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

https://doi.org/10.1021/ml100016x
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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CypScore: Quantitative Prediction of Reactivity toward Cytochromes P450 Based on Semiempirical Molecular Orbital Theory
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Fast Prediction of Cytochrome P450 Mediated Drug Metabolism
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Computational approaches for predicting CYP-related metabolism properties in the screening of new drugs
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The Chemistry Development Kit (CDK): An Open-Source Java Library for Chemo- and Bioinformatics
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Regioselectivity Prediction of CYP1A2-Mediated Phase I Metabolism
inferredcites →https://doi.org/10.1021/ct800101vopenalex-snapshot
Sulfoxide, Sulfur, and Nitrogen Oxidation and Dealkylation by Cytochrome P450
inferredcites →https://doi.org/10.1021/jm020400sopenalex-snapshot
A Model for Predicting Likely Sites of CYP3A4-mediated Metabolism on Drug-like Molecules
inferredcites →https://doi.org/10.1021/jm060551lopenalex-snapshot
Prediction of Activation Energies for Hydrogen Abstraction by Cytochrome P450
inferredcites →https://doi.org/10.1021/jm0613471openalex-snapshot
Empirical Regioselectivity Models for Human Cytochromes P450 3A4, 2D6, and 2C9
inferredcites →https://doi.org/10.1021/jp803854vopenalex-snapshot
Prediction of Activation Energies for Aromatic Oxidation by Cytochrome P450
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Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules
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Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions
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Contracted Gaussian basis sets for molecular calculations. I. Second row atoms, Z=11–18
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Self-consistent molecular orbital methods. XXIII. A polarization-type basis set for second-row elements
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Fully optimized contracted Gaussian basis sets for atoms Li to Kr
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Density-functional thermochemistry. III. The role of exact exchange
inferredcites →https://doi.org/10.1073/pnas.0603236103openalex-snapshot
Structural basis for ligand promiscuity in cytochrome P450 3A4
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State-of-the-art Tools for Computational Site of Metabolism Predictions: Comparative Analysis, Mechanistical Insights, and Future Applications
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Cytochromes P450: A Structure-Based Summary of Biotransformations Using Representative Substrates
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Abstracts
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Summary of information on human CYP enzymes: human P450 metabolism data
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Density-functional exchange-energy approximation with correct asymptotic behavior
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Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
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Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450
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Recent Developments of the Chemistry Development Kit (CDK) - An Open-Source Java Library for Chemo- and Bioinformatics

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Synergy between Experiments and Computations: A Green Channel for Revealing Metabolic Mechanism of Xenobiotics in Chemical Toxicology
inferred← citeshttps://doi.org/10.1021/acs.chemrev.8b00728openalex-snapshot
Concepts of Artificial Intelligence for Computer-Assisted Drug Discovery
inferred← citeshttps://doi.org/10.1021/acs.est.8b04643openalex-snapshot
Metabolic Susceptibility of 2-Chlorothioxanthone and Its Toxic Effects on mRNA and Protein Expression and Activities of Human CYP1A2 and CYP3A4 Enzymes
inferred← citeshttps://doi.org/10.1021/acs.jafc.4c06411openalex-snapshot
Bioaccessibility of Cafestol from Coffee Brew: A Metabolic Study Employing an In Vitro Digestion Model and LC-HRMS
inferred← citeshttps://doi.org/10.1021/acs.jafc.5c15585openalex-snapshot
Shielding Metabolic Hotspots in the Triketone–Quinoline Scaffold Yields Potent 4-Hydroxyphenylpyruvate Dioxygenase Inhibitors
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00360openalex-snapshot
Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c00361openalex-snapshot
XenoNet: Inference and Likelihood of Intermediate Metabolite Formation
inferred← citeshttps://doi.org/10.1021/acs.jcim.0c01091openalex-snapshot
Deciphering Reaction Determinants of Altered-Activity CYP2D6 Variants by Well-Tempered Metadynamics Simulation and QM/MM Calculations
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c00549openalex-snapshot
Prediction of Sites of Metabolism of CYP3A4 Substrates Utilizing Docking-Derived Geometric Features
inferred← citeshttps://doi.org/10.1021/acs.jcim.3c01588openalex-snapshot
Active Learning Approach for Guiding Site-of-Metabolism Measurement and Annotation
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c00115openalex-snapshot
DeepP450: Predicting Human P450 Activities of Small Molecules by Integrating Pretrained Protein Language Model and Molecular Representation
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c01632openalex-snapshot
Improved and Interpretable Prediction of Cytochrome P450-Mediated Metabolism by Molecule-Level Graph Modeling and Subgraph Information Bottlenecks
inferred← citeshttps://doi.org/10.1021/acs.jcim.4c02051openalex-snapshot
GLMCyp: A Deep Learning-Based Method for CYP450-Mediated Reaction Site Prediction
inferred← citeshttps://doi.org/10.1021/acs.jcim.5c00819openalex-snapshot
Automated Annotation of Sites of Metabolism from Biotransformation Data
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00233openalex-snapshot
Predicting Regioselectivity and Lability of Cytochrome P450 Metabolism Using Quantum Mechanical Simulations
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00351openalex-snapshot
Synergies Between Quantum Mechanics and Machine Learning in Reaction Prediction
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00662openalex-snapshot
MetaTox: Web Application for Predicting Structure and Toxicity of Xenobiotics’ Metabolites
inferred← citeshttps://doi.org/10.1021/acs.jcim.6b00759openalex-snapshot
Mechanism of Cytochrome P450 17A1-Catalyzed Hydroxylase and Lyase Reactions
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c01181openalex-snapshot
CypGEM: A Geometry-Aware and Edge-Enhanced Graph Transformer Model for Predicting Sites of Metabolism Mediated by Cytochromes P450
inferred← citeshttps://doi.org/10.1021/acs.jcim.6c01507openalex-snapshot
CYPMol: A Single Model Framework Integrating Functional Residues with Protein Features and Molecule Embeddings to Predict CYP Substrates, Inhibitors, and Metabolism Sites
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00165openalex-snapshot
Alignment-Based Prediction of Sites of Metabolism
inferred← citeshttps://doi.org/10.1021/acs.jcim.7b00250openalex-snapshot
FAME 2: Simple and Effective Machine Learning Model of Cytochrome P450 Regioselectivity
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00249openalex-snapshot
Comparing Molecular Patterns Using the Example of SMARTS: Applications and Filter Collection Analysis
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00250openalex-snapshot
Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00376openalex-snapshot
FAME 3: Predicting the Sites of Metabolism in Synthetic Compounds and Natural Products for Phase 1 and Phase 2 Metabolic Enzymes
inferred← citeshttps://doi.org/10.1021/acs.jcim.9b00836openalex-snapshot
The Metabolic Rainbow: Deep Learning Phase I Metabolism in Five Colors
inferred← citeshttps://doi.org/10.1021/acs.jctc.3c00710openalex-snapshot
Transferable Machine Learning Interatomic Potential for Bond Dissociation Energy Prediction of Drug-like Molecules
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.0c01174openalex-snapshot
A Chemical Probe for Dark Kinase STK17B Derives Its Potency and High Selectivity through a Unique P-Loop Conformation
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.1c01250openalex-snapshot
Optimization of TopoIV Potency, ADMET Properties, and hERG Inhibition of 5-Amino-1,3-dioxane-Linked Novel Bacterial Topoisomerase Inhibitors: Identification of a Lead with In Vivo Efficacy against MRSA
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.1c02004openalex-snapshot
Synthesis and Characterization of 5-(2-Fluoro-4-[ 11 C]methoxyphenyl)-2,2-dimethyl-3,4-dihydro-2 H -pyrano[2,3- b ]pyridine-7-carboxamide as a PET Imaging Ligand for Metabotropic Glutamate Receptor 2
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.4c02531openalex-snapshot
Development of a Second-Generation, In Vivo Chemical Probe for PIKfyve
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5c00762openalex-snapshot
Structure-Guided Optimization of 2-Aminoquinazoline Hematopoietic Progenitor Kinase 1 Inhibitors for Improved Oral Bioavailability and Synergistic Antitumor Immunity
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5c01192openalex-snapshot
SAR-Guided Development of Small-Molecule SERCA2a Activators: Discovery of Potent Indoline, Benzofuran, and Benzodioxole Analogs for Cardiovascular Applications
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.5c03051openalex-snapshot
From Discovery to Clinical Trial: YCT-529, an Oral NonHormonal Male Contraceptive Targeting the Retinoic Acid Receptor Alpha
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.6c00706openalex-snapshot
( S , S )-5-Chloro-3-((3,5-dimethylphenyl)sulfonyl)- N -(1-oxo-1-((1-(pyridin-4-yl)ethyl)amino)propan-2-yl)-1 H -indole-2-carboxamide, a New Dishevelled 1 and P-Glycoprotein Dual Inhibitor as a Anticancer Agent
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.7b01862openalex-snapshot
Design, Synthesis, and Biological Evaluation of 4-Quinoline Carboxylic Acids as Inhibitors of Dihydroorotate Dehydrogenase
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.8b01774openalex-snapshot
Identification of the Metabolic Profile of the α-Tubulin-Binding Natural Product (−)–Pironetin
inferred← citeshttps://doi.org/10.1021/acs.jmedchem.9b00510openalex-snapshot
Discovery and Development of a Series of Pyrazolo[3,4-d]pyridazinone Compounds as the Novel Covalent Fibroblast Growth Factor Receptor Inhibitors by the Rational Drug Design
inferred← citeshttps://doi.org/10.1021/acs.jpca.0c06231openalex-snapshot
Site-Level Bioactivity of Small-Molecules from Deep-Learned Representations of Quantum Chemistry
inferred← citeshttps://doi.org/10.1021/acs.molpharmaceut.5c00738openalex-snapshot
Metabolite Identification Data in Drug Discovery, Part 1: Data Generation and Trend Analysis
inferred← citeshttps://doi.org/10.1021/acs.molpharmaceut.5c00740openalex-snapshot
Metabolite Identification Data in Drug Discovery, Part 2: Site-of-Metabolism Annotation, Analysis, and Exploration for Machine Learning
inferred← citeshttps://doi.org/10.1021/acscatal.2c01741openalex-snapshot
Mechanistic Inference from Statistical Models at Different Data-Size Regimes
inferred← citeshttps://doi.org/10.1021/acscentsci.5b00131openalex-snapshot
Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning Network
inferred← citeshttps://doi.org/10.1021/acscentsci.6b00162openalex-snapshot
Modeling Reactivity to Biological Macromolecules with a Deep Multitask Network
inferred← citeshttps://doi.org/10.1021/acschemneuro.0c00448openalex-snapshot
Further Studies on Triazinoindoles as Potential Novel Multitarget-Directed Anti-Alzheimer’s Agents
inferred← citeshttps://doi.org/10.1021/acschemneuro.1c00297openalex-snapshot
Novel Positron Emission Tomography Radiotracers for Imaging Mitochondrial Complex I
inferred← citeshttps://doi.org/10.1021/acschemneuro.7b00098openalex-snapshot
Synthesis and Preliminary Studies of a Novel Negative Allosteric Modulator, 7-((2,5-Dioxopyrrolidin-1-yl)methyl)-4-(2-fluoro-4-[11C]methoxyphenyl) quinoline-2-carboxamide, for Imaging of Metabotropic Glutamate Receptor 2
inferred← citeshttps://doi.org/10.1021/acsinfecdis.2c00537openalex-snapshot
Synthesis and Testing of Analogs of the Tuberculosis Drug Candidate SQ109 against Bacteria and Protozoa: Identification of Lead Compounds against Mycobacterium abscessus and Malaria Parasites
inferred← citeshttps://doi.org/10.1021/acsmedchemlett.4c00290openalex-snapshot
Machine Learning ADME Models in Practice: Four Guidelines from a Successful Lead Optimization Case Study
inferred← citeshttps://doi.org/10.1021/acsomega.3c05377openalex-snapshot
Optimization of 3-Cyano-7-cyclopropylamino-pyrazolo[1,5- a ]pyrimidines toward the Development of an In Vivo Chemical Probe for CSNK2A
inferred← citeshttps://doi.org/10.1021/acsptsci.5c00780openalex-snapshot
Structure-Activity Relationship Studies Enable Optimization of a Small-Molecule Autophagy Activator and Evaluation of Effects on Cell Death Pathways
inferred← citeshttps://doi.org/10.1021/bk-2016-1222.ch014openalex-snapshot
Steps Toward a Virtual Rat: Predictive Absorption, Distribution, Metabolism, and Toxicity Models
inferred← citeshttps://doi.org/10.1021/ci2000488openalex-snapshot
RS-Predictor: A New Tool for Predicting Sites of Cytochrome P450-Mediated Metabolism Applied to CYP 3A4
inferred← citeshttps://doi.org/10.1021/ci200542mopenalex-snapshot
Computational Prediction of Metabolism: Sites, Products, SAR, P450 Enzyme Dynamics, and Mechanisms
inferred← citeshttps://doi.org/10.1021/ci300009zopenalex-snapshot
RS-Predictor Models Augmented with SMARTCyp Reactivities: Robust Metabolic Regioselectivity Predictions for Nine CYP Isozymes
inferred← citeshttps://doi.org/10.1021/ci3001524openalex-snapshot
2D SMARTCyp Reactivity-Based Site of Metabolism Prediction for Major Drug-Metabolizing Cytochrome P450 Enzymes
inferred← citeshttps://doi.org/10.1021/ci3003073openalex-snapshot
Development of a Computational Tool to Rival Experts in the Prediction of Sites of Metabolism of Xenobiotics by P450s
inferred← citeshttps://doi.org/10.1021/ci400050vopenalex-snapshot
Pragmatic Approaches to Using Computational Methods To Predict Xenobiotic Metabolism
inferred← citeshttps://doi.org/10.1021/ci400058sopenalex-snapshot
Prediction of Cytochrome P450 Xenobiotic Metabolism: Tethered Docking and Reactivity Derived from Ligand Molecular Orbital Analysis
inferred← citeshttps://doi.org/10.1021/ci4004688openalex-snapshot
DR-Predictor: Incorporating Flexible Docking with Specialized Electronic Reactivity and Machine Learning Techniques to Predict CYP-Mediated Sites of Metabolism
inferred← citeshttps://doi.org/10.1021/ci400472jopenalex-snapshot
Metabolism Site Prediction Based on Xenobiotic Structural Formulas and PASS Prediction Algorithm
inferred← citeshttps://doi.org/10.1021/ci400503sopenalex-snapshot
FAst MEtabolizer (FAME): A Rapid and Accurate Predictor of Sites of Metabolism in Multiple Species by Endogenous Enzymes
inferred← citeshttps://doi.org/10.1021/ci400518gopenalex-snapshot
XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks
inferred← citeshttps://doi.org/10.1021/ci5005652openalex-snapshot
Improved Prediction of CYP-Mediated Metabolism with Chemical Fingerprints
inferred← citeshttps://doi.org/10.1021/ct200462qopenalex-snapshot
IDSite: An Accurate Approach to Predict P450-Mediated Drug Metabolism
inferred← citeshttps://doi.org/10.1021/jm2006468openalex-snapshot
Structure-Based Site of Metabolism Prediction for Cytochrome P450 2D6
inferred← citeshttps://doi.org/10.1021/jm300323topenalex-snapshot
Water-Soluble Pyrazolo[4,3-e][1,2,4]triazolo[1,5-c]pyrimidines as Human A3Adenosine Receptor Antagonists
inferred← citeshttps://doi.org/10.1021/jm500700yopenalex-snapshot
Development of [18F]-Labeled Pyrazolo[4,3-e]-1,2,4- triazolo[1,5-c]pyrimidine (SCH442416) Analogs for the Imaging of Cerebral Adenosine A2AReceptors with Positron Emission Tomography
inferred← citeshttps://doi.org/10.1021/ml200246fopenalex-snapshot
Ligand-Based Site of Metabolism Prediction for Cytochrome P450 2D6
inferred← citeshttps://doi.org/10.1021/mp3005116openalex-snapshot
The Contribution of Atom Accessibility to Site of Metabolism Models for Cytochromes P450
inferred← citeshttps://doi.org/10.1021/tx5001943openalex-snapshot
Advances in the Electrochemical Simulation of Oxidation Reactions Mediated by Cytochrome P450
inferred← citeshttps://doi.org/10.1021/tx500371aopenalex-snapshot
Mechanism of the N-Hydroxylation of Primary and Secondary Amines by Cytochrome P450
inferred← citeshttps://doi.org/10.1021/tx5004062openalex-snapshot
Cooperative Binding of Aflatoxin B1 by Cytochrome P450 3A4: A Computational Study
inferred← citeshttps://doi.org/10.1038/nrd4581openalex-snapshot
Predicting drug metabolism: experiment and/or computation?
inferred← citeshttps://doi.org/10.1038/s41467-020-16201-zopenalex-snapshot
Prediction of organic homolytic bond dissociation enthalpies at near chemical accuracy with sub-second computational cost
inferred← citeshttps://doi.org/10.1038/s41570-021-00260-xopenalex-snapshot
Organic reactivity from mechanism to machine learning
inferred← citeshttps://doi.org/10.1038/s41598-017-12082-3openalex-snapshot
Pharmacological use of a novel scaffold, anomeric N,N-diarylamino tetrahydropyran: molecular similarity search, chemocentric target profiling, and experimental evidence
inferred← citeshttps://doi.org/10.1039/9781782622376-00001openalex-snapshot
How Physicochemical Properties of Drugs Affect Their Metabolism and Clearance
inferred← citeshttps://doi.org/10.1039/9781782622376-00066openalex-snapshot
Cytochrome P450 Mediated Drug Metabolism
inferred← citeshttps://doi.org/10.1039/9781782622659-00185openalex-snapshot
The Need for a Green Electronic Lab Notebook
inferred← citeshttps://doi.org/10.1039/9781837070206-00583openalex-snapshot
e-Resources Relevant to Machine Learning Tools for Medicinal Chemistry
inferred← citeshttps://doi.org/10.1039/c1md00087jopenalex-snapshot
Identification of CYP1A2 ligands by structure-based and ligand-based virtual screening
inferred← citeshttps://doi.org/10.1039/c5mb00118hopenalex-snapshot
Predicting the binding modes and sites of metabolism of xenobiotics
inferred← citeshttps://doi.org/10.1039/c5mb00784dopenalex-snapshot
Effects of protein flexibility and active site water molecules on the prediction of sites of metabolism for cytochrome P450 2C19 substrates
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