1,3-dimethyl benzimidazolones are potent, selective inhibitors of the brpf1 bromodomain

Article abstract of DOI:10.1021/ml5002932

The BRPF (bromodomain and PHD finger-containing) protein family are important scaffolding proteins for assembly of MYST histone acetyltransferase complexes. Here, we report the discovery, binding mode, and structure-activity relationship (SAR) of the firs

Full text of DOI:10.1021/ml5002932

Letter
pubs.acs.org/acsmedchemlett
Terms of Use
1
,3-Dimethyl Benzimidazolones Are Potent, Selective Inhibitors of
the BRPF1 Bromodomain
†
,‡
‡
‡
†
Emmanuel H. Demont, Paul Bamborough,* Chun-wa Chung, Peter D. Craggs, David Fallon,
Laurie J. Gordon, Paola Grandi, Clare I. Hobbs, Jameed Hussain, Emma J. Jones, Armelle Le Gall,
‡
§
‡
‡
‡
‡
§
†
†
∥
†
Anne-Marie Michon, Darren J. Mitchell, Rab K. Prinjha, Andy D. Roberts, Robert J. Sheppard,
and Robert J. Watson†
†
‡
Epinova Discovery Performance Unit and Molecular Discovery Research, GlaxoSmithKline, Gunnels Wood Road, Stevenage,
Hertfordshire SG1 2NY, U.K.
§
Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
∥DMPK, GlaxoSmithKline, Park Road, Ware SG12 0DP, U.K.
*
S Supporting Information
ABSTRACT: The BRPF (bromodomain and PHD finger-
containing) protein family are important scaffolding proteins for
assembly of MYST histone acetyltransferase complexes. Here, we
report the discovery, binding mode, and structure−activity
relationship (SAR) of the first potent, selective series of inhibitors
of the BRPF1 bromodomain.
KEYWORDS: BRPF1, BRPF2, BRD1, BRPF3, bromodomain, chemical probe, epigenetics, fragment, inhibitor
romodomain modules are found within a diverse group of
chromatin-regulator proteins and act as specific readers of
for example, the MOZ-TIF2 fusion protein, which also interacts
8
B
with BRPF1. BRPF1 is important for maintaining Hox gene
9
acetylated lysine (KAc) residues. The BET (bromodomain and
extra terminal) subfamily (BRD2/3/4/T) has received much
attention following the discovery that inhibitors found using
cellular screens bind to these targets and act by blocking their
expression and skeletal development in fish. BRPF2 (BRD1)
preferentially forms complexes with ING4 and another MYST
family HAT, HBO1. HBO1 acetylates H3K14 and promotes
10
erythroid differentiation. BRPF2 has been linked to bipolar
1
−3
11
binding to Nε-acetyl-lysine (KAc) modified histones.
BET
disorder and schizophrenia in European populations.
inhibitors such as I-BET762 and RVX-208 have progressed into
Some functions of the BRPFs have been mapped to
individual domains. The histone-binding modules include a
PZP (PHD-Zn knuckle-PHD) domain, which in BRPF1 and
1
,4
the clinic for oncology and cardiovascular disease, and their
use as chemical probes has enabled extensive biology of the
5
12
BET proteins to be elucidated.
BRPF2 binds unmodified histone H3K4. The C-terminal
The functions of other bromodomain-containing proteins
PWWP domain of BRPF1 binds H3K36me3 and localizes
9
,13
(BCPs) are less well understood. The availability of small-
BRPF1 to condensed chromatin of mitotic cells.
Like other
molecule probes for these would signficantly enhance our
bromodomains, that of BRPF1 binds KAc peptides, including
9
,14
ability to dissect their biological roles and therapeutic relevance.
H2AK5ac, H3K14ac, and H4K12ac.
Despite these impor-
6
While some disease rationale exists for a few BCPs, their
tant observations, the therapeutic opportunities of targeting the
bromodomain remain unclear. For example, deletion of the
BRPF1 bromodomain does not prevent the acetylation of
multidomain architecture and location within multiprotein
complexes makes it difficult to attribute observed functions
specifically to the bromodomain. The BRPF (bromodomain
and PHD finger-containing) family, BRPF1, BRPF2/BRD1,
and BRPF3, which operate as scaffolds to assemble complexes
of MYST-family histone acetyltransferases (HATs), are
excellent examples of this (Figure S1, Supporting Informa-
15
histone H3 by the HBO1/BRPF1 complex. We report here
the discovery of selective, potent BRPF1 bromodomain
inhibitors, which will help to unravel the functions of this
complex protein.
The BRPF bromodomains themselves are highly conserved,
sharing >65% sequence identity over their ∼100 amino acids
7
tion).
BRPF1, a component of complexes containing the MOZ/
MORF transcriptional coactivators, links the catalytic HATs to
the other subunits ING5 and hEAF6. Translocations of MOZ
Received: July 22, 2014
Accepted: August 28, 2014
8
are associated with aggressive subtypes of leukemia, producing,
©
XXXX American Chemical Society
A
dx.doi.org/10.1021/ml5002932 | ACS Med. Chem. Lett. XXXX, XXX, XXX−XXX

ACS Medicinal Chemistry Letters
Figure S1, Supporting Information). Their KAc sites closely
Letter
(
A crystal structure of BRD4 BD1 in complex with 1 was
solved. The carbonyl oxygen of the benzimidazolone makes
interactions mimicking those of the KAc side chain (Figure 1c).
Both form the same two hydrogen-bonds, with the side chain
resemble other bromodomains, including those of the BETs,
for which small-molecule inhibitors have been discovered via a
1
6,17
wide range of approaches.
The common features of the KAc binding sites of BET and
CREBBP, for example, bind fragments such as acetaminophen
NH of Asn140, and via a through-water interaction to the OH
of Tyr97. The N1-methyl group occupies the terminal methyl
pocket of the acetyl recognition site near Phe83. These
2
18
in a similar manner. In addition, BET KAc site fragments have
been optimized for potency and selectivity by targeting nearby
interactions are typical of most BET inhibitors described to
1
9−21
16,18
regions of the site.
It seemed likely that other
date.
The primary carboxamide of 1 makes no direct
bromodomains would be tractable to this approach, so we set
out to generate selective inhibitors of the BRPFs following the
strategy of optimizing the selectivity of an initially nonselective
KAc site fragment.
interactions with the protein but does H-bond indirectly to
Gln85 through a water molecule.
The residues directly interacting with fragment 1 and the
conserved waters define a recognition motif for the KAc
headgroup common to typical bromodomains (Figure S1,
Supporting Information). Fragments that bind to this site can
potentially act as scaffolds for inhibitors of multiple
bromodomains, with potency and selectivity governed by
substituents, which project into less conserved parts of the site,
One important factor to consider is that inhibition of the
BET bromodomains leads to significant and diverse phenotypic
5
responses. It is critical therefore that a BRPF1 probe molecule
has a high degree of selectivity over the BET proteins to ensure
that biological insights can be confidently ascribed to BRPF1
and not to BET. We consider that a minimum selectivity
window of 2 logs over BET is needed, preferably 3 logs if
possible.
19−21
as is the case for the BETs.
One significant difference
between BRD4 and BRPF1 is the “gatekeeper” residue that
2
forms one wall of the KAc site. In BET family BD1
The BRPF1 starting fragment 1 (Figure 1a) was initially
found in a nuclear magnetic resonance screen (STD-NMR,
bromodomains this is isoleucine (Ile146 in BRD4, Figure 1c),
and in BD2, it is valine. In the BRPF family this is a larger
phenyalanine residue, which restricts the space accessible to
inhibitors (Figure S1b, Supporting Information).
As part of our inhibitor discovery strategy, we assembled a
set of molecules targeting the bromodomain KAc site. These
included analogues derived from BET-binding fragments such
as 1, obtained by searching our compound collection and
purchased libraries. When this set was screened against the
BRPF1 bromodomain, the hits included a cluster of molecules
containing the 1,3-dimethyl benzimidazolone moiety. The hits
were also tested against BRD4 BD1. Figure 2 shows the results
Figure 2. Selectivity of initial 1,3-dimethyl benzimidazolones for
BRPF1 over BRD4 BD1, with the line of unity (dashed). Red = 5-
amides; blue = 5-sulfonamides. The size of the points is proportional
to molecular weight. Circles indicate fitted BRD4 BD1 curves, and
triangles indicate BRD4 BD1. pIC50 <4.3. Example hits 2 and 3 are
marked.
Figure 1. (A) Fragment 1. (B) Lower: STD spectrum of fragment 1
with 5 μM BRD4(1−477). Upper: same, in the presence of 1 mM
competitive ligand GW841819. (C) X-ray structure of 1 (cyan) bound
in the KAc site of BRD4 (with a DMSO molecule on the WPF shelf).
An acetylated lysine side chain from a histone peptide BRD4 complex
is superimposed (green, PDB code 3uvw). Hydrogen bonds are
indicated with dashed gray lines. The acetyl methyl pocket is ringed by
a broken magenta line.
22
for benzimidazolones from the focused set. Among the most
active hits were sulfonamides such as 2 and amides such as 3.
We chose to concentrate on the (5,6)-disubstituted benzimi-
dazolones, in particular amides related to 3, because of the large
window of selectivity of this compound for BRPF1 over BRD4.
Supplementary Methods, Supporting Information) against the
N-terminal bromodomain of BRD4 (BRD4-BD1). The STD
signal was effectively competed by the addition of GW841819,
1
5
1
Hits were tested in a N− H HSQC NMR assay
(Supplementary Methods, Supporting Information) to verify
direct binding to the BRPF1 bromodomain. Compounds 1, 2,
and 3 caused strong and specific shifts (Figure S2, Supporting
2
a BRD4 KAc site binding inhibitor (Figure 1b). The pIC50 of
fragment 1 for BRD4-BD1 was determined to be 4.1 by TR-
FRET competition binding.
B
dx.doi.org/10.1021/ml5002932 | ACS Med. Chem. Lett. XXXX, XXX, XXX−XXX

ACS Medicinal Chemistry Letters
Letter
Information). Consistent with the expected binding mode,
residues close to the KAc binding site were perturbed, e.g.,
Ile652 and Phe653, which line one side of the pocket (Figure
Very shortly afterward, a 1.65 Å resolution crystal structure
of the BRPF1 bromodomain in complex with 3 was obtained.
The whole molecule can clearly be seen in the electron density,
and the binding mode is similar in both chains of the
asymmetric unit (Figure S3, Supporting Information). The
structure shows that the benzimidazolone core of 3 binds to
BRPF1 in a very similar way as does fragment 1 to BRD4
3
). Other residues are not perturbed, for example, Leu688,
which lies >20 Å distant from the site.
(
Figure 4a). The N1-methyl group does indeed bind in the
Figure 3. 15N− H HSQC chemical shift of residues Ile652 and Phe653
of the BRPF1 bromodomain (red), which move on the addition of 1
mM 1 (blue), 2 (green), or 3 (orange). Inset: location of Ile652 and
Phe653 (magenta) within the KAc site.
1
We reasoned that the binding mode of the dimethyl
benzimidazolone core in BRPF1 would mimic that of fragment
1
in BRD4. Because the core is symmetrical, it was unclear
which of the N1 or N3 methyl groups of 3 would occupy the
conserved acetyl methyl pocket of BRPF1. Molecular modeling
suggested that this might be very substituent-dependent. To
answer that question, analogues 4 and 5, in which each of the
two N-methyl groups were removed in turn, were prepared
according to Scheme 1. Fluorinated mono- or di-N-alkylated
a
Scheme 1. Synthesis of Compounds 3, 4, and 5
Figure 4. (A) X-ray structure of BRPF1/compound 3 (blue) and of
BRD4 BD1 (orange)/fragment 1 (green). (B) The complex of BRPF1
with 3 (blue) compared to apo BRPF1 (green, PDB code 4lc2). Water
molecules in the apo structure are shown in yellow; the water
displaced by the N3-methyl group is labeled as W.
a
Reagents and conditions: (a) fuming HNO , (CH CO) O, −30 to 0
3
3
2
°
C, 71−81%; (b) piperidine, DIPEA, DMSO, 120 °C, microwaves,
5
2−79%; (c) H , Pd/C, EtOH, room temperature, 66−99%, or Fe(0),
2
acetyl methyl pocket of BRPF1 near Phe653, while the C2-
carbonyl interacts with the conserved asparagine Asn708 and
via water to Tyr665 (in the same way as that of 1 with the
equivalent BRD4 residues Asn140 and Tyr97). The replace-
ment of the Ile146 gatekeeper residue in BRD4 with the bulky
Phe714 in BRPF1 results in a tilt in binding mode of the
benzimidazolone core between the two bromodomains.
The decrease in BRPF1 potency of 0.9 logs upon removal of
the N3-methyl (compare 4 to 3) can be rationalized by
comparing the BRPF1 complex with 3 to the literature apo X-
ray structure (Figure 4b). The N3-methyl of 3 binds in a
relatively lipophilic environment, close to the side chains of
Tyr707 and Val662. A water molecule is found there in the apo
structure, so its displacement by the N3 methyl group may
allow for favorable hydrophobic interactions with these
residues. In support of this interpretation, upon binding of 3
the side chain of Val662 moves toward the N3 methyl group by
about 1 Å (Figure 4b).
NH Cl, EtOH, 90 °C, 21%; (d) 2-MeO-PhCOCl, pyridine, CH Cl or
4
2
2
DMF, room temperature, 30−55%.
23
benzimidazolones can be nitrated in a regioselective manner.
Displacement of the fluorine via SNAr by piperidine followed
by reduction of the nitro group and amide formation led to the
required analogues in good yields (Synthetic Methods,
Supporting Information).
It was expected that the methyl group occupying the acetyl
methyl pocket would be the more important group for binding.
Relative to the dimethyl parent 3, both des-methyl compounds
4
and 5 lost BRPF1 potency (Scheme 1). However, the N1−H
compound 5 lost 2.4 logs of activity with respect to 3, while the
N3−H isomer 4 lost only 0.9. We concluded that 3 probably
binds to BRPF1 with its N1-methyl buried in the acetyl methyl
pocket close to Phe653 and to BRD4 in an analogous way.
C
dx.doi.org/10.1021/ml5002932 | ACS Med. Chem. Lett. XXXX, XXX, XXX−XXX

ACS Medicinal Chemistry Letters
Letter
The X-ray structure can also help to rationalize the
structure−activity relationship (SAR) of close analogues of 3.
Table 1 summarizes variation at the benzimidazolone 5-
Table 2 shows compounds modified at the 6-position in the
5-(2-methoxyphenyl) carboxamide series. Data for 3-methoxy
a
Table 2. pIC50 at the Benzimidazolone 6-Position
a
Table 1. pIC50 at the Benzimidazolone 5-Position
R
no. BRPF1 BRD4 BD1 no. BRPF1 BRD4 BD1
R
no. BRPF1 BRD4 BD1 no. BRPF1 BRD4 BD1
2
3
-methoxy
phenyl
3
7.1
<4.3
11
7.3
≤4.7
1-piperidine
3
7.1
7.3
6.9
6.9
5.8
5.6
<4.3
≤4.7
<4.3
≤4.9
<4.3
<4.3
6
7.0
6.5
6.2
<4.3
<4.3
<4.3
1
-pyrrolidine
-morpholine
11
14
15
16
17
12
18
-methoxy
phenyl
6
7.0
<4.3
12
6.5
<4.3
4
methoxy
methyl
H
phenyl
7
8
7.0
6.5
<4.3
<4.3
19
20
5.5
5.5
<4.3
4.8
2-methyl
phenyl
a
t-butyl
9
6.2
6.4
<4.3
<4.3
See also Table S1, Supporting Information.
benzyl
10
13
6.1
<4.3
a
See also Table S1, Supporting Information.
analogues are also shown for comparison. The trends are
similar, although as outlined above the 2-methoxy compounds
are always more potent than their 3-methoxy analogues.
The 6-piperidine substituent of 3 makes few close contacts
with the bromodomain apart from a small hydrophobic patch
on the side chain methylene of Glu655 (Figure 5). The size of
the ring makes little consistent difference to BRPF1 potency
position amide substituent, when the 6-piperidine substituent
is retained (compounds 6−10). Where close analogues with
pyrrolidine at the 6-position were available, these were also
tested (Table 1, compounds 11−13).
(
1
compare 11 to 3, and 12 to 6). Interestingly, the morpholines
4 and 18 are slightly weaker than the corresponding
The 5-position amide substituent of 3 interacts with residues
of the BRPF1 ZA loop (Figure 4a). The 2-methoxy phenyl 3 is
marginally more potent than the 3-methoxy phenyl carbox-
amide 6 and unsubstituted phenyl 7. This trend is more
pronounced with other analogues tested (including the directly
analogous pyrrolidine pair, 11 and 12, and others shown
below). Any preference for the 2-methoxy phenyl substituent is
not solely a steric effect because the 2-methyl phenyl 8 is
weaker than 7. In its bound conformation, the methoxy group
forms an internal hydrogen-bond to the NH group of the
carboxamide linker, resulting in a relatively rigid planar
structure (Figure 4a). This presumably assists packing of the
face of the phenyl ring with the side chain methylene groups of
Glu661 (Figure 5). Aliphatic analogues such as the t-butyl
carboxamide 9 and the benzyl carboxamides 10 and 13, which
would be unable to pack against this side chain so efficiently,
are significantly less potent (Table 1).
piperidines 3 and 6. This is probably due to the proximity of
the backbone carbonyl of Asn651 to the 4-position of the
piperidine ring (3.5 Å, Figure 5), which would disfavor
electronegativity in this region.
Smaller 6-substituents, such as the methoxy 15, are tolerated
by BRPF1 with relatively little loss of activity, although the
methyl and hydrogen analogues 16, 17, 19, and 20 are weaker.
Rather than being due to the size of the substituents, this may
reflect the loss of an oxygen or nitrogen atom at the substituent
point itself. The piperidine N1 electrostatically favors the
bound conformation of the amide at the 5-position (Figure 5)
over the alternative where the amide carbonyl points toward
the piperidine.
Examination of the data suggests that in general compounds
with smaller 6-substituents (e.g., 15 and 17) have BRD4 pIC s
5
0
closer to the measurable threshold of 4.3 than larger ones such
as 3 and 14 (Tables 2 and S1, Supporting Information). There
is a trend toward greater selectivity for BRPF1 over BRD4 with
increasing size of this substituent. In BRD4, this vector would
point toward the narrow ZA channel between Trp81 and
Leu92 (Figure 4a), perhaps explaining this result.
All compounds are selective for BRPF1 over BRPF2/3, an
unexpected finding given the conservation between their KAc
sites. Subtle differences close to the KAc pocket must
contribute to this because even fragment 1 shows this trend
(
Table S1, Supporting Information). We speculate that the
substitution of Ser592 in BRPF2 or Asn619 in BRPF3 for
Pro658 in BRPF1 may contribute. The benzimidazolone C5
atom of 3 and the Pro658 Cδ carbon of BRPF1 are close
enough for a hydrophobic contact (Figure 4b, 3.8 Å). No X-ray
structure of BRPF3 has been solved, but in BRPF2 the
backbone NH of Ser592 H-bonds to a water molecule in chain
A. Superimposing BRPF1 and BRPF2 suggests that the
aromatic benzimidazolone ring might be unfavorably close to,
Figure 5. X-ray structure of BRPF1 with 3, showing lipophilic
interactions between the 5- and 6-substituents and the protein (E655
and E661) as yellow dotted lines.
D
dx.doi.org/10.1021/ml5002932 | ACS Med. Chem. Lett. XXXX, XXX, XXX−XXX

ACS Medicinal Chemistry Letters
Letter
or displace, this water in BRPF2 (Figure S5, Supporting
Information).
Compound 3 was tested in the BROMOscan panel of 35
bromodomain binding assays. Consistent with the data above, it
AUTHOR INFORMATION
■
Corresponding Author
(P.B.) E-mail: paul.a.bamborough@gsk.com. Tel: +44 1438
63246. Fax: +44 1438 763352.
*
7
showed excellent BRPF1 potency (pK = 8.0) and a good
d
Notes
window of selectivity over the BETs and BRPF2/3. In addition,
it was highly selective over other bromodomains tested (Table
S2, Supporting Information).
The authors declare no competing financial interest.
ACKNOWLEDGMENTS
■
A cellular protein interaction assay measuring the displace-
ment of NanoLuc-tagged BRPF1 bromodomain from Halo-
tagged histone H3.3 was employed to demonstrate cell
permeability and disruption of chromatin binding (Supple-
We thank Jacqui Men
́
dez and Danette Daniels of Promega
Corporation for facilitating NanoBRET assays, and the
DiscoveRx Corp. for BROMOscan screening. Thanks to
Heather Barnett, Mark Bird, and Tony Cooper for chemistry
and discussion, Paul Homes for fermentation, Oxana Polyakova
for BRD4 protein preparation, Richard Upton for NMR
support, Abigail Lucas, Phylicia Dassardo-Joseph, and Helena
Yong for crystallization assistance, and Melanie Leveridge for
help during manuscript preparation.
24
mentary Methods, Supporting Information). Compound 3
exhibited a dose−response curve with micromolar IC , while
50
the less active analogue 5 showed no effect (Figure 6b). When
ABBREVIATIONS
■
BD1, bromodomain; BET, bromodomain and extra-terminal;
BRD1−4, bromodomain containing 1−4; BRPF, bromodomain
and PHD finger-containing; KAc, acetyl-lysine; PWWP, Pro-
Trp-Trp-Pro
REFERENCES
Figure 6. BRPF1 isoform 1 bromodomain NanoBRET dose−response
curves of (A) compound 3 and (B) analogue 5.
■
(1) Nicodeme, E.; Jeffrey, K. L.; Schaefer, U.; Beinke, S.; Dewell, S.;
Chung, C. W.; 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.
BRPF1 isoform 2 (containing an insertion in the bromodomain
at Ser660) was used instead, neither compound showed any
effect, consistent with a KAc site competitive mode of action
(
2) Chung, C.; Coste, H.; White, J. H.; Mirguet, O.; Wilde, J.;
(
Figure S6, Supporting Information).
To conclude, in compound 3 we have discovered a potent
Gosmini, R. L.; Delves, C.; Magny, S. M.; Woodward, R.; Hughes, S.
A.; Boursier, E. V.; Flynn, H.; Bouillot, A. M.; Bamborough, P.; Brusq,
J. M.; Gellibert, F. J.; Jones, E. J.; Riou, A. M.; Homes, P.; Martin, S. L.;
Uings, I. J.; Toum, J.; Clement, C. A.; Boullay, A. B.; Grimley, R. L.;
Blandel, F. M.; Prinjha, R. K.; Lee, K.; Kirilovsky, J.; Nicodeme, E.
Discovery and characterization of small molecule inhibitors of the BET
family bromodomains. J. Med. Chem. 2011, 54, 3827−3838.
(3) Filippakopoulos, 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, T. N.;
French, C. A.; Wiest, O.; Kung, A. L.; Knapp, S.; Bradner, J. E.
Selective inhibition of BET bromodomains. Nature 2010, 468, 1067−
073.
4) McLure, K. G.; Gesner, E. M.; Tsujikawa, L.; Kharenko, O. A.;
Attwell, S.; Campeau, E.; Wasiak, S.; Stein, A.; White, A.; Fontano, E.;
Suto, R. K.; Wong, N. C.; Wagner, G. S.; Hansen, H. C.; Young, P. R.
RVX-208, an inducer of ApoA-I in humans, is a BET bromodomain
antagonist. PLoS One 2013, 8, e83190.
inhibitor of the BRPF1 bromodomain whose properties are
summarized in Table 3. It has excellent selectivity over other
Table 3. Summary of Properties of Compound 3
BRPF1/2/3 pIC50 (TR-FRET)
7.1/5.1/<4.0
<4.3/<4.3
BRD4 BD1/BD2 pIC50 (TR-FRET)
a
BRPF1 NanoBRET pIC50
6.0
BROMOscan selectivity over other
BETs, ∼3 logs
BRPF2/3, ∼2 logs
all others, >2 logs
low (25 μM)
b
bromodomains
1
(
aqueous solubility (CLND)
5
artificial membrane permeability
high (3.5 × 10− cm/s)
a
b
Promega Corp. (Figure S6, Supporting Information). DiscoveRx
Corp. (Table S2, Supporting Information).
(
5) Muller, S.; Knapp, S. Discovery of BET bromodomain inhibitors
and their role in target validation. MedChemComm 2014, 5, 228−296.
6) Chung, C.; Tough, D. Bromodomains: a new target class for
small molecule drug discovery. Drug Discovery Today: Ther. Strategies
012, 9, e111−e120.
bromodomains, is cell permeable, and displaces the BRPF1
bromodomain from Histone H3.3. Future publications will
describe the optimization of this series.
(
2
ASSOCIATED CONTENT
Supporting Information
Synthetic procedures, analytical data, methods, and figures.
This material is available free of charge via the Internet at
http://pubs.acs.org.
Accession Codes
X-ray structures have been deposited in the PDB with accession
codes 4uyd and 4uye. Compound 3 is available from Chemdiv
cat. # C301-5895) and Princeton Biomolecular Research (cat.
OSSK_ 842278).
■
(7) Carlson, S.; Glass, K. C. The MOZ histone acetyltransferase in
epigenetic signaling and disease. J. Cell Physiol 2014, 229, 1571−1574.
(8) Ullah, M.; Pelletier, N.; Xiao, L.; Zhao, S. P.; Wang, K.; Degerny,
C.; Tahmasebi, S.; Cayrou, C.; Doyon, Y.; Goh, S. L.; Champagne, N.;
Cote, J.; Yang, X. J. Molecular architecture of quartet MOZ/MORF
histone acetyltransferase complexes. Mol. Cell. Biol. 2008, 28, 6828−
*
S
6
(
843.
9) Laue, K.; Daujat, S.; Crump, J. G.; Plaster, N.; Roehl, H. H.;
Kimmel, C. B.; Schneider, R.; Hammerschmidt, M. The multidomain
protein Brpf1 binds histones and is required for Hox gene expression
and segmental identity. Development 2008, 135, 1935−1946.
(
#
E
dx.doi.org/10.1021/ml5002932 | ACS Med. Chem. Lett. XXXX, XXX, XXX−XXX

ACS Medicinal Chemistry Letters
Letter
(
10) Mishima, Y.; Miyagi, S.; Saraya, A.; Negishi, M.; Endoh, M.;
(24) Deplus, R.; Delatte, B.; Schwinn, M. K.; Defrance, M.; Mendez,
J.; Murphy, N.; Dawson, M. A.; Volkmar, M.; Putmans, P.; Calonne,
E.; Shih, A. H.; Levine, R. L.; Bernard, O.; Mercher, T.; Solary, E.; Urh,
M.; Daniels, D. L.; Fuks, F. TET2 and TET3 regulate GlcNAcylation
and H3K4 methylation through OGT and SET1/COMPASS. EMBO
J. 2013, 32, 645−655.
Endo, T. A.; Toyoda, T.; Shinga, J.; Katsumoto, T.; Chiba, T.;
Yamaguchi, N.; Kitabayashi, I.; Koseki, H.; Iwama, A. The Hbo1-Brd1/
Brpf2 complex is responsible for global acetylation of H3K14 and
required for fetal liver erythropoiesis. Blood 2011, 118, 2443−2453.
(
11) Nyegaard, M.; Severinsen, J. E.; Als, T. D.; Hedemand, A.;
Straarup, S.; Nordentoft, M.; McQuillin, A.; Bass, N.; Lawrence, J.;
Thirumalai, S.; Pereira, A. C.; Kandaswamy, R.; Lydall, G. J.; Sklar, P.;
Scolnick, E.; Purcell, S.; Curtis, D.; Gurling, H. M.; Mortensen, P. B.;
Mors, O.; Borglum, A. D. Support of association between BRD1 and
both schizophrenia and bipolar affective disorder. Am. J. Med. Genet.,
Part B 2010, 153B, 582−591.
(
12) Qin, S.; Jin, L.; Zhang, J.; Liu, L.; Ji, P.; Wu, M.; Wu, J.; Shi, Y.
Recognition of unmodified histone H3 by the first PHD finger of
bromodomain-PHD finger protein 2 provides insights into the
regulation of histone acetyltransferases monocytic leukemic zinc-finger
protein (MOZ) and MOZ-related factor (MORF). J. Biol. Chem. 2011,
2
(
86, 36944−36955.
13) Vezzoli, A.; Bonadies, N.; Allen, M. D.; Freund, S. M.; Santiveri,
C. M.; Kvinlaug, B. T.; Huntly, B. J.; Gottgens, B.; Bycroft, M.
Molecular basis of histone H3K36me3 recognition by the PWWP
domain of Brpf1. Nat. Struct. Mol. Biol. 2010, 17, 617−619.
(
14) Poplawski, A.; Hu, K.; Lee, W.; Natesan, S.; Peng, D.; Carlson,
S.; Shi, X.; Balaz, S.; Markley, J. L.; Glass, K. C. Molecular insights into
the recognition of N-terminal histone modifications by the BRPF1
bromodomain. J. Mol. Biol. 2014, 426, 1661−1676.
(
15) Lalonde, M. E.; Avvakumov, N.; Glass, K. C.; Joncas, F. H.;
Saksouk, N.; Holliday, M.; Paquet, E.; Yan, K.; Tong, Q.; Klein, B. J.;
Tan, S.; Yang, X. J.; Kutateladze, T. G.; Cote, J. Exchange of associated
factors directs a switch in HBO1 acetyltransferase histone tail
specificity. Genes Dev. 2013, 27, 2009−2024.
(
16) Hewings, D. S.; Rooney, T. P.; Jennings, L. E.; Hay, D. A.;
Schofield, C. J.; Brennan, P. E.; Knapp, S.; Conway, S. J. Progress in
the development and application of small molecule inhibitors of
bromodomain-acetyl-lysine interactions. J. Med. Chem. 2012, 55,
9
(
393−9413.
17) Garnier, J. M.; Sharp, P. P.; Burns, C. J. BET bromodomain
inhibitors: a patent review. Expert. Opin. Ther. Pat. 2014, 24, 185−199.
18) Chung, C.; Dean, A. W.; Woolven, J. M.; Bamborough, P.
(
Fragment-based discovery of bromodomain inhibitors part 1: inhibitor
binding modes and implications for lead discovery. J. Med. Chem.
2
(
012, 55, 576−586.
19) Bamborough, P.; Diallo, H.; Goodacre, J. D.; Gordon, L.; Lewis,
A.; Seal, J. T.; Wilson, D. M.; Woodrow, M. D.; Chung, C. W.
Fragment-based discovery of bromodomain inhibitors part 2:
optimization of phenylisoxazole sulfonamides. J. Med. Chem. 2012,
5
(
5, 587−596.
20) Hewings, D. S.; Fedorov, O.; Filippakopoulos, P.; Martin, S.;
Picaud, S.; Tumber, A.; Wells, C.; Olcina, M. M.; Freeman, K.; Gill, A.;
Ritchie, A. J.; Sheppard, D. W.; Russell, A. J.; Hammond, E. M.;
Knapp, S.; Brennan, P. E.; Conway, S. J. Optimization of 3,5-
dimethylisoxazole derivatives as potent bromodomain ligands. J. Med.
Chem. 2013, 56, 3217−3227.
(
21) Zhao, L.; Cao, D.; Chen, T.; Wang, Y.; Miao, Z.; Xu, Y.; Chen,
W.; Wang, X.; Li, Y.; Du, Z.; Xiong, B.; Li, J.; Xu, C.; Zhang, N.; He, J.;
Shen, J. Fragment-based drug discovery of 2-thiazolidinones as
inhibitors of the histone reader BRD4 bromodomain. J. Med. Chem.
2
(
013, 56, 3833−3851.
22) Filippakopoulos, P.; Picaud, S.; Mangos, M.; Keates, T.;
Lambert, J. P.; Barsyte-Lovejoy, D.; Felletar, I.; Volkmer, R.; Muller, 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.
(
23) Tapia, I.; Alonso-Cires, L.; Lopez-Tudanca, P. L.; Mosquera, R.;
Labeaga, L.; Innerarity, A.; Orjales, A. 2,3-Dihydro-2-oxo-1H-
benzimidazole-1-carboxamides with selective affinity for the 5-HT(4)
receptor: synthesis and structure-affinity and structure-activity relation-
ships of a new series of partial agonist and antagonist derivatives. J.
Med. Chem. 1999, 42, 2870−2880.
F
dx.doi.org/10.1021/ml5002932 | ACS Med. Chem. Lett. XXXX, XXX, XXX−XXX