Machine learning methods and docking for predicting human pregnane X receptor activation

scientific article published on 12 June 2008

Machine learning methods and docking for predicting human pregnane X receptor activation is …
instance of (P31):
scholarly articleQ13442814

External links are
P356DOI10.1021/TX800102E
P932PMC publication ID2574557
P698PubMed publication ID18547065
P5875ResearchGate publication ID5310341

P50authorSean EkinsQ7440973
Matthew D. KrasowskiQ37384288
Peter W. SwaanQ40220832
P2093author name stringMichael W Sinz
Erica J Reschly
Akash Khandelwal
P2860cites workSimilarity to molecules in the training set is a good discriminator for prediction accuracy in QSARQ81035487
Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: ranking, voting, and consensus scoringQ82694081
In silico renal clearance model using classical Volsurf approachQ83372812
SXR, a novel steroid and xenobiotic-sensing nuclear receptorQ22003995
2.1 A crystal structure of human PXR in complex with the St. John's wort compound hyperforinQ24294476
The nuclear receptor PXR is a lithocholic acid sensor that protects against liver toxicityQ24630723
Identification of a human nuclear receptor defines a new signaling pathway for CYP3A inductionQ24646162
Evolutionary selection across the nuclear hormone receptor superfamily with a focus on the NR1I subfamily (vitamin D, pregnane X, and constitutive androstane receptors).Q24815571
The human nuclear xenobiotic receptor PXR: structural determinants of directed promiscuityQ27632611
Crystal structure of the PXR–T1317 complex provides a scaffold to examine the potential for receptor antagonismQ27641100
Coactivator binding promotes the specific interaction between ligand and the pregnane X receptorQ27641809
UCSF Chimera--a visualization system for exploratory research and analysisQ27860666
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rulesQ28090714
The orphan nuclear receptor SXR coordinately regulates drug metabolism and effluxQ28186424
Structural insights into the promiscuity and function of the human pregnane X receptorQ28203830
Development and validation of a genetic algorithm for flexible dockingQ28236574
An orphan nuclear receptor activated by pregnanes defines a novel steroid signaling pathwayQ28263744
Evolution of the pregnane x receptor: adaptation to cross-species differences in biliary bile saltsQ28755660
Impact of scoring functions on enrichment in docking-based virtual screening: an application study on renin inhibitors.Q30341584
Evaluation of the FLEXX incremental construction algorithm for protein-ligand dockingQ30822076
Structure-based virtual screening of chemical libraries for drug discoveryQ33242317
Comparison of automated docking programs as virtual screening toolsQ33389993
Relative activation of human pregnane X receptor versus constitutive androstane receptor defines distinct classes of CYP2B6 and CYP3A4 inducersQ33881813
Docking and scoring in virtual screening for drug discovery: methods and applicationsQ34364227
Ketoconazole and miconazole are antagonists of the human glucocorticoid receptor: consequences on the expression and function of the constitutive androstane receptor and the pregnane X receptor.Q34512866
Can we estimate the accuracy of ADME-Tox predictions?Q34548331
A simple model to predict blood-brain barrier permeation from 3D molecular fieldsQ34707936
A ligand-based approach to understanding selectivity of nuclear hormone receptors PXR, CAR, FXR, LXRalpha, and LXRbetaQ35043486
Pharmacophore-based discovery of ligands for drug transportersQ35594214
Virtual screening for kinase targetsQ35699611
In silico tools to aid risk assessment of endocrine disrupting chemicalsQ35905735
In silico pharmacology for drug discovery: applications to targets and beyondQ35995265
Synthetic drugs and natural products as modulators of constitutive androstane receptor (CAR) and pregnane X receptor (PXR).Q36473477
Prediction of protein-ligand interactions. Docking and scoring: successes and gapsQ36605327
The role of nuclear receptors in pharmacokinetic drug-drug interactions in oncologyQ36798797
In silico pharmacology for drug discovery: methods for virtual ligand screening and profilingQ36840592
Human pregnane X receptor antagonists and agonists define molecular requirements for different binding sitesQ40118167
Discovery of a highly active ligand of human pregnane x receptor: a case study from pharmacophore modeling and virtual screening to "in vivo" biological activity.Q40119075
Attenuating pregnane X receptor (PXR) activation: a molecular modelling approachQ40136247
Valproic acid induces CYP3A4 and MDR1 gene expression by activation of constitutive androstane receptor and pregnane X receptor pathways.Q40152929
Computational models to assign biopharmaceutics drug disposition classification from molecular structureQ40175522
Effects of budesonide on P-glycoprotein expression in intestinal cell linesQ40192388
Computational approaches that predict metabolic intermediate complex formation with CYP3A4 (+b5).Q40208185
Evaluation of 170 xenobiotics as transactivators of human pregnane X receptor (hPXR) and correlation to known CYP3A4 drug interactionsQ40275355
In vitro and pharmacophore-based discovery of novel hPEPT1 inhibitorsQ40431673
Selective suppressions of human CYP3A forms, CYP3A5 and CYP3A7, by troglitazone in HepG2 cells.Q40477205
Regulation of the human CYP2B6 gene by the nuclear pregnane X receptorQ43705734
Calcium channel modulators of the dihydropyridine family are human pregnane X receptor activators and inducers of CYP3A, CYP2B, and CYP2C in human hepatocytesQ43740205
A pharmacophore for human pregnane X receptor ligandsQ43823795
CYP3A4 induction by drugs: correlation between a pregnane X receptor reporter gene assay and CYP3A4 expression in human hepatocytesQ44028568
The effect of cyclophosphamide with and without dexamethasone on cytochrome P450 3A4 and 2B6 in human hepatocytesQ44028572
Pharmacophore modeling and in silico screening for new P450 19 (aromatase) inhibitorsQ44695619
PXR and the regulation of apoA1 and HDL-cholesterol in rodentsQ44957981
Correlation of high-throughput pregnane X receptor (PXR) transactivation and binding assaysQ45081522
Structural disorder in the complex of human pregnane X receptor and the macrolide antibiotic rifampicinQ45261165
In silico prediction of pregnane X receptor activators by machine learning approaches.Q45965749
Comparative effects of fibrates on drug metabolizing enzymes in human hepatocytesQ46382825
Pharmacophore, drug metabolism, and pharmacokinetics models on non-peptide AT1, AT2, and AT1/AT2 angiotensin II receptor antagonistsQ46563183
Application of validated QSAR models of D1 dopaminergic antagonists for database miningQ46798122
A combined approach to drug metabolism and toxicity assessmentQ46871048
Structural model reveals key interactions in the assembly of the pregnane X receptor/corepressor complexQ46923329
AmineDB: large scale docking of amines with CYP2D6 and scoring for druglike properties--towards defining the scope of the chemical defense against foreign amines in humans.Q51910625
Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins.Q52132563
Insights for Human Ether-a-Go-Go-Related Gene Potassium Channel Inhibition Using Recursive Partitioning and Kohonen and Sammon Mapping TechniquesQ56512832
Three-Dimensional Quantitative Structure-Permeability Relationship Analysis for a Series of Inhibitors of Rhinovirus ReplicationQ56513693
A Stepwise Approach for Defining the Applicability Domain of SAR and QSAR ModelsQ60448876
A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitorsQ77365342
3D-QSAR studies with the aid of molecular docking for a series of non-steroidal FXR agonistsQ79792137
Crystal structure of the pregnane X receptor-estradiol complex provides insights into endobiotic recognitionQ79843123
Identification of potential pharmacological and toxicological targets differentiating structural analogs by a combination of transcriptional profiling and promoter analysis in LS-180 and Caco-2 adenocarcinoma cell linesQ79923315
P433issue7
P921main subjectmachine learningQ2539
P304page(s)1457-1467
P577publication date2008-06-12
P1433published inChemical Research in ToxicologyQ473530
P1476titleMachine learning methods and docking for predicting human pregnane X receptor activation
P478volume21

Reverse relations

cites work (P2860)
Q35206374An updated review on drug-induced cholestasis: mechanisms and investigation of physicochemical properties and pharmacokinetic parameters
Q35531564Binary and ternary combinations of anti-HIV protease inhibitors: effect on gene expression and functional activity of CYP3A4 and efflux transporters
Q28472135Challenges predicting ligand-receptor interactions of promiscuous proteins: the nuclear receptor PXR
Q37921791Computational modeling of P450s for toxicity prediction
Q33756500Elucidating the 'Jekyll and Hyde' nature of PXR: the case for discovering antagonists or allosteric antagonists
Q39747519Establishment of In Silico Prediction Models for CYP3A4 and CYP2B6 Induction in Human Hepatocytes by Multiple Regression Analysis Using Azole Compounds
Q34215650Evaluation of computational docking to identify pregnane X receptor agonists in the ToxCast database
Q38074989Evaluation of pregnane X receptor (PXR)-mediated CYP3A4 drug-drug interactions in drug development
Q51434937From Molecular Docking to 3D-Quantitative Structure-Activity Relationships (3D-QSAR): Insights into the Binding Mode of 5-Lipoxygenase Inhibitors.
Q33720954Hybrid scoring and classification approaches to predict human pregnane X receptor activators
Q36105916Identification and validation of novel human pregnane X receptor activators among prescribed drugs via ligand-based virtual screening
Q33725126Identification of clinically used drugs that activate pregnane X receptors
Q38896344In Silico Prediction of hPXR Activators Using Structure-Based Pharmacophore Modeling
Q37124197Induction of P-glycoprotein by antiretroviral drugs in human brain microvessel endothelial cells
Q56397856LASSO-ing Potential Nuclear Receptor Agonists and Antagonists: A New Computational Method for Database Screening
Q28647980Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets
Q45960608PXR ligand classification model with SFED-weighted WHIM and CoMMA descriptors.
Q37380059Polymer-drug interactions in tyrosine-derived triblock copolymer nanospheres: a computational modeling approach
Q47933969Predictive models for identifying the binding activity of structurally diverse chemicals to human pregnane X receptor.
Q38173202Progress in computational toxicology
Q39625852Regulation of human pregnane X receptor and its target gene cytochrome P450 3A4 by Chinese herbal compounds and a molecular docking study
Q35960314Screening Ingredients from Herbs against Pregnane X Receptor in the Study of Inductive Herb-Drug Interactions: Combining Pharmacophore and Docking-Based Rank Aggregation.
Q37461507The structural basis of pregnane X receptor binding promiscuity
Q34614106Thiazide-like diuretic drug metolazone activates human pregnane X receptor to induce cytochrome 3A4 and multidrug-resistance protein 1.
Q35531766Toward predicting drug-induced liver injury: parallel computational approaches to identify multidrug resistance protein 4 and bile salt export pump inhibitors
Q33755918Understanding nuclear receptors using computational methods

Search more.