Study on the synthesis of 6-alkylaminouridines via the nucleophilic aromatic substitution reaction of 6-cyanouridine derivatives

Article abstract of DOI:10.1016/j.tetlet.2011.05.033

6-Cyanouracil derivatives underwent direct substitution reactions with selective primary amines in the presence of N,N-dimethylaminopyridine as a catalyst to give the corresponding 6-alkylaminouracils. This reaction provides a facile access to versatile 6

Full text of DOI:10.1016/j.tetlet.2011.05.033

Tetrahedron Letters 52 (2011) 3969–3972
Contents lists available at ScienceDirect
Tetrahedron Letters
journal homepage: www.elsevier.com/locate/tetlet
Study on the synthesis of 6-alkylaminouridines via the nucleophilic
aromatic substitution reaction of 6-cyanouridine derivatives
⇑
Jian-Bang Lin, Jhih-Li He, Yu-Chiao Shih, Tun-Cheng Chien
Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
a r t i c l e i n f o
a b s t r a c t
Article history:
6-Cyanouracil derivatives underwent direct substitution reactions with selective primary amines in the
presence of N,N-dimethylaminopyridine as a catalyst to give the corresponding 6-alkylaminouracils. This
reaction provides a facile access to versatile 6-alkylaminouridine derivatives.
Ó 2011 Elsevier Ltd. All rights reserved.
Received 21 February 2011
Revised 25 April 2011
Accepted 9 May 2011
Available online 18 May 2011
Keywords:
6-Cyanouracil
6-Cyanouridine
6-Alkylaminouracil
6-Alkylaminouridine
Nucleophilic aromatic substitution
6-Aminouridine derivatives have received considerable atten-
tion because of their interesting chemical and biological properties.
They could serve as precursors for the synthesis of uridine-fused
bicyclic nucleosides.1–8 Besides, some of the derivatives have been
shown to exhibit a variety of biological activities.9–13 The most
intriguing is their potent inhibitory effects against orotidine 50-
monophosphate decarboxylase (ODCase) which has been corre-
lated with antiparasitic and anticancer activities.9–11
A perusal of the literature revealed that there are only few syn-
thetic routes available for the preparation of the 6-aminouridine
derivatives.4,5,8–11,13–16 The most straightforward approach has
used the direct substitution of 6-iodouridine derivatives with var-
ious amines.9–11,13,14 However, the synthesis of 6-iodouridines by
lithiation–iodination of sugar-protected uridines suffered lower
yields and limited scales,17,18 which has restricted the synthesis
of 6-aminouridines.
(A)
Me
O
O
Me
O
N
-butylamine
reflux
N
n
-Bu
n
O
N
CN
CN
N
N
H
Me
Me
1
2a
(B)
O
O
R-5'-P =
ODCase
mutant
2-O3P
O
HN
HN
O
O
N
O
N
NH-Lys-Enz
HO
OH
R-5'-P
6-CN-UMP
R-5'-P
UMP-enzyme complex
Scheme 1.
The reactions of 6-cyanouracil derivatives reported by Senda
et al. in 1970s have received our attention. When 6-cyano-1,3-dim-
ethyluracil (6-CN-1,3-DMU, 1) was reacted with n-butylamine, the
6-cyano group was substituted by the incoming nucleophile to give
6-n-butylamino-1,3-dimethyluracil (6-n-BuNH-1,3-DMU, 2a) in a
good yield (Scheme 1A).19–21 Furthermore, an enzymatic conver-
and enzymatic reactions suggested that the unique nucleophilic
substitution of 6-cyanouracils could be amenable for the synthesis
of the 6-aminouridine derivatives. Meanwhile, understanding the
chemical reactions of 6-cyanouracil derivatives could open up an
opportunity to gain a mechanistic insight of ODCase.25 Herein,
we report our studies on the synthesis of 6-alkyluridines via the
nucleophilic aromatic substitution reaction of 6-cyanouridine
derivatives.
The reaction with a non-nucleoside model was first investigated
in order to establish the reaction condition. 6-CN-1,3-DMU (1),
prepared from 5-bromouracil by the literature procedures,19–21
was heated solely with n-butylamine as the solvent to give
sion of 6-cyanouridine 50-monophosphate (6-CN-UMP) to
a
covalent Lys–UMP complex was observed by which the cyano
group of 6-CN-UMP was replaced by the Lys residue in the active
site of an ODCase mutant (Scheme 1B).22–24 Both the chemical
⇑
Corresponding author. Tel.: +886 2 7734 6126; fax: +886 2 2932 4249.
E-mail address: tcchien@ntnu.edu.tw (T.-C. Chien).
0040-4039/$ - see front matter Ó 2011 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tetlet.2011.05.033

3970
J.-B. Lin et al. / Tetrahedron Letters 52 (2011) 3969–3972
Table 1
tion product (2b) in a very good yield but surprisingly none of
the other secondary amines could react with 6-CN-1,3-DMU (1).
Primary amines with branched -carbons, including aliphatic and
aromatic primary amines, were examined and none of them could
give the desired products (entries 5–8). Only the treatment of 6-
CN-1,3-DMU (1) with allylamine or aqueous methylamine gave
the desired substituted products (2c–d) (Table 2). The survey of
the reaction indicated that 6-CN-1,3-DMU (1) could only react with
Reaction of 6-CN-1,3-DMU (1) with n-butylamine
O
O
a
-butylamine
solvent
n
Me
O
Me
O
N
N
-Bu
n
additive
reflux
N
CN
N
N
H
Me
Me
1
2a
Timea (h)
pyrrolidine and primary amines with unbranched a-carbons.
Entry
Solvent
Additive
Yieldb
Subsequently, the reaction was applied to the 6-cyanouridine
derivatives. 50-O-(tert-Butyldimethylsilyl)-20,30-O-isopropylidene-
6-cyanouridine (3), readily prepared from 5-bromouridine,26 was
heated with a variety of amines as solvents and reactants in the
presence of a catalytic amount of DMAP. As expected in accordance
with the model reactions, the sugar-protected 6-cyanouridine 3
could react with pyrrolidine (entry 2) and a variety of primary
amines with unbranched a-carbons (entries 5–9) to afford the cor-
responding sugar-protected 6-alkylaminouridines (4a–f) in good
yields (Scheme 2 and Table 3).
Although the reaction is effective, the major drawback is the use
of a large excess of alkylamines as solvents for the reaction.
1
2
3
4
5
6
—
—
—
—
—
3
84%
DMFc
>12
>12
18
23
24
N.D.d
N.R.e
22%
Dioxanec
CH3CNc
CH3CNc
EtOHc
DMAP (0.1 equiv)
DMAP (0.1 equiv)
68%
58%f
a
b
c
d
e
f
Until 6-CN-1,3-DMU (1) was completely consumed.
Isolated yield.
n-BuNH2/solvent = 1:1 (v/v).
N.D. = no desired product.
N.R. = no reaction.
Also obtained 1,3-dimethyl-6-ethoxyuracil (17%).
Table 2
O
N
O
N
Reaction of 6-CN-1,3-DMU (1) with various amines
HN
HN
O
O
R1
R2
R1
Table 3
Me
O
Me
O
NH (amine)
additive
O
CN
O
N
2b R1, R2 = -(CH2)4-
N
N
R2
1
2
TBSO
TBSO
2c
R = H, R = allyl
or
Table 4
R1
O
O
2d R1 = H, R2 = Me
N
CN
N
N
Me R2
temperature
Me
O
O
O
O
1
2b-d
Entry Amine
Additive
(0.1 equiv)
Timea
(h)
Product
(yield)b
3
4a-g
O
1
2
3
4
5
6
Diethylamine
Pyrrolidine
Piperidine
Morpholine
Isopropylamine
Cyclopentylamine DMAP
DMAP
—
DMAP
DMAP
DMAP
>12
3
N.R.c
5a R1, R2 = -(CH2)4- (N.D.)
2b (81%)
HN
TFA / H2O
= 8 : 2 (
N.R.c
1
2
>12
>12
>12
>12
>12
>12
6
5b
R = H, R = allyl (92%)
R1
)
N.R.c
v/v
O
N
N
R2
5c R1 = H, R2 = -Bu (93%)
i
n
N.R.c
1
2
5d
5e
R = H, R = -Bu (93%)
HO
0 oC ~ r. t.
N.D.d
O
1
2
R = H, R = MeO(CH2)3- (80%)
7
Cyclohexylamine
Aniline
DMAP
DMAP
DMAP
—
N.D.d
5f R1 = H, R2 = Bn (94%)
8e
9
N.R.c
1
2
5g
R = H, R = Me (76%)
HO
OH
Allylamine
2c (45%)
2d (30%)
N.D.d,h
5a-g
10
11
Methylaminef
Ammoniag
1.5
>12
DMAP
Scheme 2.
a
b
c
Until 6-CN-1,3-DMU (1) was completely consumed.
Isolated yield.
N.R. = no reaction.
N.D. = no desired product.
Reaction temperature = 150 °C.
40% aqueous solution.
d
e
f
Table 3
Reaction of 50-O-(tert-butyldimethylsilyl)-20,30-O-isopropylidene-6-cyanouridine (3)
with various amines
g
h
28% aqueous solution.
Hydrolyzed product, recovered only 1,3-dimethyluracil-6-carboxamide.
Entrya Amine
Temperature Timeb
(h)
Product
(yield)c
1
2
3
4
5
6
7
8
Diethylamine
Pyrrolidine
Piperidine
Reflux
Reflux
Reflux
120 °C
Reflux
Reflux
Reflux
Reflux
>12
6
>12
>12
8
7
6
4
N.R.d
4a (45%)
6-Bu-NH-1,3-DMU (2a) in 84% yield, which is in agreement with
Senda’s observation.25 (entry 1 in Table 1) The reaction of 6-CN-
1,3-DMU (1) with n-butylamine in various solvents was also
tested. The results showed that the use of solvents decreased the
yields. In addition, the substitution reaction could be improved
by the addition of a catalytic amount of N,N-dimethylaminopyri-
dine (DMAP). On the basis of the preliminary results, we chose to
use the alkylamines as solvents and reactants for subsequent
studies.
To explore the scope and generality, the reactions of 6-CN-1,3-
DMU (1) with a variety of alkylamines were performed and the re-
sults were summarized in Table 2. In the reactions with secondary
amines (entries 1–4), pyrrolidine was found to give the substitu-
N.R.d
Aniline
N.D.e
Allylamine
Isobutylamine
n-Butylamine
3-
Methoxypropylamine
Benzylamine
Methylaminef
4b (53%)
4c (60%)
4d (53%)
4e (56%)
9
10
100 °C
Reflux
6
>12
4f (64%)
N.D.e
a
b
c
d
e
f
Additive = DMAP (0.1 equiv).
Until 6-CN-1,3-DMU (1) was completely consumed.
Isolated yield.
N.R. = no reaction.
N.D. = no desired product.
40% aqueous solution.

J.-B. Lin et al. / Tetrahedron Letters 52 (2011) 3969–3972
3971
Table 4
Reaction of 50-O-(tert-butyldimethylsilyl)-20,30-O-isopropylidene-6-cyanouridine (3) with various amines with absolute ethanol as the solvent in a stainless steel vessel
Entrya
Amine
Solvent
Temperature
Timeb(h)
Product (yield)c
1
2
3
4
n-Butylamine
Benzylamine
EtOHd,e
EtOHd,f
EtOHg
100 °C
120 °C
80 °C
3
4
3
>12
4d (54%)
4f (57%)
4g (55%)
N.D.h
Methylamineg
Cyclopentylamine
EtOHd,f
Reflux
a
b
c
Additive = DMAP (0.1 equiv).
Until 6-CN-1,3-DMU (1) was completely consumed.
Isolated yield.
Absolute ethanol.
n-BuNH2/EtOH = 1:2 (v/v).
BnNH2/EtOH = 1:4 (v/v), BnNH2 = approximately 10 equiv.
33 wt % solution in absolute ethanol.
N.D. = no desired product.
d
e
f
g
h
Therefore, the reaction requires an appropriate solvent in order to
reduce the amine components to a stoichiometric magnitude. Our
investigation has shown that the reaction could be carried out with
ethanol as the solvent by heating above its boiling point in a sealed
stainless steel reactor. For instance, the sugar-protected 6-cyano-
uridine 3 with methylamine, n-butylamine or benzylamine in eth-
anol was heated in the sealed reactor to give the products (4d, 4f
and 4g) in good yields (Table 4). It is noteworthy that the volatile
methylamine is also applicable to the reaction. The sealed reaction
condition enhanced the reactivity of the alkylamines and allowed
the amount of alkylamines to be reduced to 10 equiv to maintain
comparable yields. Nevertheless, the reaction scope is still limited
uridine (8) was prepared from 5-bromouridine (6) and was sub-
jected to the reaction with pyrrolidine to give the sugar-
protected 6-(pyrrolidin-1-yl)uridine (9). Subsequent deprotection
with tetra-n-butylammonium fluoride (TBAF) afforded the desired
6-(pyrrolidin-1-yl)uridine (5a) (Scheme 3).
The limited scope of the alkylamine reactants for the substitu-
tion has led us to examine the reaction of 6-cyanouracil derivatives
with other strong and less hindered nitrogen nucleophiles, includ-
ing hydroxylamine and azide. The reaction of 6-CN-1,3-DMU (1)
with hydroxylamine in EtOH under reflux provided 1,3-dimethyl-
uracil-6-carboxamidoxime (10a) as the only product. Meanwhile,
6-CN-1,3-DMU (1) was heated with sodium azide and ammonium
chloride in DMF and only 1,3-dimethyl-6-(tetrazol-5-yl)uracil
(10b) was obtained from the reaction (Scheme 4). The results indi-
cated that the addition of hydroxylamine or azide to the nitrile
took place instead of the direct displacement of the cyano group
of 6-cyanouracil derivatives.
In a similar fashion, the sugar-protected 6-cyanouridine 3 was
reacted with hydroxylamine and sodium azide, respectively, to
give the corresponding carboxamidoxime (11a) and tetrazole
(11b and 11b0) adducts in good yields. It is noteworthy that the
TBS group was partially deprotected in the reaction with sodium
azide and ammonium chloride. Nonetheless, several attempts to
remove the acid-labile isopropylidene and TBS groups from 11a
and 11b/11b0 were unsuccessful. Alternatively, both reactions were
carried out with the sugar-unprotected 6-cyanouridine 12.26 While
the reaction of 6-cyanouridine 12 with hydroxylamine gave a com-
plicated result and did not afford the desired uridine-6-carbo-
xamidoxime (13a), 6-(tetrazol-5-yl)uridine (13b) was formed in a
good yield from the reaction of 6-cyanouridine 12 with sodium
azide (Scheme 5).
to the primary amines with unbranched
as an exception.
a-carbons and pyrrolidine
The acid-labile isopropylidene and t-butyldimethylsilyl (TBS)
groups of 4b–g were deblocked with aqueous trifluoroacetic acid
(TFA) to give the desired 6-alkylaminouridines 5b–g in good yields.
However, deprotection of 50-O-(tert-butyldimethylsilyl)-20,30-O-
isopropylidene-6-(pyrrolidin-1-yl)uridine (4a) under various
acidic media only resulted in the deglycosylation, which suggested
that the target compound 5a is unstable toward acidic conditions
(Scheme 2). In order to obtain the deprotected product 5a, our ini-
tial attempt was to apply the substitution reaction to the unpro-
tected 6-cyanouridine26 (12), but the reaction gave a complicated
result in which 6-(pyrrolidin-1-yl)uridine (5a) was not obtained.
This unforeseen difficulty prompted us to replace the isopropyli-
dene with two TBS groups to avoid the acidic deprotection step
in the synthesis. Hence, 20,30,50-tri-O-t-butyldimethylsilyl-6-cyano-
O
N
O
N
Br
HN
HN
In summary, our investigation has demonstrated the versatile
reactivities of 6-cyanouracil derivatives toward different nitrogen
b
O
O
CN
RO
a
TBSO
O
O
O
RO
6
7
OR
TBSO
OTBS
Me
N
R = H
R = TBS
8
N
a
b
O
N
OH
O
O
N
O
NH2
Me
Me
O
HN
HN
N
10a
c
d
O
N
N
O
N
N
CN
O
TBSO
HO
O
O
Me
Me
O
N
1
H
N
TBSO
OTBS
HO
OH
N
N
9
5a
Me
N
N
Scheme 3. Reagents and conditions: (a) TBSCl (3.3 equiv), imidazole (6.6 equiv),
DMAP (0.1 equiv), DMF, 0 °C to rt, 8 h, 85%; (b) NaCN (1.5 equiv), DMF, rt, 46 h, 88%;
(c) DMAP (0.1 equiv), pyrrolidine, reflux, 6 h, 30%; (d) 1 M TBAF in THF with 5% H2O,
0 °C to rt, 7.5 h, 92%.
10b
Scheme 4. Reagents and conditions: (a) 50 wt % NH2OH in H2O (2 equiv), EtOH,
reflux, 2 h, 80%; (b) NaN3 (1.2 equiv), NH4Cl (1.2 equiv), DMF, 100 °C, 19 h, 64%.

3972
J.-B. Lin et al. / Tetrahedron Letters 52 (2011) 3969–3972
O
N
O
N
Supplementary data
HN
HN
Supplementary data (1H and 13C NMR spectra for representative
compounds) associated with this article can be found, in the online
version, at doi:10.1016/j.tetlet.2011.05.033.
11a
for
:
R6
a
condition:
O
CN
O
TBSO
R5O
11b 11b'
:
condition:
for
/
O
O
b
References and notes
O
O
O
O
11a / 13a:
R6 =
1. Hossion, A. M. L.; Islam, R.; Kandahary, R. K.; Nagamatsu, T. Synthesis 2009,
2689–2696.
2. Nagamatsu, T.; Islam, R.; Ashida, N. Heterocycles 2007, 72, 573–588.
3. Hirano, T.; Kuroda, K.; Kodama, H.; Kataoka, M.; Hayakawa, Y. Lett. Org. Chem.
2007, 4, 530–534.
4. Itoh, T.; Ishikawa, I.; Tomii, Y.; Mizuno, Y.; Ogura, H.; Kawahara, N. Heterocycles
1990, 30, 231–235.
5. Mizuno, Y.; Watanabe, Y.; Ikeda, K. Chem. Pharm. Bull. 1974, 22, 1198–1200.
6. Jochims, J. C.; Pfleiderer, W.; Kobayashi, K.; Ritzmann, G.; Hutzenlaub, W. Chem.
Ber. 1973, 106, 2975–2981.
N
OH
3
11a R5 = TBS (70%)
NH2
5
11b
11b'
R = TBS (43%)
5
11b 11b' 13b
/
/
:
R = H (47%)
R6 =
c
N
N
HN
N
O
N
O
7. Ikeda, K.; Sumi, T.; Yokoi, K.; Mizuno, Y. Chem. Pharm. Bull. 1973, 21, 1327–
1337.
HN
HN
for 13a:
condition:
O
CN
O
N
R6
a
8. Lipkin, D.; Cori, C. F.; Rabi, J. A. J. Heterocycl. Chem. 1969, 6, 995–996.
9. Bello, A. M.; Konforte, D.; Poduch, E.; Furlonger, C.; Wei, L.; Liu, Y.; Lewis, M.;
Pai, E. F.; Paige, C. J.; Kotra, L. P. J. Med. Chem. 2009, 52, 1648–1658.
10. Bello, A. M.; Poduch, E.; Liu, Y.; Wei, L. H.; Crandall, I.; Wang, X. Y.; Dyanand, C.;
Kain, K. C.; Pai, E. F.; Kotra, L. P. J. Med. Chem. 2008, 51, 439–448.
11. Poduch, E.; Bello, A. M.; Tang, S. H.; Fujihashi, M.; Pai, E. F.; Kotra, L. P. J. Med.
Chem. 2006, 49, 4937–4945.
12. Aso, M.; Ikeno, T.; Norihisa, K.; Tanaka, M.; Koga, N.; Suemune, H. J. Org. Chem.
2001, 66, 3513–3520.
13. Pan, B.-C.; Chen, Z.-H.; Chu, E.; Chu, M.-Y. W.; Chu, S.-H. Nucleosides Nucleotides
1998, 17, 2367–2382.
14. Tanaka, H.; Hayakawa, H.; Haraguchi, K.; Miyasaka, T. Nucleosides Nucleotides
1985, 4, 607–612.
15. Miyasaka, T.; Tanaka, H.; Satoh, K.; Imahashi, M.; Yamaguchi, K.; Iitaka, Y. J.
Heterocycl. Chem. 1987, 24, 873–875.
16. Shibuya, S.; Ueda, T. Chem. Pharm. Bull. 1980, 28, 939–946.
17. Tanaka, H.; Hayakawa, H.; Shibata, S.; Haraguchi, K.; Miyasaka, T. Nucleosides
Nucleotides 1992, 11, 319–328.
18. Shih, Y. C.; Chien, T. C. Tetrahedron 2011, 67, 3915–3921.
19. Senda, S.; Hirota, K.; Asao, T. Tetrahedron Lett. 1973, 14, 2647–2650.
20. Senda, S.; Hirota, K.; Asao, T. Chem. Pharm. Bull. 1975, 23, 1708–1713.
21. Senda, S.; Hirota, K.; Asao, T. J. Org. Chem. 1975, 40, 353–356.
22. Heinrich, D.; Diederichsen, U.; Rudolph, M. G. Chem. Eur. J. 2009, 15, 6619–
6625.
HO
HO
for 13b:
condition:
O
O
b or d
HO
OH
HO
OH
12
13a
13b
(N. D.)
(b: 87% from
(d: 22% from 12)
12
)
Scheme 5. Reagents and conditions: (a) 50 wt % NH2OH in H2O, EtOH, reflux; (b)
NaN3 (1.2 equiv), NH4Cl (1.2 equiv), DMF, 95 °C; (c) TFA/H2O = 9:1 (v/v), 0 °C,
15 min, 74%; (d) NaN3 (1.2 equiv), DMF, 100 °C, 4 h (N.D. = no desired product).
nucleophiles. The reaction of 6-cyanouracil derivatives with
hydroxylamine or azide involved addition of the nitrogen nucleo-
philes at the nitrile carbons. However, the nucleophilic substitu-
tion reaction took place when 6-cyanouracil derivatives were
reacted with pyrrolidine or primary amines with unbranched
carbons. This novel reaction has provided an alternative approach
a-
toward versatile 6-alkylaminouridine derivatives.
23. Fujihashi, M.; Wei, L. H.; Kotra, L. P.; Pai, E. F. J. Mol. Biol. 2009, 387, 1199–1210.
24. Wiftmann, J. G.; Heinrich, D.; Gasow, K.; Frey, A.; Diederichsen, U.; Rudolph, M.
G. Structure 2008, 16, 82–92.
Acknowledgments
25. Wu, Y. J.; Liao, C. C.; Jen, C. H.; Shih, Y. C.; Chien, T. C. Chem. Commun. 2010, 46,
4821–4823.
26. Fujihashi, M.; Bello, A. M.; Poduch, E.; Wei, L. H.; Annedi, S. C.; Pai, E. F.; Kotra,
L. P. J. Am. Chem. Soc. 2005, 127, 15048–15050.
This work was supported by Research Grant 97-2113-M-003-
001-MY2 from the National Science Council, Taiwan. We are grate-
ful to the National Center for High-performance Computing of Tai-
wan for the electronic resources and facilities.