Benzimidazolone p38 inhibitors

Article abstract of DOI:10.1016/j.bmcl.2003.12.023

The synthesis and in vitro p38α activity of a novel series of benzimidazolone inhibitors is described. The p38α SAR is consistent with a mode of binding wherein the benzimidazolone carbonyl serves as the H-bond acceptor to Met109 of p38α in a manner analogous to the pyridine nitrogen of prototypical pyridylimidazole p38 inhibitors. Potent p38α activity comparable to that of several previously reported p38 inhibitors is observed for this novel chemotype.

Full text of DOI:10.1016/j.bmcl.2003.12.023

Bioorganic & Medicinal Chemistry Letters 14 (2004) 919–923
Benzimidazolone p38 inhibitors
Mark A. Dombroski, Michael A. Letavic,y Kim F. McClure,* John T. Barberia,
Thomas J. Carty, Santo R. Cortina, Csilla Csiki, Alan J. Dipesa, Nancy C. Elliott,
Christopher A. Gabel, Crystal K. Jordan, Jeff M. Labasi, William H. Martin,
Kevin M. Peese, Ingrid A. Stock, Linne Svensson, Francis J. Sweeney and Chul H. Yu
Pfizer Global Research and Development, Groton Laboratories, Eastern Point Road, Groton, CT 06340, USA
Received 17 October 2003; revised 21 November 2003; accepted 2 December 2003
Abstract—The synthesis and in vitro p38a activity of a novel series of benzimidazolone inhibitors is described. The p38a SARis
consistent with a mode of binding wherein the benzimidazolone carbonyl serves as the H-bond acceptor to Met109 of p38a in a
manner analogous to the pyridine nitrogen of prototypical pyridylimidazole p38 inhibitors. Potent p38a activity comparable to that
of several previously reported p38 inhibitors is observed for this novel chemotype.
# 2003 Elsevier Ltd. All rights reserved.
The proinflammatory cytokines Interleukin-1 (IL-1) and
Tumor Necrosis Factor-a (TNF-a) are thought to have
critical roles in the pathogenesis of Rheumatoid Arthritis
(RA).1 The proven clinical effectiveness of the anti-
cytokine biological agents etanercept, infliximab, anakinra,
and more recently adalimumab in patients with RA
reinforces the central role of these cytokines.2 In spite of
their success, these large protein-based agents have
limitations including cost of therapy and ease of
administration. Small molecule cytokine inhibitors such
as TACE inhibitors,3 IL-1 processing and release
inhibitors,4 and Interleukin-1b Converting Enzyme (ICE)
inhibitors such as pralnacasan5 all have the potential to
provide similar benefits in an orally administered agent.
Early work in our labs focused on the development of
tools to understand the in vivo biology of p38,18 the in
vitro biology of prototype inhibitors,19 and to identify
structurally novel antagonists. Herein we report a novel
series of benzimidazolone p38 inhibitors identified during
the course of this work.
The synthesis of the benzimidazolone nucleus begins
with the assembly of intermediates 2–6 from diamino-
benzoic acid as shown in Scheme 1. These compounds
proved to be versatile starting points for the assembly of
a variety of substituted heterocycles, including imid-
azoles, pyrazoles, oxazoles, triazoles, tetrazoles, pyrroles
and pyridines (Schemes 2–5).
Inhibitors of the mitogen activated protein (MAP)
kinase p38a6 through their downstream blockage of the
production of TNF-a, IL-1b, IL-6, cyclooxygenase-2
(COX-2), and arachadonic acid mobilization7 also have
tremendous therapeutic potential. The archetypal small
molecule p38 inhibitors are the pyridylimidazoles8 and
these structures formed the basis for much of the early
research.9ꢀ11 More recently a number of non-pyridyl
based p38 inhibitors have been described such as the
diaryl ureas,12,13 the triaza-naphthalenones,14 dihydro-
pyridopyrimidone,15 and the dihyroquinazolinones.16,17
With the completion of the benzimidazolone core the
synthesis of various imidazole analogues was conducted
as detailed in Scheme 2.
Minimally substituted benzimidazolones inhibitors
such as 12f and 12g bear close resemblance to their
pyridylimidazole counterpart 15 in terms of both
structure and intrinsic potency21 (cf. 12f and 12g with
15 Fig. 1).
Based on crude overlap of the molecules, a reasonable
hypothesis is that the imidazolone carbonyl serves as
the hydrogen bond acceptor to Met109NH of p38a in
analogy with the pyridyl nitrogen of a prototypical
pyridylimidazole. However, due to the increased size of the
benzimidazolone ring relative to pyridine the crossover
* Corresponding author. Tel.:+1-860-441-8223; fax:+1-860-715-2469;
e-mail: kim_f_mcclure@groton.pfizer.com.
y
Current address: Johnson & Johnson PR&D, 3210 Merryfield Row,
San Diego, CA 92121, USA.
0960-894X/$ - see front matter # 2003 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2003.12.023

920
M. A. Dombroski et al. / Bioorg. Med. Chem. Lett. 14 (2004) 919–923
Scheme 1. Synthesis of benzimidazolone nuclei. (a) COCl2, AcOH; (b) 3.3 equiv NaH, 3.3 equiv R–I, DMF, 50%; (c) LiBH4, MeOH/THF, reflux,
ꢁ
.
18 h, 79%; (d) TEMPO, NCS, Bu4NCl, CH2Cl2/pH 8.6 buffer, 5.5 h, 42%; (e) LiOH H2O, THF/H2O, 50 C, 2 h, 100%; (f) DPPA, Et3N, t-BuOH,
dioxane, reflux, 16 h, 37%; (g) 6N HCl, EtOH, 22 ꢁC, 24 h, 78%; (h) oxalyl chloride, Et3N, CH2Cl2/cat DMF, 1.5 h, then
ꢁ
ꢁ
ꢁ
.
CH3NHOCH3 HCl, 0–22 C, 18 h, 100%; (i) CH3MgCl, THF, 0 C, 98% (7) or ArCH2MgX, dioxane, 23–55 C, (8); (j) MsCl, Et3N, CH2Cl2,
0 ꢁC, 0.5 h, then NaCN, DMSO, 90 ꢁC, 1 h, 91%; (k) 2 M LiOH, reflux, 18 h, 83%; (l) CDI, CHCl3, 1 h, 23 ꢁC, then MeNHOMe/HCl, 18 h, 23 ꢁC,
76%; (m) R4-MgX, THF, ꢀ78–23 ꢁC.
connection or hinge region may be distorted in a man-
ner similar to what is observed for the Vertex and
Merck crystal structures14,16 rather than what is
observed in soaked23 or co-crystallized24 X-ray structures
of p38a and pyridyl imidazole analogues. Although we
have not yet obtained structural support for this
hypothesis follow-up work on the benzimidazolones
was designed to establish if the SARwas consistent with
that of pyridylimidazoles and to compare the benzimid-
azolones to other known p38 inhibitors.
Much of the early SARwork focused on the aryl group
that presumably binds the lipophilic pocket of p38a.
For convenience much of this work is presented in the
context of a benzimidazolone-imidazole with a thiophene
at C2 since the potency is unchanged relative to hydro-
gen (cf. 12b with 12h). By comparison the C4 aryl group
is more sensitive to change and has a large influence on
the overall potency. As shown in Table 1 small halogens
(F, Cl) show no particular positional preference on the
phenyl ring, while small alkyls are optimal at the meta
position (see 12d, 12e, and 12r). Alkyl groups larger
than ethyl are not well tolerated. These findings for the
Scheme 2. Synthesis of imidazole benzimidazolones. (a) m-Toluidine,
MgSO4, CH2Cl2, 90%; (b) Tos-MIC, NaH, DME, then K2CO3,
MeOH, 21%; (c) R4-CHO, KCN, EtOH/H2O 7–21%; (d) R2-CHO,
Cu(OAc)2, NH4OAc, AcOH, 41–85%; (e) Br2, AcOH, then NaOMe,
MeOH/H2O, 75%; (f) CH3I, NaH, THF, then H2, 10% Pd/C, EtOH,
6%; (g) 4-amino-1-benzylpiperidine, piperazine, a-(p-toluensulfonyl)-
4-fluorobenzylisonitrile, THF, 20 h, 20%;20 (h) 40 psi H2, Pd/C, concd
HCl, MeOH, 22 ꢁC, 4 h, 10%.
Scheme 4. Synthesis of oxazole, tetrazoles, and triazole benzimidazo-
lones. (a) a-(p-toluensulfonyl)-3-methylbenzyl-isonitrile, K2CO3, THF,
4 h 22 ꢁC, reflux, 18 h, 39%;20 (b) 4-F-5-Me-phenylmagnesium bro-
mide, THF, 22 ꢁC, 3 h, 77%; (c) TiCl4, NaN3, CH3CN, reflux, 4 h,
58%, 1:4 ratio 20 to 21;25 (d) P2O5, m-toluic acid 2-formylhydrazide,
190 ꢁC, 5 h, 21%.
Scheme 3. Synthesis of pyrazole benzimidazolones. (a) DMF-dime-
thylacetal, 90 ꢁC; (b) hydrazine hydrate, EtOH, 23 ꢁC, 18 h, 65–93%;
(c) R4-NHNH2-HCl, EtOH, 23 ꢁC, 18 h, 71%.

M. A. Dombroski et al. / Bioorg. Med. Chem. Lett. 14 (2004) 919–923
921
C4 aryl group are consistent with the published22 SAR
for pyridylimidazoles.
Other comparisons focused on the nature of the core 5-
membered heterocycle. The synthesis of many of these
analogues is shown in Schemes 3–5.
Changing the core heterocycle from imidazole to oxazole
had a detrimental effect on the potency (cf. 12d in Table
1 with 19 in Table 2). The regioisomeric pyrazoles 16
and 17 tested the published suggestion26 regarding the
need for a nitrogen atom to interact with the e-ammo-
nium group of the catalytic Lys53 in the p38a active
site. In the case of these benzimidazolone pyrazoles
the presence of this nitrogen in 16 and absence in 17 is
dramatic and supports the importance of the proposed
interaction with Lys53Ne. However, not all compounds
with this nitrogen are well tolerated. The pyrrole 26 is
substantially less active than the corresponding imid-
azole 12x, perhaps because of the obligatory presence of
a hydrogen atom, which can be avoided by imidazoles
and pyrazoles by tautomerization. In principle the tri-
azole 22, the tetrazoles 20 and 21, the isomeric pyrazole
18, and the pyridyl 27 all have a suitable nitrogen to
interact with Lys53Ne, but none of these compounds
are active. With the exception of the pyridyl analogue
27 these analogues share in common a nitrogen atom at
the connection of the core 5-membered ring and the aryl
or benzimidazolone group. One possible explanation for
the loss in potency for these compounds is that this
seemingly minor change at the linkage with the benzimid-
azolone or aryl group causes a change to the propeller
like twist of the two groups off of the central 5-membered
ring. However, electronic factors cannot be ruled out.
Of the core heterocycles explored the compounds with
the best potency are confined to certain imidazole and
pyrazole patterns, with 16e having an intrinsic potency
comparable to l-790070, one of the most potent reported
pyridylimidazole inhibitors.
Scheme 5. Synthesis of pyrrole,26 pyrrolopyridine,27 and pyridine28
benzimidazolones. (a) LiHMDS, Br2, THF, 98%; (b) 2,6-diamino-
pyridine, H2SO4, DME, 44%; (c) 2-Bromo-1-pyridin-3-yl-ethanone, 2
equiv NaH, DMA, 88%; (d) NH4OAc, AcOH, 6%; (e)
(CH3)2NCHCClCHN(CH3)2+PF6ꢀ, KOt-Bu, then AcOH, TFA, THF,
then NH4OH reflux, 23%; (f) H2, 10% Pd/C, EtOH, 30%.
Figure 1. Comparison of benzimidazolone and pyridylimidazole p38
inhibitors. 12f p38a IC50=0.14 mM; 12g p38a IC50=0.10 mM; 15 p38a
IC50=0.10 mM, 0.21 mM22
.
Table 1. Benzimidazolone imidazole SAR: C4 Aryl and C2
Sch 2 Compd
R4
R2
Rp38 a IC50 (mM)
In a separate comparison we incorporated structural
motifs similar to those found in published compounds
(Fig. 2). As shown in Table 3 none of these changes
yielded the improvements in potency observed for the
compounds after which they were modeled. In fact,
12a
12b
12c
12d
12e
12f
12g
12h
12i
H
Ph
Ph
H
H
H
H
H
H
H
Et
Me
Et
Me
Et
>1.0
0.29
0.14
0.10
0.05
0.14
0.10
0.26
0.37
0.39
0.27
0.54
0.38
0.68
15.8
1.5
6.2
0.14
1.8
0.5
8.0
>32
0.20
0.07
0.07
4.0
3-Me-Ph
3-Me-Ph
4-F-Ph
4-F-Ph
Ph
Me
Et
Table 2. Core ring SAR
2-Thiophene
2-Thiophene
2-Thiophene
2-Thiophene
2-Thiophene
2-Thiophene
2-Thiophene
2-Thiophene
2-Thiophene
2-Thiophene
2-Thiophene
2-Thiophene
2-Thiophene
2-Thiophene
2-Thiophene
3-Pyridyl
3-Pyridyl
4-Piperidyl
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Me
Et
2-F-Ph
3-F-Ph
4-F-Ph
2-Cl-Ph
3-Cl-Ph
4-Cl-Ph
3-CF3O-Ph
3-CF3-Ph
2-Me-Ph
3-Me-Ph
4-Me-Ph
3-Et-Ph
4-Et-Ph
3-i-Pr-Ph
3-Me-Ph
3-Me-Ph
3-Me-Ph
Sch 2–5 Compd
R4
R2
Rp38
a IC50 (mM)
12j
12k
12l
26
Scheme 5
4-F,5-Me-Ph
3-CF3-Ph
Ph
>1.0
0.03
0.06
0.2
16a
16b
16c
17a
16d
17b
16e
17c
22
19
20
21
11
—
—
—
—
—
—
—
—
—
—
—
—
—
—
—
Et
Et
Me
Me
Et
Et
Et
Et
Me
Et
Et
Et
Me
Et
Et
12m
12n
12o
12p
12q
12r
12s
12t
12u
12v
12w
12x
12y
12z
Ph
Ph
Ph
2.50
0.20
0.68
0.009
0.73
12.5
0.80
>1.0
>1.0
14.4
0.69
>1.0
3-Me-Ph
3-Me-Ph
3-Me-Ph
3-Me-Ph
4-F,5-Me-Ph
4-F,5-Me-Ph
3-Me-Ph
3-Me-Ph
3-Me-Ph
Et
18
27
4-F-Ph 4-Methanesulfinyl-Ph Me

922
M. A. Dombroski et al. / Bioorg. Med. Chem. Lett. 14 (2004) 919–923
Table 3. Comparison to published inhibitors
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p38a IC50 (mM)
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SB-2035808
RWJ-6835427
SB-24223529
l-79007030
12z Table 1
24
0.038
0.052
0.040
0.002
4.0
0.26
0.090
1.25
13
14
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Figure 2. Comparison of benzimidazolones with published com-
pounds.
these changes had no potency advantage over some of
the simplest benzimidazolone analogues such as 12e and
16e. A potential unifying explanation for these results,
especially where groups are projected off of the C2
position of the 5-membered ring core (e.g., 12z, 24, and
14) is that the active site cannot accommodate the span
of groups such as a sulfinylphenyl or piperidine given
the already greater length of the benzimidazolone
nucleus relative to pyridine.
In summary we have introduced a novel series of ben-
zimidazolone p38 inhibitors whose SARsuggests a
mode of binding to p38 analogous to traditional
pyridylimidazole inhibitors. Nevertheless, there are
differences likely due to the greater size of the benzimid-
azolone nucleus relative to pyridyl-based inhibitors, and
there are potentially more specific orientation require-
ments for the imidazolone carbonyl lone pairs to serve as
H-bond acceptors. Although certain benzimidazolone
analogues are as potent as selected pyridylimidazoles
further optimization specifically around the imidazolone
moiety is needed to fully explore the potential of this
series. This work will be reported in subsequent
publications.
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For the purposes of this article the p38a IC50s were
determined as follows: Activated p38a (10 ng) was added
to individual wells of 96-well Maxisorp plates that had
been pre-treated with 100 ng/well of ATF-2-GST to allow
adherence of this substrate to the bottom of the well;
reaction mixtures contained a total volume of 0.1 mL of
25 mM Hepes, pH 7.2, 25 mM MgCl2, 1 mM DTT, 20
mM b-glycerophosphate, 0.1 mM orthovanadate, 50 mM
ATP, and test compounds. After a 60-min incubation at
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