A convenient, highly selective and eco-friendly N-Boc protection of pyrimidines under microwave irradiation

Article abstract of DOI:10.1039/c4ra13033b

Protected pyrimidine nucleobases are of major importance as intermediates in the synthesis of nucleoside analogues and molecules with biological interests. We describe herein a novel practical microwave-assisted N-Boc protection of pyrimidine nucleobases under mild conditions using silica gel, avoiding treatment steps, and in increased yield.

Full text of DOI:10.1039/c4ra13033b

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A convenient, highly selective and eco-friendly N-
Boc protection of pyrimidines under microwave
irradiation†
Cite this: RSC Adv., 2014, 4, 59747
Received 5th October 2014
Accepted 5th November 2014
*
Maxime Bessieres, Vincent Roy and Luigi A. Agrofoglio
`
DOI: 10.1039/c4ra13033b
www.rsc.org/advances
Protected pyrimidine nucleobases are of major importance as inter-
Among these groups, one of the most used is the Boc; it's
mediates in the synthesis of nucleoside analogues and molecules with stable towards most nucleophiles and bases12 and it can be
biological interests. We describe herein a novel practical microwave- removed cleanly and selectively under neutral conditions.13 This
assisted N-Boc protection of pyrimidine nucleobases under mild is of particular interest when working with biolabile groups
conditions using silica gel, avoiding treatment steps, and in increased such as found in nucleoside prodrugs.14 Surprisingly, only two
yield.
teams have reported the synthesis of N-Boc-protected pyrimi-
dines under basic conditions and in two steps. Gothelf et al.15
have prepared the N3-Boc-protected thymine (6) through the
formation of N1,N3-di-Boc protected derivative and subsequent
selective deprotection of N1-Boc group with K2CO3 in dioxane,
in only 31% overall yield (Fig. 2). Porcheddhu et al.16 have
described the synthesis of N4,N4-di-Boc cytosine (7) in two steps
in moderate 60% yield, via the fully Boc protected cytosine
which was then treated with aq. NaHCO3 in MeOH at reux.
However, in spite of their potential utility, these methods suffer
from some drawbacks such (a) a long reaction time implied by
the rst step, (b) unsatisfactory yields of the deprotection step
and (c) cumbersome product isolation procedures. Thus, we
present herein, a greener practical protocol to selectively
synthesize N1-free, N3-Boc protected pyrimidine nucleobases
(5–7, 8a–c) under milder conditions, shorter reaction time and
in moderate to quantitatively yields.
Pyrimidine systems are found in many drugs which interact with
the synthesis and functions of nucleic acids such as the anti-
tumor drug uorouridine1 (1), the anti-HIV drug lamivudine2 (2)
or the anti-HBV drug telbivudine3 (3), or the antimalarial drug
pyrimethamine4 (4), (Fig. 1), to only quote some of them.
As chemical modications of nucleobases are of paramount
importance in the development of new drugs,5 their syntheses
have been largely described.6 Focusing on the base moiety, a key
step is the choice of the appropriate protecting groups for the N1
and N3 atoms of pyrimidines which have to meet several
requirements such as: a differential protection at N1 and N3, a
selective deprotection, and a removal under mild reaction condi-
tions. There is an abundant literature relating to the protection of
amino groups, such as by 9-uorenyl-methoxycarbonyl (FMOC),7
tert-butyl carbamates (Boc), benzyl carbamate, benzamide, acet-
amide,8 phtalimides,9 triphenyl methyl amide10 and tosylamide.11
The general strategy involves two steps: (1) the use of
microwave irradiation to reach quantitatively the fully protected
pyrimidines (10a, b) and (2) the subsequent selective
N1-deprotection by treatment with SiO2 (ref. 17) in
diethoxymethane/ethanol (9 : 1) as an eco-friendly surrogate to
CH2Cl2/MeOH, to desired compounds 5 and 6, respectively
Fig. 1 Chemotherapeutics containing a pyrimidine moiety.
´
´
´
ICOA UMR CNRS 7311, Universite d'Orleans, Orleans, France. E-mail: luigi.
agrofoglio@univ-orleans.fr; Tel: +33-2-3849-4582
† Electronic supplementary information (ESI) available: General procedure and
1H, 13C NMR spectra are provided. See DOI: 10.1039/c4ra13033b
Fig. 2 Structure of monoprotected pyrimidic nucleobases.
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Table 1 Preparation of N3-tert-butylcarbonyluracil (5) by selective
deprotection of 10a with SiO2
(Scheme 1). It is important to quote that microwave activation,
which ensures shorter reaction time, cleaner reactions and
which has been applied to nucleosides and their precursors,18
has never been reported for either the Boc-protection or
deprotection of pyrimidines.
Entry Solvent
Temperature Reaction time Yield (%)
1a
2a
3
DCM
RT
5 h
1 h 30 min
12 h
1 h
2 min
43
93
77
96
97
DCM/MeOH (9/1) RT
DCM/MeOH (9/1) RT
DCM/MeOH (9/1) 60 ꢀ
Thus, starting with uracil 9a, we applied the microwave
assisted, solvent-free and catalyst-free procedure reported by
Dighe et al.19 Unfortunately, in our hands, probably due to the
insolubility of uracil derivatives in Boc2O, the expected
compounds were not isolated. We moved then to a solution-
phase preparation of N1,N3-di-Boc uracil (10a) under micro-
wave irradiation in dry diethoxymethane (DEM) as a replace-
ment of THF, with an excess of Boc2O, in presence of 0.35
equivalents of 4-N,N-(dimethylamino)pyridine (DMAP) at 70 ꢀC.
It is interesting to quote that DEM is an attractive alternative to
conventional solvents as it is an eco-responsible solvent, with
unique properties,20 which make it a green industrial solvent.
Aer evaporation of all volatiles, compound 9a was almost
quantitatively converted to 10a (based on TLC) and was engaged
in the next step without the need for further purication. Table
1 summarizes the different conditions used for the N1 regio-
selective deprotection of 10a to 5.
Based on the work of Zhang et al.,17 the N1,N3-di-(Boc) uracil
(10a) was reacted with SiO2 in dichloromethane (entry 1). To
avoid the full deprotection, the reaction was performed at room
temperature and monitored by TLC. Aer 5 hours, the reaction
was stopped by simple evaporation of volatiles, affording a solid
deposit for ash chromatography. Under this condition, 5 was
obtained in 44% yield. When increasing the polarity to CH2Cl2/
MeOH (9/1), the desired compound 5 was afforded in 90
minutes at room temperature, in 93% yield (entry 2). The
benets of SiO2 was conrmed (entry 3) observing the dramat-
ically decreased yield from 93% to 77% yield obtained aer 12
hours whereas the activation of the reaction over classical
heating increases the yield and reduces the reaction time (entry
4). With our interest in shorter reaction time, the previous
conditions were optimized under microwave activation to afford
quantitatively the desired compound (entry 5).
4a
5a
C
DCM/MeOH (9/1) MW, 70 ꢀC
a
Reaction performed with SiO2 (60% w/w).
Scheme 2 Derivation at N1 position for NMR study.
Structure of 12 was determined by HMBC experiment, con-
rming the regioselectivity the deprotection step (Fig. 3).
Then we turned our attention to C5-halopyrimidines which
are of great interest as useful synthetic building blocks for
further C5 modications. Surprisingly when applying this two-
steps procedure to the C5-halogenopyrimidines (13a–c), we
observed the minor formation of the expected N3-Boc uracils
(8a–c) concomitant with the major N3-alkylation with a tert-
butyl group (14a–c, respectively) (Scheme 3).
To explain the formation of 14a–c, we hypothesized that: (1)
under our conditions (e.g. slightly acidic), the s-electron with-
drawing effect of the C5-halogens (uoro, chloro, and bromo)
can help to release the Boc at N3, and (2) the more nucleophilic
N3 obtained can react with the released isobutene under
microwave heating in closed vials. When the deprotection step
was performed under ultrasounds, due to their “degassing
Following the same procedure, N1 protected thymine (6) was
obtained in good overall yields from 9b. This straight method
offers thus a direct solid deposit for ash chromatography aer
evaporation of all volatiles, avoiding any pre-treatment.
To investigate the nal regioselectivity of the Boc derivatives
(N1 versus N3), the N1-alkylation was performed and the selec-
tivity fully determined by NMR. For instance, compound 6 was
derivatized to 12 with ethyl bromoacetate in the presence of
K2CO3) (Scheme 2).
Scheme 1 General approach to N1 free, N3-Boc-pyrimidines.
59748 | RSC Adv., 2014, 4, 59747–59749
Fig. 3 HMBC NMR analysis of 12.
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Acknowledgements
We are grateful for nancial support from the FEDER (project
COSMI), the Region Centre, the University of Orleans and the
LabEx SYNORG (ANR-11-LABX-0029).
Notes and references
1 D. K. Goette, J. Am. Acad. Dermatol., 1981, 4, 633–649.
2 W. Choi, R. Schinazi, L. J. Wilson, S. Yeola and D. C. Liotta, J.
Am. Chem. Soc., 1991, 113, 9377–9379.
Scheme 3 Deprotection of bis-Boc halogenated uracils.
3 A. Holy, Collect. Czech. Chem. Commun., 1972, 37, 4072–4087.
4 H. M. McIntosh, from The Cochrane Library, Update Soware
Ltd, 2001, Issue 4.
5 K. I. Kimura and T. D. H. Bugg, Nat. Prod. Rep., 2003, 20, 252–
273.
6 (a) D. J. Brown, The Pyrimidines, Wiley-Interscience, New
York, 1970; (b) D. J. Brown, in Comprehensive Heterocyclic
Chemistry, Pergamon Press, Oxford, 1984, vol. 3, p. 84; (c)
I. M. Lagoja, Chem. Biodiversity, 2005, 2, 1–48.
7 L. A. Carpino and G. Y. Han, J. Org. Chem., 1972, 37, 3404–
3409.
effect”, only the unprotected C5-halogenated uracils were iso-
lated in quantitatively yields.
In order to be as eco-friendly as possible, we have extended
the investigation of the DEM/EtOH solvent system, phasing out
the dichloromethane and in a less extend, the methanol. Under
our optimized conditions (e.g., slightly acidic SiO2 under
microwaves), DEM is an attractive replacement solvent for
DCM. Compared to methanol, ethanol is produced by factory
fermentation of food crops and it's more ecological than
methanol.
8 W. Green and P. G. M. Wuts, in Protective groups in Organic
Synthesis, John Wiley & Sons, New York, 3rd edn, 1999.
9 P. Y. Reddy, S. Kondo, T. Toru and Y. Ueno, J. Org. Chem.,
1997, 62, 2652–2654.
10 M. Soroka and J. Zygmunt, Synthesis, 1988, 5, 370–372.
11 B. Nyasse, L. Greyn, H. L. S. Maia, L. S. Monteiro and
U. Ragnarsson, J. Org. Chem., 1999, 64, 7135–7139.
12 (a) A. Sarkar, S. R. Roy, N. Parikh and A. K. Chakraborti, J.
Org. Chem., 2011, 76, 7132–7140; (b) E. A. Englund,
H. N. Gopi and D. H. Appella, Org. Lett., 2004, 6, 213–215;
(c) R. Moumne, S. Lavielle and P. Karoyan, J. Org. Chem.,
2006, 71, 3332–3334; (d) D. M. Shendage, R. Froehlich and
G. Haufe, Org. Lett., 2004, 6, 3675–3678.
13 J. R. Hwu, M. L. Jain, S.-C. Tsay and G. H. Hakimelahi,
Tetrahedron Lett., 1996, 37, 2035–2038.
14 M. Hamada, V. Roy, T. R. McBrayer, T. Whitaker, C. Ubina-
Blanco, S. P. Nolan, J. Balzarini, R. Snoeck, G. Andrei,
R. F. Schinazi and L. A. Agrofoglio, Eur. J. Med. Chem.,
2013, 67, 398–408.
Thus, the nal optimized conditions were SiO2 60% w/w in
DEM/EtOH (9/1) under microwaves irradiation. Applied to
cytosine, the N4,N4-di-Boc cytosine 7 was reached through 15 in
2 minutes under microwaves at 70 ꢀC with more than 97% yield
(Scheme 4).
In summary, we have accomplished a convenient, highly
selective and eco-friendly N-Boc protection of some pyrimidine
nucleobases (5–7, 8a–c) under microwave irradiation. The mild
and heterogeneous conditions are provided by SiO2, acid
enough to support the deprotection of carbamates. The micro-
wave irradiation has proved to be the most efficient synthesis
route, giving the desired compounds with quantitative (for 5–7)
or moderate (for 8a–c) yields, in short reaction times. The eco-
friendly diethoxymethane and ethanol were chosen as a
greener alternative to more toxic dichloromethane and meth-
anol, respectively. These advantages make from these reactions
some powerful ecological alternatives, optimizing the synthesis
of Boc-thymine and bis-Boc-cytosine and creating a synthetic
way for Boc-uracil. This environmentally friendly approach
represents a promising way to synthesize these necessary
building blocks for the synthesis of nucleosides, of utmost
importance in medicinal chemistry.
15 M. F. Jacobsen, M. M. Knudsen and K. V. Gothelf, J. Org.
Chem., 2006, 71, 9183–9190.
16 (a) A. Porcheddu, G. Giacomelli, I. Piredda, M. Carta and
G. Nieddu, Eur. J. Org. Chem., 2008, 5786–5797; (b) T. S. Li,
S. F. Lu, L. Xing, G.-C. Lin, Z. Ghuan and Z.-J. Yang, J.
Chin. Pharm. Sci., 2010, 19, 436–442.
17 M.-J. Zhang, X.-H. Yuan, M. Li, J.-Y. Zhao and L.-X. Gao,
Chem. Res. Chin. Univ., 2007, 12, 2330–2332.
`
18 V. Roy, U. Pradere and L. A. Agrofoglio, Future Med. Chem.,
2010, 2, 177–192.
19 S. N. Dighe and H. R. Jadhav, Tetrahedron Lett., 2012, 53,
5803–5806.
20 N. W. Boaz and B. Venepalli, Org. Process Res. Dev., 2001, 5,
127–131.
Scheme 4 Synthesis of derivative 7 under eco-friendly conditions.
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