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Emerging tools to investigate bromodomain functions.

Kougnassoukou Tchara PE, Filippakopoulos P, Lambert JP.

Methods. 2019 Nov 11. pii: S1046-2023(19)30135-5. doi: 10.1016/j.ymeth.2019.11.003. [Epub ahead of print] Review.


Evaluation of linker length effects on a BET bromodomain probe.

Traquete R, Henderson E, Picaud S, Cal PMSD, Sieglitz F, Rodrigues T, Oliveira R, Filippakopoulos P, Bernardes GJL.

Chem Commun (Camb). 2019 Aug 20;55(68):10128-10131. doi: 10.1039/c9cc05054j.


Structural Basis for Recruitment of DAPK1 to the KLHL20 E3 Ligase.

Chen Z, Picaud S, Filippakopoulos P, D'Angiolella V, Bullock AN.

Structure. 2019 Sep 3;27(9):1395-1404.e4. doi: 10.1016/j.str.2019.06.005. Epub 2019 Jul 3.


A chemical toolbox for the study of bromodomains and epigenetic signaling.

Wu Q, Heidenreich D, Zhou S, Ackloo S, Krämer A, Nakka K, Lima-Fernandes E, Deblois G, Duan S, Vellanki RN, Li F, Vedadi M, Dilworth J, Lupien M, Brennan PE, Arrowsmith CH, Müller S, Fedorov O, Filippakopoulos P, Knapp S.

Nat Commun. 2019 Apr 23;10(1):1915. doi: 10.1038/s41467-019-09672-2.


A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.

Marabelli C, Marrocco B, Pilotto S, Chittori S, Picaud S, Marchese S, Ciossani G, Forneris F, Filippakopoulos P, Schoehn G, Rhodes D, Subramaniam S, Mattevi A.

Cell Rep. 2019 Apr 9;27(2):387-399.e7. doi: 10.1016/j.celrep.2019.03.061.


Development and preclinical validation of a novel covalent ubiquitin receptor Rpn13 degrader in multiple myeloma.

Song Y, Park PMC, Wu L, Ray A, Picaud S, Li D, Wimalasena VK, Du T, Filippakopoulos P, Anderson KC, Qi J, Chauhan D.

Leukemia. 2019 Nov;33(11):2685-2694. doi: 10.1038/s41375-019-0467-z. Epub 2019 Apr 8.


Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains.

Lambert JP, Picaud S, Fujisawa T, Hou H, Savitsky P, Uusküla-Reimand L, Gupta GD, Abdouni H, Lin ZY, Tucholska M, Knight JDR, Gonzalez-Badillo B, St-Denis N, Newman JA, Stucki M, Pelletier L, Bandeira N, Wilson MD, Filippakopoulos P, Gingras AC.

Mol Cell. 2019 Feb 7;73(3):621-638.e17. doi: 10.1016/j.molcel.2018.11.006. Epub 2018 Dec 13.


Direct interaction between the PRDM3 and PRDM16 tumor suppressors and the NuRD chromatin remodeling complex.

Ivanochko D, Halabelian L, Henderson E, Savitsky P, Jain H, Marcon E, Duan S, Hutchinson A, Seitova A, Barsyte-Lovejoy D, Filippakopoulos P, Greenblatt J, Lima-Fernandes E, Arrowsmith CH.

Nucleic Acids Res. 2019 Feb 20;47(3):1225-1238. doi: 10.1093/nar/gky1192.


Nut Directs p300-Dependent, Genome-Wide H4 Hyperacetylation in Male Germ Cells.

Shiota H, Barral S, Buchou T, Tan M, Couté Y, Charbonnier G, Reynoird N, Boussouar F, Gérard M, Zhu M, Bargier L, Puthier D, Chuffart F, Bourova-Flin E, Picaud S, Filippakopoulos P, Goudarzi A, Ibrahim Z, Panne D, Rousseaux S, Zhao Y, Khochbin S.

Cell Rep. 2018 Sep 25;24(13):3477-3487.e6. doi: 10.1016/j.celrep.2018.08.069.


BRAF/MAPK and GSK3 signaling converges to control MITF nuclear export.

Ngeow KC, Friedrichsen HJ, Li L, Zeng Z, Andrews S, Volpon L, Brunsdon H, Berridge G, Picaud S, Fischer R, Lisle R, Knapp S, Filippakopoulos P, Knowles H, Steingrímsson E, Borden KLB, Patton EE, Goding CR.

Proc Natl Acad Sci U S A. 2018 Sep 11;115(37):E8668-E8677. doi: 10.1073/pnas.1810498115. Epub 2018 Aug 27.


Small molecule inhibitors reveal an indispensable scaffolding role of RIPK2 in NOD2 signaling.

Hrdinka M, Schlicher L, Dai B, Pinkas DM, Bufton JC, Picaud S, Ward JA, Rogers C, Suebsuwong C, Nikhar S, Cuny GD, Huber KV, Filippakopoulos P, Bullock AN, Degterev A, Gyrd-Hansen M.

EMBO J. 2018 Sep 3;37(17). pii: e99372. doi: 10.15252/embj.201899372. Epub 2018 Jul 19.


A TFEB nuclear export signal integrates amino acid supply and glucose availability.

Li L, Friedrichsen HJ, Andrews S, Picaud S, Volpon L, Ngeow K, Berridge G, Fischer R, Borden KLB, Filippakopoulos P, Goding CR.

Nat Commun. 2018 Jul 11;9(1):2685. doi: 10.1038/s41467-018-04849-7.


What Is the BET on Solid Tumors?

Filippakopoulos P.

J Clin Oncol. 2018 Oct 20;36(30):3040-3042. doi: 10.1200/JCO.2018.78.8695. Epub 2018 May 30. No abstract available.


BET bromodomain ligands: Probing the WPF shelf to improve BRD4 bromodomain affinity and metabolic stability.

Jennings LE, Schiedel M, Hewings DS, Picaud S, Laurin CMC, Bruno PA, Bluck JP, Scorah AR, See L, Reynolds JK, Moroglu M, Mistry IN, Hicks A, Guzanov P, Clayton J, Evans CNG, Stazi G, Biggin PC, Mapp AK, Hammond EM, Humphreys PG, Filippakopoulos P, Conway SJ.

Bioorg Med Chem. 2018 Jul 15;26(11):2937-2957. doi: 10.1016/j.bmc.2018.05.003. Epub 2018 May 15.


The C-terminal extension landscape of naturally presented HLA-I ligands.

Guillaume P, Picaud S, Baumgaertner P, Montandon N, Schmidt J, Speiser DE, Coukos G, Bassani-Sternberg M, Filippakopoulos P, Gfeller D.

Proc Natl Acad Sci U S A. 2018 May 15;115(20):5083-5088. doi: 10.1073/pnas.1717277115. Epub 2018 Apr 30.


Tryptophan-Mediated Interactions between Tristetraprolin and the CNOT9 Subunit Are Required for CCR4-NOT Deadenylase Complex Recruitment.

Bulbrook D, Brazier H, Mahajan P, Kliszczak M, Fedorov O, Marchese FP, Aubareda A, Chalk R, Picaud S, Strain-Damerell C, Filippakopoulos P, Gileadi O, Clark AR, Yue WW, Burgess-Brown NA, Dean JLE.

J Mol Biol. 2018 Mar 2;430(5):722-736. doi: 10.1016/j.jmb.2017.12.018. Epub 2017 Dec 29.


Epigenetic targeting of bromodomain protein BRD4 counteracts cancer cachexia and prolongs survival.

Segatto M, Fittipaldi R, Pin F, Sartori R, Dae Ko K, Zare H, Fenizia C, Zanchettin G, Pierobon ES, Hatakeyama S, Sperti C, Merigliano S, Sandri M, Filippakopoulos P, Costelli P, Sartorelli V, Caretti G.

Nat Commun. 2017 Nov 22;8(1):1707. doi: 10.1038/s41467-017-01645-7.


Correction for Bagarova et al., "Constitutively Active ALK2 Receptor Mutants Require Type II Receptor Cooperation".

Bagarova J, Vonner AJ, Armstrong KA, Börgermann J, Lai CSC, Deng DY, Beppu H, Alfano I, Filippakopoulos P, Morrell NW, Bullock AN, Knaus P, Mishina Y, Yu PB.

Mol Cell Biol. 2017 Sep 12;37(19). pii: e00284-17. doi: 10.1128/MCB.00284-17. Print 2017 Oct 1. No abstract available.


Structures of PGAM5 Provide Insight into Active Site Plasticity and Multimeric Assembly.

Chaikuad A, Filippakopoulos P, Marcsisin SR, Picaud S, Schröder M, Sekine S, Ichijo H, Engen JR, Takeda K, Knapp S.

Structure. 2017 Jul 5;25(7):1089-1099.e3. doi: 10.1016/j.str.2017.05.020. Epub 2017 Jun 22.


Epigenetic pathway inhibitors represent potential drugs for treating pancreatic and bronchial neuroendocrine tumors.

Lines KE, Stevenson M, Filippakopoulos P, Müller S, Lockstone HE, Wright B, Grozinsky-Glasberg S, Grossman AB, Knapp S, Buck D, Bountra C, Thakker RV.

Oncogenesis. 2017 May 15;6(5):e332. doi: 10.1038/oncsis.2017.30.


MOB1 Mediated Phospho-recognition in the Core Mammalian Hippo Pathway.

Couzens AL, Xiong S, Knight JDR, Mao DY, Guettler S, Picaud S, Kurinov I, Filippakopoulos P, Sicheri F, Gingras AC.

Mol Cell Proteomics. 2017 Jun;16(6):1098-1110. doi: 10.1074/mcp.M116.065490. Epub 2017 Apr 3.


Functions of bromodomain-containing proteins and their roles in homeostasis and cancer.

Fujisawa T, Filippakopoulos P.

Nat Rev Mol Cell Biol. 2017 Apr;18(4):246-262. doi: 10.1038/nrm.2016.143. Epub 2017 Jan 5. Review.


Multivalent Histone and DNA Engagement by a PHD/BRD/PWWP Triple Reader Cassette Recruits ZMYND8 to K14ac-Rich Chromatin.

Savitsky P, Krojer T, Fujisawa T, Lambert JP, Picaud S, Wang CY, Shanle EK, Krajewski K, Friedrichsen H, Kanapin A, Goding C, Schapira M, Samsonova A, Strahl BD, Gingras AC, Filippakopoulos P.

Cell Rep. 2016 Dec 6;17(10):2724-2737. doi: 10.1016/j.celrep.2016.11.014.


Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia.

Picaud S, Leonards K, Lambert JP, Dovey O, Wells C, Fedorov O, Monteiro O, Fujisawa T, Wang CY, Lingard H, Tallant C, Nikbin N, Guetzoyan L, Ingham R, Ley SV, Brennan P, Muller S, Samsonova A, Gingras AC, Schwaller J, Vassiliou G, Knapp S, Filippakopoulos P.

Sci Adv. 2016 Oct 12;2(10):e1600760. eCollection 2016 Oct.


Discovery and Optimization of a Selective Ligand for the Switch/Sucrose Nonfermenting-Related Bromodomains of Polybromo Protein-1 by the Use of Virtual Screening and Hydration Analysis.

Myrianthopoulos V, Gaboriaud-Kolar N, Tallant C, Hall ML, Grigoriou S, Brownlee PM, Fedorov O, Rogers C, Heidenreich D, Wanior M, Drosos N, Mexia N, Savitsky P, Bagratuni T, Kastritis E, Terpos E, Filippakopoulos P, Müller S, Skaltsounis AL, Downs JA, Knapp S, Mikros E.

J Med Chem. 2016 Oct 13;59(19):8787-8803. Epub 2016 Sep 27.


Identification of a Chemical Probe for Family VIII Bromodomains through Optimization of a Fragment Hit.

Gerstenberger BS, Trzupek JD, Tallant C, Fedorov O, Filippakopoulos P, Brennan PE, Fedele V, Martin S, Picaud S, Rogers C, Parikh M, Taylor A, Samas B, O'Mahony A, Berg E, Pallares G, Torrey AD, Treiber DK, Samardjiev IJ, Nasipak BT, Padilla-Benavides T, Wu Q, Imbalzano AN, Nickerson JA, Bunnage ME, Müller S, Knapp S, Owen DR.

J Med Chem. 2016 May 26;59(10):4800-11. doi: 10.1021/acs.jmedchem.6b00012. Epub 2016 May 3.


Dual Targeting of Bromodomain and Extraterminal Domain Proteins, and WNT or MAPK Signaling, Inhibits c-MYC Expression and Proliferation of Colorectal Cancer Cells.

Tögel L, Nightingale R, Chueh AC, Jayachandran A, Tran H, Phesse T, Wu R, Sieber OM, Arango D, Dhillon AS, Dawson MA, Diez-Dacal B, Gahman TC, Filippakopoulos P, Shiau AK, Mariadason JM.

Mol Cancer Ther. 2016 Jun;15(6):1217-26. doi: 10.1158/1535-7163.MCT-15-0724. Epub 2016 Mar 16.


Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance.

Fedorov O, Castex J, Tallant C, Owen DR, Martin S, Aldeghi M, Monteiro O, Filippakopoulos P, Picaud S, Trzupek JD, Gerstenberger BS, Bountra C, Willmann D, Wells C, Philpott M, Rogers C, Biggin PC, Brennan PE, Bunnage ME, Schüle R, Günther T, Knapp S, Müller S.

Sci Adv. 2015 Nov 13;1(10):e1500723. doi: 10.1126/sciadv.1500723. eCollection 2015 Nov.


Generation of a Selective Small Molecule Inhibitor of the CBP/p300 Bromodomain for Leukemia Therapy.

Picaud S, Fedorov O, Thanasopoulou A, Leonards K, Jones K, Meier J, Olzscha H, Monteiro O, Martin S, Philpott M, Tumber A, Filippakopoulos P, Yapp C, Wells C, Che KH, Bannister A, Robson S, Kumar U, Parr N, Lee K, Lugo D, Jeffrey P, Taylor S, Vecellio ML, Bountra C, Brennan PE, O'Mahony A, Velichko S, Müller S, Hay D, Daniels DL, Urh M, La Thangue NB, Kouzarides T, Prinjha R, Schwaller J, Knapp S.

Cancer Res. 2015 Dec 1;75(23):5106-5119. doi: 10.1158/0008-5472.CAN-15-0236. Epub 2015 Nov 9.


BET Inhibition Upregulates SIRT1 and Alleviates Inflammatory Responses.

Kokkola T, Suuronen T, Pesonen M, Filippakopoulos P, Salminen A, Jarho EM, Lahtela-Kakkonen M.

Chembiochem. 2015 Sep 21;16(14):1997-2001. doi: 10.1002/cbic.201500272. Epub 2015 Aug 13.


Beating the odds: BETs in disease.

Wang CY, Filippakopoulos P.

Trends Biochem Sci. 2015 Aug;40(8):468-79. doi: 10.1016/j.tibs.2015.06.002. Epub 2015 Jul 3. Review.


9H-purine scaffold reveals induced-fit pocket plasticity of the BRD9 bromodomain.

Picaud S, Strocchia M, Terracciano S, Lauro G, Mendez J, Daniels DL, Riccio R, Bifulco G, Bruno I, Filippakopoulos P.

J Med Chem. 2015 Mar 26;58(6):2718-36. doi: 10.1021/jm501893k. Epub 2015 Mar 5.


SPOTing Acetyl-Lysine Dependent Interactions.

Picaud S, Filippakopoulos P.

Microarrays (Basel). 2015 Aug 17;4(3):370-88. doi: 10.3390/microarrays4030370.


Molecular basis of histone tail recognition by human TIP5 PHD finger and bromodomain of the chromatin remodeling complex NoRC.

Tallant C, Valentini E, Fedorov O, Overvoorde L, Ferguson FM, Filippakopoulos P, Svergun DI, Knapp S, Ciulli A.

Structure. 2015 Jan 6;23(1):80-92. doi: 10.1016/j.str.2014.10.017. Epub 2014 Dec 18.


Discovery and optimization of small-molecule ligands for the CBP/p300 bromodomains.

Hay DA, Fedorov O, Martin S, Singleton DC, Tallant C, Wells C, Picaud S, Philpott M, Monteiro OP, Rogers CM, Conway SJ, Rooney TP, Tumber A, Yapp C, Filippakopoulos P, Bunnage ME, Müller S, Knapp S, Schofield CJ, Brennan PE.

J Am Chem Soc. 2014 Jul 2;136(26):9308-19. doi: 10.1021/ja412434f. Epub 2014 Jun 19.


A series of potent CREBBP bromodomain ligands reveals an induced-fit pocket stabilized by a cation-π interaction.

Rooney TP, Filippakopoulos P, Fedorov O, Picaud S, Cortopassi WA, Hay DA, Martin S, Tumber A, Rogers CM, Philpott M, Wang M, Thompson AL, Heightman TD, Pryde DC, Cook A, Paton RS, Müller S, Knapp S, Brennan PE, Conway SJ.

Angew Chem Int Ed Engl. 2014 Jun 10;53(24):6126-30. doi: 10.1002/anie.201402750. Epub 2014 May 12.


Targeting bromodomains: epigenetic readers of lysine acetylation.

Filippakopoulos P, Knapp S.

Nat Rev Drug Discov. 2014 May;13(5):337-56. doi: 10.1038/nrd4286. Epub 2014 Apr 22. Review.


Dual kinase-bromodomain inhibitors for rationally designed polypharmacology.

Ciceri P, Müller S, O'Mahony A, Fedorov O, Filippakopoulos P, Hunt JP, Lasater EA, Pallares G, Picaud S, Wells C, Martin S, Wodicka LM, Shah NP, Treiber DK, Knapp S.

Nat Chem Biol. 2014 Apr;10(4):305-12. doi: 10.1038/nchembio.1471. Epub 2014 Mar 2. Erratum in: Nat Chem Biol. 2014 Aug;10(8):692.


Identification of a major determinant for serine-threonine kinase phosphoacceptor specificity.

Chen C, Ha BH, Thévenin AF, Lou HJ, Zhang R, Yip KY, Peterson JR, Gerstein M, Kim PM, Filippakopoulos P, Knapp S, Boggon TJ, Turk BE.

Mol Cell. 2014 Jan 9;53(1):140-7. doi: 10.1016/j.molcel.2013.11.013. Epub 2013 Dec 26.


[1,2,4]triazolo[4,3-a]phthalazines: inhibitors of diverse bromodomains.

Fedorov O, Lingard H, Wells C, Monteiro OP, Picaud S, Keates T, Yapp C, Philpott M, Martin SJ, Felletar I, Marsden BD, Filippakopoulos P, Müller S, Knapp S, Brennan PE.

J Med Chem. 2014 Jan 23;57(2):462-76. doi: 10.1021/jm401568s. Epub 2013 Dec 30.


RVX-208, an inhibitor of BET transcriptional regulators with selectivity for the second bromodomain.

Picaud S, Wells C, Felletar I, Brotherton D, Martin S, Savitsky P, Diez-Dacal B, Philpott M, Bountra C, Lingard H, Fedorov O, Müller S, Brennan PE, Knapp S, Filippakopoulos P.

Proc Natl Acad Sci U S A. 2013 Dec 3;110(49):19754-9. doi: 10.1073/pnas.1310658110. Epub 2013 Nov 18.


Discovery of novel small-molecule inhibitors of BRD4 using structure-based virtual screening.

Vidler LR, Filippakopoulos P, Fedorov O, Picaud S, Martin S, Tomsett M, Woodward H, Brown N, Knapp S, Hoelder S.

J Med Chem. 2013 Oct 24;56(20):8073-88. doi: 10.1021/jm4011302. Epub 2013 Oct 3.


Structures of Down syndrome kinases, DYRKs, reveal mechanisms of kinase activation and substrate recognition.

Soundararajan M, Roos AK, Savitsky P, Filippakopoulos P, Kettenbach AN, Olsen JV, Gerber SA, Eswaran J, Knapp S, Elkins JM.

Structure. 2013 Jun 4;21(6):986-96. doi: 10.1016/j.str.2013.03.012. Epub 2013 May 9.


PFI-1, a highly selective protein interaction inhibitor, targeting BET Bromodomains.

Picaud S, Da Costa D, Thanasopoulou A, Filippakopoulos P, Fish PV, Philpott M, Fedorov O, Brennan P, Bunnage ME, Owen DR, Bradner JE, Taniere P, O'Sullivan B, Müller S, Schwaller J, Stankovic T, Knapp S.

Cancer Res. 2013 Jun 1;73(11):3336-46. doi: 10.1158/0008-5472.CAN-12-3292. Epub 2013 Apr 10.


Constitutively active ALK2 receptor mutants require type II receptor cooperation.

Bagarova J, Vonner AJ, Armstrong KA, Börgermann J, Lai CS, Deng DY, Beppu H, Alfano I, Filippakopoulos P, Morrell NW, Bullock AN, Knaus P, Mishina Y, Yu PB.

Mol Cell Biol. 2013 Jun;33(12):2413-24. doi: 10.1128/MCB.01595-12. Epub 2013 Apr 9. Erratum in: Mol Cell Biol. 2017 Sep 12;37(19):.


Optimization of 3,5-dimethylisoxazole derivatives as potent bromodomain ligands.

Hewings DS, Fedorov O, Filippakopoulos P, Martin S, Picaud S, Tumber A, Wells C, Olcina MM, Freeman K, Gill A, Ritchie AJ, Sheppard DW, Russell AJ, Hammond EM, Knapp S, Brennan PE, Conway SJ.

J Med Chem. 2013 Apr 25;56(8):3217-27. doi: 10.1021/jm301588r. Epub 2013 Apr 5.


Novel Inverse Binding Mode of Indirubin Derivatives Yields Improved Selectivity for DYRK Kinases.

Myrianthopoulos V, Kritsanida M, Gaboriaud-Kolar N, Magiatis P, Ferandin Y, Durieu E, Lozach O, Cappel D, Soundararajan M, Filippakopoulos P, Sherman W, Knapp S, Meijer L, Mikros E, Skaltsounis AL.

ACS Med Chem Lett. 2013 Jan 10;4(1):22-26. Epub 2012 Nov 1.


The design and synthesis of 5- and 6-isoxazolylbenzimidazoles as selective inhibitors of the BET bromodomains.

Hay D, Fedorov O, Filippakopoulos P, Martin S, Philpott M, Picaud S, Hewings DS, Uttakar S, Heightman TD, Conway SJ, Knapp S, Brennan PE.

Medchemcomm. 2013 Jan 1;4(1):140-144.


Stimulation of Hepatic Apolipoprotein A-I Production by Novel Thieno-Triazolodiazepines: Roles of the Classical Benzodiazepine Receptor, PAF Receptor, and Bromodomain Binding.

Kempen HJ, Bellus D, Fedorov O, Nicklisch S, Filippakopoulos P, Picaud S, Knapp S.

Lipid Insights. 2013 Dec 22;6:47-54. doi: 10.4137/Lpi.s13258. eCollection 2013.


Identification of a chemical probe for bromo and extra C-terminal bromodomain inhibition through optimization of a fragment-derived hit.

Fish PV, Filippakopoulos P, Bish G, Brennan PE, Bunnage ME, Cook AS, Federov O, Gerstenberger BS, Jones H, Knapp S, Marsden B, Nocka K, Owen DR, Philpott M, Picaud S, Primiano MJ, Ralph MJ, Sciammetta N, Trzupek JD.

J Med Chem. 2012 Nov 26;55(22):9831-7. doi: 10.1021/jm3010515. Epub 2012 Nov 8.

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