Full-length nuclear receptor allosteric regulation

Nuclear receptors in cancer: Unveiling theranostic potentials and innovative therapeutic strategies

Nuclear receptors (NRs) include a family of 48 transcription factors (TFs) that regulate gene expression implicated in biological processes such as cell proliferation, differentiation, metabolism, and immune response. Cancer development has been widely linked to the dysregulation of NRs and their signaling pathways, providing promising targets for therapeutic applications. Recent progress in OMIC approaches and high-throughput drug screening has facilitated the emergence of biomolecules, especially phytochemicals, as potential substitutes for synthetic anti-cancer drugs. This review aims to highlight the anticancer potency of diverse classes of biocompounds that target NRs, including phytocompounds, dietary components, venom constituents, microbial metabolites, as well as many small molecules generated from computer-aided drug design (CADD) approaches in the design of innovative and safe treatments. We examine critically the preclinical and clinical trials investigating these candidates for preventing and treating cancer, focusing on their modes of action, their proven efficacy, and their limitations. In addition, we underline significant molecular processes modulated by these natural compounds, highlighting their ability to surmount drug resistance and minimize the toxic effects of standard treatments. Overall, we believe this work has the potential to pave the way for new paradigms in identifying innovative therapeutic options for NR-mediated management of specific types of cancer.

The farnesoid X receptor activates transcription independently of RXR at non-canonical response elements

The farnesoid X receptor (FXR) is a nuclear receptor (NR) known to obligately heterodimerize with the retinoid X receptor (RXR). FXR is expressed as four isoforms (α1-α4) that drive transcription from IR-1 (inverted repeat-1) response elements (REs). Recently, we found that FXR isoforms α2/α4 also activate transcription from non-canonical ER-2 (everted repeat-2) REs, mediating most metabolic effects of general FXR activation. Here, we explored molecular determinants of regulation by FXRα2 from ER-2 REs through quantitative interaction proteomics, site-directed mutagenesis and transcriptomics. We discovered FXRα2 binds to and activates ER-2 elements in vitro and in reporter assays independently of RXR. Genome-wide binding analysis in mouse liver revealed higher ER-2 motif enrichment in FXR sites lacking RXR. Abrogation of FXRα2:RXR heterodimerization abolished IR-1, but preserved ER-2 transactivation. Transcriptome-wide, RXR overexpression inhibited 25% of FXRα2 targets in HepG2. These genes were specifically activated by the heterodimerization-deficient mutant FXRα2L434R, enriched for ER-2 motifs at their promoters, and involved in lipid metabolism and ammonia detoxification. In conclusion, RXR acts as a molecular switch, inhibiting FXRα2 activation from ER-2 while enhancing it from canonical IR-1 REs. Our results showcase FXR as the first NR with isoform-specific RXR-independent REs, highlighting a new layer of regulation and complexity for RXR-heterodimerizing NRs.

Immune-endocrine crossroads: the impact of nuclear receptors in Tuberculosis and Chagas disease

Nuclear Receptors (NRs) comprise a superfamily of proteins with essential roles in cell signaling, survival, proliferation, and metabolism. They act as transcription factors and are subclassified into families based on their ligands, DNA-binding sequences, tissue specificity, and functions. Evidence indicates that in infectious diseases, cancer, and autoimmunity, NRs modulate immune and endocrine responses, altering the transcriptional profile of cells and organs and influencing disease progression. Chronic infectious diseases, characterized by pathogen persistence, are particularly notable for an exaggerated inflammatory process. Unlike acute inflammation, which helps the host respond to pathogens, chronic inflammation leads to metabolic disorders and a dysregulated neuro-immuno-endocrine response. Over time, disturbances in cytokine, hormone, and other compound production foster an unbalanced, detrimental defensive response. This complexity underscores the significant role of ligand-dependent NRs. Tuberculosis and Chagas Disease are two critical chronic infections. The causative agents, Mycobacterium tuberculosis and Trypanosoma cruzi, have developed evasion strategies to establish chronic infections. Their clinical manifestations are associated with disrupted immuno-endocrine responses, pointing to a potential involvement of NRs. This review explores the current understanding of NRs in regulating immune-endocrine interactions within the context Tuberculosis and Chagas Disease. These diseases remain significant global health concerns, particularly in developing countries, highlighting the importance of understanding the molecular mechanisms underlying host-pathogen interactions mediated by NRs.

Enhanced dynamic coupling in a nuclear receptor underlies ligand activity

Bile acids are signaling molecules with critical roles in cholesterol and lipid metabolism, achieved by regulating the transcriptional activity of the farnesoid X receptor (FXR, NR1H4), otherwise known as the bile acid receptor. Modifications to the C6 position of the steroidal core yield bile acid derivatives with 100× improved potency over endogenous bile acids. Prevailing hypotheses suggested increased binding affinity for FXR as the driver for this activity enhancement. Our experimental results contradict this suggestion, motivating us to investigate the underlying mechanisms of enhanced ligand activity. We combined functional assays with over 200 μs of simulations, revealing an unexpected role for helix 5 in the allosteric signaling of obeticholic acid. We uncovered dynamic coupling between adjacent helices 5 and 7, which is uniquely enhanced by the bile acid modification. Ultimately, the enhanced potency of the bile acid analog can be traced to its effect on FXR dynamics. In addition to identifying a previously unknown mechanistic role for helix 5 to helix 7 coupling in FXR, these results emphasize the inextricable linkage between the activity of nuclear receptor ligands and their effects on receptor dynamics.

Allosteric communications between domains of nuclear receptors

Nuclear receptors (NRs) regulate gene expression in response to hormonal signals, influencing diverse physiological processes and diseases. Structural and dynamics investigations based on X-ray crystallography, cryo-electron microscopy (cryo-EM), hydrogen-deuterium exchange mass spectrometry, and molecular dynamics simulations, have significantly deepened our understanding of the conformational states, dynamics, and interdomain interactions of multi-domain NRs. Structural studies have examined heterodimeric complexes such as peroxisome proliferator-activated receptor gamma (PPAR-γ) with retinoid X receptor alpha (RXRα), liver X receptor beta (LXRβ) with RXRα, and retinoic acid receptor beta (RARβ) with RXRα, as well as homodimers like hepatic nuclear factor 4 alpha (HNF-4α), androgen receptor (AR), and glucocorticoid receptor (GR). These investigations highlight critical allosteric communication between ligand-binding domains (LBDs) and DNA-binding domains (DBDs), emphasizing the roles of flexible hinge regions and N-terminal segments in adapting to diverse DNA configurations. Both non-steroid receptor heterodimers and homodimers exhibit robust interdomain connections that mediate allosteric signaling. For instance, AR demonstrates three distinct conformational states that underscore its dynamic behavior, while GR exhibits unique ligand-dependent domain interactions shaping receptor signaling. The collective findings so far suggest a conserved mechanism of cross-domain communication across the NR family. Supported by complementary biophysical, spectroscopic, mutagenesis, and computational studies, this body of research has elucidated the nature of domain-domain interfaces and their pivotal roles in regulating the transcriptional activity of steroid and non-steroid receptors.

Nuclear Receptor Interdomain Communication is Mediated by the Hinge with Ligand Specificity

Nuclear receptors are ligand-induced transcription factors that bind directly to target genes and regulate their expression. Ligand binding initiates conformational changes that propagate to other domains, allosterically regulating their activity. The nature of this interdomain communication in nuclear receptors is poorly understood, largely owing to the difficulty of experimentally characterizing full-length structures. We have applied computational modeling approaches to describe and study the structure of the full-length farnesoid X receptor (FXR), approximated by the DNA binding domain (DBD) and ligand binding domain (LBD) connected by the flexible hinge region. Using extended molecular dynamics simulations (>10 microseconds) and enhanced sampling simulations, we provide evidence that ligands selectively induce domain rearrangement, leading to interdomain contact. We use protein-protein interaction assays to provide experimental evidence of these interactions, identifying a critical role of the hinge in mediating interdomain contact. Our results illuminate previously unknown aspects of interdomain communication in FXR and provide a framework to enable characterization of other full-length nuclear receptors.

Nuclear receptor interdomain communication is mediated by the hinge with ligand specificity

Nuclear receptors are ligand-induced transcription factors that bind directly to target genes and regulate their expression. Ligand binding initiates conformational changes that propagate to other domains, allosterically regulating their activity. The nature of this interdomain communication in nuclear receptors is poorly understood, largely owing to the difficulty of experimentally characterizing full-length structures. We have applied computational modeling approaches to describe and study the structure of the full length farnesoid X receptor (FXR), approximated by the DNA binding domain (DBD) and ligand binding domain (LBD) connected by the flexible hinge region. Using extended molecular dynamics simulations (> 10 microseconds) and enhanced sampling simulations, we provide evidence that ligands selectively induce domain rearrangement, leading to interdomain contact. We use protein-protein interaction assays to provide experimental evidence of these interactions, identifying a critical role of the hinge in mediating interdomain contact. Our results illuminate previously unknown aspects of interdomain communication in FXR and provide a framework to enable characterization of other full length nuclear receptors.