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Ooka M, Sakamuru S, Zhao J, Qu Y, Fang Y, Tao D, Huang R, Ferguson S, Reif D, Simeonov A, Xia M. Use of Tox21 screening data to profile PFAS bioactivities on nuclear receptors, cellular stress pathways, and cytochrome p450 enzymes. JOURNAL OF HAZARDOUS MATERIALS 2024; 473:134642. [PMID: 38776814 DOI: 10.1016/j.jhazmat.2024.134642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
Per- and poly-fluoroalkyl substances (PFAS) are synthetic chemicals widely used in commercial products. PFAS are a global concern due to their persistence in the environment and extensive associations with adverse health outcomes. While legacy PFAS have been extensively studied, many non-legacy PFAS lack sufficient toxicity information. In this study, we first analyzed the bioactivity of PFAS using Tox21 screening data surveying more than 75 assay endpoints (e.g., nuclear receptors, stress response, and metabolism) to understand the toxicity of non-legacy PFAS and investigate potential new targets of PFAS. From the Tox21 screening data analysis, we confirmed several known PFAS targets/pathways and identified several potential novel targets/pathways of PFAS. To confirm the effect of PFAS on these novel targets/pathways, we conducted several cell- and enzyme-based assays in the follow-up studies. We found PFAS inhibited cytochromes P450s (CYPs), especially CYP2C9 with IC50 values of < 1 µM. Considering PFAS affected other targets/pathways at > 10 µM, PFAS have a higher affinity to CYP2C9. This PFAS-CYP2C9 interaction was further investigated using molecular docking analysis. The result suggested that PFAS directly bind to the active sites of CYP2C9. These findings have important implications to understand the mechanism of PFAS action and toxicity.
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Affiliation(s)
- Masato Ooka
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Srilatha Sakamuru
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Jinghua Zhao
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Yanyan Qu
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Yuhong Fang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Dingyin Tao
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Stephen Ferguson
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - David Reif
- Division of Translational Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA.
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Zhang W, Hu H, Zhu Y, He Y, Yu M, Du W, Huang J. In silico study of androgen receptor N-terminal domain and exploration of its modulators. J Biomol Struct Dyn 2024:1-13. [PMID: 38661004 DOI: 10.1080/07391102.2024.2333454] [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: 11/04/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024]
Abstract
The androgen receptor (AR, Uniprot: P10275) signaling plays a key role in the progression of prostate cancer, various AR-related ligands have been reported to treat prostate cancer. However, some resistance mechanisms limited the treating effect of these ligands. Since DBD binding or the allosteric binding sites in LBD of AR may allow the circumvention of some drug resistance mechanisms, anti-resistance is expected especially through the NTD (N-terminal domain) targeting. What's more, studies have shown that compounds including EPI-001 and its derivatives which bind to the Tau-5 region on NTD could be promising molecules for AR-based therapeutics. Herein, we employed aMD (accelerated molecular dynamics) simulation to fold Tau-5 unit proteins into native structure correctly. Subsequently, based on the predicted structural features of Tau-5, the virtual screening was conducted to discover new compounds targeting AR-NTD. We picked up 8 compounds (according to their docking scores and partly similar structural consists as known AR ligands) and analyzed their interaction with Tau-5, compared with the positive control EPI-001, four of the pick-up compounds showed better glide scores. Interestingly, although compound 8 had a lower docking score, it consisted of a similar component as the ligand EIQPN and the amide derivatives, this predicts that compound 8 has also the potential to be modified into an excellent AR-NTD binding molecule. These 8 compounds were all commercially available and could be tested to check whether there was a hit compound to bind the AR-NTD and to regulate its bio-activities. Together, this study described an in silico VLS approach to discover AR-NTD ligands and provided more choices for developing AR-targeted therapies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Weidong Zhang
- Department of Pharmacy, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Hongyu Hu
- Xingzhi College, Zhejiang Normal University, Lanxi, China
| | - Yalan Zhu
- Department of Pharmacy, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Yiling He
- Department of Pharmacy, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Mingyue Yu
- Xingzhi College, Zhejiang Normal University, Lanxi, China
| | - Wenjun Du
- Department of Pharmacy, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Jiangang Huang
- Xingzhi College, Zhejiang Normal University, Lanxi, China
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Casper J, Schenk SH, Parhizkar E, Detampel P, Dehshahri A, Huwyler J. Polyethylenimine (PEI) in gene therapy: Current status and clinical applications. J Control Release 2023; 362:667-691. [PMID: 37666302 DOI: 10.1016/j.jconrel.2023.09.001] [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: 07/04/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/06/2023]
Abstract
Polyethlyenimine (PEI) was introduced 1995 as a cationic polymer for nucleic acid delivery. PEI and its derivatives are extensively used in basic research and as reference formulations in the field of polymer-based gene delivery. Despite its widespread use, the number of clinical applications to date is limited. Thus, this review aims to consolidate the past applications of PEI in DNA delivery, elucidate the obstacles that hinder its transition to clinical use, and highlight potential prospects for novel iterations of PEI derivatives. The present review article is divided into three sections. The first section examines the mechanism of action employed by PEI, examining fundamental aspects of cellular delivery including uptake mechanisms, release from endosomes, and transport into the cell nucleus, along with potential strategies for enhancing these delivery phases. Moreover, an in-depth analysis is conducted concerning the mechanism underlying cellular toxicity, accompanied with approaches to overcome this major challenge. The second part is devoted to the in vivo performance of PEI and its application in various therapeutic indications. While systemic administration has proven to be challenging, alternative localized delivery routes hold promise, such as treatment of solid tumors, application as a vaccine, or serving as a therapeutic agent for pulmonary delivery. In the last section, the outcome of completed and ongoing clinical trials is summarized. Finally, an expert opinion is provided on the potential of PEI and its future applications. PEI-based formulations for nucleic acid delivery have a promising potential, it will be an important task for the years to come to introduce innovations that address PEI-associated shortcomings by introducing well-designed PEI formulations in combination with an appropriate route of administration.
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Affiliation(s)
- Jens Casper
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Susanne H Schenk
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Elahehnaz Parhizkar
- Department of Pharmaceutics, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pascal Detampel
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
| | - Ali Dehshahri
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
| | - Jörg Huwyler
- Division of Pharmaceutical Technology, Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland.
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Mays SG, Hercules D, Ortlund EA, Okafor CD. The nuclear receptor LRH-1 discriminates between ligands using distinct allosteric signaling circuits. Protein Sci 2023; 32:e4754. [PMID: 37572334 PMCID: PMC10510465 DOI: 10.1002/pro.4754] [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: 04/05/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/14/2023]
Abstract
Nuclear receptors (NRs) are transcription factors that regulate essential biological processes in response to cognate ligands. An important part of NR function involves ligand-induced conformational changes that recruit coregulator proteins to the activation function surface (AFS), ~15 Å away from the ligand-binding pocket. Ligands must communicate with the AFS to recruit appropriate coregulators and elicit different transcriptional outcomes, but this communication is poorly understood. These studies illuminate allosteric communication networks underlying activation of liver receptor homolog-1 (LRH-1), a NR that regulates development, metabolism, cancer progression, and intestinal inflammation. Using >100 μs of all-atom molecular dynamics simulations involving 74 LRH-1 complexes, we identify distinct signaling circuits used by active and inactive ligands for AFS communication. Inactive ligands communicate via strong, coordinated motions along paths through the receptor to the AFS. Activating ligands disrupt the "inactive" circuit and induce connectivity with a second allosteric site. Ligand-contacting residues in helix 7 help mediate the switch between circuits, suggesting new avenues for developing LRH-1-targeted therapeutics. We also elucidate aspects of coregulator signaling, showing that localized, destabilizing fluctuations are induced by inappropriate ligand-coregulator pairings. These studies have uncovered novel features of LRH-1 allostery, and the quantitative approach used to analyze many simulations provides a framework to study allosteric signaling in other receptors.
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Affiliation(s)
- Suzanne G. Mays
- Department of BiochemistryEmory UniversityAtlantaGeorgiaUSA
- Department of Genome BiologyCentre for Genomic RegulationBarcelonaSpain
| | - David Hercules
- Department of BiochemistryEmory UniversityAtlantaGeorgiaUSA
| | | | - C. Denise Okafor
- Department of Molecular Biology and BiochemistryPennsylvania State UniversityState CollegePennsylvaniaUSA
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Kim H, Park C, Kim TH. Targeting Liver X Receptors for the Treatment of Non-Alcoholic Fatty Liver Disease. Cells 2023; 12:cells12091292. [PMID: 37174692 PMCID: PMC10177243 DOI: 10.3390/cells12091292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 04/29/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) refers to a range of conditions in which excess lipids accumulate in the liver, possibly leading to serious hepatic manifestations such as steatohepatitis, fibrosis/cirrhosis and cancer. Despite its increasing prevalence and significant impact on liver disease-associated mortality worldwide, no medication has been approved for the treatment of NAFLD yet. Liver X receptors α/β (LXRα and LXRβ) are lipid-activated nuclear receptors that serve as master regulators of lipid homeostasis and play pivotal roles in controlling various metabolic processes, including lipid metabolism, inflammation and immune response. Of note, NAFLD progression is characterized by increased accumulation of triglycerides and cholesterol, hepatic de novo lipogenesis, mitochondrial dysfunction and augmented inflammation, all of which are highly attributed to dysregulated LXR signaling. Thus, targeting LXRs may provide promising strategies for the treatment of NAFLD. However, emerging evidence has revealed that modulating the activity of LXRs has various metabolic consequences, as the main functions of LXRs can distinctively vary in a cell type-dependent manner. Therefore, understanding how LXRs in the liver integrate various signaling pathways and regulate metabolic homeostasis from a cellular perspective using recent advances in research may provide new insights into therapeutic strategies for NAFLD and associated metabolic diseases.
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Affiliation(s)
- Hyejin Kim
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Chaewon Park
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Tae Hyun Kim
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
- Drug Information Research Institute, Sookmyung Women's University, Seoul 04310, Republic of Korea
- Muscle Physiome Research Center, Sookmyung Women's University, Seoul 04310, Republic of Korea
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Mays SG, Hercules D, Ortlund EA, Okafor CD. The nuclear receptor LRH-1 discriminates between ligands using distinct allosteric signaling circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525934. [PMID: 36747705 PMCID: PMC9900875 DOI: 10.1101/2023.01.27.525934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Nuclear receptors (NRs) are transcription factors that regulate essential biological processes in response to cognate ligands. An important part of NR function involves ligand-induced conformational changes that recruit coregulator proteins to the activation function surface (AFS), ~15 Å away from the ligand binding pocket. Ligands must communicate with the AFS to recruit appropriate coregulators and elicit different transcriptional outcomes, but this communication is poorly understood. These studies illuminate allosteric communication networks underlying activation of liver receptor homolog-1 (LRH-1), a NR that regulates development, metabolism, cancer progression and intestinal inflammation. Using >100 microseconds of all-atom molecular dynamics simulations involving 69 LRH-1 complexes, we identify distinct signaling circuits used by active and inactive ligands for AFS communication. Inactive ligands communicate via strong, coordinated motions along paths through the receptor to the AFS. Activating ligands disrupt the "inactive" circuit by inducing connectivity elsewhere. Ligand-contacting residues in helix 7 help mediate the switch between circuits, suggesting new avenues for developing LRH-1-targeted therapeutics. We also elucidate aspects of coregulator signaling, showing that localized, destabilizing fluctuations are induced by inappropriate ligand-coregulator pairings. These studies have uncovered novel features of LRH-1 allostery, and the quantitative approach used to analyze many simulations provides a framework to study allosteric signaling in other receptors.
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7
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Sellami A, Réau M, Montes M, Lagarde N. Review of in silico studies dedicated to the nuclear receptor family: Therapeutic prospects and toxicological concerns. Front Endocrinol (Lausanne) 2022; 13:986016. [PMID: 36176461 PMCID: PMC9513233 DOI: 10.3389/fendo.2022.986016] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Being in the center of both therapeutic and toxicological concerns, NRs are widely studied for drug discovery application but also to unravel the potential toxicity of environmental compounds such as pesticides, cosmetics or additives. High throughput screening campaigns (HTS) are largely used to detect compounds able to interact with this protein family for both therapeutic and toxicological purposes. These methods lead to a large amount of data requiring the use of computational approaches for a robust and correct analysis and interpretation. The output data can be used to build predictive models to forecast the behavior of new chemicals based on their in vitro activities. This atrticle is a review of the studies published in the last decade and dedicated to NR ligands in silico prediction for both therapeutic and toxicological purposes. Over 100 articles concerning 14 NR subfamilies were carefully read and analyzed in order to retrieve the most commonly used computational methods to develop predictive models, to retrieve the databases deployed in the model building process and to pinpoint some of the limitations they faced.
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8
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Park YY. Genomic analysis of nuclear receptors and miRNAs identifies a role for the NR3C1/miR-200 axis in colon cancer. Genes Genomics 2021; 43:913-920. [PMID: 34021858 DOI: 10.1007/s13258-021-01112-0] [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: 03/03/2021] [Accepted: 04/29/2021] [Indexed: 01/14/2023]
Abstract
BACKGROUND Nuclear receptors (NRs) are crucial transcription factors involved in cell proliferation, metabolism and homeostasis. Through the development of novel genomic approaches, unknown NR functions have recently been uncovered. NR networks derived from gene expression profiles revealed that NRs are tightly linked to human disease and that targeting these links could provide new therapeutic options. MicroRNAs (miRNAs) have known functions as transcriptional regulators of NR function. OBJECTIVE I attempted to construct an NR-miRNA transcriptional network based on genomic data from human cancer. METHODS I performed comprehensive analysis with genomic data. Correlation, clustering and survival analysis were done to identify the NR and miRNA correlation in cancer. RESULTS Correlation analysis of genomic data revealed relationships between the expression levels of several NRs and miRNAs in human cancer. Based on my NR-miRNA correlation data, I found that NR3C1 expression was highly correlated with that of miR-200 in colon cancer. In most cases, miRNAs suppress expression of their target genes. Thus, miRNAs function as negative regulators during transcription. My analysis revealed that the miR-200 expression level is negatively correlated with that of NR3C1, demonstrating that miR-200 is a negative regulator of NR3C1 in colon cancer. It is known that miR-200 is a master regulator of EMT and that NR3C1 has a link with an EMT marker. CONCLUSIONS Overall, my genomic analysis revealed that the NR3C1 expression level is correlated with that of miR-200 and that this functional relationship might contribute to colon cancer cell survival. Modulating this axis could be a promising target for treating colon cancer patients.
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Affiliation(s)
- Yun-Yong Park
- Department of Life Science, College of Natural Science, Daejin University, Pocheon, 11159, Republic of Korea. .,Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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Weikum ER, Liu X, Ortlund EA. The nuclear receptor superfamily: A structural perspective. Protein Sci 2019; 27:1876-1892. [PMID: 30109749 DOI: 10.1002/pro.3496] [Citation(s) in RCA: 239] [Impact Index Per Article: 47.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 08/01/2018] [Accepted: 08/06/2018] [Indexed: 12/28/2022]
Abstract
Nuclear receptors (NRs) are a family of transcription factors that regulate numerous physiological processes such as metabolism, reproduction, inflammation, as well as the circadian rhythm. NRs sense changes in lipid metabolite levels to drive differential gene expression, producing distinct physiologic effects. This is an allosteric process whereby binding a cognate ligand and specific DNA sequences drives the recruitment of diverse transcriptional co-regulators at chromatin and ultimately transactivation or transrepression of target genes. Dysregulation of NR signaling leads to various malignances, metabolic disorders, and inflammatory disease. Given their important role in physiology and ability to respond to small lipophilic ligands, NRs have emerged as valuable therapeutic targets. Here, we summarize and discuss the recent progress on understanding the complex mechanism of action of NRs, primarily from a structural perspective. Finally, we suggest future studies to improve our understanding of NR signaling and better design drugs by integrating multiple structural and biophysical approaches.
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Affiliation(s)
- Emily R Weikum
- Department of Biochemistry, Emory School of Medicine, Atlanta, 30322, Georgia
| | - Xu Liu
- Department of Biochemistry, Emory School of Medicine, Atlanta, 30322, Georgia
| | - Eric A Ortlund
- Department of Biochemistry, Emory School of Medicine, Atlanta, 30322, Georgia
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Kozareva DA, Foley T, Moloney GM, Cryan JF, Nolan YM. TLX knockdown in the dorsal dentate gyrus of juvenile rats differentially affects adolescent and adult behaviour. Behav Brain Res 2018; 360:36-50. [PMID: 30481511 DOI: 10.1016/j.bbr.2018.11.034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 11/23/2018] [Accepted: 11/23/2018] [Indexed: 12/27/2022]
Abstract
The orphan nuclear receptor TLX is predominantly expressed in the central nervous system and is an important factor regulating the maintenance and self-renewal of neural stem cells from embryonic development through adulthood. In adolescence and adulthood, TLX expression is restricted to the neurogenic niches of the brain: the dentate gyrus of the hippocampus and the subventricular zone. The adolescent period is critical for maturation of the hippocampus with heightened levels of neurogenesis observed in rodents. Therefore, we investigated whether lentiviral silencing of TLX expression (TLX knockdown) in the dorsal dentate gyrus of juvenile rats incurred differential impairments in behaviour during late adolescence and adulthood. Our results showed that knockdown of TLX in the dorsal dentate gyrus led to a decrease in cell proliferation in the dorsal but not ventral dentate gyrus. At a behavioural level we observed differential effects in adolescence and adulthood across a number of parameters. A hyperactive phenotype was present in adolescent but not adult TLX knockdown rats, and an increase in immobility during adolescence and in swimming frequency during adulthood was observed in the forced swim test. There was an increased defecation frequency in the open field during adulthood but not adolescence. There were no changes in cognitive performance on hippocampus-dependent tasks or in anxiety-related behaviours. In conclusion, silencing of TLX in the dorsal dentate gyrus led to impairments in hippocampal-independent behaviours which either did not persist or were reversed during adulthood. The current data highlight the temporal importance and function of the nuclear receptor TLX during development.
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Affiliation(s)
- Danka A Kozareva
- Department of Anatomy and Neuroscience, University College Cork, Ireland
| | - Tara Foley
- Department of Anatomy and Neuroscience, University College Cork, Ireland
| | - Gerard M Moloney
- Department of Anatomy and Neuroscience, University College Cork, Ireland
| | - John F Cryan
- Department of Anatomy and Neuroscience, University College Cork, Ireland; APC Microbiome Ireland, University College Cork, Ireland
| | - Yvonne M Nolan
- Department of Anatomy and Neuroscience, University College Cork, Ireland; APC Microbiome Ireland, University College Cork, Ireland.
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El-Gendy BEDM, Goher SS, Hegazy LS, Arief MMH, Burris TP. Recent Advances in the Medicinal Chemistry of Liver X Receptors. J Med Chem 2018; 61:10935-10956. [DOI: 10.1021/acs.jmedchem.8b00045] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Bahaa El-Dien M. El-Gendy
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
- Chemistry Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Shaimaa S. Goher
- Chemistry Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Lamees S. Hegazy
- Department of Pharmacology and Physiology, Saint Louis University School of Medicine, St. Louis, Missouri 63104, United States
| | - Mohamed M. H. Arief
- Chemistry Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Thomas P. Burris
- Center for Clinical Pharmacology, Washington University School of Medicine and St. Louis College of Pharmacy, St. Louis, Missouri 63110, United States
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Targeting nuclear receptors in cancer-associated fibroblasts as concurrent therapy to inhibit development of chemoresistant tumors. Oncogene 2017; 37:160-173. [PMID: 28892046 PMCID: PMC5770601 DOI: 10.1038/onc.2017.319] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 07/29/2017] [Accepted: 08/06/2017] [Indexed: 12/11/2022]
Abstract
Most anticancer therapies to date focus on druggable features of tumor epithelia. Despite the increasing repertoire of treatment options, patient responses remain varied. Moreover, tumor resistance and relapse remain persistent clinical challenges. These observations imply an incomplete understanding of tumor heterogeneity. The tumor microenvironment is a major determinant of disease progression and therapy outcome. Cancer-associated fibroblasts (CAFs) are the dominant cell type within the reactive stroma of tumors. They orchestrate paracrine pro-tumorigenic signaling with adjacent tumor cells, thus exacerbating the hallmarks of cancer and accelerating tumor malignancy. Although CAF-derived soluble factors have been investigated for tumor stroma-directed therapy, the underlying transcriptional programs that enable the oncogenic functions of CAFs remain poorly understood. Nuclear receptors (NRs), a large family of ligand-responsive transcription factors, are pharmacologically viable targets for the suppression of CAF-facilitated oncogenesis. In this study, we defined the expression profiles of NRs in CAFs from clinical cutaneous squamous cell carcinoma (SCC) biopsies. We further identified a cluster of driver NRs in CAFs as important modifiers of CAF function with profound influence on cancer cell invasiveness, proliferation, drug resistance, energy metabolism and oxidative stress status. Importantly, guided by the NR profile of CAFs, retinoic acid receptor β and androgen receptor antagonists were identified for concurrent therapy with cisplatin, resulting in the inhibition of chemoresistance in recurred SCC:CAF xenografts. Our work demonstrates that treatments targeting both the tumor epithelia and the surrounding CAFs can extend the efficacy of conventional chemotherapy.
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Lagarde N, Delahaye S, Jérémie A, Ben Nasr N, Guillemain H, Empereur-Mot C, Laville V, Labib T, Réau M, Langenfeld F, Zagury JF, Montes M. Discriminating Agonist from Antagonist Ligands of the Nuclear Receptors Using Different Chemoinformatics Approaches. Mol Inform 2017; 36. [PMID: 28671755 DOI: 10.1002/minf.201700020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/30/2017] [Indexed: 11/10/2022]
Abstract
Nuclear receptors (NRs) constitute an important class of therapeutic targets. During the last 4 years, we tackled the pharmacological profile assessment of NR ligands for which we constructed the NRLiSt BDB. We evaluated and compared the performance of different virtual screening approaches: mean of molecular descriptor distribution values, molecular docking and 3D pharmacophore models. The simple comparison of the distribution profiles of 4885 molecular descriptors between the agonist and antagonist datasets didn't provide satisfying results. We obtained an overall good performance with the docking method we used, Surflex-Dock which was able to discriminate agonist from antagonist ligands. But the availability of PDB structures in the "pharmacological-profile-to-predict-bound-state" (agonist-bound or antagonist-bound) and the availability of enough ligands of both pharmacological profiles constituted limits to generalize this protocol for all NRs. Finally, the 3D pharmacophore modeling approach, allowed us to generate selective agonist pharmacophores and selective antagonist pharmacophores that covered more than 99 % of the whole NRLiSt BDB. This study allowed a better understanding of the pharmacological modulation of NRs with small molecules and could be extended to other therapeutic classes.
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Affiliation(s)
- Nathalie Lagarde
- Laboratoire Génomique Bioinformatique et Applications, Équipe d'accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003, Paris, France
| | - Solenne Delahaye
- Laboratoire Génomique Bioinformatique et Applications, Équipe d'accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003, Paris, France
| | - Aurore Jérémie
- Laboratoire Génomique Bioinformatique et Applications, Équipe d'accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003, Paris, France
| | - Nesrine Ben Nasr
- Laboratoire Génomique Bioinformatique et Applications, Équipe d'accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003, Paris, France
| | - Hélène Guillemain
- Laboratoire Génomique Bioinformatique et Applications, Équipe d'accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003, Paris, France
| | - Charly Empereur-Mot
- Laboratoire Génomique Bioinformatique et Applications, Équipe d'accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003, Paris, France
| | - Vincent Laville
- Laboratoire Génomique Bioinformatique et Applications, Équipe d'accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003, Paris, France
| | - Taoufik Labib
- Laboratoire Génomique Bioinformatique et Applications, Équipe d'accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003, Paris, France
| | - Manon Réau
- Laboratoire Génomique Bioinformatique et Applications, Équipe d'accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003, Paris, France
| | - Florent Langenfeld
- Laboratoire Génomique Bioinformatique et Applications, Équipe d'accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003, Paris, France
| | - Jean-François Zagury
- Laboratoire Génomique Bioinformatique et Applications, Équipe d'accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003, Paris, France
| | - Matthieu Montes
- Laboratoire Génomique Bioinformatique et Applications, Équipe d'accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003, Paris, France
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14
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Rudraiah S, Zhang X, Wang L. Nuclear Receptors as Therapeutic Targets in Liver Disease: Are We There Yet? Annu Rev Pharmacol Toxicol 2016; 56:605-626. [PMID: 26738480 DOI: 10.1146/annurev-pharmtox-010715-103209] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nuclear receptors (NR) are ligand-modulated transcription factors that play diverse roles in cell differentiation, development, proliferation, and metabolism and are associated with numerous liver pathologies such as cancer, steatosis, inflammation, fibrosis, cholestasis, and xenobiotic/drug-induced liver injury. The network of target proteins associated with NRs is extremely complex, comprising coregulators, small noncoding microRNAs, and long noncoding RNAs. The importance of NRs as targets of liver disease is exemplified by the number of NR ligands that are currently used in the clinics or in clinical trials with promising results. Understanding the regulation by NR during pathophysiological conditions, and identifying ligands for orphan NR, points to a potential therapeutic approach for patients with liver diseases. An overview of complex NR metabolic networks and their pharmacological implications in liver disease is presented here.
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Affiliation(s)
- Swetha Rudraiah
- Department of Physiology and Neurobiology and The Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269
| | - Xi Zhang
- Department of Physiology and Neurobiology and The Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269
| | - Li Wang
- Department of Physiology and Neurobiology and The Institute for Systems Genomics, University of Connecticut, Storrs, Connecticut 06269.,Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut 06516.,Department of Internal Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut 06520
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15
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Lagarde N, Delahaye S, Zagury JF, Montes M. Discriminating agonist and antagonist ligands of the nuclear receptors using 3D-pharmacophores. J Cheminform 2016; 8:43. [PMID: 27602059 PMCID: PMC5011875 DOI: 10.1186/s13321-016-0154-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 08/17/2016] [Indexed: 01/09/2023] Open
Abstract
Nuclear receptors (NRs) constitute an important class of therapeutic targets. We evaluated the performance of 3D structure-based and ligand-based pharmacophore models in predicting the pharmacological profile of NRs ligands using the NRLiSt BDB database. We could generate selective pharmacophores for agonist and antagonist ligands and we found that the best performances were obtained by combining the structure-based and the ligand-based approaches. The combination of pharmacophores that were generated allowed to cover most of the chemical space of the NRLiSt BDB datasets. By screening the whole NRLiSt BDB on our 3D pharmacophores, we demonstrated their selectivity towards their dedicated NRs ligands. The 3D pharmacophores herein presented can thus be used as a predictor of the pharmacological activity of NRs ligands.Graphical AbstractUsing a combination of structure-based and ligand-based pharmacophores, agonist and antagonist ligands of the Nuclear Receptors included in the NRLiSt BDB database could be separated.
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Affiliation(s)
- Nathalie Lagarde
- Laboratoire Génomique Bioinformatique et Applications, Équipe d’accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003 Paris, France
| | - Solenne Delahaye
- Laboratoire Génomique Bioinformatique et Applications, Équipe d’accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003 Paris, France
| | - Jean-François Zagury
- Laboratoire Génomique Bioinformatique et Applications, Équipe d’accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003 Paris, France
| | - Matthieu Montes
- Laboratoire Génomique Bioinformatique et Applications, Équipe d’accueil EA 4627, Conservatoire National des Arts et Métiers, 292 rue Saint Martin, 75003 Paris, France
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16
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Tice CM, Zheng YJ. Non-canonical modulators of nuclear receptors. Bioorg Med Chem Lett 2016; 26:4157-64. [PMID: 27503683 DOI: 10.1016/j.bmcl.2016.07.067] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/19/2016] [Accepted: 07/27/2016] [Indexed: 12/13/2022]
Abstract
Like G protein-coupled receptors (GPCRs) and protein kinases, nuclear receptors (NRs) are a rich source of pharmaceutical targets. Over 80 NR-targeting drugs have been approved for 18 NRs. The focus of drug discovery in NRs has hitherto been on identifying ligands that bind to the canonical ligand binding pockets of the C-terminal ligand binding domains (LBDs). Due to the development of drug resistance and selectivity concerns, there has been considerable interest in exploring other, non-canonical ligand binding sites. Unfortunately, the potencies of compounds binding at other sites have generally not been sufficient for clinical development. However, the situation has changed dramatically over the last 3years, as compounds with sufficient potency have been reported for several NR targets. Here we review recent developments in this area from a medicinal chemistry point of view in the hope of stimulating further interest in this area of research.
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Affiliation(s)
- Colin M Tice
- Vitae Pharmaceuticals, Inc., 502 West Office Center Drive, Fort Washington, PA 19034, United States
| | - Ya-Jun Zheng
- Vitae Pharmaceuticals, Inc., 502 West Office Center Drive, Fort Washington, PA 19034, United States
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17
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Banerjee M, Robbins D, Chen T. Targeting xenobiotic receptors PXR and CAR in human diseases. Drug Discov Today 2014; 20:618-28. [PMID: 25463033 DOI: 10.1016/j.drudis.2014.11.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/28/2014] [Accepted: 11/17/2014] [Indexed: 12/20/2022]
Abstract
Nuclear receptors such as the pregnane X receptor (PXR) and constitutive androstane receptor (CAR) are xenobiotic receptors regulating not only drug metabolism and disposition but also various human diseases such as cancer, diabetes, inflammatory disease, metabolic disease and liver diseases, suggesting that PXR and CAR are promising targets for drug discovery. Consequently, there is an urgent need to discover and develop small molecules that target these PXR- and/or CAR-mediated human-disease-related pathways for relevant therapeutic applications. This review proposes approaches to target PXR and CAR, either individually or simultaneously, in the context of various human diseases, taking into consideration the structural differences between PXR and CAR.
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Affiliation(s)
- Monimoy Banerjee
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Delira Robbins
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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18
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Filgueira CS, Benod C, Lou X, Gunamalai PS, Villagomez RA, Strom A, Gustafsson JÅ, Berkenstam AL, Webb P. A screening cascade to identify ERβ ligands. NUCLEAR RECEPTOR SIGNALING 2014; 12:e003. [PMID: 25422593 PMCID: PMC4242290 DOI: 10.1621/nrs.12003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 09/18/2014] [Indexed: 01/23/2023]
Abstract
The establishment of effective high throughput screening cascades to identify nuclear receptor (NR) ligands that will trigger defined, therapeutically useful sets of NR activities is of considerable importance. Repositioning of existing approved drugs with known side effect profiles can provide advantages because de novo drug design suffers from high developmental failure rates and undesirable side effects which have dramatically increased costs. Ligands that target estrogen receptor β (ERβ) could be useful in a variety of diseases ranging from cancer to neurological to cardiovascular disorders. In this context, it is important to minimize cross-reactivity with ERα, which has been shown to trigger increased rates of several types of cancer. Because of high sequence similarities between the ligand binding domains of ERα and ERβ, preferentially targeting one subtype can prove challenging. Here, we describe a sequential ligand screening approach comprised of complementary in-house assays to identify small molecules that are selective for ERβ. Methods include differential scanning fluorimetry, fluorescence polarization and a GAL4 transactivation assay. We used this strategy to screen several commercially-available chemical libraries, identifying thirty ERβ binders that were examined for their selectivity for ERβ versus ERα, and tested the effects of selected ligands in a prostate cancer cell proliferation assay. We suggest that this approach could be used to rapidly identify candidates for drug repurposing.
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Affiliation(s)
- Carly S Filgueira
- Genomic Medicine, Houston Methodist Research Institute (CSF, CB, XL, PSG, RAV, ALB, PW) and Center for Nuclear Receptors and Cell Signaling, University of Houston (AS, JAG, ALB, PW), Houston, Texas, USA
| | - Cindy Benod
- Genomic Medicine, Houston Methodist Research Institute (CSF, CB, XL, PSG, RAV, ALB, PW) and Center for Nuclear Receptors and Cell Signaling, University of Houston (AS, JAG, ALB, PW), Houston, Texas, USA
| | - Xiaohua Lou
- Genomic Medicine, Houston Methodist Research Institute (CSF, CB, XL, PSG, RAV, ALB, PW) and Center for Nuclear Receptors and Cell Signaling, University of Houston (AS, JAG, ALB, PW), Houston, Texas, USA
| | - Prem S Gunamalai
- Genomic Medicine, Houston Methodist Research Institute (CSF, CB, XL, PSG, RAV, ALB, PW) and Center for Nuclear Receptors and Cell Signaling, University of Houston (AS, JAG, ALB, PW), Houston, Texas, USA
| | - Rosa A Villagomez
- Genomic Medicine, Houston Methodist Research Institute (CSF, CB, XL, PSG, RAV, ALB, PW) and Center for Nuclear Receptors and Cell Signaling, University of Houston (AS, JAG, ALB, PW), Houston, Texas, USA
| | - Anders Strom
- Genomic Medicine, Houston Methodist Research Institute (CSF, CB, XL, PSG, RAV, ALB, PW) and Center for Nuclear Receptors and Cell Signaling, University of Houston (AS, JAG, ALB, PW), Houston, Texas, USA
| | - Jan-Åke Gustafsson
- Genomic Medicine, Houston Methodist Research Institute (CSF, CB, XL, PSG, RAV, ALB, PW) and Center for Nuclear Receptors and Cell Signaling, University of Houston (AS, JAG, ALB, PW), Houston, Texas, USA
| | - Anders L Berkenstam
- Genomic Medicine, Houston Methodist Research Institute (CSF, CB, XL, PSG, RAV, ALB, PW) and Center for Nuclear Receptors and Cell Signaling, University of Houston (AS, JAG, ALB, PW), Houston, Texas, USA
| | - Paul Webb
- Genomic Medicine, Houston Methodist Research Institute (CSF, CB, XL, PSG, RAV, ALB, PW) and Center for Nuclear Receptors and Cell Signaling, University of Houston (AS, JAG, ALB, PW), Houston, Texas, USA
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19
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Liu X, Giguère V. Inactivation of RARβ inhibits Wnt1-induced mammary tumorigenesis by suppressing epithelial-mesenchymal transitions. NUCLEAR RECEPTOR SIGNALING 2014; 12:e004. [PMID: 25422594 PMCID: PMC4242291 DOI: 10.1621/nrs.12004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/18/2014] [Indexed: 12/20/2022]
Abstract
Retinoic acid receptor β (RARβ) has been proposed to act as a tumor suppressor in
breast cancer. In contrast, recent data have shown that RARβ promotes ERBB2-induced mammary
gland tumorigenesis through remodeling of the stromal compartment and activation of
cancer-associated fibroblasts. However, it is currently unknown whether RARβ oncogenic
activity is specific to ERBB2-induced tumors, or whether it influences the initiation and
progression of other breast cancer subtypes. Accordingly, we set out to investigate the involvement
of RARβ in basal-like breast cancer using mouse mammary tumor virus (MMTV)-wingless-related
integration site 1 (Wnt1)-induced mammary gland tumorigenesis as a model system. We found that
compared with wild type mice, inactivation of Rarb resulted in a lengthy delay in
Wnt1-induced mammary gland tumorigenesis and in a significantly slower tumor growth
rate. Ablation of Rarb altered the composition of the stroma, repressed the
activation of cancer-associated fibroblasts, and reduced the recruitment of inflammatory cells and
angiogenesis. Reduced expression of IGF-1 and activity of its downstream signaling pathway
contribute to attenuate EMT in the Rarb-null tumors. Our results show that, in the
absence of retinoid signaling via RARβ, reduced IGF-1 signaling results in suppression of
epithelial-mesenchymal transition and delays tumorigenesis induced by the Wnt1
oncogene. Accordingly, our work reinforces the concept that antagonizing RARβ-dependent
retinoid signaling could provide a therapeutic avenue to treat poor outcome breast cancers.
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Affiliation(s)
- Xingxing Liu
- Goodman Cancer Research Centre, 1160 Pine Avenue West, McGill University, Montréal, Québec H3A 1A3 (XL, VG) and Departments of Biochemistry, Medicine and Oncology, 3655 Promenade Sir William Osler, McGill University, Montréal, Québec H3G 1Y6 (VG), Canada
| | - Vincent Giguère
- Goodman Cancer Research Centre, 1160 Pine Avenue West, McGill University, Montréal, Québec H3A 1A3 (XL, VG) and Departments of Biochemistry, Medicine and Oncology, 3655 Promenade Sir William Osler, McGill University, Montréal, Québec H3G 1Y6 (VG), Canada
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20
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Mahajan S, Saini A, Kalra R, Gupta P. Frienemies of infection: A chronic case of host nuclear receptors acting as cohorts or combatants of infection. Crit Rev Microbiol 2014; 42:526-34. [PMID: 25358058 DOI: 10.3109/1040841x.2014.970122] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Macrophages and dendritic cells provide critical effector functions to efficiently resist and promptly eliminate infection. Pattern recognition receptors signaling operative in these cell types is imperative for their innate properties. However, it is now emerging that besides these conventional signaling pathways, nuclear receptors coupled gene regulation and transrepression pathways assemble immune regulatory networks. A couple of these networks associated with members of nuclear receptor superfamily decide heterogeneity in macrophages and dendritic cells population and thereby play decisive role in determining protective immunity against bacteria, viruses, fungi, protozoa and helminths. Pathogens also direct shift in the expression of nuclear receptors and their target genes and this is proclaimed to be a sui generis mechanism whereby microbes disconnect the genomic component from the peripheral immune response. Many endogenous and synthetic nuclear receptor ligands have been tested in various in vitro and in vivo infection models to study their effect on pathogen burden. Here, we discuss current advances in our understanding of the composite interactions between nuclear receptor and pathogens and their implications on the causatum infectious diseases.
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Affiliation(s)
- Sahil Mahajan
- a Department of Molecular Biology , CSIR Institute of Microbial Technology , Chandigarh , India
| | - Ankita Saini
- a Department of Molecular Biology , CSIR Institute of Microbial Technology , Chandigarh , India
| | - Rashi Kalra
- a Department of Molecular Biology , CSIR Institute of Microbial Technology , Chandigarh , India
| | - Pawan Gupta
- a Department of Molecular Biology , CSIR Institute of Microbial Technology , Chandigarh , India
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21
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The human orphan nuclear receptor tailless (TLX, NR2E1) is druggable. PLoS One 2014; 9:e99440. [PMID: 24936658 PMCID: PMC4060991 DOI: 10.1371/journal.pone.0099440] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 05/14/2014] [Indexed: 12/31/2022] Open
Abstract
Nuclear receptors (NRs) are an important group of ligand-dependent transcriptional factors. Presently, no natural or synthetic ligand has been identified for a large group of orphan NRs. Small molecules to target these orphan NRs will provide unique resources for uncovering regulatory systems that impact human health and to modulate these pathways with drugs. The orphan NR tailless (TLX, NR2E1), a transcriptional repressor, is a major player in neurogenesis and Neural Stem Cell (NSC) derived brain tumors. No chemical probes that modulate TLX activity are available, and it is not clear whether TLX is druggable. To assess TLX ligand binding capacity, we created homology models of the TLX ligand binding domain (LBD). Results suggest that TLX belongs to an emerging class of NRs that lack LBD helices α1 and α2 and that it has potential to form a large open ligand binding pocket (LBP). Using a medium throughput screening strategy, we investigated direct binding of 20,000 compounds to purified human TLX protein and verified interactions with a secondary (orthogonal) assay. We then assessed effects of verified binders on TLX activity using luciferase assays. As a result, we report identification of three compounds (ccrp1, ccrp2 and ccrp3) that bind to recombinant TLX protein with affinities in the high nanomolar to low micromolar range and enhance TLX transcriptional repressive activity. We conclude that TLX is druggable and propose that our lead compounds could serve as scaffolds to derive more potent ligands. While our ligands potentiate TLX repressive activity, the question of whether it is possible to develop ligands to de-repress TLX activity remains open.
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22
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Dkhar HK, Nanduri R, Mahajan S, Dave S, Saini A, Somavarapu AK, Arora A, Parkesh R, Thakur KG, Mayilraj S, Gupta P. Mycobacterium tuberculosis keto-mycolic acid and macrophage nuclear receptor TR4 modulate foamy biogenesis in granulomas: a case of a heterologous and noncanonical ligand-receptor pair. THE JOURNAL OF IMMUNOLOGY 2014; 193:295-305. [PMID: 24907344 DOI: 10.4049/jimmunol.1400092] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The cell wall of Mycobacterium tuberculosis is configured of bioactive lipid classes that are essential for virulence and potentially involved in the formation of foamy macrophages (FMs) and granulomas. Our recent work established crosstalk between M. tuberculosis cell wall lipids and the host lipid-sensing nuclear receptor TR4. In this study, we have characterized, identified, and adopted a heterologous ligand keto-mycolic acid from among M. tuberculosis lipid repertoire for the host orphan NR TR4. Crosstalk between cell wall lipids and TR4 was analyzed by transactivation and promoter reporter assays. Mycolic acid (MA) was found to transactivate TR4 significantly compared with other cell wall lipids. Among the MA, the oxygenated form, keto-MA, was responsible for transactivation, and the identity was validated by TR4 binding assays followed by TLC and nuclear magnetic resonance. Isothermal titration calorimetry revealed that keto-MA binding to TR4 is energetically favorable. This keto-MA-TR4 axis seems to be essential to this oxygenated MA induction of FMs and granuloma formation as evaluated by in vitro and in vivo model of granuloma formation. TR4 binding with keto-MA features a unique association of host nuclear receptor with a bacterial lipid and adds to the presently known ligand repertoire beyond dietary lipids. Pharmacologic modulation of this heterologous axis may hold promise as an adjunct therapy to frontline tuberculosis drugs.
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Affiliation(s)
- Hedwin Kitdorlang Dkhar
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Ravikanth Nanduri
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Sahil Mahajan
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Sandeep Dave
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Ankita Saini
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Arun Kumar Somavarapu
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Ashish Arora
- Council of Scientific and Industrial Research-Central Drug Research Institute, Lucknow 226031, India
| | - Raman Parkesh
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Krishan Gopal Thakur
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Shanmugam Mayilraj
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
| | - Pawan Gupta
- Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh 160036, India; and
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23
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Modulation of xenobiotic receptors by steroids. Molecules 2013; 18:7389-406. [PMID: 23884115 PMCID: PMC3777271 DOI: 10.3390/molecules18077389] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Revised: 06/13/2013] [Accepted: 06/19/2013] [Indexed: 12/13/2022] Open
Abstract
Nuclear receptors (NRs) are ligand-activated transcription factors that regulate the expression of their target genes. NRs play important roles in many human diseases, including metabolic diseases and cancer, and are therefore a key class of therapeutic targets. Steroids play important roles in regulating nuclear receptors; in addition to being ligands of steroid receptors, steroids (and their metabolites) also regulate other NRs, such as the pregnane X receptor and constitutive androstane receptor (termed xenobiotic receptors), which participate in steroid metabolism. Xenobiotic receptors have promiscuous ligand-binding properties, and their structurally diverse ligands include steroids and their metabolites. Therefore, steroids, their metabolism and metabolites, xenobiotic receptors, steroid receptors, and the respective signaling pathways they regulate have functional interactions. This review discusses these functional interactions and their implications for activities mediated by steroid receptors and xenobiotic receptors, focusing on steroids that modulate pathways involving the pregnane X receptor and constitutive androstane receptor. The emphasis of the review is on structure-function studies of xenobiotic receptors bound to steroid ligands.
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