A chemical toolbox for the study of bromodomains and epigenetic signaling

[1]  S. Knapp,et al.  A structure-based approach towards identification of inhibitory fragments for eleven-nineteen-leukemia protein (ENL) YEATS domain , 2018, bioRxiv.

[2]  S. Knapp,et al.  Structure-Based Approach toward Identification of Inhibitory Fragments for Eleven-Nineteen-Leukemia Protein (ENL). , 2018, Journal of medicinal chemistry.

[3]  Jennifer A. Ward,et al.  Discovery of an MLLT1/3 YEATS Domain Chemical Probe , 2018, Angewandte Chemie.

[4]  E. Turiel,et al.  I. INTRODUCTION , 2018, Monographs of the Society for Research in Child Development.

[5]  S. Knapp,et al.  Co-targeting of BET proteins and HDACs as a novel approach to trigger apoptosis in rhabdomyosarcoma cells. , 2018, Cancer letters.

[6]  P. Valent,et al.  Hitting two oncogenic machineries in cancer cells: cooperative effects of the multi-kinase inhibitor ponatinib and the BET bromodomain blockers JQ1 or dBET1 on human carcinoma cells , 2018, Oncotarget.

[7]  R. Stam,et al.  Antileukemic Efficacy of BET Inhibitor in a Preclinical Mouse Model of MLL-AF4+ Infant ALL , 2018, Molecular Cancer Therapeutics.

[8]  J. Li,et al.  Plk1 Inhibition Enhances the Efficacy of BET Epigenetic Reader Blockade in Castration-Resistant Prostate Cancer , 2018, Molecular Cancer Therapeutics.

[9]  Anton Simeonov,et al.  Donated chemical probes for open science , 2018, eLife.

[10]  Gregory A Ross,et al.  Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo , 2018, Communications Chemistry.

[11]  Andrea Scrima,et al.  The invasin D protein from Yersinia pseudotuberculosis selectively binds the Fab region of host antibodies and affects colonization of the intestine , 2018, The Journal of Biological Chemistry.

[12]  K. Glass,et al.  Biological function and histone recognition of family IV bromodomain‐containing proteins , 2018, Journal of cellular physiology.

[13]  Jennifer A. Ward,et al.  A chemical biology toolbox to study protein methyltransferases and epigenetic signaling , 2018, bioRxiv.

[14]  K. Ozato,et al.  Brd4 binds to active enhancers to control cell identity gene induction in adipogenesis and myogenesis , 2017, Nature Communications.

[15]  Andrew J. Wilson,et al.  BET Bromodomain Inhibition Synergizes with PARP Inhibitor in Epithelial Ovarian Cancer. , 2017, Cell reports.

[16]  Christoph E. Dumelin,et al.  Isoform-Selective ATAD2 Chemical Probe with Novel Chemical Structure and Unusual Mode of Action , 2017, ACS chemical biology.

[17]  Karen E Gascoigne,et al.  GNE-781, A Highly Advanced Potent and Selective Bromodomain Inhibitor of Cyclic Adenosine Monophosphate Response Element Binding Protein, Binding Protein (CBP). , 2017, Journal of medicinal chemistry.

[18]  A. Gingras,et al.  Selective Targeting of Bromodomains of the Bromodomain-PHD Fingers Family Impairs Osteoclast Differentiation , 2017, ACS chemical biology.

[19]  F. Filipp,et al.  Metabolic profiling of triple-negative breast cancer cells reveals metabolic vulnerabilities , 2017, Cancer & metabolism.

[20]  Philip C Biggin,et al.  Statistical Analysis on the Performance of Molecular Mechanics Poisson–Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study , 2017, J. Chem. Inf. Model..

[21]  Shwu‐Yuan Wu,et al.  BRD3 and BRD4 BET Bromodomain Proteins Differentially Regulate Skeletal Myogenesis , 2017, Scientific Reports.

[22]  P. Sandy,et al.  GNE-886: A Potent and Selective Inhibitor of the Cat Eye Syndrome Chromosome Region Candidate 2 Bromodomain (CECR2). , 2017, ACS medicinal chemistry letters.

[23]  Clara D. Christ,et al.  Benzoisoquinolinediones as Potent and Selective Inhibitors of BRPF2 and TAF1/TAF1L Bromodomains , 2017, Journal of medicinal chemistry.

[24]  A. Ashworth,et al.  Marked for death: targeting epigenetic changes in cancer , 2017, Nature Reviews Drug Discovery.

[25]  P. Grandi,et al.  Discovery of a Potent, Cell Penetrant, and Selective p300/CBP-Associated Factor (PCAF)/General Control Nonderepressible 5 (GCN5) Bromodomain Chemical Probe. , 2017, Journal of medicinal chemistry.

[26]  S. Knapp,et al.  Discovery of a PCAF Bromodomain Chemical Probe , 2016, Angewandte Chemie.

[27]  M. D’Incalci,et al.  The bromodomain inhibitor OTX015 (MK-8628) exerts anti-tumor activity in triple-negative breast cancer models as single agent and in combination with everolimus , 2016, Oncotarget.

[28]  A. Gingras,et al.  Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia , 2016, Science Advances.

[29]  S. Knapp,et al.  Development of Selective CBP/P300 Benzoxazepine Bromodomain Inhibitors. , 2016, Journal of medicinal chemistry.

[30]  Yuanyuan Li,et al.  YEATS domain: Linking histone crotonylation to gene regulation , 2016, Transcription.

[31]  Andrew J. Bannister,et al.  A Chemical Probe for the ATAD2 Bromodomain. , 2016, Angewandte Chemie.

[32]  Ming-Ming Zhou,et al.  Structural Insights into Histone Crotonyl-Lysine Recognition by the AF9 YEATS Domain. , 2016, Structure.

[33]  T. Müller,et al.  Identification and Optimization of the First Highly Selective GLUT1 Inhibitor BAY‐876 , 2016, ChemMedChem.

[34]  C. Allis,et al.  The molecular hallmarks of epigenetic control , 2016, Nature Reviews Genetics.

[35]  A. Harris,et al.  The BET inhibitor JQ1 selectively impairs tumour response to hypoxia and downregulates CA9 and angiogenesis in triple negative breast cancer , 2016, Oncogene.

[36]  David J. Fallon,et al.  GSK6853, a Chemical Probe for Inhibition of the BRPF1 Bromodomain , 2016, ACS medicinal chemistry letters.

[37]  S. Knapp,et al.  Identification of a Chemical Probe for Family VIII Bromodomains through Optimization of a Fragment Hit. , 2016, Journal of medicinal chemistry.

[38]  G. Salles,et al.  Bromodomain inhibitor OTX015 in patients with lymphoma or multiple myeloma: a dose-escalation, open-label, pharmacokinetic, phase 1 study. , 2016, The Lancet. Haematology.

[39]  S. Knapp,et al.  Structure-Based Design of an in Vivo Active Selective BRD9 Inhibitor , 2016, Journal of medicinal chemistry.

[40]  Andrew J. Bannister,et al.  Discovery of I-BRD9, a Selective Cell Active Chemical Probe for Bromodomain Containing Protein 9 Inhibition. , 2016, Journal of medicinal chemistry.

[41]  Anne-Claude Gingras,et al.  BRPF3‐HBO1 regulates replication origin activation and histone H3K14 acetylation , 2016, The EMBO journal.

[42]  Karen E Gascoigne,et al.  Bromodomain inhibition of the transcriptional coactivators CBP/EP300 as a therapeutic strategy to target the IRF4 network in multiple myeloma , 2016, eLife.

[43]  Frank von Delft,et al.  A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5sc03115j , 2015, Chemical science.

[44]  Xiang-Jiao Yang,et al.  The Chromatin Regulator BRPF3 Preferentially Activates the HBO1 Acetyltransferase but Is Dispensable for Mouse Development and Survival* , 2015, The Journal of Biological Chemistry.

[45]  James E. Bradner,et al.  Response and resistance to BET bromodomain inhibitors in triple negative breast cancer , 2015, Nature.

[46]  Andrew J. Bannister,et al.  Generation of a Selective Small Molecule Inhibitor of the CBP/p300 Bromodomain for Leukemia Therapy. , 2015, Cancer research.

[47]  S. Knapp,et al.  Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance , 2015, Science Advances.

[48]  Mark A. Dawson,et al.  BET inhibitor resistance emerges from leukaemia stem cells , 2015, Nature.

[49]  Francisco J. Sánchez-Rivera,et al.  Combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma , 2015, Nature Medicine.

[50]  S. Knapp,et al.  Probing the epigenome. , 2015, Nature chemical biology.

[51]  John P. Overington,et al.  The promise and peril of chemical probes. , 2015, Nature chemical biology.

[52]  Parantu K. Shah,et al.  The SMARCA2/4 ATPase Domain Surpasses the Bromodomain as a Drug Target in SWI/SNF-Mutant Cancers: Insights from cDNA Rescue and PFI-3 Inhibitor Studies. , 2015, Cancer research.

[53]  Marie Jung,et al.  Targeting BET bromodomains for cancer treatment. , 2015, Epigenomics.

[54]  J. Strovel,et al.  BRD4 Structure-Activity Relationships of Dual PLK1 Kinase/BRD4 Bromodomain Inhibitor BI-2536. , 2015, ACS medicinal chemistry letters.

[55]  Edgar Jacoby,et al.  Extending kinome coverage by analysis of kinase inhibitor broad profiling data. , 2015, Drug discovery today.

[56]  S. Knapp,et al.  Discovery of a Chemical Tool Inhibitor Targeting the Bromodomains of TRIM24 and BRPF , 2015, Journal of medicinal chemistry.

[57]  S. Knapp,et al.  LP99: Discovery and Synthesis of the First Selective BRD7/9 Bromodomain Inhibitor** , 2015, Angewandte Chemie.

[58]  S. Knapp,et al.  LP99: Discovery and Synthesis of the First Selective BRD7/9 Bromodomain Inhibitor† , 2015, Angewandte Chemie.

[59]  Stefan Knapp,et al.  Discovery and Characterization of GSK2801, a Selective Chemical Probe for the Bromodomains BAZ2A and BAZ2B , 2015, Journal of medicinal chemistry.

[60]  Lewis R. Vidler,et al.  Structure Enabled Design of BAZ2-ICR, A Chemical Probe Targeting the Bromodomains of BAZ2A and BAZ2B , 2015, Journal of medicinal chemistry.

[61]  Raphael Gottardo,et al.  Orchestrating high-throughput genomic analysis with Bioconductor , 2015, Nature Methods.

[62]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[63]  T. Bathen,et al.  Metabolic characterization of triple negative breast cancer , 2014, BMC Cancer.

[64]  M. Dogan,et al.  The Outcome of Patients with Triple Negative Breast Cancer: The Turkish Oncology Group Experience. , 2014, The journal of breast health.

[65]  H. Harputluoglu,et al.  Outcome of 561 non-metastatic triple negative breast cancer patients: multi-center experience from Turkey. , 2014, Journal of B.U.ON. : official journal of the Balkan Union of Oncology.

[66]  Christophe Simon,et al.  The discovery of I-BET726 (GSK1324726A), a potent tetrahydroquinoline ApoA1 up-regulator and selective BET bromodomain inhibitor. , 2014, Journal of medicinal chemistry.

[67]  E. Davies,et al.  The treatment and survival of patients with triple negative breast cancer in a London population , 2014, SpringerPlus.

[68]  Ian A Blair,et al.  Akt-dependent metabolic reprogramming regulates tumor cell histone acetylation. , 2014, Cell metabolism.

[69]  S. Knapp,et al.  Discovery and Optimization of Small-Molecule Ligands for the CBP/p300 Bromodomains , 2014, Journal of the American Chemical Society.

[70]  S. Knapp,et al.  Targeting bromodomains: epigenetic readers of lysine acetylation , 2014, Nature Reviews Drug Discovery.

[71]  L. Wodicka,et al.  Dual kinase-bromodomain inhibitors for rationally designed polypharmacology , 2014, Nature chemical biology.

[72]  Rongxin Zhang,et al.  Epigenetics: the language of the cell? , 2014, Epigenomics.

[73]  S. Olesen,et al.  Acetyl-lysine Binding Site of Bromodomain-Containing Protein 4 (BRD4) Interacts with Diverse Kinase Inhibitors , 2014, ACS chemical biology.

[74]  Carsten Hopf,et al.  The commonly used PI3-kinase probe LY294002 is an inhibitor of BET bromodomains. , 2014, ACS chemical biology.

[75]  S. Knapp,et al.  [1,2,4]Triazolo[4,3-a]phthalazines: Inhibitors of Diverse Bromodomains , 2013, Journal of medicinal chemistry.

[76]  F. Dilworth,et al.  Differential modulation of cell cycle progression distinguishes members of the myogenic regulatory factor family of transcription factors , 2013, The FEBS journal.

[77]  W. Jung,et al.  Expression of cell metabolism-related genes in different molecular subtypes of triple-negative breast cancer. , 2013, Tumori.

[78]  W. Jung,et al.  Expression of cell metabolism-related genes in different molecular subtypes of triple-negative breast cancer , 2013 .

[79]  S. Knapp,et al.  PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains. , 2013, Cancer research.

[80]  Mark E Bunnage,et al.  Target validation using chemical probes. , 2013, Nature chemical biology.

[81]  David A. Orlando,et al.  Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers , 2013, Cell.

[82]  W. Jung,et al.  Metabolic phenotypes in triple-negative breast cancer , 2013, Tumor Biology.

[83]  Reid C Thompson,et al.  Inhibition of BET Bromodomain Targets Genetically Diverse Glioblastoma , 2013, Clinical Cancer Research.

[84]  M. Rudnicki,et al.  Comparative expression profiling identifies differential roles for Myogenin and p38α MAPK signaling in myogenesis. , 2012, Journal of molecular cell biology.

[85]  S. Knapp,et al.  Identification of a Chemical Probe for Bromo and Extra C-Terminal Bromodomain Inhibition through Optimization of a Fragment-Derived Hit , 2012, Journal of medicinal chemistry.

[86]  Steven J. M. Jones,et al.  Bromodomain-containing Protein 4 (BRD4) Regulates RNA Polymerase II Serine 2 Phosphorylation in Human CD4+ T Cells* , 2012, The Journal of Biological Chemistry.

[87]  S. Knapp,et al.  Progress in the development and application of small molecule inhibitors of bromodomain-acetyl-lysine interactions. , 2012, Journal of medicinal chemistry.

[88]  Julio E. Agno,et al.  Small-Molecule Inhibition of BRDT for Male Contraception , 2012, Cell.

[89]  Stefan Knapp,et al.  The bromodomain interaction module , 2012, FEBS letters.

[90]  Nathan Brown,et al.  Druggability Analysis and Structural Classification of Bromodomain Acetyl-lysine Binding Sites , 2012, Journal of medicinal chemistry.

[91]  M. Dawson,et al.  Cancer Epigenetics: From Mechanism to Therapy , 2012, Cell.

[92]  E. Nicodème,et al.  From ApoA1 upregulation to BET family bromodomain inhibition: discovery of I-BET151. , 2012, Bioorganic & medicinal chemistry letters.

[93]  David M. Wilson,et al.  Identification of a novel series of BET family bromodomain inhibitors: binding mode and profile of I-BET151 (GSK1210151A). , 2012, Bioorganic & medicinal chemistry letters.

[94]  A. Gingras,et al.  Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family , 2012, Cell.

[95]  Li Zhang,et al.  Analysis of Clinical Features and Outcome of 356 Triple-Negative Breast Cancer Patients in China , 2012, Breast Care.

[96]  Y. Doyon,et al.  Conserved Molecular Interactions within the HBO1 Acetyltransferase Complexes Regulate Cell Proliferation , 2011, Molecular and Cellular Biology.

[97]  S. Lowe,et al.  RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia , 2011, Nature.

[98]  Xiaoling Li,et al.  Mammalian Sirtuins and Energy Metabolism , 2011, International journal of biological sciences.

[99]  C. Rice,et al.  Suppression of inflammation by a synthetic histone mimic , 2010, Nature.

[100]  Rafael A. Irizarry,et al.  A framework for oligonucleotide microarray preprocessing , 2010, Bioinform..

[101]  William B. Smith,et al.  Selective inhibition of BET bromodomains , 2010, Nature.

[102]  Päivi Heikkilä,et al.  Subtyping of Breast Cancer by Immunohistochemistry to Investigate a Relationship between Subtype and Short and Long Term Survival: A Collaborative Analysis of Data for 10,159 Cases from 12 Studies , 2010, PLoS medicine.

[103]  Stephen V Frye,et al.  The art of the chemical probe. , 2010, Nature chemical biology.

[104]  Brad T. Sherman,et al.  Extracting Biological Meaning from Large Gene Lists with DAVID , 2009, Current protocols in bioinformatics.

[105]  Justin R. Cross,et al.  ATP-Citrate Lyase Links Cellular Metabolism to Histone Acetylation , 2009, Science.

[106]  Audrey Kauffmann,et al.  Bioinformatics Applications Note Arrayqualitymetrics—a Bioconductor Package for Quality Assessment of Microarray Data , 2022 .

[107]  Y. Doyon,et al.  Molecular Architecture of Quartet MOZ/MORF Histone Acetyltransferase Complexes , 2008, Molecular and Cellular Biology.

[108]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[109]  Ming-Ming Zhou,et al.  Bromodomain: an acetyl‐lysine binding domain , 2002, FEBS letters.

[110]  Lei Zeng,et al.  Structure and ligand of a histone acetyltransferase bromodomain , 1999, Nature.

[111]  I. Nonaka,et al.  Myogenin gene disruption results in perinatal lethality because of severe muscle defect , 1993, Nature.

[112]  William H. Klein,et al.  Muscle deficiency and neonatal death in mice with a targeted mutation in the myogenin gene , 1993, Nature.

[113]  K. Gupta,et al.  Cancer epigenetics: an introduction. , 2015, Methods in molecular biology.

[114]  Stefan Knapp,et al.  Kinase inhibitor selectivity profiling using differential scanning fluorimetry. , 2012, Methods in molecular biology.

[115]  W. Bickmore,et al.  Histone acetylation and the maintenance of chromatin compaction by Polycomb repressive complexes. , 2010, Cold Spring Harbor symposia on quantitative biology.

[116]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .