Synthesis and evaluation of tricyclic derivatives containing a non-aromatic amide as inhibitors of poly(ADP-ribose)polymerase-1 (PARP-1)

Article abstract of DOI:10.1016/j.bmcl.2010.02.014

Highly potent poly(ADP-ribose)polymerase-1 (PARP-1) inhibitors, including 9-hydroxy-1,2-dihydro-4H-thiopyrano[3,4-c]quinolin-5(6H)-one derivatives with a non-aromatic A-ring, were synthesized. Among the derivatives, 12a showed low nanomolar enzyme and cellular activity (IC₅₀ = 42 nM, ED₅₀ = 220 nM) with good water solubility. Further, 12a exhibited microsomal stability in vitro and brain permeability in vivo.

Full text of DOI:10.1016/j.bmcl.2010.02.014

Bioorganic & Medicinal Chemistry Letters 20 (2010) 2250–2253
Contents lists available at ScienceDirect
Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis and evaluation of tricyclic derivatives containing a non-aromatic
amide as inhibitors of poly(ADP-ribose)polymerase-1 (PARP-1)
Chun-Ho Park a, Kwangwoo Chun a,c, Bo-Young Joe a, Ji-Seon Park a, Young-Chul Kim a, Ji-Soo Choi a,
Dong-Kyu Ryu a, Seong-Ho Koh b, Goang Won Cho b, Seung Hyun Kim b, Myung-Hwa Kim a,
*
a Drug Discovery Laboratory, R&D Center, Jeil Pharmaceutical Co., Ltd. 117-1, Keungok-Ri, Baekam-Myun, Cheoin-Gu, Yongin-City, Kyunggi-Do 449-861, Republic of Korea
b Department of Neurology, Hanyang University College of Medicine, Seoul, Republic of Korea
c Department of Biotechnology, Yonsei University, Seodaemun-Gu, Seoul 120-740, Republic of Korea
a r t i c l e i n f o
a b s t r a c t
Article history:
Highly potent poly(ADP-ribose)polymerase-1 (PARP-1) inhibitors, including 9-hydroxy-1,2-dihydro-4H-
thiopyrano[3,4-c]quinolin-5(6H)-one derivatives with a non-aromatic A-ring, were synthesized. Among
the derivatives, 12a showed low nanomolar enzyme and cellular activity (IC50 = 42 nM, ED50 = 220 nM)
with good water solubility. Further, 12a exhibited microsomal stability in vitro and brain permeability
in vivo.
Received 21 October 2009
Revised 1 February 2010
Accepted 3 February 2010
Available online 8 February 2010
Ó 2010 Elsevier Ltd. All rights reserved.
Keywords:
Poly(ADP-ribose)polymerase PARP-1
Tricyclic derivatives
The poly(ADP-ribose)polymerase (PARP) family is immediately
stimulated by DNA damage.1 When DNA is damaged, PARPs use
nicotinamide adenine dinucleotide (NAD+) as substrate to synthe-
size a polymer of ADP-ribose on the PARP protein itself and various
other protein acceptors, and then carry out DNA repair, recombina-
tion, cell proliferation, or cell death and genomic stability.2 PARP
activation has been shown to mediate both ischemic brain injury
and cancer by caspase-independent cell death and DNA repair.3
PARP-1 (EC 2.4.2.30) was the first enzyme of this family to be dis-
covered, and is the most abundant member of the PARP enzyme
family in eukaryotes.2,4 The role of PARP-1 is important in a num-
ber of cellular processes, thus it is regarded as a target for treating
Figure 1. Previously reported PARP-1 inhibitors and compound 7.
* Corresponding author. Tel.: +82 31 332 4457; fax: +82 31 333 0337.
E-mail address: mhkim@jeilpharm.co.kr (M.-H. Kim).
0960-894X/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.bmcl.2010.02.014

C.-H. Park et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2250–2253
2251
Scheme 1. Reagents and conditions: (a) p-TsOH?H2O, toluene, reflux, 12 h; (b) (i) toluene, 1 h; (ii) 2 N HCl, 24 h; (c) 70% H2SO4, 14 h; (d) BBr3, CH2Cl2, 2 h; (e) K2CO3 or KOH, i-
PrOH, 24 h; (f) HCl, 1,4-dioxane, 12 h; (g) K2CO3, MeCN, 70 °C; (h) HCl, 1,4-dioxane.
( Fig. 1). The aromatic amide group of these compounds form
hydrogen bonds with the Gly-863 and Ser-904 of the PARP enzyme
and also bind to Tyr907 and Tyr896 of the nicotinamide-ribose
binding site (NI site) by a sandwiched hydrophobic interac-
tion.8,11,14 But, some of the PARP-1 inhibitors, fused uracils, had a
non-aromatic amide.16 On the basis of these compounds, we car-
ried out novel class of PARP-1 inhibitors.
In this Letter, we describe the synthesis, the structure–activity
relationship (SAR) study and the biological evaluation of tricyclic
compounds that contain non-aromatic amides as potential PARP-
1 inhibitors. Crystallographic structure of the human PARP-1 cata-
lytic domain (PDB code: 1UK0) was obtained from the Protein Data
Bank (PDB) database,11 and a docking study was performed to ap-
proach the development of potent inhibitors. The result led us to
design analogs containing a non-aromatic A-ring. The first com-
pound 7 which included a non-aromatic A-ring, fit the NI site very
well even though its conformation was not flat (Fig. 2).
To verify this docking study, tricyclic 1,2-dihydro-4H-thiopyr-
ano[3,4-c]quinolin-5(6H)-one derivatives were synthesized, as
outlined in Scheme 1. The 4-thianone 1, which was synthesized
by method in previous report, reacted with a secondary amine by
azeotropic distillation with toluene.17,18 The reaction of the enam-
ine 3 with the isocyanate 4 gave the ketoamide 5, which was cy-
clized to the thiopyranoquinolinone 6 in 70% sulfuric acid at
room temperature.19 Demethylation of 6 with Boron tribromide
in dichloromethane gave alcohol 7. Alkylation of 7 with the appro-
priate bromide 8 in the presence of base led to the Boc-protected
amine 9. Alkyl amine 11 was synthesized by deprotection under
acidic condition and coupling reaction under basic condition. Final-
Figure 2. Docking of compound 7 (red color, ball and stick) and FR257517 (blue
color, stick)11 in the catalytic domain of human PARP-1 (PDB code: 1UK0).
diseases related to ischemia-reperfusion injury and cancer. Indeed,
PARP-1 inhibitors have been shown to be effective in animal mod-
els of ischemic stroke, traumatic brain injury, Parkinson’s disease
and cancer.5–7
Recently, a variety of PARP-1 inhibitors have been reported.6,8–
Most of the PARP-1 inhibitors are competitive with NAD+ and
15
these structures are typically nicotinamide or benzamide analogs
Scheme 2. Reagents: (a) Cu(OAc)2, Et3N, MeCN; (b) HCl, 1,4-dioxane.

2252
C.-H. Park et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2250–2253
Table 1
Table 2
Enzyme and cellular activity of the synthesized compounds
Rat PK profile of 12aa (10 mg/kg), n = 3
Compound
12a
Dose (mg/kg)
AUC0–inf (h ng/ml)
CL (l/h/kg)
10
2908
3.4
t1/2 (h)
3.45
a
Values were detected by LC/MS/MS after intravenous administration.
R1
IC50
(l
M)
ED50 (lM)
a
b
Compound
15
7
—
H
0.040
0.099
1.00
NDc
Table 3
Brain/plasma concentrations of 12a in the rata (10 mg/kg), n = 3
12a
12b
0.042
0.045
0.22
0.58
Time (h)
Brain (ng/g)
Plasma (ng/ml)
Ratio
0.17
0.75
4.00
1705
391
13
2480
610
18
0.69
0.64
0.72
12c
0.071
0.74
a
The concentration was detected by LC/MS/MS.
12d
12f
0.029
0.040
1.60
1.26
Table 4
Human liver microsomal stability of 12aa
Drug
t1/2 (min)
12g
0.173
>30
Buspirone
3.8
12a
52.6
a
Microsomal activity was detected at 0, 15, 45, and 80 min by LC/MS/MS. The
incubation temperature was 37 °C. Values are the mean of triplicate experiments.
Buspirone was used as reference.
14
0.695
0.053
0.038
1.86
0.80
0.36
12h
12i
Table 1. When piperidine analogs were fused to the C-9 hydroxy
position, hydrophobic interactions with the adenine–ribose bind-
ing site (AD site) and water solubility were increased. The N-propyl
and pentyl piperidine derivatives (12a, 12b) showed good enzyme
and cellular activity, and water solubility compared to 7. Moreover,
12a was 4.5-fold more active than 15 in the cell-based assay. The
N-bulky alkyl piperidine derivative 12c was less active than 12a
due to bumping slightly to the active site. The N-(2-hydroxy) and
N-(2-methoxy)ethyl piperidine derivatives (12d, 12f) retained
moderate activity and the N-(2-piperidinyl)ethyl piperidine deriv-
ative 12g was twofold less active than 7 in the enzyme assay. How-
ever, 12d, 12f, and 12g displayed weaker activity in the cell-based
assay. Additionally, N-aryl alkyl piperidine derivatives (12h, 12i)
demonstrated good potency, but rigid or polar bulky derivatives
(14, 12j) displayed a loss of potency. Modification of the nitrogen
position (12k, 12l, 12m, and 12n) showed good potency, similar
to that of 12a. Reduction of ring size (12o, 12q) led to moderate po-
tency and 12q showed a sixfold improved potency compared to
12o.
12j
>10
9.44
12k
12l
0.028
0.039
0.025
0.056
0.080
0.013
0.89
0.58
0.28
0.74
0.73
0.35
12m
12n
12o
12q
a
We examined pharmacokinetic (PK) characteristics, brain/plas-
ma concentration, and microsomal stability of 12a. In the PK stud-
ies, 12a showed a relatively long intravenous half-life and high
AUC concentration (Table 2). The concentration of 12a in plasma
and brain was detected by LC/MS/MS after intravenous injection
in rats. The brain/plasma ratio was 0.64–0.72 over four hours (Ta-
ble 3). In the human liver microsomal stability test, 12a showed
good metabolic stability with a 52.6 min half-life (Table 4).21
In conclusion, we report the synthesis and biological evaluation
of tricyclic derivatives with a non-aromatic amide as potent PARP-
1 inhibitors. Compound 12a was found to be highly potent in en-
zyme and cell-based assays (IC50 = 42 nM, ED50 = 220 nM) with
good water solubility and brain penetration. These findings suggest
that the PARP-1 inhibitor 12a could be a useful therapeutic candi-
date for ischemic stroke and cancers. Further evaluation of this
class of derivatives is ongoing and will be reported in the near
future.
Enzymatic assays followed a commercially available protocol (Trevigen kit,
4671-096-K) in 384-well plates. Values are the mean of triplicate experiments.
b
The CHO-K1 (Chinese hamster ovary) cell line was used for cell-based assay.
Values are the mean of quadruplicate experiments.
c
ND; not determined.
ly, the N-substituted amine salt 12 was prepared by 3.7 N HCl in
1,4-dioxane to enhance water solubility. In addition to 12, the syn-
thetic procedure for phenyl amine salt 14 was outlined in Scheme
2. N-Arylation of amine 10a with phenylboronic acid in the pres-
ence of Copper(II) acetate gave phenyl amine 13, followed by
4.0 N HCl in 1,4-dioxane at room temperature to form 14.20
Recently, the indeno[1,2-c]isoquinolinone 15, reported by Ino-
teck, showed 1 nM inhibitory activity (Table 1).13 However, accord-
ing to our assay protocol, indeno[1,2-c]isoquinolinone 15 had an
IC50 value of 40 nM. The activity of various 1,2-dihydro-4H-thio-
pyrano[3,4-c]quinolin-5(6H)-one derivatives is summarized in

C.-H. Park et al. / Bioorg. Med. Chem. Lett. 20 (2010) 2250–2253
2253
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This study was supported by a grant from the Korea Healthcare
Technology R&D Project, Ministry for Health, Welfare & Family Af-
fairs, Republic of Korea (A080747-0902-0000200). We thank Pro-
fessor Gyoonhee Han (Department of Biotechnology, Yonsei
University, Republic of Korea) for his assistance with the docking
study.
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