Benzo[d]imidazole inhibitors of Coactivator Associated Arginine Methyltransferase 1 (CARM1)-Hit to Lead studies

Article abstract of DOI:10.1016/j.bmcl.2009.07.040

Hit to Lead optimization and SAR development led to the identification of the potent and selective benzo[d]imidazole inhibitor (17b) of Co-activator Associated Arginine Methyltransferase (CARM1).

Full text of DOI:10.1016/j.bmcl.2009.07.040

Bioorganic & Medicinal Chemistry Letters 19 (2009) 5063–5066
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Benzo[d]imidazole inhibitors of Coactivator Associated Arginine
Methyltransferase 1 (CARM1)—Hit to Lead studies
*
Honghe Wan , Tram Huynh, Suhong Pang, Jieping Geng, Wayne Vaccaro, Michael A. Poss, George L. Trainor,
Matthew V. Lorenzi, Marco Gottardis, Lata Jayaraman, Ashok V. Purandare
Bristol-Myers Squibb Pharmaceutical Research and Development, Princeton, NJ 08543, USA
a r t i c l e i n f o
a b s t r a c t
Article history:
Hit to Lead optimization and SAR development led to the identification of the potent and selective
benzo[d]imidazole inhibitor (17b) of Co-activator Associated Arginine Methyltransferase (CARM1).
Ó 2009 Elsevier Ltd. All rights reserved.
Received 19 May 2009
Revised 6 July 2009
Accepted 7 July 2009
Available online 10 July 2009
Keywords:
Protein arginine methyltransferase
PRMT
Co-activator associated arginine
methyltransferase 1
CARM1
Cancer
Post-translational modifications of proteins are increasingly
being recognized as essential to their function in cells. In particular,
methylation of histones which are an essential component of chro-
matin, has been shown to play an important role in the regulation
of gene transcription.1 Protein arginine methyl transferases
(PRMTs), whichtransfer a singlemethylgroupfromthemethydonor
described a pyrazole inhibitor 1 of CARM1 that showed selectivity
versus related methyltranseferases (PRMT1 and PRMT3) (Fig. 1).8
The identification of selective CARM1 inhibitors from different
chemotypes as tools to investigate CARM1 cellular function and
its relevance in disease state would be of significant interest. Here-
in, we report the Hits to Lead optimization studies that led to the
identification of a selective and potent benzo[d]imidazole inhibitor
of CARM1.
S-Adenosyl-L-Methionine (SAM) to an individual arginine residue in
the target substrate, have recently emerged as crucial players in this
process.2 The PRMT family, for which 11 different transcripts have
been identified to date, has been implicated in processes as varied
as chromatin remodeling, signal transduction, proliferation, mRNA
splicing, RNA processing, nucleo-cytoplasmic shuttling and DNA re-
pair.3–5 PRMT4 or CARM1 (Co-activator associated arginine methyl-
transferase-1) specifically drew our interest given its contributions
to nuclear hormone receptor (NHR) signaling, NF-kB signaling and
cancer. It was recently shown that CARM1 was up-regulated during
the progression of prostate cancer.6 Over-expression of CARM1 was
seen in both androgen-stimulated and castration resistant prostate
cancer tumors. We therefore rationalized that targeting CARM1
would be a viable approach for anti-cancer therapy. Hence, the
identification of selective CARM1 inhibitors as tools to understand
its function in cells is of significant interest.
During the screening campaign of the corporate compound col-
lection, benzo[d]imidazole related analogs represented by com-
pound 2 (Fig. 2) were identified as hits with modest activity (IC50
0.84 l
M) in the CARM1 mediated methylation assay.9 Based on
this hit, we initiated Hits to Lead optimization efforts to further im-
prove the in vitro potency of this series.
N
S
F3C
O
N
N
N
N
1 CARM1 IC50 0.04 µM
NH2
To date, there have been only a few publications describing
small molecule chemical modulators of CARM1.7 Earlier, we
HN
O
* Corresponding author. Tel.: +1 609 252 5759.
E-mail address: Honghe.wan@bms.com (H. Wan).
Figure 1.
0960-894X/$ - see front matter Ó 2009 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2009.07.040

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H. Wan et al. / Bioorg. Med. Chem. Lett. 19 (2009) 5063–5066
Table 1
SAR for the West end
West end
East end
H
N
N
O
O
West end
N
N
N
N
N
N
Core
Compd11
West end
CARM 1 IC50
0.84
(l
M)9
2 CARM-1 IC50 = 0.84 µM
H
N
Figure 2.
N
2
We first embarked on evaluating the West end of the molecule.
Towards this objective, West end bearing terminal amines with a
variety of dispositions and substitutions were synthesized using
the approaches depicted in Scheme 1.
HN
5
6
7
17
Very close modifications in the West end such as introduction
of
a-methyl group (as in 6 and 7) as well as removal of internal
H
N
nitrogen atom or abolishing basicity of either of nitrogen atoms
(data not shown) led to a significant loss of potency (Table 1). This
observation suggests that the binding pocket near the West end is
tight, and there is very little tolerance for any changes.
Next, we turned our attention to the center core. Towards this
end, we synthesized analogs (8 and 9) to understand the effect of
a methyl group at the 4- and 1-position of the benzo[d]imidazole.
The 4-des-methyl analog 8 and the 1-methyl analog 9 were pre-
pared from 4-bromo-6-nitroaniline and 4-bromo-N-methyl-2-ni-
tro aniline, respectively, using a similar approach as shown in
Scheme 1. Also, to evaluate the effect of introduction of a nitrogen
atom at the 4-position, imidazo-pyridine analog 14 was synthe-
sized as shown in Scheme 2.
The SAR of the core region is summarized in Table 2. The 4-des-
methyl analog (8) was slightly less potent while 1-methyl substitu-
tion at the nitrogen of the benzo[d]imidazole (as in 9) resulted in
further loss of activity. Introduction of a nitrogen atom (14) how-
ever was tolerated but did not offer any additional advantage.
We then explored the SAR of the East end (Table 3). A modified
synthetic route as depicted in Scheme 3 was used to assemble
these analogs.
N
N
>30
>30
H
N
Boc
N
Bu3Sn
NO2
NH2
NO2
NH2
Br
b
a
NO2
NH2
N
N
N
10
11
12
Boc
N
N
e, f, g
c, d
NO2
NH2
N
13
H
N
N
O
N
N
O
B
RN
N
N
O
NO2
NH2
H
N
O
H
a, b, c
N
14
N
Scheme 2. Reagents and conditions: (a) (Bu3Sn)2, Pd(PPh3)4, dioxane, microwave at
200 °C, 1 h, 54%; (b) tert-butyl 4-(trifluoromethylsulfonyloxy)-5,6-dihydropyridine-
1(2H)-carboxylate, Pd2dba3, AsPPh3, CuI, NMP, 50 °C, 55%; (c) 25% TFA/DCE; (d) tert-
butyl methyl(2-oxoethyl)carbamate, sodium triacetoxyborohydride, DCE; (e) H2
(50 psi), Pd/C (10%), MeOH; (f) 2-methoxynicotinaldehyde; (g) 25% TFA/DCE, 28%
from 12.
3 ref 10a
4 R = Boc
5 R = H
d
e, d for 2
or
f, d for 6
or
g, d for 7
H
N
SAR from this study showed that almost all of the substituted
phenyl and pyridyl groups were tolerated (only partial data
displayed). Interestingly, an unsubstituted phenyl group was not
tolerated. Within the set of substituted phenyls, compounds with
2,6-disubstituted phenyl group were preferred (as in 17b and
17d), indicating conformational preferences for the activity. Gener-
ally, phenyl ring bearing at least one hydrogen bond accepting
ortho-substituents were favored.
Compound 17b was further evaluated in biochemical assays
using other CARM1 substrates (HuR and PABP). The compound
showed a similar level of activity using these substrates.8a In order
to assess the selectivity of this series versus various closely related
PRMT’s, compound 17b was evaluated for its ability to inhibit
R1
N
O
H
N
R2
N
5
N
2 R1 = Me, R2 = H
6 R1 = H, R2 = (S) - Me
7 R1 = Me, R2 = (R) - Me
Scheme 1. Reagents and conditions: (a) tert-butyl 4-(trifluoro-methylsulfonyloxy)-
5,6-dihydropyridine-1(2H)-carboxylate,10d PdCl2dppf, Cs2CO3, DMF, 90 °C, 86%; (b)
H2 (50 psi), Pd/C (10%), MeOH, 70–80%; (c) 2-methoxynicotinaldehyde, MeOH, rt;
(d) 25% TFA/DCE; (e) tert-butyl methyl(2-oxoethyl)carbamate, sodium triacetoxy-
borohydride, DCE, 70%; (f) tert-butyl (S)-methyl(1-oxopropan-2-yl)carbamate,
sodium triacetoxyborohydride, DCE, 65%; (g) tert-butyl (R)-methyl(1-oxopropan-
2-yl)carbamate, sodium triacetoxyborohydride, DCE, 70%.

H. Wan et al. / Bioorg. Med. Chem. Lett. 19 (2009) 5063–5066
5065
Table 2
SAR for the Core
Boc
N
O
B
NO2
NH2
N
O
c
a, b, c
H
NO2
NH2
N
O
N
N
3 ref 10a
Core
15
Compd11
Core
CARM 1 IC50 (lM)
9
Boc
N
H
N
N
N
N
d, e
2
0.84
1.2
NH2
NH2
N
N
H
R
N
H
16
17a-e
N
Scheme 3. Reagents and conditions: (a) tert-butyl 4-(trifluoro-methylsulfonyloxy)-
5,6-dihydropyridine-1(2H)-carboxylate,10d PdCl2dppf, Cs2CO3, DMF, 90 °C, 89%; (b)
25% TFA/DCE; (c) tert-butyl methyl(2-oxoethyl)carbamate, sodium triacetoxyboro-
hydride, DCE, 96% over two steps; (d) H2(50 psi), Pd/C(10%), MeOH, 100%; (e)
aromatic aldehydes; (e) 25% TFA/DCE.
8
9
N
H
N
N
2.9
In summary, through Hits to Lead optimization and SAR explo-
ration, we have identified benzo[b]imidazole derivative 17b as a
potent and selective inhibitor of CARM1. Further work leading to
optimization of this series will be reported in the future.
N
14
0.7
N
H
N
References and notes
PRMT1 and PRMT3.12 Compound 17b was found to be significantly
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Table 3
SAR for the East end
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H
N
N
N
East End
N
Compd11
East end
CARM 1 IC50
0.84
(lM)
9
2
N
MeO
17a
17b
17c
17d
17e
0.41
0.07
0.26
0.12
4.6
MeO
MeO
MeO
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source for enzyme. Histone H3 (Roche Applied Science) and tritiated
F
MeO
F
Sadenosyl-L-methionine (SAM) (Amersham Pharmacia Biotech) were used as
the substrate and cofactor, respectively, for the assay. The values reported are
the average of three with <10% variability.
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A. A.; Matulenko, M. A.; Nakane, M.; Uchic, M. E.; Miller, L. N.; Chang, R.;
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MeO

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methanol-d3, 55 °C) d ppm 7.68 (t, J = 8.52 Hz, 1H) 7.52 (s, 1H) 7.35 (s, 1H)
6.95 (s, 1H), 6.93 (s, 1H), 3.96 (s, 6H) 3.50–3.57 (m, 2H) 3.40–3.45 (m, 2H)
3.20–3.28 (m, 2H), 2.96–3.04 (m, 1H) 2.84–2.95 (m, 2H) 2.80 (s, 3H), 2.65 (s,
3H) 2.07–2.17 (m, 4H) MS (ESI) m/z 514.12 (M+H).
11. (a) All compounds were characterized by LC–MS and NMR analysis. In addition,
the yields were based on the weight of pure product unless mentioned
otherwise. (b) Analytical data for compound 17b: 1H NMR (500 MHz,
12. PRMT1 and PRMT3 specific methylation assays were performed using assay
conditions as reported in Ref. 8.