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.

Current address Science for Life Laboratory Department of Cell and Molecular Biology Uppsala University 75124 Uppsala Sweden

Department of Clinical and Toxicological Analyses School of Pharmaceutical Sciences University of São Paulo Av Prof Lineu Prestes 580 05508 000 São Paulo Brazil

Department of Internal Medicine 8 University Hospital of Tübingen Otfried Müller Strasse 14 72076 Tübingen Germany

Department of Pharmacology and Toxicology Charles University Heyrovskeho 1203 50005 Hradec Kralove Czechia

Faculty of Sciences Charles University Prague Albertov 6 Prague 2 12843 Czechia

Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo náměstí 542 2 16000 Prague Czechia

Institute of Pharmacy Pharmaceutical Medicinal Chemistry and Tübingen Center for Academic Drug Discovery and Development Eberhard Karls University Tübingen Auf der Morgenstelle 8 72076 Tübingen Germany

PamGene International B 5 Wolvenhoek 10 5211HH 's Hertogenbosch Netherlands

School of Pharmacy Faculty of Health Sciences University of Eastern Finland Kuopio 70211 Finland

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