International Union of Basic and Clinical Pharmacology CXIII: Nuclear Receptor Superfamily-Update 2023

Adropin: A cardio-metabolic hormone in the periphery, a neurohormone in the brain?

Whole-body metabolic homeostasis is regulated by physiological responses across organs and tissues to proteins and peptides (<50 amino acids) released into the interstitial and circulatory spaces. These secreted factors integrate signals of metabolic status at both the cellular and systemic level, regulate the intake and distribution of ingested and stored energy substrates across tissues, and minimize toxicity from excessive excursions in circulating concentrations of energy substrates (for example, glucotoxicity and lipotoxicity). The proteins and peptides that are known to be secreted into circulation that are involved in regulating metabolic processes represent a fraction of the secretome predicted by the Human Proteome Atlas. Many undiscovered leads for targeting new therapies for metabolic diseases may therefore exist. In this review, we discuss the biology of adropin, the peptide encoded by the Energy Homeostasis Associated (ENHO) gene. First described as a feeding-responsive, liver-secreted peptide ("hepatokine") involved in metabolic homeostasis, > 2 decades of research indicate adropin is a stress-responsive peptide acting across multiple tissues, vascular, and organ systems. Adropin modulates the responses of liver and muscle to insulin and glucagon in regulating glucose homeostasis. Adropin inhibits hepatic glucose production and stimulates glycolysis but also inhibits tissue fibrosis and maintains vascular health in aging and metabolic disease states. Adropin is also highly expressed in the central nervous system where recent data suggest neuroprotective actions. Collectively, these results suggest the potential for targeting adropin in reducing risk of both metabolic (metabolic syndrome/type-2 diabetes) and neurodegenerative diseases in the context of aging and obesity.

Biased signaling in drug discovery and precision medicine

Receptors are crucial for converting chemical and environmental signals into cellular responses, making them prime targets in drug discovery, with about 70% of drugs targeting these receptors. Biased signaling, or functional selectivity, has revolutionized drug development by enabling precise modulation of receptor signaling pathways. This concept is more firmly established in G protein-coupled receptor and has now been applied to other receptor types, including ion channels, receptor tyrosine kinases, and nuclear receptors. Advances in structural biology have further refined our understanding of biased signaling. This targeted approach enhances therapeutic efficacy and potentially reduces side effects. Numerous biased drugs have been developed and approved as therapeutics to treat various diseases, demonstrating their significant therapeutic potential. This review provides a comprehensive overview of biased signaling in drug discovery and disease treatment, highlighting recent advancements and exploring the therapeutic potential of these innovative modulators across various diseases.

Targeting the ceramidase ACER3 attenuates cholestasis in mice by mitigating bile acid overload via unsaturated ceramide-mediated LXRβ signaling transduction

Bile acid overload critically drives the pathogenesis of cholestatic liver injury (CLI). While ceramide metabolism has garnered increasing interest in liver research, the role of ceramides in CLI remains unclear. This study investigates the function of alkaline ceramidase 3 (ACER3)-catalyzed hydrolysis of unsaturated ceramides in CLI. Using clinical specimens, this work finds that ACER3 expression is upregulated in the cholestatic liver and positively correlated with the severity of CLI in patients. Acer3 ablation increases ceramide(d18:1/18:1) and attenuates bile duct ligation-induced CLI in female mice with reduced hepatic necrosis, inflammation, and fibrosis. However, it does not significantly impact CLI in male mice. Moreover, ceramide(d18:1/18:1) treatment attenuates CLI in wild-type female mice. Similarly, ACER3 knockdown and ceramide(d18:1/18:1) treatment prevent lithocholic-acid-induced cell death in human-liver-derived HepG2 cells. Mechanistically, ceramide(d18:1/18:1) binds the ligand binding domain of the liver X receptor β, acting as an agonist to activate its transcriptional functions. This activation upregulates sulfotransferase 2A1-catalyzed bile acid sulfation, normalizes bile acid metabolism, and restores lipogenesis, thereby reducing bile acid overload in hepatocytes to attenuate CLI. Our findings uncover the role of ceramide(d18:1/18:1)-liver X receptor β signaling in mitigating bile acid overload in the cholestatic liver, offering mechanistic insights and suggesting therapeutic potential for targeting ACER3 and ceramide(d18:1/18:1) for CLI.

The cyclin-dependent kinase inhibitor AT7519 is a human RORγt agonist

AT7519, which inhibits multiple cyclin-dependent kinases, has been extensively investigated in various types of cancer cells. Previous studies have demonstrated the ability of this molecule to suppress the expression of the nuclear receptor retinoic acid-related orphan receptor gamma (RORγ) and several genes involved in hepatocellular carcinoma progression. In this study, we identified a distinct agonistic effect of AT7519 on RORγt, an isoform expressed by various immune cells, including T helper 17 lymphocytes. These immune cells play pivotal roles in shaping the tumor microenvironment and promoting the anticancer response of the immune system. After exposure to AT7519 during differentiation, primary human CD4+ T cells presented increased expression of IL17A/F, IFNG and GZMB and decreased expression of PDCD1 and CTLA4. These findings elucidate a previously unrecognized facet of AT7519 activity and suggest the potential incorporation of this molecule into immune therapies to augment the effectiveness of diverse anticancer strategies involving anti-programmed cell death protein 1 (anti-PD-1) and anti-cytotoxic T-lymphocyte antigen 4 (anti-CTLA4) regimens.

Activation of Genes by Nuclear Receptor/Specificity Protein (Sp) Interactions in Cancer

The human nuclear receptor (NR) superfamily consists of 48 genes that are ligand-activated transcription factors that play a key role in maintaining cellular homeostasis and in pathophysiology. NRs are important drug targets for both cancer and non-cancer endpoints as ligands for these receptors can act as agonists, antagonists or inverse agonists to modulate gene expression. With two exceptions, the classical mechanism of action of NRs involves their interactions as monomers, dimers or heterodimers with their cognate response elements (cis-elements) in target gene promoters. Several studies showed that a number of NR-regulated genes did not directly bind their corresponding cis-elements and promoter analysis identified that NR-responsive gene promoters contained GC-rich sequences that bind specificity protein 1 (Sp1), Sp3 and Sp4 transcription factors (TFs). This review is focused on identifying an important sub-set of Sp-regulated genes that are indirectly coregulated through interactions with NRs. Subsequent studies showed that many NRs directly bind Sp1 (or Sp3 and Sp4), the NR/Sp complexes bind GC-rich sites to regulate gene expression and the NR acts as a ligand-modulated nuclear cofactor. In addition, several reports show that NR-responsive genes contain cis-elements that bind both Sp TFs and NRs, and mutation of either cis-element results in loss of NR-responsive (inducible and/or basal). Regulation of these genes involves interactions between DNA-bound Sp TFs with proximal or distal DNA-bound NRs, and, in some cases, other nuclear cofactors are required for gene expression. Thus, many NR-responsive genes are regulated by NR/Sp complexes, and these genes can be targeted by ligands that target NRs and also by drugs that induce degradation of Sp1, Sp3 and Sp4.

Evaluation of N-palmitoylethanolamine (PEA) binding to nuclear receptors through docking and molecular dynamics studies

N-palmitoylethanolamine (PEA) is an endogenous bioactive compound recognized for its anti-inflammatory effects and its role in tissue protection and repair. Despite the proposal of peroxisome proliferator-activated receptor alpha (PPARα) as a potential receptor for PEA, direct evidence of binding remains insufficient. This study offers a comprehensive analysis of human nuclear receptors (NRs) through structural bioinformatics and molecular docking, evaluating a total of 367 unique NR structures across 47 subfamilies. To explore the stability and binding affinity of PEA with selected nuclear receptors, we conducted molecular dynamics simulations following initial docking assessments. The results revealed Hepatocyte Nuclear Factor 4-alpha (HNF4α) as the highest-ranking receptor with a global score of 0.884, closely followed by Hepatocyte Nuclear Factor 4-gamma (HNF4γ) at 0.871 and Retinoic Acid Receptor gamma-1 (RARγ-1) at 0.829. Among these, HNF4γ demonstrated the strongest affinity for PEA, supported by consistent simulation results. In contrast, the PPARα receptor ranked 44th with a global score of 0.519, indicating that PEA may engage more effectively with other nuclear receptors. In conclusion, this study underscores PEA's potential as a multi-target therapeutic agent through its interactions with various nuclear receptors, particularly HNF4γ and the Mineralocorticoid Receptor (MR). The ability of PEA to influence multiple signaling pathways suggests its promise in addressing complex diseases associated with inflammation and metabolic disorders. Additionally, the integration of Root Mean Square Deviation (RMSD) and Gibbs free energy (ΔG) analyses further elucidates the stability and binding affinities of PEA, providing a foundation for future research into its therapeutic applications.

Nuclear receptor profiling for subtype classification and as prognostic markers in 33 cancer types

Nuclear receptors, a group of 48 transcription factors that regulate a multitude of processes within our body, have long been employed as diagnostic markers or therapeutic targets in breast cancer, prostate cancer, and acute promyelocytic leukemia. Unfortunately, no comprehensive investigation has been conducted on their significance in other cancer types. The current study aimed to explore novel diagnostic markers by classifying nuclear receptors according to their expression patterns based on transcriptome data from The Cancer Genome Atlas on 10,071 tumor samples across 33 cancer types and investigating their association with genetic mutations, histological types, and prognosis. Our analysis showed that 21 cancers, including breast cancer, can be classified into distinct clusters based on their nuclear receptor expression profiles. Moreover, significant differences in overall survival were observed in 9 of the 21 cancer types. Overall, the results of this study indicate that previously overlooked nuclear receptors, such as NR0B1 in lung adenocarcinoma, may prove beneficial in the diagnosis of several cancers.

Agonists of the Nuclear Receptor PPARγ Can Produce Biased Signaling

Biased signaling and ligand bias, often termed functional selectivity or selective nuclear receptor modulation, have been reported for nuclear receptor partial agonists over the past 20 years. Whether signaling differences produced by partial agonists result from less intense modulation, off-target effects, or biased signaling remains unclear. A commonly postulated mechanism for biased signaling is coactivator favoritism, where agonists induce different coactivator recruitment profiles. We find that both GW1929 (full agonist) and MRL24 (partial agonist) favor recruitment of 100 to 300 residue regions from S-motif coactivators compared with a reference full agonist (rosiglitazone), yielding 95% bias value confidence intervals of 0.05-0.17 and 0.29-0.38, respectively. Calculations based on these data indicate that GW1929 and MRL24 would induce 30% to 60% higher S-motif coactivator occupancy at the receptor compared with rosiglitazone. We compare the transcriptional effects of these same three ligands on human adipocytes using RNA sequencing and exploratory Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Only 50% (rosiglitazone) and 77% (GW1929) of all gene expression changes are shared between these full agonists after 3 hours of exposure. After 24 hours of exposure, 13/98 KEGG pathways appear more intensely modulated by rosiglitazone than GW1929 (e.g., 95% confidence interval of bias in the regulation of lipolysis in adipocytes pathway is 0.03-0.09), despite similar signaling for the remaining 85 affected pathways. Similarly, rosiglitazone has an unusually large effect on several lipid metabolism-related pathways compared with the partial agonist MRL24. These data indicate that nuclear receptor full and partial agonists can induce biased signaling, likely through differences in coactivator recruitment. SIGNIFICANCE STATEMENT: Many nuclear receptor partial agonists cause fewer adverse effects and similar efficacy compared with full agonists, potentially by inducing biased agonism. Our data support the idea that partial agonists, and a full agonist, of the nuclear receptor Peroxisome proliferator-activated receptor gamma (PPARγ) are biased agonists, causing different signaling by inducing PPARγ to favor different coactivators. These data indicate that biased agonism can occur in nuclear receptors and should be considered in efforts to develop improved nuclear receptor-targeted drugs.

Leveraging nuclear receptor mediated transcriptional signaling for drug discovery: Historical insights and current advances

Nuclear receptors (NRs) are ligand-activated transcription factors that regulate gene expression in response to physiological signals, such as hormones and other chemical messengers. These receptors either activate or repress the transcription of target genes, which in turn promotes or suppresses physiological processes governing growth, differentiation, and homeostasis. NRs bind to specific DNA sequences and, in response to ligand binding, either promote or hinder the assembly of the transcriptional machinery, thereby influencing gene expression at the transcriptional level. These receptors are involved in a wide range of pathological conditions, including cancer, metabolic disorders, chronic inflammatory diseases, and immune system-related disorders. Modulation of NR function through targeted drugs has shown therapeutic benefits in treating such conditions. NR-targeted drugs, which either completely or selectively activate or block receptor function, represent a significant class of clinically valuable therapeutics. However, the pathways of NR-mediated gene expression and the resulting physiological effects are complex, involving crosstalk between various biomolecular components. As a result, NR-targeted drug discovery is challenging. With improved understanding of how NRs regulate physiological functions and deeper insights into their molecular structure, the process of NR-targeted drug discovery has evolved. While many traditional NR-targeting drugs are associated with side effects of varying severity, new drug candidates are being designed to minimize these adverse effects. Given that NR activity varies according to the tissue in which they are expressed and the specific isoform that is activated or repressed, achieving selectivity in targeting specific tissues and isoform classes may help reduce systemic side effects. In a recent breakthrough, the isoform-selective, hepato-targeted thyroid hormone-β agonist, Resmetirom (marketed as Rezdiffra), was approved for the treatment of non-alcoholic steatohepatitis. This chapter explores the structural and mechanistic principles guiding NR-targeted drug discovery and provides insights into recent developments in this field.

Central role of SUMOylation in the regulation of chromatin interactions and transcriptional outputs of the androgen receptor in prostate cancer cells

The androgen receptor (AR) is pivotal in prostate cancer (PCa) progression and represents a critical therapeutic target. AR-mediated gene regulation involves intricate interactions with nuclear proteins, with many mediating and undergoing post-translational modifications that present alternative therapeutic avenues. Through chromatin proteomics in PCa cells, we identified SUMO ligases together with nuclear receptor coregulators and pioneer transcription factors within the AR's protein network. Intriguingly, this network displayed a significant association with SUMO2/3. To elucidate the influence of SUMOylation on AR chromatin interactions and subsequent gene regulation, we inhibited SUMOylation using ML-792 (SUMOi). While androgens generally facilitated the co-occupancy of SUMO2/3 and AR on chromatin, SUMOi induced divergent effects dependent on the type of AR-binding site (ARB). SUMOi augmented AR's pioneer-like binding on inaccessible chromatin regions abundant in androgen response elements (AREs) and diminished its interaction with accessible chromatin regions sparse in AREs yet rich in pioneer transcription factor motifs. The SUMOi-impacted ARBs divergently influenced AR-regulated genes; those associated with AR-mediated activation played roles in negative regulation of cell proliferation, while those with AR-mediated repression were involved in pattern formation. In conclusion, our findings underscore the pervasive influence of SUMOylation in shaping AR's role in PCa cells, potentially unveiling new therapeutic strategies.

Mechanism of antagonist ligand binding to REV-ERBα

REV-ERBα, a therapeutically promising nuclear hormone receptor, plays a crucial role in regulating various physiological processes such as the circadian clock, inflammation, and metabolism. However, the availability of chemical probes to investigate the pharmacology of this receptor is limited, with SR8278 being the only identified synthetic antagonist. Moreover, no X-ray crystal structures are currently available that demonstrate the binding of REV-ERBα to antagonist ligands. This lack of structural information impedes the development of targeted therapeutics. To address this issue, we employed Gaussian accelerated molecular dynamics (GaMD) simulations to investigate the binding pathway of SR8278 to REV-ERBα. For comparison, we also used GaMD to observe the ligand binding process of STL1267, for which an X-ray structure is available. GaMD simulations successfully captured the binding of both ligands to the receptor's orthosteric site and predicted the ligand binding pathway and important amino acid residues involved in the antagonist SR8278 binding. This study highlights the effectiveness of GaMD in investigating protein-ligand interactions, particularly in the context of drug recognition for nuclear hormone receptors.

EP300/CREBBP acetyltransferase inhibition limits steroid receptor and FOXA1 signaling in prostate cancer cells

The androgen receptor (AR) is a primary target for treating prostate cancer (PCa), forming the bedrock of its clinical management. Despite their efficacy, resistance often hampers AR-targeted therapies, necessitating new strategies against therapy-resistant PCa. These resistances involve various mechanisms, including AR splice variant overexpression and altered activities of transcription factors like the glucocorticoid receptor (GR) and FOXA1. These factors rely on common coregulators, such as EP300/CREBBP, suggesting a rationale for coregulator-targeted therapies. Our study explores EP300/CREBBP acetyltransferase inhibition's impact on steroid receptor and FOXA1 signaling in PCa cells using genome-wide techniques. Results reveal that EP300/CREBBP inhibition significantly disrupts the AR-regulated transcriptome and receptor chromatin binding by reducing the AR-gene expression. Similarly, GR's regulated transcriptome and receptor binding were hindered, not linked to reduced GR expression but to diminished FOXA1 chromatin binding, restricting GR signaling. Overall, our findings highlight how EP300/CREBBP inhibition distinctively curtails oncogenic transcription factors' signaling, suggesting the potential of coregulatory-targeted therapies in PCa.

Structural Perspective of NR4A Nuclear Receptor Family and Their Potential Endogenous Ligands

There are 48 nuclear receptors in the human genome, and many members of this superfamily have been implicated in human diseases. The NR4A nuclear receptor family consisting of three members, NR4A1, NR4A2, and NR4A3 (formerly annotated as Nur77, Nurr1, and NOR1, respectively), are still orphan receptors but exert pathological effects on immune-related and neurological diseases. We previously reported that prostaglandin A1 (PGA1) and prostaglandin A2 (PGA2) are potent activators of NR4A3, which bind directly to the ligand-binding domain (LBD) of the receptor. Recently, the co-crystallographic structures of NR4A2-LBD bound to PGA1 and PGA2 were reported, followed by reports of the neuroprotective effects of these possible endogenous ligands in mouse models of Parkinson's disease. Based on these structures, we modeled the binding structures of the other two members (NR4A1 and NR4A3) with these potential endogenous ligands using a template-based modeling method, and reviewed the similarity and diversity of ligand-binding mechanisms in the nuclear receptor family.

RORγT agonists as immune modulators in anticancer therapy

RORγT is a transcription factor that directs the development of Th17 lymphocytes and other IL-17-expressing cells (e.g., Tc17 and ILC3 cells). These cells are involved in the body's defense against pathogenic bacteria and fungi, but they also participate in maintaining the proinflammatory environment in some autoimmune diseases and play a role in the immune system's response to cancer. Similar to other members of the nuclear receptor superfamily, the activity of RORγT is regulated by low-molecular-weight ligands. Therefore, extensive efforts have been dedicated to identifying inverse agonists that diminish the activity of this receptor and subsequently inhibit the development of autoimmune diseases. Unfortunately, in the pursuit of an ideal inverse agonist, the development of agonists has been overlooked. It is important to remember that these types of compounds, by stimulating lymphocytes expressing RORγT (Th17 and Tc17), can enhance the immune system's response to tumors. In this review, we present recent advancements in the biology of RORγT agonists and their potential application in anticancer therapy.