Synthesis of 5-acetyl-2-aminopyrrole C-deoxyribonucleoside

Article abstract of DOI:10.1016/j.tet.2007.09.082

A novel C-deoxyribonucleoside bearing 2-aminopyrrole was synthesized. The C-glycosidation between deoxyribose and pyrrole ring was carried out using palladium-catalyzed Heck coupling in the presence of excess amount of lithium chloride as an additive. The

Full text of DOI:10.1016/j.tet.2007.09.082

Tetrahedron 63 (2007) 12747–12753
Synthesis of 5-acetyl-2-aminopyrrole C-deoxyribonucleoside
*
Hiroshi Oda, Takeshi Hanami, Takashi Iwashita, Miki Kojima,
Masayoshi Itoh and Yoshihide Hayashizaki
Genome Science Laboratory, Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC),
Discovery and Research Institute, RIKEN Wako Main Campus, 2-1 Hirosawa, Wako, Saitama 351-0106, Japan
Received 21 August 2007; revised 28 September 2007; accepted 28 September 2007
Available online 2 October 2007
Abstract—A novel C-deoxyribonucleoside bearing 2-aminopyrrole was synthesized. The C-glycosidation between deoxyribose and pyrrole
ring was carried out using palladium-catalyzed Heck coupling in the presence of excess amount of lithium chloride as an additive. The
synthesized aminopyrrole nucleoside is expected to become a promising counterpart of the artificial nucleoside pair.
Ó 2007 Elsevier Ltd. All rights reserved.
1. Introduction
patterns can be depicted as shown in Figure 1 because hydro-
gen bond has the direction. However, it is possible that
pyrimidine-type bases shown in Figure 1A–C form pairs
with natural purine bases. Although type D that has gem-
diaminoethylene structure is unstable, and tautomerization
occurs easily to take an undesired hydrogen bonding pattern
as shown in Eq. 1,2 this six-membered base is promising be-
cause it is expected to form a specific base pair with unnat-
ural purine-type base.
DNA that consists of the four bases A, G, C, and T is one of
the most important biomolecules by means of coding indis-
pensable information for life. The three bases of mRNA tran-
scribed from DNA, codon, correspond to 20 kinds of amino
acids respectively, and translated to protein. Thus, if an
artificial nucleobase pair could be added to the natural
base pair system, the number of codons would be drama-
tically increased. In the past two decades, some groups
reported the trial of synthesis of enzymatically replicable ar-
tificial base pairs for a functionalized protein that includes
unnatural amino acids by such an approach.1
H2N
HN
H2N
N
ð1Þ
dR
dR
The artificial base pairs that have been reported so far can be
divided roughly into hydrogen bond type and hydrophobic
interaction type according to how to form the base pair. At
present, there is a report about highly selective PCR replica-
tion including artificial base pairs using the hydrophobic
interaction type base pair.1e However, these bases can hardly
be used in a codon because the bonding energy is quite low.
On the other hand, we recently reported the synthesis of imi-
dazo[1,2-a][1,3,5]triazin-4-one deoxyribonucleoside (Im)
as a purine-type nucleoside that only has solely lone-pair
O
N
N
N
H
N
H
O
N
N
N
H
H
O
N
dR
N
Benner et al. vigorously studied the syntheses of several
artificial nucleosides that had different hydrogen bonding
patterns from natural bases.1a–c They employed artificial
bases that had triple hydrogen bonds like the natural G/C
base pair. When isoG/isoC base pair was used for the experi-
ment of incorporation by DNA polymerase, moderate selec-
tivity was achieved in their replication.1b
N
N
H
dR
N
H
dR
dR
A
B
H
H
O
N
N
H
N
N
O
N
H
H
N
N
H
H
N
N
dR
N
dR
If a nucleoside pair is formed by using two hydrogen bonds
like the natural A/T base pair, four hydrogen bonding
dR
dR
H
C
D
* Corresponding author. Tel.: +81 48 467 9513; fax: +81 48 462 4686;
e-mail addresses: rgscerg@gsc.riken.go.jp; hoda@riken.jp
Figure 1. Base pairing of double hydrogen bonded deoxyribonucleoside.
0040–4020/$ - see front matter Ó 2007 Elsevier Ltd. All rights reserved.
doi:10.1016/j.tet.2007.09.082

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H. Oda et al. / Tetrahedron 63 (2007) 12747–12753
EWG
Ac
N
Me
N
N
N
H
H
O
H
O
N
N
N
N
dR
dR
N
N
N H
H
R
dR
N
H
Me
Figure 2. Base pairing of 2-aminopyrrole and pyrido[1,2-a][1,3,5]triazin-4-
one.
Me
Figure 4. Base pairing of 2-aminopyrrole and m2,2,7-G.
donor site located in one molecule.3a Furthermore, we
described the synthesis of pyrido[1,2-a][1,3,5]triazin-4-one
C-deoxyribonucleoside (Pt) and a DNA oligomer including
this nucleoside, and revealed that the derivative of this nucle-
oside does not form base pairs with all four natural bases
efficiently.3b When introducing the fused six/six-membered
ring into the natural DNA strand, it is preferable to employ
the five-membered ring to fit the distance between the
anomer carbons of the complementary strand to the natural
nucleoside (Fig. 2). Naturally, a triple hydrogen bond is
stronger than a double hydrogen bond. However, to consider
the secondary electrostatic interaction, nucleoside 1 is ex-
pected to form a stronger bond than an antiparallel hydrogen
bond such as A/T base pair.4
influence for the hydrogen bonding pattern in modifying the
nucleic acid, there is no problem in the reverse transcription
reaction. In the case of mRNAs that contain modified RNA
such as trimethylguanosine, the reverse transcription reac-
tion will stop at the position of the modified base. There is
a possibility to overcome the problem when triphosphate-
form of nucleoside 1 is used in the preparation of the cDNAs.
2. Results and discussion
First, we planned to synthesize 1 by the palladium-catalyzed
Heck reaction between nucleobase (or protected) halide and
silyl protected furanoid glycal for the construction of the
C-glycoside bond as a key step of the synthetic strategy as
shown in Scheme 1. 5-Acetyl-2-nitro-1H-pyrrole (3a) was
obtained along with 5-acetyl-3-nitro-1H-pyrrole (3b) by
the reaction of 2-acetylpyrrole (2) with nitric acid. Com-
pounds 3a and 3b could be separated by silica gel column
chromatography. Nitro group of 3a was reduced with iron
in acetic acid to afford 5-acetyl-2-acetylaminopyrrole (4).
This reduction reaction is advantageous for the synthetic
strategy at the point of view of the one-pot introduction of
the protecting group for the exocyclic amino group of the
halo-aminopyrrole. Compound 4 was halogenated by NBS
and NIS to obtain bromide (5a) and iodide (5b), respectively.
The furanoid glycal 6 was prepared by a method described in
the literature.7
It is difficult to design an appropriate pyrimidine-type base
that has only lone-pair acceptor sites satisfying the restric-
tion of the nucleobase such as a planarity, not markedly large
size. Thus, we planned to synthesize an artificial nucleoside
bearing 2-aminopyrrole as shown in Figure 2. Although 2-
aminopyrrole is frequently seen in the field of computational
chemistry, this compound is unstable in air. There is only one
report available where 2-aminopyrrole was confirmed in the
NMR tube.5 It is necessary to introduce an electron with-
drawing group in order to stabilize the gem-diaminoethylene
structure of 2-aminopyrrole. We used 2-acetylpyrrole as
a readily available starting pyrrole having an electron with-
drawing group, and report herein the synthesis of novel
C-deoxyribonucleoside, 5-acetyl-2-aminopyrrole C-deoxy-
ribonucleoside 1 (Fig. 3) as a promising counterpart of the
Im or Pt.
Ac
Ac
Ac
NH
The nucleoside 1 may be usable for cDNA synthesis contain-
ing modified RNA such as trimethylguanosine as shown in
Figure 4. We have previously prepared and sequenced full-
length cDNA from several organisms so far.6 However, we
may not have achieved the sequence of all cDNAs, because
mRNA contains many modified RNA residues. If there is no
a
b
NH
NH
+
NO2
NO2
2
3a
3b
Ac
Ac
NH
NH
c
O
O
Ac
Ac
N
H
N
H
N
N
N
N
X
N
N
R
N
HO
4
HO
5a ; X = Br
5b ; X = I
O
O
Ac
O
OH
OH
Im
NH
Pt
Ac
Heck reaction
N
H
Ac
O
TBSO
NH
O
TBSO
TBSO
NH2
HO
TBSO
6
7
OH
Scheme 1. Reagents and conditions: (a) HNO3, Ac2O, ꢀ40 ꢁC, 2 h, 3a
(36%), 3b (51%); (b) Fe, HOAc, 100 ꢁC, 2 h, 36%; (c) NBS, CH2Cl2,
ꢀ40 ꢁC, 1 h, 66% or NIS, CH2Cl2, ꢀ40 ꢁC, 1 h, 52%.
1
Figure 3. Artificial nucleoside.

H. Oda et al. / Tetrahedron 63 (2007) 12747–12753
12749
Table 1. Assessment of additives in the Heck reaction of 5-acetyl-3-iodo-2-
nitropyrrole 9 with protected furanoid glycal 6a
The crucial step of C-deoxyribonucleoside synthesis may
often be the C-glycosidation reaction by using the Heck re-
action. Because troublesome protection/deprotection step is
sometimes needed, it is important to avoid further functional
group interconversion of the nucleoside. Heck reaction is
also convenient to construct the configuration of the b-
anomer structure. Therefore, it is strategically superior to
construct the Heck reaction of iodide 5 into the synthetic
route. However, the Heck reaction between halide 5 and fur-
anoid glycal 6 did not afford the coupling product 7 in spite
of the wide investigation of the reaction conditions.8
Entry
Additive (equiv)
Yield of 10b (%)
1
2
3
4
5
6
Me4NCl (1)
Me4NBr (1)
Me4NI (1)
Et4NCl (1)
Et4NBr (1)
Et4NI (1)
6
15
9
19
8
6
7
8
9
Pr4NCl (1)
Pr4NBr (1)
Pr4NI (1)
9
10
5
10
11
12
13
14
15
16
17
18
19
20
Bu4NCl (1)
Bu4NBr (1)
Bu4NI (1)
LiCl (1)
NaCl (1)
KCl (1)
KCl+18-C-6 (1)
LiCl (2)
LiCl (5)
LiCl (10)
None (—)
9
18
4
19
17
5
In general, the oxidative addition of the electron rich aryl
halide to the palladium(0) species is not so easy to occur.
We assumed that the Heck reaction of 5 with 6 did not pro-
ceed because electron density over the pyrrole ring of the ha-
lide 5 was high, owing to the electron donation of the
acetylamino group. Furthermore, there might be a possibility
that the catalytic cycle was inhibited because the iodide 5
strongly coordinated to the palladium.
9
19
48
35
12
a
All reactions were carried out using 9 (0.5 mmol), 6 (0.5 mmol),
PdCl2[P(o-tol)3]2 (10 mol %), Et3N (4 equiv), and additives in DMF
(5 mL) under irradiation of microwave at 140 ꢁC for 10 min.
Isolated yield.
Because the Heck reaction between 5 and 6 did not occur, the
synthetic route was changed to carry out the Heck reaction of
5-acetyl-3-iodo-2-nitro-1H-pyrrole (9) prior to the reduction
of the nitro group. The preparation of iodide 9 is shown in
Scheme 2. Pyrrole 2 was quantitatively iodinated by NIS to
afford 2-acetyl-4-iodo-1H-pyrrole (8).9 Compound 9 was ob-
tained by the treatment of 8 with nitric acid in moderate yield.
b
C-deoxyribonucleoside (12) was obtained by diastereoselec-
tive reduction of 30-keto group of 11 in high yield.
Ac
Ac
Ac
Ac
O
Ac
NH
NH
NH
NH
NH
a
b
NH
NO2
NO2
NO2
a
TBSO
HO
HO
I
8
I
9
O
2
O
Scheme 2. Reagents and conditions: (a) NIS, CHCl3/CCl4, Amberlyst-
15DRY, 70 ꢁC, 24 h, 96%; (b) HNO3, Ac2O, ꢀ40 ꢁC, 2 h, 43%.
TBSO
10
11
Ac
The Heck coupling adduct 10 was obtained by the reaction
of iodide 9 and furanoid glycal 6 in low yield under conven-
tional conditions (ligand; triphenylphosphine, base; triethyl-
amine, solvent; DMF) using microwave at 140 ꢁC for
10 min. Tri(o-tolyl)phosphine was found to be an optimal
ligand by the assessment of the reaction condition. Triethyl-
amine and diisopropylethylamine were tolerable as bases,
whereas inorganic base such as sodium carbonate or potas-
sium phosphate was not. DMF gave best yield as a solvent.
An additive effect is depicted in Table 1. Addition of excess
amount of lithium chloride significantly increased the yield
of the Heck coupling adduct (entry 18).10 On the other hand,
addition of ammonium salt did not affect the yield even if the
quantity was increased.11
NO2
b
O
OH
12
Scheme 3. Reagents and conditions: (a) 70%-TBAFaq, HOAc, THF, rt, 10 h,
80%; (b) NaBH(OAc)3, HOAc, MeCN, ꢀ40 to 0 ꢁC, 2 h, 87%.
The nitro group of 12 could reduce by the hydrogenation with
palladium charcoal in moderate yield. However, the product
of the reduction was confirmed as a-anomer that had com-
pletely inversed at the anomeric carbon by the measurement
of the NOE spectra (Scheme 4). On the other hand, the reduc-
tion of compound 13 where the 30- and 50-hydroxyl groups
were protected by the silyl group occurred almost quantita-
tively with retention of the stereochemistry, and a-anomer
was not detected. Although 30- and 50-silyl groups of 14 could
not deprotect under usual condition by treatment of TBAF,
the removal of the silyl group was achieved by using trime-
thylsilyl triflate. However, the inversion of the anomeric
carbon occurred again, and resulting product was a-1.
The yield of the Heck reaction between iodide 9 and fura-
noid glycal 6 was improved by using an excess amount of
lithium chloride as an additive. Additives such as inorganic
salt generally enhance the reactivity by coordinating the
anion to the intermediate palladium species. However, the
effect in our case is not clear because the yield was different
depending on the counter cations of the additives.
Adduct 10 was desilylated by tetrabutylammonium
fluoride (TBAF) to afford 30-keto nucleoside (11) in
good yield (Scheme 3). 5-Acetyl-2-nitro-1H-pyrrole
The C-nucleoside sometimes causes the inversion of the
anomeric carbon by protonation to the anomeric oxygen

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H. Oda et al. / Tetrahedron 63 (2007) 12747–12753
HO
Ac
H
H
O
HO
NH
H
H
O
H
a
H
O
NH2
OH
H
H
12
HO
H
H
H
OH
H2N
N
H
Ac
Ac
H
H
α-1
N
H
OH
H2N
α-1
Figure 5. NOE correlations of compound 1 and a-1.
b
1
d
Ac
O
Ac
revealed that compound 1 has a b-conformation (Fig. 5).
No a-anomer was detected.
NH
NH
NO2
c
NH2
TBSO
TBSO
O
3. Conclusion
OTBS
13
OTBS
14
In summary, we achieved the synthesis of the novel C-nucleo-
side, 2-aminopyrrole C-deoxyribonucleoside 1. The nucleo-
side 1 does not only have a promising ability for molecular
biological use, but the synthetic route also includes some
synthetically interesting phenomena. The significant addi-
tive effect was observed in the C-glycosidation step using
palladium-catalyzed Heck coupling. To our knowledge, it
is unusual that the use of a large excess amount of additive
is effective. Although the mechanism is still unclear, epime-
rization under the condition of hydrogenation catalyzed by
palladium is also unusual. A molecular biological study
using nucleoside 1 is in progress.
Scheme 4. Reagents and conditions: (a) H2, 10%-Pd/C, H2O, rt, 40 min,
46%; (b) tert-BuMe2SiCl, imidazole, DMF, rt, overnight, 97%; (c) H2,
10%-Pd/C, MeOH, rt, 2.5 h, 96%; (d) Me3SiOTf, MeOH, Et3N, ꢀ40 ꢁC,
2 h, 84%.
on the sugar moiety under acidic conditions.12 The epimeri-
zation of C-deoxyribonucleoside, in the presence of benze-
nesulfonic acid and small amounts of water under toluene
reflux condition, have been reported by Kool et al.12a On
the other hand, Benner described that the C-nucleoside
having hydrogen at the appropriate position of the base moi-
ety epimerize to afford four isomers depending on pH, based
on the report concerned with the epimerization of pseudour-
idine.12b–d,13 We believe that the epimerization that occurred
in deprotecting nucleoside 14 took place by a similar mech-
anism to the description in Benner’s report. To our knowl-
edge, there is no report available that describes inversion
of anomeric carbon under the condition of palladium-
catalyzed hydrogenation.
4. Experimental
4.1. General
1H NMR spectra were recorded on a JEOL JNM-a400
(400 MHz) instrument. The chemical shifts are reported in
parts per million (d) downfield from tetramethylsilane
(d¼0 ppm). The signal patterns are indicated as s, singlet;
d, doublet; t, triplet; q, quartet; m, multiplet; br s, broad sin-
glet. The coupling constants (J) are given in Hertz. The 13C
NMR spectra were recorded on a JEOL JNM-a400
(100 MHz) instrument. The chemical shifts are reported in
parts per million (d) downfield from tetramethylsilane
(d¼0 ppm). FABMS spectra were measured on a JEOL
JMS-700 instrument and are reported in the order of the mo-
lecular ion peak and remarkable high peaks (intensity). The
reactions using heating in a microwave were carried out us-
ing a Biotage Initiator Sixty instrument. The products were
purified using the flash chromatography technique on Silica
Gel 60 (40–100 mm) purchased from Kanto Chemical Co.,
Inc or NH Silica (100–200 mesh) purchased from Fuji Sily-
sia Chemical Ltd. Commercial grade reagents and solvents
were used as supplied. Furanoid glycal 6 was prepared
according to the method described in the literature.5 All
reactions sensitive to oxygen or moisture were carried out
under nitrogen atmosphere.
To avoid such epimerization, the phenoxyacetyl group that
can easily be deprotected under basic conditions was intro-
duced to the amino group of the compound 14 (Scheme 5).
The desilylation of compound 15 was smoothly proceeded
to afford 16. Removal of the phenoxyacetyl group with eth-
ylene diamine gave the desired 5-acetyl-2-amino-1H-pyr-
role C-deoxyribonucleoside 1. The NOE experiments
Ac
O
NH
OPh
a
b
N
H
TBSO
14
O
OTBS
15
Ac
O
NH
OPh
N
H
c
1
HO
O
4.1.1. 5-Acetyl-2-nitro-1H-pyrrole (3a).14 To a solution of
2 (30 mmol, 3.27 g) in acetic anhydride (36 mL) was added
dropwise 70%-nitric acid (2.6 mL) at ꢀ40 ꢁC over 30 min.
The mixture was warmed to room temperature with stirring
over 2 h, and then poured into ice-cooled water and extracted
with ethyl acetate (3ꢂ50 mL). The combined organic layers
OH
16
Scheme 5. Reagents and conditions: (a) PhOCH2COCl, Et3N, THF, rt,1.5 h,
97%; (b) 70%-TBAFaq, HOAc, THF, rt, overnight, 45%; (c) H2NCH2-
CH2NH2, rt, overnight, 50%.

H. Oda et al. / Tetrahedron 63 (2007) 12747–12753
12751
were dried over anhydrous magnesium sulfate and evaporated.
Flash column chromatography (dichloromethane/ethyl
acetate¼19:1) of the residue gave 3a (36%, 1.66 g) and 3b
procedure of the preparation of 3a. Purification was carried
out by flash column chromatography (n-hexane/ethyl
acetate¼5:3). The product was obtained as an orange solid.
Yield 43% (1.11 g): 1H NMR (400 MHz, CDCl3) d 10.27 (br
s, 1H), 7.08 (d, J¼2.9 Hz, 1H), 2.52 (s, 3H); 13C NMR
(100 MHz, DMSO-d6) d 188.7, 139.9, 134.4, 124.8, 67.5,
26.7; FABMS (m/e) 281 (MH+, 54), 59 (100), 43 (78), 70
(74), 265 (25); HRMS (FAB): calcd for C6H6IN2O3
[M+H]+ 280.94177, found 280.9420.
1
(51%, 2.36 g) as a pale orange solid. Mp 234 ꢁC: (3a) H
NMR (400 MHz, CDCl3) d 10.22 (br s, 1H), 7.09 (dd, J¼
2.4, 3.9 Hz, 1H), 6.87 (d, J¼2.4, 3.9 Hz, 1H); FABMS (m/e)
155 (MH+, 3), 93 (100), 76 (38), 58 (25), 46 (20); HRMS
(FAB): calcd for C6H7N2O3 [M+H]+ 155.04512, found
1
155.0464; (3b) H NMR (400 MHz, CDCl3) d 10.01 (br s,
1H), 7.83 (dd, J¼1.0, 3.4 Hz, 1H), 7.41 (d, J¼1.5 Hz, 1H).
4.1.7. Palladium-catalyzed Heck coupling between 9 and
furanoid glycal 6. A reaction tube containing a mixture of 9
(0.5 mmol, 0.140 g), dichlorobis[tri(o-tolyl)phosphine]pal-
ladium (10 mol %, 79 mg), furanoid glycal 6 (0.5 mmol,
0.172 g), triethylamine (2 mmol, 0.202 g), and additive in
DMF (5 mL/mmol) was sealed. The mixture was heated
using a microwave at 140 ꢁC for 10 min. The solvent was
removed under reduced pressure and then the residue was
purified by flash column chromatography (n-hexane/ethyl
acetate¼4:1). The adduct 10 was obtained as a pale yellow
oil (0.119 g, 48% in the presence of 2.5 mmol of lithium
chloride as an additive): 1H NMR (400 MHz, CDCl3)
d 9.96 (br s, 1H), 7.14 (s, 1H), 6.22 (d, J¼3.4 Hz, 1H),
4.93 (s, 1H), 4.63–4.58 (m, 1H), 3.95 (d, J¼11.2 Hz, 1H),
3.78 (dd, J¼3.9, 11.2 Hz, 1H), 2.49 (s, 3H), 0.94 (s, 9H),
0.89 (s, 9H), 0.23 (s, 3H), 0.18 (s, 3H), 0.09 (s, 3H), 0.07
(s, 3H); FABMS (m/e) 497 (MH+, 11), 74 (100), 147 (43),
233 (14), 479 (11); HRMS (FAB): calcd for C23H41N2O6Si2
[M+H]+ 497.24977, found 497.2491.
4.1.2. 5-Acetyl-2-acetylamino-1H-pyrrole (4). A mixture
of 3a (6.4 mmol, 1.00 g), iron (25.8 mmol, 1.44 g), and ace-
tic acid (30 mL) was stirred at 100 ꢁC for 2 h. The solvent
was removed under reduced pressure, and the residue was
purified by flash column chromatography (ethyl acetate) to
give 4 as a red-brown solid. Yield 36% (0.385 g): 1H NMR
(400 MHz, DMSO-d6) d 10.92 (br s, 1H), 10.78 (br s, 1H),
6.95 (d, J¼3.9 Hz, 1H), 5.84 (d, J¼3.9 Hz, 1H), 2.27 (s,
3H), 2.07 (s, 3H); FABMS (m/e) 167 (MH+, 73), 154
(100), 107 (58), 89 (50), 78 (47); HRMS (FAB): calcd for
C8H11N2O2 [M+H]+ 167.08150, found 167.0827.
4.1.3. 5-Acetyl-2-acetylamino-3-bromo-1H-pyrrole (5a).
To a solution of 4 (0.41 mmol, 0.069 g) in dichloromethane
(10 mL) was added N-bromosuccinimide (0.5 mmol,
0.089 g) at ꢀ40 ꢁC. After stirring for 1 h, the mixture was al-
lowed to warm to room temperature. The mixture was evap-
orated and purified by flash column chromatography
(dichloromethane/ethyl acetate¼1:1) to give 5a as a red-
1
brown solid. Yield 66% (0.066 g), mp 218 ꢁC: H NMR
4.1.8. 2R,5R-5-(5-Acetyl-2-nitro-1H-pyrrol-3-yl)-2-hy-
droxymethyltetrahydrofuran-3-one (11). A mixture of
10 (1.6 mmol, 0.793 g), 75%-tetrabutylammonium fluoride
(6.4 mmol, 2.02 g), acetic acid (12.8 mmol, 0.763 g), and
THF (16 mL) was stirred at room temperature overnight.
After concentration in vacuo, the product was purified by
flash column chromatography (ethyl acetate) to give 11
as a pale yellow solid. Yield 80% (0.344 g), mp 240 ꢁC:
1H NMR (400 MHz, DMSO-d6) d 13.69 (s, 1H), 7.39 (s,
1H), 5.66 (dd, J¼6.3, 10.7 Hz, 1H), 5.02 (br s, 1H), 4.04
(t, J¼2.9 Hz, 1H), 3.73 (dd, J¼2.4, 12.2 Hz, 1H), 3.64
(dd, J¼3.4, 12.2 Hz, 1H), 2.92 (dd, J¼6.3, 17.6 Hz, 1H),
2.52 (s, 3H), 2.31 (dd, J¼10.7, 17.6 Hz, 1H); 13C NMR
(100 MHz, DMSO-d6) d 213.8, 189.1, 135.9, 132.5,
127.9, 114.3, 82.3, 70.1, 60.3, 43.6, 26.7; HRMS (FAB):
calcd for C11H13N2O6 [M+H]+ 269.07681, found 269.0790.
(400 MHz, CDCl3) d 10.91 (br s, 1H), 7.58 (br s, 1H), 6.82
(d, J¼2.9 Hz, 1H), 2.36 (s, 3H), 2.26 (s, 3H); FABMS
(m/e) 245 (MH+ (79Br), 68), 247 (MH+ (81Br), 67), 154
(100), 59 (78), 70 (66), 45 (58); HRMS (FAB): calcd for
C8H10BrN2O2 [M+H]+ 244.99202, found 244.9934.
4.1.4. 5-Acetyl-2-acetylamino-3-iodo-1H-pyrrole (5b).
Compound 5b was prepared by the similar procedure of 5a
by using N-iodosuccinimide instead of N-bromosuccinimide
(2.3 mmol scale; yield 52%, 0.354 g): 1H NMR (400 MHz,
CDCl3) d 10.98 (br s, 1H), 7.49 (br s, 1H), 6.89 (d,
J¼2.9 Hz, 1H), 2.36 (s, 3H), 2.27 (s, 3H); FABMS (m/e)
293 (MH+, 100), 166 (23), 250 (21), 59 (20), 107 (18);
HRMS (FAB): calcd for C8H10IN2O2 [M+H]+ 292.97815,
found 292.9796.
4.1.5. 2-Acetyl-4-iodo-1H-pyrrole (8). A mixture of 2
(10 mmol, 1.09 g), Amberlyst-15dry (0.1 g), N-iodosuccini-
mide (10 mmol, 2.25 g) in chloroform/carbon tetrachloride
(1/1, 40 mL) was stirred at 70 ꢁC for 24 h. The Amberlyst-
15dry was filtered off and the solvent was removed under re-
duced pressure. Flash column chromatography (n-hexane/
ethyl acetate¼7:3) of the residue gave 8 as a pale gray solid.
Yield 96% (2.27 g), mp 235 ꢁC: 1H NMR (400 MHz,
CDCl3) d 9.71 (br s, 1H), 7.08 (dd, J¼1.5, 2.9 Hz, 1H),
6.99 (dd, J¼1.5, 2.9 Hz, 1H), 2.42 (s, 3H); FABMS (m/e)
236 (MH+, 13), 154 (100), 107 (20), 90 (19), 78 (18);
HRMS (FAB): calcd for C6H6INO [M+H]+ 235.95669,
found 235.9590.
4.1.9. 5-Acetyl-3-(20-deoxy-b-D-ribofuranosyl)-2-nitro-
1H-pyrrole (12). To a stirring solution of 11 (4.8 mmol,
1.29 g) in acetic acid (29 mL) and acetonitrile (96 mL), so-
dium tri(acetoxy)borohydride (5.3 mmol, 1.124 g) was
slowly added at ꢀ40 ꢁC. Stirring was continued for 1 h,
and then the mixture was allowed to warm to room temper-
ature. The solvent was removed in vacuo, and the residue
was purified by flash column chromatography (ethyl ace-
tate/methanol¼9:1) to give 12 as a pale yellow solid. Yield
87% (1.13 g), mp 165 ꢁC (decomposed): 1H NMR
(400 MHz, DMSO-d6) d 13.50 (s, 1H), 7.13 (s, 1H), 5.44
(dd, J¼5.9, 9.8 Hz, 1H), 5.08 (br s, 1H), 4.79 (br s, 1H),
4.17 (td, J¼2.4, 5.4 Hz, 1H), 3.77 (dt, J¼2.4, 4.9 Hz, 1H),
3.53–3.43 (m, 2H), 2.49 (s, 3H), 2.25 (ddd, J¼2.0, 5.4,
12.2 Hz, 1H), 1.74 (ddd, J¼5.9, 9.8, 12.7 Hz, 1H); 13C
NMR (100 MHz, DMSO-d6) d 189.1, 135.5, 132.3, 130.1,
4.1.6. 5-Acetyl-3-iodo-2-nitro-1H-pyrrole (9). Compound
9 was prepared from 8 (9.3 mmol, 2.20 g) by the similar

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H. Oda et al. / Tetrahedron 63 (2007) 12747–12753
114.0, 87.5, 72.9, 72.0, 62.2, 41.5, 26.7; HRMS (FAB): calcd
for C11H15N2O6 [M+H]+ 271.09246, found 271.0938.
trimethylsilyl triflate (2.8 mmol, 0.5 mL). After stirring for
12 h at ꢀ40 ꢁC, methanol (2 mL) was added and the mixture
was stirred for 4 h. To quench the reaction, triethylamine
(0.5 mL) was added and the mixture was stirred for 2 h.
The solvent was evaporated, and the residue was purified
by silica gel column chromatography (NH silica, ethyl ace-
tate/methanol¼3:2) to give a-1. Yield 84% (0.028 g).
4.1.10. 5-Acetyl-3-[30,50-bis(tert-butyldimethylsilyl)-20-
deoxy-b-D-ribofuranosyl]-2-nitro-1H-pyrrole (13).
A
solution of 12 (3.9 mmol, 1.04 g), imidazole (24 mmol,
1.63 g), and tert-butyldimethylchlorosilane (9.7 mmol,
1.47 g) in DMF (20 mL) was stirred at room temperature
overnight. To the mixture was added ethyl acetate (100 mL)
and washed with water (3ꢂ100 mL) and brine (100 mL).
The organic layer was dried over magnesium sulfate and
evaporated. Flash column chromatography (n-hexane/ethyl
acetate¼10:1) of the residue gave 13 as a yellow oil. Yield
4.1.13. 5-Acetyl-3-[30,50-bis(tert-butyldimethylsilyl)-20-
deoxy-b-D-ribofuranosyl]-2-phenoxyacetylamino-1H-
pyrrole (15). To a solution of 14 (2.8 mmol, 1.33 g) and tri-
ethylamine (4.2 mmol, 0.59 mL) in dry-THF (40 mL) was
added dropwise phenoxyacetyl chloride (3.4 mmol,
0.47 mL). After being stirred at room temperature for
90 min, the mixture was poured into water (30 mL) and ex-
tracted with ethyl acetate (3ꢂ30 mL). The combined organic
layers were dried over magnesium sulfate and concentrated.
Flash column chromatography (dichloromethane/meth-
anol¼29:1) of the residue gave 15 as a yellow oil. Yield
1
97% (1.86 g): H NMR (400 MHz, CDCl3) d 10.02 (br s,
1H), 7.03 (d, J¼3.4 Hz, 1H), 5.64 (dd, J¼5.4, 9.8 Hz, 1H),
4.40 (dt, J¼2.4, 5.4 Hz, 1H), 3.99–3.95 (m, 1H), 3.78 (dd,
J¼3.9, 11.2 Hz, 1H), 3.70 (dd, J¼4.9, 11.2 Hz, 1H), 2.50
(s, 3H), 2.42 (ddd, J¼2.0, 5.9, 12.7 Hz, 1H), 1.77 (ddd,
J¼5.4, 9.8, 12.7 Hz, 1H), 0.92 (s, 9H), 0.91 (s, 9H), 0.112
(s, 3H), 0.106 (s, 3H), 0.104 (s, 3H), 0.095 (s, 3H); 13C
NMR (100 MHz, CDCl3) d 188.6, 130.5, 113.6, 88.0, 77.2,
74.0, 73.5, 63.5, 42.2, 25.91, 25.88, 25.8, 25.5, ꢀ4.6, ꢀ4.8,
ꢀ5.37, ꢀ5.42; HRMS (FAB): calcd for C23H43N2O6Si2
[M+H]+ 499.26542, found 499.2647.
1
97% (1.66 g): H NMR (400 MHz, CDCl3) d 10.89 (br s,
1H), 10.15 (br s, 1H), 7.37–7.31 (m, 2H), 7.06 (t,
J¼7.2 Hz, 1H), 6.98–6.93 (m, 2H), 6.56 (d, J¼3.2 Hz,
1H), 5.23 (dd, J¼5.6, 11.2 Hz, 1H), 4.61 (d, J¼6.4 Hz,
1H), 4.38 (d, J¼4.8 Hz, 1H), 4.02–3.98 (m, 1H), 3.66 (dd,
J¼4.0, 10.8 Hz, 1H), 3.44 (dd, J¼6.8, 10.8 Hz, 1H), 2.35
(s, 3H), 2.22–2.16 (m, 1H), 1.92 (ddd, J¼5.2, 10.8,
12.4 Hz, 1H), 0.92 (s, 9H), 0.80 (s, 9H), 0.12 (s, 3H), 0.11
(s, 3H), ꢀ0.06 (s, 3H), ꢀ0.10 (s, 3H); 13C NMR
(100 MHz, CDCl3) d 185.9, 166.1, 131.3, 129.9, 126.0,
122.4, 114.8, 113.5, 88.5, 86.9, 75.5, 74.1, 67.1, 63.6, 63.1,
42.7, 25.7, 25.4, 24.8, 18.2, 18.0, 13.1, ꢀ4.7, ꢀ5.5; HRMS
(FAB): calcd for C31H51N2O6Si2 [M+H]+ 603.32802, found
603.3309.
4.1.11. 5-Acetyl-2-amino-3-[30,50-bis(tert-butyldimethyl-
silyl)-20-deoxy-b-D-ribofuranosyl]-1H-pyrrole (14). A so-
lution of 13 (3.2 mmol, 1.61 g) in methanol (80 mL) was
reduced over 10% palladium on carbon (0.17 mmol,
0.18 g) under hydrogen (1 atm, balloon) at room tempera-
ture for 2 h. Removal of the catalyst and evaporation of
the solvent under reduced pressure gave 14 as a yellow oil.
1
Yield 96% (1.46 g): H NMR (400 MHz, CDCl3) d 10.45
(br s, 1H), 6.72 (s, 1H), 5.05 (dd, J¼5.6, 10.8 Hz, 1H),
4.99 (br s, 2H), 4.38 (d, J¼6.0 Hz, 1H), 3.87 (d, J¼2.0 Hz,
1H), 3.78 (dd, J¼3.2, 11.2 Hz, 1H), 3.74 (dd, J¼3.2,
11.2 Hz, 1H), 2.24 (s, 3H), 2.11 (ddd, J¼6.0, 10.8,
12.8 Hz, 1H), 1.93 (dd, J¼5.6, 12.8 Hz, 1H), 0.912 (s,
9H), 0.907 (s, 9H), 0.093 (s, 3H), 0.084 (s, 3H), 0.079 (s,
6H); HRMS (FAB): calcd for C23H45N2O4Si2 [M+H]+
469.29124, found 469.2933.
4.1.14. 5-Acetyl-3-[20-deoxy-b-D-ribofuranosyl]-2-phe-
noxyacetylamino-1H-pyrrole (16). Compound 16 was pre-
pared from 15 (2.0 mmol, 1.18 g) by the similar procedure of
the preparation of 11. Purification was carried out by flash
column chromatography (ethyl acetate). The product was
obtained as a pale yellow solid. Yield 45% (0.33 g), mp
182 ꢁC: 1H NMR (400 MHz, DMSO-d6) d 11.18 (br s,
1H), 10.44 (br s, 1H), 7.34–7.29 (m, 2H), 7.04–6.96 (m,
4H), 5.08–5.00 (m, 2H), 4.75 (s, 2H), 4.21 (br s, 1H), 3.76
(br s, 1H), 3.55–3.45 (m, 2H), 2.28 (s, 3H), 2.01–1.88 (m,
2H); 13C NMR (100 MHz, CDCl3) d 185.7, 167.3, 130.6,
130.1, 129.6, 126.0, 121.4, 114.7, 114.6, 71.0, 68.1, 67.1,
66.3, 35.7, 24.8; HRMS (FAB): calcd for C19H23N2O6
[M+H]+ 375.15506, found 375.1570.
4.1.12. 5-Acetyl-2-amino-3-(20-deoxy-a-D-ribofurano-
syl)-1H-pyrrole (a-1). (Scheme 4, path a): A solution of
12 (2.7 mmol, 0.74 g) in water (30 mL) was reduced over
10% palladium on carbon (0.27 mmol, 0.29 g) under hydro-
gen (1 atm, balloon) at room temperature for 40 min.
Removal of the catalyst and evaporation of the solvent under
reduced pressure gave an oil. The resulting oil was purified
by flash column chromatography (NH silica, ethyl acetate/
methanol¼3:2) to give a-1 as a yellow oil. Yield 46%
4.1.15. 5-Acetyl-2-amino-3-(20-deoxy-b-D-ribofurano-
syl)-1H-pyrrole (1). A solution of 16 (0.5 mmol, 0.19 g)
in ethylene diamine (5 mL) was stirred at room temperature
overnight and then concentrated under reduced pressure.
The resulting residue was purified by flash column chroma-
tography (NH silica, ethyl acetate/methanol¼7:1 to 3:1 gra-
dient) to give 1 as a yellow oil. Yield 50% (0.06 g): 1H NMR
(400 MHz, CD3OD) d 7.02 (s, 1H), 5.06 (dd, J¼5.4,
11.2 Hz, 1H), 4.37 (d, J¼5.9 Hz, 1H), 3.90 (d, J¼2.4 Hz,
1H), 3.68 (d, J¼3.9 Hz, 2H), 2.23 (s, 3H), 2.21–2.16 (m,
1H) 1.93 (dd, J¼5.4, 13.2 Hz, 1H); 13C NMR (100 MHz,
CD3OD) d 183.7, 147.8, 123.9, 123.2, 108.4, 88.8, 76.2,
74.7, 63.7, 42.2, 23.6; HRMS (FAB): calcd for
C11H17N2O4 [M+H]+ 241.11828, found 241.1168.
1
(0.30 g): H NMR (400 MHz, DMSO-d6) d 10.30 (s, 1H),
6.71 (d, J¼2.4 Hz, 1H), 5.10 (s, 2H), 4.54 (d, J¼6.4 Hz,
1H), 4.35 (d, J¼4.4 Hz, 1H), 4.16 (dd, J¼2.0, 11.2 Hz,
1H), 3.76 (dd, J¼2.0, 12.2 Hz, 1H), 3.65 (d, J¼12.2 Hz,
1H), 3.64–3.56 (m, 1H), 3.55 (br s, 1H), 2.11 (s, 3H), 1.90
(dd, J¼11.7, 23.9 Hz, 1H), 1.62–1.54 (m, 1H); 13C NMR
(100 MHz, DMSO-d6) d 181.2, 144.2, 122.5, 118.3, 107.0,
70.7, 70.2, 68.5, 67.2, 35.0, 20.8; HRMS (FAB): calcd for
C11H17N2O4 [M+H]+ 241.11828, found 241.1197.
(Scheme 4, path d): To a solution of 12 (0.14 mmol, 0.065 g)
in dichloromethane (2 mL) was cooled at ꢀ40 ꢁC and added

H. Oda et al. / Tetrahedron 63 (2007) 12747–12753
12753
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Acknowledgements
This work has been supported by a Research Grant for the
RIKEN Genome Exploration Research Project from the
Ministry of Education, Culture, Sports, Science and Tech-
nology of the Japanese Government to Y.H.
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