Novel 5-(benzyloxy)pyridin-2(1H)-one derivatives as potent c-Met inhibitors

Article abstract of DOI:10.1016/j.bmcl.2013.02.037

A series of novel 5-(benzyloxy)pyridin-2(1H)-ones were designed, synthesized and biologically evaluated for c-Met inhibition. Various amides and benzoimidazoles at C-3 position were investigated. A potent compound 12b with a c-Met IC₅₀ of 12 nM was identified. This compound exhibited potent inhibition of EBC-1 cell associated with c-Met constitutive activation and showed high selectivity for c-Met than other tested 11 kinases. The binding model 12b with c-Met was disclosed by docking analysis.

Full text of DOI:10.1016/j.bmcl.2013.02.037

Bioorganic & Medicinal Chemistry Letters 23 (2013) 2408–2413
Contents lists available at SciVerse ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Novel 5-(benzyloxy)pyridin-2(1H)-one derivatives as potent c-Met
inhibitors
Dengyou Zhang a, , Jing Ai b, , Zhongjie Liang c, , Wei Zhu a, Xia Peng b, Xianjie Chen a, YinChun Ji b,
Hualiang Jiang a,d, Cheng Luo a, Meiyu Geng b, , Hong Liu a,
⇑
⇑
a State Key Laboratory of Drug Research, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese
Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai 201203, PR China
b Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, PR China
c Center for Systems Biology, Soochow University, Jiangsu 215006, PR China
d School of Pharmacy, East China University of Science and Technology, Shanghai 200237, PR China
a r t i c l e i n f o
a b s t r a c t
Article history:
A series of novel 5-(benzyloxy)pyridin-2(1H)-ones were designed, synthesized and biologically evaluated
for c-Met inhibition. Various amides and benzoimidazoles at C-3 position were investigated. A potent
compound 12b with a c-Met IC50 of 12 nM was identified. This compound exhibited potent inhibition
of EBC-1 cell associated with c-Met constitutive activation and showed high selectivity for c-Met than
other tested 11 kinases. The binding model 12b with c-Met was disclosed by docking analysis.
Ó 2013 Elsevier Ltd. All rights reserved.
Received 20 August 2012
Revised 24 January 2013
Accepted 6 February 2013
Available online 14 February 2013
Keywords:
c-Met
EBC-1 cell
Tyrosine kinase receptor
c-Met is a unique member of receptor tyrosine kinase (RTK) ex-
pressed in both normal and malignant cells. It is a cell surface
receptor for hepatocyte growth factor (HGF), a pleiotropic cytokine
Xcovery subsequently reported a series of pyridazin-3-amines as
c-Met inhibitors,5a in which X376 (Fig. 1B, 2) with a c-Met IC50 of
0.69 nM was identified.5b Apart from the bidentate hydrogen
bonding fashion, a single hydrogen bond interaction with the hinge
region of c-Met was also proved effective. For example, 6-benzyl-
oxyquinoline analogue (Fig. 1B, 4), of which quinoline nitrogen
H-bonded with the Met 1160 residue of the hinge region, exhibited
c-Met inhibition at 23 nM.6 Similarly, researchers at Sanofi demon-
strated that 6-benzyloxybenzo[d]thiazole derivatives (Fig. 1B, 3)
were potent c-Met inhibitors (IC50 <100 nM).7 The remarkable dis-
crepancies of these structures lie in the fragments interactive with
the hing region of c-Met.
The less potency of compound 4 than crizotinib and X376 might
be ascribed to the quinoline core only providing one hydrogen
bond interactive with the hinge of c-Met. On the basis of the
pharmacophore model of compound 4, a novel pyridin-2(1H)-one
scaffold was designed (Fig. 2). We envisaged that the pyridin-
2(1H)-one scaffold might deliver bidentate hydrogen bonding with
the hinge, in which the carbonyl oxygen can act as a hydrogen
bond acceptor and NH as a donor. The bidentate hydrogen bonding
might improve the c-Met potency. Meanwhile, the 2,6-dichloro-
3-fluorobenzyloxy group was maintained owing to its potential
that conveys
a unique combination of pro-migratory, anti-
apoptotic and mitogenic signals.1 Aberrant c-Met signalling has
been identified in various human cancers. Moreover, both c-Met
over-expression and MET amplification have been associated with
poor clinical outcomes of cancers. Of particular note, HGF/c-Met
signaling is responsible for resistance to other cancer therapies.2
Without a doubt, c-Met has become an attractive target for cancer
therapy. In the past decade, a plethora of efforts have been devoted
to explore the effective means to interrupt the abnormal c-Met
pathway. Small molecule inhibitors are an important class of ther-
apeutic techniques targeting c-Met.
To date, a respectable number of c-Met inhibitors have already
been reported.2,3 A well-known compound, crizotinib (Fig. 1B, 1),
developed by scientists at Pfizer displayed c-Met inhibition with
a Ki of 2 nM.4 The cocrystal structure of crizotinib (Fig. 1A) dis-
closed its aminopyridine formed bidentate hydrogen bonds with
the hinge of c-Met, 2,6-dichloro-3-fluorobenzyloxy fragment in-
volved a
p–p interaction with activation loop residue Tyr1230
and 4-(1H-pyrazol-1-yl)piperidine reached out into the solvent.
p–p interaction with the residue Tyr 1230. The side chain R was
expected to extend to the solvent accessible region. Herein, we
disclosed our efforts to synthesis and biological evaluation
of the novel 5-(benzyloxy)pyridin-2(1H)-one derivatives against
c-Met.
⇑
Corresponding authors.
E-mail addresses: mygeng@mail.shcnc.ac.cn (M. Geng), hliu@mail.shcnc.ac.cn
(H. Liu).
These authors contributed equally to this study.
0960-894X/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmcl.2013.02.037

D. Zhang et al. / Bioorg. Med. Chem. Lett. 23 (2013) 2408–2413
2409
F
F
Cl
B
Cl
A
O
N
O
N
N
O
Cl
N
Cl
O
N
H
HN
N
NH2
2 (X376)
N
NH2
N
1(Crizotinib)
Met Ki = 2 nM
Met IC50 = 0.69 nM
F
F
Cl
Cl
O
Cl
O
Cl
O
S
H2N
HN
O
N
N
R
F
4
3
Met IC50 = 23 nM
Met IC50 < 100 nM
Figure 1. (A) Cocrystal structure of crizotinib bound to c-Met. (B) Selected examples of c-Met kinase inhibitors.
Figure 2. Design of the pyridin-2(1H)-one scaffold.
F
Cl
O
O
O
O
O
O
O
O
Br
HO
a
b
c
OH
O
O
Cl
O
O
O
N
N
N
9
N
7
F
6
8
d
F
Cl
F
Cl
Cl
O
O
O
f
e
R
O
Cl
R
O
Cl
O
O
N
H
N
O
Cl
H
HO
N
H
12a-t
O
N
N
10
11a-t
Scheme 1. Reagents and conditions: (a) benzyl alcohol, CuI, 1,10-phenanthroline, Cs2CO3, toluene, 110 °C; oxalyl chloride, DMF, CH2Cl2, 0–55 °C, MeOH, rt, 43% yield; (b) Pd/
C, H2, MeOH, 91% yield; (c) (S)-1-(2,6-dichloro-3-fluorophenyl)ethanol, DIAD, PPh3, toluene, 0 °C to rt, 85% yield; (d) LiOH, THF/MeOH/H2O (2/1/1, v/v/v), rt, 95% yield; (e)
amines, HATU, DIPEA, DMF, 0 °C to rt, 40–87% yield; (f) TMSCl, NaI, CH3CN, rt, 46–90% yield.
The construction of 5-(benzyloxy)pyridin-2(1H)-one scaffold
was described in Scheme 1. According to previous research work,5a
a series of amide chains were initially installed at C-3 position of
the 5-(benzyloxy)pyridin-2(1H)-one scaffold. Our synthesis began
with commercial available 5-bromo-2-methoxynicotinic acid. C–
O coupling of 5-bromo-2-methoxynicotinic acid 6 with benzyl
alcohol,8 followed by esterification of the resulting acid, afforded
methyl ester 7 in 43% overall yield. The hydroxyl group was
smoothly installed by debenzylation of the intermediate 7. Treat-
ment of the methyl 5-hydroxy-2-methoxynicotinate 8 with (S)-1-
(2,6-dichloro-3-fluorophenyl)ethanol under Mitsunobu conditions
gave the key intermediate 9 in 85% yield.9 Hydrolysis of the ester
9 followed by coupling with a series of amines deliver 11a–t
(40–87% yield). Finally, compounds 12a–t were obtained in

2410
D. Zhang et al. / Bioorg. Med. Chem. Lett. 23 (2013) 2408–2413
F
F
F
F
Cl
Cl
Cl
Cl
N
N
N
O
b
c
a
O
O
O
Cl
O
Cl
N
H
O
Cl
O
O
Cl
HO
O
O
N
N
O
N
13
N
9
14
16
d
F
F
c
F
Cl
Cl
Cl
O
R
HO
O
HN
N
N
N
N
N
O
Cl
O
Cl
O
e
N
H
N
H
Cl
N
H
O
N
O
N
H
O
N
15
17
18a-c
F
d
Cl
R
HN
N
O
O
Cl
N
H
O
N
H
19a-c
Scheme 2. Reagents and conditions: (a) LiAlH4, THF, À5 to 0 °C, 84% yield; (b) Dess–Martin periodinane, NaHCO3, CH2Cl2, rt, 70% yield; (c) diamines, aq NaHSO3, EtOH, reflux.
For 15, 81% yield; for 16, 70% yield; (d) TMSCl, NaI, CH3CN, rt, 64–85% yield; (e) amines, HATU, DIPEA, DMF, 0 °C to rt, 77–87% yield.
Table 1
SAR about heteroaryl/aryl amides at C-3 position
F
Cl
O
Aryl
O
Cl
N
H
O
N
H
Compound
Aryl
c-Met IC50 (nM)
EBC-1a IC50
NDc
(lM)
12a
8
1 (
3
lM)
N
N
N
N
12b
12c
12d
12
2.2 0.5
3.9 0.7
NDc
N
31 11
N
O
N
78
1
N
12e
12f
NAb
NDc
N
O
N
24
8
1.1 0.2
N
N
F3C
12g
152 53
NDc
N

D. Zhang et al. / Bioorg. Med. Chem. Lett. 23 (2013) 2408–2413
2411
M)
Table 1 (continued)
Compound
Aryl
c-Met IC50 (nM)
EBC-1a IC50
(l
N
12h
12i
12j
76 14
NDc
O
48
2
NDc
NDc
NH
F
O
142 27
NH
O
12k
23
4
2.6 0.3
N
N
N
NDc
O
12l
75 19
O
12m
27
1
5.9 0.8
O
N
N
N
12n
12o
30
27
8
2
9.8 2.4
1.1 0.3
N
N
HO
N
N
12p
14
3
1.0 0.2
HN
N
F
Cl
N
O
O
11b
NAb
NDc
O
Cl
N
H
N
a
EBC-1: human non-small-cell lung cancer cell line that expresses elevated levels of constitutively active c-Met.
b
c
NA: not active at 1.0
ND: not determined.
lM.
46–90% yield by selective demethylation of 11a–t in the presence
of TMSCl/NaI.10
ished activity, suggesting a coplanar geometric arrangement of
the pyridone core with the aniline aromatic ring seems to be pre-
ferred. Compared with 12b, the enzymatic activity was slightly
weak with the introduction of 4-[4-(methylpiperazin-1-yl)-
methyl]phenyl group (12f) but substantially decreased with the
incorporation of an additional CF3 group (12g). Appending a 3-
(piperidin-1-ylmethyl group (12h) led to a sixfold drop in potency.
Incorporation of benzamides (12i and 12j) and cyclic benzamides
(12k and 12l) was also investigated. However, there was no
significant gain in both enzymatic and cellular activity. Pyrazole
fragment is usually used to modulate physical chemical properties
in c-Met inhibitors, presumably due to its lower c logP and higher
PSA.3 Appendage of pyrazoly amides at the C-3 position of the pyri-
done exhibited enzymatic inhibition with IC50 ranging from 30 to
14 nM. It seemed that introduction of the polar tails onto the
pyrazole (12o and 12p) was more preferred over alkyl substituted
pyrazole (12n) for activity at cellular level. Compound 12p
displayed c-Met enzymatic inhibition as 12b, but showed better
cellular potency. It is worth noting that the carbonyl oxygen of
the pyridin-2(1H)-one contributed significantly to the c-Met bind-
ing affinity because block of oxygen with methyl group (11b) re-
sulted in a sharp loss of activity.
To further investigate of SAR at C-3 position of the 5-(benzyl-
oxy)pyridin-2(1H)-one scaffold, a series of benzoimidazole analogs
were prepared as illustrated in Scheme 2. Reduction of the ester 9
with LiAlH4 afforded the corresponding alcohol 13 in 84% yield. Oxi-
dation of the alcohol 13 was achieved with Dess–Martin periodinane
to give aldehyde 14 in 70% yield. Next, condensation of 14 with dia-
mines furnished the benzoimidazole intermediates 15 and 16.11
Demethylation of 15 smoothly gave the compound 17 in 85% yield.
Compounds 19a–c were prepared in a similar manner as 12a–t.
Initially, a series of aryl/heteroaryl amides at C-3 position were
biological evaluated against c-Met. The results were summarized
in Table 1. The unsubstituted phenyl amide analog 12a displayed
weak c-Met inhibition at 8 lM. Installation of the 4-(N-methylpi-
perazine) group (12b) on the phenyl of compound 12a dramati-
cally improved c-Met inhibition and showed an enzymatic IC50 of
12 nM and moderate EBC-1 cell IC50 of 2.2 lM, which suggested
a polar tail had notable impact on c-Met binding. Replacement of
phenyl ring (12b) with pyridyl group (12c and 12d) resulted in
2- to 6-fold loss of enzymatic inhibition. Interestingly, introduction
of a methoxy group adjacent to the amide (12e) completely abol-

2412
Table 2
D. Zhang et al. / Bioorg. Med. Chem. Lett. 23 (2013) 2408–2413
Table 4
SAR about alkyl amides at C-3 position
Enzyme inhibitory activity of 12b on various kinases
F
Kinase
IC50 (nM)
12
Cl
c-Met
RON
ABL
Tyro-3
Flt-1
KDR
3
446 26
281 105
>1000
>1000
>1000
>1000
>1000
>1000
>1000
>1000
>1000
>1000
O
Alkyl
N
O
Cl
H
O
N
H
PDGFR-
RET
a
EGFR
ErbB2
ErbB4
EGFR/T790M/L858R
FGFR1
Compound
Alkyl
c-Met IC50
0.32 0.10
O
12q
N
12r
12s
<50%@10
<50%@10
l
M
Next, a series of alkyl amides at C-3 position were explored.
Table 2 illustrates the enzymatic activity. Generally, the alkyl
amides were not well accommodated at the position. Tetrahydro-
pyranyl amide analog (12q) displayed c-Met inhibition with an
lM
N
O
IC50 of 0.33 lM. However, derivative bearing a 1-methylpiperi-
din-4-yl group (12r) was significantly less active. Incorporation
12t
<50%@1 lM
MeO2SHN
of benzyl amides (12s and 12t) was also proved ineffective in
c-Met enzymatic assay (inactive at 10 lM).
Although various aryl/heteroaryl/alkyl amides at C-3 position
were investigated and some compounds showed promising
enzymatic inhibition, no remarkable cellular potency was observed
presumably due to low cell permeability. We envisaged bioisoster-
ic replacement of the polar phenyl amide with less polar benzoim-
idazole might be beneficial for the cellular potency. With this in
mind, a series of benzoimidazole analog were synthesized and
evaluated for c-Met inhibition (Table 3). Compared with the parent
compound 12b, the derivative 17 was notably less active in enzy-
matic assay. It was similarly observed for analogue 19a inferior to
compound 12i. These results suggest benzoimidazole substitution
at C-3 position might be not well tolerated.
To examine whether compound 12b is a selective c-Met
inhibitor, the kinase selectivity of 12b was assessed by screening
against c-Met family member, RON, along with other 11 tyrosine
kinases (Table 4). In contrast to its high potency against c-Met
(IC50 = 12 3 nM), 12b showed more than 20-fold less potency
against RON, ABL, and barely inhibited kinase activity against the
Table 3
SAR about benzoimidazoles at C-3 position
F
Cl
R1
N
O
Cl
N
H
O
N
H
Compound
R1
c-Met IC50
0.13 0.03
(lM)
N
17
N
O
19a
19b
0.14 0.04
0.33 0.01
N
H
O
other 10 tested tyrosine kinases (IC50 >1 lM).
N
Compound 12b has been proved to be the most potent and
selective c-Met inhibitors in our research, docking simulation
was further applied to explore its binding mode in the atomic level
(Fig. 3). Here, the co-crystal structure of PF-02341066 with c-Met4
N
H
O
O
19c
N
0.36 0.12
N
H
Pro 1158
Met 1160
F
Tyr 1230
Cl
N
N
O
O
O
Cl
N
H
N
H
12b
Figure 3. A proposed structure of 12b bound to c-Met.

D. Zhang et al. / Bioorg. Med. Chem. Lett. 23 (2013) 2408–2413
2413
was selected as the model (PDB ID code: 2WGJ) by employing
Supplementary data
AutoDock4.2 software. The result found the binding model of
12b with c-Met was similar to that of PF-02341066. As expected
in our original design, the pyridone core is responsible for hydro-
gen bonding with the hinge region of c-Met. The carbonyl and
NH of the pyridone core form hydrogen bonds with the residue
Met 1160 and Pro 1158, respectively. The 2,6-dichloro-3-fluorob-
enzyloxy fragment extends to inside pocket involving a p–p inter-
action with the residue Tyr 1230. The amide side chain faces to the
solvent accessible region.
To conclude, a series of novel 5-(benzyloxy)pyridin-2(1H)-ones
were designed, synthesized and biologically evaluated for c-Met
inhibition. The carbonyl oxygen of the pyridin-2(1H)-one was
demonstrated to be an important factor for c-Met binding affinity.
In addition, various amide and benzoimidazole analogs were
explored. A potent compound 12b with an IC50 of 12 nM was iden-
tified. This compound exhibited potent inhibition of EBC-1 cell
associated with c-Met constitutive activation and showed high
selectivity for c-Met than other tested 11 kinases. Further optimi-
zation for improvement of the cellular potency and in vivo evalua-
tion are undertaken in our lab.
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.bmcl.2013. 02.037.
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Acknowledgments
We gratefully acknowledge financial support from National
Basic Research Program of China (Grants 2009CB940903, 2009
CB918502, and 2012CB518005), the National Natural Science
Foundation of China (Grants 21021063, 91229204, 81102461 and
81025017), National S&T Major Projects (2012ZX09103-101-072,
2012ZX09301001-007).
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