2025
Super‐resolution imaging of proteins inside live mammalian cells with mLIVE‐PAINT
Bhaskar H, Gidden Z, Virdi G, Kleinjan D, Rosser S, Gandhi S, Regan L, Horrocks M. Super‐resolution imaging of proteins inside live mammalian cells with mLIVE‐PAINT. Protein Science 2025, 34: e70008. PMID: 39865341, PMCID: PMC11761688, DOI: 10.1002/pro.70008.Peer-Reviewed Original Research
2024
Drug Development for Hematological Cancer Targets Using Asclepius
Crucitti D, Pérez Míguez C, Piñeiro Fiel M, Diaz Arias J, Gómez Fernández J, Mosquera Orgueira A, Zeidan A. Drug Development for Hematological Cancer Targets Using Asclepius. Blood 2024, 144: 7464-7464. DOI: 10.1182/blood-2024-198610.Peer-Reviewed Original ResearchStructure-based drug design approachBinding energy evaluationComputational chemistry calculationsBiological targetsDrug design approachMolecular dynamics simulationsFree energy techniquesSynthetic stepsChemistry calculationsSynthetic accessibilityADMET profileSynthetic costArray of moleculesMolecular dockingDynamics simulationsDrug designNovel inhibitorsDrug discoveryADMETMoleculesStructural conformationIdentified inhibitorsProtein targetsHematological cancersIntegration of artificial intelligence
2023
Design of Class I/IV Bromodomain-Targeting Degraders for Chromatin Remodeling Complexes
Zahid H, Costello J, Li Y, Kimbrough J, Actis M, Rankovic Z, Yan Q, Pomerantz W. Design of Class I/IV Bromodomain-Targeting Degraders for Chromatin Remodeling Complexes. ACS Chemical Biology 2023, 18: 1278-1293. PMID: 37260298, PMCID: PMC10698694, DOI: 10.1021/acschembio.2c00902.Peer-Reviewed Original ResearchConceptsChromatin Remodeling ComplexNon-BET bromodomainsRemodeling complexProtein degradationHeterobifunctional moleculesBET familyProtein targetsPyrimidine base analogsNumber of degradersDegradersOncogenic roleTernary complexExit vectorsWestern blottingProteinFirst exampleClass IChallenging targetComplexesCECR2ChromatinBromodomainsBPTFFamilyNanoBRET
2021
Unique N-Terminal Interactions Connect F-BOX STRESS INDUCED (FBS) Proteins to a WD40 Repeat-like Protein Pathway in Arabidopsis
Sepulveda-Garcia E, Fulton EC, Parlan EV, O’Connor L, Fleming AA, Replogle AJ, Rocha-Sosa M, Gendron JM, Thines B. Unique N-Terminal Interactions Connect F-BOX STRESS INDUCED (FBS) Proteins to a WD40 Repeat-like Protein Pathway in Arabidopsis. Plants 2021, 10: 2228. PMID: 34686037, PMCID: PMC8537223, DOI: 10.3390/plants10102228.Peer-Reviewed Original ResearchFBX proteinsSCF complexSCF-type E3 ubiquitin ligasesProtein targetsF-box domainF-box proteinsProtein degradation eventsE3 ubiquitin ligasesFBS proteinsC-terminal domainSkp proteinInteracting proteinSubstrate adaptorUbiquitin ligasesDomain interactsEnvironmental stressBiological functionsC-terminusN-terminusFacilitate recruitmentProtein pathwayFB proteinNuclear eventsArabidopsisProtein
2019
Tracking the cellular targets of platinum anticancer drugs: Current tools and emergent methods
Sutton E, McDevitt C, Yglesias M, Cunningham R, DeRose V. Tracking the cellular targets of platinum anticancer drugs: Current tools and emergent methods. Inorganica Chimica Acta 2019, 498: 118984. DOI: 10.1016/j.ica.2019.118984.Peer-Reviewed Original ResearchIn vivo CRISPR screening in CD8 T cells with AAV–Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma
Ye L, Park JJ, Dong MB, Yang Q, Chow RD, Peng L, Du Y, Guo J, Dai X, Wang G, Errami Y, Chen S. In vivo CRISPR screening in CD8 T cells with AAV–Sleeping Beauty hybrid vectors identifies membrane targets for improving immunotherapy for glioblastoma. Nature Biotechnology 2019, 37: 1302-1313. PMID: 31548728, PMCID: PMC6834896, DOI: 10.1038/s41587-019-0246-4.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntigens, CDCD8-Positive T-LymphocytesCell Line, TumorCRISPR-Cas SystemsDependovirusFemaleGene EditingGlioblastomaHumansImmunotherapy, AdoptiveLymphocyte Activation Gene 3 ProteinMaleMembrane ProteinsMiceN-AcetylglucosaminyltransferasesNeoplasm ProteinsProtein Disulfide-IsomerasesReceptors, Cell SurfaceRNA, Guide, CRISPR-Cas SystemsTransposasesXenograft Model Antitumor AssaysConceptsRNA cassetteMembrane protein targetsPrimary murine T cellsGenetic screening systemSingle-cell sequencingScreen hitsSleeping Beauty (SB) transposonCRISPR screensMembrane proteinsCell sequencingT cellsAdeno-associated virusGenomic integrationMembrane targetsMurine T cellsProtein targetsEfficient geneHuman GBM cellsGene editingT cell receptor transgenic modelGBM cellsBeauty transposonPDIA3T cell-based immunotherapyAntigen-specific killingReprogramming of Colonic Cell Metabolism by H2S
Vitvitsky V, Libiad M, Bostelaar T, Maebius A, Lee H, Lyssiotis C, Banerjee R. Reprogramming of Colonic Cell Metabolism by H2S. The FASEB Journal 2019, 33: 485.11-485.11. DOI: 10.1096/fasebj.2019.33.1_supplement.485.11.Peer-Reviewed Original ResearchOxygen consumption rateMitochondrial sulfide oxidation pathwayNumerous protein targetsSulfide oxidation pathwayEnergy metabolism pathwaysColon cancer tissuesMetabolic reprogrammingHuman colonic cellsInhibition of respirationProtein targetsStress responseNon-malignant cellsReductive carboxylationCell metabolismMetabolism pathwaysGrowth advantageInhibition of proliferationFASEB JournalCell exposurePathwayFull-text articlesColonic cellsGut microbiotaRespiratory toxinsCells
2018
Targeting Cyclin-Dependent Kinases for Treatment of Gynecologic Cancers
Lin ZP, Zhu YL, Ratner ES. Targeting Cyclin-Dependent Kinases for Treatment of Gynecologic Cancers. Frontiers In Oncology 2018, 8: 303. PMID: 30135856, PMCID: PMC6092490, DOI: 10.3389/fonc.2018.00303.Peer-Reviewed Original ResearchCDK activityCell cycleDefective cell cycle regulationCyclin-dependent kinase activityCell cycle phase transitionCell cycle regulationCyclin-dependent kinasesNormal cell cycleHomologous recombination repairHallmarks of cancerTargeting Cyclin-Dependent KinasesSynthetic lethal approachCell cycle phasesSmall molecule inhibitorsGynecologic cancerCheckpoint activationPARP inhibitorsCycle regulationHR repairKinase activityRecombination repairDNA damaging modalitiesProtein targetsCDKMajor gynecologic malignancies
2016
Induced protein degradation: an emerging drug discovery paradigm
Lai AC, Crews CM. Induced protein degradation: an emerging drug discovery paradigm. Nature Reviews Drug Discovery 2016, 16: 101-114. PMID: 27885283, PMCID: PMC5684876, DOI: 10.1038/nrd.2016.211.Peer-Reviewed Original ResearchConceptsProteolysis-targeting chimaerasProtein degradationUndruggable proteomeTarget protein degradationDifferent E3 ligasesInhibitor-based approachE3 ligasesDrug discovery platformProtein targetsProteomeDiscovery platformProtein expressionDrug discovery paradigmInhibition approachCell culturesDiscovery paradigmLigasesExact mechanismDegradationMouse modelDegradersProteinChimaerasPicomolar potency
2014
Synthesis of Stabilized Alpha-Helical Peptides
Bernal F, Katz SG. Synthesis of Stabilized Alpha-Helical Peptides. Methods In Molecular Biology 2014, 1176: 107-114. PMID: 25030922, PMCID: PMC6333094, DOI: 10.1007/978-1-4939-0992-6_9.Peer-Reviewed Original ResearchConceptsAlpha-helical peptidesImportant protein-protein interactionsSpecific amino acid residuesProtein-protein interactionsAlpha-helical motifOlefin metathesis reactionsAlpha-helical structureRing-closing olefin metathesis reactionAmino acid residuesPosttranslational modificationsProtein interactionsMetathesis reactionHost proteinsProtein targetsAcid residuesCrystal structureSecondary structureFunctional consequencesRemarkable stabilitySmall moleculesMost peptidesInteraction sitesStructural studiesCell permeabilitySynthesis
2011
The genomic binding sites of a noncoding RNA
Simon MD, Wang CI, Kharchenko PV, West JA, Chapman BA, Alekseyenko AA, Borowsky ML, Kuroda MI, Kingston RE. The genomic binding sites of a noncoding RNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 20497-20502. PMID: 22143764, PMCID: PMC3251105, DOI: 10.1073/pnas.1113536108.Peer-Reviewed Original ResearchConceptsDosage compensationCross-linked chromatin extractsMale-specific lethal (MSL) complexLevel of chromatinSpecific genomic sitesImportant regulatory roleHybridization-based techniquesLethal complexLncRNAs bindWide mappingSites of proteinsGenomic sitesChromatin extractsGenomic targetsEndogenous RNAEndogenous lncRNARNA targetsProtein targetsRegulatory roleHybridization analysisRoX2RNAChromatinProteinBinds
2010
Chapter 136 Pleckstrin Homology (PH) Domains
Lemmon M. Chapter 136 Pleckstrin Homology (PH) Domains. 2010, 1093-1101. DOI: 10.1016/b978-0-12-374145-5.00136-4.Peer-Reviewed Original ResearchPleckstrin homology domainPH domainHomology domainPH domain-containing proteinsDifferent PH domainsDomain-containing proteinsReceptor-mediated endocytosisParticular phosphoinositidesMembrane traffickingMembrane associationProtein functionSequence similarityCommon foldCellular signalingCytoskeletal organizationFunctional relatednessProtein targetsPhosphoinositidePhysiological rolePhysiological relevancePromiscuous bindingX-ray crystallographyPhospholipid modificationStructural similarityProtein
2004
PH Domains
Lemmon M, Keleti D. PH Domains. 2004, 337-363. DOI: 10.1002/3527603611.ch17.Peer-Reviewed Original Research
2001
Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking11PDB coordinates have been deposited with the RSCB with accession ID: 1F28.
Anderson A, O’Neil R, Surti T, Stroud R. Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking11PDB coordinates have been deposited with the RSCB with accession ID: 1F28. Cell Chemical Biology 2001, 8: 445-457. PMID: 11358692, DOI: 10.1016/s1074-5521(01)00023-0.Peer-Reviewed Original ResearchConceptsStructure-based drug designProtein targetsDrug designFlexible residuesHigh-resolution crystal structuresProtein/ligand complexesNew conformationDrug leadsEnzyme conformational changeThymidylate synthaseCrystal structureStructure of enzymesPossible conformationsAccession IDConformational adaptationConformational changesLigand complexesExperimental kinetic dataDrug moleculesTarget siteResiduesActive siteAntifolate inhibitorsNovel ligandsKinetic data
2000
Combinatorial Methods to Engineer Small Molecules for Functional Genomics
Ellman J. Combinatorial Methods to Engineer Small Molecules for Functional Genomics. Ernst Schering Foundation Symposium Proceedings 2000, 183-204. PMID: 11077609, DOI: 10.1007/978-3-662-04042-3_6.Peer-Reviewed Original ResearchConceptsSmall molecule librariesCell-permeable ligandsNatural substrate specificityFunctional genomicsHuman genomeSubstrate specificityComplete sequencingBiological functionsProtein targetsProteinCritical roleSmall moleculesCombinatorial librariesGenomeGenomicsPowerful toolLibrarySequencingEnzymeFunctionCellsTargetIdentification
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