N2- and C8-Substituted Oligodeoxynucleotides
J ournal of Medicinal Chemistry, 1998, Vol. 41, No. 13 2239
Syn th esis of Mon om er s. N2-Su bstitu ted 2′-Deoxygu a -
n osin e Der iva t ives. 6-O-(4-Nit r op h en et h yl)-2′-d eoxy-
gu a n osin e (4). A suspension of 2′-deoxyguanosine (3 g, 11.3
mmol) and acetic anhydride (5.0 g, 49 mmol) in 40 mL of
pyridine and 30 mL of DMF was heated at 75 °C for 4 h to
give a clear solution. TLC showed the completion of the
reaction. After cooling, the solution was concentrated to
dryness, and the solid residue obtained was washed twice with
2-propanol to give 3.2 g of 3′,5′-di-O-acetyl-2′-deoxyguanosine
(3) (yield, 81%) as a white solid. The structure was confirmed
) 6.5, 2H, -CH2-), 2.8 and 2.5 (2m, 2H, 2′-Hab), 1.91 (d, J )
3, 1H, 3′-OH).
5′-O-(4,4′-Dim e t h oxyt r it yl)-N 2-b e n zyl-2′-d e oxygu a -
n osin e (6a ). A solution of 5′-O-(4,4′-dimethoxytrityl)-6-O-(4-
nitrophenethyl)-2-fluoro-2′-deoxyguanosine (5) (2 g, 2.8 mmol)
and benzylamine (3.2 g, 30 mmol) in 50 mL of dry DMF was
stirred at room temperature for 24 h. When the reaction was
completed, the solution was concentrated under vacuum and
the residue obtained was dissolved in 300 mL of CH2Cl2. After
being washed with 100 mL of 5% aqueous NaHCO3 solution,
the organic solution was dried over Na2SO4 and concentrated.
The crude product obtained was purified with silica gel
chromatography using CH2Cl2/MeOH/Et3N ) 95/5/1 (v/v) to
give 1.9 g of 5′-O-(4,4′-dimethoxytrityl)-6-O-(4-nitrophenethyl)-
N2-benzyl-2′-deoxyguanosine as a pale-yellow foam in 84%
yield.
1
by H NMR (DMSO-d6).
3′,5′-Di-O-acetyl-2′-deoxyguanosine (3) (3.2 g, 9.1 mmol) was
suspended in 100 mL of dioxane. After triphenylphosphine
(3.6 g, 13.7 mmol) and 4-nitrophenethyl alcohol (2.3 g, 13.7
mmoL) were added, the suspension was heated at 80 °C for
30 min. Then, the suspension was cooled to 60 °C, and diethyl
azodicarboxylate (2.4 g, 13.7 mmol) was added dropwise. The
resultant mixture was heated at 60 °C for another 2 h, and a
clear-yellow solution was obtained. After cooling, the solution
was concentrated. The residue was dissolved in 300 mL of
CH2Cl2, and the organic solution obtained was washed with
200 mL of water and dried over Na2SO4. The solution was
concentrated, and the residue obtained was purified with silica
5′-O-(4,4′-Dimethoxytrityl)-6-O-(4-nitrophenethyl)-N2-ben-
zyl-2′-deoxyguanosine (1.9 g, 2.3 mmol) was dissolved in 30
mL of dry pyridine. After 2.3 g of DBU was added, the solution
obtained was stirred at room temperature for 15 h. Then, the
solution was concentrated under vacuum, and the residue
obtained was dissolved in 300 mL of CH2Cl2. After being
washed with 100 mL of 0.5 M aqueous citric acid solution and
then 100 mL of 5% aqueous NaHCO3 solution, the organic
solution was dried over Na2SO4 and concentrated. The crude
product obtained was purified with silica gel chromatography
using CH2Cl2/MeOH/Et3N ) 90/10/1 (v/v) to give 1.1 g of 5′-
O-(4,4′-dimethoxytrityl)-N2-benzyl-2′-deoxyguanosine (6a ) as
a white-yellow foam in 73% yield. 1H NMR (DMSO-d6): δ
10.59 (s, 1H, NH), 7.78 (s, 1H, 8-H), 7.1-7.4 (m, 9H, Ar-H),
6.80 (m, 5H, NH + Ar-H), 6.17 (t, J ) 6, 1H, 1′-H), 5.29 (d, J
) 4, 1H, 3′-OH), 4.33 (m, 3H, 3′-H, N-CH2-Ph), 3.91 (m, 1H,
4′-H), 3.70 (s, 6H, -OCH3), 3.0-3.3 (m, 2H, 5′-Hab), 2.7 and
2.2 (2m, 2H, 2′-Hab).
gel chromatography using CH2Cl2/MeOH ) 95/5 (v/v).
A
yellow viscous oil was obtained, and 1H NMR showed that it
contained mainly the desired product, 3′,5′-di-O-acetyl-6-O-
(4-nitrophenethyl)-2′-deoxyguanosine, contaminated by a small
amount of triphenylphosphine oxide. The crude product
thus obtained was dissolved in 150 mL of 1 M NH3/metha-
nol solution. The solution was stirred at room temperature
for 15 h. After the reaction was completed, the solvent was
evaporated and the residue was purified with silica gel
chromatography using CH2Cl2/MeOH ) 90/10 (v/v) to give
3.0 g of 6-O-(4-nitrophenethyl)-2′-deoxyguanosine (4) as a
pale-yellow foam in 79% yield. 1H NMR (DMSO-d6): δ 8.17
(d, J ) 8, 2H, Ar-H), 8.06 (s, 1H, 8-H), 7.61 (d, J ) 8, 2H,
Ar-H), 6.44 (bs, 2H, NH), 6.19 (t, J ) 6.5, 1H, 1′-H), 5.26
(bs, 1H, 3′-OH), 4.98 (bs, 1H, 5′-OH), 4.65 (t, J ) 6.5, 2H,
-CH2-), 4.34 (m, 1H, 3′-H), 3.81 (m, 1H, 4′-H), 3.4-3.6 (m,
2H, 5′-Hab), 3.24 (t, J ) 6.5, 2H, -CH2-), 2.6 and 2.2 (2m,
2H, 2′-Hab).
Compounds 6b-h were prepared with the same procedure
as above using compound 5 and 10 equiv of the corresponding
1
amines. The amine used, the product yield, and the H NMR
data of the product are as follows.
5′-O-(4,4′-Dim et h oxyt r it yl)-N2-(2-p h en ylet h yl)-2′-d e-
oxygu a n osin e (6b). Phenethylamine; yield: 85%. 1H NMR
(DMSO-d6): δ 7.79 (s, 1H, 8-H), 7.1-7.4 (m, 9H, Ar-H), 6.75
(t, J ) 9, 4H, Ar-H), 6.31 (t, J ) 5, 1H, NH), 6.21 (t, J ) 6,
1H, 1′-H), 5.32 (d, J ) 4, 1H, 3′-OH), 4.40 (m, 1H, 3′-H), 3.93
(m, 1H, 4′-H), 3.69 (s, 6H, -OCH3), 3.23 (m, 2H, N-CH2-),
3.0-3.2 (m, 2H, 5′-Hab), 2.71 (t, J ) 8, 2H, -CH2-Ph), 2.8
and 2.2 (2m, 2H, 2′-Hab).
5′-O-(4,4′-Dim et h oxyt r it yl)-6-O-(4-n it r op h en et h yl)-2-
flu or o-2′-d eoxygu a n osin e (5). Dry pyridine (4 g) was added
dropwise at -30 °C to 10 g of hydrogen fluoride-pyridine
(containing about 70% HF in pyridine; Aldrich) under stirring
to prepare 50% hydrogen fluoride-pyridine. To a suspension
of 6-O-(4-nitrophenethyl)-2′-deoxyguanosine (4) (2 g, 4.8 mmol)
in 14 g of 50% hydrogen fluoride-pyridine prepared above at
-30 °C was added 98% tert-butyl nitrite (0.7 g, 6 mmol)
dropwise, and the resultant mixture was stirred at -30 °C
for 2 h. After the bubbling stopped, a clear-yellow solution
was obtained. The solution was poured into 250 mL of ice-
water, and the mixture was extracted with CH2Cl2 (5 × 100
mL). The solvent used was removed to give 6-O-(4-nitrophen-
ethyl)-2-fluoro-2′-deoxyguanosine (2 g, 98%) as a pale-yellow
foam, which was used in the subsequent reaction without
further purification.
4,4′-Dimethoxytrityl chloride (2.0 g, 5.9 mmol) was added
to a solution of 6-O-(4-nitrophenethyl)-2-fluoro-2′-deoxygua-
nosine (2 g, 4.8 mmol) in 30 mL of dry pyridine. The solution
was stirred at room temperature for 15 h, and 5 mL of MeOH
was added. The resultant solution was concentrated, and the
residue obtained was dissolved in 300 mL of CH2Cl2. After
being washed with 100 mL of 5% aqueous NaHCO3 solution,
the organic solution was dried over Na2SO4 and concentrated.
The crude product obtained was purified with silica gel
chromatography using CH2Cl2/MeOH/Et3N ) 100/5/1 (v/v) to
give 2.5 g of 5′-O-(4,4′-dimethoxytrityl)-6-O-(4-nitrophenethyl)-
2-fluoro-2′-deoxyguanosine (5) as a pale-yellow foam with 72%
yield. 1H NMR (CDCl3): δ 8.17 (d, J ) 8.5, 2H, Ar-H), 8.03
(s, 1H, 8-H), 7.49 (d, J ) 8, 2H, Ar-H), 7.1-7.4 (m, 9H, Ar-
H), 6.80 (d, J ) 8.5, 4H, Ar-H), 6.37 (t, J ) 6.5, 1H, 1′-H),
4.83 (t, J ) 6.5, 2H, -CH2-), 4.67 (m, 1H, 3′-H), 4.12 (m, 1H,
4′-H), 3.78 (s, 6H, -OCH3), 3.2-3.5 (m, 2H, 5′-Hab), 3.29 (t, J
5′-O-(4,4′-Dim e t h oxyt r it yl)-N 2-(3-p h e n ylp r op yl)-2′-
d eoxygu a n osin e (6c). 3-Phenylpropylamine; yield: 62%. 1H
NMR (DMSO-d6): δ 10.42 (bs, 1H, NH), 7.78 (s, 1H, 8-H), 7.1-
7.4 (m, 9H, Ar-H), 6.78 (t, J ) 9, 4H, Ar-H), 6.30 (bs, 1H,
NH), 6.17 (t, J ) 6, 1H, 1′-H), 5.31 (d, J ) 4, 1H, 3′-OH), 4.40
(m, 1H, 3′-H), 3.93 (m, 1H, 4′-H), 3.70 (s, 6H, -OCH3), 3.0-
3.2 (m, 4H, N-CH2-, 5′-Hab), 2.56 (t, J ) 8, 2H, -CH2-Ph),
2.7 and 2.2 (2m, 2H, 2′-Hab), 1.7 (m, 2H, -C-CH2-C-).
5′-O-(4,4′-Dim et h oxyt r it yl)-N2-(1-n a p h t h ylm et h yl)-2′-
d eoxygu a n osin e (6d ). 1-Naphthylmethylamine; yield: 89%.
1H NMR (DMSO-d6): δ 10.45 (bs, 1H, NH), 7.8-8.1 (m, 3H,
Ar-H), 7.82 (s, 1H, 8-H), 7.1-7.6 (m, 13H, Ar-H), 6.83 (bs,
1H, NH), 6.76 (t, J ) 9, 4H, Ar-H), 6.22 (t, J ) 6, 1H, 1′-H),
5.26 (d, J ) 4, 1H, 3′-OH), 4.7-4.9 (m, 2H, -N-CH2-Ar), 4.28
(m, 1H, 3′-H), 3.91 (m, 1H, 4′-H), 3.68 (s, 6H, -OCH3), 3.0-
3.2 (m, 2H, 5′-Hab), 2.7 and 2.2 (2m, 2H, 2′-Hab).
5′-O-(4,4′-Dim et h oxyt r it yl)-N2-(2-n a p h t h ylm et h yl)-2′-
d eoxygu a n osin e (6e). 2-Naphthylmethylamine; yield: 78%.
1H NMR (DMSO-d6): δ 10.68 (bs, 1H, NH), 7.8-8.0 (m, 3H,
Ar-H), 7.80 (s, 1H, 8-H), 7.1-7.6 (m, 13H, Ar-H), 6.92 (t, J
) 5, 1H, NH), 6.77 (t, J ) 9, 4H, Ar-H), 6.19 (t, J ) 6, 1H,
1′-H), 5.30 (d, J ) 4, 1H, 3′-OH), 4.52(d, J ) 5, 2H, -N-CH2-
Ar), 4.34 (m, 1H, 3′-H), 3.92 (m, 1H, 4′-H), 3.69 (s, 6H, -OCH3),
3.0-3.2 (m, 2H, 5′-Hab), 2.7 and 2.2 (2m, 2H, 2′-Hab).
5′-O-(4,4′-Dim et h oxyt r it yl)-N2-(4-b ip h en ylm et h yl)-2′-
d eoxygu a n osin e (6f). 4-Biphenylmethylamine; yield: 73%.
1H NMR (DMSO-d6): δ 10.64 (bs, 1H, NH), 7.80 (s, 1H, 8-H),
7.1-7.7 (m, 18H, Ar-H), 6.84 (t, J ) 5, 1H, NH), 6.78 (t, J )