2024
AlphaFold2 structures guide prospective ligand discovery
Lyu J, Kapolka N, Gumpper R, Alon A, Wang L, Jain M, Barros-Álvarez X, Sakamoto K, Kim Y, DiBerto J, Kim K, Glenn I, Tummino T, Huang S, Irwin J, Tarkhanova O, Moroz Y, Skiniotis G, Kruse A, Shoichet B, Roth B. AlphaFold2 structures guide prospective ligand discovery. Science 2024, 384: eadn6354. PMID: 38753765, PMCID: PMC11253030, DOI: 10.1126/science.adn6354.Peer-Reviewed Original ResearchConceptsExperimental structuresLigand discoveryStructure-based drug designAlphaFold2 structuresAlphaFold2 modelsSample conformationsResidue conformationsDrug designLarge librariesDockingLigand recognitionLigandConformationLow energyStructureHit rateMoleculesAlphaFold2 predictionsTesting hundredsCryo-electron microscopy structureAlphaFold2Cryo-electronHitsCompare resultsEnergyA survey of generative AI for de novo drug design: new frontiers in molecule and protein generation
Tang X, Dai H, Knight E, Wu F, Li Y, Li T, Gerstein M. A survey of generative AI for de novo drug design: new frontiers in molecule and protein generation. Briefings In Bioinformatics 2024, 25: bbae338. PMID: 39007594, PMCID: PMC11247410, DOI: 10.1093/bib/bbae338.Peer-Reviewed Original ResearchDesign, Synthesis, and Mechanistic Studies of (R)‑3-Amino-5,5-difluorocyclohex-1-ene-1-carboxylic Acid as an Inactivator of Human Ornithine Aminotransferase
Devitt A, Vargas A, Zhu W, Soye B, Butun F, Alt T, Kaley N, Ferreira G, Moran G, Kelleher N, Liu D, Silverman R. Design, Synthesis, and Mechanistic Studies of (R)‑3-Amino-5,5-difluorocyclohex-1-ene-1-carboxylic Acid as an Inactivator of Human Ornithine Aminotransferase. ACS Chemical Biology 2024, 19: 1066-1081. PMID: 38630468, PMCID: PMC11274680, DOI: 10.1021/acschembio.4c00022.Peer-Reviewed Original ResearchConceptsActive siteX-ray crystallographyIntact protein mass spectrometryHuman ornithine aminotransferaseNucleophilic additionRing scaffoldMass spectrometryIntermediate speciesProtein mass spectrometryIncreased selectivityTransient state kinetic studiesX-rayMechanistic studiesAdductsSolvent accessibilityKinetic studiesHepatocellular carcinomaProgression of hepatocellular carcinomaMechanism of inactivationStructural evidencePrevalence of hepatocellular carcinomaTreatment of hepatocellular carcinomaCyclohexeneCyclopenteneCrystallography
2023
Targeting the RET tyrosine kinase in neuroblastoma: A review and application of a novel selective drug design strategy
Steen E, Basilaia M, Kim W, Getz T, Gustafson J, Zage P. Targeting the RET tyrosine kinase in neuroblastoma: A review and application of a novel selective drug design strategy. Biochemical Pharmacology 2023, 216: 115751. PMID: 37595672, PMCID: PMC10911250, DOI: 10.1016/j.bcp.2023.115751.Peer-Reviewed Original ResearchConceptsRET inhibitorsRET inhibitionSolid tumorsIncreased RET expressionAssociated with poor prognosisPediatric solid tumorsNeuroblastoma tumor cellsPapillary thyroid cancerTyrosine kinaseOncogenic RET mutationsRET tyrosine kinaseProgression of multiple typesTransmembrane receptor tyrosine kinaseRET mutationsRET expressionReceptor tyrosine kinasesThyroid cancerNeuroblastoma tumorsPoor prognosisPreclinical studiesTumor cellsBreast cancerKinase inhibitorsLung adenocarcinomaClinical trialsArtificial Intelligence in Clinical Oncology: From Data to Digital Pathology and Treatment.
Senthil Kumar K, Miskovic V, Blasiak A, Sundar R, Pedrocchi A, Pearson A, Prelaj A, Ho D. Artificial Intelligence in Clinical Oncology: From Data to Digital Pathology and Treatment. American Society Of Clinical Oncology Educational Book 2023, 43: e390084. PMID: 37235822, DOI: 10.1200/edbk_390084.Peer-Reviewed Educational MaterialsConceptsDigital pathologyClinical oncology communityArtificial intelligence (AI)-based applicationsClinical oncologyDeployment of AIDomain of digital pathologyTreatment selectionOncology communityBiomarker developmentArtificial intelligenceImprove patient outcomesAI innovationRegimen optimizationModulating dosesStandard histologyPatient outcomesDesign, synthesis, and biological testing of biphenylmethyloxazole inhibitors targeting HIV-1 reverse transcriptase
Carter Z, Hollander K, Spasov K, Anderson K, Jorgensen W. Design, synthesis, and biological testing of biphenylmethyloxazole inhibitors targeting HIV-1 reverse transcriptase. Bioorganic & Medicinal Chemistry Letters 2023, 84: 129216. PMID: 36871704, PMCID: PMC10278203, DOI: 10.1016/j.bmcl.2023.129216.Peer-Reviewed Original Research
2022
Insights from incorporating quantum computing into drug design workflows
Lau B, Emani P, Chapman J, Yao L, Lam T, Merrill P, Warrell J, Gerstein M, Lam H. Insights from incorporating quantum computing into drug design workflows. Bioinformatics 2022, 39: btac789. PMID: 36477833, PMCID: PMC9825754, DOI: 10.1093/bioinformatics/btac789.Peer-Reviewed Original ResearchConceptsQuantum machine learningComputer-aided drug designMachine-learning moduleQuantum computing methodsCommercial quantum computersMachine learningJupyter notebooksNeural networkComputing methodClassical baselinesDesign workflowQML modelsQuantum hardwarePython codeAcademic useSupplementary dataQuantum computerWorkflowJudicious partitioningModuleHardwareGitHubClassical counterpartCase studyComputerMechanism-based design of agents that selectively target drug-resistant glioma
Lin K, Gueble SE, Sundaram RK, Huseman ED, Bindra RS, Herzon SB. Mechanism-based design of agents that selectively target drug-resistant glioma. Science 2022, 377: 502-511. PMID: 35901163, PMCID: PMC9502022, DOI: 10.1126/science.abn7570.Peer-Reviewed Original Research
2021
Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme
Liu C, Shi W, Becker ST, Schatz DG, Liu B, Yang Y. Structural basis of mismatch recognition by a SARS-CoV-2 proofreading enzyme. Science 2021, 373: 1142-1146. PMID: 34315827, PMCID: PMC9836006, DOI: 10.1126/science.abi9310.Peer-Reviewed Original ResearchConceptsCryo-electron microscopy structureRNA synthesisCoronavirus RNA synthesisNascent RNAMicroscopy structureVirus life cycleMismatch recognitionRNA substratesSubstrate specificityStructural basisMolecular mechanismsNonstructural proteinsMolecular determinantsProofreading enzymeReplication fidelityMismatch correctionAnalogue inhibitorsLife cycleExoribonucleaseExonsComplexesRNARational designProteinEnzymeStructure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease
Deshmukh MG, Ippolito JA, Zhang CH, Stone EA, Reilly RA, Miller SJ, Jorgensen WL, Anderson KS. Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease. Structure 2021, 29: 823-833.e5. PMID: 34161756, PMCID: PMC8218531, DOI: 10.1016/j.str.2021.06.002.Peer-Reviewed Original ResearchConceptsMain proteaseSARS-CoV-2 main proteaseActive site flexibilityDetailed structural insightsStructure-activity relationshipsInhibitor design effortsLow micromolar rangeActive site cysteineChemical scaffoldsLow nanomolar rangeCovalent adductsStructure-guided designCrystal structureStructural insightsPharmacophoreAdductsAttractive targetScaffoldsCysteineAnaloguesMechanism of actionSupRangeStructure
2020
Quantification of SV2A Binding in Rodent Brain Using [18F]SynVesT-1 and PET Imaging
Sadasivam P, Fang XT, Toyonaga T, Lee S, Xu Y, Zheng MQ, Spurrier J, Huang Y, Strittmatter SM, Carson RE, Cai Z. Quantification of SV2A Binding in Rodent Brain Using [18F]SynVesT-1 and PET Imaging. Molecular Imaging And Biology 2020, 23: 372-381. PMID: 33258040, PMCID: PMC8105262, DOI: 10.1007/s11307-020-01567-9.Peer-Reviewed Original ResearchConceptsBrain stemAlzheimer's diseaseMin postinjectionAnimal modelsAPP/PS1 miceReference regionStandardized uptake value ratioDynamic PET imaging dataUptake value ratioRodent brain tissueStatic PET scansDifferent imaging windowsPET imaging dataWild-type controlsReference tissue modelPS1 miceAD pathogenesisTherapeutic effectMouse modelRodent modelsLittermate controlsPET scansRodent brainPreclinical imaging studiesTherapeutic drug efficacyDesigned CXCR4 mimic acts as a soluble chemokine receptor that blocks atherogenic inflammation by agonist-specific targeting
Kontos C, El Bounkari O, Krammer C, Sinitski D, Hille K, Zan C, Yan G, Wang S, Gao Y, Brandhofer M, Megens RTA, Hoffmann A, Pauli J, Asare Y, Gerra S, Bourilhon P, Leng L, Eckstein HH, Kempf WE, Pelisek J, Gokce O, Maegdefessel L, Bucala R, Dichgans M, Weber C, Kapurniotu A, Bernhagen J. Designed CXCR4 mimic acts as a soluble chemokine receptor that blocks atherogenic inflammation by agonist-specific targeting. Nature Communications 2020, 11: 5981. PMID: 33239628, PMCID: PMC7689490, DOI: 10.1038/s41467-020-19764-z.Peer-Reviewed Original ResearchMeSH KeywordsAgedAnimalsAntigens, CDAtherosclerosisBinding SitesCarotid Artery, CommonChemokine CXCL12Crystallography, X-RayDisease Models, AnimalDrug DesignDrug Evaluation, PreclinicalEndarterectomy, CarotidFemaleHumansIntramolecular OxidoreductasesMacrophage Migration-Inhibitory FactorsMaleMiceMice, Knockout, ApoEMiddle AgedPeptide FragmentsReceptors, CXCR4SialyltransferasesSignal TransductionConceptsMacrophage migration inhibitory factorCXC motif chemokine receptor 4Chemokine receptorsChemokine/receptor axisCXCR4/CXCL12 interactionHuman carotid endarterectomy specimensMigration inhibitory factorChemokine receptor 4MIF/CD74Carotid endarterectomy specimensAtherogenic inflammationCXCL12 interactionReceptor axisReceptor 4MIF inhibitorsReceptor-based strategiesAtherosclerotic plaquesAtherosclerosisAtypical chemokineLeukocyte adhesionCell activityProtective pathwaysInflammationChemokinesPlaquesHydroxamate-Based Selective Macrophage Elastase (MMP-12) Inhibitors and Radiotracers for Molecular Imaging
Gona K, Toczek J, Ye Y, Sanzida N, Golbazi A, Boodagh P, Salarian M, Jung JJ, Rajendran S, Kukreja G, Wu TL, Devel L, Sadeghi MM. Hydroxamate-Based Selective Macrophage Elastase (MMP-12) Inhibitors and Radiotracers for Molecular Imaging. Journal Of Medicinal Chemistry 2020, 63: 15037-15049. PMID: 33206510, PMCID: PMC8010999, DOI: 10.1021/acs.jmedchem.0c01514.Peer-Reviewed Original ResearchConceptsAbdominal aortic aneurysmMMP-12 inhibitorsSelective MMP-12 inhibitorMurine abdominal aortic aneurysmsRadiochemical stabilityFast blood clearanceMolecular imagingAortic aneurysmAAA progressionMMP-12Blood clearanceUpregulated MMPsAortic regionElastase inhibitorLead tracerNovel familyRupture riskMacrophage elastaseInhibitorsSelectivitySpecific bindingSynthesisVivo competitionImagingDesign, Synthesis, and Characterization of Benzimidazole Derivatives as Positron Emission Tomography Imaging Ligands for Metabotropic Glutamate Receptor 2
Yuan G, Qu X, Zheng B, Neelamegam R, Afshar S, Iyengar S, Pan C, Wang J, Kang H, Ondrechen M, Poutiainen P, Fakhri G, Zhang Z, Brownell A. Design, Synthesis, and Characterization of Benzimidazole Derivatives as Positron Emission Tomography Imaging Ligands for Metabotropic Glutamate Receptor 2. Journal Of Medicinal Chemistry 2020, 63: 12060-12072. PMID: 32981322, PMCID: PMC8629109, DOI: 10.1021/acs.jmedchem.0c01394.Peer-Reviewed Original ResearchConceptsPotential positron emission tomographyBenzimidazole derivativesPositron emission tomography imaging ligandsExcellent selectivityImaging ligandsPositive allosteric modulatorsRadiochemical yieldBinding affinityMetabotropic glutamate receptor 2C]methyl iodideMolar activityLigandDerivativesRadiochemical purityGlutamate receptor 2Brain regionsAllosteric modulatorsPositron emission tomographyC]methylationRadiochemicalIodideBrain uptakeMGluR subtypesCompoundsBindingDesigned Parasite-Selective Rhomboid Inhibitors Block Invasion and Clear Blood-Stage Malaria
Gandhi S, Baker R, Cho S, Stanchev S, Strisovsky K, Urban S. Designed Parasite-Selective Rhomboid Inhibitors Block Invasion and Clear Blood-Stage Malaria. Cell Chemical Biology 2020, 27: 1410-1424.e6. PMID: 32888502, PMCID: PMC7680425, DOI: 10.1016/j.chembiol.2020.08.011.Peer-Reviewed Original ResearchConceptsRhomboid proteolysisRhomboid intramembrane proteasesAtypical substrate specificityHost cell invasionHigh-resolution structuresRhomboid proteasesIntramembrane proteasesRhomboid inhibitorsSubstrate specificityBlocks invasionRapid invasionDisease contextsSteric clashesProteolysisUltrastructural analysisProteaseInvasionPathophysiological processesPeptide boronatesBlood-stage malariaSteric exclusionParasitesMalaria culturesSequenceTargetingRational Design of Bioavailable Photosensitizers for Manipulation and Imaging of Biological Systems
Binns TC, Ayala AX, Grimm JB, Tkachuk AN, Castillon GA, Phan S, Zhang L, Brown TA, Liu Z, Adams SR, Ellisman MH, Koyama M, Lavis LD. Rational Design of Bioavailable Photosensitizers for Manipulation and Imaging of Biological Systems. Cell Chemical Biology 2020, 27: 1063-1072.e7. PMID: 32698018, PMCID: PMC7483975, DOI: 10.1016/j.chembiol.2020.07.001.Peer-Reviewed Original ResearchConceptsBiological systemsChemical toolsRational designChemical reactionsPhotosensitizerElectron microscopyChromophore-assisted light inactivationNumerous biological experimentsHigh-resolution imagingPowerful methodPhotopolymerizationReactive oxygen speciesRhodamineOxygen speciesSynthesisTargeted destructionReactionBiological experimentsBroad rangeMicroscopyCharacterizationCell ablationDiaminobenzidineDesign of Hydrazide-Bearing HDACIs Based on Panobinostat and Their p53 and FLT3-ITD Dependency in Antileukemia Activity
Li X, Jiang Y, Peterson YK, Xu T, Himes RA, Luo X, Yin G, Inks ES, Dolloff N, Halene S, Chan SSL, Chou CJ. Design of Hydrazide-Bearing HDACIs Based on Panobinostat and Their p53 and FLT3-ITD Dependency in Antileukemia Activity. Journal Of Medicinal Chemistry 2020, 63: 5501-5525. PMID: 32321249, PMCID: PMC7684764, DOI: 10.1021/acs.jmedchem.0c00442.Peer-Reviewed Original ResearchPotent BRD4 inhibitor suppresses cancer cell-macrophage interaction
Yin M, Guo Y, Hu R, Cai WL, Li Y, Pei S, Sun H, Peng C, Li J, Ye R, Yang Q, Wang N, Tao Y, Chen X, Yan Q. Potent BRD4 inhibitor suppresses cancer cell-macrophage interaction. Nature Communications 2020, 11: 1833. PMID: 32286255, PMCID: PMC7156724, DOI: 10.1038/s41467-020-15290-0.Peer-Reviewed Original ResearchMeSH KeywordsAdministration, OralAnimalsCell CommunicationCell Cycle ProteinsCell Line, TumorCell ProliferationDisease Models, AnimalDown-RegulationDrug DesignFemaleHumansHypoxia-Inducible Factor 1, alpha SubunitMacrophage Colony-Stimulating FactorMacrophagesMice, Inbred BALB CMice, NudeNeoplasmsPhosphorylationProto-Oncogene Proteins c-mycReceptors, Granulocyte-Macrophage Colony-Stimulating FactorSignal TransductionTranscription FactorsTreatment OutcomeConceptsTumor growthMajor clinical stagesBET inhibitorsProliferation of tumorsExtraterminal domain (BET) family proteinsTumor cell proliferationClinical stageTumor shrinkageSyngeneic modelPotent BRD4 inhibitorsSmall molecule inhibitorsSolid tumorsBRD4 inhibitionTumor cellsOral bioavailabilityCancer treatmentCell proliferationBRD4 inhibitorsMolecule inhibitorsMultiple mechanismsC-MycTumorsInhibitors
2019
Toward Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-Based Convolutional Encoders
Manica M, Oskooei A, Born J, Subramanian V, Sáez-Rodríguez J, Martínez M. Toward Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-Based Convolutional Encoders. Molecular Pharmaceutics 2019, 16: 4797-4806. PMID: 31618586, DOI: 10.1021/acs.molpharmaceut.9b00520.Peer-Reviewed Original ResearchConceptsConvolutional encoderReceptor tyrosine kinasesProtein-protein interaction networkAttention-based encoderStructural similarity indexSelection of encodingDrug designDrug sensitivity predictionGene expression profilesIn silico predictionSensitivity predictionAttention weightsLeukemia cell linesSMILES sequencesInformative genesGene expression profiles of tumorsApoptotic processInteraction networkExpression profiles of tumorsBaseline modelIntracellular interactionsEncodingTyrosine kinaseDevelopment of personalized therapiesGenes
2017
Neutralization of Pathogenic Fungi with Small‐Molecule Immunotherapeutics
Chirkin E, Muthusamy V, Mann P, Roemer T, Nantermet PG, Spiegel DA. Neutralization of Pathogenic Fungi with Small‐Molecule Immunotherapeutics. Angewandte Chemie International Edition 2017, 56: 13036-13040. PMID: 28793176, DOI: 10.1002/anie.201707536.Peer-Reviewed Original ResearchConceptsImportant public health concernNovel therapeutic approachesHuman immune cellsSystemic fungal infectionsPublic health concernAntibody-recruiting moleculesFungal illnessImmune cellsNew antifungal agentsTreatment strategiesTherapeutic approachesEndogenous antibodiesRelevant functional assaysFungal infectionsHealth concernFunctional assaysAntifungal agentsNon-peptidic small moleculesC. albicans cellsCandida albicansCellsBiological evaluationAlbicans cellsImmunotherapeuticsIllness
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