A Systematic Study of the Synthesis of 2-Deoxynucleosides by Mitsunobu Reaction

Article abstract of DOI:10.1055/s-0036-1588445

The Mitsunobu reaction has emerged as an important alternative for the preparation of synthetic 2′-deoxynucleosides, which have various biological and biotechnological applications. In this work, the Mitsunobu-based synthesis of 2′-deoxynucleosides was systematically studied. The effect of phosphine, azodicarbonyl reagent, and solvent on the product yield and α/β ratio was investigated, and the highest yield and β-selectivity were obtained using (n -Bu) ₃ P and 1,1′-(azodicarbonyl)dipiperidine in DMF. The reaction was successfully applied to various nucleobase analogues.

Full text of DOI:10.1055/s-0036-1588445

SYNLETT
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©
Georg Thieme Verlag Stuttgart · New York
2017, 28, A–D
letter
A
en
Synlett
K. Seio et al.
Letter
A Systematic Study of the Synthesis of 2ʹ-Deoxynucleosides by
Mitsunobu Reaction
CANONICAL AND MODIFIED
DEOXYNUCLEOSIDES
Kohji Seio*
PURINE BASES
Munefumi Tokugawa
TBDMSO
X
N
TBDMSO
Kazuhei Kaneko
Takashi Shiozawa
Yoshiaki Masaki
TBDMSO
BASE
O
MITSUNOBU
REACTION
O
O
N
N
OH
H
OR
BASE
TBDMSO
Mitsunobu
reagents
PYRIMIDINE BASES
TBDMSO
BASE =
TBDMSO
Department of Life Science and Technology, Tokyo Institute
of Technology, 4259 Nagatsuta-cho Midori-ku, 226-8501,
Yokohama, Japan
X
N
N
N
or
N
H
N
H
N
N
seio.k.aa@m.titech.ac.jp
Mitsunobu reagents
O
H
N
C
N
P(n-Bu)3
2
Received: 30.03.2017
Accepted after revision: 09.05.2017
Published online: 07.06.2017
persilylation or are sensitive to basic conditions. Thus the
Mitsunobu reaction has emerged as a promising alternative
for the synthesis of nucleosides. For example, Szarek re-
7
DOI: 10.1055/s-0036-1588445; Art ID: st-2017-u0217-l
ported the condensation of aldo- or ketohexoses with 6-
chloropurine, and Chang described the preparation of 2′-C-
Abstract The Mitsunobu reaction has emerged as an important alter-
native for the preparation of synthetic 2′-deoxynucleosides, which have
various biological and biotechnological applications. In this work, the
Mitsunobu-based synthesis of 2′-deoxynucleosides was systematically
studied. The effect of phosphine, azodicarbonyl reagent, and solvent on
the product yield and α/β ratio was investigated, and the highest yield
8
methyl-nucleoside analogues by Mitsunobu reaction. In ad-
9
dition, Hocek and co-workers reported a systematic study
8
of the Mitsunobu-based synthesis of ribonucleosides.
More recently, we have reported the synthesis of fully pro-
tected 7-deaza-6-O-(diphenylcarbamoyl)-7-iodo-2-N-acetyl-2′-
deoxyguanosine2a (1β in Figure 1) by a Mitsunobu reaction
between 3,5-O-bis(tert-butyldimethylsilyl)-2-deoxyribose
and β-selectivity were obtained using (n-Bu) P and 1,1′-(azodicarbon-
3
yl)dipiperidine in DMF. The reaction was successfully applied to various
nucleobase analogues.
1
0
Key words nucleoside synthesis, Mitsunobu reaction, N-glycosida-
tion, stereoselectivity, solvent effects
(2)
and 7-deaza-6-O-(diphenylcarbamoyl)-7-iodo-2-N-
10
acetyl-guanine. Compound 1β was devised as a synthon
of 7-deaza-7-iodo-2′-deoxyguanosine having higher solu-
bility and reactivity in palladium-catalyzed cross-coupling
Synthetic 2′-deoxynucleosides have been widely used as
1
2a
pharmaceutical agents because of their various biological
reactions for further functionalization. In our previous
activities such as antiviral, antifungal, and anticancer prop-
erties. More recently, they have also found application as
precursors for the synthesis of functional nucleic acids such
work, the Mitsunobu reaction proved to be the best method
for the incorporation of the nucleobase containing the base-
labile diphenylcarbamoyl group.
2
as fluorescent nucleic acid probes and chemically modified
To the best of our knowledge, there has not yet been a
systematic study of the Mitsunobu synthesis of 2′-deoxy-
nucleosides. Thus, in this Letter, the use of the Mitsunobu
reaction for the synthesis of deoxynucleosides was system-
atically investigated.
3
genes. In addition to β-nucleosides, which have the same
C1′ configuration of standard deoxynucleosides, the α-iso-
mers are also useful for biotechnological applications such
as the synthesis of triplex-forming oligonucleotides.4
Therefore, methods for the preparation of deoxynucleosides
are important for the development of nucleoside- and oli-
gonucleotide-based technologies. Deoxynucleosides are
typically synthesized by N-glycosylation of a nucleobase
with a 2′-deoxyribose donor, which is activated for nucleo-
philic attack on the anomeric position. The most widely
used 2′-deoxyribose donor is α-1-chloro-3,5-di-O-toluoyl-
3
At first, the reaction between N -benzoylthymine (3)
and 2 in the presence of Ph P and diisopropyl azodicarbox-
3
ylate (DIAD) was studied in various solvents (Table 1, en-
tries 1–5). When THF was used, a mixture of thymidine de-
rivatives 4α and 4β was obtained in 50% yield and in a ratio
1
of 47:53, respectively, as determined by H NMR spectros-
copy (Table 1, entry 1), revealing a slight β-selectivity. On
the other hand, in acetonitrile (Table 1, entry 2) and di-
chloromethane (Table 1, entry 3), the yield was 42% and
57%, respectively, and the α-anomer selectivity increased,
4
deoxyribose, which reacts with nucleobases activated by
5,2b
6
an inorganic base,
such as NaH, or persilylation to ob-
tain the desired nucleosides. However, this method is not
applicable to nucleobases that are not activated by
©
Georg Thieme Verlag Stuttgart · New York — Synlett 2017, 28, A–D

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Synlett
K. Seio et al.
Letter
In the following experiments, we investigated the effect
TBSO
TBSO
O
O
N
of the phosphine structure. The reaction using Et PhP (Ta-
2
N
N
O
O
ble 1, entry 14) produced 4α and 4β in almost the same
NH
Cl
OTBS
OTBS
N
yield and ratio as with n-Bu P (Table 1, entry 6). When a
3
N
5
6
less basic phosphine, namely, MePh P (Table 1, entry 15) or
2
6
0%
α/β = 35:65
18%
α/β = 50:50
Ph P (Table 1, entry 16), was used, the yield decreased but
3
the α/β ratio did not change. In addition, Cy P (Table 1, en-
3
try 17) and (o-Tol) P (Table 1, entry 18) having large cone
3
TBSO
TBSO
O
O
angles were not effective in this reaction. We can therefore
conclude that the yield of the reaction was dependent on
the nature of the phosphine whereas the α/β ratio was not
affected.
N
N
N
O
NH2
NH2
N
OTBS
OTBS
N
N
N
7
8
6
5%
trace
α/β = 30:70
Table 1 Effect of Phosphine, Azodicarbonyl Reagent, and Solvent on
the Product Yield and α/β Ratio in the Mitsunobu-Based Deoxynucleo-
side Synthesis
TBSO
TBSO
O
O
N
N
N
O
CN
OTBS
OTBS
N
NC
NH
9
R3P (3 equiv)
C(O)X
1
0α: 42%
10β: 46%
NH2
n.d.
N
N
X(O)C
TBSO
(3 equiv)
ref. 7
TBSO
I
O
N
O
OH
O
OTBS
O
N
O
O
O
N
OTBS
2
NPh2
(
3 equiv)
TBSO
1
1
α: 23%
N
O
NHAc
N
O
O
β: 61%
solvent
N
H
NBz
r.t., 24 h
OTBS
Figure 1 Application of the Mitsunobu reaction to the synthesis of var-
ious deoxynucleosides
3
4α and 4β
Solvent
X
R3
Yield (%)a 4α/4βb
leading to a 4α/4β ratio of 59:41 and 61:39, respectively. In-
terestingly, when the amide-type solvents DMF (Table 1,
entry 4) and DMA (Table 1, entry 5) were used, the yield in-
creased to 79% and 62%, and the ratio of 4α/4β was 30:70
and 47:53, respectively. These results show that the α/β se-
lectivity was dependent on the solvent used, and DMF was
the best solvent in terms of both yield and β-selectivity.
Next, the 1,1′-(azodicarbonyl)dipiperidine (ADDP)-P(n-
Bu)311 reagent system was applied to our transformation. It
has been reported that the nitrogen anion intermediate
generated from ADDP is more basic than the corresponding
anion generated from DIAD; thus, ADDP can activate nucle-
1
2
3
4
5
6
7
8
9
THF
isopropyloxy
isopropyloxy
isopropyloxy
isopropyloxy
isopropyloxy
piperidin-1-yl
piperidin-1-yl
piperidin-1-yl
piperidin-1-yl
piperidin-1-yl
piperidin-1-yl
piperidin-1-yl
piperidin-1-yl
piperidin-1-yl
piperidin-1-yl
piperidin-1-yl
piperidin-1-yl
piperidin-1-yl
Ph3
50
42
57
79
62
95
95
25
6
47:53
59:41
61:39
30:70
47:53
37:63
50:50
61:39
66:34
58:42
63:37
70:30
54:46
38:62
32:68
32:68
–
MeCN
Ph
Ph
Ph
Ph
3
3
3
3
2 2
CH Cl
DMF
DMA
DMF
DMA
THF
n-Bu
n-Bu
n-Bu
n-Bu
n-Bu
n-Bu
3
3
3
3
3
3
1,4-dioxane
MeCN
1
0
61
13
8
11
2 2
CH Cl
ophiles with pK values >13, and is therefore expected to be
a
useful for the reaction of a wider variety of synthetic nucle-
12
13
toluene
pyridine
DMF
n-Bu3
n-Bu3
osides. As shown in Table 1, entry 6 the ADDP-P(n-Bu) sys-
3
9
tem in DMF gave the highest yield (95%) and high β-selec-
tivity (4α/4β = 37:63). The reaction in DMA (Table 1, entry
14
15
16
Et
2
Ph
94
87
34
n.d.c
n.d.c
DMF
MePh
2
7) gave the same yield, but no stereoselectivity was ob-
DMF
Ph
3
3
served. On the other hand, when THF (Table 1, entry 8), 1,4-
dioxane (Table 1, entry 9), acetonitrile (Table 1, entry 10),
dichloromethane (Table 1, entry 11), toluene (Table 1, entry
17
DMF
Cy
18
DMF
o-Tol3
–
1
2), or pyridine (Table 1, entry 13) was used, the reaction
a
Isolated yield of the mixture of 4α and 4β.
Determined by H NMR analysis.
n.d. = not detected.
b
c
1
proceeded in lower yield and with α-selectivity.
©
Georg Thieme Verlag Stuttgart · New York — Synlett 2017, 28, A–D

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Synlett
K. Seio et al.
Letter
To test the applicability of the reaction using ADDP and
the best results were originally obtained using P(n-Bu)3,
DIAD, and 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU) in
acetonitrile.9a On the other hand, our reaction proceeded
smoothly in the presence of P(n-Bu)3 and ADDP in DMF
without the need for a strong base such as DBU, because the
zwitterion generated from the addition of ADDP and P(n-
n-Bu P in DMF, we synthesized various derivatives of stan-
3
dard deoxynucleosides, and the results are shown in Figure
1
. The reaction of 2 and 6-chloropurine gave a 35:65 mix-
12
ture of 5α and 5β in 60% yield. The reaction with unpro-
13
tected thymine gave 6 in 18% yield with no stereoselectiv-
ity. Notably, a mixture of regioisomers in which the thy-
mine and deoxyribose moieties were connected at different
positions, such as N3, O2, and O4, was obtained, indicating
that N1 was the most reactive but not the only nucleophilic
position of thymine. On the other hand, the reaction of 2
with unprotected adenine gave a 30:70 mixture of 7α and
Bu) is sufficiently basic to abstract the proton from the nu-
3
cleobase. Moreover, recent study by Downey and co-work-
9b
ers reported the use of ADDP and P(n-Bu) also gave selec-
3
tively the β-anomers because of the formation of the 1′,2′-ep-
oxyribose intermediate. In our deoxynucleoside synthesis, a
mixture of α- and β-anomers was obtained in a ratio de-
pending on the solvent and the nucleobase structure be-
cause of the lack of the 2′-hydroxy group which is neces-
sary to form the epoxy intermediate. Thus, our method is
useful for the preparation of separable α- and β-anomers,
as in the case of compounds 1, 10, and 12.
In this paper, we present a systematic study of the syn-
thesis of deoxynucleosides by Mitsunobu reaction under
mild conditions. The reaction generated both α and β iso-
mers in a ratio dependent on the nucleobase structure and
the solvent. In particular, the reactions in DMF (Table 1, en-
try 6) gave the highest yield and β-selectivity. This ap-
proach is expected to be applied to the synthesis of unnatu-
ral deoxynucleosides useful for the pharmaceutical and bio-
logical applications.
1
4
7
β
in 65% yield, whereas the reaction with unprotected
cytosine or guanine to give 8 or 9, respectively, was not ef-
fective because of the low solubility of the nucleobases in
DMF.
The developed procedure was also tested for the prepa-
ration of nonstandard deoxynucleosides, namely, previous-
ly reported 1, 10 (Figure 1), and 12 (Scheme 1). Although
the α and β isomers of above natural nucleoside derivatives
could not be separated because of the similar physicochem-
ical properties of them, the isomers of the below unnatural
nucleosides could be separated by silica gel chromatogra-
phy. The reaction of 4,5-dicyanoimidazole with 2 gave im-
idazole nucleoside 10. Unlike in the case of standard deoxy-
nucleoside derivatives, the isomers of 10 were separated by
silica gel column chromatography to give 10α and 10β in
4
2% and 46% yield, respectively. As previously reported, the
reaction with a protected 7-deazaguanine derivative gave
α and 1β in 23% and 61%, respectively, after purification by
Funding Information
1
This work was supported by JSPS KAKENHI Grant Number 15H01062,
silica gel column chromatography. The Mitsunobu reaction
was also applicable to the synthesis of 5-fluorouridine de-
rivative 12. In this case, compound 2 was coupled with N -
benzoyl-5-fluorouracil (11) to give the fully protected de-
oxynucleoside, which was treated with aqueous ammonia
to afford 12α and 12β in 24% and 59% yield, respectively, af-
ter silica gel column chromatography.
15K13738, and 26288075
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S
K
A
K
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H
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Grant
1(
5
H
0
1
0
6
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S
K
A
K
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H
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Grant
1(
5
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1
3
7
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S
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Grant
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8
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Supporting Information
Supporting information for this article is available online at
https://doi.org/10.1055/s-0036-1588445.
S
u
p
p
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i
f
rm oaitn
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u
p
p
ortioIgnfmr oaitn
2
(3.0 equiv)
References and Notes
O
ADDP (3.0 equiv)
P(n-Bu)3 (3.0 equiv)
EtOH–28% NH4OH
(1:3, v/v)
F
NBz
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DMF
r.t., 2 h
r.t., 9 h
N
H
O
F
11
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TBSO
O
N
O
O
NH
OTBS
1
1
2α: 24%
2β: 59%
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Georg Thieme Verlag Stuttgart · New York — Synlett 2017, 28, A–D