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Vilas-Boas C, Sousa J, Lima E, Running L, Resende D, Ribeiro ARL, Sousa E, Santos MM, Aga DS, Tiritan ME, Ruivo R, Atilla-Gokcumen GE, Correia-da-Silva M. Preliminary hazard assessment of a new nature-inspired antifouling (NIAF) agent. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 933:172824. [PMID: 38688370 DOI: 10.1016/j.scitotenv.2024.172824] [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: 08/29/2023] [Revised: 03/29/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
A recently synthesized aminated 3,4-dioxygenated xanthone (Xantifoul2) was found to have promising antifouling (AF) effects against the settlement of the macrofouler Mytilus galloprovincialis larvae. Preliminary assessment indicated that Xantifoul2 has reduced ecotoxicological impacts: e.g., being non-toxic to the marine crustacea Artemia salina (<10 % mortality at 50 μM) and showing low bioconcentration factor in marine organisms. In order to meet the EU Biocidal Product Regulation, a preliminary hazard assessment of this new nature-inspired antifouling (NIAF) agent was conducted in this work. Xantifoul2 did not affect the swimming ability of the planktonic crustacean Daphnia magna, the growth of the diatom Phaeodactylum tricornutum, and the cellular respiration of luminescent Gram-negative bacteria Vibrio fischeri, supporting the low toxicity towards several non-target marine species. Regarding human cytotoxicity, Xantifoul2 did not affect the cell viability of retinal human cells (hTERT-RPE-1) and lipidomic studies revealed depletion of lipids involved in cell death, membrane modeling, lipid storage, and oxidative stress only at a high concentration (10 μM). Accelerated degradation studies in water were conducted under simulated sunlight to allow the understanding of putative transformation products (TPs) that could be generated in the aquatic ecosystems. Both Xantifoul2 and photolytic-treated Xantifoul2 in the aqueous matrix were therefore evaluated on several nuclear receptors (NRs). The results of this preliminary hazard assessment of Xantifoul2, combined with the high degradation rates in water, provide strong evidence of the safety of this AF agent under the evaluated conditions, and provide the support for future validation studies before this compound can be introduced in the market.
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Affiliation(s)
- Cátia Vilas-Boas
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; CIIMAR-Interdisciplinary Center for Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal
| | - João Sousa
- CIIMAR-Interdisciplinary Center for Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal
| | - Erica Lima
- CIIMAR-Interdisciplinary Center for Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal
| | - Logan Running
- Chemistry Department, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Diana Resende
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; CIIMAR-Interdisciplinary Center for Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal
| | - Ana Rita L Ribeiro
- LSRE-LCM - Laboratory of Separation and Reaction Engineering - Laboratory of Catalysis and Materials, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Emília Sousa
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; CIIMAR-Interdisciplinary Center for Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal
| | - Miguel M Santos
- CIIMAR-Interdisciplinary Center for Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal; Department of Biology, Faculty of Sciences, University of Porto, 4169-007 Porto, Portugal
| | - Diana S Aga
- Chemistry Department, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
| | - Maria Elizabeth Tiritan
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; CIIMAR-Interdisciplinary Center for Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal
| | - Raquel Ruivo
- CIIMAR-Interdisciplinary Center for Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal.
| | | | - Marta Correia-da-Silva
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; CIIMAR-Interdisciplinary Center for Marine and Environmental Research, University of Porto, 4450-208 Matosinhos, Portugal.
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2
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James BD, Medvedev AV, Makarov SS, Nelson RK, Reddy CM, Hahn ME. Moldable Plastics (Polycaprolactone) can be Acutely Toxic to Developing Zebrafish and Activate Nuclear Receptors in Mammalian Cells. ACS Biomater Sci Eng 2024. [PMID: 38981095 DOI: 10.1021/acsbiomaterials.4c00693] [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] [Indexed: 07/11/2024]
Abstract
Popularized on social media, hand-moldable plastics are formed by consumers into tools, trinkets, and dental prosthetics. Despite the anticipated dermal and oral contact, manufacturers share little information with consumers about these materials, which are typically sold as microplastic-sized resin pellets. Inherent to their function, moldable plastics pose a risk of dermal and oral exposure to unknown leachable substances. We analyzed 12 moldable plastics advertised for modeling and dental applications and determined them to be polycaprolactone (PCL) or thermoplastic polyurethane (TPU). The bioactivities of the most popular brands advertised for modeling applications of each type of polymer were evaluated using a zebrafish embryo bioassay. While water-borne exposure to the TPU pellets did not affect the targeted developmental end points at any concentration tested, the PCL pellets were acutely toxic above 1 pellet/mL. The aqueous leachates of the PCL pellets demonstrated similar toxicity. Methanolic extracts from the PCL pellets were assayed for their bioactivity using the Attagene FACTORIAL platform. Of the 69 measured end points, the extracts activated nuclear receptors and transcription factors for xenobiotic metabolism (pregnane X receptor, PXR), lipid metabolism (peroxisome proliferator-activated receptor γ, PPARγ), and oxidative stress (nuclear factor erythroid 2-related factor 2, NRF2). By nontargeted high-resolution comprehensive two-dimensional gas chromatography (GC × GC-HRT), we tentatively identified several compounds in the methanolic extracts, including PCL oligomers, a phenolic antioxidant, and residues of suspected antihydrolysis and cross-linking additives. In a follow-up zebrafish embryo bioassay, because of its stated high purity, biomedical grade PCL was tested to mitigate any confounding effects due to chemical additives in the PCL pellets; it elicited comparable acute toxicity. From these orthogonal and complementary experiments, we suggest that the toxicity was due to oligomers and nanoplastics released from the PCL rather than chemical additives. These results challenge the perceived and assumed inertness of plastics and highlight their multiple sources of toxicity.
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Affiliation(s)
- Bryan D James
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Alexander V Medvedev
- Attagene, Research Triangle Park, Morrisville, North Carolina 27709, United States
| | - Sergei S Makarov
- Attagene, Research Triangle Park, Morrisville, North Carolina 27709, United States
| | - Robert K Nelson
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Christopher M Reddy
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
| | - Mark E Hahn
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts 02543, United States
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3
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Khan O, Jones G, Lazou M, Joseph-McCarthy D, Kozakov D, Beglov D, Vajda S. Expanding FTMap for Fragment-Based Identification of Pharmacophore Regions in Ligand Binding Sites. J Chem Inf Model 2024; 64:2084-2100. [PMID: 38456842 DOI: 10.1021/acs.jcim.3c01969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The knowledge of ligand binding hot spots and of the important interactions within such hot spots is crucial for the design of lead compounds in the early stages of structure-based drug discovery. The computational solvent mapping server FTMap can reliably identify binding hot spots as consensus clusters, free energy minima that bind a variety of organic probe molecules. However, in its current implementation, FTMap provides limited information on regions within the hot spots that tend to interact with specific pharmacophoric features of potential ligands. E-FTMap is a new server that expands on the original FTMap protocol. E-FTMap uses 119 organic probes, rather than the 16 in the original FTMap, to exhaustively map binding sites, and identifies pharmacophore features as atomic consensus sites where similar chemical groups bind. We validate E-FTMap against a set of 109 experimentally derived structures of fragment-lead pairs, finding that highly ranked pharmacophore features overlap with the corresponding atoms in both fragments and lead compounds. Additionally, comparisons of mapping results to ensembles of bound ligands reveal that pharmacophores generated with E-FTMap tend to sample highly conserved protein-ligand interactions. E-FTMap is available as a web server at https://eftmap.bu.edu.
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Affiliation(s)
- Omeir Khan
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
| | - George Jones
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
| | - Maria Lazou
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Diane Joseph-McCarthy
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, United States
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, United States
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
- Acpharis Inc., Holliston, Massachusetts 01746, United States
| | - Sandor Vajda
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
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4
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Huber AD, Poudel S, Wu J, Miller DJ, Lin W, Yang L, Bwayi MN, Rimmer MA, Gee RRF, Seetharaman J, Chai SC, Chen T. A bromodomain-independent mechanism of gene regulation by the BET inhibitor JQ1: direct activation of nuclear receptor PXR. Nucleic Acids Res 2024; 52:1661-1676. [PMID: 38084912 PMCID: PMC10899790 DOI: 10.1093/nar/gkad1175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/17/2023] [Accepted: 11/23/2023] [Indexed: 02/29/2024] Open
Abstract
Bromodomain and extraterminal (BET) proteins are extensively studied in multiple pathologies, including cancer. BET proteins modulate transcription of various genes, including those synonymous with cancer, such as MYC. Thus, BET inhibitors are a major area of drug development efforts. (+)-JQ1 (JQ1) is the prototype inhibitor and is a common tool to probe BET functions. While showing therapeutic promise, JQ1 is not clinically usable, partly due to metabolic instability. Here, we show that JQ1 and the BET-inactive (-)-JQ1 are agonists of pregnane X receptor (PXR), a nuclear receptor that transcriptionally regulates genes encoding drug-metabolizing enzymes such as CYP3A4, which was previously shown to oxidize JQ1. A PXR-JQ1 co-crystal structure identified JQ1's tert-butyl moiety as a PXR anchor and explains binding by (-)-JQ1. Analogs differing at the tert-butyl lost PXR binding, validating our structural findings. Evaluation in liver cell models revealed both PXR-dependent and PXR-independent modulation of CYP3A4 expression by BET inhibitors. We have characterized a non-BET JQ1 target, a mechanism of physiological JQ1 instability, a biological function of (-)-JQ1, and BET-dependent transcriptional regulation of drug metabolism genes.
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Affiliation(s)
- Andrew D Huber
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Shyaron Poudel
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Monicah N Bwayi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mary Ashley Rimmer
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Rebecca R Florke Gee
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
- Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jayaraman Seetharaman
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Sergio C Chai
- 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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Schäfer AM, Rysz MA, Schädeli J, Hübscher M, Khosravi H, Fehr M, Seibert I, Potterat O, Smieško M, Meyer Zu Schwabedissen HE. St. John's Wort Formulations Induce Rat CYP3A23-3A1 Independent of Their Hyperforin Content. Mol Pharmacol 2023; 105:14-22. [PMID: 37863663 DOI: 10.1124/molpharm.123.000725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/08/2023] [Accepted: 09/21/2023] [Indexed: 10/22/2023] Open
Abstract
The pregnane X receptor (PXR) is a ligand-activated regulator of cytochrome P450 (CYP)3A enzymes. Among the ligands of human PXR is hyperforin, a constituent of St John's wort (SJW) extracts and potent inducer of human CYP3A4. It was the aim of this study to compare the effect of hyperforin and SJW formulations controlled for its content on CYP3A23-3A1 in rats. Hyperiplant was used as it contains a high hyperforin content and Rebalance because it is controlled for a low hyperforin content. In silico analysis revealed a weak hyperforin-rPXR binding affinity, which was further supported in cell-based reporter gene assays showing no hyperforin-mediated reporter activation in presence of rPXR. However, cellular exposure to Hyperiplant and Rebalance transactivated the CYP3A reporter 3.8-fold and 2.8-fold, respectively, and they induced Cyp3a23-3a1 mRNA expression in rat hepatoma cells compared with control 48-fold and 18-fold, respectively. In Wistar rats treated for 10 days with 400 mg/kg of Hyperiplant, we observed 1.8 times the Cyp3a23-3a1 mRNA expression, a 2.6-fold higher CYP3A23-3A1 protein amount, and a 1.6-fold increase in activity compared with controls. For Rebalance we only observed a 1.8-fold hepatic increase of CYP3A23-3A1 protein compared with control animals. Even though there are differing effects on rCyp3a23-3a1/CYP3A23-3A1 in rat liver reflecting the hyperforin content of the SJW extracts, the modulation is most likely not linked to an interaction of hyperforin with rPXR. SIGNIFICANCE STATEMENT: Treatment with St John's wort (SJW) has been reported to affect CYP3A expression and activity in rats. Our comparative study further supports this finding but shows that the pregnane X receptor-ligand hyperforin is not the driving force for changes in rat CYP3A23-3A1 expression and function in vivo and in vitro. Importantly, CYP3A induction mimics findings in humans, but our results suggest that another so far unknown constituent of SJW is responsible for the expression- and function-modifying effects in rat liver.
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Affiliation(s)
- Anima M Schäfer
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Marta A Rysz
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Julia Schädeli
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Michelle Hübscher
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Haleh Khosravi
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Michelle Fehr
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Isabell Seibert
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Olivier Potterat
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Martin Smieško
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
| | - Henriette E Meyer Zu Schwabedissen
- Biopharmacy (A.M.S., M.A.R., J.S., M.H., H.K., M.F., I.S., H.E.M.), Computational Pharmacy (M.S.), and Pharmaceutical Biology (O.P.), Department of Pharmaceutical Sciences, University of Basel, Basel, Switzerland
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6
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Vázquez-Gómez G, Petráš J, Dvořák Z, Vondráček J. Aryl hydrocarbon receptor (AhR) and pregnane X receptor (PXR) play both distinct and common roles in the regulation of colon homeostasis and intestinal carcinogenesis. Biochem Pharmacol 2023; 216:115797. [PMID: 37696457 DOI: 10.1016/j.bcp.2023.115797] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/13/2023]
Abstract
Both aryl hydrocarbon receptor (AhR) and pregnane X receptor (PXR) belong among key regulators of xenobiotic metabolism in the intestinal tissue. AhR in particular is activated by a wide range of environmental and dietary carcinogens. The data accumulated over the last two decades suggest that both of these transcriptional regulators play a much wider role in the maintenance of gut homeostasis, and that both transcription factors may affect processes linked with intestinal tumorigenesis. Intestinal epithelium is continuously exposed to a wide range of AhR, PXR and dual AhR/PXR ligands formed by intestinal microbiota or originating from diet. Current evidence suggests that specific ligands of both AhR and PXR can protect intestinal epithelium against inflammation and assist in the maintenance of epithelial barrier integrity. AhR, and to a lesser extent also PXR, have been shown to play a protective role against inflammation-induced colon cancer, or, in mouse models employing overactivation of Wnt/β-catenin signaling. In contrast, other evidence suggests that both receptors may contribute to modulation of transformed colon cell behavior, with a potential to promote cancer progression and/or chemoresistance. The review focuses on both overlapping and separate roles of the two receptors in these processes, and on possible implications of their activity within the context of intestinal tissue.
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Affiliation(s)
- Gerardo Vázquez-Gómez
- Department of Cytokinetics, Institute of Biophysics of the CAS, Královopolská 135, 61265 Brno, Czech Republic
| | - Jiří Petráš
- Department of Cytokinetics, Institute of Biophysics of the CAS, Královopolská 135, 61265 Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5, 62500 Brno, Czech Republic
| | - Zdeněk Dvořák
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, 783 71 Olomouc, Czech Republic
| | - Jan Vondráček
- Department of Cytokinetics, Institute of Biophysics of the CAS, Královopolská 135, 61265 Brno, Czech Republic.
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7
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Liang Y, Gong Y, Jiang Q, Yu Y, Zhang J. Environmental endocrine disruptors and pregnane X receptor action: A review. Food Chem Toxicol 2023; 179:113976. [PMID: 37532173 DOI: 10.1016/j.fct.2023.113976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/11/2023] [Accepted: 07/28/2023] [Indexed: 08/04/2023]
Abstract
The pregnane X receptor (PXR) is a kind of orphan nuclear receptor activated by a series of ligands. Environmental endocrine disruptors (EEDs) are a wide class of molecules present in the environment that are suspected to have adverse effects on the endocrine system by interfering with the synthesis, transport, degradation, or action of endogenous hormones. Since EEDs may modulate human/rodent PXR, this review aims to summarize EEDs as PXR modulators, including agonists and antagonists. The modular structure of PXR is also described, interestingly, the pharmacology of PXR have been confirmed to vary among different species. Furthermore, PXR play a key role in the regulation of endocrine function. Endocrine disruption of EEDs via PXR and its related pathways are systematically summarized. In brief, this review may provide a way to understand the roles of EEDs in interaction with the nuclear receptors (such as PXR) and the related pathways.
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Affiliation(s)
- Yuan Liang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Yiyao Gong
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Qiuyan Jiang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Yifan Yu
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
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8
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Lin W, Huber AD, Poudel S, Li Y, Seetharaman J, Miller DJ, Chen T. Structure-guided approach to modulate small molecule binding to a promiscuous ligand-activated protein. Proc Natl Acad Sci U S A 2023; 120:e2217804120. [PMID: 36848571 PMCID: PMC10013835 DOI: 10.1073/pnas.2217804120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/30/2023] [Indexed: 03/01/2023] Open
Abstract
Ligand-binding promiscuity in detoxification systems protects the body from toxicological harm but is a roadblock to drug development due to the difficulty in optimizing small molecules to both retain target potency and avoid metabolic events. Immense effort is invested in evaluating metabolism of molecules to develop safer, more effective treatments, but engineering specificity into or out of promiscuous proteins and their ligands is a challenging task. To better understand the promiscuous nature of detoxification networks, we have used X-ray crystallography to characterize a structural feature of pregnane X receptor (PXR), a nuclear receptor that is activated by diverse molecules (with different structures and sizes) to up-regulate transcription of drug metabolism genes. We found that large ligands expand PXR's ligand-binding pocket, and the ligand-induced expansion occurs through a specific unfavorable compound-protein clash that likely contributes to reduced binding affinity. Removing the clash by compound modification resulted in more favorable binding modes with significantly enhanced binding affinity. We then engineered the unfavorable ligand-protein clash into a potent, small PXR ligand, resulting in marked reduction in PXR binding and activation. Structural analysis showed that PXR is remodeled, and the modified ligands reposition in the binding pocket to avoid clashes, but the conformational changes result in less favorable binding modes. Thus, ligand-induced binding pocket expansion increases ligand-binding potential of PXR but is an unfavorable event; therefore, drug candidates can be engineered to expand PXR's ligand-binding pocket and reduce their safety liability due to PXR binding.
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Affiliation(s)
- Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Andrew D. Huber
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Shyaron Poudel
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Yongtao Li
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Jayaraman Seetharaman
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Darcie J. Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN38105
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN38105
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9
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Antifouling Marine Coatings with a Potentially Safer and Sustainable Synthetic Polyphenolic Derivative. Mar Drugs 2022; 20:md20080507. [PMID: 36005510 PMCID: PMC9409691 DOI: 10.3390/md20080507] [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: 06/16/2022] [Revised: 07/31/2022] [Accepted: 08/01/2022] [Indexed: 11/29/2022] Open
Abstract
The development of harmless substances to replace biocide-based coatings used to prevent or manage marine biofouling and its unwanted consequences is urgent. The formation of biofilms on submerged marine surfaces is one of the first steps in the marine biofouling process, which facilitates the further settlement of macrofoulers. Anti-biofilm properties of a synthetic polyphenolic compound, with previously described anti-settlement activity against macrofoulers, were explored in this work. In solution this new compound was able to prevent biofilm formation and reduce a pre-formed biofilm produced by the marine bacterium, Pseudoalteromonas tunicata. Then, this compound was applied to a marine coating and the formation of P. tunicata biofilms was assessed under hydrodynamic conditions to mimic the marine environment. For this purpose, polyurethane (PU)-based coating formulations containing 1 and 2 wt.% of the compound were prepared based on a prior developed methodology. The most effective formulation in reducing the biofilm cell number, biovolume, and thickness was the PU-based coating containing an aziridine-based crosslinker and 2 wt.% of the compound. To assess the marine ecotoxicity impact of this compound, its potential to disrupt endocrine processes was evaluated through the modulation of two nuclear receptors (NRs), peroxisome proliferator-activated receptor γ (PPARγ), and pregnane X receptor (PXR). Transcriptional activation of the selected NRs upon exposure to the polyphenolic compound (10 µM) was not observed, thus highlighting the eco-friendliness towards the addressed NRs of this new dual-acting anti-macro- and anti-microfouling agent towards the addressed NRs.
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10
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Dutta M, Lim JJ, Cui JY. Pregnane X Receptor and the Gut-Liver Axis: A Recent Update. Drug Metab Dispos 2022; 50:478-491. [PMID: 34862253 PMCID: PMC11022899 DOI: 10.1124/dmd.121.000415] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 12/02/2021] [Indexed: 02/04/2023] Open
Abstract
It is well-known that the pregnane X receptor (PXR)/Nr1i2 is a critical xenobiotic-sensing nuclear receptor enriched in liver and intestine and is responsible for drug-drug interactions, due to its versatile ligand binding domain (LBD) and target genes involved in xenobiotic biotransformation. PXR can be modulated by various xenobiotics including pharmaceuticals, nutraceuticals, dietary factors, and environmental chemicals. Microbial metabolites such as certain secondary bile acids (BAs) and the tryptophan metabolite indole-3-propionic acid (IPA) are endogenous PXR activators. Gut microbiome is increasingly recognized as an important regulator for host xenobiotic biotransformation and intermediary metabolism. PXR regulates and is regulated by the gut-liver axis. This review summarizes recent research advancements leveraging pharmaco- and toxico-metagenomic approaches that have redefined the previous understanding of PXR. Key topics covered in this review include: (1) genome-wide investigations on novel PXR-target genes, novel PXR-DNA interaction patterns, and novel PXR-targeted intestinal bacteria; (2) key PXR-modulating activators and suppressors of exogenous and endogenous sources; (3) novel bidirectional interactions between PXR and gut microbiome under physiologic, pathophysiological, pharmacological, and toxicological conditions; and (4) modifying factors of PXR-signaling including species and sex differences and time (age, critical windows of exposure, and circadian rhythm). The review also discusses critical knowledge gaps and important future research topics centering around PXR. SIGNIFICANCE STATEMENT: This review summarizes recent research advancements leveraging O'mics approaches that have redefined the previous understanding of the xenobiotic-sensing nuclear receptor pregnane X receptor (PXR). Key topics include: (1) genome-wide investigations on novel PXR-targeted host genes and intestinal bacteria as well as novel PXR-DNA interaction patterns; (2) key PXR modulators including microbial metabolites under physiological, pathophysiological, pharmacological, and toxicological conditions; and (3) modifying factors including species, sex, and time.
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Affiliation(s)
- Moumita Dutta
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - Joe Jongpyo Lim
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - Julia Yue Cui
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
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11
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Niu X, Wu T, Li G, Gu X, Tian Y, Cui H. Insights into the critical role of the PXR in preventing carcinogenesis and chemotherapeutic drug resistance. Int J Biol Sci 2022; 18:742-759. [PMID: 35002522 PMCID: PMC8741843 DOI: 10.7150/ijbs.68724] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 11/21/2021] [Indexed: 12/12/2022] Open
Abstract
Pregnane x receptor (PXR) as a nuclear receptor is well-established in drug metabolism, however, it has pleiotropic functions in regulating inflammatory responses, glucose metabolism, and protects normal cells against carcinogenesis. Most studies focus on its transcriptional regulation, however, PXR can regulate gene expression at the translational level. Emerging evidences have shown that PXR has a broad protein-protein interaction network, by which is implicated in the cross signaling pathways. Furthermore, the interactions between PXR and some critical proteins (e.g., p53, Tip60, p300/CBP-associated factor) in DNA damage pathway highlight its potential roles in this field. A thorough understanding of how PXR maintains genome stability and prevents carcinogenesis will help clinical diagnosis and finally benefit patients. Meanwhile, due to the regulation of CYP450 enzymes CYP3A4 and multidrug resistance protein 1 (MDR1), PXR contributes to chemotherapeutic drug resistance. It is worthy of note that the co-factor of PXR such as RXRα, also has contributions to this process, which makes the PXR-mediated drug resistance more complicated. Although single nucleotide polymorphisms (SNPs) vary between individuals, the amino acid substitution on exon of PXR finally affects PXR transcriptional activity. In this review, we have summarized the updated mechanisms that PXR protects the human body against carcinogenesis, and major contributions of PXR with its co-factors have made on multidrug resistance. Furthermore, we have also reviewed the current promising antagonist and their clinic applications in reversing chemoresistance. We believe our review will bring insight into PXR-targeted cancer therapy, enlighten the future study direction, and provide substantial evidence for the clinic in future.
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Affiliation(s)
- Xiaxia Niu
- Institute of Toxicology, School of Public Health, Lanzhou University, 730000, Lanzhou, China
| | - Ting Wu
- Institute of Toxicology, School of Public Health, Lanzhou University, 730000, Lanzhou, China
| | - Gege Li
- Institute of Toxicology, School of Public Health, Lanzhou University, 730000, Lanzhou, China
| | - Xinsheng Gu
- Department of Pharmacology, College of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Yanan Tian
- Department of Veterinary Physiology and Pharmacology, Texas A&M University, USA
| | - Hongmei Cui
- Institute of Toxicology, School of Public Health, Lanzhou University, 730000, Lanzhou, China
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12
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Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist. Comput Struct Biotechnol J 2022; 20:3004-3018. [PMID: 35782743 PMCID: PMC9218138 DOI: 10.1016/j.csbj.2022.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022] Open
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13
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Zhang J, Pavek P, Kamaraj R, Ren L, Zhang T. Dietary phytochemicals as modulators of human pregnane X receptor. Crit Rev Food Sci Nutr 2021:1-23. [PMID: 34698593 DOI: 10.1080/10408398.2021.1995322] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
As a promiscuous xenobiotic sensor, pregnane X receptor (PXR) plays a crucial role in drug metabolism. Since dietary phytochemicals exhibit the potential to modulate human PXR, this review aims to summarize the plant-derived PXR modulators, including agonists, partial agonists, and antagonists. The crystal structures of the apo and ligand-bound forms of PXR especially that of PXR complexed with binary mixtures are summarized, in order to provide the structural basis for PXR binding promiscuity and synergistic activation of PXR by composite ligands. Furthermore, this review summarizes the characterized agonists, partial agonists, and antagonists of human PXR from botanical source. Contrary to PXR agonists, there are only a few antagonists obtained from botanical source due to the promiscuity of PXR. It is worth noting that trans-resveratrol and a series of methylindoles have been identified as partial agonists of PXR, both in activating PXR function, but also inhibiting the effect of other PXR agonists. Since antagonizing PXR function plays a crucial role in the prevention of drug-drug interactions and improvement of therapeutic efficacy, further research is necessary to screen more plant-derived PXR antagonists in the future. In summary, this review may contribute to understanding the roles of phytochemicals in food-drug and herb-drug interactions.
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Affiliation(s)
- Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Petr Pavek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University, Hradec Kralove, Czech Republic
| | - Rajamanikkam Kamaraj
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University, Hradec Kralove, Czech Republic
| | - Li Ren
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun, China
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14
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Shizu R, Nishiguchi H, Tashiro S, Sato T, Sugawara A, Kanno Y, Hosaka T, Sasaki T, Yoshinari K. Helix 12 stabilization contributes to basal transcriptional activity of PXR. J Biol Chem 2021; 297:100978. [PMID: 34284062 PMCID: PMC8390552 DOI: 10.1016/j.jbc.2021.100978] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/12/2021] [Accepted: 07/16/2021] [Indexed: 11/19/2022] Open
Abstract
Pregnane X receptor (PXR) plays an important role in xenobiotic metabolism. While ligand binding induces PXR-dependent gene transcription, PXR shows constitutive transcriptional activity in the absence of ligands when expressed in cultured cells. This constitutive activity sometimes hampers investigation of PXR activation by compounds of interest. In this study, we investigated the molecular mechanism of PXR activation. In the reported crystal structures of unliganded PXR, helix 12 (H12), including a coactivator binding motif, was stabilized, while it is destabilized in the unliganded structures of other nuclear receptors, suggesting a role for H12 stabilization in the basal activity of PXR. Since Phe420, located in the loop between H11 and H12, is thought to interact with Leu411 and Ile414 to stabilize H12, we substituted alanine at Phe420 (PXR-F420A) and separately inserted three alanine residues directly after Phe420 (PXR-3A) and investigated their influence on PXR-mediated transcription. Reporter gene assays demonstrated that the mutants showed drastically reduced basal activity and enhanced responses to various ligands, which was further enhanced by coexpression of the coactivator peroxisome proliferator-activated receptor gamma coactivator 1α. Mutations of both Leu411 and Ile414 to alanine also suppressed basal activity. Mammalian two-hybrid assays showed that PXR-F420A and PXR-3A bound to corepressors and coactivators in the absence and presence of ligands, respectively. We conclude that the intramolecular interactions of Phe420 with Leu411 and Ile414 stabilize H12 to recruit coactivators even in the absence of ligands, contributing to the basal transcriptional activity of PXR. We propose that the generated mutants might be useful for PXR ligand screening.
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Affiliation(s)
- Ryota Shizu
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.
| | - Hikaru Nishiguchi
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Sarii Tashiro
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Takumi Sato
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Ayaka Sugawara
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yuichiro Kanno
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Takuomi Hosaka
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Takamitsu Sasaki
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Kouichi Yoshinari
- Laboratory of Molecular Toxicology, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan.
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15
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Goksøyr SØ, Goldstone J, Lille-Langøy R, Lock EJ, Olsvik PA, Goksøyr A, Karlsen OA. Polycyclic aromatic hydrocarbons modulate the activity of Atlantic cod (Gadus morhua) vitamin D receptor paralogs in vitro. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 238:105914. [PMID: 34304057 DOI: 10.1016/j.aquatox.2021.105914] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
Vitamin D receptor (VDR) mediates the biological function of the steroid hormone calcitriol, which is the metabolically active version of vitamin D. Calcitriol is important for a wide array of physiological functions, including calcium and phosphate homeostasis. In contrast to mammals, which harbor one VDR encoding gene, teleosts possess two orthologous vdr genes encoding Vdr alpha (Vdra) and Vdr beta (Vdrb). Genome mining identified the vdra and vdrb paralogs in the Atlantic cod (Gadus morhua) genome, which were further characterized regarding their phylogeny, tissue-specific expression, and transactivational properties induced by calcitriol. In addition, a selected set of polycyclic aromatic hydrocarbons (PAHs), including naphthalene, phenanthrene, fluorene, pyrene, chrysene, benzo[a]pyrene (BaP), and 7-methylbenzo[a]pyrene, were assessed for their ability to modulate the transcriptional activity of gmVdra and gmVdrb in vitro. Both gmVdra and gmVdrb were activated by calcitriol with similar potencies, but gmVdra produced significantly higher maximal fold activation. Notably, none of the tested PAHs showed agonistic properties towards the Atlantic cod Vdrs. However, binary exposures of calcitriol together with phenanthrene, fluorene, or pyrene, antagonized the activation of gmVdra, while chrysene and BaP significantly potentiated the calcitriol-mediated activity of both receptors. Homology modeling, solvent mapping, and docking analyses complemented the experimental data, and revealed a putative secondary binding site in addition to the canonical ligand-binding pocket (LBP). Calcitriol was predicted to interact with both binding sites, whereas PAHs docked primarily to the LBP. Importantly, our in vitro data suggest that PAHs can interact with the paralogous gmVdrs and interfere with their transcriptional activities, and thus potentially modulate the vitamin D signaling pathway and contribute to adverse effects of crude oil and PAH exposures on cardiac development and bone deformities in fish.
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Affiliation(s)
| | - Jed Goldstone
- Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | | | - Erik-Jan Lock
- Department of Biological Sciences, University of Bergen, Norway; Institute of Marine Research, Bergen, Norway
| | - Pål A Olsvik
- Institute of Marine Research, Bergen, Norway; Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Anders Goksøyr
- Department of Biological Sciences, University of Bergen, Norway
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16
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Hall A, Chanteux H, Ménochet K, Ledecq M, Schulze MSED. Designing Out PXR Activity on Drug Discovery Projects: A Review of Structure-Based Methods, Empirical and Computational Approaches. J Med Chem 2021; 64:6413-6522. [PMID: 34003642 DOI: 10.1021/acs.jmedchem.0c02245] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This perspective discusses the role of pregnane xenobiotic receptor (PXR) in drug discovery and the impact of its activation on CYP3A4 induction. The use of structural biology to reduce PXR activity on drug discovery projects has become more common in recent years. Analysis of this work highlights several important molecular interactions, and the resultant structural modifications to reduce PXR activity are summarized. The computational approaches undertaken to support the design of new drugs devoid of PXR activation potential are also discussed. Finally, the SAR of empirical design strategies to reduce PXR activity is reviewed, and the key SAR transformations are discussed and summarized. In conclusion, this perspective demonstrates that PXR activity can be greatly diminished or negated on active drug discovery projects with the knowledge now available. This perspective should be useful to anyone who seeks to reduce PXR activity on a drug discovery project.
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Affiliation(s)
- Adrian Hall
- UCB, Avenue de l'Industrie, Braine-L'Alleud 1420, Belgium
| | | | | | - Marie Ledecq
- UCB, Avenue de l'Industrie, Braine-L'Alleud 1420, Belgium
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17
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Meng R, Zhang X, Wang H, Zhang D, Zhao X. Different Inductive Effects of Praziquantel Racemate and its Enantiomers on the Enzyme CYP3A4 Mediated by Pregnane X Receptor and its Variants. Curr Drug Metab 2021; 22:232-239. [PMID: 33397228 DOI: 10.2174/1389200221999210104204057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 11/27/2020] [Accepted: 11/28/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Praziquantel (PZQ), which possesses an asymmetric center, is classified as a pyrazinoisoquinoline and has been the mainstay in the treatment of schistosomiasis since 1980. PZQ undergoes a pronounced first-pass metabolism in the liver through the CYP450 system which could be mediated by nuclear receptors. OBJECTIVE The purpose of this study was to investigate the possible different induction effects of CYP3A4 by PZQ racemate and enantiomers via the pregnane X receptor (PXR) and the effect of PXR polymorphism on the induction potency of PZQs. METHODS The dual-luciferase reporter gene systems constructed in HepG2 cells were used to measure the abilities of PZQs to induce CYP3A4 expression mediated by PXR. The mRNA and protein levels of CYP3A4 were evaluated by polymerase chain reaction (PCR) and western blotting, respectively. RESULTS In HepG2 cells transfected with PXRwt, PXR158, PXR163, PXR370 or PXR403 expression plasmids, PZQ racemate and its enantiomers up-regulated the luciferase activity in a concentration-dependent manner, while reaching saturation after transfected with PXR379 expression plasmids. The mRNA and protein expression of CYP3A4 was effectively activated in PXR-transfected HepG2 cells. The induction ability of CYP3A4 mediated by PXR activation by PZQ racemate and its enantiomers were statistically different between the same PXR group and different PXR groups. CONCLUSION The enantioselective induction effects of PZQs on CYP3A4 were related to the enantioselective activations of PXR by PZQs and were influenced by the PXR gene polymorphism. These findings provide a basis for further understanding the enantiomeric metabolism and the variable efficacy of PZQs.
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Affiliation(s)
- Ran Meng
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xueli Zhang
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Haina Wang
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Danlu Zhang
- School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xin Zhao
- School of Life Sciences, Shandong Normal University, Jinan, China
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18
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Adiwidjaja J, Boddy AV, McLachlan AJ. Potential for pharmacokinetic interactions between Schisandra sphenanthera and bosutinib, but not imatinib: in vitro metabolism study combined with a physiologically-based pharmacokinetic modelling approach. Br J Clin Pharmacol 2020; 86:2080-2094. [PMID: 32250458 DOI: 10.1111/bcp.14303] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 02/17/2020] [Accepted: 03/18/2020] [Indexed: 12/13/2022] Open
Abstract
AIMS This study aimed to investigate the potential interaction between Schisandra sphenanthera, imatinib and bosutinib combining in vitro and in silico methods. METHODS In vitro metabolism of imatinib and bosutinib using recombinant enzymes and human liver microsomes were investigated in the presence and absence of Schisandra lignans. Physiologically-based pharmacokinetic (PBPK) models for the lignans accounting for reversible and mechanism-based inhibitions and induction of CYP3A enzymes were built in the Simcyp Simulator (version 17) and evaluated for their capability to predict interactions with midazolam and tacrolimus. Their potential effect on systemic exposures of imatinib and bosutinib were predicted using PBPK in silico simulations. RESULTS Schisantherin A and schisandrol B, but not schisandrin A, potently inhibited CYP3A4-mediated metabolism of imatinib and bosutinib. All three compounds showed a strong reversible inhibition on CYP2C8 enzyme with ki of less than 0.5 μmol L-1 . The verified PBPK models were able to describe the increase in systemic exposure of midazolam and tacrolimus due to co-administration of S. sphenanthera, consistent with the reported changes in the corresponding clinical interaction study (AUC ratio of 2.0 vs 2.1 and 2.4 vs 2.1, respectively). The PBPK simulation predicted that at recommended dosing regimens of S. sphenanthera, co-administration would result in an increase in bosutinib exposure (AUC ratio 3.0) but not in imatinib exposure. CONCLUSION PBPK models for Schisandra lignans were successfully developed. Interaction between imatinib and Schisandra lignans was unlikely to be of clinical importance. Conversely, S. sphenanthera at a clinically-relevant dose results in a predicted three-fold increase in bosutinib systemic exposure.
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Affiliation(s)
- Jeffry Adiwidjaja
- Sydney Pharmacy School, The University of Sydney, Sydney, NSW, Australia
| | - Alan V Boddy
- School of Pharmacy and Medical Sciences, University of South Australia, Adelaide, SA, Australia.,University of South Australia Cancer Research Institute, University of South Australia, Adelaide, SA, Australia
| | - Andrew J McLachlan
- Sydney Pharmacy School, The University of Sydney, Sydney, NSW, Australia
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19
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Mutation of a single amino acid of pregnane X receptor switches an antagonist to agonist by altering AF-2 helix positioning. Cell Mol Life Sci 2020; 78:317-335. [PMID: 32232515 DOI: 10.1007/s00018-020-03505-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 03/04/2020] [Accepted: 03/11/2020] [Indexed: 10/24/2022]
Abstract
Pregnane X receptor (PXR) is activated by chemicals to transcriptionally regulate drug disposition and possibly decrease drug efficacy and increase resistance, suggesting therapeutic value for PXR antagonists. We previously reported the antagonist SPA70 and its analog SJB7, which unexpectedly is an agonist. Here, we describe another unexpected observation: mutating a single residue (W299A) within the PXR ligand-binding domain converts SPA70 to an agonist. After characterizing wild-type and W299A PXR activity profiles, we used molecular dynamics simulations to reveal that in wild-type PXR, agonists stabilize the activation function 2 (AF-2) helix in an "inward" position, but SPA70 displaces the AF-2. In W299A, however, SPA70 stabilizes the AF-2 "inward", like agonists. We validated our model by predicting the antagonist SJC2 to be a W299A agonist, which was confirmed experimentally. Our work correlates previously unobserved ligand-induced conformational changes to PXR cellular activity and, for the first time, reveals how PXR antagonists work.
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20
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Rampersaud A, Lodato NJ, Shin A, Waxman DJ. Widespread epigenetic changes to the enhancer landscape of mouse liver induced by a specific xenobiotic agonist ligand of the nuclear receptor CAR. Toxicol Sci 2019; 171:315-338. [PMID: 31236583 PMCID: PMC6760311 DOI: 10.1093/toxsci/kfz148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 12/13/2022] Open
Abstract
CAR (Nr1i3), a liver nuclear receptor and xenobiotic sensor, induces drug, steroid and lipid metabolism and dysregulates genes linked to hepatocellular carcinogenesis, but its impact on the liver epigenome is poorly understood. TCPOBOP, a halogenated xenochemical and highly specific CAR agonist ligand, induces localized chromatin opening or closing at several thousand mouse liver genomic regions, discovered as differential DNase-hypersensitive sites (ΔDHS). Active enhancer and promoter histone marks induced by TCPOBOP were enriched at opening DHS and TCPOBOP-inducible genes. Enrichment of CAR binding and CAR motifs was seen at opening DHS and their inducible drug/lipid metabolism gene targets, and at many constitutively open DHS located nearby. TCPOBOP-responsive cell cycle and DNA replication genes co-dependent on MET/EGFR signaling for induction were also enriched for CAR binding. A subset of opening DHS and many closing DHS mapping to TCPOBOP-responsive target genes did not bind CAR, indicating an indirect mechanism for their changes in chromatin accessibility. TCPOBOP-responsive DHS were also enriched for induced binding of RXRA, CEBPA and CEBPB, and for motifs for liver-enriched factors that may contribute to liver-specific transcriptional responses to TCPOBOP exposure. These studies elucidate the enhancer landscape of TCPOBOP-exposed liver and the widespread epigenetic changes that are induced by both direct and indirect mechanisms linked to CAR activation. The global maps of thousands of environmental chemical-induced epigenetic changes described here constitute a rich resource for further research on xenochemical effects on liver chromatin states and the epigenome.
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Affiliation(s)
- Andy Rampersaud
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA USA
| | - Nicholas J Lodato
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA USA
| | - Aram Shin
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA USA
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21
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Lille-Langøy R, Karlsen OA, Myklebust LM, Goldstone JV, Mork-Jansson A, Male R, Blumberg B, Stegeman JJ, Goksøyr A. Sequence Variations in pxr (nr1i2) From Zebrafish (Danio rerio) Strains Affect Nuclear Receptor Function. Toxicol Sci 2019; 168:28-39. [PMID: 30371853 PMCID: PMC6390661 DOI: 10.1093/toxsci/kfy269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Regulators of biotransformation are of particular interest in pharmacology and toxicology, determining in part the metabolism, disposition, and toxicity of chemicals. The nuclear receptor NR1I2 (pregnane X receptor, PXR) is a prominent xenosensor that regulates the expression of biotransformation enzymes governing elimination of many exogenous as well as endogenous compounds. Zebrafish (Danio rerio) has only one gene locus for pxr, but different genetic variants have been identified in zebrafish. However, the prevalence and significance of these variants are unknown. We hypothesize that sequence variation occurring in the Pxr gene of zebrafish may affect the action and fate of many chemicals in this species, a key model organism in various fields of research, including environmental toxicology. Here, we examine variation in Pxr sequences from four different strains of zebrafish and assess the responses of each Pxr to clotrimazole and butyl-4-aminobenzoate. The Pxr variants differed in both their ability to bind these structurally different ligands and to regulate reporter gene expression in vitro. We infer that the observed sequence variations in zebrafish Pxrs likely affect the response to putative Pxr agonists in vivo and potentially cause strain-specific biotransformation of xenobiotics in zebrafish. Thus, the choice of zebrafish strain could affect the outcome of downstream toxicological studies.
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Affiliation(s)
- Roger Lille-Langøy
- Department of Biological Sciences, University of Bergen, N-5006 Bergen, Norway
| | - Odd André Karlsen
- Department of Biological Sciences, University of Bergen, N-5006 Bergen, Norway
| | | | - Jared V Goldstone
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, U. S. A
| | - Astrid Mork-Jansson
- Department of Biological Sciences, University of Bergen, N-5006 Bergen, Norway
- Centre for Organelle Research, University of Stavanger, N-4036 Stavanger, Norway
| | - Rune Male
- Department of Biological Sciences, University of Bergen, N-5006 Bergen, Norway
| | - Bruce Blumberg
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, U. S. A
| | - John J Stegeman
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, U. S. A
| | - Anders Goksøyr
- Department of Biological Sciences, University of Bergen, N-5006 Bergen, Norway
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22
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Chai SC, Lin W, Li Y, Chen T. Drug discovery technologies to identify and characterize modulators of the pregnane X receptor and the constitutive androstane receptor. Drug Discov Today 2019; 24:906-915. [PMID: 30731240 PMCID: PMC6421094 DOI: 10.1016/j.drudis.2019.01.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/27/2018] [Accepted: 01/30/2019] [Indexed: 11/24/2022]
Abstract
The pregnane X receptor (PXR) and the constitutive androstane receptor (CAR) are ligand-activated nuclear receptors (NRs) that are notorious for their role in drug metabolism, causing unintended drug-drug interactions and decreasing drug efficacy. They control the xenobiotic detoxification system by regulating the expression of an array of drug-metabolizing enzymes and transporters that excrete exogenous chemicals and maintain homeostasis of endogenous metabolites. Much effort has been invested in recognizing potential drugs for clinical use that can activate PXR and CAR to enhance the expression of their target genes, and in identifying PXR and CAR inhibitors that can be used as co-therapeutics to prevent adverse effects. Here, we present current technologies and assays used in the quest to characterize PXR and CAR modulators, which range from biochemical to cell-based and animal models.
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Affiliation(s)
- Sergio C Chai
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Wenwei Lin
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Yongtao Li
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
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23
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Yi-Wen Z, Mei-Hua B, Xiao-Ya L, Yu C, Jing Y, Hong-Hao Z. Effects of Oridonin on Hepatic Cytochrome P450 Expression and Activities in PXR-Humanized Mice. Biol Pharm Bull 2018; 41:707-712. [PMID: 29709908 DOI: 10.1248/bpb.b17-00882] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Oridonin, the major terpene found in Rabdosia rubescens, is widely used as dietary supplement or therapeutic drug, while the effects of oridonin on CYP450 were still unclear. The pregnane X receptor (PXR) is an important regulatory factor for major drug metabolism enzyme CYPs, and it has been reported to have species-specific differences. Therefore, this study has employed more reliable models PXR-humanized mouse to investigate the influence of oridonin on PXR and downstream metabolism enzyme. Eight-week-old male PXR-humanized mice were treated with oridonin by orally (0, 25, 50, 100, 200 mg/kg) for 15 d. The effects of oridonin on major downstream CYPs of PXR were examined at both the mRNA and enzyme activity levels by RT-PCR and HPLC-MS/MS. In general, there was no significant toxic reaction in liver of PXR-humanized mice. The mRNA expression of CYPs and cytochrome P450 oxidoreductase (POR) were increased with oridonin treatment in a dose-dependent manner. CYP2c and CYP3a family catalytic activity were increased significantly in two higher doses groups. These results indicate that oridonin induced the expression and activation of CYP2c and CYP3a family, which might contribute to potential drug-drug interactions and appear to be a risk when co-administered with other clinical drugs.
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Affiliation(s)
- Zhang Yi-Wen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics.,Key Laboratory of Head & Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital
| | - Bao Mei-Hua
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics.,Department of Anatomy, Histology and Embryology, Changsha Medical University
| | - Lou Xiao-Ya
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics
| | - Cheng Yu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics
| | - Yu Jing
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics
| | - Zhou Hong-Hao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics
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24
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Narayanan B, Lade JM, Heck CJ, Dietz KD, Wade H, Bumpus NN. Probing Ligand Structure-Activity Relationships in Pregnane X Receptor (PXR): Efavirenz and 8-Hydroxyefavirenz Exhibit Divergence in Activation. ChemMedChem 2018; 13:736-747. [PMID: 29430850 PMCID: PMC6081956 DOI: 10.1002/cmdc.201700730] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 02/06/2018] [Indexed: 12/24/2022]
Abstract
Efavirenz (EFV), an antiretroviral that interacts clinically with co-administered drugs via activation of the pregnane X receptor (PXR), is extensively metabolized by the cytochromes P450. We tested whether its primary metabolite, 8-hydroxyEFV (8-OHEFV) can activate PXR and potentially contribute to PXR-mediated drug-drug interactions attributed to EFV. Luciferase reporter assays revealed that despite only differing from EFV by an oxygen atom, 8-OHEFV does not activate PXR. Corroborating this, treatment with EFV for 72 h elevated the mRNA abundance of the PXR target gene, Cyp3a11, by approximately 28-fold in primary hepatocytes isolated from PXR-humanized mice, whereas treatment with 8-OHEFV did not result in a change in Cyp3A11 mRNA levels. FRET-based competitive binding assays and isothermal calorimetry demonstrated that even with the lack of ability to activate PXR, 8-OHEFV displays an affinity for PXR (IC50 12.1 μm; KD 7.9 μm) nearly identical to that of EFV (IC50 18.7 μm; KD 12.5 μm). The use of 16 EFV analogues suggest that other discreet changes to the EFV structure beyond the 8-position are well tolerated. Molecular docking simulations implicate an 8-OHEFV binding mode that may underlie its divergence in PXR activation from EFV.
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Affiliation(s)
- Bhargavi Narayanan
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street Hunterian 709 Baltimore, MD, USA
| | - Julie M. Lade
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 N Wolfe St Biophysics 307 Baltimore, MD, USA
| | - Carley J.S. Heck
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, 725 N Wolfe St Biophysics 307 Baltimore, MD, USA
| | - Kevin D. Dietz
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street Hunterian 709 Baltimore, MD, USA
| | - Herschel Wade
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N Wolfe Street Hunterian 709 Baltimore, MD, USA
| | - Namandjé N. Bumpus
- Department of Medicine, Division of Clinical Pharmacology, Johns Hopkins University School of Medicine, 725 N Wolfe St Biophysics 307 Baltimore, MD, USA
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25
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Zhang YW, Zheng XW, Liu YJ, Fang L, Pan ZF, Bao MH, Huang P. Effect of Oridonin on Cytochrome P450 Expression and Activities in HepaRG Cell. Pharmacology 2018; 101:246-254. [PMID: 29393278 DOI: 10.1159/000486600] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 01/04/2018] [Indexed: 12/13/2022]
Abstract
Oridonin, the major terpene found in Rabdosia rubescens, is widely used as a dietary supplement or therapeutic drug. However, the effects of oridonin on major CYP450s are still unclear. As oridonin can enhance the effect of other clinical drugs, in this study, we investigated the influence of oridonin on CYP450s mRNA expression and its impact on activities in human HepaRG cell to evaluate the safety by studying its potential drug interaction. HepaRG cells were cultured with series concentrations of oridonin (1, 5, 10, and 20 μmol/L), and the major CYP450s mRNA and protein expression, as well as enzyme activities were analyzed by real-time polymerase chain reaction, Western blot analysis and UPLC-MS/MS-based metabolite assay. In general, ordonin has induced effects on the major member of CYP450s mRNA and protein expression, as well as on the enzyme activity in human HepaRG cells, especially on CYP3A4 and CYP2C9. To our knowledge, this is the first systematic research about the inductive effects of oridonin on the major member of CYP450s in human cell line. These results may provide at least partly of the basis for potential drug-drug interactions and oridonin should be used with caution to avoid potential risk.
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Affiliation(s)
- Yi-Wen Zhang
- Laboratory of Clinical Pharmacy, Zhejiang Cancer Hospital, Hangzhou, China.,Key Laboratory of Head and Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, Hangzhou, China
| | - Xiao-Wei Zheng
- Laboratory of Clinical Pharmacy, Zhejiang Cancer Hospital, Hangzhou, China
| | - Yu-Jia Liu
- Laboratory of Clinical Pharmacy, Zhejiang Cancer Hospital, Hangzhou, China
| | - Luo Fang
- Laboratory of Clinical Pharmacy, Zhejiang Cancer Hospital, Hangzhou, China
| | - Zong-Fu Pan
- Laboratory of Clinical Pharmacy, Zhejiang Cancer Hospital, Hangzhou, China
| | - Mei-Hua Bao
- Department of Anatomy, Histology and Embryology, Changsha Medical University, Changsha, China
| | - Ping Huang
- Laboratory of Clinical Pharmacy, Zhejiang Cancer Hospital, Hangzhou, China.,Key Laboratory of Head and Neck Cancer Translational Research of Zhejiang Province, Zhejiang Cancer Hospital, Hangzhou, China
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26
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Helsley RN, Zhou C. Epigenetic impact of endocrine disrupting chemicals on lipid homeostasis and atherosclerosis: a pregnane X receptor-centric view. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx017. [PMID: 29119010 PMCID: PMC5672952 DOI: 10.1093/eep/dvx017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/08/2017] [Accepted: 09/02/2017] [Indexed: 05/25/2023]
Abstract
Despite the major advances in developing diagnostic techniques and effective treatments, atherosclerotic cardiovascular disease (CVD) is still the leading cause of mortality and morbidity worldwide. While considerable progress has been achieved to identify gene variations and environmental factors that contribute to CVD, much less is known about the role of "gene-environment interactions" in predisposing individuals to CVD. Our chemical environment has significantly changed in the last few decades, and there are more than 100,000 synthetic chemicals in the market. Recent large-scale human population studies have associated exposure to certain chemicals including many endocrine disrupting chemicals (EDCs) with increased CVD risk, and animal studies have also confirmed that some EDCs can cause aberrant lipid homeostasis and increase atherosclerosis. However, the underlying mechanisms of how exposure to those EDCs influences CVD risk remain elusive. Numerous EDCs can activate the nuclear receptor pregnane X receptor (PXR) that functions as a xenobiotic sensor to regulate host xenobiotic metabolism. Recent studies have demonstrated the novel functions of PXR in lipid homeostasis and atherosclerosis. In addition to directly regulating transcription, PXR has been implicated in the epigenetic regulation of gene transcription. Exposure to many EDCs can also induce epigenetic modifications, but little is known about how the changes relate to the onset or progression of CVD. In this review, we will discuss recent research on PXR and EDCs in the context of CVD and propose that PXR may play a previously unrealized role in EDC-mediated epigenetic modifications that affect lipid homeostasis and atherosclerosis.
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Affiliation(s)
- Robert N Helsley
- Department of Pharmacology and Nutritional Sciences, Center for Metabolic Disease Research, University of Kentucky, Lexington, KY 40536, USA
- Department of Cellular and Molecular Medicine, Cleveland Clinic Lerner Research Institute, Cleveland, OH 44195, USA
| | - Changcheng Zhou
- Department of Pharmacology and Nutritional Sciences, Center for Metabolic Disease Research, University of Kentucky, Lexington, KY 40536, USA
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Lin W, Wang YM, Chai SC, Lv L, Zheng J, Wu J, Zhang Q, Wang YD, Griffin PR, Chen T. SPA70 is a potent antagonist of human pregnane X receptor. Nat Commun 2017; 8:741. [PMID: 28963450 PMCID: PMC5622171 DOI: 10.1038/s41467-017-00780-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 07/27/2017] [Indexed: 02/06/2023] Open
Abstract
Many drugs bind to and activate human pregnane X receptor (hPXR) to upregulate drug-metabolizing enzymes, resulting in decreased drug efficacy and increased resistance. This suggests that hPXR antagonists have therapeutic value. Here we report that SPA70 is a potent and selective hPXR antagonist. SPA70 inhibits hPXR in human hepatocytes and humanized mouse models and enhances the chemosensitivity of cancer cells, consistent with the role of hPXR in drug resistance. Unexpectedly, SJB7, a close analog of SPA70, is an hPXR agonist. X-ray crystallography reveals that SJB7 resides in the ligand-binding domain (LBD) of hPXR, interacting with the AF-2 helix to stabilize the LBD for coactivator binding. Differential hydrogen/deuterium exchange analysis demonstrates that SPA70 and SJB7 interact with the hPXR LBD. Docking studies suggest that the lack of the para-methoxy group in SPA70 compromises its interaction with the AF-2, thus explaining its antagonism. SPA70 is an hPXR antagonist and promising therapeutic tool.The xenobiotic-activated human pregnane X receptor (hPXR) regulates drug metabolism. Here the authors develop hPXR modulators, which are of potential therapeutic interest and functionally and structurally characterize the antagonist SPA70 and the structurally related agonist SJB7.
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Affiliation(s)
- Wenwei Lin
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105-3678, USA
| | - Yue-Ming Wang
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105-3678, USA
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105-3678, USA
| | - Lili Lv
- Structure Biology, Shanghai Medicilon Inc., Shanghai, 201299, China
| | - Jie Zheng
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL, 33458, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105-3678, USA
| | - Qijun Zhang
- Structure Biology, Shanghai Medicilon Inc., Shanghai, 201299, China
| | - Yong-Dong Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN, 38105-3678, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Scripps Florida, Jupiter, FL, 33458, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105-3678, USA.
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28
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Grewal GK, Singh KD, Kanojia N, Rawat C, Kukal S, Jajodia A, Singhal A, Misra R, Nagamani S, Muthusamy K, Kukreti R. Exploring the Carbamazepine Interaction with Human Pregnane X Receptor and Effect on ABCC2 Using in Vitro and in Silico Approach. Pharm Res 2017; 34:1444-1458. [DOI: 10.1007/s11095-017-2161-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/04/2017] [Indexed: 10/19/2022]
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29
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Sun MY, Lin JN. Relationship between NR1I2 polymorphisms and inflammatory bowel disease risk: A systematic review and meta-analysis. Clin Res Hepatol Gastroenterol 2017; 41:230-239. [PMID: 27894906 DOI: 10.1016/j.clinre.2016.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 09/21/2016] [Accepted: 10/18/2016] [Indexed: 02/04/2023]
Abstract
BACKGROUND AND OBJECTIVE Inconsistent results regarding an association between polymorphisms within the Homo sapiens nuclear receptor subfamily 1 group I member 2 (NR1I2) gene and susceptibility to inflammatory bowel disease (IBD) have been reported. A systematic review and meta-analysis was thus undertaken to determine whether NR1I2 gene polymorphisms are associated with an increased risk of IBD. METHODS Article retrieval was performed using on-line databases, such as PubMed, Embase, CENTRAL, and WOS. After extracting eligible data, Mantel-Haenszel statistics were applied to calculate the odds radio (OR), 95% confidence interval (95% CI) and P value under a random or fixed-effects model. RESULTS A total of seven articles with 4410 IBD subjects and 4028 controls were included. Compared with the control group, no significant increase in IBD susceptibility was observed for the -25385C/T (OR=0.92, 95% CI=0.78∼1.07, P=0.259), -24381A/C (OR=0.96, 95% CI=0.87∼1.06, P=0.378), +8055C/T (OR=1.06, 95% CI=0.97∼1.15, P=0.186), or +7635A/G (OR=0.96, 95% CI=0.87∼1.05, P=0.348) polymorphisms within the NR1I2 gene under the allele model. CONCLUSIONS Our meta-analysis failed to demonstrate an association between -25385C/T, -24381A/C, +8055C/T, or +7635A/G polymorphisms within the NR1I2 gene and overall IBD risk. A larger sample size is needed to validate our conclusion.
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Affiliation(s)
- Man-Yi Sun
- Department of Gastroenterology, Tianjin Union Medicine Center & Tianjin People's Hospital, 300121 Tianjin, PR China
| | - Jing-Na Lin
- Department of Endocrinology, Tianjin Union Medicine Center & Tianjin People's Hospital, Hongqiao District, Jieyuan Road No. 190, 300121 Tianjin, PR China.
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30
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Adamski CJ, Palzkill T. BLIP-II Employs Differential Hotspot Residues To Bind Structurally Similar Staphylococcus aureus PBP2a and Class A β-Lactamases. Biochemistry 2017; 56:1075-1084. [PMID: 28182405 DOI: 10.1021/acs.biochem.6b00978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The interaction of β-lactamase inhibitory protein II (BLIP-II) with β-lactamases serves as a model system to investigate the principles underlying protein-protein interactions. Previous studies have focused on identifying the determinants of binding affinity and specificity between BLIP-II and class A β-lactamases. However, interactions between BLIP-II and other bacterial proteins have yet to be explored. Here, we provide evidence that BLIP-II binds penicillin binding protein 2a (PBP2a) from methicillin-resistant Staphylococcus aureus (MRSA) with a KD in the low micromolar range. In comparison to the binding constants for the potent interaction between BLIP-II and TEM-1 β-lactamase (KD = 0.5 pM), the on-rate for BLIP-II binding PBP2a is 44 000 times slower and the off-rate is 170 times faster. Therefore, a slow association rate is a limiting factor for the potency of the interaction between BLIP-II and PBP2a. Results from alanine scanning mutagenesis of the predicted interface residues of BLIP-II indicate that charged residues on the periphery of the BLIP-II interface play a critical role for binding PBP2a, in contrast to previous findings that aromatic residues at the center of the BLIP-II interface are critical for the interaction with β-lactamases. Interestingly, many of the alanine mutants at the BLIP-II interface increase kon for binding PBP2a, consistent with the association rate being a limiting factor for affinity. In summary, the results of the study reveal that BLIP-II binds PBP2a, although weakly compared to binding of β-lactamases, and provides insights into the different binding strategies used for these targets.
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Affiliation(s)
- Carolyn J Adamski
- Department of Biochemistry and Molecular Biology, ‡Department of Pharmacology, Baylor College of Medicine , Houston, Texas 77030, United States
| | - Timothy Palzkill
- Department of Biochemistry and Molecular Biology, ‡Department of Pharmacology, Baylor College of Medicine , Houston, Texas 77030, United States
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31
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QSAR development and profiling of 72,524 REACH substances for PXR activation and CYP3A4 induction. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.comtox.2017.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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32
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Carazo A, Hyrsova L, Dusek J, Chodounska H, Horvatova A, Berka K, Bazgier V, Gan-Schreier H, Chamulitrat W, Kudova E, Pavek P. Acetylated deoxycholic (DCA) and cholic (CA) acids are potent ligands of pregnane X (PXR) receptor. Toxicol Lett 2016; 265:86-96. [PMID: 27871908 DOI: 10.1016/j.toxlet.2016.11.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/10/2016] [Accepted: 11/15/2016] [Indexed: 12/11/2022]
Abstract
The Pregnane X (PXR), Vitamin D (VDR) and Farnesoid X (FXR) nuclear receptors have been shown to be receptors of bile acids controlling their detoxification or synthesis. Chenodeoxycholic (CDCA) and lithocholic (LCA) acids are ligands of FXR and VDR, respectively, whereas 3-keto and acetylated derivates of LCA have been described as ligands for all three receptors. In this study, we hypothesized that oxidation or acetylation at position 3, 7 and 12 of bile acids DCA (deoxycholic acid), LCA, CA (cholic acid), and CDCA by detoxification enzymes or microbiome may have an effect on the interactions with bile acid nuclear receptors. We employed reporter gene assays in HepG2 cells, the TR-FRET assay with recombinant PXR and RT-PCR to study the effects of acetylated and keto bile acids on the nuclear receptors activation and their target gene expression in differentiated hepatic HepaRG cells. We demonstrate that the DCA 3,12-diacetate and CA 3,7,12-triacetate derivatives are ligands of PXR and DCA 3,12-diacetate induces PXR target genes such as CYP3A4, CYP2B6 and ABCB1/MDR1. In conclusion, we found that acetylated DCA and CA are potent ligands of PXR. Whether the acetylated bile acid derivatives are novel endogenous ligands of PXR with detoxification or physiological functions should be further studied in ongoing experiments.
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Affiliation(s)
- Alejandro Carazo
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovského 1203, Hradec Kralove CZ500 05, Czechia
| | - Lucie Hyrsova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovského 1203, Hradec Kralove CZ500 05, Czechia
| | - Jan Dusek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovského 1203, Hradec Kralove CZ500 05, Czechia
| | - Hana Chodounska
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, CZ160 00 Praha, Czechia
| | - Alzbeta Horvatova
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovského 1203, Hradec Kralove CZ500 05, Czechia
| | - Karel Berka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University in Olomouc, 17. listopadu 1131, Olomouc CZ779 00, Czechia
| | - Vaclav Bazgier
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacky University in Olomouc, 17. listopadu 1131, Olomouc CZ779 00, Czechia
| | - Hongying Gan-Schreier
- Department of Internal Medicine IV, Gastroenterology and Infectious Diseases, Im Neuenheimer Feld, Heidelberg, Germany
| | - Waleé Chamulitrat
- Department of Internal Medicine IV, Gastroenterology and Infectious Diseases, Im Neuenheimer Feld, Heidelberg, Germany
| | - Eva Kudova
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, CZ160 00 Praha, Czechia
| | - Petr Pavek
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Charles University in Prague, Heyrovského 1203, Hradec Kralove CZ500 05, Czechia.
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Zhang YM, Chang MJ, Yang XS, Han X. In silico investigation of agonist activity of a structurally diverse set of drugs to hPXR using HM-BSM and HM-PNN. JOURNAL OF HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY. MEDICAL SCIENCES = HUA ZHONG KE JI DA XUE XUE BAO. YI XUE YING DE WEN BAN = HUAZHONG KEJI DAXUE XUEBAO. YIXUE YINGDEWEN BAN 2016; 36:463-468. [PMID: 27376821 DOI: 10.1007/s11596-016-1609-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 04/28/2016] [Indexed: 10/21/2022]
Abstract
The human pregnane X receptor (hPXR) plays a critical role in the metabolism, transport and clearance of xenobiotics in the liver and intestine. The hPXR can be activated by a structurally diverse of drugs to initiate clinically relevant drug-drug interactions. In this article, in silico investigation was performed on a structurally diverse set of drugs to identify critical structural features greatly related to their agonist activity towards hPXR. Heuristic method (HM)-Best Subset Modeling (BSM) and HM-Polynomial Neural Networks (PNN) were utilized to develop the linear and non-linear quantitative structure-activity relationship models. The applicability domain (AD) of the models was assessed by Williams plot. Statistically reliable models with good predictive power and explain were achieved (for HM-BSM, r (2)=0.881, q LOO (2) =0.797, q EXT (2) =0.674; for HM-PNN, r (2)=0.882, q LOO (2) =0.856, q EXT (2) =0.655). The developed models indicated that molecular aromatic and electric property, molecular weight and complexity may govern agonist activity of a structurally diverse set of drugs to hPXR.
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Affiliation(s)
- Yi-Ming Zhang
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 210029, China
| | - Mei-Jia Chang
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Xu-Shu Yang
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
| | - Xiao Han
- School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 210029, China.
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Banerjee M, Chai SC, Wu J, Robbins D, Chen T. Tryptophan 299 is a conserved residue of human pregnane X receptor critical for the functional consequence of ligand binding. Biochem Pharmacol 2016; 104:131-8. [PMID: 26902414 DOI: 10.1016/j.bcp.2016.02.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/17/2016] [Indexed: 12/23/2022]
Abstract
PXR is a xenobiotic receptor that regulates drug metabolism by regulating the expression of drug-metabolizing enzymes including CYP3A4. It can be modulated by chemicals with different structures, functional groups and sizes. X-ray crystal structures of the ligand binding domain of human PXR (hPXR) alone or bound with agonists reveal a highly hydrophobic ligand binding pocket where the aromatic amino acid residue W299 appears to play a critical role in ligand binding. Here, we have investigated the role of W299 on the functional consequence of hPXR ligand binding. We first found that substitution of W299 with a hydrophobic residue retained its response to rifampicin, but substitution with a charged residue altered such agonist response in activating the transcription of CYP3A4. The activity of hPXR mutants on CYP3A4 expression correlates with the ability of hPXR mutants to interact with co-activator SRC-1. We further demonstrated that the effect of replacing W299 by residues with different side chains on hPXR's function varied depending on the specific agonist used. Finally we interpreted the cellular activity of the hPXR mutants by analyzing reported crystallographic data and proposing a model. Our findings reveal the essential role of W299 in the transactivation of hPXR in response to agonist binding, and provide useful information for designing modulators of hPXR.
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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
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jing Wu
- 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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Mackowiak B, Wang H. Mechanisms of xenobiotic receptor activation: Direct vs. indirect. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1859:1130-1140. [PMID: 26877237 DOI: 10.1016/j.bbagrm.2016.02.006] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Revised: 02/05/2016] [Accepted: 02/06/2016] [Indexed: 12/31/2022]
Abstract
The so-called xenobiotic receptors (XRs) have functionally evolved into cellular sensors for both endogenous and exogenous stimuli by regulating the transcription of genes encoding drug-metabolizing enzymes and transporters, as well as those involving energy homeostasis, cell proliferation, and/or immune responses. Unlike prototypical steroid hormone receptors, XRs are activated through both direct ligand-binding and ligand-independent (indirect) mechanisms by a plethora of structurally unrelated chemicals. This review covers research literature that discusses direct vs. indirect activation of XRs. A particular focus is centered on the signaling control of the constitutive androstane receptor (CAR), the pregnane X receptor (PXR), and the aryl hydrocarbon receptor (AhR). We expect that this review will shed light on both the common and distinct mechanisms associated with activation of these three XRs. This article is part of a Special Issue entitled: Xenobiotic nuclear receptors: New Tricks for An Old Dog, edited by Dr. Wen Xie.
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Affiliation(s)
- Bryan Mackowiak
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, MD 21201, United States
| | - Hongbing Wang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, MD 21201, United States.
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Transcriptional Regulation of CYP3A4/2B6/2C9 Mediated via Nuclear Receptor PXR by Helicid and Its Metabolites. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2015; 2015:797496. [PMID: 25977700 PMCID: PMC4421101 DOI: 10.1155/2015/797496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 11/23/2014] [Accepted: 12/02/2014] [Indexed: 11/17/2022]
Abstract
Objective. This study aims at establishing and validating an in vitro system to screen drug inducers of CYPs mediated via hPXR, as well as studying transcriptional regulation of CYPs mediated via hPXR by helicid and its two metabolites. Methods. Cloning the nuclear receptor hPXR and the promoters of CYP3A4, CYP2B6, CYP2C9, and inserting the trans-element to the upstream of firefly luciferase reporter gene of the pGL4.17 vectors, then cotransfecting the report vectors and hPXR expression plasmid to HepG2 cell line. After 24 hours, the transfected cells were treated with helicid (0.004, 0.04, and 0.4 μmol/L) and its metabolite I and metabolite II (0.0004, 0.004, and 0.04 μmol/L) for 48 h, while rifampin (10 μmol/L) was included as the positive control and 0.1% DMSO as the negative control group. Cells were lysized and luciferase activity was determined using a dual luciferase reporter assay kit. Results. Helicid and its metabolites did not significantly increase promoter activities of CYP3A4, CYP2B6, and CYP2C9 in HepG2 cells transfected with PXR expression plasmid (P > 0.05). Conclusion. PXR-expressed CYP3A4, CYP2B6, and CYP2C9 dual luciferase reporter gene platforms were successfully established, and helicid and its metabolites I, II do not significantly induce the transcription of CYP3A4, CYP2B6, and CYP2C9.
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Handa K, Nakagome I, Yamaotsu N, Gouda H, Hirono S. Three-Dimensional Quantitative Structure–Activity Relationship Analysis for Human Pregnane X Receptor for the Prediction of CYP3A4 Induction in Human Hepatocytes: Structure-Based Comparative Molecular Field Analysis. J Pharm Sci 2015; 104:223-32. [DOI: 10.1002/jps.24235] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 09/24/2014] [Accepted: 09/26/2014] [Indexed: 11/12/2022]
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García-Sosa AT, Maran U. Improving the use of ranking in virtual screening against HIV-1 integrase with triangular numbers and including ligand profiling with antitargets. J Chem Inf Model 2014; 54:3172-85. [PMID: 25303089 DOI: 10.1021/ci500300u] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A delicate balance exists between a drug molecule's toxicity and its activity. Indeed, efficacy, toxicity, and side effect problems are a common cause for the termination of drug candidate compounds and development projects. To address this, an antitarget interaction profile is built and combined with virtual screening and cross docking for new inhibitors of HIV-1 integrase, in order to consider possible off-target interactions as early as possible in a drug or hit discovery program. New ranking techniques using triangular numbers improve ranking information on the compounds and recovery of known inhibitors into the top compounds using different docking programs. This improved ranking arises from using consensus of ranks between docking programs and ligand efficiencies to derive a new rank, instead of using absolute score values, or average of ranks. The triangular number rerank also allowed the objective combination of results from several protein targets or screen conditions and several programs. Triangular number reranking conserves more information than other reranking methods such as average of scores or averages of ranks. In addition, the use of triangular numbers for reranking makes possible the use of thresholds with a justified leeway based on the number of available known inhibitors, so that the majority of the compounds above the threshold in ranks compare to the compounds that have known experimentally determined biological activity. The battery of anti- or off-targets can be tailored to specific molecular or drug design challenges. In silico filters can thus be deployed in successive stages, for prefiltering, activity profiling, and for further analysis and triaging of libraries of compounds.
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Zhang L, Zheng M, Zhao F, Zhai Y, Liu H. Rapid generation of privileged substructure-based compound libraries with structural diversity and drug-likeness. ACS COMBINATORIAL SCIENCE 2014; 16:184-91. [PMID: 24524741 DOI: 10.1021/co4001309] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A library of privileged-substructure-based, heterocyclic compounds was constructed by a sequence of Ugi four-component reactions incorporating the indole motif and microwave-assisted cyclizations in branched pathways. Cheminformatic analysis confirmed that the library exhibited a high degree of structural diversity and good drug-likeness.
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Affiliation(s)
- Lei Zhang
- CAS Key Laboratory of Receptor
Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Mingyue Zheng
- CAS Key Laboratory of Receptor
Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Fei Zhao
- CAS Key Laboratory of Receptor
Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yun Zhai
- CAS Key Laboratory of Receptor
Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hong Liu
- CAS Key Laboratory of Receptor
Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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Ligand promiscuity of aryl hydrocarbon receptor agonists and antagonists revealed by site-directed mutagenesis. Mol Cell Biol 2014; 34:1707-19. [PMID: 24591650 DOI: 10.1128/mcb.01183-13] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The aryl hydrocarbon receptor (AhR) is a ligand-dependent transcription factor that can be activated by structurally diverse chemicals. To examine the mechanisms responsible for the promiscuity in AhR ligand binding, we determined the effects of mutations within the AhR ligand-binding domain (LBD) on the activity of diverse AhR ligands. Site-directed mutagenesis identified Ile319 of the mouse AhR and, to a lesser extent, Phe318 as residues involved in ligand-selective modulation of AhR transformation using a panel of 12 AhR ligands. These ligands could be categorized into four distinct structurally related groups based on their ability to activate AhR mutants at position 319 in vitro. The mutation I319K was selectively activated by FICZ and not by other examined ligands in vitro and in cell culture. F318L and F318A mutations resulted in the conversion of AhR agonists β-naphthoflavone and 3-methylcholanthrene, respectively, into partial agonists/antagonists. Hsp90 binding to the AhR was decreased with several mutations and was inversely correlated with AhR ligand-binding promiscuity. Together, these data define overlapping amino acid residues within the AhR LBD involved in the selectivity of ligand binding, the agonist or antagonist mode of ligand binding, and hsp90 binding and provide insights into the ligand diversity of AhR activators.
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Chen S, He N, Chen W, Sun F, Li L, Deng R, Hu Y. Molecular insights into the promiscuous interaction of human pregnane X receptor (hPXR) with diverse environmental chemicals and drug compounds. CHEMOSPHERE 2014; 96:138-145. [PMID: 24182399 DOI: 10.1016/j.chemosphere.2013.09.084] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 08/18/2013] [Accepted: 09/20/2013] [Indexed: 06/02/2023]
Abstract
The nuclear receptor member human pregnane X receptor (hPXR) regulates enzymes and transporters involved in xenobiotic detoxification as well as maintains homeostatic balance of bile acids, thyroid and steroid hormones. hPXR can be recognized and activated by a structurally diverse array of environmental chemicals and drug compounds to initiate adverse biological effects, such as perturbing normal physiological functions and causing dangerous drug-drug interactions and exhibiting a high promiscuity in its ligand spectrum. Understanding of the molecular mechanism and biological implication underlying the promiscuous interaction of hPXR with its diverse ligands is fundamentally important for toxicological and pharmaceutical researches. In the current study, molecular docking and hybrid quantum mechanics/molecular mechanics (QM/MM) were employed to investigate the binding mode, structural basis and energetic property of hPXR interactions with various activators and non-activators. It was found that, as compared to non-activators, the activators adopt few dominant modes to tightly interact with hPXR, which are specified by few polar spots located on the hydrophobic surface of hPXR active pocket. Based on the findings, a novel method called multiple binding mode-based quantitative structure-activity relationship (MBMB-QSAR) that characterizes the nonbonded interaction profile of hPXR with its ligand in multiple binding modes was proposed to model and predict the activating potency of small-molecule compounds on hPXR. Several partial least square (PLS) predictors derived from the MBMB-QSAR modeling were demonstrated to be effective for quantitative characterization of the biological behavior of experimentally confirmed activators, and for qualitatively differentiating the activators from a large number of non-activators. From the predictor models it is suggested that the hydrophobic force and electrostatic interaction play an important role in hPXR-ligand binding, while steric factor contributes moderately to the binding.
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Affiliation(s)
- Sheng Chen
- Department of Pediatrics, Southwest Hospital, Third Military Medical University, Chongqing 400038, China
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42
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Rathod V, Jain S, Nandekar P, Sangamwar AT. Human pregnane X receptor: a novel target for anticancer drug development. Drug Discov Today 2014; 19:63-70. [DOI: 10.1016/j.drudis.2013.08.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 05/02/2013] [Accepted: 08/15/2013] [Indexed: 02/07/2023]
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43
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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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44
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Abstract
The cytosolic sulfotransferases (SULTs) are a multigene family of enzymes that catalyze the transfer of a sulfonate group from the physiologic sulfate donor, 3'-phosphoadenosine-5'-phosphosulfate, to a nucleophilic substrate to generate a polar product that is more amenable to elimination from the body. As catalysts of both xenobiotic and endogenous metabolism, the SULTs are major points of contact between the external and physiological environments, and modulation of SULT-catalyzed metabolism can not only affect xenobiotic disposition, but it can also alter endogenous metabolic processes. Therefore, it is not surprising that SULT expression is regulated by numerous members of the nuclear receptor (NR) superfamily that function as sensors of xenobiotics as well as endogenous molecules, such as fatty acids, bile acids, and oxysterols. These NRs include the peroxisome proliferator-activated receptors, pregnane X receptor, constitutive androstane receptor, vitamin D receptor, liver X receptors, farnesoid X receptor, retinoid-related orphan receptors, and estrogen-related receptors. This review summarizes current information about NR regulation of SULT expression. Because species differences in SULT subfamily composition and tissue-, sex-, development-, and inducer-dependent regulation are prominent, these differences will be emphasized throughout the review. In addition, because of the central role of the SULTs in cellular physiology, the effect of NR-mediated SULT regulation on physiological and pathophysiological processes will be discussed. Gaps in current knowledge that require further investigation are also highlighted.
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Affiliation(s)
- Melissa Runge-Morris
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan 48201, USA.
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45
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Fraccalvieri D, Soshilov AA, Karchner SI, Franks DG, Pandini A, Bonati L, Hahn ME, Denison MS. Comparative analysis of homology models of the AH receptor ligand binding domain: verification of structure-function predictions by site-directed mutagenesis of a nonfunctional receptor. Biochemistry 2013; 52:714-25. [PMID: 23286227 DOI: 10.1021/bi301457f] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that mediates the biological and toxic effects of a wide variety of structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). While significant interspecies differences in AHR ligand binding specificity, selectivity, and response have been observed, the structural determinants responsible for those differences have not been determined, and homology models of the AHR ligand-binding domain (LBD) are available for only a few species. Here we describe the development and comparative analysis of homology models of the LBD of 16 AHRs from 12 mammalian and nonmammalian species and identify the specific residues contained within their ligand binding cavities. The ligand-binding cavity of the fish AHR exhibits differences from those of mammalian and avian AHRs, suggesting a slightly different TCDD binding mode. Comparison of the internal cavity in the LBD model of zebrafish (zf) AHR2, which binds TCDD with high affinity, to that of zfAHR1a, which does not bind TCDD, revealed that the latter has a dramatically shortened binding cavity due to the side chains of three residues (Tyr296, Thr386, and His388) that reduce the amount of internal space available to TCDD. Mutagenesis of two of these residues in zfAHR1a to those present in zfAHR2 (Y296H and T386A) restored the ability of zfAHR1a to bind TCDD and to exhibit TCDD-dependent binding to DNA. These results demonstrate the importance of these two amino acids and highlight the predictive potential of comparative analysis of homology models from diverse species. The availability of these AHR LBD homology models will facilitate in-depth comparative studies of AHR ligand binding and ligand-dependent AHR activation and provide a novel avenue for examining species-specific differences in AHR responsiveness.
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Affiliation(s)
- Domenico Fraccalvieri
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
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46
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Doricakova A, Novotna A, Vrzal R, Pavek P, Dvorak Z. The role of residues T248, Y249 and T422 in the function of human pregnane X receptor. Arch Toxicol 2012; 87:291-301. [PMID: 22976785 DOI: 10.1007/s00204-012-0937-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2012] [Accepted: 08/28/2012] [Indexed: 10/27/2022]
Abstract
The pregnane X receptor (PXR) is a key xenobiotic receptor that regulates the expression of numerous drug-metabolizing enzymes. Some posttranslational mechanisms modulate its transcriptional activity. Although several kinases have been shown to directly phosphorylate this receptor, little is known about phosphorylation sites of PXR. In the present work, we examined T248, Y249 and T422 putative phosphorylation sites determined based on in silico consensus kinase site prediction analysis. T248 and T422 residues are critical for the interaction of the PXR ligand-binding domain and the activation function-2 (AF2) domain. Site-directed mutagenesis analysis was performed to generate phospho-deficient and phospho-mimetic mutants. We examined transactivation activity of the PXR mutants in gene reporter assays, formation of PXRmutant/RXRα heterodimer, binding of PXR mutants to the CYP3A4 gene response element DR3 and CYP3A4 expression in HepG2 cells after expression of the mutants. We found that T248D mutant activated CYP3A4 transactivation constitutively regardless of the presence or absence of a ligand. Contrary, T248V mutant exhibited low basal and ligand-inducible transactivation capacity as compared to wild-type PXR. Dose-response analysis revealed reduced ligand-dependent transactivation potency of PXR Y249D mutant. Transactivation of the CYP3A4 promoter was abolished with T422A/D mutants. All PXR mutants formed heterodimer with RXRα at a similar level to that observed with wild-type PXR. The ability to bind to DNA in vitro was substantially decreased in case of T248D, T422D and T248V mutants. Our data thus indicate that phosphorylation of T248, Y249 and T422 residues may be critical for the both basal and ligand-activated function of PXR.
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Affiliation(s)
- Aneta Doricakova
- Department of Cell Biology and Genetic, Palacky University Olomouc, Slechtitelu 11, 783 71 Olomouc, Czech Republic
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QSAR model for human pregnane X receptor (PXR) binding: Screening of environmental chemicals and correlations with genotoxicity, endocrine disruption and teratogenicity. Toxicol Appl Pharmacol 2012; 262:301-9. [DOI: 10.1016/j.taap.2012.05.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Revised: 05/08/2012] [Accepted: 05/13/2012] [Indexed: 02/07/2023]
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48
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Cheng J, Shah YM, Gonzalez FJ. Pregnane X receptor as a target for treatment of inflammatory bowel disorders. Trends Pharmacol Sci 2012; 33:323-30. [PMID: 22609277 PMCID: PMC3368991 DOI: 10.1016/j.tips.2012.03.003] [Citation(s) in RCA: 122] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 02/27/2012] [Accepted: 03/06/2012] [Indexed: 02/07/2023]
Abstract
Pregnane X receptor (PXR; NR1I2), a member of the nuclear receptor superfamily, has a major role in the induction of genes involved in drug transport and metabolism. Recent studies in mice have provided insight into a novel function for PXR in inflammatory bowel disease (IBD). The mechanism of the protective effect of PXR activation on IBD is not fully established, but is due in part to the attenuation of nuclear factor (NF)-κB signaling that results in lower expression of proinflammatory cytokines. Recent clinical trials with the antibiotic rifaximin, a PXR agonist in the gastrointestinal system, have revealed its potential therapeutic value in the treatment of intestinal inflammation in humans. Thus, PXR may be a novel target for IBD therapy.
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Affiliation(s)
- Jie Cheng
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Ngan CH, Bohnuud T, Mottarella SE, Beglov D, Villar EA, Hall DR, Kozakov D, Vajda S. FTMAP: extended protein mapping with user-selected probe molecules. Nucleic Acids Res 2012; 40:W271-5. [PMID: 22589414 PMCID: PMC3394268 DOI: 10.1093/nar/gks441] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Binding hot spots, protein sites with high-binding affinity, can be identified using X-ray crystallography or NMR by screening libraries of small organic molecules that tend to cluster at such regions. FTMAP, a direct computational analog of the experimental screening approaches, globally samples the surface of a target protein using small organic molecules as probes, finds favorable positions, clusters the conformations and ranks the clusters on the basis of the average energy. The regions that bind several probe clusters predict the binding hot spots, in good agreement with experimental results. Small molecules discovered by fragment-based approaches to drug design also bind at the hot spot regions. To identify such molecules and their most likely bound positions, we extend the functionality of FTMAP (http://ftmap.bu.edu/param) to accept any small molecule as an additional probe. In its updated form, FTMAP identifies the hot spots based on a standard set of probes, and for each additional probe shows representative structures of nearby low energy clusters. This approach helps to predict bound poses of the user-selected molecules, detects if a compound is not likely to bind in the hot spot region, and provides input for the design of larger ligands.
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Affiliation(s)
- Chi Ho Ngan
- Department of Biomedical Engineering, Boston University, 44 Cummington Street, Boston, MA 02215, USA
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50
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Development of in silico filters to predict activation of the pregnane X receptor (PXR) by structurally diverse drug-like molecules. Bioorg Med Chem 2012; 20:5352-65. [PMID: 22560839 DOI: 10.1016/j.bmc.2012.04.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 03/28/2012] [Accepted: 04/07/2012] [Indexed: 01/22/2023]
Abstract
The pregnane X receptor (PXR), a member of the nuclear hormone superfamily, regulates the expression of several enzymes and transporters involved in metabolically relevant processes. The significant induction of CYP450 enzymes by PXR, in particular CYP3A4, might significantly alter the metabolism of prescribed drugs. In order to early identify molecules in drug discovery with a potential to activate PXR as antitarget, we developed fast and reliable in silico filters by ligand-based QSAR techniques. Two classification models were established on a diverse dataset of 434 drug-like molecules. A second augmented set allowed focusing on interesting regions in chemical space. These classifiers are based on decision trees combined with a genetic algorithm based variable selection to arrive at predictive models. The classifier for the first dataset on 29 descriptors showed good performance on a test set with a correct classification of both 100% for PXR activators and non-activators plus 87% for activators and 83% for non-activators in an external dataset. The second classifier then correctly predicts 97% activators and 91% non-activators in a test set and 94% for activators and 64% non-activators in an external set of 50 molecules, which still qualifies for application as a filter focusing on PXR activators. Finally a quantitative model for PXR activation for a subset of these molecules was derived using a regression-tree approach combined with GA variable selection. This final model shows a predictive r(2) of 0.774 for the test set and 0.452 for an external set of 33 molecules. Thus, the combination of these filters consistently provide guidelines for lowering PXR activation in novel candidate molecules.
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