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Díaz-Holguín A, Rashidian A, Pijnenburg D, Monteiro Ferreira G, Stefela A, Kaspar M, Kudova E, Poso A, van Beuningen R, Pavek P, Kronenberger T. When Two Become One: Conformational Changes in FXR/RXR Heterodimers Bound to Steroidal Antagonists. ChemMedChem 2023; 18:e202200556. [PMID: 36398403 DOI: 10.1002/cmdc.202200556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/15/2022] [Indexed: 11/19/2022]
Abstract
Farnesoid X receptor (FXR) is a nuclear receptor with an essential role in regulating bile acid synthesis and cholesterol homeostasis. FXR activation by agonists is explained by an αAF-2-trapping mechanism; however, antagonism mechanisms are diverse. We discuss microsecond molecular dynamics (MD) simulations investigating our recently reported FXR antagonists 2a and 2 h. We study the antagonist-induced conformational changes in the FXR ligand-binding domain, when compared to the synthetic (GW4064) or steroidal (chenodeoxycholic acid, CDCA) FXR agonists in the FXR monomer or FXR/RXR heterodimer r, and in the presence and absence of the coactivator. Our MD data suggest ligand-specific influence on conformations of different FXR-LBD regions, including the α5/α6 region, αAF-2, and α9-11. Changes in the heterodimerization interface induced by antagonists seem to be associated with αAF-2 destabilization, which prevents both co-activator and co-repressor recruitment. Our results provide new insights into the conformational behaviour of FXR, suggesting that FXR antagonism/agonism shift requires a deeper assessment than originally proposed by crystal structures.
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Affiliation(s)
- Alejandro Díaz-Holguín
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland.,Current address: Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75124, Uppsala, Sweden
| | - Azam Rashidian
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Internal Medicine VIII, University Hospital of Tübingen, Otfried-Müller-Strasse 14, 72076, Tübingen, Germany
| | - Dirk Pijnenburg
- PamGene International B.V., Wolvenhoek 10, 5211HH, 's-Hertogenbosch, Netherlands
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, Av. Prof. Lineu Prestes 580, 05508-000, São Paulo, Brazil
| | - Alzbeta Stefela
- Department of Pharmacology and Toxicology, Charles University, Heyrovskeho 1203, 50005, Hradec Kralove, Czechia
| | - Miroslav Kaspar
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 16000, Prague, Czechia.,Faculty of Sciences, Charles University in Prague, Albertov 6, Prague 2, 12843, Czechia
| | - Eva Kudova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 542/2, 16000, Prague, Czechia
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Internal Medicine VIII, University Hospital of Tübingen, Otfried-Müller-Strasse 14, 72076, Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
| | - Rinie van Beuningen
- PamGene International B.V., Wolvenhoek 10, 5211HH, 's-Hertogenbosch, Netherlands
| | - Petr Pavek
- Department of Pharmacology and Toxicology, Charles University, Heyrovskeho 1203, 50005, Hradec Kralove, Czechia
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery & Development (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany.,Department of Internal Medicine VIII, University Hospital of Tübingen, Otfried-Müller-Strasse 14, 72076, Tübingen, Germany.,School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, 70211, Finland
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Allosteric Antagonism of the Pregnane X Receptor (PXR): Current-State-of-the-Art and Prediction of Novel Allosteric Sites. Cells 2022; 11:cells11192974. [PMID: 36230936 PMCID: PMC9563780 DOI: 10.3390/cells11192974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
Abstract
The pregnane X receptor (PXR, NR1I2) is a xenobiotic-activated transcription factor with high levels of expression in the liver. It not only plays a key role in drug metabolism and elimination, but also promotes tumor growth, drug resistance, and metabolic diseases. It has been proposed as a therapeutic target for type II diabetes, metabolic syndrome, and inflammatory bowel disease, and PXR antagonists have recently been considered as a therapy for colon cancer. There are currently no PXR antagonists that can be used in a clinical setting. Nevertheless, due to the large and complex ligand-binding pocket (LBP) of the PXR, it is challenging to discover PXR antagonists at the orthosteric site. Alternative ligand binding sites of the PXR have also been proposed and are currently being studied. Recently, the AF-2 allosteric binding site of the PXR has been identified, with several compounds modulating the site discovered. Herein, we aimed to summarize our current knowledge of allosteric modulation of the PXR as well as our attempt to unlock novel allosteric sites. We describe the novel binding function 3 (BF-3) site of PXR, which is also common for other nuclear receptors. In addition, we also mention a novel allosteric site III based on in silico prediction. The identified allosteric sites of the PXR provide new insights into the development of safe and efficient allosteric modulators of the PXR receptor. We therefore propose that novel PXR allosteric sites might be promising targets for treating chronic metabolic diseases and some cancers.
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