Highly efficient synthesis of allopurinol locked nucleic acid monomer by C6 deamination of 8-aza-7-bromo-7-deazaadenine locked nucleic acid monomer

Article abstract of DOI:10.1055/s-0033-1338531

An allopurinol locked nucleic acid (LNA) monomer was prepared by a novel strategy through C6 deamination of the corresponding 8-aza-7-bromo-7- deazaadenine LNA monomer with aqueous sodium hydroxide. An 8-aza-7-deazaadenine LNA monomer was also synthesized by a modification of the new synthetic pathway. N-Glycosylation at the 8-position was prevented by steric hindrance from the 7-bromo atom in the starting material 8-aza-7-bromo-7-deazaadenine. In the final step of the synthesis, the bromine was removed together with a benzyl protecting group by catalytic reduction with ammonium formate to give the required LNA monomers. Georg Thieme Verlag Stuttgart New York.

Full text of DOI:10.1055/s-0033-1338531

PAPER
▌3259
pHapiegr hly Efficient Synthesis of Allopurinol Locked Nucleic Acid Monomer by C6
Deamination of 8-Aza-7-bromo-7-deazaadenine Locked Nucleic Acid Monomer
Allopurinol Locked Nucleic Acid Monomer
Tamer Kosbar,a,b Mamdouh Sofan,b Laila Abou-Zeid,c Mohamed Waly,b Erik B. Pedersen*a
a
Department of Physics, Chemistry and Pharmacy, Nucleic Acid Center, University of Southern Denmark, Campusvej 55, 5230 Odense M,
Denmark
Fax +45 66158780; E-mail: erik@sdu.dk
b
Department of Chemistry, Faculty of Science, Damietta University, 34517 New Damietta, Damietta, Egypt
c
Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, 35516 Mansoura, Egypt
Received: 26.06.2013; Accepted after revision: 22.08.2013
and gives poor yields.10–13 To improve the regioselectivity
Abstract: An allopurinol locked nucleic acid (LNA) monomer was
of the reaction, allopurinol ribonucleoside have been syn-
prepared by a novel strategy through C6 deamination of the corre-
thesized from starting materials other than allopurinol.13–15
For example, 4,6-dichloro-1H-pyrazolo[3,4-d]pyrimidine
sponding 8-aza-7-bromo-7-deazaadenine LNA monomer with
aqueous sodium hydroxide. An 8-aza-7-deazaadenine LNA mono-
mer was also synthesized by a modification of the new synthetic has been used in the presence of trimethylsilyl triflate as a
pathway. N-Glycosylation at the 8-position was prevented by steric
hindrance from the 7-bromo atom in the starting material 8-aza-7-
bromo-7-deazaadenine. In the final step of the synthesis, the bro-
lo[3,4-d]pyrimidine13 and 4-chloro-1H-pyrazolo[3,4-
mine was removed together with a benzyl protecting group by cat-
alytic reduction with ammonium formate to give the required LNA
catalyst, but additional synthetic steps are required to pre-
pare the target compound.15 Also, 4-methoxy-1H-pyrazo-
d]pyrimidine14 have been glycosylated by using phase-
transfer methods, but both the N-8 and N-9 glycosylated
products were formed. This lack of regioselectivity also
occurred in glycosylation of 8-aza-7-deazaadenine with
1,2-di-O-acetyl-3-O-benzyl-4-C-[(mesyloxy)methyl]-5-
O-mesyl-D-erythro-pentofuranose (2) in the presence of
trimethylsilyl triflate.16 When we searched the literature
for possible solutions to this problem, we found that 7-ha-
logenated 8-aza-7-deazapurine-2,6-diamines can be gly-
cosylated in the presence of the Lewis acid boron
trifluoride etherate (BF3·Et2O) to give the N-9 isomer ex-
clusively.17 Glycosylation at the N-8 position is prevented
by the electron-withdrawing effect of the 7-halo group
and by steric hindrance.17 We therefore decided to use 8-
aza-7-bromo-7-deazaadenine18 (1) as a starting material
for the synthesis of allopurinol LNA and 8-aza-7-
deazaadenine LNA through a pathway involving an N-9
selective glycosylation followed by debromination.
monomers.
Key words: glycosylations, nucleobases, nucleosides, regioselec-
tivity
In the last two decades, a great deal of interest has been fo-
cused on the synthesis and design of modified oligonucle-
otides, with the aim of developing strong recognition of
complementary DNA or RNA sequences.1–3 Many modi-
fied oligonucleotides containing bi- and tricyclic carbohy-
drate-modified nucleotides have been studied, and their
duplexes with complementary nucleic acids have been
shown to be much more stable than those of the corre-
sponding unmodified duplexes.3 Bicyclic ribonucleotides
containing a 2′-O,4′-C-methylene bicyclic sugar moiety
were named ‘locked nucleic acids’ (LNA) when they were
introduced in 1998.4 The corresponding oligonucleotides
show unprecedented thermal stabilities when hybridized
with complementary DNA and RNA strands, increasing
the melting temperatures of the duplexes in comparison
with those of their unmodified analogues.4b,5–7 However,
the thermal stability of oligonucleotide duplexes can be
also be improved by modifying the nucleobase, as well as
by modifying carbohydrate moiety. Replacing adenine
with 8-aza-7-deazaadenine slightly increased the stability
of duplexes, whereas the incorporation of 7-substituted
derivatives leads to duplexes that are much more stable
than their adenine-containing counterparts.8,9
We achieved selective N-9 glycosylation of 8-aza-7-bro-
mo-7-deazaadenine (1) with 1,2-di-O-acetyl-3-O-benzyl-
4-C-[(mesyloxy)methyl]-5-O-mesyl-D-erythro-pentofu-
ranose (2)4g in the presence of two equivalents of tin(IV)
chloride as a Lewis acid in refluxing acetonitrile. The nu-
cleoside 3 (the N-9 isomer) was separated in 62% yield as
the only product, and no traces of the N-8 isomer were de-
tected (Scheme 1).
Treatment of nucleoside 3 with 2 M aqueous sodium hy-
droxide in 1,4-dioxane with stirring at room temperature
for one hour resulted in deacetylation and ring closure of
the sugar moiety to give the LNA monomer 4 in 88%
yield. No chromatography was necessary during the
workup, and the product could be used in the next step
without additional purification. Benzoate displacement of
the 5′-mesylate group in 4 gave the corresponding 5′-O-
benzoyl LNA monomer 5 in 84% yield (Scheme 1).
The glycosylation of allopurinol is a problem in nucleo-
side synthesis, because the reaction lacks regioselectivity
SYNTHESIS 2013, 45, 3259–3262
Advanced online publication: 13.09.2013
DOI: 10.1055/s-0033-1338531; Art ID: SS-2013-Z0438-OP
© Georg Thieme Verlag Stuttgart · New York
0
0
3
9
-
7
8
8
1
1
4
3
7
-
2
1
0
X

3260
T. Kosbar et al.
PAPER
analogue.25 Accordingly, we expected C6 deamination of
8-aza-7-bromo-7-deazaadenine to take place on treatment
with hydroxide ion. Indeed, when compound 5 was re-
fluxed in 2 M aqueous sodium hydroxide and 1,4-dioxane
for 24 hours, both 5′-O-debenzoylation and C6 deamina-
tion occurred to give the deprotected keto derivative 8 in
about 90% yield, but when compound 5 was treated with
a mixture of concentrated ammonium hydroxide and pyr-
idine at 60 °C for 24 hours, the 5′-O-debenzoylated prod-
uct 6 was obtained in 85% yield, and no C6 deamination
occurred (Scheme 2).
NH2
Br
N
MsO
MsO
O
N
OAc
SnCl4, MeCN
reflux, 24 h
+
N
H
N
BnO
OAc
1
2
NH2
Br
N
N
N
NH2
Br
N
MsO
MsO
N
NaOH (2 M)
1,4-dioxane
O
N
N
N
MsO
O
BnO
OAc
3 62%
Removal of the 3′-O-benzyl group and debromination of
compounds 6 and 8 was achieved through catalytic trans-
fer hydrogenation by stirring the compounds with ammo-
nium formate and palladium(II) hydroxide/carbon in
refluxing methanol. This gave the target products 7 and 9,
BnO
O
4 88%
BzONa (2 equiv)
DMF, 100 °C, 6 h
NH2
Br
N
N
1
respectively (Scheme 2). The H NMR and 13C NMR
N
N
BzO
BnO
spectra of compound 7 agreed with previously published
data,16 and the NMR spectra of the allopurinol part of 9
corresponded well with previously published data for al-
lopurinol nucleosides.13
O
O
5 84%
In summary, we have developed a highly efficient method
for synthesizing the allopurinol LNA monomer 9 through
C6 deamination of the 8-aza-7-bromo-7-deazaadenine
LNA monomer 5. The new method helps to overcome
problems associated with lack of regioselectivity and low
yields in glycosylation of allopurinol. In parallel, a new
synthetic pathway for 8-aza-7-deazaadenine LNA mono-
mer 7 was developed, in which the corresponding bromo
derivative 6 was debrominated after reduction with palla-
dium(II) hydroxide/carbon and ammonium formate.
Scheme 1
Enzymatic C6 deamination of adenosine analogues is a
well-known reaction.19–25 Density functional theory cal-
culations have shown that 8-aza-7-deazapurine is more
readily hydrated than are simple purines.25 Furthermore,
the hydrate of 8-aza-7-bromo-7-deazapurine has been
shown to be more stable than that of its 7-unsubstituted
NH2
Br
NMR spectra were recorded on a Bruker 400 MHz NMR spectrom-
eter at 400 MHz for 1H and at 101 MHz for 13C with TMS as an in-
ternal standard; chemical shifts (δ) are quoted in ppm. Electrospray
ionization high-resolution mass spectra were recorded on a PE SCI-
EX API Q-Star Pulsar spectrometer. For accurate determinations of
ion masses, the [M + H]+ or [M + Na]+ ion was peak matched by cal-
ibration with NaI.
N
NH4OH
pyridine
N
NaOH (2 M)
1,4-dioxane
N
N
BzO
reflux, 24 h
60 °C, 24 h
O
BnO
O
O
N
5
Br
NH2
Br
N
(2R,3R,4S)-2-(4-Amino-3-bromo-1H-pyrazolo[3,4-d]pyrimidin-
1-yl)-4-(benzyloxy)-5,5-bis[(mesyloxy)methyl]tetrahydrofuran-
3-yl Acetate (3)
NH
N
N
N
N
8-Aza-7-bromo-7-deazaadenine18 (1; 2.83 g, 13.22 mmol) and 1,2-
di-O-acetyl-3-O-benzyl-4-C-[(mesyloxy)methyl]-5-O-mesyl-D-
erythro-pentofuranose4g (2; 6.75 g, 13.22 mmol) were placed in a
dried flask under argon. Anhyd MeCN (50 mL) was added by sy-
ringe, and the mixture was stirred for 15 min. SnCl4 (3.10 mL, 26.4
mmol) was then added by syringe, and the mixture was refluxed for
24 h then cooled to r.t. The reaction was quenched with sat. aq
NaHCO3 (50 mL), and the mixture was extracted with EtOAc (3 ×
100 mL). The organic layers were combined, dried (Na2SO4), con-
centrated, and purified by flash column chromatography [silica gel,
MeOH–CH2Cl2 (1:25)] to give a white solid; yield: 62% (5.50 g);
mp 90–92 °C.
N
HO
HO
O
O
BnO
O
BnO
O
8 90%
6 85%
Pd(OH)2/C
HCOONH4
Pd(OH)2/C
HCOONH4
EtOH, reflux, 12 h
EtOH, reflux, 12 h
NH2
O
N
N
NH
N
N
N
N
N
1H NMR (400 MHz, DMSO-d6): δ = 8.26 (s, 1 H), 7.44–7.28 (m, 5
H), 6.45 (d, J = 2.6 Hz, 1 H), 5.80 (dd, J = 5.5, 2.6 Hz, 1 H), 4.89
(d, J = 5.5 Hz, 1 H), 4.69 (d, J = 11.2 Hz, 1 H), 4.62 (d, J = 11.1
Hz, 1 H), 4.53 (d, J = 11.1 Hz, 1 H), 4.47 (d, J = 11.0 Hz, 1 H), 4.38
(d, J = 10.7 Hz, 1 H), 4.29 (d, J = 10.8 Hz, 1 H), 3.21 (s, 3 H), 3.12
(s, 3 H), 2.09 (s, 3 H).
HO
HO
O
O
HO
O
HO
O
9 89%
7 87%
Scheme 2
Synthesis 2013, 45, 3259–3262
© Georg Thieme Verlag Stuttgart · New York

PAPER
Allopurinol Locked Nucleic Acid Monomer
3261
13C NMR (100 MHz, DMSO-d6): δ = 169.37, 157.39, 157.29,
154.75, 137.00, 128.28, 128.16, 127.89, 120.60, 99.70, 86.03,
83.04, 78.21, 73.35, 73.23, 68.33, 68.04, 36.79, 36.52, 20.42.
HRMS (ESI): m/z [M + Na]+ calcd for C22H26BrN5NaO10S2:
686.0197; found: 686.0172.
HRMS (ESI): m/z [M + Na]+ calcd for C18H18BrN5NaO4: 470.0434;
found: 470.0431.
(1S,3R,4R,7S)-3-(4-Amino-1H-pyrazolo[3,4-d]pyrimidin-1-yl)-
1-(hydroxymethyl)-2,5-dioxabicyclo[2.2.1]heptan-7-ol (7)
Bromo compound 6 (0.35 g, 0.78 mmol) was suspended in MeOH
(10 mL), and the mixture was cooled 0 °C. 20% Pd(OH)2/C (0.25 g)
was added in portions during 10 min and then the mixture was al-
lowed to stand for 10 min. HCO2NH4 (0.75 g) was added in small
portions, and then the mixture was allowed to warm to r.t. for 1 h.
The solution was then refluxed for 6 h, more HCO2NH4 (0.5 g) was
added, and the mixture was refluxed for a further 6 h. The hot solu-
tion was filtered through a Celite pad that was washed with boiling
MeOH. Evaporation of the filtrate gave white crystals; yield: 87%
(0.19 g); mp 244–246 °C (MeOH).
1H NMR (400 MHz, CD3OD): δ = 8.20 (s, 1 H), 8.13 (s, 1 H), 6.25
(s, 1 H), 5.11 (s, 1 H), 4.37 (s, 1 H), 4.10 (d, J = 8.0 Hz, 1 H), 3.95
(d, J = 8.0 Hz, 1 H), 3.88 (s, 2 H).
13C NMR (100 MHz, CD3OD): δ = 159.86, 157.16, 155.22, 134.81,
101.84, 88.95, 85.93, 82.14, 73.82, 73.12, 59.45.
[(1R,3R,4R,7S)-3-(4-Amino-3-bromo-1H-pyrazolo[3,4-d]py-
rimidin-1-yl)-7-(benzyloxy)-2,5-dioxabicyclo[2.2.1]hept-1-
yl]methyl Mesylate (4)
2 M aq NaOH (10 mL) was added to a solution of acetate 3 (5.0 g,
7.52 mmol) in 1,4-dioxane (40 mL). The solution was stirred at r.t.
for 1 h, and then the solvents were removed under reduced pressure.
The residue was suspended in CH2Cl2 (150 mL), washed with sat.
aq NaHCO3 (150 mL), dried (Na2SO4), and concentrated under re-
duced pressure to give a white solid; yield: 88% (3.50 g). This was
used in the next step without further purification.
1H NMR (400 MHz, CDCl3): δ = 8.32 (s, 1 H), 7.45–7.26 (m, 5 H),
6.36 (s, 1 H), 5.00 (s, 1 H), 4.78 (d, J = 11.8 Hz, 1 H), 4.72 (d,
J = 11.8 Hz, 1 H), 4.57 (d, J = 12.1 Hz, 1 H), 4.51 (d, J = 12.1 Hz,
3 H), 4.48 (s, 1 H), 4.19 (d, J = 7.9 Hz, 1 H), 4.01 (d, J = 7.9 Hz, 1
H), 3.02 (s, 3 H).
13C NMR (100 MHz, CDCl3): δ = 157.42, 157.38, 155.16, 136.95,
128.61, 128.50, 128.33, 120.19, 100.49, 84.62, 84.38, 79.02, 78.08,
72.72, 72.46, 65.82, 37.77.
HRMS (ESI): m/z [M + H]+ calcd for C19H21BrN5O6S: 526.0390;
found: 526.0388.
HRMS (ESI): m/z [M + H]+ calcd for C11H14N5O4: 280.1040; found:
280.1036.
1-{(1S,3R,4R,7S)-7-(Benzyloxy)-1-(hydroxymethyl)-2,5-dioxa-
bicyclo[2.2.1]hept-3-yl}-3-bromo-1,5-dihydro-4H-pyrazolo[3,4-
d]pyrimidin-4-one (8)
2 M aq NaOH (25 mL) and H2O (7 mL) were added to a solution of
benzoate 5 (2.7 g, 4.9 mmol) in 1,4-dioxane (25 mL). The mixture
was refluxed for 24 h, cooled to r.t., and neutralized with AcOH (4
mL). Sat. aq NaHCO3 (25 mL) was added, and the mixture was ex-
tracted with CH2Cl2 (2 × 100 mL). The organic layers were com-
bined, dried (Na2SO4), and concentrated under reduced pressure to
give a white solid; yield: 90% (2.00 g). The product was used in the
next step without further purification.
1H NMR (400 MHz, DMSO-d6): δ = 8.17 (s, 1 H), 7.45–7.31 (m, 5
H), 6.07 (s, 1 H), 4.79 (s, 1 H), 4.71 (d, J = 11.9 Hz, 1 H), 4.67 (s,
1 H), 4.66 (d, J = 11.9 Hz, 1 H), 4.50 (s, 1 H), 3.96 (d, J = 8.0 Hz,
1 H), 3.83 (d, J = 7.9 Hz, 1 H), 3.74 (d, J = 12.8 Hz, 1 H), 3.69 (d,
J = 12.6 Hz, 1 H).
13C NMR (100 MHz, DMSO-d6): δ = 156.32, 153.47, 150.12,
137.66, 128.18, 127.87, 127.61, 122.64, 104.79, 87.24, 83.97,
78.34, 77.32, 72.02, 71.21, 57.09.
HRMS (ESI): m/z [M + H]+ calcd for C18H18BrN4O5: 449.0455;
found: 449.0445.
[(1R,3R,4R,7S)-3-(4-Amino-3-bromo-1H-pyrazolo[3,4-d]py-
rimidin-1-yl)-7-(benzyloxy)-2,5-dioxabicyclo[2.2.1]hept-1-
yl]methyl Benzoate (5)
NaOBz (1.75 g, 12 mmol) was added to a solution of mesylate 4 (3.2
g, 6 mmol) in anhyd DMF (50 mL). The mixture was stirred at
100 °C for 6 h then cooled to r.t., filtered, and concentrated under
reduced pressure. The residue was suspended in EtOAc (100 mL),
washed with sat. aq NaHCO3 (3 × 50 mL), dried (Na2SO4), and con-
centrated under reduced pressure to give the desired product as a
white solid; yield: 84% (2.80 g).
1H NMR (400 MHz, CDCl3): δ = 8.31 (s, 1 H), 7.94 (d, J = 7.2 Hz,
2 H), 7.55 (t, J = 7.4 Hz, 1 H), 7.43–7.28 (m, 7 H), 6.42 (s, 1 H),
5.19 (s, 1 H), 4.81–4.66 (m, 3 H), 4.57–4.42 (m, 2 H), 4.25 (d,
J = 7.8 Hz, 1 H), 4.08 (d, J = 7.7 Hz, 1 H).
13C NMR (100 MHz, CDCl3): δ = 165.98, 157.37, 157.26, 155.18,
137.13, 133.11, 129.82, 128.51, 128.40, 128.15, 127.87, 127.57,
120.01, 100.49, 84.71, 84.52, 78.88, 78.05, 72.64, 72.62, 60.55.
HRMS (ESI): m/z [M + H]+ calcd for C25H23BrN5O5: 552.0877;
found: 552.0865.
1-[(1S,3R,4R,7S)-7-Hydroxy-1-(hydroxymethyl)-2,5-dioxabicy-
clo[2.2.1]hept-3-yl]-1,5-dihydro-4H-pyrazolo[3,4-d]pyrimidin-
4-one (9)
[(1S,3R,4R,7S)-3-(4-Amino-3-bromo-1H-pyrazolo[3,4-d]pyrim-
idin-1-yl)-7-(benzyloxy)-2,5-dioxabicyclo[2.2.1]hept-1-yl]meth-
anol (6)
Concd aq NH4OH (8 mL) was added to a solution of benzoate 5
(0.55 g, 1 mmol) in pyridine (4 mL), and the solution was heated at
60 °C for 24 h. The mixture was then concentrated under reduced
pressure, co-evaporated with toluene, and purified by column chro-
matography [silica gel, CH2Cl2–MeOH (30:1)] to give a white solid;
yield: 85% (0.38 g); mp 160–162 °C.
1H NMR (400 MHz, DMSO-d6): δ = 8.26 (s, 1 H), 7.46–7.29 (m, 5
H), 6.13 (s, 1 H), 4.96 (t, J = 5.2 Hz, 1 H), 4.81 (s, 1 H), 4.66 (s, 2
H), 4.35 (s, 1 H), 3.96 (d, J = 7.9 Hz, 1 H), 3.83 (d, J = 7.9 Hz, 1 H),
3.74 (dd, J = 5.2, 12.7 Hz, 1 H), 3.68 (dd, J = 12.9, 5.2 Hz, 1 H).
20% Pd(OH)2/C (1.28 g) and HCO2NH4 (3.8 g) were added to a sus-
pension of compound 8 (1.8 g, 4 mmol) in MeOH (30 mL), and the
solution was refluxed for 6 h. More HCO2NH4 (1.5 g) was then add-
ed and the mixture was refluxed for a further 6 h. The hot solution
was filtered through a Celite pad that was washed with boiling
MeOH. Evaporation of the filtrate gave white crystals; yield: 89%
(1.00 g); mp 196–198 °C (MeOH).
1H NMR (400 MHz, DMSO-d6): δ = 12.35 (br s, 1 H), 8.19 (s, 1 H),
8.14 (s, 1 H), 6.07 (s, 1 H), 5.70 (br s, 1 H), 4.89 (s, 1 H), 4.84 (br s,
1 H), 4.32 (s, 1 H), 3.96 (d, J = 7.8 Hz, 1 H), 3.80 (d, J = 7.8 Hz, 1
H), 3.73 (d, J = 12.7 Hz, 1 H), 3.68 (d, J = 12.7 Hz, 1 H).
13C NMR (100 MHz, DMSO-d6): δ = 157.00, 152.69, 148.69,
13C NMR (100 MHz, DMSO-d6): δ = 157.32, 157.13, 154.64,
137.70, 128.19, 128.16, 127.85, 119.76, 99.31, 87.00, 83.70, 78.41,
77.35, 72.04, 71.17, 57.14.
135.59, 105.91, 87.58, 83.80, 79.91, 71.88, 71.57, 57.54.
HRMS (ESI): m/z [M + H]+ calcd for C11H13N4O5: 281.0880; found:
281.0871.
© Georg Thieme Verlag Stuttgart · New York
Synthesis 2013, 45, 3259–3262

3262
T. Kosbar et al.
PAPER
(5) Kierzek, E.; Mathews, D. H.; Ciesielska, A.; Turner, D. H.;
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Acknowledgement
The Ministry of Higher Education of Egypt is gratefully acknowl-
edged for a predoctoral channel fellowship to Tamer Kosbar.
Supporting Information for this article is available online at
http://www.thieme-connect.com/ejournals/toc/synthesis.SnuIomprifgtooatrinSugpIoi
nnfomartit
(10) Cuny, E.; Lichtenthaler, F. W. Nucleic Acids Res., Spec.
Publ. 1975, 1, 25.
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