Predicting drug metabolism: experiment and/or computation? (Q38439385)

3 September 2017

1 reference

title

Predicting drug metabolism: experiment and/or computation? (English)

1 reference

3 September 2017

7

Robert C Glen

1 reference

3 September 2017

2

Andreas H Göller

0 references

Johannes Kirchmair

1

object named as

Johannes Kirchmair

0 references

Gisbert Schneider

8

object named as

Gisbert Schneider

1 reference

3 September 2017

5

Bernard Testa

1 reference

3 September 2017

Andreas H Göller

2

1 reference

3 September 2017

Dieter Lang

3

1 reference

3 September 2017

Jens Kunze

4

1 reference

3 September 2017

Ian D Wilson

6

1 reference

3 September 2017

language of work or name

1 reference

24 April 2015

1 reference

Nature Reviews Drug Discovery

3 September 2017

1 reference

3 September 2017

14

1 reference

3 September 2017

387-404

1 reference

3 September 2017

6

1 reference

https://scigraph.springernature.com/pub.10.1038/nrd4581

3 September 2017

0 references

cites work

Host-gut microbiota metabolic interactions

1 reference

Predicting in vivo drug interactions from in vitro drug discovery data

31 March 2020

1 reference

The role of drug metabolizing enzymes in clearance

31 March 2020

1 reference

Drug metabolism for the perplexed medicinal chemist

31 March 2020

1 reference

How do metabolites differ from their parent molecules and how are they excreted?

31 March 2020

1 reference

Reactions and enzymes in the metabolism of drugs and other xenobiotics

31 March 2020

1 reference

A critical analysis of the interplay between cytochrome P450 3A and P-glycoprotein: recent insights from knockout and transgenic mice

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

Drug metabolite profiling and identification by high-resolution mass spectrometry.

31 March 2020

1 reference

Integration of knowledge-based metabolic predictions with liquid chromatography data-dependent tandem mass spectrometry for drug metabolism studies: application to studies on the biotransformation of indinavir

31 March 2020

1 reference

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

31 March 2020

1 reference

High-throughput, computer assisted, specific MetID. A revolution for drug discovery

31 March 2020

1 reference

Enhanced metabolite identification with MS(E) and a semi-automated software for structural elucidation

31 March 2020

1 reference

Advances in metabolite identification

31 March 2020

1 reference

In silico tools for sharing data and knowledge on toxicity and metabolism: derek for windows, meteor, and vitic

31 March 2020

1 reference

SyGMa: combining expert knowledge and empirical scoring in the prediction of metabolites

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

Systems biology: Metabonomics.

31 March 2020

1 reference

The metabolomics of (+/-)-arecoline 1-oxide in the mouse and its formation by human flavin-containing monooxygenases

31 March 2020

1 reference

Isotopic enrichment enhancement in metabonomic analysis of UPLC–MS data sets

31 March 2020

1 reference

Automatic mass spectrometry method development for drug discovery: application in metabolic stability assays.

31 March 2020

1 reference

Automated high throughput ADME assays for metabolic stability and cytochrome P450 inhibition profiling of combinatorial libraries.

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

Unbiased high-throughput screening of reactive metabolites on the linear ion trap mass spectrometer using polarity switch and mass tag triggered data-dependent acquisition

31 March 2020

1 reference

Online Databases and Web Servers for Drug Metabolism Research

31 March 2020

1 reference

In silico pharmacology for drug discovery: methods for virtual ligand screening and profiling

31 March 2020

1 reference

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

31 March 2020

1 reference

The challenges involved in modeling toxicity data in silico: a review

31 March 2020

1 reference

Estimating error rates in bioactivity databases

31 March 2020

1 reference

Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms

31 March 2020

1 reference

A combined approach to drug metabolism and toxicity assessment

31 March 2020

1 reference

Algorithms for network analysis in systems-ADME/Tox using the MetaCore and MetaDrug platforms.

31 March 2020

1 reference

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

31 March 2020

1 reference

Crystal structure of human cytochrome P450 2C9 with bound warfarin

31 March 2020

1 reference

Structure-Based Methods for Predicting the Sites and Products of Metabolism

31 March 2020

1 reference

Prediction of metabolism by cytochrome P450 2C9: alignment and docking studies of a validated database of substrates

31 March 2020

1 reference

A critical assessment of docking programs and scoring functions

31 March 2020

1 reference

A computational procedure for determining energetically favorable binding sites on biologically important macromolecules

31 March 2020

1 reference

MetaSite: understanding metabolism in human cytochromes from the perspective of the chemist

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

Flexibility of human cytochromes P450: molecular dynamics reveals differences between CYPs 3A4, 2C9, and 2A6, which correlate with their substrate preferences

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

The ins and outs of cytochrome P450s.

31 March 2020

1 reference

Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force

31 March 2020

1 reference

How do substrates enter and products exit the buried active site of cytochrome P450cam? 1. Random expulsion molecular dynamics investigation of ligand access channels and mechanisms.

31 March 2020

1 reference

High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases

31 March 2020

1 reference

A new method for predicting binding affinity in computer-aided drug design

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

Emerging methods for ensemble-based virtual screening

31 March 2020

1 reference

The contribution of atom accessibility to site of metabolism models for cytochromes P450.

31 March 2020

1 reference

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

31 March 2020

1 reference

P450 enzymes: their structure, reactivity, and selectivity-modeled by QM/MM calculations

31 March 2020

1 reference

Determinants of reactivity and selectivity in soluble epoxide hydrolase from quantum mechanics/molecular mechanics modeling.

31 March 2020

1 reference

Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9,10-oxide

31 March 2020

1 reference

Molecular determinants of xenobiotic metabolism: QM/MM simulation of the conversion of 1-chloro-2,4-dinitrobenzene catalyzed by M1-1 glutathione S-transferase

31 March 2020

1 reference

Fragmentation methods: a route to accurate calculations on large systems

31 March 2020

1 reference

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

31 March 2020

1 reference

CypScore: Quantitative prediction of reactivity toward cytochromes P450 based on semiempirical molecular orbital theory

31 March 2020

1 reference

A model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules

31 March 2020

1 reference

FAst MEtabolizer (FAME): A rapid and accurate predictor of sites of metabolism in multiple species by endogenous enzymes

31 March 2020

1 reference

RS-predictor: a new tool for predicting sites of cytochrome P450-mediated metabolism applied to CYP 3A4.

31 March 2020

1 reference

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

31 March 2020

1 reference

Computational profiling of bioactive compounds using a target-dependent composite workflow.

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

Predicting drug metabolism by cytochrome P450 2C9: comparison with the 2D6 and 3A4 isoforms.

31 March 2020

1 reference

A microscale in vitro physiological model of the liver: predictive screens for drug metabolism and enzyme induction

31 March 2020

1 reference

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

31 March 2020

1 reference

Microscale culture of human liver cells for drug development.

31 March 2020

1 reference

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

31 March 2020

1 reference

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

31 March 2020

1 reference

Ion mobility spectrometry-mass spectrometry analysis for the site of aromatic hydroxylation

31 March 2020

1 reference

Soft drug design: general principles and recent applications

31 March 2020

1 reference

Prodrugs: design and clinical applications.

31 March 2020

1 reference

Prodrugs: bridging pharmacodynamic/pharmacokinetic gaps

31 March 2020

1 reference

Prodrugs--from serendipity to rational design.

31 March 2020

1 reference

Lessons learned from marketed and investigational prodrugs

31 March 2020

1 reference

Discovering drugs through biological transformation: role of pharmacologically active metabolites in drug discovery

31 March 2020

1 reference

Pharmacologically active drug metabolites: impact on drug discovery and pharmacotherapy

31 March 2020

1 reference

The biochemistry of drug metabolism--an introduction: part 1. Principles and overview.

31 March 2020

1 reference

hERG K(+) channels: structure, function, and clinical significance

31 March 2020

1 reference

Applying mechanisms of chemical toxicity to predict drug safety

31 March 2020

1 reference

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

31 March 2020

1 reference

Diet and monoamine oxidase inhibitors: a re-examination

31 March 2020

1 reference

Linezolid and serotonin syndrome

31 March 2020

1 reference

Monoamine oxidase inhibitors, opioid analgesics and serotonin toxicity

31 March 2020

1 reference

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

31 March 2020

1 reference

PocketPicker: analysis of ligand binding-sites with shape descriptors.

31 March 2020

1 reference

IDSite: An accurate approach to predict P450-mediated drug metabolism

31 March 2020

1 reference

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

31 March 2020

1 reference

The SMARTCyp cytochrome P450 metabolism prediction server

31 March 2020

1 reference

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

31 March 2020

1 reference

META. 1. A program for the evaluation of metabolic transformation of chemicals.

31 March 2020

1 reference

A systematic approach to simulating metabolism in computational toxicology. I. The TIMES heuristic modelling framework

31 March 2020

1 reference

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

31 March 2020

1 reference

Ligand-based models for the isoform specificity of cytochrome P450 3A4, 2D6, and 2C9 substrates.

31 March 2020

1 reference

Prediction of cytochrome P450 isoform responsible for metabolizing a drug molecule

31 March 2020

1 reference

WhichCyp: prediction of cytochromes P450 inhibition

31 March 2020

1 reference

VirtualToxLab - a platform for estimating the toxic potential of drugs, chemicals and natural products.

31 March 2020

1 reference

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

31 March 2020

1 reference

Development of a computational tool to rival experts in the prediction of sites of metabolism of xenobiotics by p450s

31 March 2020

1 reference

BindingDB: a web-accessible database of experimentally determined protein-ligand binding affinities

31 March 2020

1 reference

ChEMBL: a large-scale bioactivity database for drug discovery

31 March 2020

1 reference

DrugBank: a comprehensive resource for in silico drug discovery and exploration

31 March 2020

1 reference

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

31 March 2020

1 reference

HMDB: the Human Metabolome Database

31 March 2020

1 reference

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

31 March 2020

1 reference

A useful tool for drug interaction evaluation: the University of Washington Metabolism and Transport Drug Interaction Database

31 March 2020

1 reference

METLIN: a metabolite mass spectral database

31 March 2020

1 reference

PharmGKB: the Pharmacogenetics Knowledge Base

31 March 2020

1 reference

ADMET evaluation in drug discovery. 11. PharmacoKinetics Knowledge Base (PKKB): a comprehensive database of pharmacokinetic and toxic properties for drugs.

31 March 2020

1 reference

31 March 2020

The Protein Data Bank

1 reference

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

31 March 2020

1 reference

The signature molecular descriptor. 1. Using extended valence sequences in QSAR and QSPR studies

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25907346

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Lactonization is the critical first step in the disposition of the 3-hydroxy-3-methylglutaryl-CoA reductase inhibitor atorvastatin.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25907346

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

1 reference

https://pubmed.ncbi.nlm.nih.gov/25907346

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NRD4581

1 reference

3 September 2017

1 reference