A bromodomain-independent mechanism of gene regulation by the BET inhibitor JQ1: direct activation of nuclear receptor PXR

Huber, Andrew D.; Poudel, Shyaron; Wu, Jing; Miller, Darcie J.; Lin, Wenwei; Yang, Lei; Bwayi, Monicah N.; Rimmer, Mary Ashley; Gee, Rebecca R. Florke; Seetharaman, Jayaraman; Chai, Sergio C.; Chen, Taosheng

doi:10.1093/nar/gkad1175

A bromodomain-independent mechanism of gene regulation by the BET inhibitor JQ1: direct activation of nuclear receptor PXR

Journal Article · Tue Dec 12 00:00:00 EST 2023 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkad1175· OSTI ID:2229826

; Poudel, Shyaron; Wu, Jing; Miller, Darcie J.; ; Yang, Lei; Bwayi, Monicah N.; Rimmer, Mary Ashley; Gee, Rebecca R. Florke; Seetharaman, Jayaraman; ;

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.

View Journal Article

Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Organization:: National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: SC0012704

OSTI ID:: 2229826

Alternate ID(s):: OSTI ID: 2469562

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: 4 Vol. 52; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

References (58)

Improved side-chain torsion potentials for the Amber ff99SB protein force field Lindorff-Larsen, Kresten; Piana, Stefano; Palmo, Kim Proteins: Structure, Function, and Bioinformatics https://doi.org/10.1002/prot.22711	journal	January 2010
Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2−ΔΔCT Method Livak, Kenneth J.; Schmittgen, Thomas D. Methods, Vol. 25, Issue 4 https://doi.org/10.1006/meth.2001.1262	journal	December 2001
Mutation of a single amino acid of pregnane X receptor switches an antagonist to agonist by altering AF-2 helix positioning Huber, Andrew D.; Wright, William C.; Lin, Wenwei Cellular and Molecular Life Sciences, Vol. 78, Issue 1 https://doi.org/10.1007/s00018-020-03505-y	journal	March 2020
Coactivator Binding Promotes the Specific Interaction Between Ligand and the Pregnane X Receptor Watkins, Ryan E.; Davis-Searles, Paula R.; Lambert, Mill H. Journal of Molecular Biology, Vol. 331, Issue 4 https://doi.org/10.1016/S0022-2836(03)00795-2	journal	August 2003
The bromodomain revisited Jeanmougin, F. Trends in Biochemical Sciences, Vol. 22, Issue 5 https://doi.org/10.1016/S0968-0004(97)01042-6	journal	May 1997
Using TR-FRET to Investigate Protein–Protein Interactions: A Case Study of PXR-Coregulator Interaction Lin, Wenwei; Chen, Taosheng Protein-Protein Interactions in Human Disease, Part A https://doi.org/10.1016/bs.apcsb.2017.06.001	book	August 2017
Assessment of Brd4 Inhibition in Idiopathic Pulmonary Fibrosis Lung Fibroblasts and in Vivo Models of Lung Fibrosis Tang, Xiaoyan; Peng, Ruoqi; Phillips, Jonathan E. The American Journal of Pathology, Vol. 183, Issue 2 https://doi.org/10.1016/j.ajpath.2013.04.020	journal	August 2013
Serine 350 of human pregnane X receptor is crucial for its heterodimerization with retinoid X receptor alpha and transactivation of target genes in vitro and in vivo Wang, Yue-Ming; Chai, Sergio C.; Lin, Wenwei Biochemical Pharmacology, Vol. 96, Issue 4 https://doi.org/10.1016/j.bcp.2015.06.018	journal	August 2015
BET Bromodomain Inhibition as a Therapeutic Strategy to Target c-Myc Delmore, Jake E.; Issa, Ghayas C.; Lemieux, Madeleine E. Cell, Vol. 146, Issue 6 https://doi.org/10.1016/j.cell.2011.08.017	journal	September 2011
Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family Filippakopoulos, Panagis; Picaud, Sarah; Mangos, Maria Cell, Vol. 149, Issue 1 https://doi.org/10.1016/j.cell.2012.02.013	journal	March 2012
Functional Genomic Landscape of Human Breast Cancer Drivers, Vulnerabilities, and Resistance Marcotte, Richard; Sayad, Azin; Brown, Kevin R. Cell, Vol. 164, Issue 1-2 https://doi.org/10.1016/j.cell.2015.11.062	journal	January 2016
Clinical trials for BET inhibitors run ahead of the science Andrieu, Guillaume; Belkina, Anna C.; Denis, Gerald V. Drug Discovery Today: Technologies, Vol. 19 https://doi.org/10.1016/j.ddtec.2016.06.004	journal	March 2016
The Mechanisms behind the Therapeutic Activity of BET Bromodomain Inhibition Shi, Junwei; Vakoc, Christopher R. Molecular Cell, Vol. 54, Issue 5 https://doi.org/10.1016/j.molcel.2014.05.016	journal	June 2014
Targeting BET bromodomain proteins in cancer: The example of lymphomas Spriano, Filippo; Stathis, Anastasios; Bertoni, Francesco Pharmacology & Therapeutics, Vol. 215 https://doi.org/10.1016/j.pharmthera.2020.107631	journal	November 2020
Ligand flexibility and binding pocket malleability cooperate to allow selective PXR activation by analogs of a promiscuous nuclear receptor ligand Huber, Andrew D.; Poudel, Shyaron; Li, Yongtao Structure, Vol. 31, Issue 12 https://doi.org/10.1016/j.str.2023.08.020	journal	December 2023
Bromodomain-containing protein 4 contributes to renal fibrosis through the induction of epithelial-mesenchymal transition Wang, Xuan; Zhou, Yueyuan; Peng, Yi Experimental Cell Research, Vol. 383, Issue 2 https://doi.org/10.1016/j.yexcr.2019.111507	journal	October 2019
BET acetyl-lysine binding proteins control pathological cardiac hypertrophy Spiltoir, Jessica I.; Stratton, Matthew S.; Cavasin, Maria A. Journal of Molecular and Cellular Cardiology, Vol. 63 https://doi.org/10.1016/j.yjmcc.2013.07.017	journal	October 2013
Bromodomains as therapeutic targets Muller, Susanne; Filippakopoulos, Panagis; Knapp, Stefan Expert Reviews in Molecular Medicine, Vol. 13 https://doi.org/10.1017/S1462399411001992	journal	March 2011
Selective Small Molecule Induced Degradation of the BET Bromodomain Protein BRD4 Zengerle, Michael; Chan, Kwok-Ho; Ciulli, Alessio ACS Chemical Biology, Vol. 10, Issue 8 https://doi.org/10.1021/acschembio.5b00216	journal	June 2015
NanoLuc Complementation Reporter Optimized for Accurate Measurement of Protein Interactions in Cells Dixon, Andrew S.; Schwinn, Marie K.; Hall, Mary P. ACS Chemical Biology, Vol. 11, Issue 2 https://doi.org/10.1021/acschembio.5b00753	journal	December 2015
Development of BODIPY FL Vindoline as a Novel and High-Affinity Pregnane X Receptor Fluorescent Probe Lin, Wenwei; Liu, Jiuyu; Jeffries, Cynthia Bioconjugate Chemistry, Vol. 25, Issue 9 https://doi.org/10.1021/bc5002856	journal	August 2014
The Structural Basis of Pregnane X Receptor Binding Promiscuity Ngan, Chi-Ho; Beglov, Dmitri; Rudnitskaya, Aleksandra N. Biochemistry, Vol. 48, Issue 48 https://doi.org/10.1021/bi901578n	journal	November 2009
Selective inhibition of BET bromodomains Filippakopoulos, Panagis; Qi, Jun; Picaud, Sarah Nature, Vol. 468, Issue 7327 https://doi.org/10.1038/nature09504	journal	September 2010
Suppression of inflammation by a synthetic histone mimic Nicodeme, Edwige; Jeffrey, Kate L.; Schaefer, Uwe Nature, Vol. 468, Issue 7327 https://doi.org/10.1038/nature09589	journal	November 2010
RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia Zuber, Johannes; Shi, Junwei; Wang, Eric Nature, Vol. 478, Issue 7370 https://doi.org/10.1038/nature10334	journal	August 2011
SPA70 is a potent antagonist of human pregnane X receptor Lin, Wenwei; Wang, Yue-Ming; Chai, Sergio C. Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-00780-5	journal	September 2017
Bromodomains: a new target class for drug development Cochran, Andrea G.; Conery, Andrew R.; Sims, Robert J. Nature Reviews Drug Discovery, Vol. 18, Issue 8 https://doi.org/10.1038/s41573-019-0030-7	journal	July 2019
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
BRD–NUT oncoproteins: a family of closely related nuclear proteins that block epithelial differentiation and maintain the growth of carcinoma cells French, C. A.; Ramirez, C. L.; Kolmakova, J. Oncogene, Vol. 27, Issue 15 https://doi.org/10.1038/sj.onc.1210852	journal	October 2007
Origin and characterization of a human bipotent liver progenitor cell line☆ Parent, Romain; Marion, Marie-Jeanne; Furio, Laetitia Gastroenterology, Vol. 126, Issue 4 https://doi.org/10.1053/j.gastro.2004.01.002	journal	April 2004
A fast and high-quality charge model for the next generation general AMBER force field He, Xibing; Man, Viet H.; Yang, Wei The Journal of Chemical Physics, Vol. 153, Issue 11 https://doi.org/10.1063/5.0019056	journal	September 2020
BRD4 is a novel therapeutic target for liver fibrosis Ding, Ning; Hah, Nasun; Yu, Ruth T. Proceedings of the National Academy of Sciences, Vol. 112, Issue 51 https://doi.org/10.1073/pnas.1522163112	journal	December 2015
Mechanistic insights into the synergistic activation of the RXR–PXR heterodimer by endocrine disruptor mixtures Delfosse, Vanessa; Huet, Tiphaine; Harrus, Deborah Proceedings of the National Academy of Sciences, Vol. 118, Issue 1 https://doi.org/10.1073/pnas.2020551118	journal	December 2020
Bromodomain proteins regulate human cytomegalovirus latency and reactivation allowing epigenetic therapeutic intervention Groves, Ian J.; Jackson, Sarah E.; Poole, Emma L. Proceedings of the National Academy of Sciences, Vol. 118, Issue 9 https://doi.org/10.1073/pnas.2023025118	journal	February 2021
Discovery of potent BET bromodomain 1 stereoselective inhibitors using DNA-encoded chemical library selections Modukuri, Ram K.; Yu, Zhifeng; Tan, Zhi Proceedings of the National Academy of Sciences, Vol. 119, Issue 22 https://doi.org/10.1073/pnas.2122506119	journal	May 2022
Structure-guided approach to modulate small molecule binding to a promiscuous ligand-activated protein Lin, Wenwei; Huber, Andrew D.; Poudel, Shyaron Proceedings of the National Academy of Sciences, Vol. 120, Issue 10 https://doi.org/10.1073/pnas.2217804120	journal	February 2023
Infection of a human hepatoma cell line by hepatitis B virus Gripon, Philippe; Rumin, Sylvie; Urban, Stephan Proceedings of the National Academy of Sciences, Vol. 99, Issue 24 https://doi.org/10.1073/pnas.232137699	journal	November 2002
Cyclin-dependent Kinase 2 Negatively Regulates Human Pregnane X Receptor-mediated CYP3A4 Gene Expression in HepG2 Liver Carcinoma Cells Lin, Wenwei; Wu, Jing; Dong, Hanqing Journal of Biological Chemistry, Vol. 283, Issue 45 https://doi.org/10.1074/jbc.M806132200	journal	November 2008
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit Pronk, Sander; Páll, Szilárd; Schulz, Roland Bioinformatics, Vol. 29, Issue 7 https://doi.org/10.1093/bioinformatics/btt055	journal	February 2013
Metabolism of JQ1, an inhibitor of bromodomain and extra terminal bromodomain proteins, in human and mouse liver microsomes† Li, Feng; MacKenzie, Kevin R.; Jain, Prashi Biology of Reproduction, Vol. 103, Issue 2 https://doi.org/10.1093/biolre/ioaa043	journal	April 2020
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models Varadi, Mihaly; Anyango, Stephen; Deshpande, Mandar Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1061	journal	November 2021
Molecular basis of crosstalk in nuclear receptors: heterodimerization between PXR and CAR and the implication in gene regulation Bwayi, Monicah N.; Garcia-Maldonado, Efren; Chai, Sergio C. Nucleic Acids Research, Vol. 50, Issue 6 https://doi.org/10.1093/nar/gkac133	journal	February 2022
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update No authors listed Nucleic Acids Research, Vol. 50, Issue W1 https://doi.org/10.1093/nar/gkac247	journal	April 2022
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/S0021889807021206	journal	July 2007
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee; Afonine, Pavel V.; Baker, Matthew L. Acta Crystallographica Section D Structural Biology, Vol. 75, Issue 10 https://doi.org/10.1107/S2059798319011471	journal	October 2019
A Phosphomimetic Mutation at Threonine-57 Abolishes Transactivation Activity and Alters Nuclear Localization Pattern of Human Pregnane X Receptor Pondugula, Satyanarayana R.; Brimer-Cline, Cynthia; Wu, Jing Drug Metabolism and Disposition, Vol. 37, Issue 4 https://doi.org/10.1124/dmd.108.024695	journal	January 2009
CITCO Directly Binds to and Activates Human Pregnane X Receptor Lin, Wenwei; Bwayi, Monicah; Wu, Jing Molecular Pharmacology, Vol. 97, Issue 3 https://doi.org/10.1124/mol.119.118513	journal	December 2019
The Orphan Human Pregnane X Receptor Mediates the Transcriptional Activation of CYP3A4 by Rifampicin through a Distal Enhancer Module Goodwin, Bryan; Hodgson, Ecushla; Liddle, Christopher Molecular Pharmacology, Vol. 56, Issue 6 https://doi.org/10.1124/mol.56.6.1329	journal	December 1999
Phthalimide conjugation as a strategy for in vivo target protein degradation Winter, G. E.; Buckley, D. L.; Paulk, J. Science, Vol. 348, Issue 6241 https://doi.org/10.1126/science.aab1433	journal	May 2015
Regulation of NO Synthesis, Local Inflammation, and Innate Immunity to Pathogens by BET Family Proteins Wienerroither, S.; Rauch, I.; Rosebrock, F. Molecular and Cellular Biology, Vol. 34, Issue 3 https://doi.org/10.1128/MCB.01353-13	journal	November 2013
Small molecule JQ1 promotes prostate cancer invasion via BET-independent inactivation of FOXA1 Wang, Leiming; Xu, Mafei; Kao, Chung-Yang Journal of Clinical Investigation, Vol. 130, Issue 4 https://doi.org/10.1172/JCI126327	journal	March 2020
Structural Disorder in the Complex of Human Pregnane X Receptor and the Macrolide Antibiotic Rifampicin Chrencik, Jill E.; Orans, Jillian; Moore, Linda B. Molecular Endocrinology, Vol. 19, Issue 5 https://doi.org/10.1210/me.2004-0346	journal	May 2005
The HepaRG cell line: a uniquein vitrotool for understanding drug metabolism and toxicology in human Andersson, Tommy B.; Kanebratt, Kajsa P.; Kenna, John Gerry Expert Opinion on Drug Metabolism & Toxicology, Vol. 8, Issue 7 https://doi.org/10.1517/17425255.2012.685159	journal	May 2012
Evaluation of pregnane X receptor (PXR)-mediated CYP3A4 drug-drug interactions in drug development Sinz, Michael W. Drug Metabolism Reviews, Vol. 45, Issue 1 https://doi.org/10.3109/03602532.2012.743560	journal	January 2013
Bromodomain Inhibitors as Therapeutics for Herpesvirus-Related Disease: All BETs Are Off? Groves, Ian J.; Sinclair, John H.; Wills, Mark R. Frontiers in Cellular and Infection Microbiology, Vol. 10 https://doi.org/10.3389/fcimb.2020.00329	journal	July 2020
Bromodomain and Extraterminal Proteins as Novel Epigenetic Targets for Renal Diseases Morgado-Pascual, Jose Luis; Rayego-Mateos, Sandra; Tejedor, Lucia Frontiers in Pharmacology, Vol. 10 https://doi.org/10.3389/fphar.2019.01315	journal	November 2019

Similar Records

BET N-terminal bromodomain inhibition selectively blocks Th17 cell differentiation and ameliorates colitis in mice

Journal Article · Sun Mar 05 19:00:00 EST 2017 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1409528

Inhibition of the acetyl lysine-binding pocket of bromodomain and extraterminal domain proteins interferes with adipogenesis

Journal Article · Fri Apr 15 00:00:00 EDT 2016 · Biochemical and Biophysical Research Communications · OSTI ID:22596329

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Biochemistry & Molecular Biology

A bromodomain-independent mechanism of gene regulation by the BET inhibitor JQ1: direct activation of nuclear receptor PXR

Citation Formats

References (58)

Similar Records

Related Subjects