Synthesis of nucleosides containing a photolabile 2-(2-nitrophenyl)propoxycarbonyl group

Full text of DOI:10.1134/S1070428015010297

ISSN 1070-4280, Russian Journal of Organic Chemistry, 2015, Vol. 51, No. 1, pp. 141–144. © Pleiades Publishing, Ltd., 2015.
Original Russian Text © E.B. Nikolaenkova, I.A. Os’kina, V.A. Savel’ev, A.Ya. Tikhonov, V.A. Ryabinin, A.N. Sinyakov, 2015, published in Zhurnal
Organicheskoi Khimii, 2015, Vol. 51, No. 1, pp. 142–144.
SHORT
COMMUNICATIONS
Synthesis of Nucleosides Containing a Photolabile
2-(2-Nitrophenyl)propoxycarbonyl Group
E. B. Nikolaenkovaa, I. A. Os’kinaa, V. A. Savel’eva, A. Ya. Tikhonova,
V. A. Ryabininb, and A. N. Sinyakovb
a Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch, Russian Academy of Sciences,
pr. Akademika Lavrent’eva 9, Novosibirsk, 630090 Russia
e-mail: oi@nioch.nsc.ru
b Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences,
pr. Akademika Lavrent’eva 8, Novosibirsk, 630090 Russia
Received June 17, 2014
DOI: 10.1134/S1070428015010297
At present, DNA biochips are widely used in medi-
cine as diagnostic systems [1, 2]. Oligonucleotide
biochips are often obtained with the aid of photolabile
protecting groups [3–7]. The latter should be stable
under the conditions of oligonucleotide synthesis but
should be readily removed by photolysis without
involving the protected moiety. A widely used photo-
labile protecting group is the o-nitrobenzyl group
[3, 8–10]. The goal of the present work was to extend
the series of nucleosides protected by the photolabile
2-(2-nitrophenyl)propoxycarbonyl group and contain-
ing readily removable protecting groups in the aro-
matic heteroring, which can subsequently be used in
the design of oligonucleotide biochips.
We have synthesized previously unknown nucleo-
sides 4–7. Compounds 4 and 5 were obtained by acyla-
tion of 2′-deoxyguanosine and 2′-deoxyadenosine with
phenoxyacetyl chlorides 1 and 2, respectively. Nucleo-
sides 6 and 7 protected by photolabile 2-(2-nitro-
phenyl)propoxycarbonyl groups were synthesized by
treatment of compounds 4 and 5, respectively, with
2-(2-nitrophenyl)propyl chloroformate (3) which was
prepared as described in [10]. Compounds 6 and 7
were isolated as mixtures of diastereoisomers.
Scheme 1.
O
N
O
Cl
O
N
N
N
NH
NH
O
O
Me3SiCl, HOBt
+
O
HO
HO
N
NH2
N
N
H
O
O
Pr-i
i-Pr
OH
OH
1
4
NO2 Me
O
N
O
Cl
N
N
Me
NH
O
O
O
O
O
3
N
H
O
OH
O
NO2
Pr-i
6
HOBt is 1-hydroxybenzotriazole.
141

NIKOLAENKOVA et al.
142
Scheme 2.
O
N
O
NH2
HN
N
Cl
O
N
N
N
N
N
Bu-t
O
Me3SiCl
HO
HO
+
N
O
O
t-Bu
OH
OH
2
5
O
N
O
HN
N
3
N
N
Me
Bu-t
O
O
O
O
NO2
OH
7
N2-(4-Isopropylphenoxyacetyl)-2′-deoxyguano-
sine (4). 2′-Deoxyguanosine, 1.14 g (4 mmol), was
dried by double vacuum evaporation of its mixture
with 20 mL of anhydrous pyridine and was dispersed
in 20 mL of anhydrous pyridine, 2.52 g (3 mL,
20 mmol) of chloro(trimethyl)silane was added, and
the mixture was stirred for 25 min at room tem-
perature. 1-Hydroxybenzotriazole (HOBt), 0.86 g
(6.4 mmol), was dried by triple distillation of its mix-
ture with 3 mL of anhydrous acetonitrile and dispersed
in a mixture of 3 mL of anhydrous acetonitrile and
3 mL of anhydrous pyridine, and 1.28 g (6 mmol) of
(4-isopropylphenoxy)acetyl chloride was added to the
mixture. Both reactant mixtures were cooled on an ice
bath, and the suspension of 2′-deoxyguanosine was
added to the second mixture. The resulting mixture
was stirred for 8 h at room temperature (TLC), cooled
with ice-cold water, and treated with 2 mL of water
and 2.5 mL of concentrated aqueous ammonia (TLC).
The precipitate was filtered off, the filtrate was evapo-
rated, and the residue was combined with the precip-
itate and treated with water. The white voluminous
solid was filtered off, washed with water and diethyl
ether, and dried in air until constant weight. Yield
1.75 g (99%), mp 234–235°C (decomp.). IR spectrum
(KBr), ν, cm–1: 3501, 3426, 3221, 3117, 3049, 2951,
1686, 1614, 1555, 1514, 1483, 1418, 1366, 1329,
1242, 1221, 1150, 1105, 1088, 1059, 976, 928, 833,
787, 772, 644. UV spectrum (EtOH): λmax 261 nm
1.16 d (6H, CH3, J = 6.8 Hz), 2.29 m (1H, CH), 2.58 m
(1H, CH), 2.82 m (1H, CH), 3.55 m (2H, CH2), 3.84 m
(1H, CH), 4.38 m (1H, CH), 4.83 m (2H, CH2), 6.22 m
(1H, CH), 6.88 d and 7.16 d (2H each, Harom, J =
8.5 Hz), 11.79 s (1H, NH), 11.83 s (1H, NH). Found,
%: C 56.99; H 5.32; N 15.83. C21H25N5O6. Calculated,
%: C 56.87; H 5.68; N 15.79.
N6-(4-tert-Butylphenoxyacetyl)-2′-deoxyadeno-
sine (5). 2′-Deoxyadenosine, 3.96 g (15 mmol), was
dried by double vacuum evaporation of its mixture
with 50 mL of anhydrous pyridine and was dissolved
on heating in 110 mL of anhydrous pyridine. The so-
lution was cooled in a stream of argon on an ice bath,
7.7 g (9 mL, 71 mmol) of chloro(trimethyl)silane was
added dropwise, and the mixture was stirred for 30 min
at room temperature. The mixture was then cooled
again on an ice bath, 7 g (31 mmol) of (4-tert-butyl-
phenoxy)acetyl chloride was added dropwise, the mix-
ture was stirred for 2 h at room temperature and kept
for 15 h at room temperature, 200 mL of a saturated
solution of sodium hydrogen carbonate was added, and
the mixture was stirred until carbon dioxide no longer
evolved. The resulting solution was partially evapo-
rated under reduced pressure, and the residue was
extracted with methylene chloride. The extract was
dried over MgSO4 and evaporated, and residual
pyridine was removed by evaporation with toluene.
The viscous residue, 11.37 g, was purified by silica gel
column chromatography (gradient elution with chloro-
form–methanol, 0 to 5% of the latter). Yield 4.13 g
1
(logε 4.05). H NMR spectrum (DMSO-d6), δ, ppm:
RUSSIAN JOURNAL OF ORGANIC CHEMISTRY Vol. 51 No. 1 2015

SYNTHESIS OF NUCLEOSIDES
143
(62%), mp 88–89°C. IR spectrum (KBr), ν, cm–1:
3371, 2961, 2868, 1716, 1614, 1585, 1512, 1462,
1225. UV spectrum (EtOH), λmax, nm (logε): 213
(4.46), 272 (4.28). 1H NMR spectrum (CDCl3), δ, ppm:
1.28 s (9H, t-Bu), 2.37 d.d (1H, CH, J = 12, 6 Hz),
2.97 m (1H, CH), 3.80 d (1H, CH, J = 12 Hz), 3.94 d
(1H, CH, J = 12 Hz), 4.19 m (1H, CH), 4.78 d (1H,
CH, J = 4.5 Hz), 4.82 s (2H, CH2), 6.39 d.d (1H, CH,
anhydrous methylene chloride was added dropwise,
and the mixture was stirred for 5 h at –20 to –50°C and
kept for 10 h in a refrigerator. The mixture was then
treated with 50 mL of water, stirred for 30 min, and
extracted with methylene chloride, and the extract was
dried over MgSO4 and evaporated. The residue was
subjected to silica gel column chromatography
(gradient elution with methylene chloride–methanol,
0 to 10% of the latter). Yield 2.1 g (44%), mp 76–77°C.
IR spectrum (KBr), ν, cm–1: 3370, 2960, 1749, 1612,
1525, 1263, 1244. UV spectrum (EtOH): λmax 273 nm
J = 8, 6 Hz), 6.94 d and 7.32 d (2H each, Harom
,
J = 8 Hz), 8.22 s (1H, CH), 8.71 s (1H, CH), 9.59 s
(1H, NH). Found, %: C 59.47; H 5.93; N 15.67.
C22H27N5O5. Calculated, %: C 59.86; H 6.12; N 15.87.
1
(log ε 4.35). H NMR spectrum (CDCl3), δ, ppm:
N2-(4-Isopropylphenoxyacetyl)-5′-O-[2-(2-nitro-
phenyl)propoxycarbonyl]-2′-deoxyguanosine (6).
Nucleoside 4, 1.77 g (4 mmol), was dried by triple
distillation of its mixture with 15 mL of anhydrous
pyridine and was dissolved on heating in 15 mL of
anhydrous pyridine. The solution was cooled to –40°C,
a solution of 1.31 g (5.4 mmol) of compound 3 in
10 mL of anhydrous methylene chloride was added
dropwise, and the mixture was stirred for 5 h at a tem-
perature not exceeding –40°C. The mixture was then
treated with water (40 mL) and extracted twice with
methylene chloride. The combined extracts were dried
over MgSO4 and evaporated, and the residue was dried
by triple evaporation of its mixture with 40 mL of
toluene and subjected to silica gel column chromatog-
raphy (successive elution with methylene chloride and
methylene chloride–methanol, 100:1, 100:2, 100:4).
Yield 1.46 g (56%), mp 71–72°C. IR spectrum (KBr),
ν, cm–1: 3485, 3395, 3200, 2959, 1753, 1680, 1610,
1528, 1514, 1356, 1252. UV spectrum (EtOH):
1.27 s (9H, t-Bu), 1.35 d and 1.33 d (3H, CH3, J =
3 Hz), 2.56 m (1H, CH), 2.83 m (1H, CH), 3.76 m
(1H, CH), 4.15–4.40 m (5H, CH2, CH), 4.69 m (1H,
CH), 4.81 s (2H, CH2), 6.51 t (1H, CH, J = 6 Hz),
6.96 d (2H, Harom, J = 10 Hz), 7.33 m (3H, Harom),
7.45 d (1H, Harom, J = 8 Hz), 7.55 t (1H, Harom, J =
8 Hz), 7.73 d (1H, Harom, J = 8 Hz), 8.16 s and 8.21 s
(1H, 8-H), 8.74 s and 8.75 s (1H, 2-H), 9.47 s and
9.49 s (1H, NH). Found, %: C 59.29; H 5.56; N 12.59.
C32H36N6O9. Calculated, %: C 59.26; H 5.56; N 12.96.
The analytical and spectral data were obtained at
the Joint Chemical Service Center, Siberian Branch,
Russian Academy of Sciences. The IR spectra were
recorded on a Bruker Vector 22 spectrometer. The UV
spectra were measured on a Hewlett Packard 4853
1
spectrophotometer. The H NMR spectra were ob-
tained on a Bruker AV-400 instrument using the resid-
ual proton signal of the solvent as reference (CHCl3,
δ 7.26 ppm; DMSO-d5, δ 2.50 ppm). 2′-Deoxyguano-
sine, 2′-deoxyadenosine, 1-hydroxybenzotriazole,
(4-tert-butylphenoxy)acetyl chloride, (4-isopropyl-
phenoxy)acetyl chloride, and chloro(trimethyl)silane
were commercial products. Pyridine, acetonitrile, and
methylene chloride were dried according to standard
procedures.
1
λmax 256 nm (logε 4.30). H NMR spectrum (CDCl3),
δ, ppm: 1.17 d (6H, CH3, J = 6.9 Hz), 1.27 d (3H, CH3,
J = 7.0 Hz), 2.17 s (1H, OH), 2.52 m (1H, CH), 2.59–
2.71 m (1H, CH), 2.83 m (1H, CH), 3.66 m (1H, CH),
4.11–4.36 m (5H, CH2, CH), 4.69 s (2H, CH2), 4.74 m
(1H, CH), 6.27 m (1H, CH), 6.85 d and 7.12 d
(2H each, Harom, J = 8.5 Hz), 7.29 m (1H, Harom),
7.40 m (1H, Harom), 7.51 m (1H, Harom), 7.67 m (1H,
CH), 7.89 s and 7.94 s (1H, 8-H). Found, %: C 57.23;
H 4.99; N 12.97. C31H34N6O10. Calculated, %: C 57.23;
H 5.23; N 12.92.
This study was performed under financial support
by the Siberian Branch of the Russian Academy of
Sciences (integration project no. 138, 2012-2014).
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