Structure-Guided Design of a Domain-Selective Bromodomain and Extra Terminal N-Terminal Bromodomain Chemical ProbeClick to copy article linkArticle link copied!
- Erin BradleyErin BradleyGSK, Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, U.K.More by Erin Bradley
- Lucia FusaniLucia FusaniGSK, Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, U.K.More by Lucia Fusani
- Chun-wa ChungChun-wa ChungGSK, Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.More by Chun-wa Chung
- Peter D. CraggsPeter D. CraggsGSK, Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.More by Peter D. Craggs
- Emmanuel H. DemontEmmanuel H. DemontGSK, Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.More by Emmanuel H. Demont
- Philip G. Humphreys*Philip G. Humphreys*Email: [email protected]GSK, Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.More by Philip G. Humphreys
- Darren J. MitchellDarren J. MitchellGSK, Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.More by Darren J. Mitchell
- Alex PhillipouAlex PhillipouGSK, Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.More by Alex Phillipou
- Inmaculada RiojaInmaculada RiojaGSK, Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.More by Inmaculada Rioja
- Rishi R. ShahRishi R. ShahGSK, Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.More by Rishi R. Shah
- Christopher R. WellawayChristopher R. WellawayGSK, Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.More by Christopher R. Wellaway
- Rab K. PrinjhaRab K. PrinjhaGSK, Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.More by Rab K. Prinjha
- David S. PalmerDavid S. PalmerDepartment of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, U.K.More by David S. Palmer
- William J. Kerr*William J. Kerr*Email: [email protected]Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, U.K.More by William J. Kerr
- Marc ReidMarc ReidDepartment of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, U.K.More by Marc Reid
- Ian D. WallIan D. WallGSK, Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.More by Ian D. Wall
- Rosa Cookson*Rosa Cookson*Email: [email protected]GSK, Medicines Research Centre, Stevenage SG1 2NY, Hertfordshire, U.K.More by Rosa Cookson
Abstract
Small-molecule-mediated disruption of the protein–protein interactions between acetylated histone tails and the tandem bromodomains of the bromodomain and extra-terminal (BET) family of proteins is an important mechanism of action for the potential modulation of immuno-inflammatory and oncology disease. High-quality chemical probes have proven invaluable in elucidating profound BET bromodomain biology, with seminal publications of both pan- and domain-selective BET family bromodomain inhibitors enabling academic and industrial research. To enrich the toolbox of structurally differentiated N-terminal bromodomain (BD1) BET family chemical probes, this work describes an analysis of the GSK BRD4 bromodomain data set through a lipophilic efficiency lens, which enabled identification of a BD1 domain-biased benzimidazole series. Structure-guided growth targeting a key Asp/His BD1/BD2 switch enabled delivery of GSK023, a high-quality chemical probe with 300–1000-fold BET BD1 domain selectivity and a phenotypic cellular fingerprint consistent with BET bromodomain inhibition.
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License Summary*
You are free to share(copy and redistribute) this article in any medium or format and to adapt(remix, transform, and build upon) the material for any purpose, even commercially within the parameters below:
Creative Commons (CC): This is a Creative Commons license.
Attribution (BY): Credit must be given to the creator.
*Disclaimer
This summary highlights only some of the key features and terms of the actual license. It is not a license and has no legal value. Carefully review the actual license before using these materials.
License Summary*
You are free to share(copy and redistribute) this article in any medium or format and to adapt(remix, transform, and build upon) the material for any purpose, even commercially within the parameters below:
Creative Commons (CC): This is a Creative Commons license.
Attribution (BY): Credit must be given to the creator.
*Disclaimer
This summary highlights only some of the key features and terms of the actual license. It is not a license and has no legal value. Carefully review the actual license before using these materials.
Introduction
Figure 1
Figure 1. (a) Overlay of apo BRD4 BD1 in orange (pdb: 2oss) and apo BRD4 BD2 in cyan (pdb: 2ouo). Waters and ethylene glycol have been removed for clarity; (b) percent identity within the KAc binding site between the BET family bromodomains. (13) The darker the shade of blue, the higher the bromodomain identify.
Figure 2
Figure 2. Structures of selected domain-biased/selective BET BD1 and BD2 bromodomain inhibitors. Where reported, the part of the molecules that drives BET BD1 domain selectivity through interacting with Asp144 (BRD4 BD1 numbering) is colored blue for clarity.
Results and Discussion
Target Product Profile
Hit Identification
Figure 3
Figure 3. (a) Plot of BRD4 BD1 pIC50 against BRD4 BD2 pIC50 for 169 compounds with BRD4 BD1 pIC50 ≥ 7 and BRD4 BD1 domain selectivity ≥50-fold, with diagonal lines representing BD1 domain selectivity. Compounds containing substructure 10 are colored blue, and those that do not contain substructure 10 are colored green; (b) substructure 10; (c) plot of BRD4 BD1 pIC50 against chromLogDpH7.4 with diagonal lines representing different LipE values for 169 molecules. Compounds containing substructure 10 are colored blue, and those that do not contain substructure 10 are colored green; (d) comparison of median LipE values for compounds containing substructure 10 and those that do not.
Scheme 1
aReagents and conditions: (a) (R)- or (S)-1-(3-(aminomethyl)piperidin-1-yl)ethan-1-one, DIPEA, NMP, 200 °C, 1 h; (b) 1,5-dimethyl-6-oxo-1,6-dihydropyridine-3-carbaldehyde, Na2S2O4, EtOH, H2O, 100 °C, 130 min.

LipE = BRD4 BD1 pIC50–chromLogDpH7.4; LE = (1.37 × BRD4 BD1 pIC50)/heavy atom count.
Figure 4
Figure 4. (a) Structure of 14; (b) crystal structure of 14 (green) bound to BRD2 BD2 (orange) (pdb: 8px8). Water molecules are shown as red spheres and hydrogen bonds are marked in yellow; (c) As (b), but with the protein surface shown in orange; (d) overlay of the crystal structure of 13 (pink) bound to BRD2 BD2 (gray) (pdb: 8px2) and the crystal structure of 14 (green) bound to BRD2 BD2 (orange) (pdb: 8px8); (e) As (b) but with an overlay of the BRD4 BD1 protein surface (cyan) bound to 13 (pdb: 6tpy).
Figure 5
Figure 5. Two-dimensional plot of the average conformational FES of apo BRD4 BD2 (pdb: 2ouo) as calculated by metadynamics. In the boxes, representative conformations of the minima A (His437 trans), B (His437 gauche+), and C (His437 gauche+) of the apo structure are reported. The free energy is displayed every 1 kcal/mol, and the contour levels are shown up to 5 kcal/mol.
Hit Optimization
Scheme 2
aReagents and conditions: (a) tert-butyl (S)-3-(aminomethyl)piperidine-1-carboxylate, K2CO3, DMF, 80–100 °C; (b) 1,5-dimethyl-6-oxo-1,6-dihydropyridine-3-carbaldehyde, Na2S2O4, EtOH, H2O, 100 °C; (c) HCl, 1,4-dioxane, 0 °C-rt; (d) acid, HATU, DIPEA, DMF, rt or acid chloride, NEt3, THF, rt; (e) For 21–25, 27–29: HCl, 1,4-dioxane, rt.
Scheme 3
aReagents and conditions: (a) For 34: BrCH2CH2F, NaH, DMF, rt to 60 °C, 1 h, 37%; (b) For 35: BrCH2CHF2, NaH, DMF, rt to 90 °C, 37 h, 37%; (c) For 36: TFA, PhSiH3, THF, 70 °C, 19 h, 44%.


LipE = BRD4 BD1 pIC50–chromLogDpH7.4; LE = (1.37 × BRD4 BD1 pIC50)/heavy atom count.
CLND solubility.
Understanding BD1 Domain Selectivity and Activity
Figure 6
Figure 6. (a) Crystal structure of 31 (yellow) bound to BRD4 BD1 (cyan) (pdb: 8pxa). Water molecules are shown as red spheres and hydrogen bonds are marked in yellow; (b) As (a), but with the protein surface from 14 bound to BRD2 BD2 shown in orange overlaid (pdb: 8px8); (c) overlay of 31 (yellow) bound to BRD4 BD1 (pdb: 8pxa) with 14 (green) bound to BRD2 BD2 (pdb: 8px8); (d) overlay of 31 (yellow) bound to BRD4 BD1 (cyan) (pdb: 8pxa) and GSK778 (8) (gray) bound to BRD4 BD1 (blue) (pdb: 6swn). Only Asp145 and Asp144 are shown for clarity.
Figure 7
Profile of 31

TR-FRET pIC50 | fold selectivity | BROMOscan pKd | fold selectivity | |||
---|---|---|---|---|---|---|
bromodomain | BD1 | BD2 | BD1 | BD2 | ||
BRD2 | 8.0 | 5.4 | 400 | 8.5 | 5.5 | 1000 |
BRD3 | 7.7 | 5.1 | 400 | 8.4 | 5.8 | 400 |
BRD4 | 7.8 | 4.8 | 1000 | 8.1 | 5.6 | 316 |
BRDT | 7.3 | 4.5 | 630 | 8.1 | 5.5 | 400 |
EP300 | 5.0 | 1200 | ||||
20 non-BET bromodomains | ≤4.8 | ≥2000 |
Figure 8
Figure 8. (a) BioMAP profile of 31 [10 μM (red), 2.5 μM (orange), 630 nM (yellow), and 160 nM (green)] in the Diversity PLUS Panel. The X-axis lists the quantitative protein-based biomarker readouts measured in each system. The Y-axis represents a log-transformed ratio of the biomarker readouts for the drug-treated sample (n = 1) over vehicle controls (n ≥ 6). The gray region around the Y-axis represents the 95% significance envelope generated from historical vehicle controls. Biomarker activities are annotated when two or more consecutive concentrations change in the same direction relative to vehicle controls, are outside of the significance envelope, and have at least one concentration with an effect size >20% (log10 ratio >0.1). Biomarker key activities are described as modulated if these activities increase in some systems but decrease in others. No cytotoxicity was observed at the concentrations tested, and antiproliferative effects are indicated by a thick gray arrow above the X-axis; (b) As (a), but with 31 (10 μM, red) and (+)-JQ1 (120 nM, blue).
Conclusions
Experimental Section
Physicochemical Properties
Chemistry Methods
(R)-1-(3-(((2-Nitrophenyl)amino)methyl)piperidin-1-yl)ethan-1-one ((R)-11))
(S)-1-(3-(((2-Nitrophenyl)amino)methyl)piperidin-1-yl)ethan-1-one ((S)-11))
(R)-5-(1-((1-Acetylpiperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)-1,3-dimethylpyridin-2(1H)-one ((R)-12)
(S)-5-(1-((1-Acetylpiperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)-1,3-dimethylpyridin-2(1H)-one ((S)-12)
(S)-5-(1-((1-Acetylpiperidin-3-yl)methyl)-5-bromo-1H-benzo[d]imidazole-2-yl)-1,3-dimethylpyridin-2(1H)-one (14)
tert-Butyl (S)-3-(((2-Nitrophenyl)amino)methyl)piperidine-1-carboxylate (15)
tert-Butyl (S)-3-(((4-Bromo-2-nitrophenyl)amino)methyl)piperidine-1-carboxylate (16)
(S)-3-((2-(1,5-Dimethyl-6-oxo-1,6-dihydropyridin-3-yl)-H-benzo[d]imidazole-1-yl)methyl)piperidine-1-carboxylate (17)
tert-Butyl (S)-3-((5-Bromo-2-(1,5-dimethyl-6-oxo-1,6-dihydropyridin-3-yl)-1H-benzo[d]imidazole-1-yl)methyl)piperidine-1-carboxylate (18)
(R)-1,3-Dimethyl-5-(1-(piperidin-3-ylmethyl)-1H-benzo[d]imidazole-2-yl)pyridin-2(1H)-one (19)
(R)-5-(5-Bromo-1-(piperidin-3-ylmethyl)-1H-benzo[d]imidazole-2-yl)-1,3-dimethylpyridin-2(1H)-one Hydrochloride Salt (20)
(S)-5-(1-((1-(4-Aminobutanoyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)-1,3-dimethylpyridin-2(1H)-one (21)
(S)-5-(1-((1-(Azetidine-3-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)-1,3-dimethylpyridin-2(1H)-one (22)
5-(1-(((S)-1-((1r,3S)-3-Aminocyclobutane-1-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)-1,3-dimethylpyridin-2(1H)-one (23)
1,3-Dimethyl-5-(1-(((S)-1-((S)-pyrrolidine-3-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)pyridin-2(1H)-one (24)
5-(1-(((S)-1-((1S,3S)-3-Aminocyclopentane-1-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)-1,3-dimethylpyridin-2(1H)-one (25)
(S)-5-(1-((1-(1H-Imidazole-5-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazole -2-yl)-1,3-dimethylpyridin-2(1H)-one, Formic Acid Salt (26)
(S)-1,3-Dimethyl-5-(1-((1-(piperidine-4-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)pyridin-2(1H)-one (27)
5-(1-(((S)-1-((1r,4R)-4-Aminocyclohexane-1-carbonyl)piperidin-3-yl)methyl)-1H-benzo [d]imidazole-2-yl)-1,3-dimethylpyridin-2(1H)-one (28)
1,3-Dimethyl-5-(1-(((3S)-1-(1-methylpiperidine-3-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)pyridin-2(1H)-one (29)
(S)-1,3-Dimethyl-5-(1-((1-(1-methylpiperidine-4-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)pyridin-2(1H)-one (30)
(S)-5-(1-((1-(1-Isopropylpiperidine-4-carbonyl)piperidin-3-yl)methyl)-1H-benzo [d]imidazole-2-yl)-1,3-dimethylpyridin-2(1H)-one (31)
(S)-1,3-Dimethyl-5-(1-((1-(tetrahydro-2H-pyran-4-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)pyridin-2(1H)-one (32)
(S)-5-(1-((1-(1-Acetylpiperidine-4-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)-1,3-dimethylpyridin-2(1H)-one (33)
(S)-5-(1-((1-(1-(2-Fluoroethyl)piperidine-4-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)-1,3-dimethylpyridin-2(1H)-one (34)
(S)-5-(1-((1-(1-(2,2-Difluoroethyl)piperidine-4-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)-1,3-dimethylpyridin-2(1H)-one (35)
(S)-1,3-Dimethyl-5-(1-((1-(1-(2,2,2-trifluoroethyl)piperidine-4-carbonyl)piperidin-3-yl)methyl)-1H-benzo[d]imidazole-2-yl)pyridin-2(1H)-one (36)
Computational Methods
Complex Preparation
Metadynamics
Docking Calculations
WaterMap
BioMAP Phenotypic Profile
In Vitro Assays
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jmedchem.3c00906.
All screening statistics, full BROMOscan and selectivity data, 1H and 13C NMR spectra for 31, representative LCMS traces of target compounds, and X-ray data collection and refinement statistics (PDF)
Molecular formula strings (CSV)
Docking of compound 12 into BRD4 BD1 (PDB)
Coordinates have been deposited with the Protein Data Bank under accession codes 8px2 (BRD2 BD2/13 complex), 8px8 (BRD2 BD2/14 complex), and 8pxa (BRD4 BD1/31 complex). The authors will release atomic coordinates and experimental data upon article publication.
Terms & Conditions
Most electronic Supporting Information files are available without a subscription to ACS Web Editions. Such files may be downloaded by article for research use (if there is a public use license linked to the relevant article, that license may permit other uses). Permission may be obtained from ACS for other uses through requests via the RightsLink permission system: http://pubs.acs.org/page/copyright/permissions.html.
Acknowledgments
E.B. and L.F. are grateful to GSK, Stevenage, and the University of Strathclyde for a Ph.D. studentship, and we thank the EPSRC for funding via Prosperity Partnership EP/S035990/1. For the purpose of open access, the authors have applied a Creative Commons Attribution (CC BY) licence to any Author Accepted Manuscript version arising from this submission. We also thank Sean Lynn and Richard Upton for assistance with NMR; Steve Jackson and Eric Hortense for chiral HPLC, Tony Cook for high resolution mass spectrometry support, and the GSK Physchem Team for physicochemical data generation.
aq | aqueous |
BD1 | bromodomain 1 (N-terminal bromodomain) |
BD2 | bromodomain 2 (C-terminal bromodomain) |
BRD2 | bromodomain containing protein 2 |
BRD3 | bromodomain containing protein 3 |
BRD4 | bromodomain containing protein 4 |
BRDT | bromodomain containing protein, testis-specific |
CAD | charged aerosol detection |
CLND | chemiluminescent nitrogen detection |
CV | collective variables |
EP300 | E1A-associated protein p300 |
FES | free energy surface |
hWB | human whole blood |
LCMS | liquid chromatography mass spectrometry |
LE | ligand efficiency |
LipE | lipophilic efficiency |
MCP-1 | monocyte chemoattractant protein-1 |
MDAP | mass-directed auto preparation |
pIC50 | –log10(IC50) |
pdb | protein data bank |
TR-FRET | time-resolved Fürster resonance energy transfer |
WPF | tryptophan-proline-phenylalanine |
References
This article references 58 other publications.
- 1Filippakopoulos, P.; Picaud, S.; Mangos, M.; Keates, T.; Lambert, J.-P.; Barsyte-Lovejoy, D.; Felletar, I.; Volkmer, R.; Müller, S.; Pawson, T.; Gingras, A.-C.; Arrowsmith, C. H.; Knapp, S. Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family. Cell 2012, 149, 214– 231, DOI: 10.1016/j.cell.2012.02.013Google Scholar1https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XltVamurs%253D&md5=05583a01a1cd4c3b59fc59c00e4c4777Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain FamilyFilippakopoulos, Panagis; Picaud, Sarah; Mangos, Maria; Keates, Tracy; Lambert, Jean-Philippe; Barsyte-Lovejoy, Dalia; Felletar, Ildiko; Volkmer, Rudolf; Muller, Susanne; Pawson, Tony; Gingras, Anne-Claude; Arrowsmith, Cheryl H.; Knapp, StefanCell (Cambridge, MA, United States) (2012), 149 (1), 214-231CODEN: CELLB5; ISSN:0092-8674. (Cell Press)Bromodomains (BRDs) are protein interaction modules that specifically recognize ε-N-lysine acetylation motifs, a key event in the reading process of epigenetic marks. The 61 BRDs in the human genome cluster into eight families based on structure/sequence similarity. Here, we present 29 high-resoln. crystal structures, covering all BRD families. These proteins are: ASH1L, ATAD2, BAZ2B, BPTF, BRD1, BRD3(1), BRD3(2), BRD4(1), BRD4(2), BRD9, BRDT(1), CECR2, EP300, CREBBP, GCN5L2, KIAA1240, PB1(1), PB1(2), PB1(3), PB1(4), PB1(5), PB1(6), PCAF, PHIP(2), TAF1(2), WDR9(2), BRD4(1). Comprehensive crossfamily structural anal. identifies conserved and family-specific structural features that are necessary for specific acetylation-dependent substrate recognition. Screening of more than 30 representative BRDs against systematic histone-peptide arrays identifies new BRD substrates and reveals a strong influence of flanking posttranslational modifications, such as acetylation and phosphorylation, suggesting that BRDs recognize combinations of marks rather than singly acetylated sequences. We further uncovered a structural mechanism for the simultaneous binding and recognition of diverse diacetyl-contg. peptides by BRD4. These data provide a foundation for structure-based drug design of specific inhibitors for this emerging target family.
- 2Zaware, N.; Zhou, M.-M. Bromodomain Biology and Drug Discovery. Nat. Struct. Mol. Biol. 2019, 26, 870– 879, DOI: 10.1038/s41594-019-0309-8Google Scholar2https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvFSnsL3E&md5=7ccf3a3a2ff7147ead1148ee71fa2806Bromodomain biology and drug discoveryZaware, Nilesh; Zhou, Ming-MingNature Structural & Molecular Biology (2019), 26 (10), 870-879CODEN: NSMBCU; ISSN:1545-9993. (Nature Research)The bromodomain (BrD) is a conserved structural module found in chromatin- and transcription-assocd. proteins that acts as the primary reader for acetylated lysine residues. This basic activity endows BrD proteins with versatile functions in the regulation of protein-protein interactions mediating chromatin-templated gene transcription, DNA recombination, replication and repair. Consequently, BrD proteins are involved in the pathogenesis of numerous human diseases. In this Review, we highlight our current understanding of BrD biol., and discuss the latest development of small-mol. inhibitors targeting BrDs as emerging epigenetic therapies for cancer and inflammatory disorders.
- 3Belkina, A. C.; Denis, G. V. BET Domain Co-Regulators in Obesity, Inflammation and Cancer. Nat. Rev. Cancer 2012, 12, 465– 477, DOI: 10.1038/nrc3256Google Scholar3https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XovFyks7s%253D&md5=d06d88ef0d5d4d71115f40a2f901f53dBET domain co-regulators in obesity, inflammation and cancerBelkina, Anna C.; Denis, Gerald V.Nature Reviews Cancer (2012), 12 (7), 465-477CODEN: NRCAC4; ISSN:1474-175X. (Nature Publishing Group)A review. The bromodomain is a highly conserved motif of 110 amino acids that is bundled into four anti-parallel α-helixes and found in proteins that interact with chromatin, such as transcription factors, histone acetylases and nucleosome remodelling complexes. Bromodomain proteins are chromatin 'readers'; they recruit chromatin-regulating enzymes, including 'writers' and 'erasers' of histone modification, to target promoters and to regulate gene expression. Conventional wisdom held that complexes involved in chromatin dynamics are not 'druggable' targets. However, small mols. that inhibit bromodomain and extraterminal (BET) proteins have been described. We examine these developments and discuss the implications for small mol. epigenetic targeting of chromatin networks in cancer.
- 4Jain, A. K.; Barton, M. C. Bromodomain Histone Readers and Cancer. J. Mol. Biol. 2017, 429, 2003– 2010, DOI: 10.1016/j.jmb.2016.11.020Google Scholar4https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvFOisbbI&md5=2d1d3efa959f66eeb8789b48daf96325Bromodomain histone readers and cancerJain, Abhinav K.; Barton, Michelle C.Journal of Molecular Biology (2017), 429 (13), 2003-2010CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)A review. Lysine acetylation of histone proteins is a fundamental post-translational modification that regulates chromatin structure and plays an important role in gene transcription. Aberrant levels of histone lysine acetylation are assocd. with the development of several diseases. Acetyl-lysine modifications create docking sites for bromodomains, which are structurally conserved modules present in transcription-assocd. proteins that are termed "reader" proteins. Bromodomain-contg. reader proteins are part of multiprotein complexes that regulate transcription programs, which are often assocd. with profound phenotypic changes. Many bromodomain-contg. proteins are aberrantly expressed in diseases, as best studied in cancers, where bromodomain proteins impact the expression of oncogenes and anti-apoptotic proteins. Thus, bromodomain readers of histone acetylation have emerged as attractive targets for cancer drug discovery, prompting immense interest in epigenetic-focused, medicinal chem. to develop structurally guided chem. probes of bromodomains. Here, we describe bromodomain-contg. proteins with defined roles in cancer and highlight recent progress in the development of bromodomain inhibitors.
- 5Conery, A. R.; Centore, R. C.; Neiss, A.; Keller, P. J.; Joshi, S.; Spillane, K. L.; Sandy, P.; Hatton, C.; Pardo, E.; Zawadzke, L.; Bommi-Reddy, A.; Gascoigne, K. E.; Bryant, B. M.; Mertz, J. A.; Sims, R. J., III Bromodomain Inhibition of the Transcriptional Coactivators CBP/EP300 as a Therapeutic Strategy to Target the IRF4 Network in Multiple Myeloma. eLife 2016, 5, e10483 DOI: 10.7554/elife.10483Google Scholar5https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXnslahtro%253D&md5=d0037d5abb6fbd85ce1ce2763c535370Bromodomain inhibition of the transcriptional coactivators CBP/EP300 as atherapeutic strategy to target the IRF4 network in multiple myelomaConery, Andrew R.; Centore, Richard C.; Neiss, Adrianne; Keller, Patricia J.; Joshi, Shivangi; Spillane, Kerry L.; Sandy, Peter; Hatton, Charlie; Pardo, Eneida; Zawadzke, Laura; Bommi-Reddy, Archana; Gascoigne, Karen E.; Bryant, Barbara M.; Mertz, Jennifer A.; Sims, Robert J., IIIeLife (2016), 5 (), e10483/1-e10483/17CODEN: ELIFA8; ISSN:2050-084X. (eLife Sciences Publications Ltd.)Pharmacol. inhibition of chromatin co-regulatory factors represents a clin. validated strategy to modulate oncogenic signaling through selective attenuation of gene expression. Here, we demonstrate that CBP/EP300 bromodomain inhibition preferentially abrogates the viability of multiple myeloma cell lines. Selective targeting of multiple myeloma cell lines through CBP/EP300 bromodomain inhibition is the result of direct transcriptional suppression of the lymphocyte-specific transcription factor IRF4, which is essential for the viability of myeloma cells, and the concomitant repression of the IRF4 target gene c-MYC. Ectopic expression of either IRF4 or MYC antagonizes the phenotypic and transcriptional effects of CBP/EP300 bromodomain inhibition, highlighting the IRF4/MYC axis as a key component of its mechanism of action. These findings suggest that CBP/EP300 bromodomain inhibition represents a viable therapeutic strategy for targeting multiple myeloma and other lymphoid malignancies dependent on the IRF4 network.
- 6Zeng, L.; Li, J.; Muller, M.; Yan, S.; Mujtaba, S.; Pan, C.; Wang, Z.; Zhou, M.-M. Selective Small Molecules Blocking HIV-1 Tat and Coactivator PCAF Association. J. Am. Chem. Soc. 2005, 127, 2376– 2377, DOI: 10.1021/ja044885gGoogle Scholar6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXps12lsQ%253D%253D&md5=98329586e5772042c8b7184d8e9a560eSelective Small Molecules Blocking HIV-1 Tat and Coactivator PCAF AssociationZeng, Lei; Li, Jiaming; Muller, Michaela; Yan, Sherry; Mujtaba, Shiraz; Pan, Chongfeng; Wang, Zhiyong; Zhou, Ming-MingJournal of the American Chemical Society (2005), 127 (8), 2376-2377CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Development of drug resistance from mutations in the targeted viral proteins leads to continuation of viral prodn. by chronically infected cells, contributing to HIV-mediated immune dysfunction. Targeting a host cell protein essential for viral reprodn., rather than a viral protein, may minimize the viral drug resistance problem as obsd. with HIV protease inhibitors. The authors report here the development of a novel class of N1-aryl-propane-1,3-diamine compds. using a structure-based approach that selectively inhibit the activity of the bromodomain of the human transcriptional coactivator PCAF, of which assocn. with the HIV trans-activator Tat is essential for transcription and replication of the integrated HIV provirus.
- 7Filippakopoulos, P.; Qi, J.; Picaud, S.; Shen, Y.; Smith, W. B.; Fedorov, O.; Morse, E. M.; Keates, T.; Hickman, T. T.; Felletar, I.; Philpott, M.; Munro, S.; McKeown, M. R.; Wang, Y.; Christie, A. L.; West, N.; Cameron, M. J.; Schwartz, B.; Heightman, T. D.; La Thangue, N.; French, C. A.; Wiest, O.; Kung, A. L.; Knapp, S.; Bradner, J. E. Selective Inhibition of BET Bromodomains. Nature 2010, 468, 1067– 1073, DOI: 10.1038/nature09504Google Scholar7https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXotlGmtA%253D%253D&md5=bd9cadac86124d2c6c3cd5b2a92d68c2Selective inhibition of BET bromodomainsFilippakopoulos, Panagis; Qi, Jun; Picaud, Sarah; Shen, Yao; Smith, William B.; Fedorov, Oleg; Morse, Elizabeth M.; Keates, Tracey; Hickman, Tyler T.; Felletar, Ildiko; Philpott, Martin; Munro, Shongah; McKeown, Michael R.; Wang, Yuchuan; Christie, Amanda L.; West, Nathan; Cameron, Michael J.; Schwartz, Brian; Heightman, Tom D.; La Thangue, Nicholas; French, Christopher; Wiest, Olaf; Kung, Andrew L.; Knapp, Stefan; Bradner, James E.Nature (London, United Kingdom) (2010), 468 (7327), 1067-1073CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Epigenetic proteins are intently pursued targets in ligand discovery. So far, successful efforts have been limited to chromatin modifying enzymes, or so-called epigenetic 'writers' and 'erasers'. Potent inhibitors of histone binding modules have not yet been described. Here the authors report a cell-permeable small mol. (I,JQ1) that binds competitively to acetyl-lysine recognition motifs, or bromodomains. High potency and specificity towards a subset of human bromodomains is explained by co-crystal structures with bromodomain and extra-terminal (BET) family member BRD4, revealing excellent shape complementarity with the acetyl-lysine binding cavity. Recurrent translocation of BRD4 is obsd. in a genetically-defined, incurable subtype of human squamous carcinoma. Competitive binding by JQ1 displaces the BRD4 fusion oncoprotein from chromatin, prompting squamous differentiation and specific antiproliferative effects in BRD4-dependent cell lines and patient-derived xenograft models. These data establish proof-of-concept for targeting protein-protein interactions of epigenetic 'readers', and provide a versatile chem. scaffold for the development of chem. probes more broadly throughout the bromodomain family.
- 8Nicodeme, E.; Jeffrey, K. L.; Schaefer, U.; Beinke, S.; Dewell, S.; Chung, C.; Chandwani, R.; Marazzi, I.; Wilson, P.; Coste, H.; White, J.; Kirilovsky, J.; Rice, C. M.; Lora, J. M.; Prinjha, R. K.; Lee, K.; Tarakhovsky, A. Suppression of Inflammation by a Synthetic Histone Mimic. Nature 2010, 468, 1119– 1123, DOI: 10.1038/nature09589Google Scholar8https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhtl2rtb%252FP&md5=0dfccd9d01b87859512bf591e1c5a93cSuppression of inflammation by a synthetic histone mimicNicodeme, Edwige; Jeffrey, Kate L.; Schaefer, Uwe; Beinke, Soren; Dewell, Scott; Chung, Chun-wa; Chandwani, Rohit; Marazzi, Ivan; Wilson, Paul; Coste, Herve; White, Julia; Kirilovsky, Jorge; Rice, Charles M.; Lora, Jose M.; Prinjha, Rab K.; Lee, Kevin; Tarakhovsky, AlexanderNature (London, United Kingdom) (2010), 468 (7327), 1119-1123CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Interaction of pathogens with cells of the immune system results in activation of inflammatory gene expression. This response, although vital for immune defense, is frequently deleterious to the host due to the exaggerated prodn. of inflammatory proteins. The scope of inflammatory responses reflects the activation state of signaling proteins upstream of inflammatory genes as well as signal-induced assembly of nuclear chromatin complexes that support mRNA expression. Recognition of post-translationally modified histones by nuclear proteins that initiate mRNA transcription and support mRNA elongation is a crit. step in the regulation of gene expression. Here we present a novel pharmacol. approach that targets inflammatory gene expression by interfering with the recognition of acetylated histones by the bromodomain and extra terminal domain (BET) family of proteins. We describe a synthetic compd. (I-BET) that by mimicking' acetylated histones disrupts chromatin complexes responsible for the expression of key inflammatory genes in activated macrophages, and confers protection against lipopolysaccharide-induced endotoxic shock and bacteria-induced sepsis. Our findings suggest that synthetic compds. specifically targeting proteins that recognize post-translationally modified histones can serve as a new generation of immunomodulatory drugs.
- 9Prinjha, R. K.; Witherington, J.; Lee, K. Place Your BETs: The Therapeutic Potential of Bromodomains. Trends Pharmacol. Sci. 2012, 33, 146– 153, DOI: 10.1016/j.tips.2011.12.002Google Scholar9https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XjtlOlt74%253D&md5=ea1e9e5740b1131239aa0407748d549bPlace your BETs: the therapeutic potential of bromodomainsPrinjha, R. K.; Witherington, J.; Lee, K.Trends in Pharmacological Sciences (2012), 33 (3), 146-153CODEN: TPHSDY; ISSN:0165-6147. (Elsevier Ltd.)A review. Therapeutic targeting of the processes that regulate histone modification is a growing area of scientific exploration. Although most interest has concd. on the various families of enzymes that contribute to these processes, this review focuses on emerging data demonstrating the chem. tractability and therapeutic potential of a hitherto underexplored family of proteins, namely the bromodomain (BRD) family of reader proteins. These proteins perform a crucial role in translating histone modifications with powerful transcriptional consequences. We review current knowledge of the biol. of this emergent target class and highlight recent breakthroughs that now make the BRD family of reader proteins attractive for drug discovery.
- 10Garnier, J.-M.; Sharp, P. P.; Burns, C. J. BET Bromodomain Inhibitors: A Patent Review. Exp. Opin. Ther. Pat. 2014, 24, 185– 199, DOI: 10.1517/13543776.2014.859244Google Scholar10https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXptlWgtg%253D%253D&md5=bb33008eefa34f3689e0ee4a49a2539eBET bromodomain inhibitors: a patent reviewGarnier, Jean-Marc; Sharp, Phillip P.; Burns, Christopher J.Expert Opinion on Therapeutic Patents (2014), 24 (2), 185-199CODEN: EOTPEG; ISSN:1354-3776. (Informa Healthcare)A review. Introduction: The bromodomain (BRD) and extra-C terminal domain (BET) protein family consists of four members (BRD2, BRD3, BRD4 and BRDT). These "epigenetic readers" bind to acetyllysine (KAc) residues on the tails of histones H3 and H4, and regulate chromatin structure and gene expression. There is increasing evidence of their role in human disease, and recently a no. of small-mol. inhibitors have been reported. There is increasing interest in the inhibition of BET proteins for a variety of therapeutic applications that have resulted in considerable patent activity from academia and biotechnol. and pharmaceutical companies. Areas covered: Data supporting the use of BET inhibitors in treating disease are outlined, and the current patent literature is discussed. The survey is focused on patents claiming compds. as BET inhibitors and addnl. patents covering compds. now reported as BET inhibitors have been included. Expert opinion: There is now compelling preclin. data demonstrating BET inhibition as a strategy to target processes known to be involved in disease development and progression with clin. trials of two bona fide BET inhibitors now underway. Patent activity in this area is increasing with initial activity focused on variations to reported BET inhibitors and more recent patents disclosing novel chemotypes as BET inhibitors.
- 11Chen, H.; Liu, Z.; Zheng, L.; Wang, R.; Shi, L. BET Inhibitors: An Updated Patent Review (2018–2021). Exp. Opin. Ther. Pat. 2022, 32, 953– 968, DOI: 10.1080/13543776.2022.2115354Google ScholarThere is no corresponding record for this reference.
- 12Watson, R. J.; Bamborough, P.; Barnett, H.; Chung, C.; Davis, R.; Gordon, L.; Grandi, P.; Petretich, M.; Phillipou, A.; Prinjha, R. K.; Rioja, I.; Soden, P.; Werner, T.; Demont, E. H. GSK789: A Selective Inhibitor of the First Bromodomains (BD1) of the Bromo and Extra Terminal Domain (BET) Proteins. J. Med. Chem. 2020, 63, 9045– 9069, DOI: 10.1021/acs.jmedchem.0c00614Google Scholar12https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhsVWrsLzJ&md5=c86b4d2c85dcfa62854debf225c8076cGSK789: A Selective Inhibitor of the First Bromodomains (BD1) of the Bromo and Extra Terminal Domain (BET) ProteinsWatson, Robert J.; Bamborough, Paul; Barnett, Heather; Chung, Chun-wa; Davis, Rob; Gordon, Laurie; Grandi, Paola; Petretich, Massimo; Phillipou, Alex; Prinjha, Rab K.; Rioja, Inmaculada; Soden, Peter; Werner, Thilo; Demont, Emmanuel H.Journal of Medicinal Chemistry (2020), 63 (17), 9045-9069CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)Pan-bromodomain and extra terminal (BET) inhibitors interact equipotently with all eight bromodomains of the BET family of proteins. They have shown profound efficacy in vitro and in vivo in oncol. and immunomodulatory models, and a no. of them are currently in clin. trials where significant safety signals have been reported. It is therefore important to understand the functional contribution of each bromodomain to assess the opportunity to tease apart efficacy and toxicity. This article discloses the in vitro and cellular activity profiles of GSK789(I), a potent, cell-permeable, and highly selective inhibitor of the first bromodomains of the BET family.
- 14Piha-Paul, S. A.; Hann, C. L.; French, C. A.; Cousin, S.; Braña, I.; Cassier, P. A.; Moreno, V.; de Bono, J. S.; Harward, S. D.; Ferron-Brady, G.; Barbash, O.; Wyce, A.; Wu, Y.; Horner, T.; Annan, M.; Parr, N. J.; Prinjha, R. K.; Carpenter, C. L.; Hilton, J.; Hong, D. S.; Haas, N. B.; Markowski, M. C.; Dhar, A.; O’Dwyer, P. J.; Shapiro, G. I. Phase 1 Study of Molibresib (GSK525762), a Bromodomain and Extra-Terminal Domain Protein Inhibitor, in NUT Carcinoma and Other Solid Tumors. JNCI Cancer Spectrum 2020, 4, pkz093, DOI: 10.1093/jncics/pkz093Google ScholarThere is no corresponding record for this reference.
- 15Shorstova, T.; Foulkes, W. D.; Witcher, M. Achieving Clinical Success with BET Inhibitors as Anti-Cancer Agents. Br. J. Cancer 2021, 124, 1478– 1490, DOI: 10.1038/s41416-021-01321-0Google Scholar15https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXmsFKiu7c%253D&md5=3bac6e1d949af466cb01f96382318f42Achieving clinical success with BET inhibitors as anti-cancer agentsShorstova, Tatiana; Foulkes, William D.; Witcher, MichaelBritish Journal of Cancer (2021), 124 (9), 1478-1490CODEN: BJCAAI; ISSN:0007-0920. (Nature Portfolio)A review. The transcriptional upregulation of oncogenes is a driving force behind the progression of many tumors. However, until a decade ago, the concept of 'switching off' these oncogenic pathways represented a formidable challenge. Research has revealed that members of the bromo- and extra-terminal domain (BET) motif family are key activators of oncogenic networks in a spectrum of cancers; their function depends on their recruitment to chromatin through two bromodomains (BD1 and BD2). The advent of potent inhibitors of BET proteins (BETi), which target either one or both bromodomains, represents an important step towards the goal of suppressing oncogenic networks within tumors. Here, we discuss the biol. of BET proteins, advances in BETi design and highlight potential biomarkers predicting their activity. We also outline the logic of incorporating BETi into combination therapies to enhance its efficacy. We suggest that understanding mechanisms of activity, defining predictive biomarkers and identifying potent synergies represents a roadmap for clin. success using BETi.
- 16Postel-Vinay, S.; Herbschleb, K.; Massard, C.; Woodcock, V.; Soria, J.-C.; Walter, A. O.; Ewerton, F.; Poelman, M.; Benson, N.; Ocker, M.; Wilkinson, G.; Middleton, M. First-in-Human Phase I Study of the Bromodomain and Extraterminal Motif Inhibitor BAY 1238097: Emerging Pharmacokinetic/Pharmacodynamic Relationship and Early Termination Due to Unexpected Toxicity. Eur. J. Cancer 2019, 109, 103– 110, DOI: 10.1016/j.ejca.2018.12.020Google Scholar16https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhslCltLo%253D&md5=c5969b7827810fd1146338b84c8f8621First-in-human phase I study of the bromodomain and extraterminal motif inhibitor BAY 1238097: emerging pharmacokinetic/pharmacodynamic relationship and early termination due to unexpected toxicityPostel-Vinay, Sophie; Herbschleb, Karin; Massard, Christophe; Woodcock, Victoria; Soria, Jean-Charles; Walter, Annette O.; Ewerton, Flavio; Poelman, Martine; Benson, Neil; Ocker, Matthias; Wilkinson, Gary; Middleton, MarkEuropean Journal of Cancer (2019), 109 (), 103-110CODEN: EJCAEL; ISSN:0959-8049. (Elsevier Ltd.)Bromodomain and extraterminal motif protein inhibition is a promising cancer treatment strategy, notably for targeting MYC- or BRD4-driven diseases. A first-in-human study investigated the safety, pharmacokinetics, max. tolerated dose and recommended phase II dose of the BET inhibitor BAY 1238097 in patients with advanced malignancies.In this phase I, open-label, non-randomised, multicentre study, patients with cytol. or histol. confirmed advanced refractory malignancies received oral BAY 1238097 twice weekly in 21-day cycles using an adaptive dose-escalation design at a starting dose of 10 mg/wk. Both patients receiving 80 mg/wk had dose-limiting toxicities (grade 3 vomiting, grade 3 headache and grade 2/3 back pain). The most common adverse events were nausea, vomiting, headache, back pain and fatigue. Pharmacokinetic anal. indicated a linear dose response with increasing dose. Two patients displayed prolonged stable disease; no responses were obsd. Biomarker evaluation of MYC and HEXIM1 expression demonstrated an emerging pharmacokinetic/pharmacodynamic relationship, with a trend towards decreased MYC and increased HEXIM1 expression in response to treatment.The study was prematurely terminated because of the occurrence of DLTs at a dose below targeted drug exposure. Pharmacokinetic modeling indicated that an alternate dosing schedule whereby DLTs could be avoided while reaching efficacious exposure was not feasible.
- 17Chen, J.; Tang, P.; Wang, Y.; Wang, J.; Yang, C.; Li, Y.; Yang, G.; Wu, F.; Zhang, J.; Ouyang, L. Targeting Bromodomain-Selective Inhibitors of BET Proteins in Drug Discovery and Development. J. Med. Chem. 2022, 65, 5184– 5211, DOI: 10.1021/acs.jmedchem.1c01835Google Scholar17https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XnvVKhsr0%253D&md5=bd2bb412aad23fa184778d41fc957a21Targeting Bromodomain-Selective Inhibitors of BET Proteins in Drug Discovery and DevelopmentChen, Juncheng; Tang, Pan; Wang, Yuxi; Wang, Jiaxing; Yang, Chengcan; Li, Yang; Yang, Gaoxia; Wu, Fengbo; Zhang, Jifa; Ouyang, LiangJournal of Medicinal Chemistry (2022), 65 (7), 5184-5211CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)A review. Blocking the interactions between bromodomain and extraterminal (BET) proteins and acetylated lysines of histones by small mols. has important implications for the treatment of cancers and other diseases. Many pan-BET inhibitors have shown satisfactory results in clin. trials, but their potential for poor tolerability and toxicity persist. However, recently reported studies illustrate that some BET bromodomain (BET-BD1 or BET-BD2)-selective inhibitors have advantage over pan-inhibitors, including reduced toxicity concerns. Furthermore, some selective BET inhibitors have similar or even better therapeutic efficacy in inflammatory diseases or cancers. Therefore, the development of selective BET inhibitors has become a hot spot for medicinal chemists. Here, we summarize the known selective BET-BD1 and BET-BD2 inhibitors and review the methods for enhancing the selectivity and potency of these inhibitors based on their different modes of interactions with BET-BD1 or BET-BD2. Finally, we discuss prospective strategies that selectively target the bromodomains of BET proteins.
- 18Gilan, O.; Rioja, I.; Knezevic, K.; Bell, M. J.; Yeung, M. M.; Harker, N. R.; Lam, E. Y. N.; Chung, C.; Bamborough, P.; Petretich, M.; Urh, M.; Atkinson, S. J.; Bassil, A. K.; Roberts, E. J.; Vassiliadis, D.; Burr, M. L.; Preston, A. G. S.; Wellaway, C.; Werner, T.; Gray, J. R.; Michon, A.-M.; Gobbetti, T.; Kumar, V.; Soden, P. E.; Haynes, A.; Vappiani, J.; Tough, D. F.; Taylor, S.; Dawson, S.-J.; Bantscheff, M.; Lindon, M.; Drewes, G.; Demont, E. H.; Daniels, D. L.; Grandi, P.; Prinjha, R. K.; Dawson, M. A. Selective Targeting of BD1 and BD2 of the BET Proteins in Cancer and Immunoinflammation. Science 2020, 368, 387– 394, DOI: 10.1126/science.aaz8455Google Scholar18https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXnslKrtrg%253D&md5=d78cfea091fcf5ee18735b02b2120dd7Selective targeting of BD1 and BD2 of the BET proteins in cancer and immunoinflammationGilan, Omer; Rioja, Inmaculada; Knezevic, Kathy; Bell, Matthew J.; Yeung, Miriam M.; Harker, Nicola R.; Lam, Enid Y. N.; Chung, Chun-wa; Bamborough, Paul; Petretich, Massimo; Urh, Marjeta; Atkinson, Stephen J.; Bassil, Anna K.; Roberts, Emma J.; Vassiliadis, Dane; Burr, Marian L.; Preston, Alex G. S.; Wellaway, Christopher; Werner, Thilo; Gray, James R.; Michon, Anne-Marie; Gobbetti, Thomas; Kumar, Vinod; Soden, Peter E.; Haynes, Andrea; Vappiani, Johanna; Tough, David F.; Taylor, Simon; Dawson, Sarah-Jane; Bantscheff, Marcus; Lindon, Matthew; Drewes, Gerard; Demont, Emmanuel H.; Daniels, Danette L.; Grandi, Paola; Prinjha, Rab K.; Dawson, Mark A.Science (Washington, DC, United States) (2020), 368 (6489), 387-394CODEN: SCIEAS; ISSN:1095-9203. (American Association for the Advancement of Science)The two tandem bromodomains of the BET (bromodomain and extraterminal domain) proteins enable chromatin binding to facilitate transcription. Drugs that inhibit both bromodomains equally have shown efficacy in certain malignant and inflammatory conditions. To explore the individual functional contributions of the first (BD1) and second (BD2) bromodomains in biol. and therapy, we developed selective BD1 and BD2 inhibitors. We found that steady-state gene expression primarily requires BD1, whereas the rapid increase of gene expression induced by inflammatory stimuli requires both BD1 and BD2 of all BET proteins. BD1 inhibitors phenocopied the effects of pan-BET inhibitors in cancer models, whereas BD2 inhibitors were predominantly effective in models of inflammatory and autoimmune disease. These insights into the differential requirement of BD1 and BD2 for the maintenance and induction of gene expression may guide future BET-targeted therapies.
- 19Picaud, 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, P. E.; Knapp, S.; Filippakopoulos, P. RVX-208, an Inhibitor of BET Transcriptional Regulators with Selectivity for the Second Bromodomain. Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 19754– 19759, DOI: 10.1073/pnas.1310658110Google Scholar19https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvFKms7zN&md5=c918702c9fdb91241bc837732730f7f6RVX-208, an inhibitor of BET transcriptional regulators with selectivity for the second bromodomainPicaud, Sarah; Wells, Christopher; Felletar, Ildiko; Brotherton, Deborah; Martin, Sarah; Savitsky, Pavel; Diez-Dacal, Beatriz; Philpott, Martin; Bountra, Chas; Lingard, Hannah; Fedorov, Oleg; Muller, Susanne; Brennan, Paul E.; Knapp, Stefan; Filippakopoulos, PanagisProceedings of the National Academy of Sciences of the United States of America (2013), 110 (49), 19754-19759,S19754/1-S19754/10CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Bromodomains have emerged as attractive candidates for the development of inhibitors targeting gene transcription. Inhibitors of the bromo and extraterminal (BET) family recently showed promising activity in diverse disease models. However, the pleiotropic nature of BET proteins regulating tissue-specific transcription has raised safety concerns and suggested that attempts should be made for domain-specific targeting. Here, we report that RVX-208, a compd. currently in phase II clin. trials, is a BET bromodomain inhibitor specific for second bromodomains (BD2s). Cocrystal structures revealed binding modes of RVX-208 and its synthetic precursor, and fluorescent recovery after photobleaching demonstrated that RVX-208 displaces BET proteins from chromatin. However, gene-expression data showed that BD2 inhibition only modestly affects BET-dependent gene transcription. Our data demonstrate the feasibility of specific targeting within the BET family resulting in different transcriptional outcomes and highlight the importance of BD1 in transcriptional regulation.
- 20http://www.clinicaltrials.gov/ct2/show/NCT04894266 (accessed April 4, 2023).Google ScholarThere is no corresponding record for this reference.
- 21Sheppard, G. S.; Wang, L.; Fidanze, S. D.; Hasvold, L. A.; Liu, D.; Pratt, J. K.; Park, C. H.; Longenecker, K.; Qiu, W.; Torrent, M.; Kovar, P. J.; Bui, M.; Faivre, E.; Huang, X.; Lin, X.; Wilcox, D.; Zhang, L.; Shen, Y.; Albert, D. H.; Magoc, T. J.; Rajaraman, G.; Kati, W. M.; McDaniel, K. F. Discovery of N-Ethyl-4-[2-(4-Fluoro-2,6-Dimethyl-Phenoxy)-5-(1-Hydroxy-1-Methyl-Ethyl)Phenyl]-6-Methyl-7-Oxo-1H-Pyrrolo[2,3-c]Pyridine-2-Carboxamide (ABBV-744), a BET Bromodomain Inhibitor with Selectivity for the Second Bromodomain. J. Med. Chem. 2020, 63, 5585– 5623, DOI: 10.1021/acs.jmedchem.0c00628Google Scholar21https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXnvVeisrk%253D&md5=675827659c3c7b6099ccd667f4c60f95Discovery of N-Ethyl-4-[2-(4-fluoro-2,6-dimethyl-phenoxy)-5-(1-hydroxy-1-methyl-ethyl)phenyl]-6-methyl-7-oxo-1H-pyrrolo[2,3-c]pyridine-2-carboxamide (ABBV-744), a BET Bromodomain Inhibitor with Selectivity for the Second BromodomainSheppard, George S.; Wang, Le; Fidanze, Steven D.; Hasvold, Lisa A.; Liu, Dachun; Pratt, John K.; Park, Chang H.; Longenecker, Kenton; Qiu, Wei; Torrent, Maricel; Kovar, Peter J.; Bui, Mai; Faivre, Emily; Huang, Xiaoli; Lin, Xiaoyu; Wilcox, Denise; Zhang, Lu; Shen, Yu; Albert, Daniel H.; Magoc, Terrance J.; Rajaraman, Ganesh; Kati, Warren M.; McDaniel, Keith F.Journal of Medicinal Chemistry (2020), 63 (10), 5585-5623CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)The BET family of proteins consists of BRD2, BRD3, BRD4, and BRDt. Each protein contains two distinct bromodomains (BD1 and BD2). BET family bromodomain inhibitors under clin. development for oncol. bind to each of the eight bromodomains with similar affinities. We hypothesized that it may be possible to achieve an improved therapeutic index by selectively targeting subsets of the BET bromodomains. Both BD1 and BD2 are highly conserved across family members (>70% identity), whereas BD1 and BD2 from the same protein exhibit a larger degree of divergence (~ 40% identity), suggesting selectivity between BD1 and BD2 of all family members would be more straightforward to achieve. Exploiting the Asp144/His437 and Ile146/Val439 sequence differences (BRD4 BD1/BD2 numbering) allowed the identification of compd. 27 demonstrating greater than 100-fold selectivity for BRD4 BD2 over BRD4 BD1. Further optimization to improve BD2 selectivity and oral bioavailability resulted in the clin. development compd. 46 (ABBV-744).
- 22Faivre, E. J.; McDaniel, K. F.; Albert, D. H.; Mantena, S. R.; Plotnik, J. P.; Wilcox, D.; Zhang, L.; Bui, M. H.; Sheppard, G. S.; Wang, L.; Sehgal, V.; Lin, X.; Huang, X.; Lu, X.; Uziel, T.; Hessler, P.; Lam, L. T.; Bellin, R. J.; Mehta, G.; Fidanze, S.; Pratt, J. K.; Liu, D.; Hasvold, L. A.; Sun, C.; Panchal, S. C.; Nicolette, J. J.; Fossey, S. L.; Park, C. H.; Longenecker, K.; Bigelow, L.; Torrent, M.; Rosenberg, S. H.; Kati, W. M.; Shen, Y. Selective Inhibition of the BD2 Bromodomain of BET Proteins in Prostate Cancer. Nature 2020, 578, 306– 310, DOI: 10.1038/s41586-020-1930-8Google Scholar22https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXis1Smsr0%253D&md5=800d9106c33084390fd8cbf1ac7f1766Selective inhibition of the BD2 bromodomain of BET proteins in prostate cancerFaivre, Emily J.; McDaniel, Keith F.; Albert, Daniel H.; Mantena, Srinivasa R.; Plotnik, Joshua P.; Wilcox, Denise; Zhang, Lu; Bui, Mai H.; Sheppard, George S.; Wang, Le; Sehgal, Vasudha; Lin, Xiaoyu; Huang, Xiaoli; Lu, Xin; Uziel, Tamar; Hessler, Paul; Lam, Lloyd T.; Bellin, Richard J.; Mehta, Gaurav; Fidanze, Steve; Pratt, John K.; Liu, Dachun; Hasvold, Lisa A.; Sun, Chaohong; Panchal, Sanjay C.; Nicolette, John J.; Fossey, Stacey L.; Park, Chang H.; Longenecker, Kenton; Bigelow, Lance; Torrent, Maricel; Rosenberg, Saul H.; Kati, Warren M.; Shen, YuNature (London, United Kingdom) (2020), 578 (7794), 306-310CODEN: NATUAS; ISSN:0028-0836. (Nature Research)Abstr.: Proteins of the bromodomain and extra-terminal (BET) domain family are epigenetic readers that bind acetylated histones through their bromodomains to regulate gene transcription. Dual-bromodomain BET inhibitors (DbBi) that bind with similar affinities to the first (BD1) and second (BD2) bromodomains of BRD2, BRD3, BRD4 and BRDt have displayed modest clin. activity in monotherapy cancer trials. A reduced no. of thrombocytes in the blood (thrombocytopenia) as well as symptoms of gastrointestinal toxicity are dose-limiting adverse events for some types of DbBi1-5. Given that similar haematol. and gastrointestinal defects were obsd. after genetic silencing of Brd4 in mice6, the platelet and gastrointestinal toxicities may represent on-target activities assocd. with BET inhibition. The two individual bromodomains in BET family proteins may have distinct functions7-9 and different cellular phenotypes after pharmacol. inhibition of one or both bromodomains have been reported10,11, suggesting that selectively targeting one of the bromodomains may result in a different efficacy and tolerability profile compared with DbBi. Available compds. that are selective to individual domains lack sufficient potency and the pharmacokinetics properties that are required for in vivo efficacy and tolerability assessment10-13. Here we carried out a medicinal chem. campaign that led to the discovery of ABBV-744, a highly potent and selective inhibitor of the BD2 domain of BET family proteins with drug-like properties. In contrast to the broad range of cell growth inhibition induced by DbBi, the antiproliferative activity of ABBV-744 was largely, but not exclusively, restricted to cell lines of acute myeloid leukemia and prostate cancer that expressed the full-length androgen receptor (AR). ABBV-744 retained robust activity in prostate cancer xenografts, and showed fewer platelet and gastrointestinal toxicities than the DbBi ABBV-07514. Analyses of RNA expression and chromatin immunopptn. followed by sequencing revealed that ABBV-744 displaced BRD4 from AR-contg. super-enhancers and inhibited AR-dependent transcription, with less impact on global transcription compared with ABBV-075. These results underscore the potential value of selectively targeting the BD2 domain of BET family proteins for cancer therapy.
- 23Gacias, M.; Gerona-Navarro, G.; Plotnikov, A. N.; Zhang, G.; Zeng, L.; Kaur, J.; Moy, G.; Rusinova, E.; Rodriguez, Y.; Matikainen, B.; Vincek, A.; Joshua, J.; Casaccia, P.; Zhou, M.-M. Selective Chemical Modulation of Gene Transcription Favors Oligodendrocyte Lineage Progression. Chem. Biol. 2014, 21, 841– 854, DOI: 10.1016/j.chembiol.2014.05.009Google Scholar23https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtVemtLrK&md5=6b377663a8d0d07441ab4f8a5d8191b3Selective Chemical Modulation of Gene Transcription Favors Oligodendrocyte Lineage ProgressionGacias, Mar; Gerona-Navarro, Guillermo; Plotnikov, Alexander N.; Zhang, Guangtao; Zeng, Lei; Kaur, Jasbir; Moy, Gregory; Rusinova, Elena; Rodriguez, Yoel; Matikainen, Bridget; Vincek, Adam; Joshua, Jennifer; Casaccia, Patrizia; Zhou, Ming-MingChemistry & Biology (Oxford, United Kingdom) (2014), 21 (7), 841-854CODEN: CBOLE2; ISSN:1074-5521. (Elsevier Ltd.)Lysine acetylation regulates gene expression through modulating protein-protein interactions in chromatin. Chem. inhibition of acetyl-lysine binding bromodomains of the major chromatin regulators BET (bromodomain and extraterminal domain) proteins has been shown to effectively block cell proliferation in cancer and inflammation. However, whether selective inhibition of individual BET bromodomains has distinctive functional consequences remains only partially understood. In this study, we show that selective chem. inhibition of the first bromodomain of BET proteins using our small-mol. inhibitor, Olinone, accelerated the progression of mouse primary oligodendrocyte progenitors toward differentiation, whereas inhibition of both bromodomains of BET proteins hindered differentiation. This effect was target specific, as it was not detected in cells treated with inactive analogs and independent of any effect on proliferation. Therefore, selective chem. modulation of individual bromodomains, rather than use of broad-based inhibitors, may enhance regenerative strategies in disorders characterized by myelin loss such as aging and neurodegeneration.
- 24Rodríguez, Y.; Gerona-Navarro, G.; Osman, R.; Zhou, M.-M. In Silico Design and Molecular Basis for the Selectivity of Olinone toward the First over the Second Bromodomain of BRD4. Proteins: Struct., Funct., Bioinf. 2020, 88, 414– 430, DOI: 10.1002/prot.25818Google Scholar24https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvFymt7jE&md5=3347bcb89a938a3aa25ba6bfd2bea8dbIn silico design and molecular basis for the selectivity of Olinone toward the first over the second bromodomain of BRD4Rodriguez, Yoel; Gerona-Navarro, Guillermo; Osman, Roman; Zhou, Ming-MingProteins: Structure, Function, and Bioinformatics (2020), 88 (3), 414-430CODEN: PSFBAF; ISSN:1097-0134. (Wiley-Blackwell)Bromodomains (BrDs), a conserved structural module in chromatin-assocd. proteins, are well known for recognizing ε-N-acetyl lysine residues on histones. One of the most relevant BrDs is BRD4, a tandem BrD contg. protein (BrD1 and BrD2) that plays a crit. role in numerous diseases including cancer. Growing evidence shows that the two BrDs of BRD4 have different biol. functions; hence selective ligands that can be used to study their functions are of great interest. Here, as a follow-up of our previous work, we first provide a detailed characterization study of the in silico rational design of Olinone as part of a series of five tetrahydropyrido indole-based compds. as BRD4 BrD1 inhibitors. Addnl., we investigated the mol. basis for Olinone's selective recognition by BrD1 over BrD2. Mol. dynamics simulations, free energy calcns., and conformational analyses of the apo-BRD4-BrD1|2 and BRD4-BrD1|2/Olinone complexes showed that Olinone's selectivity is facilitated by five key residues: Leu92 in BrD1|385 in BrD2 of ZA loop, Asn140|433, Asp144|His437 and Asp145|Glu438 of BC loop, and Ile146|Val49 of helix C. Furthermore, the difference in hydrogen bonds no. and in mobility of the ZA and BC loops of the acetyl-lysine binding site between BRD4 BrD1/Olinone and BrD2/Olinone complexes also contribute to the difference in Olinone's binding affinity and selectivity toward BrD1 over BrD2. Altogether, our computer-aided mol. design techniques can effectively guide the development of small-mol. BRD4 BrD1 inhibitors, explain their selectivity origin, and further open doors to the design of new therapeutically improved derivs.
- 25Divakaran, A.; Talluri, S. K.; Ayoub, A. M.; Mishra, N. K.; Cui, H.; Widen, J. C.; Berndt, N.; Zhu, J.-Y.; Carlson, A. S.; Topczewski, J. J.; Schonbrunn, E. K.; Harki, D. A.; Pomerantz, W. C. K. Molecular Basis for the N-Terminal Bromodomain-and-Extra-Terminal-Family Selectivity of a Dual Kinase-Bromodomain Inhibitor. J. Med. Chem. 2018, 61, 9316– 9334, DOI: 10.1021/acs.jmedchem.8b01248Google Scholar25https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhvVSis7fM&md5=5176ef754a898b3e03fc56e2662ab399Molecular Basis for the N-Terminal Bromodomain-and-Extra-Terminal-Family Selectivity of a Dual Kinase-Bromodomain InhibitorDivakaran, Anand; Talluri, Siva K.; Ayoub, Alex M.; Mishra, Neeraj K.; Cui, Huarui; Widen, John C.; Berndt, Norbert; Zhu, Jin-Yi; Carlson, Angela S.; Topczewski, Joseph J.; Schonbrunn, Ernst K.; Harki, Daniel A.; Pomerantz, William C. K.Journal of Medicinal Chemistry (2018), 61 (20), 9316-9334CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)As regulators of transcription, epigenetic proteins that interpret post-translational modifications to N-terminal histone tails are essential for maintaining cellular homeostasis. When dysregulated, "reader" proteins become drivers of disease. In the case of bromodomains, which recognize N-ε-acetylated lysine, selective inhibition of individual bromodomain-and-extra-terminal (BET)-family bromodomains has proven challenging. We describe the >55-fold N-terminal-BET bromodomain selectivity of 1,4,5-trisubstituted-imidazole dual kinase-bromodomain inhibitors. Selectivity for the BRD4 N-terminal bromodomain (BRD4(1)) over its second bromodomain (BRD4(2)) arises from the displacement of ordered waters and the conformational flexibility of lysine-141 in BRD4(1). Cellular efficacy was demonstrated via redn. of c-Myc expression, inhibition of NF-κB signaling, and suppression of IL-8 prodn. through potential synergistic inhibition of BRD4(1) and p38α. These dual inhibitors provide a new scaffold for domain-selective inhibition of BRD4, the aberrant function of which plays a key role in cancer and inflammatory signaling.
- 26Cipriano, A.; Milite, C.; Feoli, A.; Viviano, M.; Pepe, G.; Campiglia, P.; Sarno, G.; Picaud, S.; Imaide, S.; Makukhin, N.; Filippakopoulos, P.; Ciulli, A.; Castellano, S.; Sbardella, G. Discovery of Benzo[d]Imidazole-6-Sulfonamides as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the First Bromodomain. ChemMedChem 2022, 17, e202200343 DOI: 10.1002/cmdc.202200343Google Scholar26https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XisVSnsLrJ&md5=a4628e3e7597053c1658915561fdd2dbDiscovery of Benzo[d]imidazole-6-sulfonamides as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the First BromodomainCipriano, Alessandra; Milite, Ciro; Feoli, Alessandra; Viviano, Monica; Pepe, Giacomo; Campiglia, Pietro; Sarno, Giuliana; Picaud, Sarah; Imaide, Satomi; Makukhin, Nikolai; Filippakopoulos, Panagis; Ciulli, Alessio; Castellano, Sabrina; Sbardella, GianlucaChemMedChem (2022), 17 (20), e202200343CODEN: CHEMGX; ISSN:1860-7179. (Wiley-VCH Verlag GmbH & Co. KGaA)The bromodomain and extra-terminal (BET) family of proteins includes BRD2, BRD3, BRD4, and the testis-specific protein, BRDT, each contg. two N-terminal tandem bromodomain (BRD) modules. Potent and selective inhibitors targeting the two bromodomains are required to elucidate their biol. role(s), with potential clin. applications. In this study, we designed and synthesized a series of benzimidazole-6-sulfonamides starting from the azobenzene compds. MS436 (7 a) and MS611 (7 b) that exhibited preference for the first (BD1) over the second (BD2) BRD of BET family members. The most-promising compd. (9 a) showed good binding potency and improved metabolic stability and selectivity towards BD1 with respect to the parent compds.
- 27Cui, H.; Carlson, A. S.; Schleiff, M. A.; Divakaran, A.; Johnson, J. A.; Buchholz, C. R.; Zahid, H.; Vail, N. R.; Shi, K.; Aihara, H.; Harki, D. A.; Miller, G. P.; Topczewski, J. J.; Pomerantz, W. C. K. 4-Methyl-1,2,3-Triazoles as N-Acetyl-Lysine Mimics Afford Potent BET Bromodomain Inhibitors with Improved Selectivity. J. Med. Chem. 2021, 64, 10497– 10511, DOI: 10.1021/acs.jmedchem.1c00933Google Scholar27https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhs1WmtbnK&md5=6dfafd833706b5a418e5998f73c2eb944-Methyl-1,2,3-Triazoles as N-Acetyl-Lysine Mimics Afford Potent BET Bromodomain Inhibitors with Improved SelectivityCui, Huarui; Carlson, Angela S.; Schleiff, Mary A.; Divakaran, Anand; Johnson, Jorden A.; Buchholz, Caroline R.; Zahid, Huda; Vail, Nora R.; Shi, Ke; Aihara, Hideki; Harki, Daniel A.; Miller, Grover P.; Topczewski, Joseph J.; Pomerantz, William C. K.Journal of Medicinal Chemistry (2021), 64 (14), 10497-10511CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)The bromodomain and extra terminal (BET) protein family recognizes acetylated lysines within histones and transcription factors using two N-terminal bromodomains, D1 and D2. The protein-protein interactions between BET bromodomains, acetylated histones, and transcription factors are therapeutic targets for BET-related diseases, including inflammatory disease and cancer. Prior work demonstrated that methylated-1,2,3-triazoles are suitable N-acetyl lysine mimetics for BET inhibition. Here we describe a structure-activity relationship study of triazole-based inhibitors that improve affinity, D1 selectivity, and microsomal stability. These outcomes were accomplished by targeting a nonconserved residue, Asp144 and a conserved residue, Met149, on BRD4 D1. The lead inhibitors DW34 and 26 have a BRD4 D1 Kd of 12 and 6.4 nM, resp. Cellular activity was demonstrated through suppression of c-Myc expression in MM.1S cells and downregulation of IL-8 in TNF-α-stimulated A549 cells. These data indicate that DW34 (I) and 26 (II) are new leads to investigate the anticancer and anti-inflammatory activity of BET proteins.
- 28Seal, J.; Lamotte, Y.; Donche, F.; Bouillot, A.; Mirguet, O.; Gellibert, F.; Nicodeme, E.; Krysa, G.; Kirilovsky, J.; Beinke, S.; McCleary, S.; Rioja, I.; Bamborough, P.; Chung, C.-W.; Gordon, L.; Lewis, T.; Walker, A. L.; Cutler, L.; Lugo, D.; Wilson, D. M.; Witherington, J.; Lee, K.; Prinjha, R. K. Identification of a Novel Series of BET Family Bromodomain Inhibitors: Binding Mode and Profile of I-BET151 (GSK1210151A). Bioorg. Med. Chem. Lett. 2012, 22, 2968– 2972, DOI: 10.1016/j.bmcl.2012.02.041Google Scholar28https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XktFOqsr8%253D&md5=a8037c89bcb93948d663208bd1ebfd55Identification of a novel series of BET family bromodomain inhibitors: Binding mode and profile of I-BET151 (GSK1210151A)Seal, Jonathan; Lamotte, Yann; Donche, Frederic; Bouillot, Anne; Mirguet, Olivier; Gellibert, Francoise; Nicodeme, Edwige; Krysa, Gael; Kirilovsky, Jorge; Beinke, Soren; McCleary, Scott; Rioja, Inma; Bamborough, Paul; Chung, Chun-Wa; Gordon, Laurie; Lewis, Toni; Walker, Ann L.; Cutler, Leanne; Lugo, David; Wilson, David M.; Witherington, Jason; Lee, Kevin; Prinjha, Rab K.Bioorganic & Medicinal Chemistry Letters (2012), 22 (8), 2968-2972CODEN: BMCLE8; ISSN:0960-894X. (Elsevier B.V.)A novel series of quinoline isoxazole BET family bromodomain inhibitors are discussed. Crystallog. is used to illustrate binding modes and rationalize their SAR. One member, I-BET151 (GSK1210151A), shows good oral bioavailability in both the rat and minipig as well as demonstrating efficient suppression of bacterial induced inflammation and sepsis in a murine in vivo endotoxemia model.
- 29Wellaway, C. R.; Bamborough, P.; Bernard, S. G.; Chung, C.; Craggs, P. D.; Cutler, L.; Demont, E. H.; Evans, J. P.; Gordon, L.; Karamshi, B.; Lewis, A. J.; Lindon, M. J.; Mitchell, D. J.; Rioja, I.; Soden, P. E.; Taylor, S.; Watson, R. J.; Willis, R.; Woolven, J. M.; Wyspiańska, B. S.; Kerr, W. J.; Prinjha, R. K. Structure-Based Design of a Bromodomain and Extraterminal Domain (BET) Inhibitor Selective for the N-Terminal Bromodomains That Retains an Anti-Inflammatory and Antiproliferative Phenotype. J. Med. Chem. 2020, 63, 9020– 9044, DOI: 10.1021/acs.jmedchem.0c00566Google Scholar29https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhsV2lt77M&md5=52b2505bb0a36f526a08bb9bad1f2c26Structure-Based Design of a Bromodomain and Extraterminal Domain (BET) Inhibitor Selective for the N-Terminal Bromodomains That Retains an Anti-inflammatory and Antiproliferative PhenotypeWellaway, Christopher R.; Bamborough, Paul; Bernard, Sharon G.; Chung, Chun-wa; Craggs, Peter D.; Cutler, Leanne; Demont, Emmanuel H.; Evans, John P.; Gordon, Laurie; Karamshi, Bhumika; Lewis, Antonia J.; Lindon, Matthew J.; Mitchell, Darren J.; Rioja, Inmaculada; Soden, Peter E.; Taylor, Simon; Watson, Robert J.; Willis, Rob; Woolven, James M.; Wyspianska, Beata S.; Kerr, William J.; Prinjha, Rab K.Journal of Medicinal Chemistry (2020), 63 (17), 9020-9044CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)The bromodomain and extraterminal domain (BET) family of epigenetic regulators comprises four proteins (BRD2, BRD3, BRD4, BRDT), each contg. tandem bromodomains. To date, small mol. inhibitors of these proteins typically bind all eight bromodomains of the family with similar affinity, resulting in a diverse range of biol. effects. To enable further understanding of the broad phenotype characteristic of pan-BET inhibition, the development of inhibitors selective for individual, or sets of, bromodomains within the family is required. In this regard, we report the discovery of a potent probe mol. possessing up to 150-fold selectivity for the N-terminal bromodomains (BD1s) over the C-terminal bromodomains (BD2s) of the BETs. Guided by structural information, a specific amino acid difference between BD1 and BD2 domains was targeted for selective interaction with chem. functionality appended to the previously developed I-BET151 scaffold. Data presented herein demonstrate that selective inhibition of BD1 domains is sufficient to drive anti-inflammatory and antiproliferative effects.
- 30Liu, Z.; Chen, H.; Wang, P.; Li, Y.; Wold, E. A.; Leonard, P. G.; Joseph, S.; Brasier, A. R.; Tian, B.; Zhou, J. Discovery of Orally Bioavailable Chromone Derivatives as Potent and Selective BRD4 Inhibitors: Scaffold Hopping, Optimization, and Pharmacological Evaluation. J. Med. Chem. 2020, 63, 5242– 5256, DOI: 10.1021/acs.jmedchem.0c00035Google Scholar30https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXmsVOhsbs%253D&md5=95cb6c3f150a5ee9e65a76fd36a559fdDiscovery of Orally Bioavailable Chromone Derivatives as Potent and Selective BRD4 Inhibitors: Scaffold Hopping, Optimization, and Pharmacological EvaluationLiu, Zhiqing; Chen, Haiying; Wang, Pingyuan; Li, Yi; Wold, Eric A.; Leonard, Paul G.; Joseph, Sarah; Brasier, Allan R.; Tian, Bing; Zhou, JiaJournal of Medicinal Chemistry (2020), 63 (10), 5242-5256CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)Arylquinazolinones and arylchromenones such as I (X = CH2, MeN) were prepd. as selective inhibitors of bromodomain-contg. protein 4 (BRD4) for potential use as orally bioavailable antiinflammatory agents. I inhibited BRD4 with IC50 values of 67-84 nM and were selective for BRD1 over binding domains of BRD2, BRD3, and BRDT and over CBP; I inhibited the expression of Toll-like receptor (TLR3)-induced inflammatory genes in vitro and inhibited airway inflammation in mice. The pharmacokinetics (t1/2, AUC, Cmax, and clearance), metabolic stability of I (X = NMe) in murine and human cells, and inhibition of cytochrome P450 enzymes and hERG by I (X = MeN) were detd. The structure of I (X = NMe) bound to human BRD4 binding domain 1 was detd. by X-ray crystallog.
- 31Cui, H.; Divakaran, A.; Pandey, A. K.; Johnson, J. A.; Zahid, H.; Hoell, Z. J.; Ellingson, M. O.; Shi, K.; Aihara, H.; Harki, D. A.; Pomerantz, W. C. K. Selective N-Terminal BET Bromodomain Inhibitors by Targeting Non-Conserved Residues and Structured Water Displacement. Angew. Chem., Int. Ed. 2021, 60, 1220– 1226, DOI: 10.1002/anie.202008625Google Scholar31https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitlOqtLjI&md5=0f0379a17c98e5c1b9c436dc0952e9a7Selective N-Terminal BET Bromodomain Inhibitors by Targeting Non-Conserved Residues and Structured Water Displacement**Cui, Huarui; Divakaran, Anand; Pandey, Anil K.; Johnson, Jorden A.; Zahid, Huda; Hoell, Zachariah J.; Ellingson, Mikael O.; Shi, Ke; Aihara, Hideki; Harki, Daniel A.; Pomerantz, William C. K.Angewandte Chemie, International Edition (2021), 60 (3), 1220-1226CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)Bromodomain and extra-terminal (BET) family proteins, BRD2-4 and T, are important drug targets; however, the biol. functions of each bromodomain remain ill-defined. Chem. probes that selectively inhibit a single BET bromodomain are lacking, although pan inhibitors of the first (D1), and second (D2), bromodomain are known. Here, we develop selective BET D1 inhibitors with preferred binding to BRD4 D1. In competitive inhibition assays, we show that our lead compd. is 9-33 fold selective for BRD4 D1 over the other BET bromodomains. X-ray crystallog. supports a role for the selectivity based on reorganization of a non-conserved lysine and displacement of an addnl. structured water in the BRD4 D1 binding site relative to our prior lead. Whereas pan-D1 inhibitors displace BRD4 from MYC enhancers, BRD4 D1 inhibition in MM.1S cells is insufficient for stopping Myc expression and may lead to its upregulation. Future anal. of BRD4 D1 gene regulation may shed light on differential BET bromodomain functions.
- 32Cui, H.; Divakaran, A.; Hoell, Z. J.; Ellingson, M. O.; Scholtz, C. R.; Zahid, H.; Johnson, J. A.; Griffith, E. C.; Gee, C. T.; Lee, A. L.; Khanal, S.; Shi, K.; Aihara, H.; Shah, V. H.; Lee, R. E.; Harki, D. A.; Pomerantz, W. C. K. A Structure-Based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes. J. Med. Chem. 2022, 65, 2342– 2360, DOI: 10.1021/acs.jmedchem.1c01779Google Scholar32https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38Xms1Smtg%253D%253D&md5=f27226c5728fc1d627f797f56eac2690A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical ProbesCui, Huarui; Divakaran, Anand; Hoell, Zachariah J.; Ellingson, Mikael O.; Scholtz, Cole R.; Zahid, Huda; Johnson, Jorden A.; Griffith, Elizabeth C.; Gee, Clifford T.; Lee, Amani L.; Khanal, Shalil; Shi, Ke; Aihara, Hideki; Shah, Vijay H.; Lee, Richard E.; Harki, Daniel A.; Pomerantz, William C. K.Journal of Medicinal Chemistry (2022), 65 (3), 2342-2360CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)Chem. probes for epigenetic proteins are essential tools for dissecting the mol. mechanisms for gene regulation and therapeutic development. The bromodomain and extra-terminal (BET) proteins are master transcriptional regulators. Despite promising therapeutic targets, selective small mol. inhibitors for a single bromodomain remain an unmet goal due to their high sequence similarity. Here, we address this challenge via a structure-activity relationship study using 1,4,5-trisubstituted imidazoles against the BRD4 N-terminal bromodomain (D1). Leading compds. 26 and 30 have 15 and 18 nM affinity against BRD4 D1 and over 500-fold selectivity against BRD2 D1 and BRD4 D2 via ITC. Broader BET selectivity was confirmed by fluorescence anisotropy, thermal shift, and CETSA. Despite BRD4 engagement, BRD4 D1 inhibition was unable to reduce c-Myc expression at low concn. in multiple myeloma cells. Conversely, for inflammation, IL-8 and chemokine downregulation were obsd. These results provide new design rules for selective inhibitors of an individual BET bromodomain.
- 33Schiedel, M.; Moroglu, M.; Ascough, D. M. H.; Chamberlain, A. E. R.; Kamps, J. J. A. G.; Sekirnik, A. R.; Conway, S. J. Chemical Epigenetics: The Impact of Chemical and Chemical Biology Techniques on Bromodomain Target Validation. Angew. Chem., Int. Ed. 2019, 58, 17930– 17952, DOI: 10.1002/anie.201812164Google Scholar33https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXitFKrt77N&md5=d26cbf7f78d9542b2c98b9b74d979761Chemical Epigenetics: The Impact of Chemical and Chemical Biology Techniques on Bromodomain Target ValidationSchiedel, Matthias; Moroglu, Mustafa; Ascough, David M. H.; Chamberlain, Anna E. R.; Kamps, Jos J. A. G.; Sekirnik, Angelina R.; Conway, Stuart J.Angewandte Chemie, International Edition (2019), 58 (50), 17930-17952CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)A review. Epigenetics is currently the focus of intense research interest across a broad range of disciplines due to its importance in a multitude of biol. processes and disease states. Epigenetic functions result partly from modification of the nucleobases in DNA and RNA, and/or post-translational modifications of histone proteins. These modifications are dynamic, with cellular machinery identified to modulate and interpret the marks. The authors' focus is on bromodomains, which bind to acetylated lysine residues. Progress in the study of bromodomains, and the development of bromodomain ligands, has been rapid. These advances have been underpinned by many disciplines, but chem. and chem. biol. have undoubtedly played a significant role. Herein, the authors review the key chem. and chem. biol. approaches that have furthered the authors' study of bromodomains, enabled the development of bromodomain ligands, and played a crit. role in the validation of bromodomains as therapeutic targets.
- 34Arrowsmith, C. H.; Audia, J. E.; Austin, C.; Baell, J.; Bennett, J.; Blagg, J.; Bountra, C.; Brennan, P. E.; Brown, P. J.; Bunnage, M. E.; Buser-Doepner, C.; Campbell, R. M.; Carter, A. J.; Cohen, P.; Copeland, R. A.; Cravatt, B.; Dahlin, J. L.; Dhanak, D.; Edwards, A. M.; Frederiksen, M.; Frye, S. V.; Gray, N.; Grimshaw, C. E.; Hepworth, D.; Howe, T.; Huber, K. V. M.; Jin, J.; Knapp, S.; Kotz, J. D.; Kruger, R. G.; Lowe, D.; Mader, M. M.; Marsden, B.; Mueller-Fahrnow, A.; Müller, S.; O’Hagan, R. C.; Overington, J. P.; Owen, D. R.; Rosenberg, S. H.; Ross, R.; Roth, B.; Schapira, M.; Schreiber, S. L.; Shoichet, B.; Sundström, M.; Superti-Furga, G.; Taunton, J.; Toledo-Sherman, L.; Walpole, C.; Walters, M. A.; Willson, T. M.; Workman, P.; Young, R. N.; Zuercher, W. J. The Promise and Peril of Chemical Probes. Nat. Chem. Biol. 2015, 11, 536– 541, DOI: 10.1038/nchembio.1867Google Scholar34https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht1Wlu7zO&md5=d8c7a7af94921ab4cdcc871487cceaddThe promise and peril of chemical probesArrowsmith, Cheryl H.; Audia, James E.; Austin, Christopher; Baell, Jonathan; Bennett, Jonathan; Blagg, Julian; Bountra, Chas; Brennan, Paul E.; Brown, Peter J.; Bunnage, Mark E.; Buser-Doepner, Carolyn; Campbell, Robert M.; Carter, Adrian J.; Cohen, Philip; Copeland, Robert A.; Cravatt, Ben; Dahlin, Jayme L.; Dhanak, Dashyant; Edwards, Aled M.; Frye, Stephen V.; Gray, Nathanael; Grimshaw, Charles E.; Hepworth, David; Howe, Trevor; Huber, Kilian V. M.; Jin, Jian; Knapp, Stefan; Kotz, Joanne D.; Kruger, Ryan G.; Lowe, Derek; Mader, Mary M.; Marsden, Brian; Mueller-Fahrnow, Anke; Muller, Susanne; O'Hagan, Ronan C.; Overington, John P.; Owen, Dafydd R.; Rosenberg, Saul H.; Roth, Brian; Ross, Ruth; Schapira, Matthieu; Schreiber, Stuart L.; Shoichet, Brian; Sundstrom, Michael; Superti-Furga, Giulio; Taunton, Jack; Toledo-Sherman, Leticia; Walpole, Chris; Walters, Michael A.; Willson, Timothy M.; Workman, Paul; Young, Robert N.; Zuercher, William J.Nature Chemical Biology (2015), 11 (8), 536-541CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)Chem. probes are powerful reagents with increasing impacts on biomedical research. However, probes of poor quality or that are used incorrectly generate misleading results. To help address these shortcomings, we will create a community-driven wiki resource to improve quality and convey current best practice.
- 35Blagg, J.; Workman, P. Choose and Use Your Chemical Probe Wisely to Explore Cancer Biology. Cancer Cell 2017, 32, 9– 25, DOI: 10.1016/j.ccell.2017.06.005Google Scholar35https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtFGmsLvI&md5=468848d484d5d91c52330949d5778b1dChoose and Use Your Chemical Probe Wisely to Explore Cancer BiologyBlagg, Julian; Workman, PaulCancer Cell (2017), 32 (1), 9-25CODEN: CCAECI; ISSN:1535-6108. (Elsevier Inc.)Small-mol. chem. probes or tools have become progressively more important in recent years as valuable reagents to investigate fundamental biol. mechanisms and processes causing disease, including cancer. Chem. probes have also achieved greater prominence alongside complementary biol. reagents for target validation in drug discovery. However, there is evidence of widespread continuing misuse and promulgation of poor-quality and insufficiently selective chem. probes, perpetuating a worrisome and misleading pollution of the scientific literature. We discuss current challenges with the selection and use of chem. probes, and suggest how biologists can and should be more discriminating in the probes they employ.
- 36Bunnage, M. E.; Chekler, E. L. P.; Jones, L. H. Target Validation Using Chemical Probes. Nat. Chem. Biol. 2013, 9, 195– 199, DOI: 10.1038/nchembio.1197Google Scholar36https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXktFagsr4%253D&md5=af0c362882191de96a8e8698ff2c9ce8Target validation using chemical probesBunnage, Mark E.; Chekler, Eugene L. Piatnitski; Jones, Lyn H.Nature Chemical Biology (2013), 9 (4), 195-199CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)A review on the fully profiled chem. probes essential to support the unbiased interpretation of biol. expts. necessary for rigorous preclin. target validation. We believe that by developing a 'chem. probe tool kit', and a framework for its use, chem. biol. can have a more central role in identifying targets of potential relevance to disease, avoiding many of the biases that complicate target validation as practiced currently.
- 37Müller, S.; Ackloo, S.; Al Chawaf, A.; Al-Lazikani, B.; Antolin, A.; Baell, J. B.; Beck, H.; Beedie, S.; Betz, U. A. K.; Bezerra, G. A.; Brennan, P. E.; Brown, D.; Brown, P. J.; Bullock, A. N.; Carter, A. J.; Chaikuad, A.; Chaineau, M.; Ciulli, A.; Collins, I.; Dreher, J.; Drewry, D.; Edfeldt, K.; Edwards, A. M.; Egner, U.; Frye, S. V.; Fuchs, S. M.; Hall, M. D.; Hartung, I. V.; Hillisch, A.; Hitchcock, S. H.; Homan, E.; Kannan, N.; Kiefer, J. R.; Knapp, S.; Kostic, M.; Kubicek, S.; Leach, A. R.; Lindemann, S.; Marsden, B. D.; Matsui, H.; Meier, J. L.; Merk, D.; Michel, M.; Morgan, M. R.; Mueller-Fahrnow, A.; Owen, D. R.; Perry, B. G.; Rosenberg, S. H.; Saikatendu, K. S.; Schapira, M.; Scholten, C.; Sharma, S.; Simeonov, A.; Sundström, M.; Superti-Furga, G.; Todd, M. H.; Tredup, C.; Vedadi, M.; von Delft, F.; Willson, T. M.; Winter, G. E.; Workman, P.; Arrowsmith, C. H. Target 2035─Update on the Quest for a Probe for Every Protein. RSC Med. Chem. 2022, 13, 13– 21, DOI: 10.1039/D1MD00228GGoogle Scholar37https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXis1CmtLvE&md5=537ffb7c73c37f5f69cb5db0b2ea6cbbTarget 2035 - update on the quest for a probe for every proteinMueller, Susanne; Ackloo, Suzanne; Al Chawaf, Arij; Al-Lazikani, Bissan; Antolin, Albert; Baell, Jonathan B.; Beck, Hartmut; Beedie, Shaunna; Betz, Ulrich A. K.; Bezerra, Gustavo Arruda; Brennan, Paul E.; Brown, David; Brown, Peter J.; Bullock, Alex N.; Carter, Adrian J.; Chaikuad, Apirat; Chaineau, Mathilde; Ciulli, Alessio; Collins, Ian; Dreher, Jan; Drewry, David; Edfeldt, Kristina; Edwards, Aled M.; Egner, Ursula; Frye, Stephen V.; Fuchs, Stephen M.; Hall, Matthew D.; Hartung, Ingo V.; Hillisch, Alexander; Hitchcock, Stephen H.; Homan, Evert; Kannan, Natarajan; Kiefer, James R.; Knapp, Stefan; Kostic, Milka; Kubicek, Stefan; Leach, Andrew R.; Lindemann, Sven; Marsden, Brian D.; Matsui, Hisanori; Meier, Jordan L.; Merk, Daniel; Michel, Maurice; Morgan, Maxwell R.; Mueller-Fahrnow, Anke; Owen, Dafydd R.; Perry, Benjamin G.; Rosenberg, Saul H.; Saikatendu, Kumar Singh; Schapira, Matthieu; Scholten, Cora; Sharma, Sujata; Simeonov, Anton; Sundstroem, Michael; Superti-Furga, Giulio; Todd, Matthew H.; Tredup, Claudia; Vedadi, Masoud; von Delft, Frank; Willson, Timothy M.; Winter, Georg E.; Workman, Paul; Arrowsmith, Cheryl H.RSC Medicinal Chemistry (2022), 13 (1), 13-21CODEN: RMCSEZ; ISSN:2632-8682. (Royal Society of Chemistry)Twenty years after the publication of the first draft of the human genome, our knowledge of the human proteome is still fragmented. The challenge of translating the wealth of new knowledge from genomics into new medicines is that proteins, and not genes, are the primary executers of biol. function. Therefore, much of how biol. works in health and disease must be understood through the lens of protein function. Accordingly, a subset of human proteins has been at the heart of research interests of scientists over the centuries, and we have accumulated varying degrees of knowledge about approx. 65% of the human proteome. Nevertheless, a large proportion of proteins in the human proteome (∼35%) remains uncharacterized, and less than 5% of the human proteome has been successfully targeted for drug discovery. This highlights the profound disconnect between our abilities to obtain genetic information and subsequent development of effective medicines. Target 2035 is an international federation of biomedical scientists from the public and private sectors, which aims to address this gap by developing and applying new technologies to create by year 2035 chemogenomic libraries, chem. probes, and/or biol. probes for the entire human proteome.
- 38Hartung, I. V.; Rudolph, J.; Mader, M. M.; Mulder, M. P. C.; Workman, P. Expanding Chemical Probe Space: Quality Criteria for Covalent and Degrader Probes. J. Med. Chem. 2023, 66, 9297– 9312, DOI: 10.1021/acs.jmedchem.3c00550Google Scholar38https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3sXhtlKltrbF&md5=ac21f68535b0c75c78921ef471319a61Expanding Chemical Probe Space: Quality Criteria for Covalent and Degrader ProbesHartung, Ingo V.; Rudolph, Joachim; Mader, Mary M.; Mulder, Monique P. C.; Workman, PaulJournal of Medicinal Chemistry (2023), 66 (14), 9297-9312CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)A review. Within druggable target space, new small-mol. modalities, particularly covalent inhibitors and targeted degraders, have expanded the repertoire of medicinal chemists. Mols. with such modes of action have a large potential not only as drugs but also as chem. probes. Criteria have previously been established to describe the potency, selectivity, and properties of small-mol. probes that are qualified to enable the interrogation and validation of drug targets. These definitions have been tailored to reversibly acting modulators but fall short in their applicability to other modalities. While initial guidelines have been proposed, we delineate here a full set of criteria for the characterization of covalent, irreversible inhibitors as well as heterobifunctional degraders ("proteolysis-targeting chimeras", or PROTACs) and mol. glue degraders. We propose modified potency and selectivity criteria compared to those for reversible inhibitors. We discuss their relevance and highlight examples of suitable probe and pathfinder compds.
- 39Nguyen, T. H.; Maltby, S.; Eyers, F.; Foster, P. S.; Yang, M. Bromodomain and Extra Terminal (BET) Inhibitor Suppresses Macrophage-Driven Steroid-Resistant Exacerbations of Airway Hyper-Responsiveness and Inflammation. PLoS One 2016, 11, e0163392 DOI: 10.1371/journal.pone.0163392Google Scholar39https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXitV2kurk%253D&md5=d46c12f7d2d30f01bd65614fe5de3e0bBromodomain and extra terminal (BET) inhibitor suppresses macrophage-driven steroid-resistant exacerbations of airway hyper-responsiveness and inflammationNguyen, Thi Hiep; Maltby, Steven; Eyers, Fiona; Foster, Paul S.; Yang, MingPLoS One (2016), 11 (9), e0163392/1-e0163392/15CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)Background: Exacerbations of asthma are linked to significant decline in lung function and are often poorly controlled by corticosteroid treatment. Clin. investigations indicate that viral and bacterial infections play crucial roles in the onset of steroid-resistant inflammation and airways hyperresponsiveness (AHR) that are hallmark features of exacerbations.We have previously shown that interferon γ (IFNγ) and lipopolysaccharide (LPS) cooperatively activate pulmonary macrophages and induce steroid-resistant airway inflammation and AHR in mouse models. Furthermore, we have established a mouse model of respiratory syncytial virus (RSV)-induced exacerbation of asthma, which exhibits macrophage-dependent, steroid- resistant lung disease. Emerging evidence has demonstrated a key role for bromoand extra-terminal (BET) proteins in the regulation of inflammatory gene expression in macrophages. We hypothesised that BET proteins may be involved in the regulation of AHR and airway inflammation in our steroid-resistant exacerbation models. Methodol./Principal Findings: We investigated the effects of a BET inhibitor (I-BET-762) on the development of steroidresistant AHR and airway inflammation in two mouse models. I-BET-762 administration decreased macrophage and neutrophil infiltration into the airways, and suppressed key inflammatory cytokines in bothmodels. I-BET treatment also suppressed key inflammatory cytokines linked to the development of steroid-resistant inflammation such as monocyte chemoattractant protein 1 (MCP-1), keratinocyte-derived protein chemokine (KC), IFNγ, and interleukin 27 (IL-27). Attenuation of inflammation was assocd. with suppression of AHR. Conclusions/Significance: Our results suggest that BET proteins play an important role in the regulation of steroidresistant exacerbations of airway inflammation and AHR. BET proteins may be potential targets for the development of future therapies to treat steroid-resistant inflammatory components of asthma.
- 40Clegg, M. A.; Tomkinson, N. C. O.; Prinjha, R. K.; Humphreys, P. G. Advancements in the Development of Non-BET Bromodomain Chemical Probes. ChemMedChem 2019, 14, 362– 385, DOI: 10.1002/cmdc.201800738Google Scholar40https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXit1Ohs70%253D&md5=a93505759fe45ffd0352de2f0e17885aAdvancements in the Development of non-BET Bromodomain Chemical ProbesClegg, Michael A.; Tomkinson, Nicholas C. O.; Prinjha, Rab K.; Humphreys, Philip G.ChemMedChem (2019), 14 (4), 362-385CODEN: CHEMGX; ISSN:1860-7179. (Wiley-VCH Verlag GmbH & Co. KGaA)A review. The bromodomain and extra terminal (BET) family of bromodomain-contg. proteins (BCPs) have been the subject of extensive research over the past decade, resulting in a plethora of high-quality chem. probes for their tandem bromodomains. In turn, these chem. probes have helped reveal the profound biol. role of the BET bromodomains and their role in disease, ultimately leading to a no. of mols. in active clin. development. However, the BET subfamily represents just 8/61 of the known human bromodomains, and attention has now expanded to the biol. role of the remaining 53 non-BET bromodomains. Rapid growth of this research area has been accompanied by a greater understanding of the requirements for an effective bromodomain chem. probe and has led to a no. of new non-BET bromodomain chem. probes being developed. Advances since Dec. 2015 are discussed, highlighting the strengths/caveats of each mol., and the value they add toward validating the non-BET bromodomains as tractable therapeutic targets.
- 41Bayliss, M. K.; Butler, J.; Feldman, P. L.; Green, D. V. S.; Leeson, P. D.; Palovich, M. R.; Taylor, A. J. Quality Guidelines for Oral Drug Candidates: Dose, Solubility and Lipophilicity. Drug Disc. Today 2016, 21, 1719– 1727, DOI: 10.1016/j.drudis.2016.07.007Google ScholarThere is no corresponding record for this reference.
- 42Johnson, T. W.; Gallego, R. A.; Edwards, M. P. Lipophilic Efficiency as an Important Metric in Drug Design. J. Med. Chem. 2018, 61, 6401– 6420, DOI: 10.1021/acs.jmedchem.8b00077Google Scholar42https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXmsVahsbg%253D&md5=29f38880914fa75c33be3a640ace4309Lipophilic Efficiency as an Important Metric in Drug DesignJohnson, Ted W.; Gallego, Rebecca A.; Edwards, Martin P.Journal of Medicinal Chemistry (2018), 61 (15), 6401-6420CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)A review. Lipophilic efficiency (LipE) is an important metric that has been increasingly applied in drug discovery medicinal chem. lead optimization programs. In this perspective, using literature drug discovery examples, we discuss the concept of rigorously applying LipE to guide medicinal chem. lead optimization toward drug candidates with potential for superior in vivo efficacy and safety, esp. when guided by physiochem. property-based optimization (PPBO). Also highlighted are examples of small structural modifications such as addn. of single atoms, small functional groups, and cyclizations that produce large increases in LipE. Understanding the factors that may contribute to LipE changes through anal. of ligand-protein crystal structures and using structure-based drug design (SBDD) to increase LipE by design is also discussed. Herein we advocate for use of LipE anal. coupled with PPBO and SBDD as an efficient mechanism for drug design.
- 43Freeman-Cook, K. D.; Hoffman, R. L.; Johnson, T. W. Lipophilic Efficiency: The Most Important Efficiency Metric in Medicinal Chemistry. Future Med. Chem. 2013, 5, 113– 115, DOI: 10.4155/fmc.12.208Google Scholar43https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhs1aiu7g%253D&md5=36170decfa1f1e3ef09ecf772322a210Lipophilic efficiency: the most important efficiency metric in medicinal chemistryFreeman-Cook, Kevin D.; Hoffman, Robert L.; Johnson, Ted W.Future Medicinal Chemistry (2013), 5 (2), 113-115CODEN: FMCUA7; ISSN:1756-8919. (Future Science Ltd.)A review is given on the crit. role of lipophilicity in drug discovery and optimization of general absorption, distribution, metab. and excretion properties, toxicol. profiles and ultimately pharmacol. response. Math. equations are presented concerning the impact of lipophilicity on the dose and the calcn. of the lipophilic ligand efficiency (LipE).
- 44Scott, J. S.; Waring, M. J. Practical Application of Ligand Efficiency Metrics in Lead Optimisation. Bioorg. Med. Chem. 2018, 26, 3006– 3015, DOI: 10.1016/j.bmc.2018.04.004Google Scholar44https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXnsVent7g%253D&md5=50bba76316f6f2ec3c89e06f6717c388Practical application of ligand efficiency metrics in lead optimisationScott, James S.; Waring, Michael J.Bioorganic & Medicinal Chemistry (2018), 26 (11), 3006-3015CODEN: BMECEP; ISSN:0968-0896. (Elsevier B.V.)The use of composite metrics that normalize biol. potency values in relation to markers of physicochem. properties, such as size or lipophilicity, has gained a significant amt. of traction with many medicinal chemists in recent years. However, there is no consensus on best practice in the area and their application has attracted some criticism. Here we present our approach to their application in lead optimization projects, provide an objective discussion of the principles we consider important and illustrate how our use of lipophilic ligand efficiency enabled the progression of a no. of our successful drug discovery projects. We derive, from this and some recent literature highlights, a set of heuristic guidelines for lipophilicity based optimization that we believe are generally applicable across chem. series and protein targets.
- 45Wellaway, C. R.; Amans, D.; Bamborough, P.; Barnett, H.; Bit, R. A.; Brown, J. A.; Carlson, N. R.; Chung, C.; Cooper, A. W. J.; Craggs, P. D.; Davis, R. P.; Dean, T. W.; Evans, J. P.; Gordon, L.; Harada, I. L.; Hirst, D. J.; Humphreys, P. G.; Jones, K. L.; Lewis, A. J.; Lindon, M. J.; Lugo, D.; Mahmood, M.; McCleary, S.; Medeiros, P.; Mitchell, D. J.; O’Sullivan, M.; Le Gall, A.; Patel, V. K.; Patten, C.; Poole, D. L.; Shah, R. R.; Smith, J. E.; Stafford, K. A. J.; Thomas, P. J.; Vimal, M.; Wall, I. D.; Watson, R. J.; Wellaway, N.; Yao, G.; Prinjha, R. K. Discovery of a Bromodomain and Extraterminal Inhibitor with a Low Predicted Human Dose through Synergistic Use of Encoded Library Technology and Fragment Screening. J. Med. Chem. 2020, 63, 714– 746, DOI: 10.1021/acs.jmedchem.9b01670Google Scholar45https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXivFagtw%253D%253D&md5=826ebe53a3091893c9e6c6c4830ac388Discovery of a Bromodomain and Extraterminal Inhibitor with a Low Predicted Human Dose through Synergistic Use of Encoded Library Technology and Fragment ScreeningWellaway, Christopher R.; Amans, Dominique; Bamborough, Paul; Barnett, Heather; Bit, Rino A.; Brown, Jack A.; Carlson, Neil R.; Chung, Chun-wa; Cooper, Anthony W. J.; Craggs, Peter D.; Davis, Robert P.; Dean, Tony W.; Evans, John P.; Gordon, Laurie; Harada, Isobel L.; Hirst, David J.; Humphreys, Philip G.; Jones, Katherine L.; Lewis, Antonia J.; Lindon, Matthew J.; Lugo, Dave; Mahmood, Mahnoor; McCleary, Scott; Medeiros, Patricia; Mitchell, Darren J.; O'Sullivan, Michael; Le Gall, Armelle; Patel, Vipulkumar K.; Patten, Chris; Poole, Darren L.; Shah, Rishi R.; Smith, Jane E.; Stafford, Kayleigh A. J.; Thomas, Pamela J.; Vimal, Mythily; Wall, Ian D.; Watson, Robert J.; Wellaway, Natalie; Yao, Gang; Prinjha, Rab K.Journal of Medicinal Chemistry (2020), 63 (2), 714-746CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)The bromodomain and extraterminal (BET) family of bromodomain-contg. proteins are important regulators of the epigenome through their ability to recognize N-acetyl lysine (KAc) post-translational modifications on histone tails. These interactions have been implicated in various disease states and, consequently, disruption of BET-KAc binding has emerged as an attractive therapeutic strategy with a no. of small mol. inhibitors now under investigation in the clinic. However, until the utility of these advanced candidates is fully assessed by these trials, there remains scope for the discovery of inhibitors from new chemotypes with alternative physicochem., pharmacokinetic, and pharmacodynamic profiles. Herein, we describe the discovery of a candidate-quality dimethylpyridone benzimidazole compd. which originated from the hybridization of a dimethylphenol benzimidazole series, identified using encoded library technol., with an N-Me pyridone series identified through fragment screening. Optimization via structure- and property-based design led to I-BET469, which possesses favorable oral pharmacokinetic properties, displays activity in vivo, and is projected to have a low human efficacious dose.
- 46Barducci, A.; Bussi, G.; Parrinello, M. Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method. Phys. Rev. Lett. 2008, 100, 020603, DOI: 10.1103/PhysRevLett.100.020603Google Scholar46https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXovFensQ%253D%253D&md5=701ccfeee476c2e9a5d1e5a6b0e82197Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy MethodBarducci, Alessandro; Bussi, Giovanni; Parrinello, MichelePhysical Review Letters (2008), 100 (2), 020603/1-020603/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)We present a method for detg. the free-energy dependence on a selected no. of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only on the phys. relevant regions of the order parameter space. The algorithm is tested on the reconstruction of an alanine dipeptide free-energy landscape.
- 47Laio, A.; Parrinello, M. Escaping Free-Energy Minima. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562– 12566, DOI: 10.1073/pnas.202427399Google Scholar47https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XnvFGiurc%253D&md5=48d5bc7436f3ef9d78369671e70fa608Escaping free-energy minimaLaio, Alessandro; Parrinello, MicheleProceedings of the National Academy of Sciences of the United States of America (2002), 99 (20), 12562-12566CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the min. in the FES, allowing the efficient exploration and accurate detn. of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissocn. of a NaCl mol. in water and in the study of the conformational changes of a dialanine in soln.
- 48Gillis, E. P.; Eastman, K. J.; Hill, M. D.; Donnelly, D. J.; Meanwell, N. A. Applications of Fluorine in Medicinal Chemistry. J. Med. Chem. 2015, 58, 8315– 8359, DOI: 10.1021/acs.jmedchem.5b00258Google Scholar48https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht1ajs7%252FK&md5=9995829a94a8c0b8d9fb0d21bdfd5a1dApplications of Fluorine in Medicinal ChemistryGillis, Eric P.; Eastman, Kyle J.; Hill, Matthew D.; Donnelly, David J.; Meanwell, Nicholas A.Journal of Medicinal Chemistry (2015), 58 (21), 8315-8359CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)A review with meta-anal. The role of fluorine in drug design and development is expanding rapidly as we learn more about the unique properties assocd. with this unusual element and how to deploy it with greater sophistication. The judicious introduction of fluorine into a mol. can productively influence conformation, pKa, intrinsic potency, membrane permeability, metabolic pathways, and pharmacokinetic properties. In addn., 18F has been established as a useful positron emitting isotope for use with in vivo imaging technol. that potentially has extensive application in drug discovery and development, often limited only by convenient synthetic accessibility to labeled compds. The wide ranging applications of fluorine in drug design are providing a strong stimulus for the development of new synthetic methodologies that allow more facile access to a wide range of fluorinated compds. In this review, we provide an update on the effects of the strategic incorporation of fluorine in drug mols. and applications in positron emission tomog.
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Compound 22 from ref (31) shows a direct salt bridge between a pendant basic amine and BRD4 BD1 Asp144 (pdb: 7rxt). However, no BD1/BD2 selectivity data for this compound is reported and the research focus is the design of BRD4 BD1 selective chemicals probes, not BET BD1 chemical probes.
There is no corresponding record for this reference. - 50Abel, R.; Young, T.; Farid, R.; Berne, B. J.; Friesner, R. A. Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding. J. Am. Chem. Soc. 2008, 130, 2817– 2831, DOI: 10.1021/ja0771033Google Scholar50https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhvFWgurk%253D&md5=8eefe76547a82bccaea38f2c84e6cd5fRole of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand BindingAbel, Robert; Young, Tom; Farid, Ramy; Berne, Bruce J.; Friesner, Richard A.Journal of the American Chemical Society (2008), 130 (9), 2817-2831CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Understanding the underlying physics of the binding of small-mol. ligands to protein active sites is a key objective of computational chem. and biol. It is widely believed that displacement of water mols. from the active site by the ligand is a principal (if not the dominant) source of binding free energy. Although continuum theories of hydration are routinely used to describe the contributions of the solvent to the binding affinity of the complex, it is still an unsettled question as to whether or not these continuum solvation theories describe the underlying mol. physics with sufficient accuracy to reliably rank the binding affinities of a set of ligands for a given protein. Here we develop a novel, computationally efficient descriptor of the contribution of the solvent to the binding free energy of a small mol. and its assocd. receptor that captures the effects of the ligand displacing the solvent from the protein active site with at. detail. This descriptor quant. predicts (R2 = 0.81) the binding free energy differences between congeneric ligand pairs for the test system factor Xa, elucidates phys. properties of the active site solvent that appear to be missing in most continuum theories of hydration, and identifies several features of the hydration of the factor Xa active site relevant to the structure-activity relationship of its inhibitors.
- 51Young, T.; Abel, R.; Kim, B.; Berne, B. J.; Friesner, R. A. Motifs for Molecular Recognition Exploiting Hydrophobic Enclosure in Protein-Ligand Binding. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 808– 813, DOI: 10.1073/pnas.0610202104Google Scholar51https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhtVegtr4%253D&md5=1109e3f48670cd910885f7fd527eb880Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand bindingYoung, Tom; Abel, Robert; Kim, Byungchan; Berne, Bruce J.; Friesner, Richard A.Proceedings of the National Academy of Sciences of the United States of America (2007), 104 (3), 808-813CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)The thermodn. properties and phase behavior of water in confined regions can vary significantly from that obsd. in the bulk. This is particularly true for systems in which the confinement is on the mol.-length scale. In this study, we use mol. dynamics simulations and a powerful solvent anal. technique based on inhomogeneous solvation theory to investigate the properties of water mols. that solvate the confined regions of protein active sites. Our simulations and anal. indicate that the solvation of protein active sites that are characterized by hydrophobic enclosure and correlated hydrogen bonds induce atypical entropic and enthalpic penalties of hydration. These penalties apparently stabilize the protein-ligand complex with respect to the independently solvated ligand and protein, which leads to enhanced binding affinities. Our anal. elucidates several challenging cases, including the super affinity of the streptavidin-biotin system.
- 52BROMOscan recombinant protein binding assays were carried out at DiscoverX. http://www.discoverx.com (accessed April 4, 2023).Google ScholarThere is no corresponding record for this reference.
- 53Berg, E. L.; Kunkel, E. J.; Hytopoulos, E.; Plavec, I. Characterization of Compound Mechanisms and Secondary Activities by BioMAP Analysis. J. Pharmacol. Toxicol. Methods 2006, 53, 67– 74, DOI: 10.1016/j.vascn.2005.06.003Google Scholar53https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XhvFyisw%253D%253D&md5=48f71e46491af636d6cdc4bc12dadec9Characterization of compound mechanisms and secondary activities by BioMAP analysisBerg, Ellen L.; Kunkel, Eric J.; Hytopoulos, Evangelos; Plavec, IvanJournal of Pharmacological and Toxicological Methods (2006), 53 (1), 67-74CODEN: JPTMEZ; ISSN:1056-8719. (Elsevier B.V.)Introduction: Unexpected drug activities account for many of the failures of new chem. entities in clin. trials. These activities can be target-dependent, resulting from feedback mechanisms downstream of the primary target, or they can occur as a result of unanticipated secondary target(s). Methods that would provide rapid and efficient characterization of compds. with respect to a broad range of biol. pathways and mechanisms relevant to human disease have the potential to improve preclin. and clin. success rates. BioMAP assays contg. primary human cells (endothelial cells and co-cultures with peripheral blood leukocytes) were stimulated in complex formats (specific combinations of inflammatory mediators) for 24 h in the presence or absence of test agents (drugs, exptl. compds., etc.). The levels of selected protein readouts (adhesion receptors, cytokines, enzymes, etc.) were measured and activity profiles (normalized data sets comprising BioMAP profiles) were generated for each test agent. The resulting profiles were compared by statistical methods to identify similarities and mechanistic insights. Compds. with known mechanisms including inhibitors of histamine H1 receptor, angiotensin converting enzyme, IκB kinase-2, β2 adrenergic receptor and others were shown to generate reproducible and distinguishable BioMAP activity profiles. Similarities were obsd. between compds. targeting components within the same signal transduction pathway (e.g. NFκB), and also between compds. that share secondary targets (e.g. ibuprofen and FMOC-L-leucine, a PPARγ agonist). Complex primary cell-based assays can be applied for detecting and distinguishing unexpected activities that may be of relevance to drug action in vivo. The ability to rapidly test compds. prior to animal or clin. studies may reduce the no. of compds. that unexpectedly fail in preclin. or clin. studies.
- 54Kleinstreuer, N. C.; Yang, J.; Berg, E. L.; Knudsen, T. B.; Richard, A. M.; Martin, M. T.; Reif, D. M.; Judson, R. S.; Polokoff, M.; Dix, D. J.; Kavlock, R. J.; Houck, K. A. Phenotypic Screening of the ToxCast Chemical Library to Classify Toxic and Therapeutic Mechanisms. Nat. Biotechnol. 2014, 32, 583– 591, DOI: 10.1038/nbt.2914Google Scholar54https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXotFeqsrc%253D&md5=09336f8e859668a0374d8a27ca4a0ff6Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanismsKleinstreuer, Nicole C.; Yang, Jian; Berg, Ellen L.; Knudsen, Thomas B.; Richard, Ann M.; Martin, Matthew T.; Reif, David M.; Judson, Richard S.; Polokoff, Mark; Dix, David J.; Kavlock, Robert J.; Houck, Keith A.Nature Biotechnology (2014), 32 (6), 583-591CODEN: NABIF9; ISSN:1087-0156. (Nature Publishing Group)Addressing the safety aspects of drugs and environmental chems. has historically been undertaken through animal testing. However, the quantity of chems. in need of assessment and the challenges of species extrapolation require the development of alternative approaches. Our approach, the US Environmental Protection Agency's ToxCast program, utilizes a large suite of in vitro and model organism assays to interrogate important chem. libraries and computationally analyze bioactivity profiles. Here we evaluated one component of the ToxCast program, the use of primary human cell systems, by screening for chems. that disrupt physiol. important pathways. Chem.-response signatures for 87 endpoints covering mol. functions relevant to toxic and therapeutic pathways were generated in eight cell systems for 641 environmental chems. and 135 ref. pharmaceuticals and failed drugs. Computational clustering of the profiling data provided insights into the polypharmacol. and potential off-target effects for many chems. that have limited or no toxicity information. The endpoints measured can be closely linked to in vivo outcomes, such as the upregulation of tissue factor in endothelial cell systems by compds. linked to the risk of thrombosis in vivo. Our results demonstrate that assaying complex biol. pathways in primary human cells can identify potential chem. targets, toxicol. liabilities and mechanisms useful for elucidating adverse outcome pathways.
- 55Seal, J. T.; Atkinson, S. J.; Aylott, H.; Bamborough, P.; Chung, C.-W.; Copley, R. C. B.; Gordon, L.; Grandi, P.; Gray, J. R.; Harrison, L. A.; Hayhow, T. G.; Lindon, M.; Messenger, C.; Michon, A.-M.; Mitchell, D.; Preston, A.; Prinjha, R. K.; Rioja, I.; Taylor, S.; Wall, I. D.; Watson, R. J.; Woolven, J. M.; Demont, E. H. The Optimization of a Novel, Weak Bromo and Extra Terminal Domain (BET) Bromodomain Fragment Ligand to a Potent and Selective Second Bromodomain (BD2) Inhibitor. J. Med. Chem. 2020, 63, 9093– 9126, DOI: 10.1021/acs.jmedchem.0c00796Google Scholar55https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhsVCmurzI&md5=c562a8c9e4c38abac04149ee96e2f594The Optimization of a Novel, Weak Bromo and Extra Terminal Domain (BET) Bromodomain Fragment Ligand to a Potent and Selective Second Bromodomain (BD2) InhibitorSeal, Jonathan T.; Atkinson, Stephen J.; Aylott, Helen; Bamborough, Paul; Chung, Chun-wa; Copley, Royston C. B.; Gordon, Laurie; Grandi, Paola; Gray, James R. J.; Harrison, Lee A.; Hayhow, Thomas G.; Lindon, Matthew; Messenger, Cassie; Michon, Anne-Marie; Mitchell, Darren; Preston, Alex; Prinjha, Rab K.; Rioja, Inmaculada; Taylor, Simon; Wall, Ian D.; Watson, Robert J.; Woolven, James M.; Demont, Emmanuel H.Journal of Medicinal Chemistry (2020), 63 (17), 9093-9126CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)The profound efficacy, yet assocd. toxicity of pan-BET inhibitors is well documented. The possibility of an ameliorated safety profile driven by significantly selective (>100-fold) inhibition of a subset of the eight bromodomains is enticing, but challenging given the close homol. Herein, we describe the X-ray crystal structure-directed optimization of a novel weak fragment ligand with a pan-second bromodomain (BD2) bias, to potent and highly BD2 selective inhibitors. A template hopping approach, enabled by our parallel research into an orthogonal template (15, GSK046, I), was the basis for the high selectivity obsd. This culminated in two tool mols., 20 (GSK620) and 56 (GSK549), which showed an anti-inflammatory phenotype in human whole blood, confirming their cellular target engagement. Excellent broad selectivity, developability, and in vivo oral pharmacokinetics characterize these tools, which we hope will be of broad utility to the field of epigenetics research.
- 56Roos, K.; Wu, C.; Damm, W.; Reboul, M.; Stevenson, J. M.; Lu, C.; Dahlgren, M. K.; Mondal, S.; Chen, W.; Wang, L.; Abel, R.; Friesner, R. A.; Harder, E. D. OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules. J. Chem. Theory Comput. 2019, 15, 1863– 1874, DOI: 10.1021/acs.jctc.8b01026Google Scholar56https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXjtFKlsrs%253D&md5=5c91547ddc0c975f9616cfba56a5454fOPLS3e: Extending Force Field Coverage for Drug-Like Small MoleculesRoos, Katarina; Wu, Chuanjie; Damm, Wolfgang; Reboul, Mark; Stevenson, James M.; Lu, Chao; Dahlgren, Markus K.; Mondal, Sayan; Chen, Wei; Wang, Lingle; Abel, Robert; Friesner, Richard A.; Harder, Edward D.Journal of Chemical Theory and Computation (2019), 15 (3), 1863-1874CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)Building upon the OPLS3 force field we report on an enhanced model, OPLS3e, that further extends its coverage of medicinally relevant chem. space by addressing limitations in chemotype transferability. OPLS3e accomplishes this by incorporating new parameter types that recognize moieties with greater chem. specificity and integrating an on-the-fly parametrization approach to the assignment of partial charges. As a consequence, OPLS3e leads to greater accuracy against performance benchmarks that assess small mol. conformational propensities, solvation, and protein-ligand binding.
- 57Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy. J. Med. Chem. 2004, 47, 1739– 1749, DOI: 10.1021/jm0306430Google Scholar57https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhsFyit74%253D&md5=8cc2f0022318b12dd972e9c493375bf9Glide: A new approach for rapid, accurate docking and scoring. 1. method and assessment of docking accuracyFriesner, Richard A.; Banks, Jay L.; Murphy, Robert B.; Halgren, Thomas A.; Klicic, Jasna J.; Mainz, Daniel T.; Repasky, Matthew P.; Knoll, Eric H.; Shelley, Mee; Perry, Jason K.; Shaw, David E.; Francis, Perry; Shenkin, Peter S.Journal of Medicinal Chemistry (2004), 47 (7), 1739-1749CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)A review. Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand. In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses. The very best candidates are further refined via a Monte Carlo sampling of pose conformation; in some cases, this is crucial to obtaining an accurate docked pose. Selection of the best docked pose uses a model energy function that combines empirical and force-field-based terms. Docking accuracy is assessed by redocking ligands from 282 cocrystd. PDB complexes starting from conformationally optimized ligand geometries that bear no memory of the correctly docked pose. Errors in geometry for the top-ranked pose are less than 1 Å in nearly half of the cases and are greater than 2 Å in only about one-third of them. Comparisons to published data on rms deviations show that Glide is nearly twice as accurate as GOLD and more than twice as accurate as FlexX for ligands having up to 20 rotatable bonds. Glide is also found to be more accurate than the recently described Surflex method.
- 58Kunkel, E. J.; Plavec, I.; Nguyen, D.; Melrose, J.; Rosler, E. S.; Kao, L. T.; Wang, Y.; Hytopoulos, E.; Bishop, A. C.; Bateman, R.; Shokat, K. M.; Butcher, E. C.; Berg, E. L. Rapid Structure-Activity and Selectivity Analysis of Kinase Inhibitors by BioMAP Analysis in Complex Human Primary Cell-Based Models. Assay Drug Dev. Technol. 2004, 2, 431– 442, DOI: 10.1089/adt.2004.2.431Google Scholar58https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXntlGksLY%253D&md5=eae8485e89ea69af97d5e60738bee209Rapid Structure-Activity and Selectivity Analysis of Kinase Inhibitors by BioMAP Analysis in Complex Human Primary Cell-Based ModelsKunkel, Eric J.; Plavec, Ivan; Nguyen, Dat; Melrose, Jennifer; Rosler, Elen S.; Kao, Leon T.; Wang, Yuker; Hytopoulos, Evangelos; Bishop, Anthony C.; Bateman, Raynard; Shokat, Kevan M.; Butcher, Eugene C.; Berg, Ellen L.Assay and Drug Development Technologies (2004), 2 (4), 431-441CODEN: ADDTAR; ISSN:1540-658X. (Mary Ann Liebert, Inc.)A review. Rapid, quant. methods for characterizing the biol. activities of kinase inhibitors in complex human cell systems could allow the biol. consequences of differential target selectivity to be monitored early in development, improving the selection of drug candidates. We have previously shown that Biol. Multiplexed Activity Profiling (BioMAP) permits rapid characterization of drug function based on statistical anal. of protein expression data sets from complex primary human cell based models of disease biol. Here, using four such model systems contg. primary human endothelial cells and peripheral blood mononuclear cells in which multiple signaling pathways relevant to inflammation and immune responses are simultaneously activated, we demonstrate that BioMAP anal. can detect and distinguish a wide range of inhibitors directed against different kinase targets. Using a panel of p38 mitogen-activated protein kinase antagonists as a test set, we show further that related compds. can be distinguished by unique features of the biol. responses they induce in complex systems, and can be classified according to their induction of shared (on-target) and secondary activities. Statistical comparisons of quant. BioMAP profiles and anal. of profile features allow correlation of induced biol. effects with chem. structure and mapping of biol. responses to chem. series or substituents on a common scaffold. Integration of automated BioMAP anal. for prioritization of hits and for structure-activity relation studies may improve and accelerate the design and selection of optimal therapeutic candidates.
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(34)
, 36177-36184. https://doi.org/10.1021/acsomega.4c01495
- David J. Hirst, Paul Bamborough, Niam Al-Mahdi, Davina C. Angell, Heather A. Barnett, Andrew Baxter, Rino A. Bit, Jack A. Brown, Chun-wa Chung, Peter D. Craggs, Robert P. Davis, Emmanuel H. Demont, Alan Ferrie, Laurie J. Gordon, Isobel Harada, Tim C. T. Ho, Ian D. Holyer, Edward Hooper-Greenhill, Katherine L. Jones, Matthew J. Lindon, Cerys Lovatt, David Lugo, Claire Maller, Grant McGonagle, Cassie Messenger, Darren J. Mitchell, David D. Pascoe, Vipulkumar K. Patel, Christopher Patten, Darren L. Poole, Rishi R. Shah, Inmaculada Rioja, Kayleigh A. J. Stafford, Daniel Tape, Simon Taylor, Natalie H. Theodoulou, Laura Tomlinson, Ian D. Wall, Christopher R. Wellaway, Gemma White, Rab K. Prinjha, Philip G. Humphreys. Structure- and Property-Based Optimization of Efficient Pan-Bromodomain and Extra Terminal Inhibitors to Identify Oral and Intravenous Candidate I-BET787. Journal of Medicinal Chemistry 2024, 67
(12)
, 10464-10489. https://doi.org/10.1021/acs.jmedchem.4c00959
- Laura C. Paterson, Philip G. Humphreys, Henry A. Kelly, William J. Kerr. Collaborative GSK–University of Strathclyde doctoral research and training programmes: Transforming approaches to industry–academia engagement. Drug Discovery Today 2024, 29
(11)
, 104162. https://doi.org/10.1016/j.drudis.2024.104162
- Yanli Wang, Yongle Wang, Yulong Xu, Leyi Kang, Darcy Tocci, Changning Wang. The Development and Evaluation of a Novel Highly Selective PET Radiotracer for Targeting BET BD1. Pharmaceuticals 2024, 17
(10)
, 1289. https://doi.org/10.3390/ph17101289
- Rebecca A. Gallego, Martin P. Edwards, T. Patrick Montgomery. An update on lipophilic efficiency as an important metric in drug design. Expert Opinion on Drug Discovery 2024, 19
(8)
, 917-931. https://doi.org/10.1080/17460441.2024.2368744
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Abstract
Figure 1
Figure 1. (a) Overlay of apo BRD4 BD1 in orange (pdb: 2oss) and apo BRD4 BD2 in cyan (pdb: 2ouo). Waters and ethylene glycol have been removed for clarity; (b) percent identity within the KAc binding site between the BET family bromodomains. (13) The darker the shade of blue, the higher the bromodomain identify.
Figure 2
Figure 2. Structures of selected domain-biased/selective BET BD1 and BD2 bromodomain inhibitors. Where reported, the part of the molecules that drives BET BD1 domain selectivity through interacting with Asp144 (BRD4 BD1 numbering) is colored blue for clarity.
Figure 3
Figure 3. (a) Plot of BRD4 BD1 pIC50 against BRD4 BD2 pIC50 for 169 compounds with BRD4 BD1 pIC50 ≥ 7 and BRD4 BD1 domain selectivity ≥50-fold, with diagonal lines representing BD1 domain selectivity. Compounds containing substructure 10 are colored blue, and those that do not contain substructure 10 are colored green; (b) substructure 10; (c) plot of BRD4 BD1 pIC50 against chromLogDpH7.4 with diagonal lines representing different LipE values for 169 molecules. Compounds containing substructure 10 are colored blue, and those that do not contain substructure 10 are colored green; (d) comparison of median LipE values for compounds containing substructure 10 and those that do not.
Scheme 1
Scheme 1. Synthesis of (R)-12 and (S)-12aaReagents and conditions: (a) (R)- or (S)-1-(3-(aminomethyl)piperidin-1-yl)ethan-1-one, DIPEA, NMP, 200 °C, 1 h; (b) 1,5-dimethyl-6-oxo-1,6-dihydropyridine-3-carbaldehyde, Na2S2O4, EtOH, H2O, 100 °C, 130 min.
Figure 4
Figure 4. (a) Structure of 14; (b) crystal structure of 14 (green) bound to BRD2 BD2 (orange) (pdb: 8px8). Water molecules are shown as red spheres and hydrogen bonds are marked in yellow; (c) As (b), but with the protein surface shown in orange; (d) overlay of the crystal structure of 13 (pink) bound to BRD2 BD2 (gray) (pdb: 8px2) and the crystal structure of 14 (green) bound to BRD2 BD2 (orange) (pdb: 8px8); (e) As (b) but with an overlay of the BRD4 BD1 protein surface (cyan) bound to 13 (pdb: 6tpy).
Figure 5
Figure 5. Two-dimensional plot of the average conformational FES of apo BRD4 BD2 (pdb: 2ouo) as calculated by metadynamics. In the boxes, representative conformations of the minima A (His437 trans), B (His437 gauche+), and C (His437 gauche+) of the apo structure are reported. The free energy is displayed every 1 kcal/mol, and the contour levels are shown up to 5 kcal/mol.
Scheme 2
Scheme 2. Synthesis of Benzimidazoles 14 and 21–33aaReagents and conditions: (a) tert-butyl (S)-3-(aminomethyl)piperidine-1-carboxylate, K2CO3, DMF, 80–100 °C; (b) 1,5-dimethyl-6-oxo-1,6-dihydropyridine-3-carbaldehyde, Na2S2O4, EtOH, H2O, 100 °C; (c) HCl, 1,4-dioxane, 0 °C-rt; (d) acid, HATU, DIPEA, DMF, rt or acid chloride, NEt3, THF, rt; (e) For 21–25, 27–29: HCl, 1,4-dioxane, rt.
Scheme 3
Scheme 3. Synthesis of Benzimidazoles 34–36aaReagents and conditions: (a) For 34: BrCH2CH2F, NaH, DMF, rt to 60 °C, 1 h, 37%; (b) For 35: BrCH2CHF2, NaH, DMF, rt to 90 °C, 37 h, 37%; (c) For 36: TFA, PhSiH3, THF, 70 °C, 19 h, 44%.
Figure 6
Figure 6. (a) Crystal structure of 31 (yellow) bound to BRD4 BD1 (cyan) (pdb: 8pxa). Water molecules are shown as red spheres and hydrogen bonds are marked in yellow; (b) As (a), but with the protein surface from 14 bound to BRD2 BD2 shown in orange overlaid (pdb: 8px8); (c) overlay of 31 (yellow) bound to BRD4 BD1 (pdb: 8pxa) with 14 (green) bound to BRD2 BD2 (pdb: 8px8); (d) overlay of 31 (yellow) bound to BRD4 BD1 (cyan) (pdb: 8pxa) and GSK778 (8) (gray) bound to BRD4 BD1 (blue) (pdb: 6swn). Only Asp145 and Asp144 are shown for clarity.
Figure 7
Figure 8
Figure 8. (a) BioMAP profile of 31 [10 μM (red), 2.5 μM (orange), 630 nM (yellow), and 160 nM (green)] in the Diversity PLUS Panel. The X-axis lists the quantitative protein-based biomarker readouts measured in each system. The Y-axis represents a log-transformed ratio of the biomarker readouts for the drug-treated sample (n = 1) over vehicle controls (n ≥ 6). The gray region around the Y-axis represents the 95% significance envelope generated from historical vehicle controls. Biomarker activities are annotated when two or more consecutive concentrations change in the same direction relative to vehicle controls, are outside of the significance envelope, and have at least one concentration with an effect size >20% (log10 ratio >0.1). Biomarker key activities are described as modulated if these activities increase in some systems but decrease in others. No cytotoxicity was observed at the concentrations tested, and antiproliferative effects are indicated by a thick gray arrow above the X-axis; (b) As (a), but with 31 (10 μM, red) and (+)-JQ1 (120 nM, blue).
References
This article references 58 other publications.
- 1Filippakopoulos, P.; Picaud, S.; Mangos, M.; Keates, T.; Lambert, J.-P.; Barsyte-Lovejoy, D.; Felletar, I.; Volkmer, R.; Müller, S.; Pawson, T.; Gingras, A.-C.; Arrowsmith, C. H.; Knapp, S. Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family. Cell 2012, 149, 214– 231, DOI: 10.1016/j.cell.2012.02.0131https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XltVamurs%253D&md5=05583a01a1cd4c3b59fc59c00e4c4777Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain FamilyFilippakopoulos, Panagis; Picaud, Sarah; Mangos, Maria; Keates, Tracy; Lambert, Jean-Philippe; Barsyte-Lovejoy, Dalia; Felletar, Ildiko; Volkmer, Rudolf; Muller, Susanne; Pawson, Tony; Gingras, Anne-Claude; Arrowsmith, Cheryl H.; Knapp, StefanCell (Cambridge, MA, United States) (2012), 149 (1), 214-231CODEN: CELLB5; ISSN:0092-8674. (Cell Press)Bromodomains (BRDs) are protein interaction modules that specifically recognize ε-N-lysine acetylation motifs, a key event in the reading process of epigenetic marks. The 61 BRDs in the human genome cluster into eight families based on structure/sequence similarity. Here, we present 29 high-resoln. crystal structures, covering all BRD families. These proteins are: ASH1L, ATAD2, BAZ2B, BPTF, BRD1, BRD3(1), BRD3(2), BRD4(1), BRD4(2), BRD9, BRDT(1), CECR2, EP300, CREBBP, GCN5L2, KIAA1240, PB1(1), PB1(2), PB1(3), PB1(4), PB1(5), PB1(6), PCAF, PHIP(2), TAF1(2), WDR9(2), BRD4(1). Comprehensive crossfamily structural anal. identifies conserved and family-specific structural features that are necessary for specific acetylation-dependent substrate recognition. Screening of more than 30 representative BRDs against systematic histone-peptide arrays identifies new BRD substrates and reveals a strong influence of flanking posttranslational modifications, such as acetylation and phosphorylation, suggesting that BRDs recognize combinations of marks rather than singly acetylated sequences. We further uncovered a structural mechanism for the simultaneous binding and recognition of diverse diacetyl-contg. peptides by BRD4. These data provide a foundation for structure-based drug design of specific inhibitors for this emerging target family.
- 2Zaware, N.; Zhou, M.-M. Bromodomain Biology and Drug Discovery. Nat. Struct. Mol. Biol. 2019, 26, 870– 879, DOI: 10.1038/s41594-019-0309-82https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvFSnsL3E&md5=7ccf3a3a2ff7147ead1148ee71fa2806Bromodomain biology and drug discoveryZaware, Nilesh; Zhou, Ming-MingNature Structural & Molecular Biology (2019), 26 (10), 870-879CODEN: NSMBCU; ISSN:1545-9993. (Nature Research)The bromodomain (BrD) is a conserved structural module found in chromatin- and transcription-assocd. proteins that acts as the primary reader for acetylated lysine residues. This basic activity endows BrD proteins with versatile functions in the regulation of protein-protein interactions mediating chromatin-templated gene transcription, DNA recombination, replication and repair. Consequently, BrD proteins are involved in the pathogenesis of numerous human diseases. In this Review, we highlight our current understanding of BrD biol., and discuss the latest development of small-mol. inhibitors targeting BrDs as emerging epigenetic therapies for cancer and inflammatory disorders.
- 3Belkina, A. C.; Denis, G. V. BET Domain Co-Regulators in Obesity, Inflammation and Cancer. Nat. Rev. Cancer 2012, 12, 465– 477, DOI: 10.1038/nrc32563https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XovFyks7s%253D&md5=d06d88ef0d5d4d71115f40a2f901f53dBET domain co-regulators in obesity, inflammation and cancerBelkina, Anna C.; Denis, Gerald V.Nature Reviews Cancer (2012), 12 (7), 465-477CODEN: NRCAC4; ISSN:1474-175X. (Nature Publishing Group)A review. The bromodomain is a highly conserved motif of 110 amino acids that is bundled into four anti-parallel α-helixes and found in proteins that interact with chromatin, such as transcription factors, histone acetylases and nucleosome remodelling complexes. Bromodomain proteins are chromatin 'readers'; they recruit chromatin-regulating enzymes, including 'writers' and 'erasers' of histone modification, to target promoters and to regulate gene expression. Conventional wisdom held that complexes involved in chromatin dynamics are not 'druggable' targets. However, small mols. that inhibit bromodomain and extraterminal (BET) proteins have been described. We examine these developments and discuss the implications for small mol. epigenetic targeting of chromatin networks in cancer.
- 4Jain, A. K.; Barton, M. C. Bromodomain Histone Readers and Cancer. J. Mol. Biol. 2017, 429, 2003– 2010, DOI: 10.1016/j.jmb.2016.11.0204https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC28XhvFOisbbI&md5=2d1d3efa959f66eeb8789b48daf96325Bromodomain histone readers and cancerJain, Abhinav K.; Barton, Michelle C.Journal of Molecular Biology (2017), 429 (13), 2003-2010CODEN: JMOBAK; ISSN:0022-2836. (Elsevier Ltd.)A review. Lysine acetylation of histone proteins is a fundamental post-translational modification that regulates chromatin structure and plays an important role in gene transcription. Aberrant levels of histone lysine acetylation are assocd. with the development of several diseases. Acetyl-lysine modifications create docking sites for bromodomains, which are structurally conserved modules present in transcription-assocd. proteins that are termed "reader" proteins. Bromodomain-contg. reader proteins are part of multiprotein complexes that regulate transcription programs, which are often assocd. with profound phenotypic changes. Many bromodomain-contg. proteins are aberrantly expressed in diseases, as best studied in cancers, where bromodomain proteins impact the expression of oncogenes and anti-apoptotic proteins. Thus, bromodomain readers of histone acetylation have emerged as attractive targets for cancer drug discovery, prompting immense interest in epigenetic-focused, medicinal chem. to develop structurally guided chem. probes of bromodomains. Here, we describe bromodomain-contg. proteins with defined roles in cancer and highlight recent progress in the development of bromodomain inhibitors.
- 5Conery, A. R.; Centore, R. C.; Neiss, A.; Keller, P. J.; Joshi, S.; Spillane, K. L.; Sandy, P.; Hatton, C.; Pardo, E.; Zawadzke, L.; Bommi-Reddy, A.; Gascoigne, K. E.; Bryant, B. M.; Mertz, J. A.; Sims, R. J., III Bromodomain Inhibition of the Transcriptional Coactivators CBP/EP300 as a Therapeutic Strategy to Target the IRF4 Network in Multiple Myeloma. eLife 2016, 5, e10483 DOI: 10.7554/elife.104835https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXnslahtro%253D&md5=d0037d5abb6fbd85ce1ce2763c535370Bromodomain inhibition of the transcriptional coactivators CBP/EP300 as atherapeutic strategy to target the IRF4 network in multiple myelomaConery, Andrew R.; Centore, Richard C.; Neiss, Adrianne; Keller, Patricia J.; Joshi, Shivangi; Spillane, Kerry L.; Sandy, Peter; Hatton, Charlie; Pardo, Eneida; Zawadzke, Laura; Bommi-Reddy, Archana; Gascoigne, Karen E.; Bryant, Barbara M.; Mertz, Jennifer A.; Sims, Robert J., IIIeLife (2016), 5 (), e10483/1-e10483/17CODEN: ELIFA8; ISSN:2050-084X. (eLife Sciences Publications Ltd.)Pharmacol. inhibition of chromatin co-regulatory factors represents a clin. validated strategy to modulate oncogenic signaling through selective attenuation of gene expression. Here, we demonstrate that CBP/EP300 bromodomain inhibition preferentially abrogates the viability of multiple myeloma cell lines. Selective targeting of multiple myeloma cell lines through CBP/EP300 bromodomain inhibition is the result of direct transcriptional suppression of the lymphocyte-specific transcription factor IRF4, which is essential for the viability of myeloma cells, and the concomitant repression of the IRF4 target gene c-MYC. Ectopic expression of either IRF4 or MYC antagonizes the phenotypic and transcriptional effects of CBP/EP300 bromodomain inhibition, highlighting the IRF4/MYC axis as a key component of its mechanism of action. These findings suggest that CBP/EP300 bromodomain inhibition represents a viable therapeutic strategy for targeting multiple myeloma and other lymphoid malignancies dependent on the IRF4 network.
- 6Zeng, L.; Li, J.; Muller, M.; Yan, S.; Mujtaba, S.; Pan, C.; Wang, Z.; Zhou, M.-M. Selective Small Molecules Blocking HIV-1 Tat and Coactivator PCAF Association. J. Am. Chem. Soc. 2005, 127, 2376– 2377, DOI: 10.1021/ja044885g6https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2MXps12lsQ%253D%253D&md5=98329586e5772042c8b7184d8e9a560eSelective Small Molecules Blocking HIV-1 Tat and Coactivator PCAF AssociationZeng, Lei; Li, Jiaming; Muller, Michaela; Yan, Sherry; Mujtaba, Shiraz; Pan, Chongfeng; Wang, Zhiyong; Zhou, Ming-MingJournal of the American Chemical Society (2005), 127 (8), 2376-2377CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Development of drug resistance from mutations in the targeted viral proteins leads to continuation of viral prodn. by chronically infected cells, contributing to HIV-mediated immune dysfunction. Targeting a host cell protein essential for viral reprodn., rather than a viral protein, may minimize the viral drug resistance problem as obsd. with HIV protease inhibitors. The authors report here the development of a novel class of N1-aryl-propane-1,3-diamine compds. using a structure-based approach that selectively inhibit the activity of the bromodomain of the human transcriptional coactivator PCAF, of which assocn. with the HIV trans-activator Tat is essential for transcription and replication of the integrated HIV provirus.
- 7Filippakopoulos, P.; Qi, J.; Picaud, S.; Shen, Y.; Smith, W. B.; Fedorov, O.; Morse, E. M.; Keates, T.; Hickman, T. T.; Felletar, I.; Philpott, M.; Munro, S.; McKeown, M. R.; Wang, Y.; Christie, A. L.; West, N.; Cameron, M. J.; Schwartz, B.; Heightman, T. D.; La Thangue, N.; French, C. A.; Wiest, O.; Kung, A. L.; Knapp, S.; Bradner, J. E. Selective Inhibition of BET Bromodomains. Nature 2010, 468, 1067– 1073, DOI: 10.1038/nature095047https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3MXotlGmtA%253D%253D&md5=bd9cadac86124d2c6c3cd5b2a92d68c2Selective inhibition of BET bromodomainsFilippakopoulos, Panagis; Qi, Jun; Picaud, Sarah; Shen, Yao; Smith, William B.; Fedorov, Oleg; Morse, Elizabeth M.; Keates, Tracey; Hickman, Tyler T.; Felletar, Ildiko; Philpott, Martin; Munro, Shongah; McKeown, Michael R.; Wang, Yuchuan; Christie, Amanda L.; West, Nathan; Cameron, Michael J.; Schwartz, Brian; Heightman, Tom D.; La Thangue, Nicholas; French, Christopher; Wiest, Olaf; Kung, Andrew L.; Knapp, Stefan; Bradner, James E.Nature (London, United Kingdom) (2010), 468 (7327), 1067-1073CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Epigenetic proteins are intently pursued targets in ligand discovery. So far, successful efforts have been limited to chromatin modifying enzymes, or so-called epigenetic 'writers' and 'erasers'. Potent inhibitors of histone binding modules have not yet been described. Here the authors report a cell-permeable small mol. (I,JQ1) that binds competitively to acetyl-lysine recognition motifs, or bromodomains. High potency and specificity towards a subset of human bromodomains is explained by co-crystal structures with bromodomain and extra-terminal (BET) family member BRD4, revealing excellent shape complementarity with the acetyl-lysine binding cavity. Recurrent translocation of BRD4 is obsd. in a genetically-defined, incurable subtype of human squamous carcinoma. Competitive binding by JQ1 displaces the BRD4 fusion oncoprotein from chromatin, prompting squamous differentiation and specific antiproliferative effects in BRD4-dependent cell lines and patient-derived xenograft models. These data establish proof-of-concept for targeting protein-protein interactions of epigenetic 'readers', and provide a versatile chem. scaffold for the development of chem. probes more broadly throughout the bromodomain family.
- 8Nicodeme, E.; Jeffrey, K. L.; Schaefer, U.; Beinke, S.; Dewell, S.; Chung, C.; Chandwani, R.; Marazzi, I.; Wilson, P.; Coste, H.; White, J.; Kirilovsky, J.; Rice, C. M.; Lora, J. M.; Prinjha, R. K.; Lee, K.; Tarakhovsky, A. Suppression of Inflammation by a Synthetic Histone Mimic. Nature 2010, 468, 1119– 1123, DOI: 10.1038/nature095898https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3cXhtl2rtb%252FP&md5=0dfccd9d01b87859512bf591e1c5a93cSuppression of inflammation by a synthetic histone mimicNicodeme, Edwige; Jeffrey, Kate L.; Schaefer, Uwe; Beinke, Soren; Dewell, Scott; Chung, Chun-wa; Chandwani, Rohit; Marazzi, Ivan; Wilson, Paul; Coste, Herve; White, Julia; Kirilovsky, Jorge; Rice, Charles M.; Lora, Jose M.; Prinjha, Rab K.; Lee, Kevin; Tarakhovsky, AlexanderNature (London, United Kingdom) (2010), 468 (7327), 1119-1123CODEN: NATUAS; ISSN:0028-0836. (Nature Publishing Group)Interaction of pathogens with cells of the immune system results in activation of inflammatory gene expression. This response, although vital for immune defense, is frequently deleterious to the host due to the exaggerated prodn. of inflammatory proteins. The scope of inflammatory responses reflects the activation state of signaling proteins upstream of inflammatory genes as well as signal-induced assembly of nuclear chromatin complexes that support mRNA expression. Recognition of post-translationally modified histones by nuclear proteins that initiate mRNA transcription and support mRNA elongation is a crit. step in the regulation of gene expression. Here we present a novel pharmacol. approach that targets inflammatory gene expression by interfering with the recognition of acetylated histones by the bromodomain and extra terminal domain (BET) family of proteins. We describe a synthetic compd. (I-BET) that by mimicking' acetylated histones disrupts chromatin complexes responsible for the expression of key inflammatory genes in activated macrophages, and confers protection against lipopolysaccharide-induced endotoxic shock and bacteria-induced sepsis. Our findings suggest that synthetic compds. specifically targeting proteins that recognize post-translationally modified histones can serve as a new generation of immunomodulatory drugs.
- 9Prinjha, R. K.; Witherington, J.; Lee, K. Place Your BETs: The Therapeutic Potential of Bromodomains. Trends Pharmacol. Sci. 2012, 33, 146– 153, DOI: 10.1016/j.tips.2011.12.0029https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XjtlOlt74%253D&md5=ea1e9e5740b1131239aa0407748d549bPlace your BETs: the therapeutic potential of bromodomainsPrinjha, R. K.; Witherington, J.; Lee, K.Trends in Pharmacological Sciences (2012), 33 (3), 146-153CODEN: TPHSDY; ISSN:0165-6147. (Elsevier Ltd.)A review. Therapeutic targeting of the processes that regulate histone modification is a growing area of scientific exploration. Although most interest has concd. on the various families of enzymes that contribute to these processes, this review focuses on emerging data demonstrating the chem. tractability and therapeutic potential of a hitherto underexplored family of proteins, namely the bromodomain (BRD) family of reader proteins. These proteins perform a crucial role in translating histone modifications with powerful transcriptional consequences. We review current knowledge of the biol. of this emergent target class and highlight recent breakthroughs that now make the BRD family of reader proteins attractive for drug discovery.
- 10Garnier, J.-M.; Sharp, P. P.; Burns, C. J. BET Bromodomain Inhibitors: A Patent Review. Exp. Opin. Ther. Pat. 2014, 24, 185– 199, DOI: 10.1517/13543776.2014.85924410https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXptlWgtg%253D%253D&md5=bb33008eefa34f3689e0ee4a49a2539eBET bromodomain inhibitors: a patent reviewGarnier, Jean-Marc; Sharp, Phillip P.; Burns, Christopher J.Expert Opinion on Therapeutic Patents (2014), 24 (2), 185-199CODEN: EOTPEG; ISSN:1354-3776. (Informa Healthcare)A review. Introduction: The bromodomain (BRD) and extra-C terminal domain (BET) protein family consists of four members (BRD2, BRD3, BRD4 and BRDT). These "epigenetic readers" bind to acetyllysine (KAc) residues on the tails of histones H3 and H4, and regulate chromatin structure and gene expression. There is increasing evidence of their role in human disease, and recently a no. of small-mol. inhibitors have been reported. There is increasing interest in the inhibition of BET proteins for a variety of therapeutic applications that have resulted in considerable patent activity from academia and biotechnol. and pharmaceutical companies. Areas covered: Data supporting the use of BET inhibitors in treating disease are outlined, and the current patent literature is discussed. The survey is focused on patents claiming compds. as BET inhibitors and addnl. patents covering compds. now reported as BET inhibitors have been included. Expert opinion: There is now compelling preclin. data demonstrating BET inhibition as a strategy to target processes known to be involved in disease development and progression with clin. trials of two bona fide BET inhibitors now underway. Patent activity in this area is increasing with initial activity focused on variations to reported BET inhibitors and more recent patents disclosing novel chemotypes as BET inhibitors.
- 11Chen, H.; Liu, Z.; Zheng, L.; Wang, R.; Shi, L. BET Inhibitors: An Updated Patent Review (2018–2021). Exp. Opin. Ther. Pat. 2022, 32, 953– 968, DOI: 10.1080/13543776.2022.2115354There is no corresponding record for this reference.
- 12Watson, R. J.; Bamborough, P.; Barnett, H.; Chung, C.; Davis, R.; Gordon, L.; Grandi, P.; Petretich, M.; Phillipou, A.; Prinjha, R. K.; Rioja, I.; Soden, P.; Werner, T.; Demont, E. H. GSK789: A Selective Inhibitor of the First Bromodomains (BD1) of the Bromo and Extra Terminal Domain (BET) Proteins. J. Med. Chem. 2020, 63, 9045– 9069, DOI: 10.1021/acs.jmedchem.0c0061412https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhsVWrsLzJ&md5=c86b4d2c85dcfa62854debf225c8076cGSK789: A Selective Inhibitor of the First Bromodomains (BD1) of the Bromo and Extra Terminal Domain (BET) ProteinsWatson, Robert J.; Bamborough, Paul; Barnett, Heather; Chung, Chun-wa; Davis, Rob; Gordon, Laurie; Grandi, Paola; Petretich, Massimo; Phillipou, Alex; Prinjha, Rab K.; Rioja, Inmaculada; Soden, Peter; Werner, Thilo; Demont, Emmanuel H.Journal of Medicinal Chemistry (2020), 63 (17), 9045-9069CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)Pan-bromodomain and extra terminal (BET) inhibitors interact equipotently with all eight bromodomains of the BET family of proteins. They have shown profound efficacy in vitro and in vivo in oncol. and immunomodulatory models, and a no. of them are currently in clin. trials where significant safety signals have been reported. It is therefore important to understand the functional contribution of each bromodomain to assess the opportunity to tease apart efficacy and toxicity. This article discloses the in vitro and cellular activity profiles of GSK789(I), a potent, cell-permeable, and highly selective inhibitor of the first bromodomains of the BET family.
- 14Piha-Paul, S. A.; Hann, C. L.; French, C. A.; Cousin, S.; Braña, I.; Cassier, P. A.; Moreno, V.; de Bono, J. S.; Harward, S. D.; Ferron-Brady, G.; Barbash, O.; Wyce, A.; Wu, Y.; Horner, T.; Annan, M.; Parr, N. J.; Prinjha, R. K.; Carpenter, C. L.; Hilton, J.; Hong, D. S.; Haas, N. B.; Markowski, M. C.; Dhar, A.; O’Dwyer, P. J.; Shapiro, G. I. Phase 1 Study of Molibresib (GSK525762), a Bromodomain and Extra-Terminal Domain Protein Inhibitor, in NUT Carcinoma and Other Solid Tumors. JNCI Cancer Spectrum 2020, 4, pkz093, DOI: 10.1093/jncics/pkz093There is no corresponding record for this reference.
- 15Shorstova, T.; Foulkes, W. D.; Witcher, M. Achieving Clinical Success with BET Inhibitors as Anti-Cancer Agents. Br. J. Cancer 2021, 124, 1478– 1490, DOI: 10.1038/s41416-021-01321-015https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXmsFKiu7c%253D&md5=3bac6e1d949af466cb01f96382318f42Achieving clinical success with BET inhibitors as anti-cancer agentsShorstova, Tatiana; Foulkes, William D.; Witcher, MichaelBritish Journal of Cancer (2021), 124 (9), 1478-1490CODEN: BJCAAI; ISSN:0007-0920. (Nature Portfolio)A review. The transcriptional upregulation of oncogenes is a driving force behind the progression of many tumors. However, until a decade ago, the concept of 'switching off' these oncogenic pathways represented a formidable challenge. Research has revealed that members of the bromo- and extra-terminal domain (BET) motif family are key activators of oncogenic networks in a spectrum of cancers; their function depends on their recruitment to chromatin through two bromodomains (BD1 and BD2). The advent of potent inhibitors of BET proteins (BETi), which target either one or both bromodomains, represents an important step towards the goal of suppressing oncogenic networks within tumors. Here, we discuss the biol. of BET proteins, advances in BETi design and highlight potential biomarkers predicting their activity. We also outline the logic of incorporating BETi into combination therapies to enhance its efficacy. We suggest that understanding mechanisms of activity, defining predictive biomarkers and identifying potent synergies represents a roadmap for clin. success using BETi.
- 16Postel-Vinay, S.; Herbschleb, K.; Massard, C.; Woodcock, V.; Soria, J.-C.; Walter, A. O.; Ewerton, F.; Poelman, M.; Benson, N.; Ocker, M.; Wilkinson, G.; Middleton, M. First-in-Human Phase I Study of the Bromodomain and Extraterminal Motif Inhibitor BAY 1238097: Emerging Pharmacokinetic/Pharmacodynamic Relationship and Early Termination Due to Unexpected Toxicity. Eur. J. Cancer 2019, 109, 103– 110, DOI: 10.1016/j.ejca.2018.12.02016https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhslCltLo%253D&md5=c5969b7827810fd1146338b84c8f8621First-in-human phase I study of the bromodomain and extraterminal motif inhibitor BAY 1238097: emerging pharmacokinetic/pharmacodynamic relationship and early termination due to unexpected toxicityPostel-Vinay, Sophie; Herbschleb, Karin; Massard, Christophe; Woodcock, Victoria; Soria, Jean-Charles; Walter, Annette O.; Ewerton, Flavio; Poelman, Martine; Benson, Neil; Ocker, Matthias; Wilkinson, Gary; Middleton, MarkEuropean Journal of Cancer (2019), 109 (), 103-110CODEN: EJCAEL; ISSN:0959-8049. (Elsevier Ltd.)Bromodomain and extraterminal motif protein inhibition is a promising cancer treatment strategy, notably for targeting MYC- or BRD4-driven diseases. A first-in-human study investigated the safety, pharmacokinetics, max. tolerated dose and recommended phase II dose of the BET inhibitor BAY 1238097 in patients with advanced malignancies.In this phase I, open-label, non-randomised, multicentre study, patients with cytol. or histol. confirmed advanced refractory malignancies received oral BAY 1238097 twice weekly in 21-day cycles using an adaptive dose-escalation design at a starting dose of 10 mg/wk. Both patients receiving 80 mg/wk had dose-limiting toxicities (grade 3 vomiting, grade 3 headache and grade 2/3 back pain). The most common adverse events were nausea, vomiting, headache, back pain and fatigue. Pharmacokinetic anal. indicated a linear dose response with increasing dose. Two patients displayed prolonged stable disease; no responses were obsd. Biomarker evaluation of MYC and HEXIM1 expression demonstrated an emerging pharmacokinetic/pharmacodynamic relationship, with a trend towards decreased MYC and increased HEXIM1 expression in response to treatment.The study was prematurely terminated because of the occurrence of DLTs at a dose below targeted drug exposure. Pharmacokinetic modeling indicated that an alternate dosing schedule whereby DLTs could be avoided while reaching efficacious exposure was not feasible.
- 17Chen, J.; Tang, P.; Wang, Y.; Wang, J.; Yang, C.; Li, Y.; Yang, G.; Wu, F.; Zhang, J.; Ouyang, L. Targeting Bromodomain-Selective Inhibitors of BET Proteins in Drug Discovery and Development. J. Med. Chem. 2022, 65, 5184– 5211, DOI: 10.1021/acs.jmedchem.1c0183517https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XnvVKhsr0%253D&md5=bd2bb412aad23fa184778d41fc957a21Targeting Bromodomain-Selective Inhibitors of BET Proteins in Drug Discovery and DevelopmentChen, Juncheng; Tang, Pan; Wang, Yuxi; Wang, Jiaxing; Yang, Chengcan; Li, Yang; Yang, Gaoxia; Wu, Fengbo; Zhang, Jifa; Ouyang, LiangJournal of Medicinal Chemistry (2022), 65 (7), 5184-5211CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)A review. Blocking the interactions between bromodomain and extraterminal (BET) proteins and acetylated lysines of histones by small mols. has important implications for the treatment of cancers and other diseases. Many pan-BET inhibitors have shown satisfactory results in clin. trials, but their potential for poor tolerability and toxicity persist. However, recently reported studies illustrate that some BET bromodomain (BET-BD1 or BET-BD2)-selective inhibitors have advantage over pan-inhibitors, including reduced toxicity concerns. Furthermore, some selective BET inhibitors have similar or even better therapeutic efficacy in inflammatory diseases or cancers. Therefore, the development of selective BET inhibitors has become a hot spot for medicinal chemists. Here, we summarize the known selective BET-BD1 and BET-BD2 inhibitors and review the methods for enhancing the selectivity and potency of these inhibitors based on their different modes of interactions with BET-BD1 or BET-BD2. Finally, we discuss prospective strategies that selectively target the bromodomains of BET proteins.
- 18Gilan, O.; Rioja, I.; Knezevic, K.; Bell, M. J.; Yeung, M. M.; Harker, N. R.; Lam, E. Y. N.; Chung, C.; Bamborough, P.; Petretich, M.; Urh, M.; Atkinson, S. J.; Bassil, A. K.; Roberts, E. J.; Vassiliadis, D.; Burr, M. L.; Preston, A. G. S.; Wellaway, C.; Werner, T.; Gray, J. R.; Michon, A.-M.; Gobbetti, T.; Kumar, V.; Soden, P. E.; Haynes, A.; Vappiani, J.; Tough, D. F.; Taylor, S.; Dawson, S.-J.; Bantscheff, M.; Lindon, M.; Drewes, G.; Demont, E. H.; Daniels, D. L.; Grandi, P.; Prinjha, R. K.; Dawson, M. A. Selective Targeting of BD1 and BD2 of the BET Proteins in Cancer and Immunoinflammation. Science 2020, 368, 387– 394, DOI: 10.1126/science.aaz845518https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXnslKrtrg%253D&md5=d78cfea091fcf5ee18735b02b2120dd7Selective targeting of BD1 and BD2 of the BET proteins in cancer and immunoinflammationGilan, Omer; Rioja, Inmaculada; Knezevic, Kathy; Bell, Matthew J.; Yeung, Miriam M.; Harker, Nicola R.; Lam, Enid Y. N.; Chung, Chun-wa; Bamborough, Paul; Petretich, Massimo; Urh, Marjeta; Atkinson, Stephen J.; Bassil, Anna K.; Roberts, Emma J.; Vassiliadis, Dane; Burr, Marian L.; Preston, Alex G. S.; Wellaway, Christopher; Werner, Thilo; Gray, James R.; Michon, Anne-Marie; Gobbetti, Thomas; Kumar, Vinod; Soden, Peter E.; Haynes, Andrea; Vappiani, Johanna; Tough, David F.; Taylor, Simon; Dawson, Sarah-Jane; Bantscheff, Marcus; Lindon, Matthew; Drewes, Gerard; Demont, Emmanuel H.; Daniels, Danette L.; Grandi, Paola; Prinjha, Rab K.; Dawson, Mark A.Science (Washington, DC, United States) (2020), 368 (6489), 387-394CODEN: SCIEAS; ISSN:1095-9203. (American Association for the Advancement of Science)The two tandem bromodomains of the BET (bromodomain and extraterminal domain) proteins enable chromatin binding to facilitate transcription. Drugs that inhibit both bromodomains equally have shown efficacy in certain malignant and inflammatory conditions. To explore the individual functional contributions of the first (BD1) and second (BD2) bromodomains in biol. and therapy, we developed selective BD1 and BD2 inhibitors. We found that steady-state gene expression primarily requires BD1, whereas the rapid increase of gene expression induced by inflammatory stimuli requires both BD1 and BD2 of all BET proteins. BD1 inhibitors phenocopied the effects of pan-BET inhibitors in cancer models, whereas BD2 inhibitors were predominantly effective in models of inflammatory and autoimmune disease. These insights into the differential requirement of BD1 and BD2 for the maintenance and induction of gene expression may guide future BET-targeted therapies.
- 19Picaud, 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, P. E.; Knapp, S.; Filippakopoulos, P. RVX-208, an Inhibitor of BET Transcriptional Regulators with Selectivity for the Second Bromodomain. Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 19754– 19759, DOI: 10.1073/pnas.131065811019https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhvFKms7zN&md5=c918702c9fdb91241bc837732730f7f6RVX-208, an inhibitor of BET transcriptional regulators with selectivity for the second bromodomainPicaud, Sarah; Wells, Christopher; Felletar, Ildiko; Brotherton, Deborah; Martin, Sarah; Savitsky, Pavel; Diez-Dacal, Beatriz; Philpott, Martin; Bountra, Chas; Lingard, Hannah; Fedorov, Oleg; Muller, Susanne; Brennan, Paul E.; Knapp, Stefan; Filippakopoulos, PanagisProceedings of the National Academy of Sciences of the United States of America (2013), 110 (49), 19754-19759,S19754/1-S19754/10CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)Bromodomains have emerged as attractive candidates for the development of inhibitors targeting gene transcription. Inhibitors of the bromo and extraterminal (BET) family recently showed promising activity in diverse disease models. However, the pleiotropic nature of BET proteins regulating tissue-specific transcription has raised safety concerns and suggested that attempts should be made for domain-specific targeting. Here, we report that RVX-208, a compd. currently in phase II clin. trials, is a BET bromodomain inhibitor specific for second bromodomains (BD2s). Cocrystal structures revealed binding modes of RVX-208 and its synthetic precursor, and fluorescent recovery after photobleaching demonstrated that RVX-208 displaces BET proteins from chromatin. However, gene-expression data showed that BD2 inhibition only modestly affects BET-dependent gene transcription. Our data demonstrate the feasibility of specific targeting within the BET family resulting in different transcriptional outcomes and highlight the importance of BD1 in transcriptional regulation.
- 20http://www.clinicaltrials.gov/ct2/show/NCT04894266 (accessed April 4, 2023).There is no corresponding record for this reference.
- 21Sheppard, G. S.; Wang, L.; Fidanze, S. D.; Hasvold, L. A.; Liu, D.; Pratt, J. K.; Park, C. H.; Longenecker, K.; Qiu, W.; Torrent, M.; Kovar, P. J.; Bui, M.; Faivre, E.; Huang, X.; Lin, X.; Wilcox, D.; Zhang, L.; Shen, Y.; Albert, D. H.; Magoc, T. J.; Rajaraman, G.; Kati, W. M.; McDaniel, K. F. Discovery of N-Ethyl-4-[2-(4-Fluoro-2,6-Dimethyl-Phenoxy)-5-(1-Hydroxy-1-Methyl-Ethyl)Phenyl]-6-Methyl-7-Oxo-1H-Pyrrolo[2,3-c]Pyridine-2-Carboxamide (ABBV-744), a BET Bromodomain Inhibitor with Selectivity for the Second Bromodomain. J. Med. Chem. 2020, 63, 5585– 5623, DOI: 10.1021/acs.jmedchem.0c0062821https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXnvVeisrk%253D&md5=675827659c3c7b6099ccd667f4c60f95Discovery of N-Ethyl-4-[2-(4-fluoro-2,6-dimethyl-phenoxy)-5-(1-hydroxy-1-methyl-ethyl)phenyl]-6-methyl-7-oxo-1H-pyrrolo[2,3-c]pyridine-2-carboxamide (ABBV-744), a BET Bromodomain Inhibitor with Selectivity for the Second BromodomainSheppard, George S.; Wang, Le; Fidanze, Steven D.; Hasvold, Lisa A.; Liu, Dachun; Pratt, John K.; Park, Chang H.; Longenecker, Kenton; Qiu, Wei; Torrent, Maricel; Kovar, Peter J.; Bui, Mai; Faivre, Emily; Huang, Xiaoli; Lin, Xiaoyu; Wilcox, Denise; Zhang, Lu; Shen, Yu; Albert, Daniel H.; Magoc, Terrance J.; Rajaraman, Ganesh; Kati, Warren M.; McDaniel, Keith F.Journal of Medicinal Chemistry (2020), 63 (10), 5585-5623CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)The BET family of proteins consists of BRD2, BRD3, BRD4, and BRDt. Each protein contains two distinct bromodomains (BD1 and BD2). BET family bromodomain inhibitors under clin. development for oncol. bind to each of the eight bromodomains with similar affinities. We hypothesized that it may be possible to achieve an improved therapeutic index by selectively targeting subsets of the BET bromodomains. Both BD1 and BD2 are highly conserved across family members (>70% identity), whereas BD1 and BD2 from the same protein exhibit a larger degree of divergence (~ 40% identity), suggesting selectivity between BD1 and BD2 of all family members would be more straightforward to achieve. Exploiting the Asp144/His437 and Ile146/Val439 sequence differences (BRD4 BD1/BD2 numbering) allowed the identification of compd. 27 demonstrating greater than 100-fold selectivity for BRD4 BD2 over BRD4 BD1. Further optimization to improve BD2 selectivity and oral bioavailability resulted in the clin. development compd. 46 (ABBV-744).
- 22Faivre, E. J.; McDaniel, K. F.; Albert, D. H.; Mantena, S. R.; Plotnik, J. P.; Wilcox, D.; Zhang, L.; Bui, M. H.; Sheppard, G. S.; Wang, L.; Sehgal, V.; Lin, X.; Huang, X.; Lu, X.; Uziel, T.; Hessler, P.; Lam, L. T.; Bellin, R. J.; Mehta, G.; Fidanze, S.; Pratt, J. K.; Liu, D.; Hasvold, L. A.; Sun, C.; Panchal, S. C.; Nicolette, J. J.; Fossey, S. L.; Park, C. H.; Longenecker, K.; Bigelow, L.; Torrent, M.; Rosenberg, S. H.; Kati, W. M.; Shen, Y. Selective Inhibition of the BD2 Bromodomain of BET Proteins in Prostate Cancer. Nature 2020, 578, 306– 310, DOI: 10.1038/s41586-020-1930-822https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXis1Smsr0%253D&md5=800d9106c33084390fd8cbf1ac7f1766Selective inhibition of the BD2 bromodomain of BET proteins in prostate cancerFaivre, Emily J.; McDaniel, Keith F.; Albert, Daniel H.; Mantena, Srinivasa R.; Plotnik, Joshua P.; Wilcox, Denise; Zhang, Lu; Bui, Mai H.; Sheppard, George S.; Wang, Le; Sehgal, Vasudha; Lin, Xiaoyu; Huang, Xiaoli; Lu, Xin; Uziel, Tamar; Hessler, Paul; Lam, Lloyd T.; Bellin, Richard J.; Mehta, Gaurav; Fidanze, Steve; Pratt, John K.; Liu, Dachun; Hasvold, Lisa A.; Sun, Chaohong; Panchal, Sanjay C.; Nicolette, John J.; Fossey, Stacey L.; Park, Chang H.; Longenecker, Kenton; Bigelow, Lance; Torrent, Maricel; Rosenberg, Saul H.; Kati, Warren M.; Shen, YuNature (London, United Kingdom) (2020), 578 (7794), 306-310CODEN: NATUAS; ISSN:0028-0836. (Nature Research)Abstr.: Proteins of the bromodomain and extra-terminal (BET) domain family are epigenetic readers that bind acetylated histones through their bromodomains to regulate gene transcription. Dual-bromodomain BET inhibitors (DbBi) that bind with similar affinities to the first (BD1) and second (BD2) bromodomains of BRD2, BRD3, BRD4 and BRDt have displayed modest clin. activity in monotherapy cancer trials. A reduced no. of thrombocytes in the blood (thrombocytopenia) as well as symptoms of gastrointestinal toxicity are dose-limiting adverse events for some types of DbBi1-5. Given that similar haematol. and gastrointestinal defects were obsd. after genetic silencing of Brd4 in mice6, the platelet and gastrointestinal toxicities may represent on-target activities assocd. with BET inhibition. The two individual bromodomains in BET family proteins may have distinct functions7-9 and different cellular phenotypes after pharmacol. inhibition of one or both bromodomains have been reported10,11, suggesting that selectively targeting one of the bromodomains may result in a different efficacy and tolerability profile compared with DbBi. Available compds. that are selective to individual domains lack sufficient potency and the pharmacokinetics properties that are required for in vivo efficacy and tolerability assessment10-13. Here we carried out a medicinal chem. campaign that led to the discovery of ABBV-744, a highly potent and selective inhibitor of the BD2 domain of BET family proteins with drug-like properties. In contrast to the broad range of cell growth inhibition induced by DbBi, the antiproliferative activity of ABBV-744 was largely, but not exclusively, restricted to cell lines of acute myeloid leukemia and prostate cancer that expressed the full-length androgen receptor (AR). ABBV-744 retained robust activity in prostate cancer xenografts, and showed fewer platelet and gastrointestinal toxicities than the DbBi ABBV-07514. Analyses of RNA expression and chromatin immunopptn. followed by sequencing revealed that ABBV-744 displaced BRD4 from AR-contg. super-enhancers and inhibited AR-dependent transcription, with less impact on global transcription compared with ABBV-075. These results underscore the potential value of selectively targeting the BD2 domain of BET family proteins for cancer therapy.
- 23Gacias, M.; Gerona-Navarro, G.; Plotnikov, A. N.; Zhang, G.; Zeng, L.; Kaur, J.; Moy, G.; Rusinova, E.; Rodriguez, Y.; Matikainen, B.; Vincek, A.; Joshua, J.; Casaccia, P.; Zhou, M.-M. Selective Chemical Modulation of Gene Transcription Favors Oligodendrocyte Lineage Progression. Chem. Biol. 2014, 21, 841– 854, DOI: 10.1016/j.chembiol.2014.05.00923https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXhtVemtLrK&md5=6b377663a8d0d07441ab4f8a5d8191b3Selective Chemical Modulation of Gene Transcription Favors Oligodendrocyte Lineage ProgressionGacias, Mar; Gerona-Navarro, Guillermo; Plotnikov, Alexander N.; Zhang, Guangtao; Zeng, Lei; Kaur, Jasbir; Moy, Gregory; Rusinova, Elena; Rodriguez, Yoel; Matikainen, Bridget; Vincek, Adam; Joshua, Jennifer; Casaccia, Patrizia; Zhou, Ming-MingChemistry & Biology (Oxford, United Kingdom) (2014), 21 (7), 841-854CODEN: CBOLE2; ISSN:1074-5521. (Elsevier Ltd.)Lysine acetylation regulates gene expression through modulating protein-protein interactions in chromatin. Chem. inhibition of acetyl-lysine binding bromodomains of the major chromatin regulators BET (bromodomain and extraterminal domain) proteins has been shown to effectively block cell proliferation in cancer and inflammation. However, whether selective inhibition of individual BET bromodomains has distinctive functional consequences remains only partially understood. In this study, we show that selective chem. inhibition of the first bromodomain of BET proteins using our small-mol. inhibitor, Olinone, accelerated the progression of mouse primary oligodendrocyte progenitors toward differentiation, whereas inhibition of both bromodomains of BET proteins hindered differentiation. This effect was target specific, as it was not detected in cells treated with inactive analogs and independent of any effect on proliferation. Therefore, selective chem. modulation of individual bromodomains, rather than use of broad-based inhibitors, may enhance regenerative strategies in disorders characterized by myelin loss such as aging and neurodegeneration.
- 24Rodríguez, Y.; Gerona-Navarro, G.; Osman, R.; Zhou, M.-M. In Silico Design and Molecular Basis for the Selectivity of Olinone toward the First over the Second Bromodomain of BRD4. Proteins: Struct., Funct., Bioinf. 2020, 88, 414– 430, DOI: 10.1002/prot.2581824https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXhvFymt7jE&md5=3347bcb89a938a3aa25ba6bfd2bea8dbIn silico design and molecular basis for the selectivity of Olinone toward the first over the second bromodomain of BRD4Rodriguez, Yoel; Gerona-Navarro, Guillermo; Osman, Roman; Zhou, Ming-MingProteins: Structure, Function, and Bioinformatics (2020), 88 (3), 414-430CODEN: PSFBAF; ISSN:1097-0134. (Wiley-Blackwell)Bromodomains (BrDs), a conserved structural module in chromatin-assocd. proteins, are well known for recognizing ε-N-acetyl lysine residues on histones. One of the most relevant BrDs is BRD4, a tandem BrD contg. protein (BrD1 and BrD2) that plays a crit. role in numerous diseases including cancer. Growing evidence shows that the two BrDs of BRD4 have different biol. functions; hence selective ligands that can be used to study their functions are of great interest. Here, as a follow-up of our previous work, we first provide a detailed characterization study of the in silico rational design of Olinone as part of a series of five tetrahydropyrido indole-based compds. as BRD4 BrD1 inhibitors. Addnl., we investigated the mol. basis for Olinone's selective recognition by BrD1 over BrD2. Mol. dynamics simulations, free energy calcns., and conformational analyses of the apo-BRD4-BrD1|2 and BRD4-BrD1|2/Olinone complexes showed that Olinone's selectivity is facilitated by five key residues: Leu92 in BrD1|385 in BrD2 of ZA loop, Asn140|433, Asp144|His437 and Asp145|Glu438 of BC loop, and Ile146|Val49 of helix C. Furthermore, the difference in hydrogen bonds no. and in mobility of the ZA and BC loops of the acetyl-lysine binding site between BRD4 BrD1/Olinone and BrD2/Olinone complexes also contribute to the difference in Olinone's binding affinity and selectivity toward BrD1 over BrD2. Altogether, our computer-aided mol. design techniques can effectively guide the development of small-mol. BRD4 BrD1 inhibitors, explain their selectivity origin, and further open doors to the design of new therapeutically improved derivs.
- 25Divakaran, A.; Talluri, S. K.; Ayoub, A. M.; Mishra, N. K.; Cui, H.; Widen, J. C.; Berndt, N.; Zhu, J.-Y.; Carlson, A. S.; Topczewski, J. J.; Schonbrunn, E. K.; Harki, D. A.; Pomerantz, W. C. K. Molecular Basis for the N-Terminal Bromodomain-and-Extra-Terminal-Family Selectivity of a Dual Kinase-Bromodomain Inhibitor. J. Med. Chem. 2018, 61, 9316– 9334, DOI: 10.1021/acs.jmedchem.8b0124825https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXhvVSis7fM&md5=5176ef754a898b3e03fc56e2662ab399Molecular Basis for the N-Terminal Bromodomain-and-Extra-Terminal-Family Selectivity of a Dual Kinase-Bromodomain InhibitorDivakaran, Anand; Talluri, Siva K.; Ayoub, Alex M.; Mishra, Neeraj K.; Cui, Huarui; Widen, John C.; Berndt, Norbert; Zhu, Jin-Yi; Carlson, Angela S.; Topczewski, Joseph J.; Schonbrunn, Ernst K.; Harki, Daniel A.; Pomerantz, William C. K.Journal of Medicinal Chemistry (2018), 61 (20), 9316-9334CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)As regulators of transcription, epigenetic proteins that interpret post-translational modifications to N-terminal histone tails are essential for maintaining cellular homeostasis. When dysregulated, "reader" proteins become drivers of disease. In the case of bromodomains, which recognize N-ε-acetylated lysine, selective inhibition of individual bromodomain-and-extra-terminal (BET)-family bromodomains has proven challenging. We describe the >55-fold N-terminal-BET bromodomain selectivity of 1,4,5-trisubstituted-imidazole dual kinase-bromodomain inhibitors. Selectivity for the BRD4 N-terminal bromodomain (BRD4(1)) over its second bromodomain (BRD4(2)) arises from the displacement of ordered waters and the conformational flexibility of lysine-141 in BRD4(1). Cellular efficacy was demonstrated via redn. of c-Myc expression, inhibition of NF-κB signaling, and suppression of IL-8 prodn. through potential synergistic inhibition of BRD4(1) and p38α. These dual inhibitors provide a new scaffold for domain-selective inhibition of BRD4, the aberrant function of which plays a key role in cancer and inflammatory signaling.
- 26Cipriano, A.; Milite, C.; Feoli, A.; Viviano, M.; Pepe, G.; Campiglia, P.; Sarno, G.; Picaud, S.; Imaide, S.; Makukhin, N.; Filippakopoulos, P.; Ciulli, A.; Castellano, S.; Sbardella, G. Discovery of Benzo[d]Imidazole-6-Sulfonamides as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the First Bromodomain. ChemMedChem 2022, 17, e202200343 DOI: 10.1002/cmdc.20220034326https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38XisVSnsLrJ&md5=a4628e3e7597053c1658915561fdd2dbDiscovery of Benzo[d]imidazole-6-sulfonamides as Bromodomain and Extra-Terminal Domain (BET) Inhibitors with Selectivity for the First BromodomainCipriano, Alessandra; Milite, Ciro; Feoli, Alessandra; Viviano, Monica; Pepe, Giacomo; Campiglia, Pietro; Sarno, Giuliana; Picaud, Sarah; Imaide, Satomi; Makukhin, Nikolai; Filippakopoulos, Panagis; Ciulli, Alessio; Castellano, Sabrina; Sbardella, GianlucaChemMedChem (2022), 17 (20), e202200343CODEN: CHEMGX; ISSN:1860-7179. (Wiley-VCH Verlag GmbH & Co. KGaA)The bromodomain and extra-terminal (BET) family of proteins includes BRD2, BRD3, BRD4, and the testis-specific protein, BRDT, each contg. two N-terminal tandem bromodomain (BRD) modules. Potent and selective inhibitors targeting the two bromodomains are required to elucidate their biol. role(s), with potential clin. applications. In this study, we designed and synthesized a series of benzimidazole-6-sulfonamides starting from the azobenzene compds. MS436 (7 a) and MS611 (7 b) that exhibited preference for the first (BD1) over the second (BD2) BRD of BET family members. The most-promising compd. (9 a) showed good binding potency and improved metabolic stability and selectivity towards BD1 with respect to the parent compds.
- 27Cui, H.; Carlson, A. S.; Schleiff, M. A.; Divakaran, A.; Johnson, J. A.; Buchholz, C. R.; Zahid, H.; Vail, N. R.; Shi, K.; Aihara, H.; Harki, D. A.; Miller, G. P.; Topczewski, J. J.; Pomerantz, W. C. K. 4-Methyl-1,2,3-Triazoles as N-Acetyl-Lysine Mimics Afford Potent BET Bromodomain Inhibitors with Improved Selectivity. J. Med. Chem. 2021, 64, 10497– 10511, DOI: 10.1021/acs.jmedchem.1c0093327https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXhs1WmtbnK&md5=6dfafd833706b5a418e5998f73c2eb944-Methyl-1,2,3-Triazoles as N-Acetyl-Lysine Mimics Afford Potent BET Bromodomain Inhibitors with Improved SelectivityCui, Huarui; Carlson, Angela S.; Schleiff, Mary A.; Divakaran, Anand; Johnson, Jorden A.; Buchholz, Caroline R.; Zahid, Huda; Vail, Nora R.; Shi, Ke; Aihara, Hideki; Harki, Daniel A.; Miller, Grover P.; Topczewski, Joseph J.; Pomerantz, William C. K.Journal of Medicinal Chemistry (2021), 64 (14), 10497-10511CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)The bromodomain and extra terminal (BET) protein family recognizes acetylated lysines within histones and transcription factors using two N-terminal bromodomains, D1 and D2. The protein-protein interactions between BET bromodomains, acetylated histones, and transcription factors are therapeutic targets for BET-related diseases, including inflammatory disease and cancer. Prior work demonstrated that methylated-1,2,3-triazoles are suitable N-acetyl lysine mimetics for BET inhibition. Here we describe a structure-activity relationship study of triazole-based inhibitors that improve affinity, D1 selectivity, and microsomal stability. These outcomes were accomplished by targeting a nonconserved residue, Asp144 and a conserved residue, Met149, on BRD4 D1. The lead inhibitors DW34 and 26 have a BRD4 D1 Kd of 12 and 6.4 nM, resp. Cellular activity was demonstrated through suppression of c-Myc expression in MM.1S cells and downregulation of IL-8 in TNF-α-stimulated A549 cells. These data indicate that DW34 (I) and 26 (II) are new leads to investigate the anticancer and anti-inflammatory activity of BET proteins.
- 28Seal, J.; Lamotte, Y.; Donche, F.; Bouillot, A.; Mirguet, O.; Gellibert, F.; Nicodeme, E.; Krysa, G.; Kirilovsky, J.; Beinke, S.; McCleary, S.; Rioja, I.; Bamborough, P.; Chung, C.-W.; Gordon, L.; Lewis, T.; Walker, A. L.; Cutler, L.; Lugo, D.; Wilson, D. M.; Witherington, J.; Lee, K.; Prinjha, R. K. Identification of a Novel Series of BET Family Bromodomain Inhibitors: Binding Mode and Profile of I-BET151 (GSK1210151A). Bioorg. Med. Chem. Lett. 2012, 22, 2968– 2972, DOI: 10.1016/j.bmcl.2012.02.04128https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC38XktFOqsr8%253D&md5=a8037c89bcb93948d663208bd1ebfd55Identification of a novel series of BET family bromodomain inhibitors: Binding mode and profile of I-BET151 (GSK1210151A)Seal, Jonathan; Lamotte, Yann; Donche, Frederic; Bouillot, Anne; Mirguet, Olivier; Gellibert, Francoise; Nicodeme, Edwige; Krysa, Gael; Kirilovsky, Jorge; Beinke, Soren; McCleary, Scott; Rioja, Inma; Bamborough, Paul; Chung, Chun-Wa; Gordon, Laurie; Lewis, Toni; Walker, Ann L.; Cutler, Leanne; Lugo, David; Wilson, David M.; Witherington, Jason; Lee, Kevin; Prinjha, Rab K.Bioorganic & Medicinal Chemistry Letters (2012), 22 (8), 2968-2972CODEN: BMCLE8; ISSN:0960-894X. (Elsevier B.V.)A novel series of quinoline isoxazole BET family bromodomain inhibitors are discussed. Crystallog. is used to illustrate binding modes and rationalize their SAR. One member, I-BET151 (GSK1210151A), shows good oral bioavailability in both the rat and minipig as well as demonstrating efficient suppression of bacterial induced inflammation and sepsis in a murine in vivo endotoxemia model.
- 29Wellaway, C. R.; Bamborough, P.; Bernard, S. G.; Chung, C.; Craggs, P. D.; Cutler, L.; Demont, E. H.; Evans, J. P.; Gordon, L.; Karamshi, B.; Lewis, A. J.; Lindon, M. J.; Mitchell, D. J.; Rioja, I.; Soden, P. E.; Taylor, S.; Watson, R. J.; Willis, R.; Woolven, J. M.; Wyspiańska, B. S.; Kerr, W. J.; Prinjha, R. K. Structure-Based Design of a Bromodomain and Extraterminal Domain (BET) Inhibitor Selective for the N-Terminal Bromodomains That Retains an Anti-Inflammatory and Antiproliferative Phenotype. J. Med. Chem. 2020, 63, 9020– 9044, DOI: 10.1021/acs.jmedchem.0c0056629https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhsV2lt77M&md5=52b2505bb0a36f526a08bb9bad1f2c26Structure-Based Design of a Bromodomain and Extraterminal Domain (BET) Inhibitor Selective for the N-Terminal Bromodomains That Retains an Anti-inflammatory and Antiproliferative PhenotypeWellaway, Christopher R.; Bamborough, Paul; Bernard, Sharon G.; Chung, Chun-wa; Craggs, Peter D.; Cutler, Leanne; Demont, Emmanuel H.; Evans, John P.; Gordon, Laurie; Karamshi, Bhumika; Lewis, Antonia J.; Lindon, Matthew J.; Mitchell, Darren J.; Rioja, Inmaculada; Soden, Peter E.; Taylor, Simon; Watson, Robert J.; Willis, Rob; Woolven, James M.; Wyspianska, Beata S.; Kerr, William J.; Prinjha, Rab K.Journal of Medicinal Chemistry (2020), 63 (17), 9020-9044CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)The bromodomain and extraterminal domain (BET) family of epigenetic regulators comprises four proteins (BRD2, BRD3, BRD4, BRDT), each contg. tandem bromodomains. To date, small mol. inhibitors of these proteins typically bind all eight bromodomains of the family with similar affinity, resulting in a diverse range of biol. effects. To enable further understanding of the broad phenotype characteristic of pan-BET inhibition, the development of inhibitors selective for individual, or sets of, bromodomains within the family is required. In this regard, we report the discovery of a potent probe mol. possessing up to 150-fold selectivity for the N-terminal bromodomains (BD1s) over the C-terminal bromodomains (BD2s) of the BETs. Guided by structural information, a specific amino acid difference between BD1 and BD2 domains was targeted for selective interaction with chem. functionality appended to the previously developed I-BET151 scaffold. Data presented herein demonstrate that selective inhibition of BD1 domains is sufficient to drive anti-inflammatory and antiproliferative effects.
- 30Liu, Z.; Chen, H.; Wang, P.; Li, Y.; Wold, E. A.; Leonard, P. G.; Joseph, S.; Brasier, A. R.; Tian, B.; Zhou, J. Discovery of Orally Bioavailable Chromone Derivatives as Potent and Selective BRD4 Inhibitors: Scaffold Hopping, Optimization, and Pharmacological Evaluation. J. Med. Chem. 2020, 63, 5242– 5256, DOI: 10.1021/acs.jmedchem.0c0003530https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXmsVOhsbs%253D&md5=95cb6c3f150a5ee9e65a76fd36a559fdDiscovery of Orally Bioavailable Chromone Derivatives as Potent and Selective BRD4 Inhibitors: Scaffold Hopping, Optimization, and Pharmacological EvaluationLiu, Zhiqing; Chen, Haiying; Wang, Pingyuan; Li, Yi; Wold, Eric A.; Leonard, Paul G.; Joseph, Sarah; Brasier, Allan R.; Tian, Bing; Zhou, JiaJournal of Medicinal Chemistry (2020), 63 (10), 5242-5256CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)Arylquinazolinones and arylchromenones such as I (X = CH2, MeN) were prepd. as selective inhibitors of bromodomain-contg. protein 4 (BRD4) for potential use as orally bioavailable antiinflammatory agents. I inhibited BRD4 with IC50 values of 67-84 nM and were selective for BRD1 over binding domains of BRD2, BRD3, and BRDT and over CBP; I inhibited the expression of Toll-like receptor (TLR3)-induced inflammatory genes in vitro and inhibited airway inflammation in mice. The pharmacokinetics (t1/2, AUC, Cmax, and clearance), metabolic stability of I (X = NMe) in murine and human cells, and inhibition of cytochrome P450 enzymes and hERG by I (X = MeN) were detd. The structure of I (X = NMe) bound to human BRD4 binding domain 1 was detd. by X-ray crystallog.
- 31Cui, H.; Divakaran, A.; Pandey, A. K.; Johnson, J. A.; Zahid, H.; Hoell, Z. J.; Ellingson, M. O.; Shi, K.; Aihara, H.; Harki, D. A.; Pomerantz, W. C. K. Selective N-Terminal BET Bromodomain Inhibitors by Targeting Non-Conserved Residues and Structured Water Displacement. Angew. Chem., Int. Ed. 2021, 60, 1220– 1226, DOI: 10.1002/anie.20200862531https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXitlOqtLjI&md5=0f0379a17c98e5c1b9c436dc0952e9a7Selective N-Terminal BET Bromodomain Inhibitors by Targeting Non-Conserved Residues and Structured Water Displacement**Cui, Huarui; Divakaran, Anand; Pandey, Anil K.; Johnson, Jorden A.; Zahid, Huda; Hoell, Zachariah J.; Ellingson, Mikael O.; Shi, Ke; Aihara, Hideki; Harki, Daniel A.; Pomerantz, William C. K.Angewandte Chemie, International Edition (2021), 60 (3), 1220-1226CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)Bromodomain and extra-terminal (BET) family proteins, BRD2-4 and T, are important drug targets; however, the biol. functions of each bromodomain remain ill-defined. Chem. probes that selectively inhibit a single BET bromodomain are lacking, although pan inhibitors of the first (D1), and second (D2), bromodomain are known. Here, we develop selective BET D1 inhibitors with preferred binding to BRD4 D1. In competitive inhibition assays, we show that our lead compd. is 9-33 fold selective for BRD4 D1 over the other BET bromodomains. X-ray crystallog. supports a role for the selectivity based on reorganization of a non-conserved lysine and displacement of an addnl. structured water in the BRD4 D1 binding site relative to our prior lead. Whereas pan-D1 inhibitors displace BRD4 from MYC enhancers, BRD4 D1 inhibition in MM.1S cells is insufficient for stopping Myc expression and may lead to its upregulation. Future anal. of BRD4 D1 gene regulation may shed light on differential BET bromodomain functions.
- 32Cui, H.; Divakaran, A.; Hoell, Z. J.; Ellingson, M. O.; Scholtz, C. R.; Zahid, H.; Johnson, J. A.; Griffith, E. C.; Gee, C. T.; Lee, A. L.; Khanal, S.; Shi, K.; Aihara, H.; Shah, V. H.; Lee, R. E.; Harki, D. A.; Pomerantz, W. C. K. A Structure-Based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes. J. Med. Chem. 2022, 65, 2342– 2360, DOI: 10.1021/acs.jmedchem.1c0177932https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB38Xms1Smtg%253D%253D&md5=f27226c5728fc1d627f797f56eac2690A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical ProbesCui, Huarui; Divakaran, Anand; Hoell, Zachariah J.; Ellingson, Mikael O.; Scholtz, Cole R.; Zahid, Huda; Johnson, Jorden A.; Griffith, Elizabeth C.; Gee, Clifford T.; Lee, Amani L.; Khanal, Shalil; Shi, Ke; Aihara, Hideki; Shah, Vijay H.; Lee, Richard E.; Harki, Daniel A.; Pomerantz, William C. K.Journal of Medicinal Chemistry (2022), 65 (3), 2342-2360CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)Chem. probes for epigenetic proteins are essential tools for dissecting the mol. mechanisms for gene regulation and therapeutic development. The bromodomain and extra-terminal (BET) proteins are master transcriptional regulators. Despite promising therapeutic targets, selective small mol. inhibitors for a single bromodomain remain an unmet goal due to their high sequence similarity. Here, we address this challenge via a structure-activity relationship study using 1,4,5-trisubstituted imidazoles against the BRD4 N-terminal bromodomain (D1). Leading compds. 26 and 30 have 15 and 18 nM affinity against BRD4 D1 and over 500-fold selectivity against BRD2 D1 and BRD4 D2 via ITC. Broader BET selectivity was confirmed by fluorescence anisotropy, thermal shift, and CETSA. Despite BRD4 engagement, BRD4 D1 inhibition was unable to reduce c-Myc expression at low concn. in multiple myeloma cells. Conversely, for inflammation, IL-8 and chemokine downregulation were obsd. These results provide new design rules for selective inhibitors of an individual BET bromodomain.
- 33Schiedel, M.; Moroglu, M.; Ascough, D. M. H.; Chamberlain, A. E. R.; Kamps, J. J. A. G.; Sekirnik, A. R.; Conway, S. J. Chemical Epigenetics: The Impact of Chemical and Chemical Biology Techniques on Bromodomain Target Validation. Angew. Chem., Int. Ed. 2019, 58, 17930– 17952, DOI: 10.1002/anie.20181216433https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXitFKrt77N&md5=d26cbf7f78d9542b2c98b9b74d979761Chemical Epigenetics: The Impact of Chemical and Chemical Biology Techniques on Bromodomain Target ValidationSchiedel, Matthias; Moroglu, Mustafa; Ascough, David M. H.; Chamberlain, Anna E. R.; Kamps, Jos J. A. G.; Sekirnik, Angelina R.; Conway, Stuart J.Angewandte Chemie, International Edition (2019), 58 (50), 17930-17952CODEN: ACIEF5; ISSN:1433-7851. (Wiley-VCH Verlag GmbH & Co. KGaA)A review. Epigenetics is currently the focus of intense research interest across a broad range of disciplines due to its importance in a multitude of biol. processes and disease states. Epigenetic functions result partly from modification of the nucleobases in DNA and RNA, and/or post-translational modifications of histone proteins. These modifications are dynamic, with cellular machinery identified to modulate and interpret the marks. The authors' focus is on bromodomains, which bind to acetylated lysine residues. Progress in the study of bromodomains, and the development of bromodomain ligands, has been rapid. These advances have been underpinned by many disciplines, but chem. and chem. biol. have undoubtedly played a significant role. Herein, the authors review the key chem. and chem. biol. approaches that have furthered the authors' study of bromodomains, enabled the development of bromodomain ligands, and played a crit. role in the validation of bromodomains as therapeutic targets.
- 34Arrowsmith, C. H.; Audia, J. E.; Austin, C.; Baell, J.; Bennett, J.; Blagg, J.; Bountra, C.; Brennan, P. E.; Brown, P. J.; Bunnage, M. E.; Buser-Doepner, C.; Campbell, R. M.; Carter, A. J.; Cohen, P.; Copeland, R. A.; Cravatt, B.; Dahlin, J. L.; Dhanak, D.; Edwards, A. M.; Frederiksen, M.; Frye, S. V.; Gray, N.; Grimshaw, C. E.; Hepworth, D.; Howe, T.; Huber, K. V. M.; Jin, J.; Knapp, S.; Kotz, J. D.; Kruger, R. G.; Lowe, D.; Mader, M. M.; Marsden, B.; Mueller-Fahrnow, A.; Müller, S.; O’Hagan, R. C.; Overington, J. P.; Owen, D. R.; Rosenberg, S. H.; Ross, R.; Roth, B.; Schapira, M.; Schreiber, S. L.; Shoichet, B.; Sundström, M.; Superti-Furga, G.; Taunton, J.; Toledo-Sherman, L.; Walpole, C.; Walters, M. A.; Willson, T. M.; Workman, P.; Young, R. N.; Zuercher, W. J. The Promise and Peril of Chemical Probes. Nat. Chem. Biol. 2015, 11, 536– 541, DOI: 10.1038/nchembio.186734https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht1Wlu7zO&md5=d8c7a7af94921ab4cdcc871487cceaddThe promise and peril of chemical probesArrowsmith, Cheryl H.; Audia, James E.; Austin, Christopher; Baell, Jonathan; Bennett, Jonathan; Blagg, Julian; Bountra, Chas; Brennan, Paul E.; Brown, Peter J.; Bunnage, Mark E.; Buser-Doepner, Carolyn; Campbell, Robert M.; Carter, Adrian J.; Cohen, Philip; Copeland, Robert A.; Cravatt, Ben; Dahlin, Jayme L.; Dhanak, Dashyant; Edwards, Aled M.; Frye, Stephen V.; Gray, Nathanael; Grimshaw, Charles E.; Hepworth, David; Howe, Trevor; Huber, Kilian V. M.; Jin, Jian; Knapp, Stefan; Kotz, Joanne D.; Kruger, Ryan G.; Lowe, Derek; Mader, Mary M.; Marsden, Brian; Mueller-Fahrnow, Anke; Muller, Susanne; O'Hagan, Ronan C.; Overington, John P.; Owen, Dafydd R.; Rosenberg, Saul H.; Roth, Brian; Ross, Ruth; Schapira, Matthieu; Schreiber, Stuart L.; Shoichet, Brian; Sundstrom, Michael; Superti-Furga, Giulio; Taunton, Jack; Toledo-Sherman, Leticia; Walpole, Chris; Walters, Michael A.; Willson, Timothy M.; Workman, Paul; Young, Robert N.; Zuercher, William J.Nature Chemical Biology (2015), 11 (8), 536-541CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)Chem. probes are powerful reagents with increasing impacts on biomedical research. However, probes of poor quality or that are used incorrectly generate misleading results. To help address these shortcomings, we will create a community-driven wiki resource to improve quality and convey current best practice.
- 35Blagg, J.; Workman, P. Choose and Use Your Chemical Probe Wisely to Explore Cancer Biology. Cancer Cell 2017, 32, 9– 25, DOI: 10.1016/j.ccell.2017.06.00535https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXhtFGmsLvI&md5=468848d484d5d91c52330949d5778b1dChoose and Use Your Chemical Probe Wisely to Explore Cancer BiologyBlagg, Julian; Workman, PaulCancer Cell (2017), 32 (1), 9-25CODEN: CCAECI; ISSN:1535-6108. (Elsevier Inc.)Small-mol. chem. probes or tools have become progressively more important in recent years as valuable reagents to investigate fundamental biol. mechanisms and processes causing disease, including cancer. Chem. probes have also achieved greater prominence alongside complementary biol. reagents for target validation in drug discovery. However, there is evidence of widespread continuing misuse and promulgation of poor-quality and insufficiently selective chem. probes, perpetuating a worrisome and misleading pollution of the scientific literature. We discuss current challenges with the selection and use of chem. probes, and suggest how biologists can and should be more discriminating in the probes they employ.
- 36Bunnage, M. E.; Chekler, E. L. P.; Jones, L. H. Target Validation Using Chemical Probes. Nat. Chem. Biol. 2013, 9, 195– 199, DOI: 10.1038/nchembio.119736https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXktFagsr4%253D&md5=af0c362882191de96a8e8698ff2c9ce8Target validation using chemical probesBunnage, Mark E.; Chekler, Eugene L. Piatnitski; Jones, Lyn H.Nature Chemical Biology (2013), 9 (4), 195-199CODEN: NCBABT; ISSN:1552-4450. (Nature Publishing Group)A review on the fully profiled chem. probes essential to support the unbiased interpretation of biol. expts. necessary for rigorous preclin. target validation. We believe that by developing a 'chem. probe tool kit', and a framework for its use, chem. biol. can have a more central role in identifying targets of potential relevance to disease, avoiding many of the biases that complicate target validation as practiced currently.
- 37Müller, S.; Ackloo, S.; Al Chawaf, A.; Al-Lazikani, B.; Antolin, A.; Baell, J. B.; Beck, H.; Beedie, S.; Betz, U. A. K.; Bezerra, G. A.; Brennan, P. E.; Brown, D.; Brown, P. J.; Bullock, A. N.; Carter, A. J.; Chaikuad, A.; Chaineau, M.; Ciulli, A.; Collins, I.; Dreher, J.; Drewry, D.; Edfeldt, K.; Edwards, A. M.; Egner, U.; Frye, S. V.; Fuchs, S. M.; Hall, M. D.; Hartung, I. V.; Hillisch, A.; Hitchcock, S. H.; Homan, E.; Kannan, N.; Kiefer, J. R.; Knapp, S.; Kostic, M.; Kubicek, S.; Leach, A. R.; Lindemann, S.; Marsden, B. D.; Matsui, H.; Meier, J. L.; Merk, D.; Michel, M.; Morgan, M. R.; Mueller-Fahrnow, A.; Owen, D. R.; Perry, B. G.; Rosenberg, S. H.; Saikatendu, K. S.; Schapira, M.; Scholten, C.; Sharma, S.; Simeonov, A.; Sundström, M.; Superti-Furga, G.; Todd, M. H.; Tredup, C.; Vedadi, M.; von Delft, F.; Willson, T. M.; Winter, G. E.; Workman, P.; Arrowsmith, C. H. Target 2035─Update on the Quest for a Probe for Every Protein. RSC Med. Chem. 2022, 13, 13– 21, DOI: 10.1039/D1MD00228G37https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3MXis1CmtLvE&md5=537ffb7c73c37f5f69cb5db0b2ea6cbbTarget 2035 - update on the quest for a probe for every proteinMueller, Susanne; Ackloo, Suzanne; Al Chawaf, Arij; Al-Lazikani, Bissan; Antolin, Albert; Baell, Jonathan B.; Beck, Hartmut; Beedie, Shaunna; Betz, Ulrich A. K.; Bezerra, Gustavo Arruda; Brennan, Paul E.; Brown, David; Brown, Peter J.; Bullock, Alex N.; Carter, Adrian J.; Chaikuad, Apirat; Chaineau, Mathilde; Ciulli, Alessio; Collins, Ian; Dreher, Jan; Drewry, David; Edfeldt, Kristina; Edwards, Aled M.; Egner, Ursula; Frye, Stephen V.; Fuchs, Stephen M.; Hall, Matthew D.; Hartung, Ingo V.; Hillisch, Alexander; Hitchcock, Stephen H.; Homan, Evert; Kannan, Natarajan; Kiefer, James R.; Knapp, Stefan; Kostic, Milka; Kubicek, Stefan; Leach, Andrew R.; Lindemann, Sven; Marsden, Brian D.; Matsui, Hisanori; Meier, Jordan L.; Merk, Daniel; Michel, Maurice; Morgan, Maxwell R.; Mueller-Fahrnow, Anke; Owen, Dafydd R.; Perry, Benjamin G.; Rosenberg, Saul H.; Saikatendu, Kumar Singh; Schapira, Matthieu; Scholten, Cora; Sharma, Sujata; Simeonov, Anton; Sundstroem, Michael; Superti-Furga, Giulio; Todd, Matthew H.; Tredup, Claudia; Vedadi, Masoud; von Delft, Frank; Willson, Timothy M.; Winter, Georg E.; Workman, Paul; Arrowsmith, Cheryl H.RSC Medicinal Chemistry (2022), 13 (1), 13-21CODEN: RMCSEZ; ISSN:2632-8682. (Royal Society of Chemistry)Twenty years after the publication of the first draft of the human genome, our knowledge of the human proteome is still fragmented. The challenge of translating the wealth of new knowledge from genomics into new medicines is that proteins, and not genes, are the primary executers of biol. function. Therefore, much of how biol. works in health and disease must be understood through the lens of protein function. Accordingly, a subset of human proteins has been at the heart of research interests of scientists over the centuries, and we have accumulated varying degrees of knowledge about approx. 65% of the human proteome. Nevertheless, a large proportion of proteins in the human proteome (∼35%) remains uncharacterized, and less than 5% of the human proteome has been successfully targeted for drug discovery. This highlights the profound disconnect between our abilities to obtain genetic information and subsequent development of effective medicines. Target 2035 is an international federation of biomedical scientists from the public and private sectors, which aims to address this gap by developing and applying new technologies to create by year 2035 chemogenomic libraries, chem. probes, and/or biol. probes for the entire human proteome.
- 38Hartung, I. V.; Rudolph, J.; Mader, M. M.; Mulder, M. P. C.; Workman, P. Expanding Chemical Probe Space: Quality Criteria for Covalent and Degrader Probes. J. Med. Chem. 2023, 66, 9297– 9312, DOI: 10.1021/acs.jmedchem.3c0055038https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3sXhtlKltrbF&md5=ac21f68535b0c75c78921ef471319a61Expanding Chemical Probe Space: Quality Criteria for Covalent and Degrader ProbesHartung, Ingo V.; Rudolph, Joachim; Mader, Mary M.; Mulder, Monique P. C.; Workman, PaulJournal of Medicinal Chemistry (2023), 66 (14), 9297-9312CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)A review. Within druggable target space, new small-mol. modalities, particularly covalent inhibitors and targeted degraders, have expanded the repertoire of medicinal chemists. Mols. with such modes of action have a large potential not only as drugs but also as chem. probes. Criteria have previously been established to describe the potency, selectivity, and properties of small-mol. probes that are qualified to enable the interrogation and validation of drug targets. These definitions have been tailored to reversibly acting modulators but fall short in their applicability to other modalities. While initial guidelines have been proposed, we delineate here a full set of criteria for the characterization of covalent, irreversible inhibitors as well as heterobifunctional degraders ("proteolysis-targeting chimeras", or PROTACs) and mol. glue degraders. We propose modified potency and selectivity criteria compared to those for reversible inhibitors. We discuss their relevance and highlight examples of suitable probe and pathfinder compds.
- 39Nguyen, T. H.; Maltby, S.; Eyers, F.; Foster, P. S.; Yang, M. Bromodomain and Extra Terminal (BET) Inhibitor Suppresses Macrophage-Driven Steroid-Resistant Exacerbations of Airway Hyper-Responsiveness and Inflammation. PLoS One 2016, 11, e0163392 DOI: 10.1371/journal.pone.016339239https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2sXitV2kurk%253D&md5=d46c12f7d2d30f01bd65614fe5de3e0bBromodomain and extra terminal (BET) inhibitor suppresses macrophage-driven steroid-resistant exacerbations of airway hyper-responsiveness and inflammationNguyen, Thi Hiep; Maltby, Steven; Eyers, Fiona; Foster, Paul S.; Yang, MingPLoS One (2016), 11 (9), e0163392/1-e0163392/15CODEN: POLNCL; ISSN:1932-6203. (Public Library of Science)Background: Exacerbations of asthma are linked to significant decline in lung function and are often poorly controlled by corticosteroid treatment. Clin. investigations indicate that viral and bacterial infections play crucial roles in the onset of steroid-resistant inflammation and airways hyperresponsiveness (AHR) that are hallmark features of exacerbations.We have previously shown that interferon γ (IFNγ) and lipopolysaccharide (LPS) cooperatively activate pulmonary macrophages and induce steroid-resistant airway inflammation and AHR in mouse models. Furthermore, we have established a mouse model of respiratory syncytial virus (RSV)-induced exacerbation of asthma, which exhibits macrophage-dependent, steroid- resistant lung disease. Emerging evidence has demonstrated a key role for bromoand extra-terminal (BET) proteins in the regulation of inflammatory gene expression in macrophages. We hypothesised that BET proteins may be involved in the regulation of AHR and airway inflammation in our steroid-resistant exacerbation models. Methodol./Principal Findings: We investigated the effects of a BET inhibitor (I-BET-762) on the development of steroidresistant AHR and airway inflammation in two mouse models. I-BET-762 administration decreased macrophage and neutrophil infiltration into the airways, and suppressed key inflammatory cytokines in bothmodels. I-BET treatment also suppressed key inflammatory cytokines linked to the development of steroid-resistant inflammation such as monocyte chemoattractant protein 1 (MCP-1), keratinocyte-derived protein chemokine (KC), IFNγ, and interleukin 27 (IL-27). Attenuation of inflammation was assocd. with suppression of AHR. Conclusions/Significance: Our results suggest that BET proteins play an important role in the regulation of steroidresistant exacerbations of airway inflammation and AHR. BET proteins may be potential targets for the development of future therapies to treat steroid-resistant inflammatory components of asthma.
- 40Clegg, M. A.; Tomkinson, N. C. O.; Prinjha, R. K.; Humphreys, P. G. Advancements in the Development of Non-BET Bromodomain Chemical Probes. ChemMedChem 2019, 14, 362– 385, DOI: 10.1002/cmdc.20180073840https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXit1Ohs70%253D&md5=a93505759fe45ffd0352de2f0e17885aAdvancements in the Development of non-BET Bromodomain Chemical ProbesClegg, Michael A.; Tomkinson, Nicholas C. O.; Prinjha, Rab K.; Humphreys, Philip G.ChemMedChem (2019), 14 (4), 362-385CODEN: CHEMGX; ISSN:1860-7179. (Wiley-VCH Verlag GmbH & Co. KGaA)A review. The bromodomain and extra terminal (BET) family of bromodomain-contg. proteins (BCPs) have been the subject of extensive research over the past decade, resulting in a plethora of high-quality chem. probes for their tandem bromodomains. In turn, these chem. probes have helped reveal the profound biol. role of the BET bromodomains and their role in disease, ultimately leading to a no. of mols. in active clin. development. However, the BET subfamily represents just 8/61 of the known human bromodomains, and attention has now expanded to the biol. role of the remaining 53 non-BET bromodomains. Rapid growth of this research area has been accompanied by a greater understanding of the requirements for an effective bromodomain chem. probe and has led to a no. of new non-BET bromodomain chem. probes being developed. Advances since Dec. 2015 are discussed, highlighting the strengths/caveats of each mol., and the value they add toward validating the non-BET bromodomains as tractable therapeutic targets.
- 41Bayliss, M. K.; Butler, J.; Feldman, P. L.; Green, D. V. S.; Leeson, P. D.; Palovich, M. R.; Taylor, A. J. Quality Guidelines for Oral Drug Candidates: Dose, Solubility and Lipophilicity. Drug Disc. Today 2016, 21, 1719– 1727, DOI: 10.1016/j.drudis.2016.07.007There is no corresponding record for this reference.
- 42Johnson, T. W.; Gallego, R. A.; Edwards, M. P. Lipophilic Efficiency as an Important Metric in Drug Design. J. Med. Chem. 2018, 61, 6401– 6420, DOI: 10.1021/acs.jmedchem.8b0007742https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXmsVahsbg%253D&md5=29f38880914fa75c33be3a640ace4309Lipophilic Efficiency as an Important Metric in Drug DesignJohnson, Ted W.; Gallego, Rebecca A.; Edwards, Martin P.Journal of Medicinal Chemistry (2018), 61 (15), 6401-6420CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)A review. Lipophilic efficiency (LipE) is an important metric that has been increasingly applied in drug discovery medicinal chem. lead optimization programs. In this perspective, using literature drug discovery examples, we discuss the concept of rigorously applying LipE to guide medicinal chem. lead optimization toward drug candidates with potential for superior in vivo efficacy and safety, esp. when guided by physiochem. property-based optimization (PPBO). Also highlighted are examples of small structural modifications such as addn. of single atoms, small functional groups, and cyclizations that produce large increases in LipE. Understanding the factors that may contribute to LipE changes through anal. of ligand-protein crystal structures and using structure-based drug design (SBDD) to increase LipE by design is also discussed. Herein we advocate for use of LipE anal. coupled with PPBO and SBDD as an efficient mechanism for drug design.
- 43Freeman-Cook, K. D.; Hoffman, R. L.; Johnson, T. W. Lipophilic Efficiency: The Most Important Efficiency Metric in Medicinal Chemistry. Future Med. Chem. 2013, 5, 113– 115, DOI: 10.4155/fmc.12.20843https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC3sXhs1aiu7g%253D&md5=36170decfa1f1e3ef09ecf772322a210Lipophilic efficiency: the most important efficiency metric in medicinal chemistryFreeman-Cook, Kevin D.; Hoffman, Robert L.; Johnson, Ted W.Future Medicinal Chemistry (2013), 5 (2), 113-115CODEN: FMCUA7; ISSN:1756-8919. (Future Science Ltd.)A review is given on the crit. role of lipophilicity in drug discovery and optimization of general absorption, distribution, metab. and excretion properties, toxicol. profiles and ultimately pharmacol. response. Math. equations are presented concerning the impact of lipophilicity on the dose and the calcn. of the lipophilic ligand efficiency (LipE).
- 44Scott, J. S.; Waring, M. J. Practical Application of Ligand Efficiency Metrics in Lead Optimisation. Bioorg. Med. Chem. 2018, 26, 3006– 3015, DOI: 10.1016/j.bmc.2018.04.00444https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1cXnsVent7g%253D&md5=50bba76316f6f2ec3c89e06f6717c388Practical application of ligand efficiency metrics in lead optimisationScott, James S.; Waring, Michael J.Bioorganic & Medicinal Chemistry (2018), 26 (11), 3006-3015CODEN: BMECEP; ISSN:0968-0896. (Elsevier B.V.)The use of composite metrics that normalize biol. potency values in relation to markers of physicochem. properties, such as size or lipophilicity, has gained a significant amt. of traction with many medicinal chemists in recent years. However, there is no consensus on best practice in the area and their application has attracted some criticism. Here we present our approach to their application in lead optimization projects, provide an objective discussion of the principles we consider important and illustrate how our use of lipophilic ligand efficiency enabled the progression of a no. of our successful drug discovery projects. We derive, from this and some recent literature highlights, a set of heuristic guidelines for lipophilicity based optimization that we believe are generally applicable across chem. series and protein targets.
- 45Wellaway, C. R.; Amans, D.; Bamborough, P.; Barnett, H.; Bit, R. A.; Brown, J. A.; Carlson, N. R.; Chung, C.; Cooper, A. W. J.; Craggs, P. D.; Davis, R. P.; Dean, T. W.; Evans, J. P.; Gordon, L.; Harada, I. L.; Hirst, D. J.; Humphreys, P. G.; Jones, K. L.; Lewis, A. J.; Lindon, M. J.; Lugo, D.; Mahmood, M.; McCleary, S.; Medeiros, P.; Mitchell, D. J.; O’Sullivan, M.; Le Gall, A.; Patel, V. K.; Patten, C.; Poole, D. L.; Shah, R. R.; Smith, J. E.; Stafford, K. A. J.; Thomas, P. J.; Vimal, M.; Wall, I. D.; Watson, R. J.; Wellaway, N.; Yao, G.; Prinjha, R. K. Discovery of a Bromodomain and Extraterminal Inhibitor with a Low Predicted Human Dose through Synergistic Use of Encoded Library Technology and Fragment Screening. J. Med. Chem. 2020, 63, 714– 746, DOI: 10.1021/acs.jmedchem.9b0167045https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXivFagtw%253D%253D&md5=826ebe53a3091893c9e6c6c4830ac388Discovery of a Bromodomain and Extraterminal Inhibitor with a Low Predicted Human Dose through Synergistic Use of Encoded Library Technology and Fragment ScreeningWellaway, Christopher R.; Amans, Dominique; Bamborough, Paul; Barnett, Heather; Bit, Rino A.; Brown, Jack A.; Carlson, Neil R.; Chung, Chun-wa; Cooper, Anthony W. J.; Craggs, Peter D.; Davis, Robert P.; Dean, Tony W.; Evans, John P.; Gordon, Laurie; Harada, Isobel L.; Hirst, David J.; Humphreys, Philip G.; Jones, Katherine L.; Lewis, Antonia J.; Lindon, Matthew J.; Lugo, Dave; Mahmood, Mahnoor; McCleary, Scott; Medeiros, Patricia; Mitchell, Darren J.; O'Sullivan, Michael; Le Gall, Armelle; Patel, Vipulkumar K.; Patten, Chris; Poole, Darren L.; Shah, Rishi R.; Smith, Jane E.; Stafford, Kayleigh A. J.; Thomas, Pamela J.; Vimal, Mythily; Wall, Ian D.; Watson, Robert J.; Wellaway, Natalie; Yao, Gang; Prinjha, Rab K.Journal of Medicinal Chemistry (2020), 63 (2), 714-746CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)The bromodomain and extraterminal (BET) family of bromodomain-contg. proteins are important regulators of the epigenome through their ability to recognize N-acetyl lysine (KAc) post-translational modifications on histone tails. These interactions have been implicated in various disease states and, consequently, disruption of BET-KAc binding has emerged as an attractive therapeutic strategy with a no. of small mol. inhibitors now under investigation in the clinic. However, until the utility of these advanced candidates is fully assessed by these trials, there remains scope for the discovery of inhibitors from new chemotypes with alternative physicochem., pharmacokinetic, and pharmacodynamic profiles. Herein, we describe the discovery of a candidate-quality dimethylpyridone benzimidazole compd. which originated from the hybridization of a dimethylphenol benzimidazole series, identified using encoded library technol., with an N-Me pyridone series identified through fragment screening. Optimization via structure- and property-based design led to I-BET469, which possesses favorable oral pharmacokinetic properties, displays activity in vivo, and is projected to have a low human efficacious dose.
- 46Barducci, A.; Bussi, G.; Parrinello, M. Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method. Phys. Rev. Lett. 2008, 100, 020603, DOI: 10.1103/PhysRevLett.100.02060346https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXovFensQ%253D%253D&md5=701ccfeee476c2e9a5d1e5a6b0e82197Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy MethodBarducci, Alessandro; Bussi, Giovanni; Parrinello, MichelePhysical Review Letters (2008), 100 (2), 020603/1-020603/4CODEN: PRLTAO; ISSN:0031-9007. (American Physical Society)We present a method for detg. the free-energy dependence on a selected no. of collective variables using an adaptive bias. The formalism provides a unified description which has metadynamics and canonical sampling as limiting cases. Convergence and errors can be rigorously and easily controlled. The parameters of the simulation can be tuned so as to focus the computational effort only on the phys. relevant regions of the order parameter space. The algorithm is tested on the reconstruction of an alanine dipeptide free-energy landscape.
- 47Laio, A.; Parrinello, M. Escaping Free-Energy Minima. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12562– 12566, DOI: 10.1073/pnas.20242739947https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD38XnvFGiurc%253D&md5=48d5bc7436f3ef9d78369671e70fa608Escaping free-energy minimaLaio, Alessandro; Parrinello, MicheleProceedings of the National Academy of Sciences of the United States of America (2002), 99 (20), 12562-12566CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)We introduce a powerful method for exploring the properties of the multidimensional free energy surfaces (FESs) of complex many-body systems by means of coarse-grained non-Markovian dynamics in the space defined by a few collective coordinates. A characteristic feature of these dynamics is the presence of a history-dependent potential term that, in time, fills the min. in the FES, allowing the efficient exploration and accurate detn. of the FES as a function of the collective coordinates. We demonstrate the usefulness of this approach in the case of the dissocn. of a NaCl mol. in water and in the study of the conformational changes of a dialanine in soln.
- 48Gillis, E. P.; Eastman, K. J.; Hill, M. D.; Donnelly, D. J.; Meanwell, N. A. Applications of Fluorine in Medicinal Chemistry. J. Med. Chem. 2015, 58, 8315– 8359, DOI: 10.1021/acs.jmedchem.5b0025848https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2MXht1ajs7%252FK&md5=9995829a94a8c0b8d9fb0d21bdfd5a1dApplications of Fluorine in Medicinal ChemistryGillis, Eric P.; Eastman, Kyle J.; Hill, Matthew D.; Donnelly, David J.; Meanwell, Nicholas A.Journal of Medicinal Chemistry (2015), 58 (21), 8315-8359CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)A review with meta-anal. The role of fluorine in drug design and development is expanding rapidly as we learn more about the unique properties assocd. with this unusual element and how to deploy it with greater sophistication. The judicious introduction of fluorine into a mol. can productively influence conformation, pKa, intrinsic potency, membrane permeability, metabolic pathways, and pharmacokinetic properties. In addn., 18F has been established as a useful positron emitting isotope for use with in vivo imaging technol. that potentially has extensive application in drug discovery and development, often limited only by convenient synthetic accessibility to labeled compds. The wide ranging applications of fluorine in drug design are providing a strong stimulus for the development of new synthetic methodologies that allow more facile access to a wide range of fluorinated compds. In this review, we provide an update on the effects of the strategic incorporation of fluorine in drug mols. and applications in positron emission tomog.
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Compound 22 from ref (31) shows a direct salt bridge between a pendant basic amine and BRD4 BD1 Asp144 (pdb: 7rxt). However, no BD1/BD2 selectivity data for this compound is reported and the research focus is the design of BRD4 BD1 selective chemicals probes, not BET BD1 chemical probes.
There is no corresponding record for this reference. - 50Abel, R.; Young, T.; Farid, R.; Berne, B. J.; Friesner, R. A. Role of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand Binding. J. Am. Chem. Soc. 2008, 130, 2817– 2831, DOI: 10.1021/ja077103350https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD1cXhvFWgurk%253D&md5=8eefe76547a82bccaea38f2c84e6cd5fRole of the Active-Site Solvent in the Thermodynamics of Factor Xa Ligand BindingAbel, Robert; Young, Tom; Farid, Ramy; Berne, Bruce J.; Friesner, Richard A.Journal of the American Chemical Society (2008), 130 (9), 2817-2831CODEN: JACSAT; ISSN:0002-7863. (American Chemical Society)Understanding the underlying physics of the binding of small-mol. ligands to protein active sites is a key objective of computational chem. and biol. It is widely believed that displacement of water mols. from the active site by the ligand is a principal (if not the dominant) source of binding free energy. Although continuum theories of hydration are routinely used to describe the contributions of the solvent to the binding affinity of the complex, it is still an unsettled question as to whether or not these continuum solvation theories describe the underlying mol. physics with sufficient accuracy to reliably rank the binding affinities of a set of ligands for a given protein. Here we develop a novel, computationally efficient descriptor of the contribution of the solvent to the binding free energy of a small mol. and its assocd. receptor that captures the effects of the ligand displacing the solvent from the protein active site with at. detail. This descriptor quant. predicts (R2 = 0.81) the binding free energy differences between congeneric ligand pairs for the test system factor Xa, elucidates phys. properties of the active site solvent that appear to be missing in most continuum theories of hydration, and identifies several features of the hydration of the factor Xa active site relevant to the structure-activity relationship of its inhibitors.
- 51Young, T.; Abel, R.; Kim, B.; Berne, B. J.; Friesner, R. A. Motifs for Molecular Recognition Exploiting Hydrophobic Enclosure in Protein-Ligand Binding. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 808– 813, DOI: 10.1073/pnas.061020210451https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2sXhtVegtr4%253D&md5=1109e3f48670cd910885f7fd527eb880Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand bindingYoung, Tom; Abel, Robert; Kim, Byungchan; Berne, Bruce J.; Friesner, Richard A.Proceedings of the National Academy of Sciences of the United States of America (2007), 104 (3), 808-813CODEN: PNASA6; ISSN:0027-8424. (National Academy of Sciences)The thermodn. properties and phase behavior of water in confined regions can vary significantly from that obsd. in the bulk. This is particularly true for systems in which the confinement is on the mol.-length scale. In this study, we use mol. dynamics simulations and a powerful solvent anal. technique based on inhomogeneous solvation theory to investigate the properties of water mols. that solvate the confined regions of protein active sites. Our simulations and anal. indicate that the solvation of protein active sites that are characterized by hydrophobic enclosure and correlated hydrogen bonds induce atypical entropic and enthalpic penalties of hydration. These penalties apparently stabilize the protein-ligand complex with respect to the independently solvated ligand and protein, which leads to enhanced binding affinities. Our anal. elucidates several challenging cases, including the super affinity of the streptavidin-biotin system.
- 52BROMOscan recombinant protein binding assays were carried out at DiscoverX. http://www.discoverx.com (accessed April 4, 2023).There is no corresponding record for this reference.
- 53Berg, E. L.; Kunkel, E. J.; Hytopoulos, E.; Plavec, I. Characterization of Compound Mechanisms and Secondary Activities by BioMAP Analysis. J. Pharmacol. Toxicol. Methods 2006, 53, 67– 74, DOI: 10.1016/j.vascn.2005.06.00353https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD28XhvFyisw%253D%253D&md5=48f71e46491af636d6cdc4bc12dadec9Characterization of compound mechanisms and secondary activities by BioMAP analysisBerg, Ellen L.; Kunkel, Eric J.; Hytopoulos, Evangelos; Plavec, IvanJournal of Pharmacological and Toxicological Methods (2006), 53 (1), 67-74CODEN: JPTMEZ; ISSN:1056-8719. (Elsevier B.V.)Introduction: Unexpected drug activities account for many of the failures of new chem. entities in clin. trials. These activities can be target-dependent, resulting from feedback mechanisms downstream of the primary target, or they can occur as a result of unanticipated secondary target(s). Methods that would provide rapid and efficient characterization of compds. with respect to a broad range of biol. pathways and mechanisms relevant to human disease have the potential to improve preclin. and clin. success rates. BioMAP assays contg. primary human cells (endothelial cells and co-cultures with peripheral blood leukocytes) were stimulated in complex formats (specific combinations of inflammatory mediators) for 24 h in the presence or absence of test agents (drugs, exptl. compds., etc.). The levels of selected protein readouts (adhesion receptors, cytokines, enzymes, etc.) were measured and activity profiles (normalized data sets comprising BioMAP profiles) were generated for each test agent. The resulting profiles were compared by statistical methods to identify similarities and mechanistic insights. Compds. with known mechanisms including inhibitors of histamine H1 receptor, angiotensin converting enzyme, IκB kinase-2, β2 adrenergic receptor and others were shown to generate reproducible and distinguishable BioMAP activity profiles. Similarities were obsd. between compds. targeting components within the same signal transduction pathway (e.g. NFκB), and also between compds. that share secondary targets (e.g. ibuprofen and FMOC-L-leucine, a PPARγ agonist). Complex primary cell-based assays can be applied for detecting and distinguishing unexpected activities that may be of relevance to drug action in vivo. The ability to rapidly test compds. prior to animal or clin. studies may reduce the no. of compds. that unexpectedly fail in preclin. or clin. studies.
- 54Kleinstreuer, N. C.; Yang, J.; Berg, E. L.; Knudsen, T. B.; Richard, A. M.; Martin, M. T.; Reif, D. M.; Judson, R. S.; Polokoff, M.; Dix, D. J.; Kavlock, R. J.; Houck, K. A. Phenotypic Screening of the ToxCast Chemical Library to Classify Toxic and Therapeutic Mechanisms. Nat. Biotechnol. 2014, 32, 583– 591, DOI: 10.1038/nbt.291454https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC2cXotFeqsrc%253D&md5=09336f8e859668a0374d8a27ca4a0ff6Phenotypic screening of the ToxCast chemical library to classify toxic and therapeutic mechanismsKleinstreuer, Nicole C.; Yang, Jian; Berg, Ellen L.; Knudsen, Thomas B.; Richard, Ann M.; Martin, Matthew T.; Reif, David M.; Judson, Richard S.; Polokoff, Mark; Dix, David J.; Kavlock, Robert J.; Houck, Keith A.Nature Biotechnology (2014), 32 (6), 583-591CODEN: NABIF9; ISSN:1087-0156. (Nature Publishing Group)Addressing the safety aspects of drugs and environmental chems. has historically been undertaken through animal testing. However, the quantity of chems. in need of assessment and the challenges of species extrapolation require the development of alternative approaches. Our approach, the US Environmental Protection Agency's ToxCast program, utilizes a large suite of in vitro and model organism assays to interrogate important chem. libraries and computationally analyze bioactivity profiles. Here we evaluated one component of the ToxCast program, the use of primary human cell systems, by screening for chems. that disrupt physiol. important pathways. Chem.-response signatures for 87 endpoints covering mol. functions relevant to toxic and therapeutic pathways were generated in eight cell systems for 641 environmental chems. and 135 ref. pharmaceuticals and failed drugs. Computational clustering of the profiling data provided insights into the polypharmacol. and potential off-target effects for many chems. that have limited or no toxicity information. The endpoints measured can be closely linked to in vivo outcomes, such as the upregulation of tissue factor in endothelial cell systems by compds. linked to the risk of thrombosis in vivo. Our results demonstrate that assaying complex biol. pathways in primary human cells can identify potential chem. targets, toxicol. liabilities and mechanisms useful for elucidating adverse outcome pathways.
- 55Seal, J. T.; Atkinson, S. J.; Aylott, H.; Bamborough, P.; Chung, C.-W.; Copley, R. C. B.; Gordon, L.; Grandi, P.; Gray, J. R.; Harrison, L. A.; Hayhow, T. G.; Lindon, M.; Messenger, C.; Michon, A.-M.; Mitchell, D.; Preston, A.; Prinjha, R. K.; Rioja, I.; Taylor, S.; Wall, I. D.; Watson, R. J.; Woolven, J. M.; Demont, E. H. The Optimization of a Novel, Weak Bromo and Extra Terminal Domain (BET) Bromodomain Fragment Ligand to a Potent and Selective Second Bromodomain (BD2) Inhibitor. J. Med. Chem. 2020, 63, 9093– 9126, DOI: 10.1021/acs.jmedchem.0c0079655https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BB3cXhsVCmurzI&md5=c562a8c9e4c38abac04149ee96e2f594The Optimization of a Novel, Weak Bromo and Extra Terminal Domain (BET) Bromodomain Fragment Ligand to a Potent and Selective Second Bromodomain (BD2) InhibitorSeal, Jonathan T.; Atkinson, Stephen J.; Aylott, Helen; Bamborough, Paul; Chung, Chun-wa; Copley, Royston C. B.; Gordon, Laurie; Grandi, Paola; Gray, James R. J.; Harrison, Lee A.; Hayhow, Thomas G.; Lindon, Matthew; Messenger, Cassie; Michon, Anne-Marie; Mitchell, Darren; Preston, Alex; Prinjha, Rab K.; Rioja, Inmaculada; Taylor, Simon; Wall, Ian D.; Watson, Robert J.; Woolven, James M.; Demont, Emmanuel H.Journal of Medicinal Chemistry (2020), 63 (17), 9093-9126CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)The profound efficacy, yet assocd. toxicity of pan-BET inhibitors is well documented. The possibility of an ameliorated safety profile driven by significantly selective (>100-fold) inhibition of a subset of the eight bromodomains is enticing, but challenging given the close homol. Herein, we describe the X-ray crystal structure-directed optimization of a novel weak fragment ligand with a pan-second bromodomain (BD2) bias, to potent and highly BD2 selective inhibitors. A template hopping approach, enabled by our parallel research into an orthogonal template (15, GSK046, I), was the basis for the high selectivity obsd. This culminated in two tool mols., 20 (GSK620) and 56 (GSK549), which showed an anti-inflammatory phenotype in human whole blood, confirming their cellular target engagement. Excellent broad selectivity, developability, and in vivo oral pharmacokinetics characterize these tools, which we hope will be of broad utility to the field of epigenetics research.
- 56Roos, K.; Wu, C.; Damm, W.; Reboul, M.; Stevenson, J. M.; Lu, C.; Dahlgren, M. K.; Mondal, S.; Chen, W.; Wang, L.; Abel, R.; Friesner, R. A.; Harder, E. D. OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules. J. Chem. Theory Comput. 2019, 15, 1863– 1874, DOI: 10.1021/acs.jctc.8b0102656https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BC1MXjtFKlsrs%253D&md5=5c91547ddc0c975f9616cfba56a5454fOPLS3e: Extending Force Field Coverage for Drug-Like Small MoleculesRoos, Katarina; Wu, Chuanjie; Damm, Wolfgang; Reboul, Mark; Stevenson, James M.; Lu, Chao; Dahlgren, Markus K.; Mondal, Sayan; Chen, Wei; Wang, Lingle; Abel, Robert; Friesner, Richard A.; Harder, Edward D.Journal of Chemical Theory and Computation (2019), 15 (3), 1863-1874CODEN: JCTCCE; ISSN:1549-9618. (American Chemical Society)Building upon the OPLS3 force field we report on an enhanced model, OPLS3e, that further extends its coverage of medicinally relevant chem. space by addressing limitations in chemotype transferability. OPLS3e accomplishes this by incorporating new parameter types that recognize moieties with greater chem. specificity and integrating an on-the-fly parametrization approach to the assignment of partial charges. As a consequence, OPLS3e leads to greater accuracy against performance benchmarks that assess small mol. conformational propensities, solvation, and protein-ligand binding.
- 57Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shelley, M.; Perry, J. K.; Shaw, D. E.; Francis, P.; Shenkin, P. S. Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy. J. Med. Chem. 2004, 47, 1739– 1749, DOI: 10.1021/jm030643057https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXhsFyit74%253D&md5=8cc2f0022318b12dd972e9c493375bf9Glide: A new approach for rapid, accurate docking and scoring. 1. method and assessment of docking accuracyFriesner, Richard A.; Banks, Jay L.; Murphy, Robert B.; Halgren, Thomas A.; Klicic, Jasna J.; Mainz, Daniel T.; Repasky, Matthew P.; Knoll, Eric H.; Shelley, Mee; Perry, Jason K.; Shaw, David E.; Francis, Perry; Shenkin, Peter S.Journal of Medicinal Chemistry (2004), 47 (7), 1739-1749CODEN: JMCMAR; ISSN:0022-2623. (American Chemical Society)A review. Unlike other methods for docking ligands to the rigid 3D structure of a known protein receptor, Glide approximates a complete systematic search of the conformational, orientational, and positional space of the docked ligand. In this search, an initial rough positioning and scoring phase that dramatically narrows the search space is followed by torsionally flexible energy optimization on an OPLS-AA nonbonded potential grid for a few hundred surviving candidate poses. The very best candidates are further refined via a Monte Carlo sampling of pose conformation; in some cases, this is crucial to obtaining an accurate docked pose. Selection of the best docked pose uses a model energy function that combines empirical and force-field-based terms. Docking accuracy is assessed by redocking ligands from 282 cocrystd. PDB complexes starting from conformationally optimized ligand geometries that bear no memory of the correctly docked pose. Errors in geometry for the top-ranked pose are less than 1 Å in nearly half of the cases and are greater than 2 Å in only about one-third of them. Comparisons to published data on rms deviations show that Glide is nearly twice as accurate as GOLD and more than twice as accurate as FlexX for ligands having up to 20 rotatable bonds. Glide is also found to be more accurate than the recently described Surflex method.
- 58Kunkel, E. J.; Plavec, I.; Nguyen, D.; Melrose, J.; Rosler, E. S.; Kao, L. T.; Wang, Y.; Hytopoulos, E.; Bishop, A. C.; Bateman, R.; Shokat, K. M.; Butcher, E. C.; Berg, E. L. Rapid Structure-Activity and Selectivity Analysis of Kinase Inhibitors by BioMAP Analysis in Complex Human Primary Cell-Based Models. Assay Drug Dev. Technol. 2004, 2, 431– 442, DOI: 10.1089/adt.2004.2.43158https://chemport.cas.org/services/resolver?origin=ACS&resolution=options&coi=1%3ACAS%3A528%3ADC%252BD2cXntlGksLY%253D&md5=eae8485e89ea69af97d5e60738bee209Rapid Structure-Activity and Selectivity Analysis of Kinase Inhibitors by BioMAP Analysis in Complex Human Primary Cell-Based ModelsKunkel, Eric J.; Plavec, Ivan; Nguyen, Dat; Melrose, Jennifer; Rosler, Elen S.; Kao, Leon T.; Wang, Yuker; Hytopoulos, Evangelos; Bishop, Anthony C.; Bateman, Raynard; Shokat, Kevan M.; Butcher, Eugene C.; Berg, Ellen L.Assay and Drug Development Technologies (2004), 2 (4), 431-441CODEN: ADDTAR; ISSN:1540-658X. (Mary Ann Liebert, Inc.)A review. Rapid, quant. methods for characterizing the biol. activities of kinase inhibitors in complex human cell systems could allow the biol. consequences of differential target selectivity to be monitored early in development, improving the selection of drug candidates. We have previously shown that Biol. Multiplexed Activity Profiling (BioMAP) permits rapid characterization of drug function based on statistical anal. of protein expression data sets from complex primary human cell based models of disease biol. Here, using four such model systems contg. primary human endothelial cells and peripheral blood mononuclear cells in which multiple signaling pathways relevant to inflammation and immune responses are simultaneously activated, we demonstrate that BioMAP anal. can detect and distinguish a wide range of inhibitors directed against different kinase targets. Using a panel of p38 mitogen-activated protein kinase antagonists as a test set, we show further that related compds. can be distinguished by unique features of the biol. responses they induce in complex systems, and can be classified according to their induction of shared (on-target) and secondary activities. Statistical comparisons of quant. BioMAP profiles and anal. of profile features allow correlation of induced biol. effects with chem. structure and mapping of biol. responses to chem. series or substituents on a common scaffold. Integration of automated BioMAP anal. for prioritization of hits and for structure-activity relation studies may improve and accelerate the design and selection of optimal therapeutic candidates.
Supporting Information
Supporting Information
The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jmedchem.3c00906.
All screening statistics, full BROMOscan and selectivity data, 1H and 13C NMR spectra for 31, representative LCMS traces of target compounds, and X-ray data collection and refinement statistics (PDF)
Molecular formula strings (CSV)
Docking of compound 12 into BRD4 BD1 (PDB)
Coordinates have been deposited with the Protein Data Bank under accession codes 8px2 (BRD2 BD2/13 complex), 8px8 (BRD2 BD2/14 complex), and 8pxa (BRD4 BD1/31 complex). The authors will release atomic coordinates and experimental data upon article publication.
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