Exploration of the 5-bromopyrimidin-4(3H)-ones as potent inhibitors of PDE5

Article abstract of DOI:10.1016/j.bmcl.2013.06.062

The substituents both at the 6-position of the 5-bromopyrimidinone ring and at the 5′-position of the phenyl ring of 5-bromopyrimidin-4(3H)-ones were explored. 5-Bromo-6-isopropyl-2-(2-propoxy-phenyl)pyrimidin-4(3H)-one was identified as a new scaffold fo

Full text of DOI:10.1016/j.bmcl.2013.06.062

Bioorganic & Medicinal Chemistry Letters 23 (2013) 4944–4947
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Exploration of the 5-bromopyrimidin-4(3H)-ones as potent
inhibitors of PDE5
Xudong Gong a, , Guan Wang b, , Jing Ren b, , Zheng Liu c, Zhen Wang b, Tiantian Chen b, Xiaojun Yang c,
Xiangrui Jiang b, Jingshan Shen b, Hualiang Jiang b, Haji Akber Aisa a, aisa@ms.xjb.ac.cn, Yechun Xu b,
⇑
⇑
,
Jianfeng Li b,
⇑
a Key Laboratory of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumiqi
830011, China
b CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
c Vitargeta Therapeutics Inc., Plainsboro, NJ 08536, United States
a r t i c l e i n f o
a b s t r a c t
The substituents both at the 6-position of the 5-bromopyrimidinone ring and at the 50-position of the
phenyl ring of 5-bromopyrimidin-4(3H)-ones were explored. 5-Bromo-6-isopropyl-2-(2-propoxy-
phenyl)pyrimidin-4(3H)-one was identified as a new scaffold for potent PDE5 inhibitors. The crystal
structures of PDE5/2e and PDE5/10a complexes provided a structural basis for the inhibition of 5-bromo-
pyrimidinones to PDE5. In addition, it was also found that there is a great tolerance for the substitution at
the 50-position of the phenyl ring of 5-bormopyrimidinones and the resulted compound 13a has the high-
est inhibition activity to PDE5 (IC50, 1.7 nM).
Article history:
Received 16 January 2013
Revised 3 June 2013
Accepted 21 June 2013
Available online 29 June 2013
Keywords:
PDE5 inhibitors
5-Bromopyrimidin-4(3H)-ones
Ó 2013 Elsevier Ltd. All rights reserved.
Since sildenafil launched in 1998, inhibitors of PDE5 have been
approved for the treatment of ED, PAH, and lower urinary tract
symptoms (LUTS) in men with benign prostatic hyperplasia
(BPH).1–3 In addition, avanafil has received FDA approval to treat
ED as a second generation PDE5 inhibitors in April 2012.4 The clin-
ical success of these inhibitors evidenced that the inhibition of
PDE5 is an effective therapy for the diseases mentioned above,
resulting in continuing interest in discovering novel PDE5
inhibitors.
In the course of our effort to seek novel inhibitors of PDE5 with
improved potency and selectivity, we have disclosed the design,
synthesis, and pharmacological evaluation of monocyclic pyrimid-
inones as novel inhibitors of PDE5.2 It is interesting that introduc-
ing a halogen atom except for fluorine at the 5-position of the
pyrimidinone ring led to a remarkable increase in potency com-
pared with that of the 5-hydrogenpyrimidinones (Scheme 1).5 It
has been verified that the increase of potency is attributed to the
halogen bond formed between the halogen atom of the compound
and the hydroxyl oxygen atom of Y612 in the active site of PDE5.5
Although the order of halogen-binding contribution to IC50 of these
compounds to PDE5 is I > Br > Cl > F, the potency of bromo deriva-
tive is comparable to that of the iodo ones. Moreover, the bromo
derivative is more drug-like than the iodo derivative. Hereupon,
we decided to further examine the SAR of this series of 5-bromo-
pyrimidinones as PDE5 inhibitors.
O
N
O
N
H
R
Br
NH OPr
O2S
OPr
NH
R
O2S
N
N
1a R=Et, IC50= 52 nM
1b R=i-Pr, IC50= 31.5 nM
2a R=Et, IC50= 13 nM
2b R=i-Pr, IC50 = 7.2 nM
N
N
Me
Me
Scheme 1.
O
O
N
Br
NH OPr or Et
Br2 / Py
N
NH OPr or Et
R
R
CH2Cl2
⇑
Corresponding authors. Tel.: +86 991 3835679; fax: +86 991 3838957 (H.A.A.);
tel.: +86 21 50801267; fax: +86 21 50807188 (Y.X.); tel./fax: +86 21 20231000 2407
(J.L.).
O2S
O2S
N
N
N
2c-g
N
Me
E-mail addresses: haji@ms.xjb.ac.cn (H.A. Aisa), ycxu@mail.shcnc.ac.cn (Y. Xu),
jfli@mail.shcnc.ac.cn (J. Li).
Me
These authors contributed equally to this work.
Scheme 2.
0960-894X/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmcl.2013.06.062

X. Gong et al. / Bioorg. Med. Chem. Lett. 23 (2013) 4944–4947
4945
Table 1
tial to determine the potency of monocyclic pyrimidin-4(3H)-ones
to PDE5 activity inhibition. The various types of substituents, such
as alkyl, aryl, and the strongly electron-withdrawing trifluoro-
methyl, were introduced at this position. Synthesis of these com-
pounds is outlined in Scheme 2. 5-Hydrogenpyrimidinones,
which were synthesized following the procedure we previously
reported,2 were treated with bromine in the presence of pyridine
in dichloromethane to obtain the 5-bromopyrimidinones.
SAR of substitution at the 6-position of 5-bromopyrimidinone ring
O
Br
NH OR1
R
N
O2S
N
The inhibition activities of these 5-bromopyrimidinones to
PDE5 were presented in Table 1. The 5-bromo substituted com-
pounds are more potent to PDE5 than the 5-hydrogen substituted
ones. As shown in Scheme 1 and Table 1, the effect of substituents
at the 6-position of the 5-bromopyrimidinones to the inhibition
potency is similar to that of the 5-hydrogenpyrimidinones, and
the compound 2b bearing an isopropyl group at the 6-position
showed the highest potency (IC50 = 7.2 nM). Additionally, we have
evaluated the effect of the O-alkyl side-chain at the 20-position of
the phenyl ring on its hydrophobic interaction with the enzyme.2
It was found that a 3-carbon chain at this position gives the best
efficacy. On the basis of these results, we identified that compound
2b is the most potent compound and measured the inhibition of 2b
to PDE5 as well as PDE6. The IC50 of compound 2b to PDE6 is
7.4 nM, which is similar to the inhibition of the compound to
PDE5. The selectivity of compound 2b to PDE5 over PDE6 is thus
much lower than that of 5,6-diethyl-2-[2-n-propoxy-5-(4-
N
Me
Compound
R1
R
PDE5 IC50 (nM)
Sildenafil
2aa
2ba
2c
2d
2e
—
—
Et
i-Pr
Me
3.9
13
7.2
48
10.2
77
74
n-Pr
n-Pr
n-Pr
n-Pr
Et
n-Pr
n-Oct
Ph
2f
2g
Et
n-Pr
CF3
272
Data are the mean of two independent assays, each performed in duplicate.
Compounds have been reported in our previous study.2
a
Firstly, we devoted our efforts to investigate the substituent at
the 6-position of the 5-bromopyrimidinone ring, due to its poten-
O
O
O
O
Br
Br
NH OPr
Br
NH OPr
a
NH OPr
b
c
NH OPr
O2S
i-Pr
N
i-Pr
N
i-Pr
N
i-Pr
N
SO2Cl
3
d
4
5
6a-g
R
O
O
O
O
N
Br
i-Pr
Br
NH OC3H7
NH OC3H7
Br
i-Pr
Br
e
NH OC3H7
NH OC3H7
f
g
N
i-Pr
N
N
i-Pr
Br
R1
O
CH3
Br
7
8
O
O
10a, 10b
9
R1
N
N
N CH3
10a
10b
O
Scheme 3. Reagents and conditions: (a) Br2, Et3N, DCM, 0 °C, 95%; (b) HSO3Cl, 0 °C; (c) the corresponding amine moiety, Et3N, DCM, 0 °C, 59–86%; (d) Br2, AcOH, 60 °C, 76%;
(e) (i) vinyl n-butyl ether, Pd(OAc)2, bis(diphenylphosphino)butane, Et3N; (ii) hydrochloric acid (10%); (f) Br2, AcOH, 30 °C, 18%; (g) N-methylpiperazine or morpholine, Et3N,
39–50%.
O
N
4
O
N
O
N
O
N
Br
Br
Br
NH OC3H7
NH OC3H
NH OC3H7
Br
7 b
NH OC3H7
a
c
i-Pr
i-Pr
i-Pr
i-Pr
NO2
NH2
13a
12
11
NH
MeSO2
d
e
O
N
O
Br
i-Pr
NH
OC3H7
O
Br
OH
OH
NH
OC3H7
13c
HO
HO
OH
O
i-Pr
N
OH
OH
HN
NHPh
13d
13c 13d
13b
OH
NHR
S
Scheme 4. Reagents and conditions: (a) H2SO4, HNO3, 90%; (b) Fe, HCl, 82%; (c) CH3SO2Cl, Et3N, 36%; (d) phenyl isothiocynate, Et3N, 89%; (e) CH3COOH, n-butanol, glucose or
mannose, 21–35%.

4946
X. Gong et al. / Bioorg. Med. Chem. Lett. 23 (2013) 4944–4947
methyl-1-piperazinylsulfonyl)phenyl]pyrimid-4(3H)-one.2
According to our previous study, modifying the sulfamide group
may improve the selectivity over PDE6 of PDE5 inhibitors using sil-
denafil as a starting template.6
We fixed the 5-bromo-6-isopropyl-2-(2-propoxyphenyl)pyrim-
idin-4(3H)-one and focused on exploration of the effect of substit-
uents at the 50-position of the phenyl ring to obtain both potent
and selective PDE5 inhibitors. The solved crystal structures of
PDE5 catalytic domain in complex with the inhibitors also indicate
that there might be a great tolerance for the substitution at this po-
sition.7–10 We therefore synthesized three types of inhibitors bear-
ing various series of substitutions and evaluated their bioactivities.
Compounds 6a–g were synthesized as shown in Scheme 3. The
key intermediate 4, which was prepared following the procedure
we previously reported,2 was treated with chlorosulfonic acid,
and then followed by the corresponding amine moiety, resulting
in the compounds 6a–g. The intermediate 7, prepared through bro-
mation of 4 in acetic acid at 60 °C,11 was coupled with vinyl n-butyl
ether by Pd(OAc)2-catalyzed coupling reaction in the presence of
bis(diphenylphosphino)butane and triethylamine, and then the re-
sulted products were treated with hydrochloric acid (10%) to ob-
tain 8.12 The solution of 8 and bromine in acetic acid was stirred
for 3 h at 30 °C, giving the intermediate 9.13 Compounds 10a and
10b were obtained by the reaction of 9 with N-methylpiperazine
or morpholine.14
The intermediate 4 was nitrated and hydrogenated to give 12.15
Compound 13a was obtained by the sulfonylation of 12 employing
methanesulfonyl chloride.11
The alcoholic solution of 12 was treated with triethylamine and
phenylisothiocyanate to give 13b.16 Compounds 13c and 13d were
formed through the glucosylation and mannosylation of the amine
group in 12, respectively (Scheme 4).17
The inhibition activities of those substituted compounds to
PDE5 were summarized in Table 2. Although the value of IC50 var-
ied in a wide range from 1.7 to 29.3 nM, there is at least one potent
inhibitor (IC50 <10 nM) for each type of substituents at the 50-posi-
tion of the phenyl ring. This result is consistent with the previous
suggestion that there is tolerance for such substitution. Two com-
pounds, 6e and 13a, were chosen to test the selectivity of PDE5
over PDE6, and compound 13a showed an excellent selectivity
(PDE6/5 = 941).
The crystal structures of the catalytic domain of PDE5 in com-
plex with compounds 2e and 10a were determined by soaking
the compounds into the apo crystals of the protein (Fig. 1). The pro-
tocol for solving the 3D structures of PDE5/2e and PDE5/10a com-
plexes was the same as that described in our previous
publications.2,5 The complete statistics, as well as the quality of
the two solved structures, are shown in Supplementary data (Sup-
plementary Table S1). The binding position of the two compounds
inside the catalytic domain of PDE5 is very similar to that of silde-
nafil as well as our previously reported PDE5 inhibitors. Briefly, the
protein–ligand interactions include the conserved bidentate
hydrogen bonds (H-bonds) between the pyrimidinone rings and
the side chain of Q817, a H-bond between the carbonyl oxygen
of the pyrimidinone ring and the side chain of Q775 via a water
molecule, a face-to-face
p–p stacking interactions between the
pyrimidinone ring and the phenyl ring of F820, and hydrophobic
interactions between the compounds and other residues nearby.
Moreover, a halogen bond between the bromo atom substituted
at the 5-position of the pyrimidinone ring and the hydroxyl oxygen
of the residue Y612 which simultaneously H-bonds to D764
through a water molecule is formed (Fig. 1C). For the compound
2e, its long alkyl chain substituted at the 6-position of the pyrimid-
inone ring fits into the cavity toward the hydrophobic residue L725
as shown in Figure 1A. Hydrophobic interactions are formed be-
tween the alkyl chain and residues such as L725. In the complex
Figure 1. Crystal structures of PDE5/2e and PDE5/10a complexes. (A, B) Molecular
surface representation of the binding pocket of compounds 2e (A) and 10a (B) in the
catalytic domain of PDE5. (C) The H-bonding and hydrophobic interactions between
the compound 10a and the residues of PDE5.
of PDE5/10a, there are no strong interaction observed between
the substituent at 50-position of the phenyl ring of 10a and the

X. Gong et al. / Bioorg. Med. Chem. Lett. 23 (2013) 4944–4947
4947
Table 2
In summary, we have designed as well as synthesized a series of
5-bormopyrimidinones, and identified the 5-bromo-6-isopropyl-2-
(2-propoxy-phenyl)pyrimidin-4(3H)-one as a new scaffold of po-
tent PDE5 inhibitors. The different substitutions at the 50-position
of the phenyl ring were also explored, which verified that there
is a great tolerance for the substitution at this position and the sub-
stituents play an important role in the selectivity of PDE5 over
PDE6. The resulted 5-bromo-6-isopropyl-2-(2-propoxyphenyl)pyr-
imidin-4(3H)-one analog 13a showed the highest activity with an
IC50 value of 1.7 nM and an excellent selectivity over PDE6
(PDE6/5 = 941). The crystal structures of PDE5/2e and PDE5/10a
complexes give insight into the binding mode of 5-bormopyrimid-
inones with the catalytic domain of PDE5. With this available
structure information, further modifications on the compound
13a are ongoing.
SAR of substitution at the 50-position of the phenyl ring
O
Br
NH OPr
i-Pr
N
R
Compound
R
IC50 (nM)
PDE5
3.9
PDE6
39.2
Sildenafil
—
O2S
N
2b
7.2
7.4
N
Me
Me
Acknowledgments
O2S
N
6a
6b
6c
25.5
6.2
—
—
—
This study was supported by the ‘100 Talents Project’ of CAS (to
Y.X.), the National Science and Technology Major Project
(2011ZX09102-005-02 and 2012ZX09301001-001), the National
High Technology Research and Development Program of China
(2012AA020302), the National Natural Science Foundation of Chi-
na (No. 91013010 and 21172233), Innovation Fund for Technology
Based Firms of Shanghai City (No. 1002H117400).
O2S
O2S
N
N
O
29.3
N
Ph
O2S
N
Me
6d
11.1
—
Supplementary data
Me
Supplementary data associated with this article can be found, in
O2S
N
6e
6f
2.8
4.5
2.2
—
the
online
version,
at
http://dx.doi.org/10.1016/
HOOC
j.bmcl.2013.06.062.
O
O2S
N
References and notes
N
H
Et
N
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O2S
6g
9.6
—
—
N
H
Et
Me
N
O
10a
18.2
N
N
O
O
10b
13a
8.8
1.7
—
NH
1600
MeSO2
H
HN
S
N
13b
13c
Ph
4.0
—
—
HN
HO
O
OH
OH
21.3
OH
O
HN
HO
OH
OH
13d
17.4
—
11. Dumaitre, B.; Dodic, N. J. Med. Chem. 1996, 39, 1635.
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Data are the mean of two independent assays, each performed in duplicate.
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and PDE5/10a complexes revealed the detailed binding mode of
the two inhibitors with the catalytic domain of PDE5, though only
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inhibition activities (77 and 18.2 nM) of the two compounds.
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