator of NR-induced transcription.
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Affiliation(s)
- Jonathan M Tsai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob D Aguirre
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Yen-Der Li
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Jared Brown
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Vivian Focht
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Lukas Kater
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Brittany Sandoval
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stefan Schmitt
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Justine C Rutter
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pius Galli
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Science, University of Basel, Basel, Switzerland
| | - Colby R Sandate
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jevon A Cutler
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Charles Zou
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ryan J Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Paul M C Park
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Quinlan Sievers
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlie Hatton
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Ener
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Brandon D Regalado
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Micah T Sperling
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Mikołaj Słabicki
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeonghyeon Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Rebecca Zon
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Zinan Zhang
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Peter G Miller
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Roger Belizaire
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Division of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Adam S Sperling
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Rafael Irizarry
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Scott A Armstrong
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Benjamin L Ebert
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA.
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Xi L, Shi A, Shen T, Wang G, Wei Y, Guo J. Licraside as novel potent FXR agonist for relieving cholestasis: structure-based drug discovery and biological evaluation studies. Front Pharmacol 2023; 14:1197856. [PMID: 37397498 PMCID: PMC10309033 DOI: 10.3389/fphar.2023.1197856] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/06/2023] [Indexed: 07/04/2023] Open
Abstract
Cholestasis is a common clinical disease caused by a disorder in bile acids (BAs) homeostasis, which promotes its development. The Farnesoid X receptor (FXR) plays a critical role in regulating BAs homeostasis, making it an essential target for cholestasis treatment. Although several active FXR agonists have been identified, effective drugs for cholestasis are still lacking. To address this, a molecular docking-based virtual screening method was used to identify potential FXR agonists. A hierarchical screening strategy was employed to improve the screening accuracy, and six compounds were selected for further evaluation. Dual-luciferase reporter gene assay was used to demonstrate FXR activation by the screened compounds, and their cytotoxicity was then evaluated. Among the compounds, licraside showed the best performance and was selected for in vivo evaluation using an ANIT-induced cholestasis animal model. Results demonstrated that licraside significantly reduced biliary TBA, serum ALT, AST, GGT, ALP, TBIL, and TBA levels. Liver histopathological analysis showed that licraside also had a therapeutic effect on ANIT-induced liver injury. Overall, these findings suggest that licraside is an FXR agonist with potential therapeutic effects on cholestasis. This study provides valuable insights into the development of novel lead compounds from traditional Chinese medicine for cholestasis treatment.
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Affiliation(s)
- Lili Xi
- Office of Institution of Drug Clinical Trial, The First Hospital of Lanzhou University, Lanzhou, China
| | - Axi Shi
- Department of Pharmacy, The First Hospital of Lanzhou University, Lanzhou, China
| | - Tiantian Shen
- The First School of Clinical Medicine, Lanzhou University, Lanzhou, China
| | - Guoxu Wang
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Yuhui Wei
- Department of Pharmacy, The First Hospital of Lanzhou University, Lanzhou, China
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, Macao, China
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9
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The marionette mechanism of domain-domain communication in the antagonist, agonist, and coactivator responses of the estrogen receptor. Proc Natl Acad Sci U S A 2023; 120:e2216906120. [PMID: 36730193 PMCID: PMC9963092 DOI: 10.1073/pnas.2216906120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The human estrogen receptor α (hERα) is involved in the regulation of growth, development, and tissue homeostasis. Agonists that bind to the receptor's ligand-binding domain (LBD) lead to recruitment of coactivators and the enhancement of gene expression. In contrast, antagonists bind to the LBD and block the binding of coactivators thus decreasing gene expressions. In this work, we carry out simulations using the AWSEM (Associative memory, Water mediated, Structure and Energy Model)-Suite force field along with the 3SPN.2C force field for DNA to predict the structure of hERα and study its dynamics when binding to DNA and coactivators. Using simulations of antagonist-bound hERα and agonist-bound hERα by themselves and also along with bound DNA and coactivators, principal component analyses and free energy landscape analyses capture the pathway of domain-domain communication for agonist-bound hERα. This communication is mediated through the hinge domains that are ordinarily intrinsically disordered. These disordered segments manipulate the hinge domains much like the strings of a marionette as they twist in different ways when antagonists or agonists are bound to the ligand-binding domain.
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10
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Feng Y, Cui J, Jin B, Li X, Zhang X, Liu L, Zhang L. In Vitro Binding Effects of the Ecdysone Receptor-Binding Domain and PonA in Plutella xylostella. Molecules 2023; 28:molecules28031426. [PMID: 36771090 PMCID: PMC9920912 DOI: 10.3390/molecules28031426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
Both insect ecdysone receptors and ultraspiracle belong to the nuclear receptor family. They form a nanoscale self-assembling complex with ecdysteroids in cells, transit into the nucleus, bind with genes to initiate transcription, and perform specific biological functions to regulate the molting, metamorphosis, and growth processes of insects. Therefore, this complex is an important target for the development of eco-friendly insecticides. The diamondback moth (Plutella xylostella) is a devastating pest of cruciferous vegetable crops, wreaking havoc worldwide and causing severe economic losses, and this pest has developed resistance to most chemical insecticides. In this study, highly pure EcR and USP functional domains were obtained by constructing a prokaryotic expression system for the diamondback moth EcR and USP functional domain genes, and the differences between EcR and USP binding domain monomers and dimers were analyzed using transmission electron microscopy and zeta potential. Radioisotope experiments further confirmed that the binding affinity of PonA to the EcR/USP dimer was enhanced approximately 20-fold compared with the binding affinity to the PxGST-EcR monomer. The differences between PonA and tebufenozide in binding with EcR/USP were examined. Molecular simulations showed that the hydrogen bonding network formed by Glu307 and Arg382 on the EcR/USP dimer was a key factor in the affinity enhancement. This study provides a rapid and sensitive method for screening ecdysone agonists for ecdysone receptor studies in vitro.
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Affiliation(s)
- Yanjiao Feng
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Jialin Cui
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Binyan Jin
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Xiuzhen Li
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Xiaoming Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Libing Liu
- Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
- Correspondence: (L.L.); (L.Z.)
| | - Li Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
- Correspondence: (L.L.); (L.Z.)
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Li X, Liu S, Qi D, Qi H, Wang Y, Zhao K, Tian F. Genome-wide identification and expression of the peroxisome proliferator-activated receptor gene family in the Tibetan highland fish Gymnocypris przewalskii. FISH PHYSIOLOGY AND BIOCHEMISTRY 2022; 48:1685-1699. [PMID: 36469183 DOI: 10.1007/s10695-022-01152-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 11/27/2022] [Indexed: 06/17/2023]
Abstract
Peroxisome proliferator-activated receptor (PPAR) plays an important role in the regulation of lipid metabolism and has been widely identified in diverse species. Gymnocypris przewalskii is a native fish of the Qinghai Tibetan Plateau that survives in a chronically cold environment. In the current study, we conducted genome-wide identification of PPAR genes, revealing the existence of seven PPARs in the G. przewalskii genome. Collinearity was observed between two copies of PPARαb and PPARγ in G. przewalskii, suggesting that the additional copy might be gained through whole genome duplication. Both phylogenetic and multiple sequence alignment analyses indicated that PPARs in G. przewalskii were conserved with teleosts. The cold treatment (10 °C and 4 °C) led to the developmental delay of G. przewalskii embryos. Continuous expression of PPARs was observed during the embryonic development of G. przewalskii under normal and cold conditions, with significantly different transcriptional patterns. These results indicated that PPARs participated in the embryonic development of G. przewalskii, and were involved in the cold response during development. The current study proposed a potential role of PPARs in the cold response in the embryonic development of G. przewalskii, which shed light on understanding cold adaptation in Tibetan highland fish.
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Affiliation(s)
- Xiaohuan Li
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810001, Qinghai, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Sijia Liu
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810001, Qinghai, China
| | - Delin Qi
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, Qinghai, China
| | - Hongfang Qi
- Qinghai Provincial Key Laboratory of Breeding and Protection of Gymnocypris Przewalskii, Xining, Qinghai, China
| | - Yang Wang
- Qinghai Provincial Key Laboratory of Breeding and Protection of Gymnocypris Przewalskii, Xining, Qinghai, China
| | - Kai Zhao
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810001, Qinghai, China.
| | - Fei Tian
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, 810001, Qinghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
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12
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Jayaprakash S, Hegde M, Girisa S, Alqahtani MS, Abbas M, Lee EHC, Yap KCH, Sethi G, Kumar AP, Kunnumakkara AB. Demystifying the Functional Role of Nuclear Receptors in Esophageal Cancer. Int J Mol Sci 2022; 23:ijms231810952. [PMID: 36142861 PMCID: PMC9501100 DOI: 10.3390/ijms231810952] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/14/2022] [Accepted: 09/14/2022] [Indexed: 11/16/2022] Open
Abstract
Esophageal cancer (EC), an aggressive and poorly understood disease, is one of the top causes of cancer-related fatalities. GLOBOCAN 2020 reports that there are 544,076 deaths and 604,100 new cases expected worldwide. Even though there are various advancements in treatment procedures, this cancer has been reported as one of the most difficult cancers to cure, and to increase patient survival; treatment targets still need to be established. Nuclear receptors (NRs) are a type of transcription factor, which has a key role in several biological processes such as reproduction, development, cellular differentiation, stress response, immunity, metabolism, lipids, and drugs, and are essential regulators of several diseases, including cancer. Numerous studies have demonstrated the importance of NRs in tumor immunology and proved the well-known roles of multiple NRs in modulating proliferation, differentiation, and apoptosis. There are surplus of studies conducted on NRs and their implications in EC, but only a few studies have demonstrated the diagnostic and prognostic potential of NRs. Therefore, there is still a paucity of the role of NRs and different ways to target them in EC cells to stop them from spreading malignancy. This review emphasizes the significance of NRs in EC by discussing their diverse agonists as well as antagonists and their response to tumor progression. Additionally, we emphasize NRs’ potential to serve as a novel therapeutic target and their capacity to treat and prevent EC.
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Affiliation(s)
- Sujitha Jayaprakash
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati 781039, Assam, India
| | - Mangala Hegde
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati 781039, Assam, India
| | - Sosmitha Girisa
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati 781039, Assam, India
| | - Mohammed S. Alqahtani
- Radiological Sciences Department, College of Applied Medical Sciences, King Khalid University, Abha 61421, Saudi Arabia
- BioImaging Unit, Space Research Centre, Michael Atiyah Building, University of Leicester, Leicester LE1 7RH, UK
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, Abha 61421, Saudi Arabia
- Electronics and Communications Department, College of Engineering, Delta University for Science and Technology, Gamasa 35712, Egypt
| | - E. Hui Clarissa Lee
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Kenneth Chun-Hong Yap
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
- Correspondence: (A.P.K.); (A.B.K.)
| | - Ajaikumar B. Kunnumakkara
- Cancer Biology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology (IIT) Guwahati, Guwahati 781039, Assam, India
- Correspondence: (A.P.K.); (A.B.K.)
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13
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Yao B, Yang C, Pan C, Li Y. Thyroid hormone resistance: Mechanisms and therapeutic development. Mol Cell Endocrinol 2022; 553:111679. [PMID: 35738449 DOI: 10.1016/j.mce.2022.111679] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 05/03/2021] [Accepted: 05/09/2022] [Indexed: 10/18/2022]
Abstract
As an essential primary hormone, thyroid hormone (TH) is indispensable for human growth, development and metabolism. Impairment of TH function in several aspects, including TH synthesis, activation, transportation and receptor-dependent transactivation, can eventually lead to thyroid hormone resistance syndrome (RTH). RTH is a rare syndrome that manifests as a reduced target cell response to TH signaling. The majority of RTH cases are related to thyroid hormone receptor β (TRβ) mutations, and only a few RTH cases are associated with thyroid hormone receptor α (TRα) mutations or other causes. Patients with RTH suffer from goiter, mental retardation, short stature and bradycardia or tachycardia. To date, approximately 170 mutated TRβ variants and more than 20 mutated TRα variants at the amino acid level have been reported in RTH patients. In addition to these mutated proteins, some TR isoforms can also reduce TH function by competing with primary TRs for TRE and RXR binding. Fortunately, different treatments for RTH have been explored with structure-activity relationship (SAR) studies and drug design, and among these treatments. With thyromimetic potency but biochemical properties that differ from those of primary TH (T3 and T4), these TH analogs can bypass specific defective transporters or reactive mutant TRs. However, these compounds must be carefully applied to avoid over activating TRα, which is associated with more severe heart impairment. The structural mechanisms of mutation-induced RTH in the TR ligand-binding domain are summarized in this review. Furthermore, strategies to overcome this resistance for therapeutic development are also discussed.
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Affiliation(s)
- Benqiang Yao
- The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, 361005, China
| | - Chunyan Yang
- The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, 361005, China.
| | - Chengxi Pan
- The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, 361005, China
| | - Yong Li
- The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian, 361005, China.
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14
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Oehler D, Spychala A, Gödecke A, Lang A, Gerdes N, Ruas J, Kelm M, Szendroedi J, Westenfeld R. Full-length transcriptomic analysis in murine and human heart reveals diversity of PGC-1α promoters and isoforms regulated distinctly in myocardial ischemia and obesity. BMC Biol 2022; 20:169. [PMID: 35907957 PMCID: PMC9338484 DOI: 10.1186/s12915-022-01360-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/23/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α) acts as a transcriptional coactivator and regulates mitochondrial function. Various isoforms are generated by alternative splicing and differentially regulated promoters. In the heart, total PGC-1α deficiency knockout leads to dilatative cardiomyopathy, but knowledge on the complexity of cardiac isoform expression of PGC-1α remains sparse. Thus, this study aims to generate a reliable dataset on cardiac isoform expression pattern by long-read mRNA sequencing, followed by investigation of differential regulation of PGC-1α isoforms under metabolic and ischemic stress, using high-fat-high-sucrose-diet-induced obesity and a murine model of myocardial infarction. RESULTS Murine (C57Bl/6J) or human heart tissue (obtained during LVAD-surgery) was used for long-read mRNA sequencing, resulting in full-length transcriptomes including 58,000 mRNA isoforms with 99% sequence accuracy. Automatic bioinformatic analysis as well as manual similarity search against exonic sequences leads to identification of putative coding PGC-1α isoforms, validated by PCR and Sanger sequencing. Thereby, 12 novel transcripts generated by hitherto unknown splicing events were detected. In addition, we postulate a novel promoter with homologous and strongly conserved sequence in human heart. High-fat diet as well as ischemia/reperfusion (I/R) injury transiently reduced cardiac expression of PGC-1α isoforms, with the most pronounced effect in the infarcted area. Recovery of PGC-1α-isoform expression was even more decelerated when I/R was performed in diet-induced obese mice. CONCLUSIONS We deciphered for the first time a complete full-length transcriptome of the murine and human heart, identifying novel putative PGC-1α coding transcripts including a novel promoter. These transcripts are differentially regulated in I/R and obesity suggesting transcriptional regulation and alternative splicing that may modulate PGC-1α function in the injured and metabolically challenged heart.
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Affiliation(s)
- Daniel Oehler
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany.
- Cardiovascular Research Institute Düsseldorf (CARID), Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany.
| | - André Spychala
- Department of Cardiovascular Physiology, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Axel Gödecke
- Cardiovascular Research Institute Düsseldorf (CARID), Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
- Department of Cardiovascular Physiology, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexander Lang
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
- Cardiovascular Research Institute Düsseldorf (CARID), Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Norbert Gerdes
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
- Cardiovascular Research Institute Düsseldorf (CARID), Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Jorge Ruas
- Molecular and Cellular Exercise Physiology, Department of Physiology and Pharmacology, Karolinska Institutet, SE-17177, Stockholm, Sweden
| | - Malte Kelm
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany
- Cardiovascular Research Institute Düsseldorf (CARID), Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - Julia Szendroedi
- Joint Heidelberg-IDC Translational Diabetes Program, Internal Medicine, Heidelberg University Hospital, Heidelberg, Germany
- German Center for Diabetes Research, Neuherberg, Germany
| | - Ralf Westenfeld
- Division of Cardiology, Pulmonology, and Vascular Medicine, Medical Faculty, Heinrich-Heine University, Moorenstr. 5, 40225, Düsseldorf, Germany.
- Cardiovascular Research Institute Düsseldorf (CARID), Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany.
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15
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Estrogen Induces c-myc Transcription by Binding to Upstream ERE Element in Promoter. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12146853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Estrogen Receptor α(ERα) is reported to regulate the expression of many target genes by binding to specific estrogen response elements (EREs) in their promoters. c-myc is known to be over-expressed in most of the human carcinomas due to dysregulated transcription, translation, or protein stability. Estrogen (E) can induce the c-myc expression by binding to an upstream enhancer element in its promoter. This suggests that elevated estradiol (E2), a potent form of estrogen, levels could induce the expression of c-myc in breast cancer (BC). The expression of c-myc and estradiol were induced at Stage III and Stage IV of breast cancer. c-myc and estradiol expression was also associated with the established risk factors of breast cancer, such as BMI. Age at the time of the disease was alsocorrelated with the relative expression of c-myc and estradiol (p < 0.0007 and p < 0.000001). The correlation coefficient (R = 0.462) shows a positive relationship between estradiol bound ER, ER, and c-myc. Docking energy −229 kJ/mol suggests the binding affinity of estradiol bound ER binding to 500 bp upstream of proximal promotor of c-myc at three distinct positions. The data presented in this study proposed that the expression of c-myc and estradiol are directly correlated in breast cancer. The prognostic utility of an induced level of c-myc associated with the normal status of the c-myc gene and estradiol for patients with metastatic carcinoma should be explored further.
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16
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Tian SY, Chen SM, Pan CX, Li Y. FXR: structures, biology, and drug development for NASH and fibrosis diseases. Acta Pharmacol Sin 2022; 43:1120-1132. [PMID: 35217809 PMCID: PMC9061771 DOI: 10.1038/s41401-021-00849-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 12/21/2021] [Indexed: 12/11/2022] Open
Abstract
The nuclear receptor farnesoid-X-receptor (FXR) plays an essential role in bile acid, glucose, and lipid homeostasis. In the last two decades, several diseases, such as obesity, type 2 diabetes, nonalcoholic fatty liver disease, cholestasis, and chronic inflammatory diseases of the liver and intestine, have been revealed to be associated with alterations in FXR functions. FXR has become a promising therapeutic drug target, particularly for enterohepatic diseases. Despite the large number of FXR modulators reported, only obeticholic acid (OCA) has been approved for primary biliary cholangitis (PBC) therapy as FXR modulator. In this review, we summarize the structure and function of FXR, the development of FXR modulators, and the structure-activity relationships of FXR modulators. Based on the structural analysis, we discuss potential strategies for developing future therapeutic FXR modulators to overcome current limitations, providing new perspectives for enterohepatic and metabolic diseases treatment.
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Affiliation(s)
- Si-yu Tian
- grid.12955.3a0000 0001 2264 7233The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Shu-ming Chen
- grid.12955.3a0000 0001 2264 7233The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Cheng-xi Pan
- grid.12955.3a0000 0001 2264 7233The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361005 China
| | - Yong Li
- The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, 361005, China.
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17
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Wei KL, Gao GL, Chou YT, Lin CY, Chen SC, Chen YL, Choi HQ, Cheng CC, Su JGJ. Sorafenib is an antagonist of the aryl hydrocarbon receptor. Toxicology 2022; 470:153118. [DOI: 10.1016/j.tox.2022.153118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 01/29/2022] [Accepted: 02/02/2022] [Indexed: 02/07/2023]
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18
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Hunt JP, Galiardi J, Free TJ, Yang SO, Poole D, Zhao EL, Andersen JL, Wood DW, Bundy BC. Mechanistic discoveries and simulation-guided assay optimization of portable hormone biosensors with cell-free protein synthesis. Biotechnol J 2021; 17:e2100152. [PMID: 34761537 DOI: 10.1002/biot.202100152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/19/2021] [Accepted: 11/08/2021] [Indexed: 01/10/2023]
Abstract
Nuclear receptors (NRs) influence nearly every system of the body and our lives depend on correct NR signaling. Thus, a key environmental and pharmaceutical quest is to identify and detect chemicals which interact with nuclear hormone receptors, including endocrine disrupting chemicals (EDCs), therapeutic receptor modulators, and natural hormones. Previously reported biosensors of nuclear hormone receptor ligands facilitated rapid detection of NR ligands using cell-free protein synthesis (CFPS). In this work, the advantages of CFPS are further leveraged and combined with kinetic analysis, autoradiography, and western blot to elucidate the molecular mechanism of this biosensor. Additionally, mathematical simulations of enzyme kinetics are used to optimize the biosensor assay, ultimately lengthening its readable window by five-fold and improving sensor signal strength by two-fold. This approach enabled the creation of an on-demand thyroid hormone biosensor with an observable color-change readout. This mathematical and experimental approach provides insight for engineering rapid and field-deployable CFPS biosensors and promises to improve methods for detecting natural hormones, therapeutic receptor modulators, and EDCs.
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Affiliation(s)
- John Porter Hunt
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Jackelyn Galiardi
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA
| | - Tyler J Free
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Seung Ook Yang
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Daniel Poole
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - Emily Long Zhao
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Joshua L Andersen
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA
| | - David W Wood
- Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
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19
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Königshofer P, Brusilovskaya K, Petrenko O, Hofer BS, Schwabl P, Trauner M, Reiberger T. Nuclear Receptors in Liver Fibrosis. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166235. [PMID: 34339839 DOI: 10.1016/j.bbadis.2021.166235] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/18/2021] [Accepted: 07/27/2021] [Indexed: 12/12/2022]
Abstract
Nuclear receptors are ligand-activated transcription factors that regulate gene expression of a variety of key molecular signals involved in liver fibrosis. The primary cellular driver of liver fibrogenesis are activated hepatic stellate cells. Different NRs regulate the hepatic expression of pro-inflammatory and pro-fibrogenic cytokines that promote the transformation of hepatic stellate cells into fibrogenic myofibroblasts. Importantly, nuclear receptors regulate gene expression circuits that promote hepatic fibrogenesis and/or allow liver fibrosis regression. In this review, we highlight the direct and indirect influence of nuclear receptors on liver fibrosis, with a focus on hepatic stellate cells, and discuss potential therapeutic effects of nuclear receptor modulation in regard to anti-fibrotic and anti-inflammatory effects. Further research on nuclear receptors-related signaling may lead to the clinical development of effective anti-fibrotic therapies for patients with liver disease.
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Affiliation(s)
- Philipp Königshofer
- Division of Gastroenterology and Hepatology, Department of Medicine III, Medical University of Vienna, Vienna, Austria; Vienna Experimental Hepatic Hemodynamic Lab (HEPEX), Medical University of Vienna, Vienna, Austria; Christian Doppler Lab for Portal Hypertension and Liver Fibrosis, Medical University of Vienna, Vienna, Austria
| | - Ksenia Brusilovskaya
- Division of Gastroenterology and Hepatology, Department of Medicine III, Medical University of Vienna, Vienna, Austria; Vienna Experimental Hepatic Hemodynamic Lab (HEPEX), Medical University of Vienna, Vienna, Austria; Christian Doppler Lab for Portal Hypertension and Liver Fibrosis, Medical University of Vienna, Vienna, Austria
| | - Oleksandr Petrenko
- Division of Gastroenterology and Hepatology, Department of Medicine III, Medical University of Vienna, Vienna, Austria; Vienna Experimental Hepatic Hemodynamic Lab (HEPEX), Medical University of Vienna, Vienna, Austria; Christian Doppler Lab for Portal Hypertension and Liver Fibrosis, Medical University of Vienna, Vienna, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Benedikt Silvester Hofer
- Division of Gastroenterology and Hepatology, Department of Medicine III, Medical University of Vienna, Vienna, Austria; Vienna Experimental Hepatic Hemodynamic Lab (HEPEX), Medical University of Vienna, Vienna, Austria; Christian Doppler Lab for Portal Hypertension and Liver Fibrosis, Medical University of Vienna, Vienna, Austria
| | - Philipp Schwabl
- Division of Gastroenterology and Hepatology, Department of Medicine III, Medical University of Vienna, Vienna, Austria; Vienna Experimental Hepatic Hemodynamic Lab (HEPEX), Medical University of Vienna, Vienna, Austria; Christian Doppler Lab for Portal Hypertension and Liver Fibrosis, Medical University of Vienna, Vienna, Austria
| | - Michael Trauner
- Division of Gastroenterology and Hepatology, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Thomas Reiberger
- Division of Gastroenterology and Hepatology, Department of Medicine III, Medical University of Vienna, Vienna, Austria; Vienna Experimental Hepatic Hemodynamic Lab (HEPEX), Medical University of Vienna, Vienna, Austria; Christian Doppler Lab for Portal Hypertension and Liver Fibrosis, Medical University of Vienna, Vienna, Austria; Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria; CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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20
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La Sala G, Gunnarsson A, Edman K, Tyrchan C, Hogner A, Frolov AI. Unraveling the Allosteric Cross-Talk between the Coactivator Peptide and the Ligand-Binding Site in the Glucocorticoid Receptor. J Chem Inf Model 2021; 61:3667-3680. [PMID: 34156843 DOI: 10.1021/acs.jcim.1c00323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The glucocorticoid receptor (GR) is a nuclear receptor that controls critical biological processes by regulating the transcription of specific genes. There is a known allosteric cross-talk between the ligand and coregulator binding sites within the GR ligand-binding domain that is crucial for the control of the functional response. However, the molecular mechanisms underlying such an allosteric control remain elusive. Here, molecular dynamics (MD) simulations, bioinformatic analysis, and biophysical measurements are integrated to capture the structural and dynamic features of the allosteric cross-talk within the GR. We identified a network of evolutionarily conserved residues that enables the allosteric signal transduction, in agreement with experimental data. MD simulations clarify how such a network is dynamically interconnected and offer a mechanistic explanation of how different peptides affect the intensity of the allosteric signal. This study provides useful insights to elucidate the GR allosteric regulation, ultimately providing a foundation for designing novel drugs.
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Affiliation(s)
- Giuseppina La Sala
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Gunnarsson
- Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Karl Edman
- Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Christian Tyrchan
- Medicinal Chemistry, Research and Early Development, Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Anders Hogner
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Andrey I Frolov
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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21
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Xu C, Chen H, Zhou S, Sun C, Xia X, Peng Y, Zhuang J, Fu X, Zeng H, Zhou H, Cao Y, Yu Q, Li Y, Hu L, Zhou G, Yan F, Chen G, Li J. Pharmacological Activation of RXR-α Promotes Hematoma Absorption via a PPAR-γ-dependent Pathway After Intracerebral Hemorrhage. Neurosci Bull 2021; 37:1412-1426. [PMID: 34142331 DOI: 10.1007/s12264-021-00735-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/16/2021] [Indexed: 12/26/2022] Open
Abstract
Endogenously eliminating the hematoma is a favorable strategy in addressing intracerebral hemorrhage (ICH). This study sought to determine the role of retinoid X receptor-α (RXR-α) in the context of hematoma absorption after ICH. Our results showed that pharmacologically activating RXR-α with bexarotene significantly accelerated hematoma clearance and alleviated neurological dysfunction after ICH. RXR-α was expressed in microglia/macrophages, neurons, and astrocytes. Mechanistically, bexarotene promoted the nuclear translocation of RXR-α and PPAR-γ, as well as reducing neuroinflammation by modulating microglia/macrophage reprograming from the M1 into the M2 phenotype. Furthermore, all the beneficial effects of RXR-α in ICH were reversed by the PPAR-γ inhibitor GW9662. In conclusion, the pharmacological activation of RXR-α confers robust neuroprotection against ICH by accelerating hematoma clearance and repolarizing microglia/macrophages towards the M2 phenotype through PPAR-γ-related mechanisms. Our data support the notion that RXR-α might be a promising therapeutic target for ICH.
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Affiliation(s)
- Chaoran Xu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Huaijun Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Shengjun Zhou
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Chenjun Sun
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Xiaolong Xia
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Yucong Peng
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Jianfeng Zhuang
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Xiongjie Fu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Hanhai Zeng
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Hang Zhou
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Yang Cao
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Qian Yu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Yin Li
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Libin Hu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Guoyang Zhou
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Feng Yan
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China
| | - Gao Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China.
| | - Jianru Li
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, 310052, China.
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22
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Eide M, Zhang X, Karlsen OA, Goldstone JV, Stegeman J, Jonassen I, Goksøyr A. The chemical defensome of five model teleost fish. Sci Rep 2021; 11:10546. [PMID: 34006915 PMCID: PMC8131381 DOI: 10.1038/s41598-021-89948-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/04/2021] [Indexed: 12/13/2022] Open
Abstract
How an organism copes with chemicals is largely determined by the genes and proteins that collectively function to defend against, detoxify and eliminate chemical stressors. This integrative network includes receptors and transcription factors, biotransformation enzymes, transporters, antioxidants, and metal- and heat-responsive genes, and is collectively known as the chemical defensome. Teleost fish is the largest group of vertebrate species and can provide valuable insights into the evolution and functional diversity of defensome genes. We have previously shown that the xenosensing pregnane x receptor (pxr, nr1i2) is lost in many teleost species, including Atlantic cod (Gadus morhua) and three-spined stickleback (Gasterosteus aculeatus), but it is not known if compensatory mechanisms or signaling pathways have evolved in its absence. In this study, we compared the genes comprising the chemical defensome of five fish species that span the teleosteii evolutionary branch often used as model species in toxicological studies and environmental monitoring programs: zebrafish (Danio rerio), medaka (Oryzias latipes), Atlantic killifish (Fundulus heteroclitus), Atlantic cod, and three-spined stickleback. Genome mining revealed evolved differences in the number and composition of defensome genes that can have implication for how these species sense and respond to environmental pollutants, but we did not observe any candidates of compensatory mechanisms or pathways in cod and stickleback in the absence of pxr. The results indicate that knowledge regarding the diversity and function of the defensome will be important for toxicological testing and risk assessment studies.
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Affiliation(s)
- Marta Eide
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Xiaokang Zhang
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital-Radiumhospitalet, Oslo, Norway
| | - Odd André Karlsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Jared V Goldstone
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - John Stegeman
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Inge Jonassen
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
| | - Anders Goksøyr
- Department of Biological Sciences, University of Bergen, Bergen, Norway.
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23
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Großkopf H, Walter K, Karkossa I, von Bergen M, Schubert K. Non-Genomic AhR-Signaling Modulates the Immune Response in Endotoxin-Activated Macrophages After Activation by the Environmental Stressor BaP. Front Immunol 2021; 12:620270. [PMID: 33868237 PMCID: PMC8045971 DOI: 10.3389/fimmu.2021.620270] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/15/2021] [Indexed: 12/16/2022] Open
Abstract
Emerging studies revealed that the Aryl hydrocarbon receptor (AhR), a receptor sensing environmental contaminants, is executing an immunomodulatory function. However, it is an open question to which extent this is achieved by its role as a transcription factor or via non-genomic signaling. We utilized a multi-post-translational modification-omics approach to examine non-genomic AhR-signaling after activation with endogenous (FICZ) or exogenous (BaP) ligand in endotoxin-activated (LPS) monocyte-derived macrophages. While AhR activation affected abundances of few proteins, regulation of ubiquitination and phosphorylation were highly pronounced. Although the number and strength of effects depended on the applied AhR-ligand, both ligands increased ubiquitination of Rac1, which participates in PI3K/AKT-pathway-dependent macrophage activation, resulting in a pro-inflammatory phenotype. In contrast, co-treatment with ligand and LPS revealed a decreased AKT activity mediating an anti-inflammatory effect. Thus, our data show an immunomodulatory effect of AhR activation through a Rac1ubiquitination-dependent mechanism that attenuated AKT-signaling, resulting in a mitigated inflammatory response.
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Affiliation(s)
- Henning Großkopf
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Katharina Walter
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Isabel Karkossa
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany.,Institute of Biochemistry, Leipzig University, Leipzig, Germany
| | - Kristin Schubert
- Department of Molecular Systems Biology, Helmholtz Centre for Environmental Research, Leipzig, Germany
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24
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Alatshan A, Benkő S. Nuclear Receptors as Multiple Regulators of NLRP3 Inflammasome Function. Front Immunol 2021; 12:630569. [PMID: 33717162 PMCID: PMC7952630 DOI: 10.3389/fimmu.2021.630569] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/08/2021] [Indexed: 12/11/2022] Open
Abstract
Nuclear receptors are important bridges between lipid signaling molecules and transcription responses. Beside their role in several developmental and physiological processes, many of these receptors have been shown to regulate and determine the fate of immune cells, and the outcome of immune responses under physiological and pathological conditions. While NLRP3 inflammasome is assumed as key regulator for innate and adaptive immune responses, and has been associated with various pathological events, the precise impact of the nuclear receptors on the function of inflammasome is hardly investigated. A wide variety of factors and conditions have been identified as modulators of NLRP3 inflammasome activation, and at the same time, many of the nuclear receptors are known to regulate, and interact with these factors, including cellular metabolism and various signaling pathways. Nuclear receptors are in the focus of many researches, as these receptors are easy to manipulate by lipid soluble molecules. Importantly, nuclear receptors mediate regulatory mechanisms at multiple levels: not only at transcription level, but also in the cytosol via non-genomic effects. Their importance is also reflected by the numerous approved drugs that have been developed in the past decade to specifically target nuclear receptors subtypes. Researches aiming to delineate mechanisms that regulate NLRP3 inflammasome activation draw a wide range of attention due to their unquestionable importance in infectious and sterile inflammatory conditions. In this review, we provide an overview of current reports and knowledge about NLRP3 inflammasome regulation from the perspective of nuclear receptors, in order to bring new insight to the potentially therapeutic aspect in targeting NLRP3 inflammasome and NLRP3 inflammasome-associated diseases.
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Affiliation(s)
- Ahmad Alatshan
- Departments of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Cellular and Immune Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Szilvia Benkő
- Departments of Physiology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
- Doctoral School of Molecular Cellular and Immune Biology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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25
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Piir G, Sild S, Maran U. Binary and multi-class classification for androgen receptor agonists, antagonists and binders. CHEMOSPHERE 2021; 262:128313. [PMID: 33182081 DOI: 10.1016/j.chemosphere.2020.128313] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/24/2020] [Accepted: 09/10/2020] [Indexed: 06/11/2023]
Abstract
Androgens and androgen receptor regulate a variety of biological effects in the human body. The impaired functioning of androgen receptor may have different adverse health effects from cancer to infertility. Therefore, it is important to determine whether new chemicals have any binding activity and act as androgen agonists or antagonists before commercial use. Due to the large number of chemicals that require experimental testing, the computational methods are a viable alternative. Therefore, the aim of the present study was to develop predictive QSAR models for classifying compounds according to their activity at the androgen receptor. A large data set of chemicals from the CoMPARA project was used for this purpose and random forest classification models have been developed for androgen binding, agonistic, and antagonistic activity. In addition, a unique effort has been made for multi-class approach that discriminates between inactive compounds, agonists and antagonists simultaneously. For the evaluation set, the classification models predicted agonists with 80% of accuracy and for the antagonists' and binders' the respective metrics were 72% and 78%. Combining agonists, antagonists and inactive compounds into a multi-class approach added complexity to the modelling task and resulted to 64% prediction accuracy for the evaluation set. Considering the size of the training data sets and their imbalance, the achieved evaluation accuracy is very good. The final classification models are available for exploring and predicting at QsarDB repository (https://doi.org/10.15152/QDB.236).
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Affiliation(s)
- Geven Piir
- University of Tartu, Institute of Chemistry, Ravila 14A, Tartu, 50411, Estonia
| | - Sulev Sild
- University of Tartu, Institute of Chemistry, Ravila 14A, Tartu, 50411, Estonia
| | - Uko Maran
- University of Tartu, Institute of Chemistry, Ravila 14A, Tartu, 50411, Estonia.
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26
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Guo F, Xu S, Zhu Y, Zheng X, Lu Y, Tu J, He Y, Jin L, Li Y. PPARγ Transcription Deficiency Exacerbates High-Fat Diet-Induced Adipocyte Hypertrophy and Insulin Resistance in Mice. Front Pharmacol 2020; 11:1285. [PMID: 32973516 PMCID: PMC7466717 DOI: 10.3389/fphar.2020.01285] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/03/2020] [Indexed: 12/29/2022] Open
Abstract
Background The transcriptional factor peroxisome proliferator–activated receptor γ (PPARγ) is an important therapeutic target for the treatment of type 2 diabetes. However, the role of the PPARγ transcriptional activity remains ambiguous in its metabolic regulation. Methods Based on the crystal structure of PPARγ bound with the DNA target of PPARγ response element (PPRE), Arg134, Arg135, and Arg138, three crucial DNA binding sites for PPARγ, were mutated to alanine (3RA), respectively. In vitro AlphaScreen assay and cell-based reporter assay validated that PPARγ 3RA mutant cannot bind with PPRE and lost transcriptional activity, while can still bind ligand (rosiglitazone) and cofactors (SRC1, SRC2, and NCoR). By using CRISPR/Cas9, we created mice that were heterozygous for PPARγ-3RA (PPARγ3RA/+). The phenotypes of chow diet and high-fat diet fed PPARγ3RA/+ mice were investigated, and the molecular mechanism were analyzed by assessing the PPARγ transcriptional activity. Results Homozygous PPARγ-3RA mutant mice are embryonically lethal. The mRNA levels of PPARγ target genes were significantly decreased in PPARγ3RA/+ mice. PPARγ3RA/+ mice showed more severe adipocyte hypertrophy, insulin resistance, and hepatic steatosis than wild type mice when fed with high-fat diet. These phenotypes were ameliorated after the transcription activity of PPARγ was restored by rosiglitazone, a PPARγ agonist. Conclusion The current report presents a novel mouse model for investigating the role of PPARγ transcription in physiological functions. The data demonstrate that the transcriptional activity plays an indispensable role for PPARγ in metabolic regulation.
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Affiliation(s)
- Fusheng Guo
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Shuangshuang Xu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yanlin Zhu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Xing Zheng
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Yi Lu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
| | - Jui Tu
- Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States
| | - Ying He
- Laboratory Animal Center, Xiamen University, Xiamen, China
| | - Lihua Jin
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China.,Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, United States
| | - Yong Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Xiamen, China
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27
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Ning X, Wang Y, Zhu N, Li G, Sang N. Risk assessment of the lipid metabolism-disrupting effects of nitro-PAHs. JOURNAL OF HAZARDOUS MATERIALS 2020; 396:122611. [PMID: 32353732 DOI: 10.1016/j.jhazmat.2020.122611] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/18/2020] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Nitro-polycyclic aromatic hydrocarbons (NPAHs) are of increasing global concern due to their ubiquitous occurrence and long-range transport in the environment. However, their potential metabolism-disrupting effects, especially nuclear receptor-related lipid disorders, are still poorly understood. Targeting estrogen receptor α (ERα), this study for the first time evaluated the lipid metabolic effects of NPAHs using in vitro and in vivo models. The results indicated that four of the five NPAHs tested exhibited significant ERα agonistic activities, and induced increased secretion of 17β-estradiol (E2) in HepG2 cells. Furthermore, lipidomic analysis showed that exposure to the candidate NPAH (3-nitrofluoranthene, 3-NFA) led to elevated hepatic levels of triacylglycerols (TAGs) and cholesteryl esters (CEs). Importantly, the lipid overload induced by 3-NFA was verified in the livers of zebrafish larvae using Oil Red O staining. Additionally, significant increases in E2 production and the expression levels of associated genes (17βHSD and C/EBP-α) further supported the involvement of the ERα signaling pathway in the lipid metabolic perturbation induced by 3-NFA. These results provide novel insight into the lipid metabolism-disrupting effects induced by NPAHs and may offer a better understanding of the environmental risks of NPAHs.
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Affiliation(s)
- Xia Ning
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Yue Wang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Na Zhu
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
| | - Guangke Li
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China.
| | - Nan Sang
- College of Environment and Resource, Research Center of Environment and Health, Shanxi University, Taiyuan, Shanxi 030006, PR China
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28
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Yao B, Zhang S, Wei Y, Tian S, Lu Z, Jin L, He Y, Xie W, Li Y. Structural Insights into the Specificity of Ligand Binding and Coactivator Assembly by Estrogen-Related Receptor β. J Mol Biol 2020; 432:5460-5472. [PMID: 32795533 DOI: 10.1016/j.jmb.2020.08.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 01/20/2023]
Abstract
Estrogen-related receptor β (ERRβ) is a nuclear receptor critical for many biological processes. Despite the biological and pharmaceutical importance of ERRβ, deciphering the structure of ERRβ has been hampered by the difficulties in obtaining a pure and stable protein for structural studies. In fact, the ERRβ ligand-binding domain remains the last unsolved ERR structure and also one of only a few unknown nuclear receptor structures. Here, we report the identification of a critical single-residue mutation resulted in robust solubility and stability of an active ERRβ ligand-binding domain, thereby providing a protein tool enabling the first probe into the biochemical and structural studies of this important receptor. The crystal structure reveals key structural features that have enabled the integration of the molecular determinants of signals transduced across the ligand binding and coregulator recruitment by all three ERR subtypes, which also provides a framework for the rational design of selective and potent ligands for the treatment of various ERR-mediated diseases.
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Affiliation(s)
- Benqiang Yao
- The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Shuchi Zhang
- The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Yijuan Wei
- The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Siyu Tian
- The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Zhou Lu
- The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Lihua Jin
- The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Ying He
- The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Wen Xie
- Center for Pharmacogenetics and Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yong Li
- The State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China.
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29
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Leijten-van de Gevel IA, Brunsveld L. Delineation of the molecular determinants of the unique allosteric binding site of the orphan nuclear receptor RORγt. J Biol Chem 2020; 295:9183-9191. [PMID: 32439807 PMCID: PMC7335795 DOI: 10.1074/jbc.ra120.013581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/17/2020] [Indexed: 12/12/2022] Open
Abstract
Nuclear receptors (NRs) are high-interest targets in drug discovery because of their involvement in numerous biological processes and diseases. Classically, NRs are targeted via their hydrophobic, orthosteric pocket. Although successful, this approach comes with challenges, including off-target effects due to lack of selectivity. Allosteric modulation of NR activity constitutes a promising pharmacological strategy. The retinoic acid receptor-related orphan receptor-γt (RORγt) is a constitutively active NR that positively regulates the expression of interleukin-17 in T helper 17 cells. Inhibiting this process is an emerging strategy for managing autoimmune diseases. Recently, an allosteric binding pocket in the C-terminal region of the ligand-binding domain (LBD) of RORγt was discovered that is amenable to small-molecule drug discovery. Compounds binding this pocket induce a reorientation of helix 12, thereby preventing coactivator recruitment. Therefore, inverse agonists binding this site with high affinity are actively being pursued. To elucidate the pocket formation mechanism, verify the uniqueness of this pocket, and substantiate the relevance of targeting this site, here we identified the key characteristics of the RORγt allosteric region. We evaluated the effects of substitutions in the LBD on coactivator, orthosteric, and allosteric ligand binding. We found that two molecular elements unique to RORγt, the length of helix 11' and a Gln-487 residue, are crucial for the formation of the allosteric pocket. The unique combination of elements present in RORγt suggests a high potential for subtype-selective targeting of this NR to more effectively treat patients with autoimmune diseases.
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Affiliation(s)
- Iris A Leijten-van de Gevel
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, the Netherlands
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems, Technische Universiteit Eindhoven, Eindhoven, the Netherlands.
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30
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Zhu Y, Xu S, Lu Y, Wei Y, Yao B, Guo F, Zheng X, Wang Y, He Y, Jin L, Li Y. Repositioning an Immunomodulatory Drug Vidofludimus as a Farnesoid X Receptor Modulator With Therapeutic Effects on NAFLD. Front Pharmacol 2020; 11:590. [PMID: 32477115 PMCID: PMC7240069 DOI: 10.3389/fphar.2020.00590] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/16/2020] [Indexed: 12/12/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) has become the most common chronic liver disorder, and yet with no pharmacological treatment approved worldwide. The repositioning of old drugs provides a safe approach for drug development. Vidofludimus, an inhibitor for dihydroorotate dehydrogenase (DHODH) for the treatment of autoimmune disorders, is herein uncovered as a novel modulator for farnesoid X receptor (FXR) by biochemical and crystallographic analysis. We further revealed that vidofludimus exerts in vivo therapeutic effects on dextran sodium sulfate (DSS)-induced colitis in an FXR-dependent manner. Notably, vidofludimus also possesses remarkable beneficial effects in reducing NAFLD by targeting FXR, which may represent a unique approach in developing the treatment for NAFLD. Our findings not only reveal a promising template for the design of novel FXR ligands in treating autoimmune disorders, but also uncover a novel therapeutic effect for vidofludimus on NAFLD based on the newly established relationships among drugs, targets, and diseases.
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Affiliation(s)
- Yanlin Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
| | - Shuangshuang Xu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
| | - Yi Lu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Neonatal Diseases, Xiamen Children's Hospital, Xiamen, China
| | - Yijuan Wei
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
| | - Benqiang Yao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
| | - Fusheng Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
| | - Xing Zheng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
| | - Yumeng Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
| | - Ying He
- Laboratory Animal Center, Xiamen University, Xiamen, China
| | - Lihua Jin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China.,Department of Diabetes Complications and Metabolism, Diabetes and Metabolism Research Institute, Beckman Research Institute, City of Hope National Medical Center, Duarte, USA
| | - Yong Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
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31
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Fan Q, Nørgaard RC, Grytten I, Ness CM, Lucas C, Vekterud K, Soedling H, Matthews J, Lemma RB, Gabrielsen OS, Bindesbøll C, Ulven SM, Nebb HI, Grønning-Wang LM, Sæther T. LXRα Regulates ChREBPα Transactivity in a Target Gene-Specific Manner through an Agonist-Modulated LBD-LID Interaction. Cells 2020; 9:cells9051214. [PMID: 32414201 PMCID: PMC7290792 DOI: 10.3390/cells9051214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/19/2020] [Accepted: 05/07/2020] [Indexed: 01/02/2023] Open
Abstract
The cholesterol-sensing nuclear receptor liver X receptor (LXR) and the glucose-sensing transcription factor carbohydrate responsive element-binding protein (ChREBP) are central players in regulating glucose and lipid metabolism in the liver. More knowledge of their mechanistic interplay is needed to understand their role in pathological conditions like fatty liver disease and insulin resistance. In the current study, LXR and ChREBP co-occupancy was examined by analyzing ChIP-seq datasets from mice livers. LXR and ChREBP interaction was determined by Co-immunoprecipitation (CoIP) and their transactivity was assessed by real-time quantitative polymerase chain reaction (qPCR) of target genes and gene reporter assays. Chromatin binding capacity was determined by ChIP-qPCR assays. Our data show that LXRα and ChREBPα interact physically and show a high co-occupancy at regulatory regions in the mouse genome. LXRα co-activates ChREBPα and regulates ChREBP-specific target genes in vitro and in vivo. This co-activation is dependent on functional recognition elements for ChREBP but not for LXR, indicating that ChREBPα recruits LXRα to chromatin in trans. The two factors interact via their key activation domains; the low glucose inhibitory domain (LID) of ChREBPα and the ligand-binding domain (LBD) of LXRα. While unliganded LXRα co-activates ChREBPα, ligand-bound LXRα surprisingly represses ChREBPα activity on ChREBP-specific target genes. Mechanistically, this is due to a destabilized LXRα:ChREBPα interaction, leading to reduced ChREBP-binding to chromatin and restricted activation of glycolytic and lipogenic target genes. This ligand-driven molecular switch highlights an unappreciated role of LXRα in responding to nutritional cues that was overlooked due to LXR lipogenesis-promoting function.
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Affiliation(s)
- Qiong Fan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (Q.F.); (K.V.); (C.B.)
| | - Rikke Christine Nørgaard
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Ivar Grytten
- Department of Informatics, Faculty of Mathematics and Natural Sciences, University of Oslo, N-0317 Oslo, Norway;
| | - Cecilie Maria Ness
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Christin Lucas
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Kristin Vekterud
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (Q.F.); (K.V.); (C.B.)
| | - Helen Soedling
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Jason Matthews
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Roza Berhanu Lemma
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, N-0317 Oslo, Norway; (R.B.L.); (O.S.G.)
| | - Odd Stokke Gabrielsen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, N-0317 Oslo, Norway; (R.B.L.); (O.S.G.)
| | - Christian Bindesbøll
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (Q.F.); (K.V.); (C.B.)
| | - Stine Marie Ulven
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Hilde Irene Nebb
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Line Mariann Grønning-Wang
- Department of Nutrition, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (R.C.N.); (C.M.N.); (C.L.); (H.S.); (J.M.); (S.M.U.); (H.I.N.); (L.M.G.-W.)
| | - Thomas Sæther
- Department of Molecular Medicine, Institute of Basic Medical Sciences, Faculty of Medicine, University of Oslo, N-0317 Oslo, Norway; (Q.F.); (K.V.); (C.B.)
- Correspondence: ; Tel.: +47-22-851510
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Yao B, Wei Y, Zhang S, Tian S, Xu S, Wang R, Zheng W, Li Y. Revealing a Mutant-Induced Receptor Allosteric Mechanism for the Thyroid Hormone Resistance. iScience 2019; 20:489-496. [PMID: 31655060 PMCID: PMC6806671 DOI: 10.1016/j.isci.2019.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 09/19/2019] [Accepted: 09/30/2019] [Indexed: 12/13/2022] Open
Abstract
Resistance to thyroid hormone (RTH) is a clinical disorder without specific and effective therapeutic strategy, partly due to the lack of structural mechanisms for the defective ligand binding by mutated thyroid hormone receptors (THRs). We herein uncovered the prescription drug roxadustat as a novel THRβ-selective ligand with therapeutic potentials in treating RTH, thereby providing a small molecule tool enabling the first probe into the structural mechanisms of RTH. Despite a wide distribution of the receptor mutation sites, different THRβ mutants induce allosteric conformational modulation on the same His435 residue, which disrupts a critical hydrogen bond required for the binding of thyroid hormones. Interestingly, roxadustat retains hydrophobic interactions with THRβ via its unique phenyl extension, enabling the rescue of the activity of the THRβ mutants. Our study thus reveals a critical receptor allosterism mechanism for RTH by mutant THRβ, providing a new and viable therapeutic strategy for the treatment of RTH. We identified a novel THR ligand that effectively binds to THRβ mutants Structures revealed mechanisms for the RTH controlled by a key residue switch Roxadustat retains unique hydrophobic interactions with THRβ mutants We provide a promising approach to design THR ligands in treating RTH
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Affiliation(s)
- Benqiang Yao
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Yijuan Wei
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Shuchi Zhang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Siyu Tian
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Shuangshuang Xu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Weili Zheng
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Yong Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China.
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Singam ERA, Tachachartvanich P, Merrill MAL, Smith MT, Durkin KA. Structural Dynamics of Agonist and Antagonist Binding to the Androgen Receptor. J Phys Chem B 2019; 123:7657-7666. [PMID: 31431014 PMCID: PMC6742532 DOI: 10.1021/acs.jpcb.9b05654] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Androgen receptor (AR) is a steroid hormone nuclear receptor which upon binding its endogenous androgenic ligands (agonists), testosterone and dihydrotestosterone (DHT), alters gene transcription, producing a diverse range of biological effects. Antiandrogens, such as the pharmaceuticals bicalutamide and hydroxyflutamide, act as agonists in the absence of androgens and as antagonists in their presence or in high concentration. The atomic level mechanism of action by agonists and antagonists of AR is less well characterized. Therefore, in this study, multiple 1 μs molecular dynamics (MD), docking simulations, and perturbation-response analyses were performed to more fully explore the nature of interaction between agonist or antagonist and AR and the conformational changes induced in the AR upon interaction with different ligands. We characterized the mechanism of the ligand entry/exit and found that helix-12 and nearby structural motifs respond dynamically in that process. Modeling showed that the agonist and antagonist/agonist form a hydrogen bond with Thr877/Asn705 and that this interaction is absent for antagonists. Agonist binding to AR increases the mobility of residues at allosteric sites and coactivator binding sites, while antagonist binding decreases mobility at these important sites. A new site was also identified as a potential surface for allosteric binding. These results shed light on the effect of agonists and antagonists on the structure and dynamics of AR.
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Affiliation(s)
| | | | | | - Martyn T. Smith
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, CA, USA
| | - Kathleen A. Durkin
- Molecular Graphics and Computation Facility, College of Chemistry, University of California, Berkeley, CA, USA
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Shamilov R, Aneskievich BJ. Intrinsic Disorder in Nuclear Receptor Amino Termini: From Investigational Challenge to Therapeutic Opportunity. NUCLEAR RECEPTOR RESEARCH 2019. [DOI: 10.32527/2019/101417] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Rambon Shamilov
- Graduate Program in Pharmacology & Toxicology, University of Connecticut, Storrs, CT 06269-3092, USA
| | - Brian J. Aneskievich
- Department of Pharmaceutical Sciences, University of Connecticut, Storrs, CT 06269-3092, USA
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35
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Fouache A, Zabaiou N, De Joussineau C, Morel L, Silvente-Poirot S, Namsi A, Lizard G, Poirot M, Makishima M, Baron S, Lobaccaro JMA, Trousson A. Flavonoids differentially modulate liver X receptors activity-Structure-function relationship analysis. J Steroid Biochem Mol Biol 2019; 190:173-182. [PMID: 30959154 DOI: 10.1016/j.jsbmb.2019.03.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/27/2019] [Accepted: 03/31/2019] [Indexed: 12/30/2022]
Abstract
Liver X receptors (LXRs) α (NR1H3) and β (NR1H2) are nuclear receptors that have been involved in the regulation of many physiological processes, principally in the control of cholesterol homeostasis, as well as in the control of the cell death and proliferation balance. These receptors are thus promising therapeutic targets in various pathologies such as dyslipidemia, atherosclerosis, diabetes and/or cancers. These receptors are known to be activated by specific oxysterol compounds. The screening for LXR-specific ligands is a challenging process: indeed, these molecules should present a specificity towards each LXR-isoform. Because some natural products have significant effects in the regulation of the LXR-regulated homeostasis and are enriched in flavonoids, we have decided to test in cell culture the effects of 4 selected flavonoids (galangin, quercetin, apigenin and naringenin) on the modulation of LXR activity using double-hybrid experiments. In silico, molecular docking suggests specific binding pattern between agonistic and antagonistic molecules. Altogether, these results allow a better understanding of the ligand binding pocket of LXRα/β. They also improve our knowledge about flavonoid mechanism of action, allowing the selection and development of better LXR selective ligands.
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Affiliation(s)
- Allan Fouache
- Université Clermont Auvergne, GReD, CNRS UMR 6293, INSERM U1103, 28, place Henri Dunant, BP38, F63001, Clermont-Ferrand, France; Centre de Recherche en Nutrition Humaine d'Auvergne, 58 Boulevard Montalembert, F-63009, Clermont-Ferrand, France.
| | - Nada Zabaiou
- Université Clermont Auvergne, GReD, CNRS UMR 6293, INSERM U1103, 28, place Henri Dunant, BP38, F63001, Clermont-Ferrand, France; Laboratory of Molecular Toxicology, Department of Molecular and Cellular Biology, Faculty of Science, Université Mohamed Seddik Ben Yahia, 18000, Jijel, Algeria.
| | - Cyrille De Joussineau
- Université Clermont Auvergne, GReD, CNRS UMR 6293, INSERM U1103, 28, place Henri Dunant, BP38, F63001, Clermont-Ferrand, France; Centre de Recherche en Nutrition Humaine d'Auvergne, 58 Boulevard Montalembert, F-63009, Clermont-Ferrand, France.
| | - Laurent Morel
- Université Clermont Auvergne, GReD, CNRS UMR 6293, INSERM U1103, 28, place Henri Dunant, BP38, F63001, Clermont-Ferrand, France; Centre de Recherche en Nutrition Humaine d'Auvergne, 58 Boulevard Montalembert, F-63009, Clermont-Ferrand, France.
| | | | - Amira Namsi
- University Tunis El Manar, Faculty of Sciences of Tunis, UR/11ES09, Lab. 'Functional Neurophysiology and Pathology', 2092, Tunis, Tunisia.
| | - Gérard Lizard
- Team Bio-peroxIL, "Biochemistry of the Peroxisome, Inflammation and Lipid Metabolism" (EA7270)/University Bourgogne Franche-Comté/Inserm, 21000, Dijon, France.
| | - Marc Poirot
- Cancer Research Center of Toulouse, UMR 1037 INSERM-University of Toulouse, Toulouse, France.
| | - Makoto Makishima
- Nihon University School of Medicine, Division of Biochemistry, Department of Biomedical Sciences, 30-1 Oyaguchi-kamicho, Itabashi-ku, Tokyo, 173-8610, Japan.
| | - Silvère Baron
- Université Clermont Auvergne, GReD, CNRS UMR 6293, INSERM U1103, 28, place Henri Dunant, BP38, F63001, Clermont-Ferrand, France; Centre de Recherche en Nutrition Humaine d'Auvergne, 58 Boulevard Montalembert, F-63009, Clermont-Ferrand, France.
| | - Jean-Marc A Lobaccaro
- Université Clermont Auvergne, GReD, CNRS UMR 6293, INSERM U1103, 28, place Henri Dunant, BP38, F63001, Clermont-Ferrand, France; Centre de Recherche en Nutrition Humaine d'Auvergne, 58 Boulevard Montalembert, F-63009, Clermont-Ferrand, France.
| | - Amalia Trousson
- Université Clermont Auvergne, GReD, CNRS UMR 6293, INSERM U1103, 28, place Henri Dunant, BP38, F63001, Clermont-Ferrand, France; Centre de Recherche en Nutrition Humaine d'Auvergne, 58 Boulevard Montalembert, F-63009, Clermont-Ferrand, France.
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Jin LH, Fang ZP, Fan MJ, Huang WD. Bile-ology: from bench to bedside. J Zhejiang Univ Sci B 2019; 20:414-427. [PMID: 31090267 PMCID: PMC6568232 DOI: 10.1631/jzus.b1900158] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 04/05/2019] [Indexed: 12/13/2022]
Abstract
Bile acids (BAs) are originally known as detergents essential for the digestion and absorption of lipids. In recent years, extensive research has unveiled new functions of BAs as gut hormones that modulate physiological and pathological processes, including glucose and lipid metabolism, energy expenditure, inflammation, tumorigenesis, cardiovascular disease, and even the central nervous system in addition to cholesterol homeostasis, enterohepatic protection and liver regeneration. BAs are closely linked with gut microbiota which might explain some of their crucial roles in organs. The signaling actions of BAs can also be mediated through specific nuclear receptors and membrane-bound G protein-coupled receptors. Several pharmacological agents or bariatric surgeries have demonstrated efficacious therapeutic effects on metabolic diseases through targeting BA signaling. In this mini-review, we summarize recent advances in bile-ology, focusing on its translational studies.
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Affiliation(s)
- Li-hua Jin
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- State Key Laboratory of Cellular Stress Biology; Innovation Center for Cell Signaling Network; School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Zhi-peng Fang
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Min-jie Fan
- College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Wen-dong Huang
- Department of Diabetes Complications and Metabolism, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
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37
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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: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [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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38
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Abstract
As plant-derived natural products, saponins have been widely applied for the dietary modification of metabolic syndrome. However, the underlying mechanisms of their preventive and therapeutic effects are still largely unclear. Nuclear receptors have been identified as potential pharmaceutical targets for treating various types of metabolic disorders. With similar structure to endogenous hormones, several saponins may serve as selective ligands for nuclear receptors. Recently, a series of saponins are proved to exert their physiological activities through binding to nuclear receptors. This review summarizes the biological and pharmacological activities of typical saponins mediated by some of the most well described nuclear receptors, including the classical steroid hormone receptors (ER, GR, MR, and AR) and the adopted orphan receptors (PPAR, LXR, FXR, and PXR).
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Affiliation(s)
- Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Shuning Zhong
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Tiezhu Li
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun, China
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39
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Adamidou T, Arvaniti KO, Glykos NM. Folding Simulations of a Nuclear Receptor Box-Containing Peptide Demonstrate the Structural Persistence of the LxxLL Motif Even in the Absence of Its Cognate Receptor. J Phys Chem B 2017; 122:106-116. [DOI: 10.1021/acs.jpcb.7b10292] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Triantafyllia Adamidou
- Department of Molecular Biology
and Genetics, Democritus University of Thrace, University campus, 68100 Alexandroupolis, Greece
| | - Konstantina-Olympia Arvaniti
- Department of Molecular Biology
and Genetics, Democritus University of Thrace, University campus, 68100 Alexandroupolis, Greece
| | - Nicholas M. Glykos
- Department of Molecular Biology
and Genetics, Democritus University of Thrace, University campus, 68100 Alexandroupolis, Greece
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40
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Lu Y, Zheng W, Lin S, Guo F, Zhu Y, Wei Y, Liu X, Jin S, Jin L, Li Y. Identification of an Oleanane-Type Triterpene Hedragonic Acid as a Novel Farnesoid X Receptor Ligand with Liver Protective Effects and Anti-inflammatory Activity. Mol Pharmacol 2017; 93:63-72. [DOI: 10.1124/mol.117.109900] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 11/15/2017] [Indexed: 12/26/2022] Open
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41
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Zheng W, Lu Y, Lin S, Wang R, Qiu L, Zhu Y, Yao B, Guo F, Jin S, Jin L, Li Y. A Novel Class of Natural FXR Modulators with a Unique Mode of Selective Co-regulator Assembly. Chembiochem 2017; 18:721-725. [PMID: 28186695 DOI: 10.1002/cbic.201700059] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Indexed: 12/13/2022]
Abstract
The farnesoid X receptor (FXR) is an important target for drug discovery. Small molecules induce a conformational change in FXR that modulates its binding to co-regulators, thus resulting in distinct FXR functional profiles. However, the mechanisms for selectively recruiting co-regulators by FXR remain elusive, partly because of the lack of FXR-selective modulators. We report the identification of two natural terpenoids, tschimgine and feroline, as novel FXR modulators. Remarkably, their crystal structures uncovered a secondary binding pocket important for ligand binding. Further, tschimgine or feroline induced dynamic conformational changes in the activation function 2 (AF-2) surface, thus leading to differential co-regulator recruiting profiles, modulated by both hydrophobic and selective hydrogen-bond interactions unique to specific co-regulators. Our findings thus provide a novel structure template for optimization for FXR-selective modulators of clinical value.
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Affiliation(s)
- Weili Zheng
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yi Lu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, 361005, China
| | - Shengchen Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, 361005, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, 361005, China
| | - Lin Qiu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yanlin Zhu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, 361005, China
| | - Benqiang Yao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, 361005, China
| | - Fusheng Guo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, 361005, China
| | - Shikai Jin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, 361005, China
| | - Lihua Jin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, 361005, China
| | - Yong Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, Fujian, 361005, China
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42
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Wu Y, Doering JA, Ma Z, Tang S, Liu H, Zhang X, Wang X, Yu H. Identification of androgen receptor antagonists: In vitro investigation and classification methodology for flavonoid. CHEMOSPHERE 2016; 158:72-79. [PMID: 27258897 DOI: 10.1016/j.chemosphere.2016.05.059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 05/17/2016] [Accepted: 05/20/2016] [Indexed: 06/05/2023]
Abstract
A tremendous gap exists between the number of potential endocrine disrupting chemicals (EDCs) possibly in the environment and the limitation of traditional regulatory testing. In this study, the anti-androgenic potencies of 21 flavonoids were analyzed in vitro, and another 32 flavonoids from the literature were selected as additional chemicals. Molecular dynamic simulations were employed to obtain four different separation approaches based on the different behaviors of ligands and receptors during the process of interaction. Specifically, ligand-receptor complex which highlighted the discriminating features of ligand escape or retention via "mousetrap" mechanism, hydrogen bonds formed during simulation times, ligand stability and the stability of the helix-12 of the receptor were investigated. Together, a methodology was generated that 87.5% of flavonoids could be discriminated as active versus inactive antagonists, and over 90% inactive antagonists could be filtered out before QSAR study. This methodology could be used as a "proof of concept" to identify inactive anti-androgenic flavonoids, as well could be beneficial for rapid risk assessment and regulation of multiple new chemicals for androgenicity.
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Affiliation(s)
- Yang Wu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Jon A Doering
- Toxicology Centre, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Zhiyuan Ma
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Song Tang
- School of Environment and Sustainability, University of Saskatchewan, Saskatoon, SK S7N 5B3, Canada
| | - Hongling Liu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China.
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Xiaoxiang Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China.
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43
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Belorusova A, Osz J, Petoukhov MV, Peluso-Iltis C, Kieffer B, Svergun DI, Rochel N. Solution Behavior of the Intrinsically Disordered N-Terminal Domain of Retinoid X Receptor α in the Context of the Full-Length Protein. Biochemistry 2016; 55:1741-1748. [PMID: 26937780 DOI: 10.1021/acs.biochem.5b01122] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Retinoid X receptors (RXRs) are transcription factors with important functions in embryonic development, metabolic processes, differentiation, and apoptosis. A particular feature of RXRs is their ability to act as obligatory heterodimerization partners of class II nuclear receptors. At the same time, these receptors are also able to form homodimers that bind to direct repeat separated by one nucleotide hormone response elements. Since the discovery of RXRs, most of the studies focused on its ligand binding and DNA binding domains, while its N-terminal domain (NTD) harboring a ligand-independent activation function remained poorly characterized. Here, we investigated the solution properties of the NTD of RXRα alone and in the context of the full-length receptor using small-angle X-ray scattering and nuclear magnetic resonance spectroscopy. We report the solution structure of the full-length homodimeric RXRα on DNA and show that the NTD remains highly flexible within this complex.
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Affiliation(s)
- Anna Belorusova
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
| | - Judit Osz
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
| | - Maxim V Petoukhov
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Carole Peluso-Iltis
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
| | - Bruno Kieffer
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
| | - Dmitri I Svergun
- European Molecular Biology Laboratory, Hamburg Outstation, Notkestrasse 85, 22603 Hamburg, Germany
| | - Natacha Rochel
- Department of Integrative Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Institut National de la Santé et de la Recherche Médicale (INSERM) U964 / Centre National de la Recherche Scientifique (CNRS) UMR 7104 / Université de Strasbourg, 67404 Illkirch, France
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44
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Carter EL, Gupta N, Ragsdale SW. High Affinity Heme Binding to a Heme Regulatory Motif on the Nuclear Receptor Rev-erbβ Leads to Its Degradation and Indirectly Regulates Its Interaction with Nuclear Receptor Corepressor. J Biol Chem 2015; 291:2196-222. [PMID: 26670607 DOI: 10.1074/jbc.m115.670281] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Indexed: 01/11/2023] Open
Abstract
Rev-erbα and Rev-erbβ are heme-binding nuclear receptors (NR) that repress the transcription of genes involved in regulating metabolism, inflammation, and the circadian clock. Previous gene expression and co-immunoprecipitation studies led to a model in which heme binding to Rev-erbα recruits nuclear receptor corepressor 1 (NCoR1) into an active repressor complex. However, in contradiction, biochemical and crystallographic studies have shown that heme decreases the affinity of the ligand-binding domain of Rev-erb NRs for NCoR1 peptides. One explanation for this discrepancy is that the ligand-binding domain and NCoR1 peptides used for in vitro studies cannot replicate the key features of the full-length proteins used in cellular studies. However, the combined in vitro and cellular results described here demonstrate that heme does not directly promote interactions between full-length Rev-erbβ (FLRev-erbβ) and an NCoR1 construct encompassing all three NR interaction domains. NCoR1 tightly binds both apo- and heme-replete FLRev-erbβ·DNA complexes; furthermore, heme, at high concentrations, destabilizes the FLRev-erbβ·NCoR1 complex. The interaction between FLRev-erbβ and NCoR1 as well as Rev-erbβ repression at the Bmal1 promoter appear to be modulated by another cellular factor(s), at least one of which is related to the ubiquitin-proteasome pathway. Our studies suggest that heme is involved in regulating the degradation of Rev-erbβ in a manner consistent with its role in circadian rhythm maintenance. Finally, the very slow rate constant (10(-6) s(-1)) of heme dissociation from Rev-erbβ rules out a prior proposal that Rev-erbβ acts as an intracellular heme sensor.
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Affiliation(s)
- Eric L Carter
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Nirupama Gupta
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
| | - Stephen W Ragsdale
- From the Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109
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Jin L, Wang R, Zhu Y, Zheng W, Han Y, Guo F, Ye FB, Li Y. Selective targeting of nuclear receptor FXR by avermectin analogues with therapeutic effects on nonalcoholic fatty liver disease. Sci Rep 2015; 5:17288. [PMID: 26620317 PMCID: PMC4664883 DOI: 10.1038/srep17288] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 10/28/2015] [Indexed: 12/18/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) has become a predictive factor of death from many diseases. Farnesoid X receptor (FXR) is an ideal target for NAFLD drug development due to its crucial roles in lipid metabolism. The aim of this work is to examine the molecular mechanisms and functional roles of FXR modulation by avermectin analogues in regulating metabolic syndromes like NAFLD. We found that among avermectin analogues studied, the analogues that can bind and activate FXR are effective in regulating metabolic parameters tested, including reducing hepatic lipid accumulation, lowering serum cholesterol and glucose levels, and improving insulin sensitivity, in a FXR dependent manner. Mechanistically, the avermectin analogues that interact with FXR exhibited features as partial agonists, with distinctive properties in modulating coregulator recruitment. Structural features critical for avermectin analogues to selectively bind to FXR were also revealed. This study indicated that in addition to antiparasitic activity, avermectin analogues are promising drug candidates to treat metabolism syndrome including NAFLD by directly targeting FXR. Additionally, the structural features that discriminate the selective binding of FXR by avermectin analogues may provide a unique safe approach to design drugs targeting FXR signaling.
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Affiliation(s)
- Lihua Jin
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China.,State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Rui Wang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Yanlin Zhu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Weili Zheng
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Yaping Han
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Fusheng Guo
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Frank Bin Ye
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
| | - Yong Li
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, School of Life Sciences, Xiamen University, Fujian 361005, China
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46
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Biological functions of thyroid hormone in placenta. Int J Mol Sci 2015; 16:4161-79. [PMID: 25690032 PMCID: PMC4346950 DOI: 10.3390/ijms16024161] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 02/03/2015] [Accepted: 02/04/2015] [Indexed: 12/16/2022] Open
Abstract
The thyroid hormone, 3,3,5-triiodo-l-thyronine (T3), modulates several physiological processes, including cellular growth, differentiation, metabolism, inflammation and proliferation, via interactions with thyroid hormone response elements (TREs) in the regulatory regions of target genes. Infection and inflammation are critical processes in placental development and pregnancy-related diseases. In particular, infection is the leading cause of neonatal mortality and morbidity worldwide. However, to date, no successful approach has been developed for the effective diagnosis of infection in preterm infants. Pre-eclampsia (PE) is a serious disorder that adversely affects ~5% of human pregnancies. Recent studies identified a multiprotein complex, the inflammasome, including the Nod-like receptor (NLR) family of cytosolic pattern recognition receptors, the adaptor protein apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) and caspase-1, which plays a vital role in the placenta. The thyroid hormone modulates inflammation processes and is additionally implicated in placental development and disease. Therefore, elucidation of thyroid hormone receptor-regulated inflammation-related molecules, and their underlying mechanisms in placenta, should facilitate the identification of novel predictive and therapeutic targets for placental disorders. This review provides a detailed summary of current knowledge with respect to identification of useful biomarkers and their physiological significance in placenta.
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Classical nuclear hormone receptor activity as a mediator of complex concentration response relationships for endocrine active compounds. Curr Opin Pharmacol 2014; 19:112-9. [PMID: 25299165 DOI: 10.1016/j.coph.2014.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/08/2014] [Accepted: 09/16/2014] [Indexed: 02/07/2023]
Abstract
Nonmonotonic concentration response relationships are frequently observed for endocrine active ligands that act via nuclear receptors. The curve of best fit for nonmonotonic concentration response relationships are often inverted U-shaped with effects at intermediate concentrations that are different from effects at higher or lower concentrations. Cytotoxicity is a major mode of action responsible for inverted U-shaped concentration response relationships. However, evidence suggests that ligand selectivity, activation of multiple molecular targets, concerted regulation of multiple opposing endpoints, and multiple ligand binding sites within nuclear receptors also contribute to nonmonotonic concentration response relationships of endocrine active ligands. This review reports the current understanding of mechanisms involved in classical nuclear receptor mediated nonmonotonic concentration response relationships with a focus on studies published between 2012 and 2014.
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48
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Gerlach T, Knaust J, Kaiser C, Körner M, Hettwer K, Uhlig S, Simon K, Baronian K, Kunze G. Development and assessment of a novel Arxula adeninivorans androgen screen (A-YAS) assay and its application in analysis of cattle urine. THE SCIENCE OF THE TOTAL ENVIRONMENT 2014; 490:1073-1081. [PMID: 24927152 DOI: 10.1016/j.scitotenv.2014.05.100] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 05/21/2014] [Accepted: 05/21/2014] [Indexed: 06/03/2023]
Abstract
The novel A-YAS assay for the detection of androgenic activity in liquid samples such as urine has been developed and assessed. The assay is based on transgenic Arxula adeninivorans yeast cells as the bio-component. The cells were engineered to co-express the human androgen receptor (hAR) gene and the inducible phytase reporter gene (phyK, derived from Klebsiella sp. ASR1), under the control of an Arxula derived glucoamylase (GAA) promoter, which had been modified by the insertion of hormone-responsive elements (HREs). The Arxula transformation/expression platform Xplor®2 was used to select stable mitotic resistance marker free transformants and the most suitable cells were characterized for performance as a sensor bio-component. The assay is easy-to-use, fast (6-25 h) and is currently the most sensitive yeast-based androgen screen with an EC50, limit of detection and of quantification values for 5α-dihydrotestosterone (DHT) of 277.1±53.0, 56.5±4.1 and 76.5±6.7 ng L(-1), respectively. Furthermore, the assay allows the determination of androgenic and anti-androgenic activity of various compounds such as naturally occurring androgens and estrogens, pharmaceuticals and biocides. The robustness of the A-YAS assay enables it to be used for analysis of complex samples such as urine. The results of the analysis of a number of cattle urine samples achieved by the A-YAS assay correlate well with GC-MS analysis of the same samples.
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Affiliation(s)
- Torsten Gerlach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany
| | - Jacqueline Knaust
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany
| | - Christian Kaiser
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany
| | - Martina Körner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany
| | - Karina Hettwer
- Quo Data GmbH, Kaitzer Str. 135, D-01187 Dresden, Germany
| | - Steffen Uhlig
- Quo Data GmbH, Kaitzer Str. 135, D-01187 Dresden, Germany
| | - Kirsten Simon
- New Diagnostics GmbH, Moosstr. 92c, D-85356 Freising, Germany
| | - Keith Baronian
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Gotthard Kunze
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, D-06466 Gatersleben, Germany.
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49
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Abstract
The six members of the family of insulin-like growth factor (IGF) binding proteins (IGFBPs) were originally characterized as passive reservoirs of circulating IGFs, but they are now understood to have many actions beyond their endocrine role in IGF transport. IGFBPs also function in the pericellular and intracellular compartments to regulate cell growth and survival - they interact with many proteins, in addition to their canonical ligands IGF-I and IGF-II. Intranuclear roles of IGFBPs in transcriptional regulation, induction of apoptosis and DNA damage repair point to their intimate involvement in tumour development, progression and resistance to treatment. Tissue or circulating IGFBPs might also be useful as prognostic biomarkers.
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Affiliation(s)
- Robert C Baxter
- Kolling Institute of Medical Research, University of Sydney, Royal North Shore Hospital, St Leonards, New South Wales 2065, Australia
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50
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Wheeler JLH, Martin KC, Resseguie E, Lawrence BP. Differential consequences of two distinct AhR ligands on innate and adaptive immune responses to influenza A virus. Toxicol Sci 2014; 137:324-34. [PMID: 24194396 PMCID: PMC3908724 DOI: 10.1093/toxsci/kft255] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 10/26/2013] [Indexed: 12/30/2022] Open
Abstract
Immune modulation by the aryl hydrocarbon receptor (AhR) has been primarily studied using 2,3,7,8 tetrachlorodibenzo-p-dioxin (TCDD). Recent reports suggest another AhR ligand, 6-formylindolo[3,2-b]carbazole (FICZ), exhibits distinct immunomodulatory properties, but side-by-side comparisons of these 2 structurally distinct, high-affinity ligands are limited. In this study, the effects of in vivo AhR activation with TCDD and FICZ were directly compared in a mouse model of influenza virus infection using 3 key measures of the host response to infection: pulmonary neutrophilia, inducible nitric oxide synthase (iNOS) levels, and the virus-specific CD8(+) T-cell response. By this approach, the consequences of AhR activation on innate and adaptive immune responses to the same antigenic challenge were compared. A single dose of TCDD elicited AhR activation that is sustained for the duration of the host's response to infection and modulated all 3 responses to infection. In contrast, a single dose of FICZ induced transient AhR activation and had no effect on the immune response to infection. Micro-osmotic pumps and Cyp1a1-deficient mice were utilized to augment FICZ-mediated AhR activation in vivo, in order to assess the effect of transient versus prolonged AhR activation. Prolonged AhR activation with FICZ did not affect neutrophil recruitment or pulmonary iNOS levels. However, FICZ-mediated AhR activation diminished the CD8(+) T-cell response in Cyp1a1-deficient mice in a similar manner to TCDD. These results demonstrate that immunomodulatory differences in the action of these 2 ligands are likely due to not only the duration of AhR activation but also the cell types in which the receptor is activated.
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Affiliation(s)
- Jennifer L. H. Wheeler
- Department of Environmental Medicine and Toxicology Graduate Program, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
| | - Kyle C. Martin
- Department of Environmental Medicine and Toxicology Graduate Program, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
| | - Emily Resseguie
- Department of Environmental Medicine and Toxicology Graduate Program, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
| | - B. Paige Lawrence
- Department of Environmental Medicine and Toxicology Graduate Program, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642
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