2024
Estimating Position-Dependent and Anisotropic Diffusivity Tensors from Molecular Dynamics Trajectories: Existing Methods and Future Outlook
Domingues T, Coifman R, Haji-Akbari A. Estimating Position-Dependent and Anisotropic Diffusivity Tensors from Molecular Dynamics Trajectories: Existing Methods and Future Outlook. Journal Of Chemical Theory And Computation 2024, 20: 4427-4455. PMID: 38815171, DOI: 10.1021/acs.jctc.4c00148.Peer-Reviewed Original ResearchKernel-based methodsMolecular dynamicsMolecular dynamics trajectoriesAnisotropic diffusion tensorPhysicochemical properties of materialsClosed-form analytical solutionMD trajectoriesMobility statisticsComputational chemistryHeuristic extensionMD simulationsProperties of materialsAlgorithmDynamics trajectoriesDiffusion tensorEstimated diffusivityVariable spaceMaterial propertiesDiscretization techniqueNatural extensionPosition-dependentFokker-Planck equationSpatial binsAnalytical solutionTracer particlesTransacylation and hydrolysis of the acyl glucuronides of ibuprofen and its α-methyl-substituted analogues investigated by 1H NMR spectroscopy and computational chemistry: Implications for drug design
Richards S, Bradshaw P, Johnson C, Stachulski A, Athersuch T, Nicholson J, Lindon J, Wilson I. Transacylation and hydrolysis of the acyl glucuronides of ibuprofen and its α-methyl-substituted analogues investigated by 1H NMR spectroscopy and computational chemistry: Implications for drug design. Journal Of Pharmaceutical And Biomedical Analysis 2024, 246: 116238. PMID: 38805849, DOI: 10.1016/j.jpba.2024.116238.Peer-Reviewed Original ResearchAcyl migrationDensity functional theoryAcyl glucuronideBuffered aqueous solutionIndividual rate constantsNMR spectroscopyTransition stateComputational chemistryFunctional theoryPositional isomersHPLC-MS studiesDimethyl analoguesRate constantsDrug metabolitesHydrolysis reactionAqueous solutionDrug designActivation energySpontaneous acyl migrationAnomerisationHuman plasmaHPLC-MSTransacylation reactionAcylTransacylation
2021
PaccMannRL: De novo generation of hit-like anticancer molecules from transcriptomic data via reinforcement learning
Born J, Manica M, Oskooei A, Cadow J, Markert G, Martínez M. PaccMannRL: De novo generation of hit-like anticancer molecules from transcriptomic data via reinforcement learning. IScience 2021, 24: 102269. PMID: 33851095, PMCID: PMC8022157, DOI: 10.1016/j.isci.2021.102269.Peer-Reviewed Original ResearchDrug designSimilarity to compoundsReinforcement learning methodDeep generative modelsDeep learning approachMolecular designStructurally similar to compoundsDrug-likenessComputational chemistryBridging systems biologyMolecule generationReinforcement learningReward functionLearning methodsGenerative modelLearning approachCompoundsAnticancer moleculesChemical propertiesMoleculesIncorporating informationCandidate drugsSynthesizabilityAnticancer drugsPrediction modelPotent Noncovalent Inhibitors of the Main Protease of SARS-CoV‑2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations
Zhang CH, Stone EA, Deshmukh M, Ippolito JA, Ghahremanpour MM, Tirado-Rives J, Spasov KA, Zhang S, Takeo Y, Kudalkar SN, Liang Z, Isaacs F, Lindenbach B, Miller SJ, Anderson KS, Jorgensen WL. Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV‑2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations. ACS Central Science 2021, 7: 467-475. PMID: 33786375, PMCID: PMC7931627, DOI: 10.1021/acscentsci.1c00039.Peer-Reviewed Original ResearchFree energy perturbation calculationsX-ray crystal structurePotent noncovalent inhibitorMain proteaseHigh-resolution X-ray crystal structuresCell-based antiviral assaysComputational chemistryLigand complexesNoncovalent inhibitorsCrystal structureNonpeptidic inhibitorsLead optimizationDrug discoveryPerturbation calculationsNM ICPotent analoguesKinetic assaysPossible therapeutic significanceNoncovalentChemistryAnaloguesValuable guidanceCalculationsCompoundsComplexes
2013
The Roles of Counterion and Water in a Stereoselective Cysteine‐Catalyzed Rauhut–Currier Reaction: A Challenge for Computational Chemistry
Osuna S, Dermenci A, Miller SJ, Houk KN. The Roles of Counterion and Water in a Stereoselective Cysteine‐Catalyzed Rauhut–Currier Reaction: A Challenge for Computational Chemistry. Chemistry - A European Journal 2013, 19: 14245-14253. PMID: 24038400, PMCID: PMC3918516, DOI: 10.1002/chem.201300745.Peer-Reviewed Original ResearchConceptsRauhut-Currier reactionCysteine derivativesComplete reaction pathwayRole of counterionsPresence of counterionsRate-determining eliminationMichael addition productsDensity functional theoryComputational chemistryExplicit water solvationWater solvationPotassium counterionsReaction conditionsReaction pathwaysAddition productsEnantiomer pairsThiol catalystCatalyst eliminationPossible stereoisomersCurrier ReactionFunctional theoryCounterionsNucleophilesReactionDerivatives
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