3,5-Disubstituted quinolines as novel c-Jun N-terminal kinase inhibitors

Article abstract of DOI:10.1016/j.bmcl.2007.08.054

The structure-based design and synthesis of a novel series of c-Jun N-terminal kinase (JNK) inhibitors with selectivity against p38 is reported. The unique structure of 3,5-disubstituted quinolines (2) was developed from the previously reported 4-(2,7-phenanthrolin-9-yl)phenol (1). The X-ray crystal structure of 16a in JNK3 reveals an unexpected binding mode for this new scaffold with protein.

Full text of DOI:10.1016/j.bmcl.2007.08.054

Available online at www.sciencedirect.com
Bioorganic & Medicinal Chemistry Letters 17 (2007) 6378–6382
3,5-Disubstituted quinolines as novel c-Jun N-terminal
kinase inhibitors
Rong Jiang,a,* Derek Duckett,b Weiming Chen,b Jeff Habel,b Yuan Yuan Ling,b
Philip LoGrassob and Theodore M. Kameneckaa
aDepartment of Medicinal Chemistry, Scripps Florida, 5353 Parkside Drive, RF-2, Jupiter, FL 33458, USA
bDepartment of Molecular Therapeutics, Scripps Florida, 5353 Parkside Drive, RF-2, Jupiter, FL 33458, USA
Received 29 June 2007; revised 21 August 2007; accepted 23 August 2007
Available online 26 August 2007
Abstract—The structure-based design and synthesis of a novel series of c-Jun N-terminal kinase (JNK) inhibitors with selectivity
against p38 is reported. The unique structure of 3,5-disubstituted quinolines (2) was developed from the previously reported 4-
(2,7-phenanthrolin-9-yl)phenol (1). The X-ray crystal structure of 16a in JNK3 reveals an unexpected binding mode for this new
scaffold with protein.
ꢀ 2007 Elsevier Ltd. All rights reserved.
As a member of the mitogen-activated protein kinase
(MAPK) family, the c-Jun N-terminal kinases (JNKs)
regulate the serine/threonine phosphorylation of several
transcription factors when they are activated via up-
stream kinase signaling cascade in response to environ-
mental stress. Three distinct genes encoding JNKs
have been identified (jnk1, jnk2, and jnk3).1 JNK1 and
JNK2 are ubiquitously expressed, while JNK3 is pri-
marily localized in neuronal tissues and to a lesser extent
in the heart and testis.2,3
Therefore, developing JNK inhibitors as therapeutics
has gained considerable interest over the past few
years.14–20 Evaluation of the primary and patent litera-
ture reveals limited structural diversity amongst JNK
inhibitors, though this is not unusual for kinase targets
given that most are ATP-competitive inhibitors.21 Previ-
ously, 4-(2,7-phenanthrolin-9-yl)phenol (1, Fig. 1), dis-
covered by screening the Merck compound collection,
was reported as a 590-nM JNK3 inhibitor with no
detectable activity against p38.22 We were particularly
interested in this compound not only because its unique
structure is strikingly different from most of the kinase
inhibitors published in literature, but also because its
relatively small size provides plenty of opportunities to
improve potency and selectivity by rational structure-
based design. Herein, we report a novel series of JNK
inhibitors based on the 3,5-disubstituted quinoline scaf-
fold (2, Fig. 1) which was derived from phenanthroline
(1).
In recent studies, JNK-1, often in concert with JNK-2,
has been suggested to play a central role in the develop-
ment of obesity-induced insulin resistance which implies
therapeutic inhibition of JNK1 may provide a potential
solution in type-2 diabetes mellitus.4,5 JNK2 has been
described in the pathology of autoimmune disorders
such as rheumatoid arthritis and asthma, and it also
has been implicated to play a role in cancer, as well as
in a broad range of diseases with an inflammatory com-
ponent.6–10 JNK3 has been shown to mediate neuronal
apoptosis and make inhibiting this isoform a promising
therapeutic target for neurodegenerative diseases such as
Parkinson’s disease, Alzheimer’s disease, and other CNS
disorders.11–13
The initial SAR strategy was to maintain the core struc-
ture of 1 (the a, b, c ring system), since 2-key hydrogen
HO
2 N
c
R
HN
5
Ar
3
a
7 N
b
N
Keywords: c-Jun N-terminal kinase; 3,5-disubstituted quinolines.
*
2
1
Corresponding author. Tel.: +1 561 799 8495; fax: +1 561 799
8980; e-mail: rjiang@scripps.edu
Figure 1. Novel JNK scaffolds.
0960-894X/$ - see front matter ꢀ 2007 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2007.08.054

R. Jiang et al. / Bioorg. Med. Chem. Lett. 17 (2007) 6378–6382
Table 1. Inhibition of JNK3 by phenanthroline derivatives 1
6379
bonding interactions were identified between the two
nitrogen atoms of 1 and the main chain of the JNK3
ATP binding site as illustrated in the co-crystal structure
of 1 and JNK3.22,23 Thus, our first attempt was to mod-
ify the phenol group at the C-9 position of the phenan-
a,24
a,24
Compound
R
JNK3 IC50
(lM)
p38 IC50
(lM)
1
OH
H
0.59 0.04
1.0 0.17
>20
>20
>20
nt
1a
1b
1c
1d
1e
1f
1g
1h
1i
throline. Compound
1
and analogs 1a–i were
Phenyl
5-Pyrazolyl
Morpholino
NH2
synthesized in four steps as described in Scheme 1. Pom-
eranz–Fritsch isoquinoline synthesis of 3-bromobenzal-
dehyde and 2,2-dimethoxyethylamine provided two
separable isomers, 7- and 8-bromoisoquinoline. Amina-
tion of 7-bromoisoquinoline followed by Combes quin-
oline synthesis and deprotection furnished 1.
3.6 0.68
1.3 0.22
0.51 0.03
1.6 0.27
0.53 0.08
0.93 0.10
0.21 0.02
nt
nt
>20
nt
NAc2
NHAc
NHMs
NMs2
>20
>20
>20
a Values are means of three experiments; nt, not tested.
Nine analogs of compound 1 have been tested for JNK3
inhibitory activities which are shown in Table 1. Substit-
uents such as hydrogen, phenyl, pyrazole, and mopholi-
no failed to improve potency against JNK3 (1a–d), but
small polar hydrogen bond donor groups such as
NH2, NHAc, and NHMs (1e, 1g, 1h) had comparable
activities to the parent compound 1. The sulfonamide
1i, was nearly 3· as potent, but exhibited poor solubility
as did other analogs. Other modifications including
ortho- and meta-substituted phenyl derivatives (not
shown) as well as substitutions on the b-ring failed to
improve JNK3 inhibitory activity. This series of inhibi-
tors also suffered from poor rodent pharmacokinetics
(high Clp, short t1/2, low %F).
R5
R
N
MsHN
R5
R3
N
N
N
4
5
3
Figure 2. Modifications to phenanthroline scaffold.
para-phenylmethanesulfonamide was chosen as a stan-
dard R3 (5, Fig. 2).
The initial round of compounds was N-linked through
C-5 of the quinoline ring, and the synthesis is outlined
in Scheme 2. Regioselective bromination of commer-
To improve the overall physicochemical properties of
the molecules as well as to facilitate chemical SAR, the
b-ring of 1 was eliminated, resulting in compounds of
type 3 (Fig. 2). These compounds (data not shown) were
considerably more soluble; however, despite synthesiz-
ing numerous analogs, we were unable to improve
JNK3 inhibition below 10 lM even though the nitrogen
atoms from the two pyridyl rings are still present as
hydrogen bond acceptors. Presumably, some degree of
planarity in 1 is required for potency that is lost in struc-
ture 3. To slightly increase conformational rigidity, we
decided to keep the a- and b-rings of 1, and this time,
break down the c-ring (4, Fig. 2). Introduction of sub-
stituents at the 5-position of the quinoline would hope-
fully pick up the purported hydrogen bonding
interaction of the phenanthroline N-2, with the
quinoline nitrogen atom maintaining the conserved
hydrogen bond with Met 149 in the hinge region.22 In
order to explore the SAR of the R5 position efficiently,
NO2
NO2
H
N
O
Br
S
O
NO2
b
a
N
N
6
7
8
N
c
H
N
H
N
O
R
d
O
S
O
HN
S
O
NH2
N
N
9
10
Scheme 2. Reagents: (a) Br2, pyridine; (b) 4-(methylsulfonami-
do)phenylboronic acid, Pd(PPh3)4, K2CO3, DME; (c) Pd/C, MeOH;
(d) Pd2dba3, Cs2CO3, Xantphos, DME.
OMe
a
+
N
N
N
NH2
Br
MeO
Br
CHO
Br
b
R
N
c
R
H2N
N
R=OMe
OHC CHO
d
1
R=OH,
Scheme 1. Reagents and conditions: (a) i—Toluene, 120 ꢁC; ii—concd H2SO4, P2O5; (b) i—Pd2dba3, BINAP, NaOtBu, Ph2C@NH, toluene; ii—1 N
HCl, THF; (c) HOAc, 120 ꢁC; ii—concd H2SO4, 100 ꢁC; (d) BBr3, Et2O, 0 ꢁC.

6380
R. Jiang et al. / Bioorg. Med. Chem. Lett. 17 (2007) 6378–6382
Table 3. Inhibition of JNK3 by pyridyl derivatives 13
cially available 5-nitro-quinoline (6) with bromine in
pyridine at elevated temperature provided 3-bromo-5-
nitro-quinoline (7) which was subsequently treated with
4-(methylsulfonamido)phenylboronic acid under Suzuki
conditions to afford compound 8. Reduction of 8 fol-
lowed by acylation or Buchwald amination furnished
compound 10. The rapid synthesis of the core quinoline
allowed us to evaluate a series of analogs with a variety
of R5-substituents.
a
a
Compound
R
JNK3 IC50 (lM)
p38 IC50 (lM)
13a
>20
nt
N
13b
13c
5.2 0.39
5.0 0.37
>20
>20
N
N
The SAR for this class of compounds revealed that a 2-
pyridyl-amino group at C-5 (10a, Table 2) slightly im-
proved potency compared to 1. This was a significant
breakthrough as this was the first time we were able to
get away from the phenanthroline ring system and main-
tain inhibitory activity against JNK3. Introduction of
an extra nitrogen atom in the ring (10b) is tolerable,
but the 2-pyridinylamide (10c) is not. Five-membered
ring heterocycles are also allowed (10d). The largest
improvements in potency came with small meta-substi-
tuted 2-pyridylamine groups (10g and 10h), whereas
large substituents or substitution at other positions
diminished activity (10e, 10f, and 10i). Fortunately, con-
version of the phenanthroline to a quinoline scaffold did
not pick up p38 activity, as all analogs tested were essen-
tially inactive.
a Values are means of three experiments; nt, not tested.
acid (Scheme 3). The 2-pyridyl analog, 13a, could then
place its nitrogen atom in the same position in space
as phenanthroline 1 as observed in a 2-dimensional
overlap. It was surprising that the 13a was completely
inactive versus JNK3, whereas the 3- and 4-pyridyl ana-
logs (13b and 13c), though slightly better, were still con-
siderably less active than the N-linked analogs 10a–i. At
this time, it was unclear what role the NH-group played
in conferring potency to analogs described in Table 2.
Having somewhat optimized the C-5 substituent, we
continued to probe the 4-substituted phenyl group at
the C-3 position. Following the procedure described in
Scheme 4, the inverse sulfonamide 16 was synthesized
from 3-bromo-5-nitro-quinoline (6) in three steps. Elim-
ination of the t-butyl group with 90% trifluoroacetic
acid in dichloromethane generated primary sulfonamide
17. The inverse sulfonamide t-butyl analog 16a was 3·
more potent than 10a, and 4· more potent than 1 (Table
4). Unfortunately, installation of the potency enhancing
m-chloro substituent in 16b did not result in any boost in
potency as seen for 10a ! 10g.
Attempts were then made to eliminate the C-5 amino
group and to attach the pyridyl ring directly to the quin-
oline core (Table 3). Analogs 13 were synthesized in two
steps from 5-amino-quinoline 11 by Sandmeyer reaction
followed by Suzuki coupling with 2-pyridine boronic
Table 2. Inhibition of JNK3 by phenanthroline derivatives 10
a
a
Compound
R
JNK3 IC50 (lM) p38 IC50 (lM)
A crystal structure of 16a was pursued in an attempt to
help explain its binding mode and further aid in struc-
ture-based drug design. Surprisingly, compound 16a
bound in a completely unexpected manner, and quite dif-
ferently from phenanthroline 1 (Fig. 3). Apparently the
newly introduced 2-aminopyridine group binds to the
hinge region in JNK3, much like many other kinase inhib-
itors. This forces the rest of the molecule to wrap around
the hinge region and extend out into solvent exposed
space. The sulfonamide group picks up additional hydro-
gen bonding interactions outside the active site. We antic-
ipate using this crystal structure to design and synthesize
new, more potent analogs which might take advantage of
the rest of the currently unoccupied ATP binding site.
10a
0.44 0.09
0.48 0.06
>20
>20
N
N
N
10b
10c
10d
3.6 0.32
nt
nt
N
O
S
NO2
0.76 0.15
N
Cl
10e
15 0.17
nt
N
N
In summary, a series of 3,5-disubstituted quinolines as a
new structural type of JNK3 inhibitors has been devel-
oped from structure-based drug design originating from
a published compound 1. Optimization by introduction
of an aminopyridinyl group at the 5-position of the
quinoline led to the discovery of compounds 10a and
16a as more potent JNK3 inhibitors. These compounds
have a completely different binding mode from 1 and
most other kinase inhibitors by not taking advantage
of most of the ATP binding site, which, perhaps will
lead to unanticipated selectivities against other closely
related kinases. Synthesis and characterization of more
10f
10g
10h
10i
6.5 0.53
0.12 0.02
0.14 0.02
0.49 0.06
nt
Cl
Cl
>20
nt
N
N
N
F
CF3
nt
a Values are means of three experiments; nt, not tested.

R. Jiang et al. / Bioorg. Med. Chem. Lett. 17 (2007) 6378–6382
6381
N
MsHN
MsHN
MsHN
Br
NH2
a
b
N
12
N
13
N
11
Scheme 3. Reagents: (a) i—NaNO2, HBr; ii—CuBr; (b) Pd(PPh3)4, DME, Na2CO3, ArB(OH)2.
O
S
O
O
S
O
NO2
N
H
NH2
N
H
NO2
Br
a
b
N
N
c
N
6
14
15
O
S
O
O
S
O
R
R
N
H
HN
H2N
HN
d
N
N
17
16
Scheme 4. Reagents and condition: (a) N-t-butyl-4-(4,5-dimethyl-1,3,2-dioxaborolan-2-yl)benzenesulfonamide, Pd(PPh3)4, K2CO3, DME, micro-
wave; (b) Pd/C, MeOH; (c) RX, Pd2dba3, Cs2CO3, Xantphos, DME, microwave; (d) 90% TFA in CH2Cl2.
potent analogs will continue and will be reported in due
course.
Table 4. Inhibition of JNK3 by inverse sulfonamides 16 and 17
a
a
Compound
R
JNK3 IC50 (lM) p38 IC50 (lM)
16a
0.15 0.02
0.25 0.03
0.20 0.02
0.24 0.01
>20
>20
nt
Acknowledgments
N
N
N
N
The authors thank Dr. Michael Cameron and Li Lin for
rat PK data of compound 1, Prof. William R. Roush
and Mr. Tomas Vojkovsky for helpful discussion of
chemistry. The authors would like to acknowledge Dr.
Gloria Borgstahl of the Eppley Institute for Cancer Re-
search and Allied Diseases for helpful discussions and
guidance during structure refinement.
Cl
Cl
16b
17a
17b
nt
a Values are means of three experiments; nt, not tested.
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biotinylated-ATF2 and ATP were 0.3 nM, 0.4 nM, and
1 lM, respectively. Final assay concentrations of p38,
biotinylated-ATF2, and ATP were 1 nM, 0.4 nM, and
11.5 lM, respectively. In both assays, the phosphor-
Thr71-ATF-2 product was detected by a Europium-
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Streptavidin–allophycocyanin–XL was used as the accep-
tor. A 10-point dose–response curve for each compound
was generated in duplicate and data were fit to a four-
parameter logistic.