ArticleScientific reports2018
Exploring the PXR ligand binding mechanism with advanced Molecular Dynamics methods.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 37 citations in OpenAlex.
- Exploring the Therapeutic Role of Pregnane X Receptor Activation in Acute Kidney Injury: Mechanisms and Clinical Implications.Current molecular medicine · 2026Review
- Discovery of PXR Antagonist MI891 and PXR Degrader MI1013 and Their Roles in Hepatic Gene Regulation.Journal of medicinal chemistry · 2025Article
- Impact of Persistent Endocrine-Disrupting Chemicals on Human Nuclear Receptors: Insights from In Silico and Experimental Characterization.International journal of molecular sciences · 2025Article
- The hypolipidemic effect of MI-883, the combined CAR agonist/ PXR antagonist, in diet-induced hypercholesterolemia model.Nature communications · 2025Article
- Illuminating ligand-induced dynamics in nuclear receptors through MD simulations.Biochimica et biophysica acta. Gene regulatory mechanisms · 2024Review
- Predicting Endocrine Disruption Using Conformal Prediction - A Prioritization Strategy to Identify Hazardous Chemicals with Confidence.Chemical research in toxicology · 2023Article
- Ligand-induced shifts in conformational ensembles that describe transcriptional activation.eLife · 2022Article
- Review
- Nuclear Receptor Pathways Mediating the Development of Boar Taint.Metabolites · 2022Review
- PathDetect-SOM: A Neural Network Approach for the Identification of Pathways in Ligand Binding Simulations.Journal of chemical theory and computation · 2022Article
- A concise review on hPXR ligand-recognizing residues and structure-based strategies to alleviate hPXR transactivation risk.RSC medicinal chemistry · 2022Review
- Discrepancy in interactions and conformational dynamics of pregnane X receptor (PXR) bound to an agonist and a novel competitive antagonist.Computational and structural biotechnology journal · 2022Article
- Review
- Immunoproteasome and Non-Covalent Inhibition: Exploration by Advanced Molecular Dynamics and Docking Methods.Molecules (Basel, Switzerland) · 2021Article
- Mutation of a single amino acid of pregnane X receptor switches an antagonist to agonist by altering AF-2 helix positioning.Cellular and molecular life sciences : CMLS · 2021Article
- PXR: a center of transcriptional regulation in cancer.Acta pharmaceutica Sinica. B · 2020Review
- In Silico Predictions of Endocrine Disruptors Properties.Endocrinology · 2019Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The Pregnane X Receptor (PXR) is a ligand-activated transcription factor belonging to the nuclear receptor family. PXR can bind diverse drugs and environmental toxicants with different binding modes, making it an intriguing target for drug discovery. Here we investigated the binding mechanism of the SR12813 ligand to elucidate the significant steps, from the ligand entrance pathway into the binding cavity, to the ligand-induced conformational changes, and to the exploration of its alternative binding geometries. We used the advanced Molecular Dynamics-based methods implemented in the BiKi suite and developed specific methodological approaches to overcome the complexity induced by the buried and flexible binding cavity. The adopted methods provided a full dynamic description of the binding event and allowed rationalization of the observed multiple binding modes. These results suggest that the same approach could be exploited for the study of other binding processes with similar characteristics.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.