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Chemical Epigenetics pp 287–337Cite as

Applied Biophysics for Bromodomain Drug Discovery

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Part of the book series: Topics in Medicinal Chemistry ((TMC,volume 33))

Abstract

The dynamic regulation of epigenetic processes is dictated by the addition, removal, and recognition of posttranslational modifications on proteins and nucleic acids. These processes further regulate how our genetic information is accessed within chromatin. The recognition of acetylated histones by bromodomain modules is one such process that has been significantly evaluated as a promising interaction to disrupt for developing epigenetic therapies. The discovery of such inhibitors has been aided by the application of a wealth of biophysical and computational tools leading to insights into the structural biology of bromodomains and potent inhibitors that are advancing in the clinic. This chapter will first provide a brief historical overview on the discovery and characterization of bromodomains, followed by several of the seminal discoveries of bromodomain inhibitors. The remainder of the chapter will provide descriptions of the experimental and computational tools that are available to scientists interested in biophysical analysis of bromodomain inhibitor discovery for developing new drugs and chemical probes. The field of chemical epigenetics is rapidly expanding, and the goal of this chapter is to help researchers keep abreast of the new methods being used to study this important epigenetic protein domain.

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Abbreviations

3FY:

3-Fluorotyrosine

4FF:

4-Fluorophenylalanine

5FW:

5-Fluorotryptophan

BET:

Bromodomain and extraterminal domain

BRET:

Bioluminescence resonance energy transfer

Brm :

Brahma

CBP:

CREB-binding protein

CPMG:

Carr-Purcell-Meiboom-Gill

Cryo-TEM:

Cryo-transmission electron microscopy

DSF:

Differential scanning fluorimetry

FP:

Fluorescence polarization

FRAP:

Fluorescence recovery after photobleaching

GEM:

Group epitope mapping

GST:

Glutathione S-transferase

HDAC:

Histone deacetylase

HTR-FRET:

Homogeneous time-resolved fluorescence resonance energy transfer

IC50:

Inhibitory constant

ITC:

Isothermal calorimetry

K d :

Dissociation constant

LPS:

Lipopolysaccharide

NMC:

NUT-midline carcinoma

NOE:

Nuclear Overhauser effect

NTA:

Nickel nitrilotriacetic acid

PrOF NMR:

Protein-observed NMR

SPR:

Surface plasmon resonance

STD:

Saturation transfer difference

T 2 :

Transverse relaxation time

Τ c :

Rotational correlation time

T m :

Thermal melting temperature

References

  1. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403(6765):41–45. https://doi.org/10.1038/47412

    Article  CAS  PubMed  Google Scholar 

  2. Allis CD, Muir TW (2011) Spreading chromatin into chemical biology. Chembiochem 12(2):264–279. https://doi.org/10.1002/cbic.201000761

    Article  CAS  PubMed  Google Scholar 

  3. Phillips DM (1963) Presence of acetyl groups in histones. Biochem J 87(2):258. https://doi.org/10.1042/bj0870258

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Johns EW, Phillips DM, Simpson P, Butler JAW (1961) The electrophoresis of histones and histone fractions on starch gel. Biochem J 80:189–192

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Allfrey VG, Faulkner R, Mirsky AE (1964) Acetylation + methylation of histones + their possible role in regulation of RNA synthesis. Proc Natl Acad Sci U S A 51(5):786–794. https://doi.org/10.1073/pnas.51.5.786

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Filippakopoulos P, Knapp S (2012) The bromodomain interaction module. FEBS Lett 586(17):2692–2704. https://doi.org/10.1016/j.febslet.2012.04.045

    Article  CAS  PubMed  Google Scholar 

  7. Li YY, Sabari BR, Panchenko T, Wen H, Zhao D, Guan HP, Wan LL, Huang H, Tang ZY, Zhao YM, Roeder RG, Shi XB, Allis CD, Li HT (2016) Molecular coupling of histone Crotonylation and active transcription by AF9 YEATS domain. Mol Cell 62(2):181–193. https://doi.org/10.1016/j.molcel.2016.03.028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Fujimori DG, Conway SJ (2016) Editorial overview: chemical genetics and epigenetics. Curr Opin Chem Biol 33:VI–VII. https://doi.org/10.1016/j.cbpa.2016.08.008

    Article  CAS  PubMed  Google Scholar 

  9. Filippakopoulos P, Qi J, Picaud S, Shen Y, Smith WB, Fedorov O, Morse EM, Keates T, Hickman TT, Felletar I, Philpott M, Munro S, McKeown MR, Wang YC, Christie AL, West N, Cameron MJ, Schwartz B, Heightman TD, La Thangue N, French CA, Wiest O, Kung AL, Knapp S, Bradner JE (2010) Selective inhibition of BET bromodomains. Nature 468(7327):1067–1073. https://doi.org/10.1038/nature09504

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Nicodeme E, Jeffrey KL, Schaefer U, Beinke S, Dewell S, Chung CW, Chandwani R, Marazzi I, Wilson P, Coste H, White J, Kirilovsky J, Rice CM, Lora JM, Prinjha RK, Lee K, Tarakhovsky A (2010) Suppression of inflammation by a synthetic histone mimic. Nature 468(7327):1119–1123. https://doi.org/10.1038/nature09589

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Arrowsmith CH, Bountra C, Fish PV, Lee K, Schapira M (2012) Epigenetic protein families: a new frontier for drug discovery. Nat Rev Drug Discov 11(5):384–400. https://doi.org/10.1038/nrd3674

    Article  CAS  PubMed  Google Scholar 

  12. Belkina AC, Denis GV (2012) BET domain co-regulators in obesity, inflammation and cancer. Nat Rev Cancer 12(7):465–477. https://doi.org/10.1038/nrc3256

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Brand M, Measures AM, Wilson BG, Cortopassi WA, Alexander R, Hoess M, Hewings DS, Rooney TPC, Paton RS, Conway SJ (2015) Small molecule inhibitors of bromodomain-acetyl-lysine interactions. ACS Chem Biol 10(1):22–39. https://doi.org/10.1021/cb500996u

    Article  CAS  PubMed  Google Scholar 

  14. Zhang G, Smith SG, Zhou M-M (2015) Discovery of chemical inhibitors of human bromodomains. Chem Rev 115(21):11625–11668. https://doi.org/10.1021/acs.chemrev.5b00205

    Article  CAS  PubMed  Google Scholar 

  15. Chung C-W, Witherington J (2011) Progress in the discovery of small-molecule inhibitors of bromodomain-histone interactions. J Biomol Screen 16(10):1170–1185. https://doi.org/10.1177/1087057111421372

    Article  CAS  PubMed  Google Scholar 

  16. Zeng L, Li JM, Muller M, Yan S, Mujtaba S, Pan CF, Wang ZY, Zhou MM (2005) Selective small molecules blocking HIV-1 Tat and coactivator PCAF association. J Am Chem Soc 127(8):2376–2377. https://doi.org/10.1021/ja044885g

    Article  CAS  PubMed  Google Scholar 

  17. Tamkun JW, Deuring R, Scott MP, Kissinger M, Pattatucci AM, Kaufman TC, Kennison JA (1992) Brahma - a regulator of drosophila homeotic genes structurally related to the yeast transcriptional activator SNF2 SW12. Cell 68(3):561–572. https://doi.org/10.1016/0092-8674(92)90191-e

    Article  CAS  PubMed  Google Scholar 

  18. Owen DJ, Ornaghi P, Yang JC, Lowe N, Evans PR, Ballario P, Neuhaus D, Filetici P, Travers AA (2000) The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase Gcn5p. EMBO J 19(22):6141–6149. https://doi.org/10.1093/emboj/19.22.6141

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Randazzo FM, Khavari P, Crabtree G, Tamkun J, Rossant J (1994) BRG1: a putative murine homolog of the drosophila brahma gene, a homeotic gene regulator. Dev Biol 161(1):229–242. https://doi.org/10.1006/dbio.1994.1023

    Article  PubMed  Google Scholar 

  20. Filippakopoulos P, Picaud S, Mangos M, Keates T, Lambert JP, Barsyte-Lovejoy D, Felletar I, Volkmer R, Muller S, Pawson T, Gingras AC, Arrowsmith CH, Knapp S (2012) Histone recognition and large-scale structural analysis of the human bromodomain family. Cell 149(1):214–231. https://doi.org/10.1016/j.cell.2012.02.013

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Jeanmougin F, Wurtz JM, LeDouarin B, Chambon P, Losson R (1997) The bromodomain revisited. Trends Biochem Sci 22(5):151–153. https://doi.org/10.1016/s0968-0004(97)01042-6

    Article  CAS  PubMed  Google Scholar 

  22. Dhalluin C, Carlson JE, Zeng L, He C, Aggarwal AK, Zhou MM (1999) Structure and ligand of a histone acetyltransferase bromodomain. Nature 399(6735):491–496

    Article  CAS  PubMed  Google Scholar 

  23. Jacobson RH, Ladurner AG, King DS, Tjian R (2000) Structure and function of a human TAF(II)250 double bromodomain module. Science 288(5470):1422–1425. https://doi.org/10.1126/science.288.5470.1422

    Article  CAS  PubMed  Google Scholar 

  24. Ornaghi P, Ballario P, Lena AM, Gonzalez A, Filetici P (1999) The bromodomain of Gcn5p interacts in vitro with specific residues in the N terminus of histone H4. J Mol Biol 287(1):1–7. https://doi.org/10.1006/jmbi.1999.2577

    Article  CAS  PubMed  Google Scholar 

  25. Hudson BP, Martinez-Yamout MA, Dyson HJ, Wright PE (2000) Solution structure and acetyl-lysine binding activity of the GCN5 bromodomain. J Mol Biol 304(3):355–370. https://doi.org/10.1006/jmbi.2000.4207

    Article  CAS  PubMed  Google Scholar 

  26. Vidler LR, Brown N, Knapp S, Hoelder S (2012) Druggability analysis and structural classification of bromodomain acetyl-lysine binding sites. J Med Chem 55(17):7346–7359. https://doi.org/10.1021/jm300346w

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Liu J, Li F, Bao H, Jiang Y, Zhang S, Ma R, Gao J, Wu J, Ruan K (2017) The polar warhead of a TRIM24 bromodomain inhibitor rearranges a water-mediated interaction network. FEBS J 284(7):1082–1095. https://doi.org/10.1111/febs.14041

    Article  CAS  PubMed  Google Scholar 

  28. 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 (2015) Selective targeting of the BRG/PB1 bromodomains impairs embryonic and trophoblast stem cell maintenance. Sci Adv 1(10):e1500723. https://doi.org/10.1126/sciadv.1500723

    Article  PubMed  PubMed Central  Google Scholar 

  29. Crawford TD, Tsui V, Flynn EM, Wang S, Taylor AM, Cote A, Audia JE, Beresini MH, Burdick DJ, Cummings R, Dakin LA, Duplessis M, Good AC, Hewitt MC, Huang H-R, Jayaram H, Kiefer JR, Jiang Y, Murray J, Nasveschuk CG, Pardo E, Poy F, Romero FA, Tang Y, Wang J, Xu Z, Zawadzke LE, Zhu X, Albrecht BK, Magnuson SR, Bellon S, Cochran AG (2016) Diving into the water: inducible binding conformations for BRD4, TAF1(2), BRD9, and CECR2 bromodomains. J Med Chem 59(11):5391–5402. https://doi.org/10.1021/acs.jmedchem.6b00264

    Article  CAS  PubMed  Google Scholar 

  30. Divakaran A, Talluri SK, Ayoub AM, Mishra NK, Cui H, Widen JC, Berndt N, Zhu J-Y, Carlson AS, Topczewski JJ, Schonbrunn EK, Harki DA, Pomerantz WCK (2018) Molecular basis for the N-terminal bromodomain-and-extra-terminal-family selectivity of a dual kinase–bromodomain inhibitor. J Med Chem 61(20):9316–9334. https://doi.org/10.1021/acs.jmedchem.8b01248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Aldeghi M, Ross GA, Bodkin MJ, Essex JW, Knapp S, Biggin PC (2018) Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo. Commun Chem 1(1):19. https://doi.org/10.1038/s42004-018-0019-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Ruthenburg AJ, Li H, Patel DJ, Allis CD (2007) Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol 8(12):983–994. https://doi.org/10.1038/nrm2298

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Qin S, Jin L, Zhang J, Liu L, Ji P, Wu M, Wu J, Shi Y (2011) Recognition of unmodified histone H3 by the first PHD finger of bromodomain-PHD finger protein 2 provides insights into the regulation of histone acetyltransferases monocytic leukemic zinc-finger protein (MOZ) and MOZ-related factor (MORF). J Biol Chem 286(42):36944–36955. https://doi.org/10.1074/jbc.M111.244400

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Paz JC, Park S-H, Phillips N, Matsumura S, Tsai W-W, Kasper L, Brindle PK, Zhang G, Zhou M-M, Wright PE, Montminy M (2014) Combinatorial regulation of a signal-dependent activator by phosphorylation and acetylation. Proc Natl Acad Sci U S A 111(48):17116–17121. https://doi.org/10.1073/pnas.1420389111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Miller TCR, Simon B, Rybin V, Groetsch H, Curtet S, Khochbin S, Carlomagno T, Mueller CW (2016) A bromodomain-DNA interaction facilitates acetylation-dependent bivalent nucleosome recognition by the BET protein BRDT. Nat Commun 7. https://doi.org/10.1038/ncomms13855

  36. Mujtaba S, He Y, Zeng L, Yan S, Plotnikova O, Sachchidanand, Sanchez R, Zeleznik-Le NJ, Ronai Z, Zhou MM (2004) Structural mechanism of the bromodomain of the coactivator CBP in p53 transcriptional activation. Mol Cell 13(2):251–263. https://doi.org/10.1016/s1097-2765(03)00528-8

    Article  CAS  PubMed  Google Scholar 

  37. Mujtaba S, He Y, Zeng L, Farooq A, Carlson JE, Ott M, Verdin E, Zhou MM (2002) Structural basis of lysine-acetylated HIV-1 Tat recognition by PCAF bromodomain. Mol Cell 9(3):575–586. https://doi.org/10.1016/s1097-2765(02)00483-5

    Article  CAS  PubMed  Google Scholar 

  38. Huang B, Yang X-D, Zhou M-M, Ozato K, Chen L-F (2009) Brd4 coactivates transcriptional activation of NF-kappa B via specific binding to acetylated RelA. Mol Cell Biol 29(5):1375–1387. https://doi.org/10.1128/mcb.01365-08

    Article  CAS  PubMed  Google Scholar 

  39. Shi J, Wang YF, Zeng L, Wu YD, Deng J, Zhang Q, Lin YW, Li JL, Kang TB, Tao M, Rusinova E, Zhang GT, Wang C, Zhu HN, Yao J, Zeng YX, Evers BM, Zhou MM, Zhou BHP (2014) Disrupting the interaction of BRD4 with diacetylated twist suppresses tumorigenesis in basal-like breast cancer. Cancer Cell 25(2):210–225. https://doi.org/10.1016/j.ccr.2014.01.028

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Asangani IA, Dommeti VL, Wang XJ, Malik R, Cieslik M, Yang RD, Escara-Wilke J, Wilder-Romans K, Dhanireddy S, Engelke C, Iyer MK, Jing XJ, Wu YM, Cao XH, Qin ZHS, Wang SM, Feng FY, Chinnaiyan AM (2014) Therapeutic targeting of BET bromodomain proteins in castration-resistant prostate cancer. Nature 510(7504):278. https://doi.org/10.1038/nature13229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Hu P, Wang X, Zhang B, Zhang S, Wang Q, Wang Z (2014) Fluorescence polarization for the evaluation of small-molecule inhibitors of PCAF BRD/Tat-AcK50 association. ChemMedChem 9(5):928–931. https://doi.org/10.1002/cmdc.201300499

    Article  CAS  PubMed  Google Scholar 

  42. Moustakim M, Clark PGK, Trulli L, de Arriba ALF, Ehebauer MT, Chaikuad A, Murphy EJ, Mendez-Johnson J, Daniels D, Hou CFD, Lin YH, Walker JR, Hui R, Yang HB, Dorrell L, Rogers CM, Monteiro OP, Fedorov O, Huber KVM, Knapp S, Heer J, Dixon DJ, Brennan PE (2017) Discovery of a PCAF bromodomain chemical probe. Angew Chem Int Ed 56(3):827–831. https://doi.org/10.1002/anie.201610816

    Article  CAS  Google Scholar 

  43. Picaud S, Leonards K, Lambert J-P, Dovey O, Wells C, Fedorov O, Monteiro O, Fujisawa T, Wang C-Y, Lingard H, Tallant C, Nikbin N, Guetzoyan L, Ingham R, Ley SV, Brennan P, Muller S, Samsonova A, Gingras A-C, Schwaller J, Vassiliou G, Knapp S, Filippakopoulos P (2016) Promiscuous targeting of bromodomains by bromosporine identifies BET proteins as master regulators of primary transcription response in leukemia. Sci Adv 2(10):e1600760. https://doi.org/10.1126/sciadv.1600760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Humphreys PG, Bamborough P, Chung C-W, Crags PD, Gordon L, Grandi P, Hayhow TG, Hussain J, Jones KL, Lindon M, Michon A-M, Renaux JF, Suckling CJ, Tough DF, Prinjha RK (2017) Discovery of a potent, cell penetrant, and selective p300/CBP-associated factor (PCAF)/general control nonderepressible 5 (GCN5) bromodomain chemical probe. J Med Chem 60(2):695–709. https://doi.org/10.1021/acs.jmedchem.6b01566

    Article  CAS  PubMed  Google Scholar 

  45. Goodman RH, Smolik S (2000) CBP/p300 in cell growth, transformation, and development. Genes Dev 14(13):1553–1577

    CAS  PubMed  Google Scholar 

  46. Zhang ZW, Hofmann C, Casanova E, Schutz G, Lutz B (2004) Generation of a conditional allele of the CBP gene in mouse. Genesis 40(2):82–89. https://doi.org/10.1002/gene.20068

    Article  CAS  PubMed  Google Scholar 

  47. Korzus E (2017) Rubinstein-Taybi syndrome and epigenetic alterations. Adv Exp Med Biol 978:39–62. https://doi.org/10.1007/978-3-319-53889-1_3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Sachchidanand, Resnick-Silverman L, Yan S, Mutjaba S, Liu WJ, Zeng L, Manfredi JJ, Zhou MM (2006) Target structure-based discovery of small molecules that block human p53 and CREB binding protein association. Chem Biol 13(1):81–90. https://doi.org/10.1016/j.chembiol.2005.10.014

    Article  CAS  PubMed  Google Scholar 

  49. Shankar DB, Cheng JC, Sakamoto KM (2005) Role of cyclic AMP response element binding protein in human leukemias. Cancer 104(9):1819–1824. https://doi.org/10.1002/cncr.21401

    Article  CAS  PubMed  Google Scholar 

  50. Iyer NG, Ozdag H, Caldas C (2004) p300/CBP and cancer. Oncogene 23(24):4225–4231. https://doi.org/10.1038/sj.onc.1207118

    Article  CAS  PubMed  Google Scholar 

  51. Gerona-Navarro G, Yoel R, Mujtaba S, Frasca A, Patel J, Zeng L, Plotnikov AN, Osman R, Zhou M-M (2011) Rational design of cyclic peptide modulators of the transcriptional coactivator CBP: a new class of p53 inhibitors. J Am Chem Soc 133(7):2040–2043. https://doi.org/10.1021/ja107761h

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Borah JC, Mujtaba S, Karakikes I, Zeng L, Muller M, Patel J, Moshkina N, Morohashi K, Zhang W, Gerona-Navarro G, Hajjar RJ, Zhou M-M (2011) A small molecule binding to the coactivator CREB-binding protein blocks apoptosis in cardiomyocytes. Chem Biol 18(4):531–541. https://doi.org/10.1016/j.chembiol.2010.12.021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Fedorov O, Lingard H, Wells C, Monteiro OP, Picaud S, Keates T, Yapp C, Philpott M, Martin SJ, Felletar I, Marsden BD, Filippakopoulos P, Mueller S, Knapp S, Brennan PE (2014) 1,2,4 Triazolo 4,3-a phthalazines: inhibitors of diverse bromodomains. J Med Chem 57(2):462–476. https://doi.org/10.1021/jm401568s

    Article  CAS  PubMed  Google Scholar 

  54. Rooney TPC, 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, Mueller S, Knapp S, Brennan PE, Conway SJ (2014) A series of potent CREBBP bromodomain ligands reveals an induced-fit pocket stabilized by a cation-pi interaction. Angew Chem Int Ed 53(24):6126–6130. https://doi.org/10.1002/anie.201402750

    Article  CAS  Google Scholar 

  55. 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, Mueller S, Hay D, Daniels DL, Urh M, La Thangue NB, Kouzarides T, Prinjha R, Schwaller J, Knapp S (2015) Generation of a selective small molecule inhibitor of the CBP/p300 bromodomain for leukemia therapy. Cancer Res 75(23):5106–5119. https://doi.org/10.1158/0008-5472.Can-15-0236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Perez-Salvia M, Esteller M (2017) Bromodomain inhibitors and cancer therapy: from structures to applications. Epigenetics 12(5):323–339. https://doi.org/10.1080/15592294.2016.1265710

    Article  PubMed  Google Scholar 

  57. Ember SWJ, Zhu JY, Olesen SH, Martin MP, Becker A, Berndt N, Georg GI, Schonbrunn E (2014) Acetyl-lysine binding site of bromodomain-containing protein 4 (BRD4) interacts with diverse kinase inhibitors. ACS Chem Biol 9(5):1160–1171. https://doi.org/10.1021/cb500072z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Ciceri P, Muller 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 (2014) Dual kinase-bromodomain inhibitors for rationally designed polypharmacology. Nat Chem Biol 10(4):305–312. https://doi.org/10.1038/nchembio.1471

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Ferguson FM, Fedorov O, Chaikuad A, Philpott M, Muniz JRC, Felletar I, von Delft F, Heightman T, Knapp S, Abell C, Ciulli A (2013) Targeting low-druggability bromodomains: fragment based screening and inhibitor design against the BAZ2B bromodomain. J Med Chem 56(24):10183–10187. https://doi.org/10.1021/jm401582c

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Ouyang L, Zhang L, Liu J, Fu L, Yao D, Zhao Y, Zhang S, Wang G, He G, Liu B (2017) Discovery of a small-molecule bromodomain-containing protein 4 (BRD4) inhibitor that induces AMP-activated protein kinase-modulated autophagy-associated cell death in breast cancer. J Med Chem 60(24):9990–10012. https://doi.org/10.1021/acs.jmedchem.7b00275

    Article  CAS  PubMed  Google Scholar 

  61. Zhang GT, Plotnikov AN, Rusinova E, Shen T, Morohashi K, Joshua J, Zeng L, Mujtaba S, Ohlmeyer M, Zhou MM (2013) Structure-guided design of potent diazobenzene inhibitors for the BET bromodomains. J Med Chem 56(22):9251–9264. https://doi.org/10.1021/jm401334s

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Gacias M, Gerona-Navarro G, Plotnikov AN, Zhang G, Zeng L, Kaur J, Moy G, Rusinova E, Rodriguez Y, Matikainen B, Vincek A, Joshua J, Casaccia P, Zhou M-M (2014) Selective chemical modulation of gene transcription favors oligodendrocyte lineage progression. Chem Biol 21(7):841–854. https://doi.org/10.1016/j.chembiol.2014.05.009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Picaud S, Wells C, Felletar I, Brotherton D, Martin S, Savitsky P, Diez-Dacal B, Philpott M, Bountra C, Lingard H, Fedorov O, Mueller S, Brennan PE, Knapp S, Filippakopoulos P (2013) RVX-208, an inhibitor of BET transcriptional regulators with selectivity for the second bromodomain. Proc Natl Acad Sci U S A 110(49):19754–19759. https://doi.org/10.1073/pnas.1310658110

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Kharenko OA, Gesner EM, Patel RG, Norek K, White A, Fontano E, Suto RK, Young PR, McLure KG, Hansen HC (2016) RVX-297-a novel BD2 selective inhibitor of BET bromodomains. Biochem Biophys Res Commun 477(1):62–67. https://doi.org/10.1016/j.bbrc.2016.06.021

    Article  CAS  PubMed  Google Scholar 

  65. Endo J, Hikawa H, Hamada M, Ishibuchi S, Fujie N, Sugiyama N, Tanaka M, Kobayashi H, Sugahara K, Oshita K, Iwata K, Ooike S, Murata M, Sumichika H, Chiba K, Adachi K (2016) A phenotypic drug discovery study on thienodiazepine derivatives as inhibitors of T cell proliferation induced by CD28 co-stimulation leads to the discovery of a first bromodomain inhibitor. Bioorg Med Chem Lett 26(5):1365–1370. https://doi.org/10.1016/j.bmcl.2016.01.084

    Article  CAS  PubMed  Google Scholar 

  66. Zuber J, Shi JW, Wang E, Rappaport AR, Herrmann H, Sison EA, Magoon D, Qi J, Blatt K, Wunderlich M, Taylor MJ, Johns C, Chicas A, Mulloy JC, Kogan SC, Brown P, Valent P, Bradner JE, Lowe SW, Vakoc CR (2011) RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 478(7370):524–U124. https://doi.org/10.1038/nature10334

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Delmore JE, Issa GC, Lemieux ME, Rahl PB, Shi JW, Jacobs HM, Kastritis E, Gilpatrick T, Paranal RM, Qi J, Chesi M, Schinzel AC, McKeown MR, Heffernan TP, Vakoc CR, Bergsagel PL, Ghobrial IM, Richardson PG, Young RA, Hahn WC, Anderson KC, Kung AL, Bradner JE, Mitsiades CS (2011) BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 146(6):903–916. https://doi.org/10.1016/j.cell.2011.08.017

    Article  CAS  Google Scholar 

  68. Loven J, Hoke HA, Lin CY, Lau A, Orlando DA, Vakoc CR, Bradner JE, Lee TI, Young RA (2013) Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153(2):320–334. https://doi.org/10.1016/j.cell.2013.03.036

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Berkovits BD, Wolgemuth DJ (2011) The first bromodomain of the testis-specific double bromodomain protein Brdt is required for chromocenter organization that is modulated by genetic background. Dev Biol 360(2):358–368. https://doi.org/10.1016/j.ydbio.2011.10.005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Devaiah BN, Lewis BA, Cherman N, Hewitt MC, Albrecht BK, Robey PG, Ozato K, Sims III RJ, Singer DS (2012) BRD4 is an atypical kinase that phosphorylates Serine2 of the RNA polymerase II carboxy-terminal domain. Proc Natl Acad Sci U S A 109(18):6927–6932. https://doi.org/10.1073/pnas.1120422109

    Article  PubMed  PubMed Central  Google Scholar 

  71. Urick AK, Hawk LML, Cassel MK, Mishra NK, Liu S, Adhikari N, Zhang W, Dos Santos CO, Hall JL, Pomerantz WCK (2015) Dual screening of BPTF and Brd4 using protein-observed fluorine NMR uncovers new bromodomain probe molecules. ACS Chem Biol 10(10):2246–2256. https://doi.org/10.1021/acschembio.5b00483

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Andrews FH, Singh AR, Joshi S, Smith CA, Morales GA, Garlich JR, Durden DL, Kutateladze TG (2017) Dual-activity PI3K-BRD4 inhibitor for the orthogonal inhibition of MYC to block tumor growth and metastasis. Proc Natl Acad Sci U S A 114(7):E1072–E1080. https://doi.org/10.1073/pnas.1613091114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Carlino L, Rastelli G (2016) Dual kinase-bromodomain inhibitors in anticancer drug discovery: a structural and pharmacological perspective. J Med Chem 59(20):9305–9320. https://doi.org/10.1021/acs.jmedchem.6b00438

    Article  CAS  PubMed  Google Scholar 

  74. Shadrick WR, Slavish PJ, Chai SC, Connelly M, Low JA, Young BM, Bharatham N, Boyd VA, Chen T, Lee RE, Kiplin GR, Potter PM, Waddell B, Tallant C, Knapp S, Morfouace M, Roussel MF, Shelat AA (2018) Exploiting a water network to achieve enthalpy-driven, bromodomain-selective BET inhibitors. Bioorg Med Chem 26:25–36

    Article  CAS  PubMed  Google Scholar 

  75. Vidler LR, Filippakopoulos P, Fedorov O, Picaud S, Martin S, Tomsett M, Woodward H, Brown N, Knapp S, Hoelder S (2013) Discovery of novel small-molecule inhibitors of BRD4 using structure-based virtual screening. J Med Chem 56(20):8073–8088. https://doi.org/10.1021/jm4011302

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Marchand J-R, Vedove AD, Lolli G, Caflisch A (2017) Discovery of inhibitors of four bromodomains by fragment-anchored ligand docking. J Chem Inf Model 57(10):2584–2597. https://doi.org/10.1021/acs.jcim.7b00336

    Article  CAS  PubMed  Google Scholar 

  77. Aldeghi M, Heifetz A, Bodkin MJ, Knapp S, Biggin PC (2017) Predictions of ligand selectivity from absolute binding free energy calculations. J Am Chem Soc 139(2):946–957. https://doi.org/10.1021/jacs.6b11467

    Article  CAS  PubMed  Google Scholar 

  78. Giblin KA, Hughes SJ, Boyd H, Hansson P, Bender A (2018) Prospectively validated proteochemometric models for the prediction of small-molecule binding to bromodomain proteins. J Chem Inf Model 58(9):1870–1888. https://doi.org/10.1021/acs.jcim.8b00400

    Article  CAS  PubMed  Google Scholar 

  79. Allen BK, Mehta S, Ember SWJ, Zhu J-Y, Schönbrunn E, Ayad NG, Schürer SC (2017) Identification of a novel class of BRD4 inhibitors by computational screening and binding simulations. ACS Omega 2(8):4760–4771. https://doi.org/10.1021/acsomega.7b00553

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Ayoub AM, Hawk LML, Herzig RJ, Jiang J, Wisniewski AJ, Gee CT, Zhao P, Zhu JY, Berndt N, Offei-Addo NK, Scott TG, Qi J, Bradner JE, Ward TR, Schonbrunn E, Georg GI, Pomerantz WCK (2017) BET bromodomain inhibitors with one-step synthesis discovered from virtual screen. J Med Chem 60(12):4805–4817. https://doi.org/10.1021/acs.jmedchem.6b01336

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Hasvold LA, Sheppard GS, Wang L, Fidanze SD, Liu D, Pratt JK, Mantei RA, Wada CK, Hubbard R, Shen Y, Lin X, Huang X, Warder SE, Wilcox D, Li L, Buchanan FG, Smithee L, Albert DH, Magoc TJ, Park CH, Petros AM, Panchal SC, Sun C, Kovar P, Soni NB, Elmore SW, Kati WM, McDaniel KF (2017) Methylpyrrole inhibitors of BET bromodomains. Bioorg Med Chem Lett 27(10):2225–2233. https://doi.org/10.1016/j.bmcl.2017.02.057

    Article  CAS  PubMed  Google Scholar 

  82. Harner MJ, Chauder BA, Phan J, Fesik SW (2014) Fragment-based screening of the bromodomain of ATAD2. J Med Chem 57(22):9687–9692. https://doi.org/10.1021/jm501035j

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Yu J-L, Chen T-T, Zhou C, Lian F-L, Tang X-L, Wen Y, Shen J-K, Xu Y-C, Xiong B, Zhang N-X (2016) NMR-based platform for fragment-based lead discovery used in screening BRD4-targeted compounds. Acta Pharmacol Sin 37(7):984–993. https://doi.org/10.1038/aps.2016.19

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Poplawski A, Hu K, Lee W, Natesan S, Peng D, Carlson S, Shi X, Balaz S, Markley JL, Glass KC (2014) Molecular insights into the recognition of N-terminal histone modifications by the BRPF1 bromodomain. J Mol Biol 426(8):1661–1676. https://doi.org/10.1016/j.jmb.2013.12.007

    Article  CAS  PubMed  Google Scholar 

  85. Charlop-Powers Z, Zeng L, Zhang Q, Zhou M-M (2010) Structural insights into selective histone H3 recognition by the human polybromo bromodomain 2. Cell Res 20:529. https://doi.org/10.1038/cr.2010.43

    Article  CAS  PubMed  Google Scholar 

  86. Liu Y, Wang X, Zhang J, Huang H, Ding B, Wu J, Shi Y (2008) Structural basis and binding properties of the second bromodomain of Brd4 with acetylated histone tails. Biochemistry 47(24):6403–6417. https://doi.org/10.1021/bi8001659

    Article  CAS  PubMed  Google Scholar 

  87. Sun H, Liu J, Zhang J, Shen W, Huang H, Xu C, Dai H, Wu J, Shi Y (2007) Solution structure of BRD7 bromodomain and its interaction with acetylated peptides from histone H3 and H4. Biochem Biophys Res Commun 358(2):435–441. https://doi.org/10.1016/j.bbrc.2007.04.139

    Article  CAS  PubMed  Google Scholar 

  88. Ferguson FM, Dias DM, Rodrigues JPGLM, Wienk H, Boelens R, Bonvin AMJJ, Abell C, Ciulli A (2014) Binding hotspots of BAZ2B bromodomain: histone interaction revealed by solution NMR driven docking. Biochemistry 53(42):6706–6716. https://doi.org/10.1021/bi500909d

    Article  CAS  PubMed  Google Scholar 

  89. Marsh ENG, Suzuki Y (2014) Using 19F NMR to probe biological interactions of proteins and peptides. ACS Chem Biol 9(6):1242–1250. https://doi.org/10.1021/cb500111u

    Article  CAS  PubMed  Google Scholar 

  90. Gerig JT. (2001) Fluorine NMR. Online textbook; http://www.biophysics.org/img/jtg2001-2.pdf

  91. Moreira IS, Martins JM, Ramos RM, Fernandes PA, Ramos MJ (2013) Understanding the importance of the aromatic amino-acid residues as hot-spots. Biochim Biophys Acta 1834(1):404–414. https://doi.org/10.1016/j.bbapap.2012.07.005

    Article  CAS  PubMed  Google Scholar 

  92. Bogan AA, Thorn KS (1998) Anatomy of hot spots in protein interfaces11Edited by J. Wells. J Mol Biol 280(1):1–9. https://doi.org/10.1006/jmbi.1998.1843

    Article  CAS  PubMed  Google Scholar 

  93. Arntson KE, Pomerantz WCK (2016) Protein-observed fluorine NMR: a bioorthogonal approach for small molecule discovery. J Med Chem 59(11):5158–5171. https://doi.org/10.1021/acs.jmedchem.5b01447

    Article  CAS  PubMed  Google Scholar 

  94. Urick AK, Calle LP, Espinosa JF, Hu H, Pomerantz WCK (2016) Protein-observed fluorine NMR is a complementary ligand discovery method to 1H CPMG ligand-observed NMR. ACS Chem Biol 11(11):3154–3164. https://doi.org/10.1021/acschembio.6b00730

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  95. Zartler ER, Hanson J, Jones BE, Kline AD, Martin G, Mo H, Shapiro MJ, Wang R, Wu H, Yan J (2003) RAMPED-UP NMR: multiplexed NMR-based screening for drug discovery. J Am Chem Soc 125(36):10941–10946. https://doi.org/10.1021/ja0348593

    Article  CAS  PubMed  Google Scholar 

  96. Frey WD, Chaudhry A, Slepicka PF, Ouellette AM, Kirberger SE, Pomerantz WCK, Hannon GJ, dos Santos CO (2017) BPTF maintains chromatin accessibility and the self-renewal capacity of mammary gland stem cells. Stem Cell Rep 9(1):23–31. https://doi.org/10.1016/j.stemcr.2017.04.031

    Article  CAS  Google Scholar 

  97. Mayer M, Meyer B (2001) Group epitope mapping by saturation transfer difference NMR to identify segments of a ligand in direct contact with a protein receptor. J Am Chem Soc 123(25):6108–6117. https://doi.org/10.1021/ja0100120

    Article  CAS  PubMed  Google Scholar 

  98. Geist L, Mayer M, Cockcroft X-L, Wolkerstorfer B, Kessler D, Engelhardt H, McConnell DB, Konrat R (2017) Direct NMR probing of hydration shells of protein ligand interfaces and its application to drug design. J Med Chem 60(21):8708–8715. https://doi.org/10.1021/acs.jmedchem.7b00845

    Article  CAS  PubMed  Google Scholar 

  99. Spiliotopoulos D, Wamhoff E-C, Lolli G, Rademacher C, Caflisch A (2017) Discovery of BAZ2A bromodomain ligands. Eur J Med Chem 139(Supplement C):564–572. https://doi.org/10.1016/j.ejmech.2017.08.028

    Article  CAS  PubMed  Google Scholar 

  100. Spiliotopoulos D, Zhu J, Wamhoff E-C, Deerain N, Marchand J-R, Aretz J, Rademacher C, Caflisch A (2017) Virtual screen to NMR (VS2NMR): discovery of fragment hits for the CBP bromodomain. Bioorg Med Chem Lett 27(11):2472–2478. https://doi.org/10.1016/j.bmcl.2017.04.001

    Article  CAS  PubMed  Google Scholar 

  101. Wang N, Li F, Bao H, Li J, Wu J, Ruan K (2016) NMR fragment screening hit induces plasticity of BRD7/9 bromodomains. Chembiochem 17(15):1456–1463. https://doi.org/10.1002/cbic.201600184

    Article  CAS  PubMed  Google Scholar 

  102. Gossert AD, Jahnke W (2016) NMR in drug discovery: a practical guide to identification and validation of ligands interacting with biological macromolecules. Prog Nucl Magn Reson Spectrosc 97(Supplement C):82–125. https://doi.org/10.1016/j.pnmrs.2016.09.001

    Article  CAS  PubMed  Google Scholar 

  103. Perell GT, Mishra NK, Sudhamalla B, Ycas PD, Islam K, Pomerantz WCK (2017) Specific acetylation patterns of H2A.Z form transient interactions with the BPTF bromodomain. Biochemistry 56(35):4607–4615. https://doi.org/10.1021/acs.biochem.7b00648

    Article  CAS  PubMed  Google Scholar 

  104. Navratilova I, Aristotelous T, Hopkins AL, Picaud S, Chaikuad A, Knapp S, Filappakopoulos P (2016) Discovery of new bromodomain scaffolds by biosensor fragment screening. ACS Med Chem Lett 7(12):1213–1218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. 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 (2013) PFI-1, a highly selective protein interaction inhibitor, targeting BET bromodomains. Cancer Res 73(11):3336–3346. https://doi.org/10.1158/0008-5472.can-12-3292

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Ember SWJ, Zhu J-Y, Olesen SH, Martin MP, Becker A, Berndt N, Georg GI, Schönbrunn E (2014) Acetyl-lysine binding site of bromodomain-containing protein 4 (BRD4) interacts with diverse kinase inhibitors. ACS Chem Biol 9(5):1160–1171. https://doi.org/10.1021/cb500072z

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. 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 (2016) Identification of a chemical probe for family VIII bromodomains through optimization of a fragment hit. J Med Chem 59(10):4800–4811. https://doi.org/10.1021/acs.jmedchem.6b00012

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Chaikuad A, Lang S, Brennan PE, Temperini C, Fedorov O, Hollander J, Nachane R, Abell C, Müller S, Siegal G, Knapp S (2016) Structure-based identification of inhibitory fragments targeting the p300/CBP-associated factor bromodomain. J Med Chem 59(4):1648–1653. https://doi.org/10.1021/acs.jmedchem.5b01719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Martin LJ, Koegl M, Bader G, Cockcroft X-L, Fedorov O, Fiegen D, Gerstberger T, Hofmann MH, Hohmann AF, Kessler D, Knapp S, Knesl P, Kornigg S, Müller S, Nar H, Rogers C, Rumpel K, Schaaf O, Steurer S, Tallant C, Vakoc CR, Zeeb M, Zoephel A, Pearson M, Boehmelt G, McConnell D (2016) Structure-based design of an in vivo active selective BRD9 inhibitor. J Med Chem 59(10):4462–4475. https://doi.org/10.1021/acs.jmedchem.5b01865

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  110. Chen P, Chaikuad A, Bamborough P, Bantscheff M, Bountra C, Chung C-w, Fedorov O, Grandi P, Jung D, Lesniak R, Lindon M, Müller S, Philpott M, Prinjha R, Rogers C, Selenski C, Tallant C, Werner T, Willson TM, Knapp S, Drewry DH (2016) Discovery and characterization of GSK2801, a selective chemical probe for the bromodomains BAZ2A and BAZ2B. J Med Chem 59(4):1410–1424. https://doi.org/10.1021/acs.jmedchem.5b00209

    Article  CAS  PubMed  Google Scholar 

  111. Bamborough P, Diallo H, Goodacre JD, Gordon L, Lewis A, Seal JT, Wilson DM, Woodrow MD, Chung C-w (2012) Fragment-based discovery of bromodomain inhibitors part 2: optimization of phenylisoxazole sulfonamides. J Med Chem 55(2):587–596. https://doi.org/10.1021/jm201283q

    Article  CAS  PubMed  Google Scholar 

  112. Chung C-w, Dean AW, Woolven JM, Bamborough P (2012) Fragment-based discovery of bromodomain inhibitors part 1: inhibitor binding modes and implications for lead discovery. J Med Chem 55(2):576–586. https://doi.org/10.1021/jm201320w

    Article  CAS  PubMed  Google Scholar 

  113. Molina DM, Jafari R, Ignatushchenko M, Seki T, Larsson EA, Dan C, Sreekumar L, Cao Y, Nordlund P (2013) Monitoring drug target engagement in cells and tissues using the cellular thermal shift assay. Science 341(6141):84–87. https://doi.org/10.1126/science.1233606

    Article  CAS  Google Scholar 

  114. Jafari R, Almqvist H, Axelsson H, Ignatushchenko M, Lundbäck T, Nordlund P, Molina DM (2014) The cellular thermal shift assay for evaluating drug target interactions in cells. Nat Protoc 9:2100. https://doi.org/10.1038/nprot.2014.138. https://www.nature.com/articles/nprot.2014.138#supplementary-information

    Article  CAS  PubMed  Google Scholar 

  115. Philpott M, Yang J, Tumber T, Fedorov O, Uttarkar S, Filippakopoulos P, Picaud S, Keates T, Felletar I, Ciulli A, Knapp S, Heightman TD (2011) Bromodomain-peptide displacement assays for interactome mapping and inhibitor discovery. Mol BioSyst 7(10):2899–2908. https://doi.org/10.1039/c1mb05099k

    Article  CAS  PubMed  Google Scholar 

  116. Roberts JM, Bradner JE (2015) A bead-based proximity assay for BRD4 ligand discovery. Curr Protoc Chem Biol 7(4):263–278. https://doi.org/10.1002/9780470559277.ch150024

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  117. Fedorov O, Lingard H, Wells C, Monteiro OP, Picaud S, Keates T, Yapp C, Philpott M, Martin SJ, Felletar I, Marsden BD, Filippakopoulos P, Muller S, Knapp S, Brennan PE (2014) [1,2,4]Triazolo[4,3-a]phthalazines: inhibitors of diverse bromodomains. J Med Chem 57(2):462–476. https://doi.org/10.1021/jm401568s

    Article  CAS  PubMed  Google Scholar 

  118. Ciceri P, Mueller 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 (2014) Dual kinase-bromodomain inhibitors for rationally designed polypharmacology. Nat Chem Biol 10(4):305–312. https://doi.org/10.1038/nchembio.1471

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Crawford TD, Audia JE, Bellon S, Burdick DJ, Bommi-Reddy A, Cote A, Cummings RT, Duplessis M, Flynn EM, Hewitt M, Huang H-R, Jayaram H, Jiang Y, Joshi S, Kiefer JR, Murray J, Nasveschuk CG, Neiss A, Pardo E, Romero FA, Sandy P, Sims RJ, Tang Y, Taylor AM, Tsui V, Wang J, Wang S, Wang Y, Xu Z, Zawadzke L, Zhu X, Albrecht BK, Magnuson SR, Cochran AG (2017) GNE-886: a potent and selective inhibitor of the cat eye syndrome chromosome region candidate 2 bromodomain (CECR2). ACS Med Chem Lett 8(7):737–741. https://doi.org/10.1021/acsmedchemlett.7b00132

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Chen P, Chaikuad A, Bamborough P, Bantscheff M, Bountra C, Chung C-w, Fedorov O, Grandi P, Jung D, Lesniak R, Lindon M, Muller S, Philpott M, Prinjha R, Rogers C, Selenski C, Tallant C, Werner T, Willson TM, Knapp S, Drewry DH (2016) Discovery and characterization of GSK2801, a selective chemical probe for the bromodomains BAZ2A and BAZ2B. J Med Chem 59(4):1410–1424. https://doi.org/10.1021/acs.jmedchem.5b00209

    Article  CAS  PubMed  Google Scholar 

  121. Crawford TD, Romero FA, Lai KW, Tsui V, Taylor AM, de Leon Boenig G, Noland CL, Murray J, Ly J, Choo EF, Hunsaker TL, Chan EW, Merchant M, Kharbanda S, Gascoigne KE, Kaufman S, Beresini MH, Liao J, Liu W, Chen KX, Chen Z, Conery AR, Cote A, Jayaram H, Jiang Y, Kiefer JR, Kleinheinz T, Li Y, Maher J, Pardo E, Poy F, Spillane KL, Wang F, Wang J, Wei X, Xu Z, Xu Z, Yen I, Zawadzke L, Zhu X, Bellon S, Cummings R, Cochran AG, Albrecht BK, Magnuson S (2016) Discovery of a potent and selective in vivo probe (GNE-272) for the bromodomains of CBP/EP300. J Med Chem 59(23):10549–10563. https://doi.org/10.1021/acs.jmedchem.6b01022

    Article  CAS  PubMed  Google Scholar 

  122. Humphreys PG, Bamborough P, Chung C-w, Craggs PD, Gordon L, Grandi P, Hayhow TG, Hussain J, Jones KL, Lindon M, Michon A-M, Renaux JF, Suckling CJ, Tough DF, Prinjha RK (2017) Discovery of a potent, cell penetrant, and selective p300/CBP-associated factor (PCAF)/general control nonderepressible 5 (GCN5) bromodomain chemical probe. J Med Chem 60(2):695–709. https://doi.org/10.1021/acs.jmedchem.6b01566

    Article  CAS  PubMed  Google Scholar 

  123. Theodoulou NH, Bamborough P, Bannister AJ, Becher I, Bit RA, Che KH, Chung C-w, Dittmann A, Drewes G, Drewry DH, Gordon L, Grandi P, Leveridge M, Lindon M, Michon A-M, Molnar J, Robson SC, Tomkinson NCO, Kouzarides T, Prinjha RK, Humphreys PG (2016) Discovery of I-BRD9, a selective cell active chemical probe for bromodomain containing protein 9 inhibition. J Med Chem 59(4):1425–1439. https://doi.org/10.1021/acs.jmedchem.5b00256

    Article  CAS  PubMed  Google Scholar 

  124. Kenakin TP (1993) Pharmacological analysis of drug-receptor interaction. Raven, New York

    Google Scholar 

  125. Chung C-W, Coste H, White JH, Mirguet O, Wilde J, Gosmini RL, Delves C, Magny SM, Woodward R, Hughes SA, Boursier EV, Flynn H, Bouillot AM, Bamborough P, Brusq J-MG, Gellibert FJ, Jones EJ, Riou AM, Homes P, Martin SL, Uings IJ, Toum J, Clément CA, Boullay A-B, Grimley RL, Blandel FM, Prinjha RK, Lee K, Kirilovsky J, Nicodeme E (2011) Discovery and characterization of small molecule inhibitors of the BET family bromodomains. J Med Chem 54(11):3827–3838. https://doi.org/10.1021/jm200108t

    Article  CAS  PubMed  Google Scholar 

  126. Xinyi H (2003) Fluorescence polarization competition assay: the range of resolvable inhibitor potency is limited by the affinity of the fluorescent ligand. J Biomol Screen 8(1):34–38. https://doi.org/10.1177/1087057102239666

    Article  CAS  Google Scholar 

  127. Cox OB, Krojer T, Collins P, Monteiro O, Talon R, Bradley A, Fedorov O, Amin J, Marsden BD, Spencer J, von Delft F, Brennan PE (2016) A poised fragment library enables rapid synthetic expansion yielding the first reported inhibitors of PHIP(2), an atypical bromodomain. Chem Sci 7(3):2322–2330. https://doi.org/10.1039/C5SC03115J

    Article  CAS  PubMed  Google Scholar 

  128. Zhao L, Cao D, Chen T, Wang Y, Miao Z, Xu Y, Chen W, Wang X, Li Y, Du Z, Xiong B, Li J, Xu C, Zhang N, He J, Shen J (2013) Fragment-based drug discovery of 2-thiazolidinones as inhibitors of the histone reader BRD4 bromodomain. J Med Chem 56(10):3833–3851. https://doi.org/10.1021/jm301793a

    Article  CAS  PubMed  Google Scholar 

  129. 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 (2012) Identification of a chemical probe for bromo and extra C-terminal bromodomain inhibition through optimization of a fragment-derived hit. J Med Chem 55(22):9831–9837. https://doi.org/10.1021/jm3010515

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  130. Daguer JP, Zambaldo C, Abegg D, Barluenga S, Tallant C, Muller S, Adibekian A, Winssinger N (2015) Identification of covalent bromodomain binders through DNA display of small molecules. Angew Chem Int Ed Engl 54(20):6057–6061. https://doi.org/10.1002/anie.201412276

    Article  CAS  PubMed  Google Scholar 

  131. Rhyasen GW, Hattersley MM, Yao Y, Dulak A, Wang W, Petteruti P, Dale IL, Boiko S, Cheung T, Zhang J, Wen S, Castriotta L, Lawson D, Collins M, Bao L, Ahdesmaki MJ, Walker G, O’Connor G, Yeh TC, Rabow AA, Dry JR, Reimer C, Lyne P, Mills GB, Fawell SE, Waring MJ, Zinda M, Clark E, Chen H (2016) AZD5153: a novel bivalent BET bromodomain inhibitor highly active against hematologic malignancies. Mol Cancer Ther 15(11):2563–2574. https://doi.org/10.1158/1535-7163.mct-16-0141

    Article  CAS  PubMed  Google Scholar 

  132. Waring MJ, Chen H, Rabow AA, Walker G, Bobby R, Boiko S, Bradbury RH, Callis R, Clark E, Dale I, Daniels DL, Dulak A, Flavell L, Holdgate G, Jowitt TA, Kikhney A, McAlister M, Méndez J, Ogg D, Patel J, Petteruti P, Robb GR, Robers MB, Saif S, Stratton N, Svergun DI, Wang W, Whittaker D, Wilson DM, Yao Y (2016) Potent and selective bivalent inhibitors of BET bromodomains. Nat Chem Biol 12:1097. https://doi.org/10.1038/nchembio.2210. https://www.nature.com/articles/nchembio.2210#supplementary-information

    Article  CAS  PubMed  Google Scholar 

  133. Tanaka M, Roberts JM, Seo HS, Souza A, Paulk J, Scott TG, DeAngelo SL, Dhe-Paganon S, Bradner JE (2016) Design and characterization of bivalent BET inhibitors. Nat Chem Biol 12(12):1089–1096. https://doi.org/10.1038/nchembio.2209

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  134. Lu J, Qian Y, Altieri M, Dong H, Wang J, Raina K, Hines J, Winkler JD, Crew AP, Coleman K, Crews CM (2015) Hijacking the E3 ubiquitin ligase cereblon to efficiently target BRD4. Chem Biol 22(6):755–763. https://doi.org/10.1016/j.chembiol.2015.05.009

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Zengerle M, Chan K-H, Ciulli A (2015) Selective small molecule induced degradation of the BET bromodomain protein BRD4. ACS Chem Biol 10(8):1770–1777. https://doi.org/10.1021/acschembio.5b00216

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  136. Winter GE, Buckley DL, Paulk J, Roberts JM, Souza A, Dhe-Paganon S, Bradner JE (2015) Drug development. Phthalimide conjugation as a strategy for in vivo target protein degradation. Science 348(6241):1376–1381. https://doi.org/10.1126/science.aab1433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  137. Toure M, Crews CM (2016) Small-molecule PROTACS: new approaches to protein degradation. Angew Chem Int Ed 55(6):1966–1973. https://doi.org/10.1002/anie.201507978

    Article  CAS  Google Scholar 

  138. Remillard D, Buckley DL, Paulk J, Dastjerdi S, Bradner JE, Brien GL, Armstrong SA, Sonnett M, Sonnett M, Wuhr M, Seo H-S, Dhe-Paganon S, Wuhr M (2017) Degradation of the BAF complex factor BRD9 by heterobifunctional ligands. Angew Chem Int Ed Engl 56(21):5738–5743

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  139. Gechijian LN, Buckley DL, Lawlor MA, Reyes JM, Paulk J, Ott CJ, Winter GE, Erb MA, Scott TG, Xu M, Seo HS, Dhe-Paganon S, Kwiatkowski NP, Perry JA, Qi J, Gray NS, Bradner JE (2018) Functional TRIM24 degrader via conjugation of ineffectual bromodomain and VHL ligands. Nat Chem Biol. https://doi.org/10.1038/s41589-018-0010-y

  140. Tekel SJ, Haynes KA (2017) Molecular structures guide the engineering of chromatin. Nucleic Acids Res 45(13):7555–7570. https://doi.org/10.1093/nar/gkx531

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Authors and Affiliations

  1. Department of Chemistry, University of Minnesota, Minneapolis, MN, USA

    William C. K. Pomerantz, Jorden A. Johnson & Peter D. Ycas

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  1. William C. K. Pomerantz
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  2. Jorden A. Johnson
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  3. Peter D. Ycas
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Correspondence to William C. K. Pomerantz .

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  1. Sapienza University of Rome, Rome, Italy

    Antonello Mai

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Funding: This study was funded by the National Institute of General Medical Sciences of the National Institutes under the award number R01GM121414 (W.C.K.P and P.D.Y). J.A.J. was supported by a National Institutes of Health Biotechnology training grant 5T32GM008347-23.

Conflict of Interest: All authors declare that they have no conflicts of interest.

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Pomerantz, W.C.K., Johnson, J.A., Ycas, P.D. (2019). Applied Biophysics for Bromodomain Drug Discovery. In: Mai, A. (eds) Chemical Epigenetics. Topics in Medicinal Chemistry, vol 33. Springer, Cham. https://doi.org/10.1007/7355_2019_79

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