Preparation of 2′-Alkylselenouridine Derivatives via a 2-(Trimethylsilyl)ethylselenation Approach

Article abstract of DOI:10.1055/s-0036-1588937

2′-O-Methylation of nucleotides is well-known to increase siRNA stability against nuclease activities. Recently, selenium-containing biomolecules have been recognized as unique biological and medicinal agents for humans. In this study, 2′-alkylselenouridine derivatives were prepared through 2-(trimethylsilyl)ethylselenation at the C2′ position of 5′-DMT-2,2′-O-cyclouridine, followed by alkylation with various haloalkanes utilizing the characteristics of a Si atom. Overall, we demonstrated the versatility of a 2-(trimethylsilyl)ethylselenyl group for the synthesis of 2′-alkylselenouridines.

Full text of DOI:10.1055/s-0036-1588937

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S. Fukuno et al.
Letter
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Preparation of 2′-Alkylselenouridine Derivatives via a 2-(Trimethyl-
silyl)ethylselenation Approach
Shota Fukunoa
Masayuki Ninomiyaa,b
Mamoru Koketsu*a,b
a Department of Materials Science and Technology,
Faculty of Engineering, Gifu University, 1-1 Yanagido,
Gifu 501-1193, Japan
koketsu@gifu-u.ac.jp
b Department of Chemistry and Biomolecular Science,
Faculty of Engineering, Gifu University, 1-1 Yanagido,
Gifu 501-1193, Japan
Received: 22.11.2016
Accepted after revision: 22.12.2016
Published online: 17.01.2017
activity. The replacement of an oxygen atom by homolo-
gous sulfur and selenium atoms affects the chemical prop-
erties and often leads to useful alterations of its efficacy.
Within the scope of our ongoing program aimed at the syn-
thetic study of selenium-containing nucleosides,17,18 we
herein describe the strategy for the synthesis of 2′-al-
kylselenouridine derivatives.
For alkylselenation, most of previous reports employed
alkyl diselenides (R–Se–Se–R).19–21 However, in this meth-
odology, alkyl diselenides must be prepared with respect to
each alkyl functional group. Depending on the functional-
ities, it is difficult to prepare respective alkyl diselenides.
We therefore planned to use 2-(trimethylsilyl)ethyl (TSE)
diselenide (TSE–Se–Se–TSE, 1) as a selenating reagent
which has two latent sites of reactivity. Our strategy is out-
lined in Scheme 1. The initial step commences with in situ
generation of a TSE selenolate anion (TSE–Se–) from TSE
diselenide (1) by hydride reduction. This anion is expected
DOI: 10.1055/s-0036-1588937; Art ID: st-2016-u0784-l
Abstract 2′-O-Methylation of nucleotides is well-known to increase
siRNA stability against nuclease activities. Recently, selenium-contain-
ing biomolecules have been recognized as unique biological and medic-
inal agents for humans. In this study, 2′-alkylselenouridine derivatives
were prepared through 2-(trimethylsilyl)ethylselenation at the C2′ posi-
tion of 5′-DMT-2,2′-O-cyclouridine, followed by alkylation with various
haloalkanes utilizing the characteristics of a Si atom. Overall, we
demonstrated the versatility of a 2-(trimethylsilyl)ethylselenyl group for
the synthesis of 2′-alkylselenouridines.
Key words selenium-containing biomolecule, 2-(trimethylsilyl)ethyl-
selenyl group, selenation, 2′-alkylselenouridine derivative, phosphora-
midite monomer
Small interfering RNAs (siRNAs) play an important role
in the cellular RNA interference (RNAi) pathway to regulate
gene expression.1,2 RNA is unstable compared to DNA, be-
cause 2′-OH group in RNA promotes RNA hydrolysis under
acidic and basic conditions.3 Although this 2′-OH group in
the pentose sugar is not very necessary for siRNAs activity,4
the C2′ position holds the possibilities to strengthen nucle-
ase resistance and to enhance duplex stability. Improve-
ment of siRNAs stability is a primary factor direction for the
therapeutic advantages.5 Chemical modifications at the C2′
position have been intensively investigated;6–10 especially,
2′-O-methylation stabilized siRNAs in serum with mainte-
nance of RNA interference potency.11
hydride
reduction
Si
Si
Si
Se
Se Se
1
O
N
O
N
O
N
NH
NH
O
N
PGO
O
O
O
PGO
PGO
The element selenium is essential in the nutrition of hu-
mans.12,13 The glutathione peroxidase (GPx) having Se in its
catalytic center14 reduces hydroperoxides and participates
in the antioxidant protection of cells.15 In recent years, sele-
nium-containing biomolecules have been documented as
promising pharmacological agents.16 Minor changes in mo-
lecular structures can cause extensive changes in biological
F
R–X
O
O
OH
OH Se
OH SeR
Si
Scheme 1 Synthetic strategy for the synthesis of 2′-alkylselenouridine
derivatives
© Georg Thieme Verlag Stuttgart · New York — Synlett 2017, 28, A–D

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to attack to the C2′ position of 2,2′-O-cyclouridine, resulting
in introduction of TSE selenyl moiety onto ribose in uridine
skeleton. The second step involves Se-alkylation using high
affinity of Si to F.
ed N-methylated uridine analogue 5 as a major product, in-
dicating the need to protect an imide group. It was consid-
ered that basicity of TBAF accelerates N-methylation. Fol-
lowing N3-protection using benzyloxymethyl chloride
(BOMCl, 1.5 equiv) and 1,8-diazabicyclo[5.4.0]undec-7-ene
(DBU, 2.0 equiv), we tried Se-methylation again. Under
slightly modified conditions (40 °C for 5 h), N3-BOM-pro-
tected compound 6 favorably accepted a methyl group on
the Se atom in 92% yield (7a, Scheme 2).23
After successful methylation of 6, the stage was now set
for the comparative screening of the reactivity of 6 with
various alkyl halides. Results are summarized in Table 1.
Reactions with MeI, EtI, i-PrI, allyl bromide, and propargyl
bromide afforded the corresponding Se-alkylated products
(7a–e) in good to excellent yields (Table 1, entries 1–5).
Comparing with these results, treatment with bromoaceto-
nitrile furnished the respective product 7f in 19% yield,
while the yield was decreased considerably (Table 1, entry
6). With 3-bromopropionitrile (an additional one carbon of
bromoacetonitrile), 6 did not react at all (Table 1, entry 7).
When 2-bromoethyl methyl ether was used, the good yield
of 72% (7h) was achieved (Table 1, entry 8).
TSE diselenide (1) was prepared according to our proce-
dure as reported previously;17 following treatment of ele-
mental selenium with sodium borohydride (NaBH4), alkyla-
tion of the activated selenium with 2-(bromoethyl)trimeth-
yl silane provided the desired selenating reagent 1 in 71%
yield. Since 2,2′-O-cyclouridine (2) has a primary alcohol at
the C5′ position, 4,4′-dimethoxytrityl (DMT) protection was
initially conducted.20 It is noteworthy that treatment of 5′-
DMT-2,2′-O-cyclouridine (3) with TSE diselenide (1, 1.2
equiv) in the presence of NaBH4 (1.2 equiv) at 60 °C for one
hour proceeded smoothly to afford 2-(trimethylsilyl)eth-
ylselenated uridine (4) in 98% yield.22 The 77Se NMR signal
observed at δ = 150.3 ppm clearly revealed that a TSE sele-
nolate anion attacked to the C2′ position rather than the C2
position. Methylation of 4 by means of iodomethane (MeI,
5.0 equiv) and tetrabutylammonium fluoride (TBAF, 3.0
equiv) at room temperature for one hour gave an unsolicit-
O
O
Table 1 Reactivity of 6 with Various Alkyl Halides
N
N
O
O
N
O
N
O
N
DMTCl
(1.5 equiv)
BOM
O
BOM
O
HO
DMTO
N
N
R–X
TBAF
(3.0 equiv)
O
O
pyridine
r.t., 4 h
72%
N
DMTO
DMTO
OH
OH
1 (1.2 equiv)
3
O
O
DMF, 40 °C
2
DMF, 60 °C
1 h, 98%
NaBH4 (1.2 equiv)
EtOH (3.0 equiv)
OH Se
OH SeR
Si
7a–h
6
O
O
BOM
O
Entry
Electrophile (equiv)
Time (h)
Yield (%)
N
NH
1
2
3
4
5
6
7
8
MeI (5.0)
1.0
0.5
5.0
1.5
0.5
4.0
4.0
4.0
7a 92
7b 98
7c 70
7d 73
7e 65
7f 19
7g 0
BOMCl
(1.5 equiv)
DBU
N
N
O
EtI (5.0)
DMTO
DMTO
O
O
(2.0 equiv)
i-PrI (3.0)
CH2=CHCH2Br (3.0)
CH≡CCH2Br (3.0)
N≡CCH2Br (3.0)
N≡CCH2CH2Br (3.0)
MeOCH2CH2Br (3.0)
DMF, 0.5 h
0 °C to r.t.
89%
OH Se
OH Se
Si
Si
6
4
TBAF
TBAF
(3.0 equiv)
MeI
(5.0 equiv)
DMF, 40 °C
5 h, 92%
(3.0 equiv)
MeI
(5.0 equiv)
DMF, r.t.
1 h, 64%
7h 72
O
O
BOM
In order to verify the practical effectiveness of a TSE
group, we next examined the reactivity of 6 with benzyl
bromides bearing a variety of functional groups on the ben-
zene ring. Upon treatment of benzyl and 4-methylbenzyl
bromides, the Se-benzylated products (7i and 7j) were ob-
tained in 81% and 69% yields, respectively (Table 2, entries 1
and 2). With 2-, 3-, and 4-nitro-substituted benzyl bro-
mides, the yields were reduced (Table 2, entries 3–5). The
electron-withdrawing properties of nitro substitutions
NMe
O
N
N
N
O
DMTO
DMTO
O
O
OH Se
OH SeMe
Si
5
7a
Scheme 2 Synthesis of 2′-methylselenouridine derivatives
© Georg Thieme Verlag Stuttgart · New York — Synlett 2017, 28, A–D

C
S. Fukuno et al.
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Synlett
have a negative effect on the reaction progress. Chloro sub-
stitutions on the benzene ring slightly increased the yields
(Table 2, entries 6–8). When 2-(bromomethyl)naphthalene
was used, the reaction could easily access to the product
(7q) in 76% yield (Table 2, entry 9). Furthermore, by using
α-haloketone (phenacyl bromide) and ester (methyl bro-
moacetate), the yields were poor in both cases (Table 2, en-
tries 10 and 11).
Table 2 Reactivity of 6 with Various Benzyl Bromides, α-Bromoketone,
and α-Bromoester
O
O
BOM
O
BOM
O
N
N
R–X
(3.0 equiv)
TBAF
N
N
DMTO
DMTO
(3.0 equiv)
O
O
In addition, we attempted Se-acetylation of 6 to expand
the feasibility of the approach, however, the reaction with
acetyl chloride using TBAF under the same conditions with
Table 2 produced the 3′-OAc product instead of 2′-Se-acetyl-
ated compound. Even when silver(I) tetrafluoroborate
(AgBF4)24 was employed as a promoter, 2′-Se-acetylation did
not progress.
Interest in oligonucleotide phosphoramidite synthetic
chemistry has grown over last thirty years.25–27 Nucleosidic
phosphoramidites are powerful tools for the automated sol-
id-phase synthesis of oligonucleotide-based antisense
drugs. With 4 in hand, we turned our attention to synthe-
size a fully protected phosphoramidite monomer of 2′-
methylselenouridine for the assembly of its oligonucle-
otide. (Pivaloyloxy)methyl (POM) as a suitable protective
group for an imide group was employed.28 From 4 as the
starting point, treatment with POMCl (1.5 equiv) in the
presence of K2CO3 (2.0 equiv) for five hours afforded the N3-
POM product 8 in 31% yield. Subsequent Se-methylation of-
fered easy access to the N3-POM-2′-Se-methylated uridine
(9, 83% yield), which was phosphitylated by the standard
procedure,11,29 to yield the corresponding phosphoramidite
(10, 56% yield) as a diastereomeric mixture (Scheme 3).30
DMF, 40 °C, 4 h
Si
OH SeR
OH Se
6
7i–s
Entry
Electrophile
Yield (%)
1
2
BnBr
7i 81
4-MeC6H4CH2Br
2-O2NC6H4CH2Br
3-O2NC6H4CH2Br
4-O2NC6H4CH2Br
2-ClC6H4CH2Br
3-ClC6H4CH2Br
4-ClC6H4CH2Br
NaphCH2Br
7j 69
7k 39
7l 11
3
4
5
7m 45
7n 82
7o 72
7p 55
7q 76
7r 30
7s 22
6
7
8
9
10a
11a
Ph(C=O)CH2Br
MeO(C=O)CH2Br
a 10 equiv of electrophiles were used for 0.5 h.
In conclusion, we have demonstrated a valuable route
for the synthesis of 2′-alkylselenouridine derivatives. The
simplified methodology in this article has a wide applica-
O
O
POM
N
NH
POMCl (1.5 equiv)
K2CO3 (2.0 equiv)
N
O
N
O
DMTO
DMTO
DMF, 0 °C to r.t., 5 h
31%
O
O
OH Se
OH Se
Si
Si
8
4
TBAF (3.0 equiv)
MeI (5.0 equiv)
DMF, 40 °C
5 h, 83%
O
N
(i-Pr)2N
Cl
POM
O
P
N
O
O
NC
POM
N
(2.0 equiv)
DMTO
DMAP (5.0 equiv)
O
N
O
DMTO
THF, r.t., 2.5 h
56%
(i-Pr)2N
O
P
SeMe
O
O
OH SeMe
NC
10
9
Scheme 3 Synthesis of a 2′-methylselenouridine phosphoramidite
© Georg Thieme Verlag Stuttgart · New York — Synlett 2017, 28, A–D

D
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tion for incorporation of an alkylselenyl moiety into bio-
molecule frameworks. Our findings highlight the great ver-
satility and limitations of a 2-(trimethylsilyl)ethylselenyl
group.
mmol), NaBH4 (1.14 mmol), and EtOH (2.85 mmol) in DMF (5
mL) at 0 °C for 30 min, 3 (0.95 mmol) was added to the solution,
and the reaction was continued at 60 °C for an additional 1 h.
The resultant solution was quenched by 5% NH3Cl aq, and then
was poured into distilled water, partitioned with EtOAc, and
washed with brine. The organic layer was dried over anhydrous
Na2SO4 and concentrated in vacuo. The residue was purified
using silica gel column chromatography eluted with n-hexane–
EtOAc (3:1 to 1:1) to afford 4 (98% yield) as a white amorphous
powder. [α]D +79.39 (c 0.64, CHCl3). IR (film): νmax = 3407, 2924,
Acknowledgment
This work was supported by a Grant-in-Aid for Science Research from
the Ministry of Education, Culture, Sports, Science and Technology of
Japan (No. 15K07856) to which we are grateful.
1
1685 cm–1. H NMR (600 MHz, CDCl3): δ = 8.79 (br s, 1 H, NH),
7.89 (d, 1 H, J = 7.6 Hz, H5), 7.36 (d, 2 H, J = 6.8 Hz, Ph), 7.30 (t, 2
H, J = 7.6 Hz, Ph), 7.26–7.23 (m, 5 H, Ph), 6.84 (d, 4 H, J = 8.9 Hz,
Ph), 6.19 (d, 1 H, J = 8.3 Hz, H1′), 5.36 (d, 1 H, J = 8.2 Hz, H6), 4.37
(dd, 1 H, J = 2.8, 4.8 Hz, H3′), 4.18 (d, 1 H, J = 2.7 Hz, H4′), 3.79 (s,
6 H, 2 OMe), 3.66 (dd, 2 H, J = 4.8, 7.6 Hz, H2′), 3.51 (dd, 1 H, J =
2.7, 11.0 Hz, H5′a), 3.47 (dd, 2 H, J = 2.7, 11.0 Hz, H5′b), 2.85 (d, 1
H, J = 3.5 Hz, OH), 2.78–2.71 (m, 2 H, SeCH2CH2TMS), 1.03–0.95
(m, 2 H, SeCH2CH2TMS), 0.008 (s, 9 H, SiMe3). 13C NMR (150
MHz, CDCl3): δ = 163.1, 158.9, 150.4, 144.4, 140.0, 135.2, 135.0,
130.21, 130.16, 128.2, 127.4, 113.5, 102.7, 88.1, 87.4, 84.7, 71.6,
63.5, 55.4, 50.4, 20.8, 19.2, –1.8. 77Se NMR (115 MHz, CDCl3): δ =
Supporting Information
Supporting information for this article is available online at
http://dx.doi.org/10.1055/s-0036-1588937.
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References and Notes
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150.3. HRMS (ESI, TOF): m/z calcd for
733.1824; found: 733.1816 [M + Na]+.
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C35H42N2O7SeNa,
TBAF (1.0 M in THF, 0.15 mmol) was added to a solution of 6
(0.05 mmol) and MeI (0.25 mmol) in DMF (0.5 ml). After stir-
ring at 40 °C for 5 h, the resultant solution was poured into dis-
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.
NMR (400 MHz, CDCl3): δ = 7.78 (d, 1 H, J = 8.0 Hz, H5), 7.38–
7.25 (m, 14 H, Ph), 6.84 (d, 4 H, J = 8.9 Hz, Ph), 6.21 (d, 1 H, J = 6.7
Hz, H1′), 5.47 (s, 2 H, CH2OCH2Ph), 5.40 (d, 1 H, J = 8.1 Hz, H6),
4.69 (s, 2 H, CH2OCH2Ph), 4.38 (d, 1 H, J = 5.4 Hz, H3′), 4.15 (d, 1
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and H5′), 2.75 (d, 1 H, J = 4.0 Hz, OH), 2.14 (s, 3 H, SeMe). 13C
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138.0, 135.3, 135.1, 130.2, 128.4, 128.2, 127.8, 127.4, 113.4,
102.4, 102.3, 88.8, 87.4, 84.5, 72.3, 71.3, 70.5, 63.0, 55.4, 51.0,
4.9. 77Se NMR (75 MHz, CDCl3): δ = 27.9. HRMS (ESI, TOF): m/z
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After stirring of 2-(trimethylsilyl)ethyl diselenide (1, 1.14
© Georg Thieme Verlag Stuttgart · New York — Synlett 2017, 28, A–D