Predicting drug metabolism: experiment and/or computation?

The role of drug metabolizing enzymes in clearance

(2014) Li Di   Expert Opinion on Drug Metabolism & Toxicology

MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics

(2014) Stephan Beisken et al.   Molecular Informatics

Identifying the macromolecular targets of de novo-designed chemical entities through self-organizing map consensus

(2014) D. Reker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

WhichCyp: prediction of cytochromes P450 inhibition

(2013) Michał Rostkowski et al.   BIOINFORMATICS

Organic Stereochemistry. Part 8

(2013) Bernard Testa   HELVETICA CHIMICA ACTA

Organic Stereochemistry. Part 7

(2013) Bernard Testa   HELVETICA CHIMICA ACTA

How Do Metabolites Differ from Their Parent Molecules and How Are They Excreted?

(2013) Johannes Kirchmair et al.   Journal of Chemical Information and Modeling

Computational Profiling of Bioactive Compounds Using a Target-Dependent Composite Workflow

(2013) Jamel Meslamani et al.   Journal of Chemical Information and Modeling

Estimating Error Rates in Bioactivity Databases

(2013) Pekka Tiikkainen et al.   Journal of Chemical Information and Modeling

FAst MEtabolizer (FAME): A Rapid and Accurate Predictor of Sites of Metabolism in Multiple Species by Endogenous Enzymes

(2013) Johannes Kirchmair et al.   Journal of Chemical Information and Modeling

The Contribution of Atom Accessibility to Site of Metabolism Models for Cytochromes P450

(2013) Patrik Rydberg et al.   MOLECULAR PHARMACEUTICS

Genetically humanized mouse models of drug metabolizing enzymes and transporters and their applications

(2013) Nico Scheer et al.   XENOBIOTICA

Current status of prediction of drug disposition and toxicity in humans using chimeric mice with humanized liver

(2013) Shigeyuki Kitamura et al.   XENOBIOTICA

Identification of drug metabolites in human plasma or serum integrating metabolite prediction, LC–HRMS and untargeted data processing

(2013) Peter L Jacobs et al.   Bioanalysis

Determinants of Reactivity and Selectivity in Soluble Epoxide Hydrolase from Quantum Mechanics/Molecular Mechanics Modeling

(2012) Richard Lonsdale et al.   BIOCHEMISTRY

RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules

(2012) J. Zaretzki et al.   BIOINFORMATICS

Predicting Drug Metabolism by Cytochrome P450 2C9: Comparison with the 2D6 and 3A4 Isoforms

(2012) Patrik Rydberg et al.   ChemMedChem

Multiple, Ligand-dependent Routes from the Active Site of Cytochrome P450 2C9

(2012) Vlad Cojocaru et al.   CURRENT DRUG METABOLISM

Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450 Probed by Molecular Dynamics Simulations

(2012) Tereza Hendrychova et al.   CURRENT DRUG METABOLISM

The Challenges Involved in Modeling Toxicity Data In Silico: A Review

(2012) M. Paul Gleeson et al.   CURRENT PHARMACEUTICAL DESIGN

Reactions and enzymes in the metabolism of drugs and other xenobiotics

(2012) Bernard Testa et al.   DRUG DISCOVERY TODAY

The promiscuous binding of pharmaceutical drugs and their transporter-mediated uptake into cells: what we (need to) know and how we can do so

(2012) Douglas B. Kell et al.   DRUG DISCOVERY TODAY

Rationalization of stereospecific binding of propranolol to cytochrome P450 2D6 by free energy calculations

(2012) Gabor Nagy et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

ADMET Evaluation in Drug Discovery. 11. PharmacoKinetics Knowledge Base (PKKB): A Comprehensive Database of Pharmacokinetic and Toxic Properties for Drugs

(2012) Dongyue Cao et al.   Journal of Chemical Information and Modeling

Free Energy Calculations Give Insight into the Stereoselective Hydroxylation of α-Ionones by Engineered Cytochrome P450 BM3 Mutants

(2012) Stephanie B.A. de Beer et al.   Journal of Chemical Information and Modeling

Development of a Computational Tool to Rival Experts in the Prediction of Sites of Metabolism of Xenobiotics by P450s

(2012) Valérie Campagna-Slater et al.   Journal of Chemical Information and Modeling

Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms

(2012) Johannes Kirchmair et al.   Journal of Chemical Information and Modeling

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

Binding of quinidine radically increases the stability and decreases the flexibility of the cytochrome P450 2D6 active site

(2012) Karel Berka et al.   JOURNAL OF INORGANIC BIOCHEMISTRY

hERG K+ Channels: Structure, Function, and Clinical Significance

(2012) Jamie I. Vandenberg et al.   PHYSIOLOGICAL REVIEWS

Host-Gut Microbiota Metabolic Interactions

(2012) J. K. Nicholson et al.   SCIENCE

VirtualToxLab — A platform for estimating the toxic potential of drugs, chemicals and natural products

(2012) Angelo Vedani et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Structural Alert/Reactive Metabolite Concept as Applied in Medicinal Chemistry to Mitigate the Risk of Idiosyncratic Drug Toxicity: A Perspective Based on the Critical Examination of Trends in the Top 200 Drugs Marketed in the United States

(2011) Antonia F. Stepan et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Fragmentation Methods: A Route to Accurate Calculations on Large Systems

(2011) Mark S. Gordon et al.   CHEMICAL REVIEWS

Microfluidic devices for in vitro studies on liver drug metabolism and toxicity

(2011) Paul M. van Midwoud et al.   Integrative Biology

Drug Metabolite Profiling and Identification by High-resolution Mass Spectrometry

(2011) Mingshe Zhu et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RS-Predictor: A New Tool for Predicting Sites of Cytochrome P450-Mediated Metabolism Applied to CYP 3A4

(2011) Jed Zaretzki et al.   Journal of Chemical Information and Modeling

IDSite: An Accurate Approach to Predict P450-Mediated Drug Metabolism

(2011) Jianing Li et al.   Journal of Chemical Theory and Computation

From in silico target prediction to multi-target drug design: Current databases, methods and applications

(2011) Alexios Koutsoukas et al.   Journal of Proteomics

The University of Minnesota Pathway Prediction System: multi-level prediction and visualization

(2011) J. Gao et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

ChEMBL: a large-scale bioactivity database for drug discovery

(2011) A. Gaulton et al.   NUCLEIC ACIDS RESEARCH

A Critical Analysis of the Interplay between Cytochrome P450 3A and P-Glycoprotein: Recent Insights from Knockout and Transgenic Mice

(2011) R. A. B. van Waterschoot et al.   PHARMACOLOGICAL REVIEWS

Prodrugs--from Serendipity to Rational Design

(2011) K. M. Huttunen et al.   PHARMACOLOGICAL REVIEWS

Addressing the challenge of limited sample volumes inin vitrostudies with capillary-scale microfluidic LC–MS/MS

(2011) Paul D Rainville et al.   Bioanalysis

Advances in metabolite identification

(2011) David S Wishart   Bioanalysis

Ligand-Based Site of Metabolism Prediction for Cytochrome P450 2D6

(2011) Patrik Rydberg et al.   ACS Medicinal Chemistry Letters

The SMARTCyp cytochrome P450 metabolism prediction server

(2010) Patrik Rydberg et al.   BIOINFORMATICS

Emerging Methods for Ensemble-Based Virtual Screening

(2010) Rommie Amaro et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Human Cytochrome P450 2E1 Structures with Fatty Acid Analogs Reveal a Previously Unobserved Binding Mode

(2010) Patrick R. Porubsky et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A review of LC–MS techniques and high-throughput approaches used to investigate drug metabolism by cytochrome P450s

(2010) Kuresh A. Youdim et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES

Site of metabolism prediction on cytochrome P450 2C9: a knowledge-based docking approach

(2010) Ákos Tarcsay et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Sites of metabolic substitution: investigating metabolite structures utilising ion mobility and molecular modelling

(2010) Gordon J. Dear et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

Enhanced metabolite identification with MSE and a semi-automated software for structural elucidation

(2010) Britta Bonn et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

SMARTCyp: A 2D Method for Prediction of Cytochrome P450-Mediated Drug Metabolism

(2010) Patrik Rydberg et al.   ACS Medicinal Chemistry Letters

Prediction of cytochrome P450 isoform responsible for metabolizing a drug molecule

(2010) Nitish K Mishra et al.   BMC Pharmacology & Toxicology

P450 Enzymes: Their Structure, Reactivity, and Selectivity—Modeled by QM/MM Calculations

(2009) Sason Shaik et al.   CHEMICAL REVIEWS

Drug Metabolism for the Perplexed Medicinal Chemist

(2009) Bernard Testa   CHEMISTRY & BIODIVERSITY

CypScore: Quantitative Prediction of Reactivity toward Cytochromes P450 Based on Semiempirical Molecular Orbital Theory

(2009) Matthias Hennemann et al.   ChemMedChem

Prodrugs: bridging pharmacodynamic/pharmacokinetic gaps

(2009) Bernard Testa   CURRENT OPINION IN CHEMICAL BIOLOGY

Metabolic bioactivation and drug-related adverse effects: current status and future directions from a pharmaceutical research perspective

(2009) Wei Tang et al.   DRUG METABOLISM REVIEWS

Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients, Geometry Optimization, and First Principles Molecular Dynamics

(2009) Ivan S. Ufimtsev et al.   Journal of Chemical Theory and Computation

The University of Minnesota Biocatalysis/Biodegradation Database: improving public access

(2009) Junfeng Gao et al.   NUCLEIC ACIDS RESEARCH

SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions

(2009) Saskia Preissner et al.   NUCLEIC ACIDS RESEARCH

Unbiased High-Throughput Screening of Reactive Metabolites on the Linear Ion Trap Mass Spectrometer Using Polarity Switch and Mass Tag Triggered Data-Dependent Acquisition

(2008) Zhengyin Yan et al.   ANALYTICAL CHEMISTRY

Recent advances in applications of liquid chromatography–tandem mass spectrometry to the analysis of reactive drug metabolites

(2008) Shuguang Ma et al.   CHEMICO-BIOLOGICAL INTERACTIONS

SyGMa: Combining Expert Knowledge and Empirical Scoring in the Prediction of Metabolites

(2008) Lars Ridder et al.   ChemMedChem

Prediction of Metabolism by Cytochrome P450 2C9: Alignment and Docking Studies of a Validated Database of Substrates

(2008) Matthew J. Sykes et al.   JOURNAL OF MEDICINAL CHEMISTRY

Flexibility of Human Cytochromes P450: Molecular Dynamics Reveals Differences between CYPs 3A4, 2C9, and 2A6, which Correlate with Their Substrate Preferences

(2008) Josef Skopalík et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Systems biology: Metabonomics

(2008) Jeremy K. Nicholson et al.   NATURE

Prodrugs: design and clinical applications

(2008) Jarkko Rautio et al.   NATURE REVIEWS DRUG DISCOVERY

IsoScore: automated localization of biotransformations by mass spectrometry using product ion scoring of virtual regioisomers

(2008) Laurent Leclercq et al.   RAPID COMMUNICATIONS IN MASS SPECTROMETRY

An evaluation of the implementation of the Cramer classification scheme in the Toxtree software

(2008) G. Patlewicz et al.   SAR AND QSAR IN ENVIRONMENTAL RESEARCH

In Silico Tools for Sharing Data and Knowledge on Toxicity and Metabolism: Derek for Windows, Meteor, and Vitic

(2008) Carol A. Marchant et al.   TOXICOLOGY MECHANISMS AND METHODS