Improved synthesis of N1-substituted orotic acid derivatives

Article abstract of DOI:10.1016/j.tetlet.2013.05.136

An improved method for the synthesis of N1-substituted orotic acid derivatives is reported. The method involves sequential incorporation of nitrogen atoms to the pyrimidine structure from simple starting materials and thus allows the synthesis of N1-subst

Full text of DOI:10.1016/j.tetlet.2013.05.136

Accepted Manuscript
Improved synthesis of N1-substituted orotic acid derivatives
Nicholas A. Senger, Jeannette T. Bowler, Rene S. Mercado, Sidney Lin,
Weiming Wu
PII:
S0040-4039(13)00927-1
DOI:
http://dx.doi.org/10.1016/j.tetlet.2013.05.136
TETL 43036
Reference:
To appear in:
Tetrahedron Letters
Received Date:
Accepted Date:
14 May 2013
29 May 2013
Please cite this article as: Senger, N.A., Bowler, J.T., Mercado, R.S., Lin, S., Wu, W., Improved synthesis of N1-
substituted orotic acid derivatives, Tetrahedron Letters (2013), doi: http://dx.doi.org/10.1016/j.tetlet.2013.05.136
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Graphical Abstract
.

Tetrahedron Letters
1
TETRAHEDRON
LETTERS
Pergamon
Improved synthesis of N1-substituted orotic acid derivatives
Nicholas A. Senger, Jeannette T. Bowler, Rene S. Mercado, Sidney Lin and Weiming Wu*
Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132 USA
Abstract— An improved method for the synthesis of N1-substituted orotic acid derivatives is reported. The method involves sequential
incorporation of nitrogen atoms to the pyrimidine structure from simple starting materials and thus allows the synthesis of N1-substituted
orotic acid derivatives with single 15N label at either N-1 or N-3. © 2013 Elsevier Science. All rights reserved
of a primary amine to acrylate that yields adduct 5.17,20 The
Keywords: Orotic acid, orotidine, 1-substituted orotic acid,
amino group is converted to the urea group via reaction
with cyanate. Cyclization as a result of the reaction of the
urea group with the ester group gives the 5,6-dihydrouracil
6. Bromination of 6 produces 7, which undergoes thermal
elimination to yield uracil 2.
1-substituted uracil, dihydrouracil, 5-bromouracil
The decarboxylation of orotic acid and its analogues has
been investigated as
a model for the enzymatic
decarboxylation catalyzed by orotidine-5’-monophosphate
decarboxylase (ODCase).1-12 Part of the mechanistic
investigation requires N1-substituted orotic acid derivatives
(structure 1 in Scheme I) as substrates. Direct alkylation of
O
O
H
O
RNH2
KCNO
HCl
OCH3
CH3O
N
orotic acid, unfortunately, produces
a
mixture of
O
HN
R
N
R
6
disubstituted and N3-substituted orotic acid derivatives
because N3 is the more reactive site.13 N1-Substituted
orotic acid derivatives are commonly synthesized from N1-
substituted uracil 2 via 5-bromouracil 3 and 6-cyanouracil 4
as shown in Scheme 1.11,14-16 In this Letter, we report a
simplified synthetic method for such orotic acid derivatives
from readily available 5,6-dihydrouracil derivatives.
5
O
O
H
O
Br
H
Br2
heat
DMF
N
N
HOAc
N
R
7
O
N
R
2
O
O
O
H
O
H
O
Br
H
O
Br2
KCN
DMF
N
N
N
Scheme 2
DMF
N
R
2
N
R
3
N
R
4
CN
In the process of synthesizing N1-substituted uracil
derivatives following this reported synthetic route, we
observed that the bromination of 5,6-dihydrouracil 6
yielded desired product 7 mixed with dibrominated product
8 as shown in Scheme 3. Further experiments of purified
dibromide 8 illustrated that it underwent elimination upon
heating to produce 5-bromouracil 3, analogous to the
conversion of bromide 7 to 2. We have thus thought to
shorten the synthetic route employing 5,5-dibromo-5,6-
dihydrouracil 8 as a synthetic intermediate.
O
4
H
O
1) NaOH
N
2
3
5
6
1
+
2) H3O
N
R
1
CO2H
Scheme 1
A few methods for the synthesis of N1-substituted uracil
derivatives have been reported.17-19 One of the methods
involves sequential integration of the two nitrogen atoms
from simple starting materials (as shown in Scheme 2) and
15
thus will allow incorporation of N at one position only.17
The reported synthesis starts with the conjugated addition
* Corresponding author. Tel.: 1-415-338-1436; fax: 1-415-338-2384; e-mail: wuw@sfsu.edu.

2
Tetrahedron Letters
O
O
O
derivatives or the enzymatic decarboxylation catalyzed by
ODCase.
Br
Br
H
O
H
O
H
O
Br
Br2
N
N
N
HOAc
N
R
6
N
R
8
N
R
3
Experimental Details
All reagents were obtained from commercial sources
and used without further purification. Only the
experimental procedures for the conversion of
Scheme 3
dihydrouracil 6 to 5-bromouracil 3 are described here using
The
products were purified through recrystallization or column
chromatography. Procedures for other synthetic steps were
described in literature and were employed without
modification.
1-cyclohexyl-5,6-dihydrouracil as an example.
The dibromination of 6 to 8 was effected by using more
than two equivalents of bromine. Interestingly, it was
observed that a fraction of dibromide 8 underwent
elimination spontaneously to produce bromouracil 3 under
the reaction conditions (acetic acid, 100 °C). We thought
to further simplify the synthetic route by combining the
bromination and elimination steps. The bromination
reaction was thus carried out in boiling acetic acid. Under
the new reaction condition, dihydrouracil 6 was converted
to 5-bromouracil 3 in one step, in contrast to the three-step
sequence in the original synthesis. The yields for the one-
step reactions were excellent for various primary and
secondary substituting groups (tertiary groups were found
to be labile under the highly acidic reaction conditions as
expected) tested as shown in Table 1. In the case when
cyclohexyl was the substituting group, the yields for the
two synthetic routes were directly compared. The direct
conversion of 6a to 3a (R = cyclohexyl) was found to be
quantitative (the yield is 89% if purified by
recrystallization), whereas the reported yields for the three
synthetic steps were 69% (6a to 7a), 85% (7a to 2a), and
75% (2a to 3a), respectively, giving an overall yield of
44% from 6a to 3a.14,17 Therefore, the modified one-step
Typical experimental procedure: 1-Cyclohexyl-5,6-
dihydrouracil (1.00 g, 5.1 mmol) was dissolved in 12 mL
acetic acid in a round-bottomed flask. A solution of
bromine (3.24 g, 20.2 mmol) in 10 mL acetic acid was
added to the reaction flask and the reaction mixture was
refluxed. The reaction usually took five to six hours and
was followed by thin layer chromatography (TLC). Upon
completion of the reaction, the reaction mixture was
evaporated to dryness under reduced pressure. The solid
residue was purified by either column chromatography
(10% ethyl acetate/methylene chloride as solvent) or
recrystallization from ethanol to produce 5-bromo-1-
cyclohexyluracil as colorless flakes; mp 220-222 °C, lit.
mp 225 °C.17
Acknowledgments
procedure reported here represents
a
significantly
simplified and improved method to synthesize N1-
substituted orotic acid derivatives.
This investigation was supported by the National Institutes
of Health, Grant SC1 GM095419. N.A.S. and J.T.B. were
supported by the Beckman Scholarship. R.S.M. and S.L.
were summer students supported by the BRIDGE Program
(funded by NIH) and Project SEED (the American
Chemical Society), respectively. The NMR facility was
funded by the National Science Foundation (DUE-9451624
and DBI 0521342). We thank Professor Ihsan Erden
(SFSU) for helpful discussions.
Table 1. Yields for the one-step conversion of 5,6-
dihydrouracil 6 to 5-bromouracil 321
Entry 1-Substituted
dihydrouracils (6)
5,6- Yield (isolated)
(%)
1
2
3
4
5
100 (89)a
85
6a, R = cyclohexyl
6b, R = n-butyl
6c, R = n-propyl
6d, R = isobutyl
6e, R = sec-butyl
References
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It should be pointed out again that this synthetic route
allows the incorporation of a single 15N label at either N1 or
N3. Such labeled compounds may aid in the mechanistic
investigation of the model decarboxylation of orotic acid

Tetrahedron Letters
10. Wong, F. M.; Capule, C. C.; Chen, D. X.; Gronert, S.; Wu, 1-n-Propyl-5,6-dihydrouracil 6c. 7.5 (bs, 1H, NH); δ3.4 (m,
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0.9 (t, 3H, CH3).
1-Isobutyl-5,6-dihydrouracil 6d. δ7.6 (s, 1H, NH); 3.4 (t, 2H,
NCH2 ring; 3.2 (d, 2H, NCH2 side chain); 2.7 (t, 2H, CH2CO);
2.0 (sept, 1H, CH); 0.9 (6H, CH3 x 2).
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1-sec-Butyl-5,6-dihydrouracil 6e. δ8.1 (s, 1H, NH); 4.4 (1H,
sext, NCH); 3.3 (2H, m, NCH2); 2.6 (t, 2H, CH2CO); 1.5
(quint, 2H, CH3CH2); 1.2 (d, 3H, CHCH3); 0.9 (t, 3H,
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CH); 3.8 (t, 2H, NCH2); 1.7 (quin, 2H, NCH2CH2), 1.4 (sext,
2H, CH2CH3); 1.0 (t, 3H, CH3).
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CH); 3.7 (t, 2H, NCH2); 1.7 (sext, 2H, CH2CH3); 1.0 (t, 3H,
CH3).
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CH3 x 2).
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1H, H-6); 4.6 (1H, sext, NCH); 1.7 (quint, 2H, CH3CH2); 1.3
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1
21. H NMR data of 6 and 3 in CDCl3:
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4H, CH2NCH2); 2.7 (t, 2H, CH2CO); 1.6 (quin, 2H,
NCH2CH2), 1.3 (sext, 2H, CH2CH3); 0.9 (t, 3H, CH3).

Graphical Abstract
.
Leave this area blank for abstract info.
Improved synthesis of N1-substituted orotic acid
derivatives
Nicholas A. Senger, Jeannette T. Bowler, Rene S. Mercado, Sidney Lin and Weiming Wu*
Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, CA 94132 USA
O
O
O
O
Br
Br
H
O
H
O
H
O
Br
H
O
Br2
N
N
N
N
HOAc
N
R
N
R
N
R
N
R
CO2H