Ligand flexibility and binding pocket malleability cooperate to allow selective PXR activation by analogs of a promiscuous nuclear receptor ligand

Impact of Persistent Endocrine-Disrupting Chemicals on Human Nuclear Receptors: Insights from In Silico and Experimental Characterization

Endocrine-disrupting chemicals (EDCs) are notable for their persistence, bioaccumulation, and associations with cancer. Human nuclear receptors (hNRs) are primary targets disrupted by these persistent EDCs, resulting in alterations to xenobiotic metabolism, lipid homeostasis, and endocrine function, which can lead to carcinogenic effects. Despite their hazardous effects, comprehensive studies on EDC interactions and their impacts on hNRs remain limited. Here, we profiled the interactions of persistent EDCs, including PFAS, plastic additives, bisphenols, polybrominated diphenyl ethers, and phthalates, with key hNRs such as PXR, CAR, PPARα, PPARγ, PPARδ, AR, and RORγt. Through controlled molecular docking simulations, we observed strong binding of the EDCs to these receptors. Further analysis showed that EDCs exhibit strong binding activity towards hNRs by preferentially interacting with hydrophobic amino acids, namely leucine, isoleucine, methionine, and phenylalanine. PFAS demonstrated the highest binding affinity, characterized by a combination of complementary hydrophobic interactions from their fluorinated carbon chains and polar interactions from their functional groups (e.g., carboxylate, sulfonate) across all receptors. Distinct polycyclic and hydrophobic trends, contributing to strong NR binding, were evident in non-PFAS and nonplastic EDCs. The hNR activity assay in HepG2 cells revealed agonistic effects of dicyclohexyl phthalate (DCHP) and di-2-ethylhexyl phthalate (DEHP) on most receptors, except for PPARα. The hNR transcription factor pathway assay in HepG2 cells demonstrated increased gene expression of VDRE and PXR, suggesting potential chronic effects on xenobiotic metabolism and calcium homeostasis. Overall, our findings demonstrate the need for further research into the endocrine disruption and carcinogenic effects of these persistent EDCs.

A two-in-one expression construct for biophysical and structural studies of the human pregnane X receptor ligand-binding domain, a pharmaceutical and environmental target

The ligand-binding domain (LBD) of the human nuclear receptor pregnane X receptor (PXR) is known to crystallize in two different crystal forms, P212121 or P43212, depending on the construct and the strategy used for protein production, as well as the presence or absence of the coactivator-derived peptide SRC-1. In order to facilitate biophysical and structural studies, a versatile construct was designed that allows access to both forms. This was achieved by introducing a thrombin cleavage site between the PXRLBD and the SRC-1 peptide fused to its C-terminus. Here, we describe the expression, purification and crystallization processes of this novel construct and report two new structures of PXRLBD that were obtained thanks to this strategy.

PROTAC-mediated activation, rather than degradation, of a nuclear receptor reveals complex ligand-receptor interaction network

Proteolysis-targeting chimeras (PROTACs) are heterobifunctional molecules containing a ligand for a protein of interest linked to an E3 ubiquitin ligase ligand that induce protein degradation through E3 recruitment to the target protein. Small changes in PROTAC linkers can have drastic consequences, including loss of degradation activity, but the structural mechanisms governing such changes are unclear. To study this phenomenon, we screened PROTACs of diverse targeting modalities and identified dTAG-13 as an activator of the xenobiotic-sensing pregnane X receptor (PXR), which promiscuously binds various ligands. Characterization of dTAG-13 analogs and precursors revealed interplay between the PXR-binding moiety, linker, and E3 ligand that altered PXR activity without inducing degradation. A crystal structure of PXR ligand binding domain bound to a precursor ligand showed ligand-induced binding pocket distortions and a linker-punctured tunnel to the protein exterior at a region incompatible with E3 complex formation, highlighting the effects of linker environment on PROTAC activity.

Novel antagonists reveal the mechanism of PXR inhibition

The pregnane X receptor (PXR) is a key regulator of metabolism, but the mechanisms underlying its antagonism remain unclear. Garcia-Maldonado et al. reported potent new antagonists and their co-crystal structures, revealing molecular determinants of PXR antagonism and paving the way for developing antagonists as therapeutics and preventing undesirable PXR activation.

Computationally-Assisted Discovery and Assignment of a New Class of 6/6/5/5 Fused-Ring Diterpene Acting as Pregnane X Receptor Ligands from Isodon serra

We report here the orchestration of molecular ion networking (MoIN) and a set of computationally assisted structural elucidation approaches in the discovery and assignment of a new class of rearranged 4,5-seco-abietane diterpenoids including serra A (1), which possesses an unusual 6/6/5/5 fused-ring skeleton system, together with two previously unreported diterpenoids serras B-C (2-3) and five known compounds were isolated from Isodon serra (I. serra). The structures were elucidated by spectroscopic analysis in conjunction with computationally assisted structure elucidation tools. In silico, serras A-C (1-3) bind well to PXR, suggesting their potential role in reducing inflammation. The results of serra A (1) with hPXR demonstrated agonist activity with an EC50 value of 15 μM. Serra A (1), graciliflorin F (4), gerardianin C (5), 11,12,15-trihydroxy-8,11,13-abietatrien-7-one (6), rabdosin D (7), and 15-hydroxysalprionin (8) exhibited promising anti-inflammatory activities in lipopolysaccharide (LPS)-induced RAW 267.4 cells, and their inhibition rates on NO production were more than 65% at 10 μM.

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

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.

Regulation of PXR in drug metabolism: chemical and structural perspectives

INTRODUCTION

Pregnane X receptor (PXR) is a master xenobiotic sensor that transcriptionally controls drug metabolism and disposition pathways. PXR activation by pharmaceutical drugs, natural products, environmental toxins, etc. may decrease drug efficacy and increase drug-drug interactions and drug toxicity, indicating a therapeutic value for PXR antagonists. However, PXR's functions in physiological events, such as intestinal inflammation, indicate that PXR activators may be useful in certain disease contexts.

AREAS COVERED

We review the reported roles of PXR in various physiological and pathological processes including drug metabolism, cancer, inflammation, energy metabolism, and endobiotic homeostasis. We then highlight specific cellular and chemical routes that modulate PXR activity and discuss the functional consequences. Databases searched and inclusive dates: PubMed, 1 January 1980 to 10 January 2024.

EXPERT OPINION

Knowledge of PXR's drug metabolism function has helped drug developers produce small molecules without PXR-mediated metabolic liabilities, and further understanding of PXR's cellular functions may offer drug development opportunities in multiple disease settings.

Go big and go home: A bulky extension makes promiscuous ligands settle down

Synthetic ligands often show undesired polypharmacology, affecting the function of multiple targets. In this issue of Structure, Huber et al. developed a PXR-specific agonist based on a promiscuous ligand. Their structure-guided approach exploited the malleability of the PXR ligand-binding pocket, which unlike other nuclear receptors could accommodate bulkier ligands.