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Structure-Based CoMFA As a Predictive Model - CYP2C9 Inhibitors As a Test Case

https://doi.org/10.1021/ci800313h
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Outgoing claims: the papers this work cites, builds on, or argues with.

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The Probability of Chance Correlation Using Partial Least Squares (PLS)
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Arginines 97 and 108 in CYP2C9 Are Important Determinants of the Catalytic Function
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Knowledge-based scoring function to predict protein-ligand interactions
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The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
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SCORE: A New Empirical Method for Estimating the Binding Affinity of a Protein-Ligand Complex
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AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
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Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
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Comparative molecular field analysis (CoMFA). 2. Toward its use with 3D-structural databases
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Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming
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Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors
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A survey of active site access channels in cytochromes P450
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Automatic atom type and bond type perception in molecular mechanical calculations
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Molecular insight into pseudolysin inhibition using the MM-PBSA and LIE methods
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Inhibitory Effects of Azelastine and Its Metabolites on Drug Oxidation Catalyzed by Human Cytochrome P-450 Enzymes
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Three-dimensional quantitative structure-activity relationship for inhibitors of cytochrome P4502C9.
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Consensus scoring for ligand/protein interactions
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Inversion of receptor binding preferences by mutagenesis: Free energy thermodynamic integration studies on sugar binding to L-arabinose binding proteins
inferredcites →https://doi.org/10.1021/bi049651oopenalex-snapshot
Quantitative Binding Models for CYP2C9 Based on Benzbromarone Analogues
inferredcites →https://doi.org/10.1021/ci050283kopenalex-snapshot
Comparison of Consensus Scoring Strategies for Evaluating Computational Models of Protein−Ligand Complexes
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High-Throughput Calculation of Protein−Ligand Binding Affinities: Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid Computing
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MedusaScore: An Accurate Force Field-Based Scoring Function for Virtual Drug Screening
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Free energy calculations: Applications to chemical and biochemical phenomena
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Structural and Dynamical Basis of Broad Substrate Specificity, Catalytic Mechanism, and Inhibition of Cytochrome P450 3A4
inferredcites →https://doi.org/10.1021/jm000048nopenalex-snapshot
A Refined 3-Dimensional QSAR of Cytochrome P450 2C9: Computational Predictions of Drug Interactions
inferredcites →https://doi.org/10.1021/jm000241hopenalex-snapshot
Binding of a Diverse Set of Ligands to Avidin and Streptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models
inferredcites →https://doi.org/10.1021/jm00050a010openalex-snapshot
Molecular Similarity Indices in a Comparative Analysis (CoMSIA) of Drug Molecules to Correlate and Predict Their Biological Activity
inferredcites →https://doi.org/10.1021/jm049081qopenalex-snapshot
Validation and Use of the MM-PBSA Approach for Drug Discovery
inferredcites →https://doi.org/10.1021/jm050306mopenalex-snapshot
Evaluating the Molecular Mechanics Poisson−Boltzmann Surface Area Free Energy Method Using a Congeneric Series of Ligands to p38 MAP Kinase
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A Multistep Approach to Structure-Based Drug Design: Studying Ligand Binding at the Human Neutrophil Elastase
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Insight through Molecular Mechanics Poisson−Boltzmann Surface Area Calculations into the Binding Affinity of Triclosan and Three Analogues for FabI, the E. coli Enoyl Reductase
inferredcites →https://doi.org/10.1021/jm060522aopenalex-snapshot
Accurate Prediction of the Relative Potencies of Members of a Series of Kinase Inhibitors Using Molecular Docking and MM-GBSA Scoring
inferredcites →https://doi.org/10.1021/jm0608210openalex-snapshot
Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field
inferredcites →https://doi.org/10.1021/jm980536jopenalex-snapshot
A General and Fast Scoring Function for Protein−Ligand Interactions: A Simplified Potential Approach
inferredcites →https://doi.org/10.1021/jm990352kopenalex-snapshot
Consensus Scoring: A Method for Obtaining Improved Hit Rates from Docking Databases of Three-Dimensional Structures into Proteins
inferredcites →https://doi.org/10.1023/a:1007996124545openalex-snapshot
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
inferredcites →https://doi.org/10.1023/a:1011115820450openalex-snapshot
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
inferredcites →https://doi.org/10.1023/a:1016357811882openalex-snapshot
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
inferredcites →https://doi.org/10.1038/300341a0openalex-snapshot
The hydrophobic interaction is long range, decaying exponentially with distance
inferredcites →https://doi.org/10.1038/nature01862openalex-snapshot
Crystal structure of human cytochrome P450 2C9 with bound warfarin
inferredcites →https://doi.org/10.1038/sj.bjp.0701633openalex-snapshot
Ipriflavone as an inhibitor of human cytochrome P450 enzymes
inferredcites →https://doi.org/10.1046/j.1365-2125.1998.00721.xopenalex-snapshot
Cytochrome P4502C9: an enzyme of major importance in human drug metabolism
inferredcites →https://doi.org/10.1063/1.439486openalex-snapshot
Molecular dynamics simulations at constant pressure and/or temperature
inferredcites →https://doi.org/10.1063/1.445869openalex-snapshot
Comparison of simple potential functions for simulating liquid water
inferredcites →https://doi.org/10.1063/1.448118openalex-snapshot
Molecular dynamics with coupling to an external bath
inferredcites →https://doi.org/10.1063/1.464397openalex-snapshot
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
inferredcites →https://doi.org/10.1063/1.470043openalex-snapshot
Accuracy and efficiency of the particle mesh Ewald method
inferredcites →https://doi.org/10.1074/jbc.m401413200openalex-snapshot
Glycogen Synthase Kinase-3β Regulates Growth, Calcium Homeostasis, and Diastolic Function in the Heart
inferredcites →https://doi.org/10.1074/jbc.m405427200openalex-snapshot
The Structure of Human Cytochrome P450 2C9 Complexed with Flurbiprofen at 2.0-Å Resolution
inferredcites →https://doi.org/10.1107/s0021889883010985openalex-snapshot
Analytical molecular surface calculation
inferredcites →https://doi.org/10.1124/dmd.31.9.1090openalex-snapshot
INHIBITORY EFFECT OF GLYBURIDE ON HUMAN CYTOCHROME P450 ISOFORMS IN HUMAN LIVER MICROSOMES
inferredcites →https://doi.org/10.1124/mol.65.4.842openalex-snapshot
Differential Roles of Arg97, Asp293, and Arg108 in Enzyme Stability and Substrate Specificity of CYP2C9
inferredcites →https://doi.org/10.1248/bpb.31.1552openalex-snapshot
Determination of Ligand-Binding Sites on Proteins Using Long-Range Hydrophobic Potential
inferredcites →https://doi.org/10.3109/03602539709037596openalex-snapshot
Modeling the Active Sites of Cytochrome P450s and GlutathioneS-Transferases, two of the Most Important Biotransformation Enzymes

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Quantitative Structure–Activity Relationship (QSAR) Methods for the Prediction of Substrates, Inhibitors, and Inducers of Metabolic Enzymes
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Challenges and advances in computational docking: 2009 in review
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Three-Dimensional Quantitative Structure–Activity Relationship Analysis for Human Pregnane X Receptor for the Prediction of CYP3A4 Induction in Human Hepatocytes: Structure-Based Comparative Molecular Field Analysis
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Molecular Modeling and Drug Design Techniques in Microbial Drug Discovery
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Exploration of the binding of proton pump inhibitors to human P450 2C9 based on docking and molecular dynamics simulation
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Exploration of the binding of curcumin analogues to human P450 2C9 based on docking and molecular dynamics simulation
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Warfarin: history, tautomerism and activity
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Molecular dynamics directed CoMFA studies on carbocyclic neuraminidase inhibitors
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Impact of chemoinformatics approaches and tools on current chemical research
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Precise prediction of activators for the human constitutive androstane receptor using structure-based three-dimensional quantitative structure–activity relationship methods
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Computational prediction of cytochrome P450 inhibition and induction
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Structure-based ligand design to overcome CYP inhibition in drug discovery projects
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Predicting the structures of complexes between phosphoinositide 3-kinase (PI3K) and romidepsin-related compounds for the drug design of PI3K/histone deacetylase dual inhibitors using computational docking and the ligand-based drug design approach
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Minimizing CYP2C9 Inhibition of Exposed-Pyridine NAMPT (Nicotinamide Phosphoribosyltransferase) Inhibitors
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In Silico Toxicology in Drug Discovery — Concepts Based on Three-dimensional Models
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Three-dimensional Quantitative Structure–Activity Relationship Analysis of Inhibitors of Human and Rat Cytochrome P4503A Enzymes
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Quinic acid from Annona muricata Fruit Inhibits Cyclophosphamide Metabolism through Modulation of Cytochrome P450: Implications for Herbal-Drug Interaction
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