Synthetic routes to a series of proximal and distal 2′-deoxy fleximers

Article abstract of DOI:10.1055/s-0032-1316791

Two series of innovative 2-deoxy nucleoside analogues have been designed where the nucleobase has been split into its imidazole and pyrimidine subunits. This structural modification serves to introduce flexibility into the nucleobase scaffold while still

Full text of DOI:10.1055/s-0032-1316791

3496▌
PAPER
paper
Synthetic Routes to a Series of Proximal and Distal 2′-Deoxy Fleximers
Synthetic Routes to Proximal and Distal 2′-Deoxy Fleximers
Orrette R. Wauchope, Melvin Velasquez, Katherine Seley-Radtke*
Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
Fax +1(410)4552608; E-mail: kseley@umbc.edu
Received: 31.07.2012; Accepted after revision: 10.09.2012
of the parent ribose series are shown in Figure 1 below
Abstract: Two series of innovative 2′-deoxy nucleoside analogues
(adenosine analogues 1 and 2).
have been designed where the nucleobase has been split into its im-
idazole and pyrimidine subunits. This structural modification serves
to introduce flexibility into the nucleobase scaffold while still re-
taining the elements required for recognition. The synthetic efforts
to realize these analogues are described within.
This new class of modified nucleosides introduced flexi-
bility to the heteroaromatic base by deconstructing the pu-
rine ring system into its two components, an imidazole
and pyrimidine ring. This modification confers additional
degrees of conformational freedom and torsional flexibil-
ity to the ligand while still retaining the molecular ele-
ments necessary for recognition.
Key words: flexible nucleosides, fleximers, nucleobase, guano-
sine, adenosine, resistance
In addition, by virtue of their inherent flexibility, these
novel nucleosides should be able to sample more favor-
able enzyme–ligand interactions. More importantly, they
should be able to overcome viral resistance mechanisms
due to their ability to engage secondary amino acid resi-
dues not previously involved in an enzyme’s mechanism
of action, thereby retaining their activity when confronted
with a point mutation in the active site of an enzyme.
Drug resistance poses a particularly difficult problem in
the development of chemotherapeutics for the treatment
of bacterial, viral, or parasitic infections.1 Consequently,
there is an urgent unmet medical need for the develop-
ment of drugs aimed at combating resistant mutations as
well as fighting emerging new viral diseases.2–4 Notably,
it was recently shown that flexible nucleoside and nucleo-
base inhibitors (e.g., tenofovir and etravirine) could over-
come viral HIV resistant mutations,1,5,6 by adapting
conformationally and positionally to the mutations in the
HIV reverse transcriptase (RT) nucleoside and nonnucle-
oside binding sites, thereby retaining their activity.1,5–7
Recently, the fleximer concept was adapted by Hudson et
al.8 where they were cleverly able to construct a modified
fleximer scaffold using click chemistry. Husdon’s ana-
logues focused on a triazole ring connected by a single
bond to several different aromatic ring systems. Their
preparation and fluorescent and luminescent properties
were reported. These analogues were proposed for use in
gaining a better understanding of the interactions between
oligonucleotides and various biologically significant en-
zymes.8
As an extension of those findings, and a possible answer
to the on-going problem of resistance in many viral dis-
eases, a series of flexible nucleoside analogues called
‘fleximers’ were designed. Two representative examples
In our own laboratories it was observed that the distal ri-
bofuranose guanosine fleximer, Flex-G 3a (Figure 1)
served as an inhibitor of S-adenosylhomocysteine hydro-
lase (SAHase).9 This observation is unprecedented, since
to our knowledge no other guanosine nucleoside has ever
been reported to inhibit SAHase, an adenosine metaboliz-
ing enzyme. SAHase is an attractive biological target as it
has been implicated in viral and parasitic replication.9–11
H2N
N
4
N
N
N
N
NH2
5
N
6
N
5
HO
HO
N
O
O
HO
OH
HO
OH
1, proximal adenosine
2, distal adenosine
Additionally, the triphosphate of the guanosine fleximer
3b (Figure 1) was investigated with GTP fucose pyro-
phosphorylase (GFPP). This enzyme catalyzes the revers-
ible condensation of guanosine triphosphate and β-L-
fucose-1-phosphate to form the nucleotide sugar GDP-β-
L-fucose. This enzyme functions primarily in the mamma-
lian liver and kidney to salvage free L-fucose during the
breakdown of glycolipids and glycoproteins.12–14 It was
observed that 3b served as a superior substrate for human
GFPP, with a catalytic efficiency twice of the natural sub-
strate, GTP.15,16 Additionally, it was observed that despite
the mutation of a critical amino acid in the active site of
N
N
O
NH
RO
N
O
NH2
HO
OH
3a, R = H (Flex-G)
3b, R = triphosphate (Flex-GTP)
Figure 1 Fleximer numbering and nomenclature designations
SYNTHESIS 2012, 44, 3496–3504
Advanced online publication: 02.10.2012
0
0
3
9
-
7
8
8
1
1
4
3
7
-
2
1
0
X
DOI: 10.1055/s-0032-1316791; Art ID: SS-2012-M0627-OP
© Georg Thieme Verlag Stuttgart · New York

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Synthetic Routes to Proximal and Distal 2′-Deoxy Fleximers
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GFPP, Flex-GTP remained potent, while the natural sub- with the ribose distal fleximers.17,18 Since our initial re-
strate GTP was rendered completely inactive.15,16
ported approach, we have developed a shorter synthetic
route20 thereby facilitating the speed by which the 2′-de-
oxy distal fleximers could be obtained.
This demonstrates that conformational flexibility can in-
deed facilitate increased affinity and allow for the engage-
ment of secondary amino acids not previously involved in
the mechanism of action. More importantly, these results
confirm that flexibility facilitates retention of activity de-
spite binding site mutations. Consequently, this provided
additional motivation to pursue the synthesis of the corre-
sponding 2′-deoxy analogues in the hopes of increasing
the library of active compounds as well as to study the ef-
fects of substrate/inhibitor flexibility on DNA viruses.
N
N
S
N
N
O
O
NH
NH2
NH
NH2
PMBO
PMBO
N
N
O
O
a
PMBO
PMBO
13
12
b
N
O
The proposed 2′-deoxy targets are shown in Figures 2 and
3 for the distal and proximal fleximers, respectively.
N
NH
NH2
HO
N
O
N
N
N
N
O
NH2
HO
NH
NH2
N
4
HO
HO
N
N
O
O
Scheme 1 Reagents and conditions: (a) Raney Ni, MeOH, 65%; (b)
HO
HO
Pd/C, ammonium formate, EtOH, 80%.
4
5
N
N
N
O
O
It should be noted that the removal of the sulfur made de-
protection of the 4-methoxybenzyl (PMB) groups facile
utilizing standard hydrogenation conditions of palladium-
on-carbon and ammonium formate to give the distal gua-
nosine 4 in good yield (Scheme 1).
N
NH
NH
HO
HO
N
HN
O
O
O
HO
HO
7
6
Figure 2 2′-Deoxy distal fleximer targets
N
N
S
O
N
N
S
NH2
NH
N
O
PMBO
H2N
PMBO
N
N
NH
N
O
O
a
NH2
N
N
N
N
N
PMBO
PMBO
14
N
15
HO
HO
O
O
b
b
N
N
N
O
NH2
HO
HO
8
9
N
NH
N
RO
RO
O
N
N
O
O
O
NH
NH
NH
N
O
N
N
N
RO
RO
N
16, R = PMB
5, R = H
17, R = PMB
6, R = H
HO
c
HO
c
O
O
Scheme 2 Reagents and conditions: (a) (i) 2,4,6-i-Pr3C6H2SO2Cl,
DMAP, Et3N, MeCN, 3 h; (ii) NH3, r.t., 18 h; (b) Raney Ni, EtOH,
60% (16), 70% (17); (c) Pd/C, ammonium formate, EtOH, 50% (5),
75% (6).
HO
HO
11
10
Figure 3 2′-Deoxy proximal fleximer targets
The distal adenosine and inosine targets were obtained in
a similar fashion (Scheme 2). Once the previously report-
ed inosine tricycle 1420 was in hand, analogous to the gua-
nosine intermediate, standard desulfurization followed by
deprotection afforded the inosine target 6 (Scheme 2). The
adenosine tricycle was obtained by converting the carbon-
yl of 1420 into the relatively labile 2,4,6-triisopropylphe-
nylsulfonyl group followed by displacement with
ammonia to provide 15.20 Standard deblocking protocols
were then used in order to obtain the adenosine fleximer
target 5.
The synthetic approach to distal fleximers mirrors the
route previously employed to realize the ribofuranose
fleximers,17,18 and is outlined in Scheme 1 for the guano-
sine analogue, 4. It should be noted that this route was ini-
tially chosen due to the use of our previously reported
tricyclic nucleosides, which could serve as facile interme-
diates.18,19
Synthesis of the tricyclic intermediate 1220 was pursued
first and the desired fleximer 4 was subsequently obtained
through desulfurization with Raney nickel as was reported
© Georg Thieme Verlag Stuttgart · New York
Synthesis 2012, 44, 3496–3504

3498
O. R. Wauchope et al.
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Next, attention turned to the synthesis of the 2′-deoxyxan- 75% yield. Stepwise deprotection of the benzyl and tert-
thosine fleximer. Surprisingly, the xanthosine tricycle re- butyldimethylsilyl protecting groups of 23 was conducted
sisted all attempts at desulfurization under several to give the xanthosine target 7 in 53% for the two deblock-
different sets of conditions, including increasing reaction ing steps.
times and temperatures. As a result, a new route was con-
sidered. The shortest approach appeared to be via cross-
The approach to realize the 2′-deoxy proximal targets did
not involve the expanded purine tricyclic nucleosides.
coupling methodology (e.g., the Suzuki coupling) to con-
Since the Suzuki reaction had previously been successful
nect the imidazole and pyrimidine subunits.
in making the ribose derivatives,17,24,25 efforts turned to
synthesizing the requisite coupling partners. As shown in
I
N
N
N
N
Scheme 5, the synthesis of the imidazole synthon was
analogous to that utilized for the ribose series.24,25
I
N
a
TolO
RO
b
I
O
O
I
I
I
I
N
H
I
N
N
N
N
N
N
TolO
RO
19, R = Tol
20, R = TBDMS
18
21
BnO
HO
a
BnO
b
O
O
O
Scheme 3 Reagents and conditions: (a) (i) NaH, MeCN; (ii) 2-de-
oxy-3,5-di-O-toluoyl-β-D-ribofuranosyl chloride; (b) (i) NaOMe,
MeOH; (ii) TBDMSCl, imidazole, DMF, 86% (2 steps).
BnO
HO
BnO
25
24
26
Scheme 5 Reagents and conditions: (a) (i) NaH, THF; (ii) TBAI,
BnBr, 85%; (b) (i) EtMgBr, THF, 0 °C; (ii) EtOH, 80%.
Starting with a standard literature procedure, 4,5-diiodo-
1H-imidazole was reduced with sodium sulfite to give 18
(Scheme 3).21 Reaction of the sodium salt of 18 with the
2′-deoxy chlorosugar gave a mixture of isomeric com-
pounds 19 and 21. Using NOE NMR techniques, the de-
sired isomer 19 was delineated from 21 by irradiation of
the 1′-proton, which showed no correlation with any of the
aromatic hydrogens in the imidazole ring. The opposite
was shown for isomer 21, where a clear correlation was
observed between the anomeric proton and the H5 of the
imidazole ring. Intermediate 19 was then deprotected un-
der basic conditions and then protected with the common
tert-butyldimethylsilyl protecting group with a yield of
86% for the two steps. It should be noted that tert-butyldi-
methylsilyl was chosen to facilitate ease of removal at the
end of the scheme. The pyrimidine subunit, 22 was made
as previously reported.22,23
The hydroxy groups of 2420 were protected with the robust
benzyl groups using standard benzylation conditions of
sodium hydride, followed by the in situ generation of ben-
zyl iodide from benzyl bromide and tetrabutylammonium
iodide to provide 25 in good yield (Scheme 5).25 The pro-
tected 4-iodoimidazole synthon 26 was then achieved by
treating 25 with ethylmagnesium bromide followed by
quenching with ethanol.24,25
Next, synthesis of the pyrimidine partner was undertaken.
Beginning with the proximal 2′-deoxy guanosine target 8,
the pyrimidine subunit was planned as shown in Scheme
6.
O
O
O
Br
Br
HN
a
HN
b
HN
H2N
N
H2N
N
OBn
N
N
N
OR2
Me
N
N
28
27
29
N
N
N
I
Me
N
R1O
BnO
N
22
a
B(OH)2
R1O
O
N
c
O
OR2
R1O
OBn
R1O
OBn
19, R1 = Tol
B(OH)2
20, R1 = TBDMS
N
Br
23, R1 = TBDMS, R2 = Bn
7, R1 = R2 = H
N
b
N
N
N
N
Me
31
Scheme 4 Reagents and conditions: (a) (i) Pd(PPh3)4, DME (ii) 22,
NaHCO3, 75%; (b) (i) Pd/C, ammonium formate, EtOH; (ii) TBAF,
THF, 53% (2 steps).
N
Me
30
N
Me
Me
Scheme 6 Reagents and conditions: (a) Br2, H2O, 75%; (b) DMF-
DMA, DMF, 60%; (c) DIAD, Ph3P, BnOH, DMF, 80%; (d) (i) B(Oi-
Pr)3, THF, toluene, –78 °C, (ii) BuLi, (iii) aq HCl.
Initially, the toluoyl-protected imidazole synthon 19 was
used in the Suzuki coupling reaction in the hopes that the
reaction was basic enough to simultaneously deprotect the
ester groups during the formation of the coupled product.
However, the coupling reaction did not proceed with 19 so
the protecting group was exchanged to employ the tert-
butyldimethylsilyl group instead (Scheme 4). Coupling of
20 with boronic acid 22 proved successful and gave 23 in
Commercially available isocytosine 27 was brominated
under standard conditions of bromine and water to give
28.26 Once 28 was in hand, the exocyclic amine was pro-
tected with N,N-dimethylformamide dimethyl acetal
(DMF-DMA) to give 29. To reduce the risk of any acidic
Synthesis 2012, 44, 3496–3504
© Georg Thieme Verlag Stuttgart · New York

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Synthetic Routes to Proximal and Distal 2′-Deoxy Fleximers
3499
NH2
protons possibly interfering with the Suzuki coupling, 29
was converted into 30 using standard Mitsunobu condi-
tions in 80% yield.27 These reactions were also conducted
with a C5 iodo group instead of the bromine with similar
reactivity and yields. It was important that the amino
group be protected before the Mitsunobu reaction, as ami-
no groups are known to react under these conditions. Dis-
appointingly, 30 (either with the 5-Br or 5-I) could not be
converted into the boronic acid even under many different
reaction conditions.
NH2
NH2
N
I
Sn(Bu)3
N
a
N
b
N
N
N
34
36
35
Scheme 8 Reagents and conditions: (a) NIS, AcOH, 79%; (b)
(Bu3Sn)2, Pd2dba3·CHCl3, DMF, 65%.
analogue 33 gave the analogous adenosine intermediate
37 (Scheme 9). Typical deprotection protocols then gave
Searching for a new approach, examination of other work the target 9 in 70% yield.
done in our laboratories for another project,24,25 as well as
NH2
the literature from others revealed an article by Matsuda
et al.28 where they had successfully used an organotin py-
rimidine moiety in a Stille coupling reaction. As shown in
Scheme 7, the protected guanosine analogue 8 was suc-
cessfully achieved via Stille coupling of the protected im-
idazole synthon 26 with 3228 in moderate yield.
Sn(Bu)3
H2N
N
N
I
N
N
N
N
N
N
36
BnO
a
RO
O
O
BnO
RO
26
OMe
MeO
37, R = Bn
9, R = H
I
b
N
N
N
Sn(Bu)3
N
NH2
N
N
N
Scheme 9 Reagents and conditions: (a) Pd2dba3·CHCl3, DMF, 100
°C, 65%; (b) Pd/C, ammonium formate, EtOH, reflux, 70%.
H2N
N
32
a
BnO
O
BnO
O
BnO
After successfully making the guanosine and adenosine
targets, attention then turned towards the 2′-deoxy proxi-
mal inosine target 10. Since the Stille coupling had been
proven to work for the guanosine and adenosine ana-
logues, there was motivation to attempt to make the 5-(tri-
butylstannyl)pyrimidine intermediate and then subject it
to Stille coupling with the imidazole synthon. Iodination29
of commercially available 38 followed by protection uti-
lizing Mitsunobu conditions27 was then conducted. Utiliz-
ing standard literature procedures 41 was obtained
(Scheme 10). The transformation to the 5-tributylstannyl
intermediate 41 was also done in an analogous manner to
the other previously employed tin compounds, with the
exception that tetrakis(triphenylphosphine)palladium(0)
was used as the catalyst instead of tris(dibenzylideneace-
tone)dipalladium–chloroform as the former resulted in a
higher yield.30
26
BnO
33
b
O
NH
NH2
N
N
N
HO
O
HO
8
Scheme 7 Reagents and conditions: (a) Pd2dba3·CHCl3, DMF, 100
°C, 65%; (b) Pd/C, ammonium formate, EtOH, reflux, 80%.
Additionally, this route did not require the protection of
the exocyclic amino group as had been necessary in the
other attempted approaches. Moreover, the overall route
proved to be relatively short and the yields reasonable
enough to allow for scaleup. The 2′-deoxyguanosine tar-
get, 8 was then achieved following hydrogenation
(Scheme 7) in 80% yield.
O
O
OBn
I
I
HN
a
HN
b
N
N
N
N
38
39
40
Once the guanosine analogue 8 was achieved, the adenos-
ine target 9 was pursued. Since it was observed that the
Stille coupling could be performed without protection of
amine groups, the approach to realize the adenosine flex-
imer was much more straightforward.
c
OBn
N
Sn(Bu)3
N
Iodination of commercially available 4-aminopyrimidine
34 using N-iodosuccinimide in acetic acid gave 35
(Scheme 8). As was utilized for the guanosine analogue,
35 was converted into the 5-tributylstannyl intermediate
36 under palladium-catalyzed conditions. Stille coupling
under the identical conditions for the protected guanosine
41
Scheme 10 Reagent and conditions: (a) NaOH, I2, 70%; (b) DIAD,
Ph3P, BnOH, DMF, 77%; (c) (Bu3Sn)2, Pd(PPh3)4, toluene, 60%.
© Georg Thieme Verlag Stuttgart · New York
Synthesis 2012, 44, 3496–3504

3500
O. R. Wauchope et al.
PAPER
The Stille coupling was then performed as before with the All chemicals were obtained from commercial sources and used
without further purification unless otherwise noted. Anhyd DMF,
MeOH, DMSO, and toluene were purchased or obtained using a
guanosine and adenosine analogues as summarized in
Scheme 11. Finally, the inosine target, 10 was obtained
from deprotection of 42 in 60% yield.
solvent purification system (mBraun Labmaster 130). Melting
1
points are uncorrected. All H and 13C NMR spectra were refer-
enced to internal TMS (δ = 0.0 ppm); primed assignments refer to
furanose positions, Him to imidazole protons, and Hpyr to pyrimidine
protons. Reactions were monitored by TLC. Column chromatogra-
OBn
RO
Sn(Bu)3
N
N
phy was performed using commercial silica gel and eluted with the
indicated solvent system. Yields refer to chromatographically and
spectroscopically (1H and 13C NMR) homogeneous materials.
I
N
N
N
N
N
N
41
BnO
RO
a
O
O
2-Amino-6-{1-[2-deoxy-3,5-di-O-(4-methoxybenzyl)-β-D-ribo-
furanosyl]-1H-imidazol-5-yl}pyrimidin-4(3H)-one (13); Typi-
cal Procedure
BnO
RO
26
42, R = Bn
10, R = H
To a soln of 12 (300 mg, 0.532 mmol) in anhyd MeOH (25 mL) was
added washed Raney Ni. The mixture was heated under reflux for
18 h. The mixture was then filtered through Celite and the Celite
pad was washed several times with hot EtOH. The EtOH washings
were combined and the solvent was removed under reduced pres-
sure to give 13 (184 mg, 0.344 mmol, 65%) as a colorless syrup,
which was used in the next step without purification.
b
Scheme 11 Reagents and conditions:(a) Pd2dba3·CHCl3, DMF, 100
°C, 60%; (b) Pd/C, ammonium formate, EtOH, reflux, 60%.
1H NMR (400 MHz, DMSO-d6): δ = 2.34 (m, 2 H, H2′), 3.56 (m, 1
H, H3′), 3.63 (m, 1 H, H5′), 3.70–3.71 (s, 6 H, 2 OCH3), 4.12 (m, 1
H, H5′), 4.23 (m, 1 H, H4′), 4.38 (m, 2 H, PMB-CH2), 4.45 (s, 2 H,
PMB-CH2), 5.67 (br s, 2 H, NH2), 6.04 (s, 1 H, H1′), 6.85 (s, 1 H,
H4im), 6.82–6.89 (m, 4 H, HPMB), 7.15 (m, 2 H, HPMB), 7.22 (m, 2 H,
The final proximal 2′-deoxy target was the xanthosine
fleximer 11. This target initially appeared straightforward
since there were no sensitive groups on the pyrimidine
subunit to consider during the synthesis. The requisite py-
rimidine coupling partner 4325 was synthesized using pre-
viously reported procedures.25 Coupling was then
successfully carried out with tetrakis(triphenylphos-
phine)palladium(0) in refluxing 1,2-dimethoxyethane and
saturated aqueous sodium hydrogen carbonate to give 44
(64%) (Scheme 12).24,25 Removal of all five of the benzyl
groups with palladium-on-carbon and ammonium formate
in ethanol was accomplished in 52% yield to give the 2′-
deoxy proximal xanthosine fleximer 11 directly (Scheme
12).
HPMB), 7.51 (s, 1 H, H5pyr), 8.24 (s, 1 H, H2im).
13C NMR (100 MHz, DMSO-d6): δ = 68.3, 71.6, 74.8, 84.6, 87.0,
99.2, 113.8, 114.2, 114.5, 128.4, 128.5, 128.7, 129.4, 129.6, 129.8,
130.2, 139.9, 141.2, 142.3, 146.2, 150.1, 159.6, 159.8.
HRMS (FAB): m/z [M + H] calcd for C28H32N5O6: 534.2353; found:
534.2354.
2-Amino-6-[1-(2-deoxy-β-D-ribofuranosyl)-1H-imidazol-5-
yl]pyrimidin-4(3H)-one (4); Typical Procedure
A mixture of 13 (0.20 g, 0.37 mmol), 10% Pd/C (0.20 g), and am-
monium formate (0.20 g, 3.2 mmol) in EtOH (50 mL) was heated
under reflux for 18 h. The mixture was filtered through Celite and
the Celite pad was washed several times with hot EtOH. The com-
bined filtrate was evaporated under reduced pressure. The residue
was purified by column chromatography (EtOAc–EtOH–acetone–
H2O, 4:1:1:1) to give 4 (87 mg, 0.297 mmol, 80%) as hygroscopic
white needles.
RO
OBn
N
B(OH)2
OR
N
a
I
N
N
N
N
N
BnO
N
43
RO
BnO
1H NMR (400 MHz, D2O): δ = 3.70 (dd, J = 2.4, 10.5 Hz, 2 H, H2′),
3.87 (dd, J = 1.8, 10.5 Hz, 1 H, H3′), 4.07– 4.16 (m, 2 H, H5′), 4.29
(dd, 1 H, H4′), 6.11 (s, 1 H, H1′), 6.38 (d, J = 1.2 Hz, 1 H, H4im),
7.84 (s, 1 H, H2im), 9.14 (s, 1 H, H6pyr).
O
O
RO
BnO
26
44, R = Bn
11, R = OH
b
13C NMR (100 MHz, D2O): δ = 10.1, 32.3, 41.2, 60.1, 70.4, 75.6,
85.4, 92.3, 102.8, 122.5, 130.0, 135.8, 145.3, 154.0, 163.4.
Scheme 12 Reagents and conditions: (a) Pd(PPh3)4, NaHCO3,
DME, reflux, 4 h, 64%; (b) Pd/C, ammonium formate, EtOH, reflux,
52%.
HRMS (FAB): m/z [M + H] calcd for C12H16N5O4: 294.1202; found:
294.1204.
6-{1-[2-Deoxy-3,5-di-O-(4-methoxybenzyl)-β-D-ribofuranosyl]-
1H-imidazol-5-yl}pyrimidin-4-amine (16)
Following the typical procedure for 13 using 15 (400 mg, 0.730
mmol), anhyd EtOH (25 mL) and Raney Ni gave 16 (227 mg, 0.439
mmol, 60%) as a colorless syrup, which was used in the next step
without purification.
1H NMR (400 MHz, DMSO-d6): δ = 2.34 (m, 2 H, H2′), 3.56 (d, J =
2.4 Hz, 1 H, H3′), 3.63 (d, J = 2.4 Hz, 1 H, H5′), 3.70–3.71 (s, 6 H,
2 OCH3), 4.12 (m, 1 H, H5′), 4.23 (m, 1 H, H4′), 4.38 (m, 2 H, PMB-
CH2), 4.45 (s, 2 H, PMB-CH2), 5.67 (br s, 2 H, NH2), 6.04 (t, J = 4.5
Hz, 1 H, H1′), 6.95 (s, 1 H, H4im), 6.82–6.89 (m, 4 H, HPMB), 7.15
(m, 2 H, HPMB), 7.22 (m, 2 H, HPMB), 7.45 (s, 1 H, H5pyr), 8.26 (s, 1
H, H2im), 8.28 (s, 1 H, H2pyr).
In summary, two series of 2′-deoxy fleximers were syn-
thesized using optimized procedures and in some cases,
new coupling approaches. Biological testing is currently
underway for the newly synthesized 2′-deoxy fleximers,
including against resistant strains. These results will be
evaluated as they become available, and it is our hope that
they will provide additional insight toward increasing our
understanding of enzyme/ligand structure and function,
and as such, may serve as the foundation for the design of
a new generation of chemotherapeutic agents.
Synthesis 2012, 44, 3496–3504
© Georg Thieme Verlag Stuttgart · New York

PAPER
Synthetic Routes to Proximal and Distal 2′-Deoxy Fleximers
3501
13C NMR (100 MHz, DMSO-d6): δ = 32.8, 42.6, 43.6, 60.1, 68.9,
75.9, 85.4, 91.6, 104.9, 105.0, 122.5, 126.6, 126.7, 127.2, 129.6,
130.1, 130.5, 135.8, 145.3, 145.4, 153.9, 163.4.
h at r.t.. TLC analysis (hexane–EtOAc, 1:1) indicated the presence
of two strongly fluorescent spots. The spots were isolated by chro-
matography using the same TLC system as above to give the iso-
mers as a yellow foam and a yellow oil. NMR analysis, both 1D and
2D (COSY, NOESY), was used to identify the products following
separation by chromatography.
HRMS (FAB): m/z [M + H] calcd for C28H32N5O5: 518.2403; found:
518.2406.
1H NMR (400 MHz, CDCl3): δ = 2.40 (s, 6 H, 2 C6H4CH3), 2.61–
2.67 (m, 2 H, H2′), 4.59–4.60 (m, 1 H, H3′), 4.60–4.61 (m, 2 H,
H5′), 5.61–5.63 (m, 1 H, H4′), 6.07 (t, J = 4.5 Hz, 1 H, H1′), 7.12 (s,
1 H, H4), 7.24–7.25 (m, 4 H, HPh), 7.54 (s, 1 H, H2), 7.85–7.92 (m,
4 H, HPh).
13C NMR (100 MHz, CDCl3): δ = 21.8, 21.9, 29.8, 39.5, 39.6, 63.9,
74.9, 83.0, 86.4, 122.1, 126.4, 129.4, 129.6, 129.7, 129.9, 137.4,
144.4, 144.7, 165.9, 166.2.
6-[1-(2-Deoxy-β-D-ribofuranosyl)-1H-imidazol-5-yl]pyrimidin-
4-amine (5)
Following the typical procedure for 4 using 16 (95 mg, 1.205
mmol), 10% Pd/C (100 mg), ammonium formate (115 mg, 1.83
mmol), and anhyd EtOH; during the standard work up the Celite
pad was washed repeatedly with hot EtOH. Column chromatogra-
phy (EtOAc–acetone–EtOH–H2, 6:1:1:1) gave 5 (25 mg, 0.090
mmol, 50%) as a white powder; mp 195–196 °C.
1H NMR (400 MHz, D2O): δ = 3.65 (dd, J = 2.4, 10.5 Hz, 2 H, H2′),
3.97 (m, 1 H, H3′), 4.07–4.16 (m, 2 H, H5′), 4.29 (m, 1 H, H4′), 6.11
(t, J = 4.5 Hz, 1 H, H1′), 6.38 (s, 1 H, H4pyr), 7.25 (s, 1 H, H2pyr),
8.21 (s, 1 H, H2im), 8.24 (s, 1 H, H6im).
13C NMR (100 MHz, D2O): δ = 60.7, 66.1, 73.4, 74.5, 75.6, 84.9,
90.5, 110.4, 124.9, 127.7, 136.5, 150.2, 157.9, 162.8.
HRMS (ESI): m/z [M + H] calcd for C24H24IN2O5: 547.0730; found:
547.0726.
1-[3,5-Di-O-(tert-butyldimethylsilyl)-2-deoxy-β-D-ribofurano-
syl]-5-iodo-1H-imidazole (20)
To a soln 19 (368 mg, 0.674 mmol) in anhyd MeOH (20 mL) was
added NaOMe (75 mg, 1.347 mmol) was added and the resulting
soln was stirred for 4 h at r.t. Then the solvent was evaporated and
purified by flash chromatography (silica gel, EtOAc–MeOH, 4:1) to
give the deprotected product (0.188 g, 90%) as colorless solid. The
deprotected product (188 mg, 0.606 mmol) and imidazole (272 mg,
4.00 mmol) were then dissolved in the minimum amount of DMF
and the soln was cooled and stirred at 0 °C. TBDMSCl (301 mg, 2
mmol) was added portionwise at 0 °C. The mixture was allowed to
warm up to r.t. and stirred overnight. H2O was added and the organ-
ic layer was extracted with hexanes (4 × 10 mL). The combined or-
ganic layers were dried (MgSO4) and filtered and the solvent
removed to give 20 (310 mg, 0.576 mmol, 95%) as a yellow oil.
HRMS (FAB): m/z [M + H] calcd for C12H16N5O3: 278.1253; found:
278.1255.
6-{1-[2-Deoxy-3,5-di-O-(4-methoxybenzyl)-β-D-ribofuranosyl]-
1H-imidazol-5-yl}pyrimidin-4(3H)-one (17)
Following the typical procedure for 13 using 14 (300 mg, 0.547
mmol), anhyd EtOH (25 mL), and Raney nickel gave 17 (198 mg,
0.382 mmol, 70%) as a colorless syrup, which was used in the next
step without purification.
1H NMR (400 MHz, DMSO): δ = 2.37 (m, 2 H, H2′), 3.48 (m, 1 H,
H3′), 3.65 (m, 2 H, H5′), 3.70–3.71 (m, 6 H, 2 OCH3), 4.36 (m, 1 H,
H4′), 4.39 (s, 2 H, PMB-CH2), 4.49 (s, 2 H, PMB-CH2), 6.48 (t, J =
4.5 Hz, 1 H, H1′), 6.82–6.89 (m, 4 H, HPMB), 7.25 (m, 2 H, HPMB),
7.29 (m, 2 H, HPMB), 7.44 (s, 1 H, H4im), 8.35 (s, 1 H, H2pyr), 8.42,
(s, 1 H, H2im), 9.46 (s, 1 H, H5pyr).
13C NMR (100 MHz, DMSO): δ = 55.6, 68.1, 71.4, 74.7, 75.6, 77.4,
78.9, 84.8, 87.0, 99.2, 113.8, 114.5, 114.3, 127.4, 127.5, 127.6,
128.0, 129.6, 129.8, 129.9, 131.2, 139.4, 146.5, 150.3, 159.6, 159.8.
1H NMR (400 MHz, CDCl3): δ = 0.08–0.09 (m, 12 H, 4 SiCH3),
0.89–0.91 [m, 18 H, 2 SiC(CH3)3], 2.26–2.29 (m, 2 H, H2′), 2.88 (s,
1 H, H3′), 3.72–3.76 (m, 2 H, H5′), 4.48–4.49 (m, 1 H, H4′), 5.93–
5.96 (t, J = 4.5 Hz, 1 H, H1′), 7.25 (s, 1 H, H4), 7.55 (s, 1 H, H2).
13C NMR (100 MHz, CDCl3): δ = –4.7, 25.8, 26.1, 42.8, 63.4, 72.2,
86.5, 78.8, 122.3, 137.3, 137.4.
HRMS (FAB): m/z [M + H] calcd for C28H31N4O6: 519.2244; found:
HRMS (FAB): m/z [M + H] calcd for C20H40IN2O3Si2: 539.1622;
519.2243.
found: 539.1623.
6-[1-(2-Deoxy-β-D-ribofuranosyl)-1H-imidazol-5-yl]pyrimidin-
4(3H)-one (6)
2,4-Bis(benzyloxy)-6-{1-[3,5-di-O-(4-tert-butyldimethylsilyl)-2-
deoxy-β-D-ribofuranosyl]-1H-imidazol-5-yl}pyrimidine (23)
A mixture of 20 (310 mg, 0.576 mmol) and Pd(PPh3)4 (67 mg,
0.0576 mmol) in DME (20 mL) was stirred at r.t. under argon for 10
min. To this mixture was added 2,6-bis(benzyloxy)pyrimidin-4-yl-
boronic acid (22, 1.39 mmol) in DME (20 mL). Sat. aq NaHCO3 (15
mL) was added and the mixture refluxed under argon for 4 h. The
soln was cooled to r.t. and the DME layer separated and set aside.
The aqueous layer was then extracted with EtOAc (3 × 50 mL), and
the organic extracts were combined with the DME layer, washed
with brine (100 mL), and dried (MgSO4). The solvent was removed
to give a pale brown syrup. Column chromatography (2% EtOH–
CH2Cl2) gave 23 (290 mg, 0.413 mmol, 75%) as a yellow syrup.
1H NMR (400 MHz, CDCl3): δ = 0.08–0.09 (m, 12 H, 2 SiCH3),
0.89–0.91 [m, 18 H, SiC(CH3)3], 1.59 (s, 1 H), 2.26–2.29 (m, 2 H,
H2′), 3.72–3.76 (m, 2 H, H5′), 3.95–3.97 (m, 1 H, H3′), 4.48–4.49
(m, 1 H, H4′), 5.39–5.42 (m, 4 H, 2 PhCH2), 5.93–5.96 (t, J = 4.5
Hz, 1 H, H1′), 6.43 (s, 1 H, H4), 7.36 (s, 1 H, H5), 7.37–7.38 (m, 10
H, HPh), 8.34 (s, 1 H, H2).
Following the typical procedure for 4 using 17 (0.250 g, 0.482
mmol), Pd/C (662 mg), ammonium formate (300 mg, 4.82 mmol)
in anhyd EtOH (50 mL); during the standard workup the Celite pad
was washed repeatedly with hot EtOH. Column chromatography
(EtOAc–acetone–EtOH–H2, 8:1:1:0.5) gave 6 (100 mg, 0.360
mmol, 75%) as a white powder; mp 135–137 °C.
1H NMR (400 MHz, D2O): δ = 3.67 (dd, J = 2.4, 10.5 Hz, 2 H, H2′),
3.94 (m, 1 H, H3′), 4.06–4.16 (m, 2 H, H5′), 4.26 (m, 1 H, H4′), 6.11
(t, J = 4.5 Hz, 1 H, H1′), 6.83 (s, 1 H, H4im), 7.25 (s, 1 H, H2pyr),
8.22 (s, 1 H, H2im), 8.25 (s, 1 H, H5pyr).
13C NMR (100 MHz, D2O): δ = 60.7, 66.1, 73.4, 74.5, 75.6, 84.9,
90.5, 110.4, 124.9, 127.7, 136.5, 150.2, 157.9, 162.8.
HRMS (FAB): m/z [M + H] calcd for C12H15N4O4: 279.1093; found:
279.1095.
1-(2-Deoxy-3,5-di-O-toluoyl-β-D-ribofuranosyl)-5-iodo-1H-im-
idazole (19)
Monoiodoimidazole 18 (2.29 g, 11.78 mmol) was added to anhyd
MeCN (25 mL) under N2. The mixture was allowed to stir at 0 °C
for 15 min. NaH (60%, 283 mg, 11.78 mmol) was added portion-
wise over 5 min and the resulting mixture was stirred at 0 °C under
N2 for 30 min. Then 2-deoxy-3,5-di-O-toluoyl-β-D-ribofuranosyl
chloride (5.04 g, 12.96 mmol) was added in portions (2 × 30 min in-
tervals) to the mixture. The mixture was then stirred under N2 for 18
13C NMR (100 MHz, CDCl3): δ = –4.7, 25.8, 25.9, 26.0, 26.1, 42.7,
67.4, 68.3, 69.2, 72.2, 86.7, 102.6, 121.2, 128.2, 128.3, 128.5,
136.1, 136.7, 158.8, 170.9.
HRMS (FAB): m/z [M + H] calcd for C38H55N4O5Si2: 703.3711;
found: 703.3713.
© Georg Thieme Verlag Stuttgart · New York
Synthesis 2012, 44, 3496–3504

3502
O. R. Wauchope et al.
PAPER
5-Bromo-N2-[(dimethylamino)methylene]isocytosine (29)
To a soln of 5-bromoisocytosine (1.5 g, 7.89 mmol) in anhyd DMF
(25 mL) was added DMF-DMA (1.3 mL, 9.47 mmol). The mixture
was stirred at r.t. for 18 h. The solvent was removed under reduced
pressure and the product was purified by column chromatography
(EtOAc–MeOH (10:1) to give 29 (1.16 g, 4.75 mmol, 60%) as a
white solid; mp 110–112 °C.
6-[1-(2-Deoxy-1-β-D-ribofuranosyl)-1H-imidazol-5-yl]uracil (7)
Following the typical procedure for 4 using 23 (400 mg, 0.569
mmol), 10% Pd/C (400 mg), ammonium formate (359 mg, 5.69
mmol), in anhyd EtOH (30 mL) gave the debenzylated product (208
mg, 70%). The product used in the next reaction without further pu-
rification, as it was quite pure.
1H NMR (400 MHz, DMSO-d6): δ = 0.01–0.06 (m, 12 H), 0.81–
0.87 (m, 18 H), 2.45–2.46 (m, 1 H), 2.47–2.48 (m, 1 H), 3.61–3.62
(m, 2 H), 3.78–3.79 (m, 1 H), 4.41–4.43 (m, 1 H), 6.01 (t, 1 H), 7.61
(s, 1 H), 7.76 (s, 1 H), 7.78 (s, 1 H), 10.9 (s, 1 H), 11.2 (s, 1 H).
1H NMR (400 MHz, DMSO-d6): δ = 3.06 (s, 3 H, CH3), 3.10 (s, 3
H, CH3), 7.85 (s, 1 H, N=CH–NMe2), 7.93 (s, 1 H, H6), 11.26 (br s,
1 H, NH).
13C NMR (100 MHz, DMSO-d6): δ = 17.4, 18.6, 19.3, 25.9, 26.4,
61.5, 71.3, 75.4, 85.4, 89.3, 106.3, 113.5, 133.7, 135.7, 136.8,
150.5, 162.4.
13C NMR (100 MHz, DMSO-d6): δ = 35.1, 41.3, 71.5, 156.7, 157.5,
160.2, 161.1.
HRMS (FAB): m/z [M + H] calcd for C7H10BrN4O: 245.0038;
found: 245.0039.
HRMS (FAB): m/z [M + H]+ calcd for C22H43N4O5Si2: 523.2772;
found: 523.2772.
4-(Benzyloxy)-5-bromo-N2-[(dimethylamino)methylene]isocy-
tosine (30)
To a soln of the debenzylated product (200 mg, 0.383 mmol) in an-
hyd THF (25 mL) was added 1 M TBAF in THF (0.8 mL, 0.765
mmol). The mixture was stirred at r.t. for 4 h and the solvent was
removed under reduced pressure. The product was purified by col-
umn chromatography (EtOAc–acetone–EtOH–H2O) to give 7 (84
mg, 0.286 mmol, 75%) as a white solid; mp 251–252 °C.
1H NMR (400 MHz, DMSO-d6): δ = 3.46–3.49 (m, 2 H, H2′, OH),
3.74–3.75 (m, 1 H, H2′), 4.08–4.19 (m, 2 H, H5′), 4.37 (br s, 1 H,
OH), 4.90 (s, 1 H, H3′), 5.23–5.24 (m, 1 H, H4′), 6.04 (t, J = 4.5 Hz,
1 H), 7.66 (s, 1 H, H4im), 7.87 (s, 1 H, H5pyr), 7.93 (s, 1 H, H2), 11.06
(s, 1 H, NH), 11.24 (s, 1 H, NH).
A mixture of 5-bromo-N2-[(dimethylamino)methylene]isocytosine
(1.16 g, 4.73 mmol) and Ph3P (1.5 g, 5.68 mmol) was dissolved in
anhyd DMF. DIAD (1.2 mL, 5.68 mmol) was added dropwise fol-
lowed by the addition of BnOH (0.6 mL, 5.68 mmol) at 0 °C. The
mixture was then allowed to warm up to r.t. and stirred for 1.5 h.
The solvent was removed under vacuum and the product was puri-
fied by column chromatography (EtOAc–hexanes, 1:3) to give 30
(1.26 g, 3.77 mmol, 80%) as a colorless syrup.
1H NMR (400 MHz, DMSO-d6): δ = 3.08 (s, 3 H, CH3), 3.14 (s, 3
H, CH3), 5.15 (s, 2 H, PhCH2), 7.33–7.38 (m, 5 H, HPh), 7.87 (s, 1
H, CH), 7.96 (s, 1 H, H6).
13C NMR (100 MHz, DMSO-d6): δ = 7.7, 32.5, 42.2, 60.5, 69.3,
75.0, 86.9, 113.3, 126.7, 151.7, 157.6.
13C NMR (100 MHz, DMSO-d6): δ = 35.3, 41.5, 71.6, 128.0, 128.1,
128.2, 128.5, 128.6, 156.6, 157.4, 160.6, 161.1.
HRMS (FAB): m/z [M + H] calcd for C12H15N4O5: 295.1042; found:
295.1043.
HRMS (FAB): m/z [M + H] calcd for C14H16BrN4O: 335.0508;
found: 335.0505.
1-[3,5-Di-O-benzyl-2-deoxy-β-D-ribofuranosyl]-4-iodo-1H-im-
idazole (26)
5-{1-[3,5-Di-O-benzyl-2-deoxy-β-D-ribofuranosyl]-1H-imidaz-
ol-4-yl}-4-methoxypyrimidin-2-amine (33)
To a soln of 25 (1.295 g, 2.642 mmol) in anhyd THF (20 mL) was
added 3 M EtMgBr (1.06 mL, 3.17 mmol) dropwise. The mixture
was stirred at r.t. for 3 h and then quenched with EtOH (5 mL). The
solvent was removed under vacuum. Sat. NH4Cl (20 mL) was added
and the mixture was extracted with CH2Cl2 (3 × 25 mL). The organ-
ic layers were combined, washed with brine, and dried (MgBr2) to
give 26 (1.0 g, 2.04 mmol, 80%) as a colorless syrup.
A mixture of 26 (1.08 g, 2.21 mmol), 32 (1.37 g, 3.31 mmol) and
Pd2dba3·CHCl3 (274 mg, 0.26 mmol) in anhyd DMF (20 mL) was
heated at 100 °C for 11 h. The mixture was filtered through Celite,
diluted with EtOAc (30 mL), washed with brine, and dried
(MgSO4). The organic solvents were removed and the product was
purified by column chromatography (CH2Cl2–MeOH, 3:1) to give
33 (183 mg, 0.376 mmol, 65%) as a yellow oil.
1H NMR (400 MHz, acetone-d6): δ = 2.50–2.55 (m, 2 H, H2′), 3.65–
3.67 (m, 1 H, H3′), 4.26–4.27 (m, 2 H, H5′), 4.36–4.37 (m, 1 H,
H4′), 4.56 (s, 2 H, PhCH2), 4.59 (s, 2 H, PhCH2), 6.09 (t, J = 4.5 Hz,
1 H, H1′), 7.34–7.41 (m, 10 H, HPh), 7.41 (s, 1 H, H2), 7.69 (s, 1 H,
H5).
13C NMR (100 MHz, acetone-d6): δ = 60.3, 72.4, 72.7, 73.7, 76.7,
77.4, 77.7, 81.7, 82.8, 127.9, 128.1, 128.2, 128.6, 137.5, 137.8,
171.0.
1H NMR (400 MHz, acetone-d6): δ = 3.62 (m, 2 H, H2′), 3.75 (m, 1
H, H3′), 3.84 (s, 3 H, CH3), 4.29 (br s, 2 H, H5′), 4.33–4.36 (m, 1 H,
H4′), 4.49–4.69 (m, 4 H, PhCH2), 6.68 (s, 1 H), 6.87 (t, J = 4.5 Hz,
1 H, H1′), 6.95 (br s, 2 H, NH2), 7.19–7.33 (m, 10 H, HPh), 7.43 (s,
1 H, H5im), 8.23 (s, 1 H, H2im), 8.62 (s, 1 H, H6pyr).
13C NMR (100 MHz, acetone-d6): δ = 67.4, 72.4, 72.6, 73.5, 75.5,
82.9, 103.6, 127.7, 128.1, 128.4, 128.3, 128.6, 137.8, 137.9, 138.4,
158.3, 166.5.
HRMS (FAB): m/z [M + H] calcd for C22H24IN2O3: 491.0832;
found: 491.0833.
HRMS (FAB): m/z [M + H] calcd for C27H30N5O4: 488.2298; found:
488.2300.
5-Bromoisocytosine (28)
Isocytosine (650 mg, 5.85 mmol) was suspended in H2O (10 mL)
and Br2 (0.93 g, 5.85 mmol) was added. The mixture was stirred at
r.t. for 2 h and refrigerated overnight. NH4OH (5 mL) was added
and the mixture was concentrated to give 28 (0.780 g, 4.13 mmol,
75%) as a white solid; mp 235–237 °C (dec.).
1H NMR (400 MHz, DMSO-d6): δ = 6.70 (br s, 2 H, NH2), 7.93 (s,
1 H, H6), 11.26 (br s, 1 H, NH).
5-[1-(2-Deoxy-β-D-ribofuranosyl)-1H-imidazol-4-yl]-4-meth-
oxypyrimidin-2-amine (8)
Following the typical procedure for 4 using 33 (0.21 g, 0.41 mmol),
10% Pd/C (0.21 g), and ammonium formate (0.20 g, 3.2 mmol) in
MeOH (50 mL). Purification by column chromatography (EtOAc–
EtOH–acetone–H2, 4:1:1:1) gave 8 (96 mg, 0.328 mmol, 80%) as
hygroscopic white needles.
13C NMR (100 MHz, DMSO-d6): δ = 71.3, 156.8, 160.0, 161.4.
1H NMR (400 MHz, D2O): δ = 3.73 (dd, J = 2.4, 10.5 Hz, 2 H, H2′),
3.85 (dd, J = 1.8, 10.5 Hz, 1 H, H3′), 4.07– 4.16 (m, 2 H, H5′), 4.26
(m, 1 H, H4′), 6.13 (t, J = 4.5 Hz, 1 H, H1′), 7.35 (s, 1 H, H5im), 8.10
(s, 1 H, H2im), 9.16 (s, 1 H, H6pyr).
HRMS (FAB): m/z [M + H] calcd for C4H5BrN3O: 189.9616;
found: 189.9617.
13C NMR (100 MHz, D2O): δ = 7.74, 32.5, 42.3, 60.5, 69.3, 75.0,
91.0, 113.4, 151.7, 157.6.
Synthesis 2012, 44, 3496–3504
© Georg Thieme Verlag Stuttgart · New York

PAPER
Synthetic Routes to Proximal and Distal 2′-Deoxy Fleximers
3503
HRMS (FAB): m/z [M + H] calcd for C12H16N5O4: 294.1202; found:
294.1203.
13C NMR (400 MHz, D2O): δ = 62.1, 70.7, 74.8, 86.6, 89.5, 127.9,
145.4, 149.3, 155.1, 158.9.
HRMS (FAB): m/z [M + H] calcd for C12H16N5O3: 278.1253; found:
278.1255.
4-Amino-5-iodopyrimidine (35)
To a soln of 4-aminopyrimidine (34; 147 mg, 1.55 mmol) in AcOH
(10 mL) was added NIS (417 mg, 1.85 mmol). The mixture was
then heated at 80 °C for 2.5 h. The solvent was removed under vac-
uum and the residue was partitioned between CHCl3 and 5% aq
Na2S2O3 (10 mL total volume). The organic layers were washed
with brine, dried, and filtered, and the solvent was removed to give
35 (273 mg, 1.236 mmol, 79%) as a light yellow oil.
5-Iodopyrimidin-3(4H)-one (39)29
A mixture of pyrimidin-3(4H)-one (1.44 g, 15 mmol), I2 (3.81 g, 15
mmol), and NaOH (800 mg, 20 mmol) was heated at 80 °C for 18
h. After neutralization with AcOH, the precipitate was recrystal-
lized (EtOH) to give 39 (2.3 g, 10.4 mmol, 70%) as a white solid.
Spectral data were in agreement with literature values.29
1H NMR (400 MHz, acetone-d6): δ = 5.65 (br s, 2 H, NH2), 8.18 (s,
1 H, H6), 8.35 (s, 1 H, H2).
13C NMR (100 MHz, acetone-d6): δ = 113.5, 164.5, 162.5, 167.8.
1H NMR (400 MHz, DMSO-d6): δ = 8.15 (s, 1 H, H6), 8.37 (s, 1 H,
H2), 11.25 (s, 1 H, NH).
13C NMR (100 MHz, DMSO-d6): δ = 81.4, 150.3, 151.5, 162.3.
HRMS (FAB): m/z [M + H] calcd for C4H5IN3: 221.9528; found:
221.9529.
4-(Benzyloxy)-5-iodopyrimidine (40)
Pyrimidine 39 (1.67 g, 7.52 mmol) and Ph3P (2.37 g, 9.03 mmol)
were dissolved in DMF (20 mL) while stirring at 0 °C. DIAD (1.79
mL, 9.03 mmol) was added dropwise, followed by the addition of
BnOH (0.94 mL, 9.03 mmol) at 0 °C. The mixture was stirred at r.t.
and monitored. After the reaction was complete, the solvents were
removed under vacuum. Column chromatography (80% EtOAc–
hexanes) gave 40 (1.81 g, 5.80 mmol, 77%) as a yellow oil.
1H NMR (400 MHz, acetone-d6): δ = 5.21 (s, 2 H, PhCH2), 7.35–
7.40 (m, 5 H, HPh), 8.39 (s, 1 H, H6), 8.52 (s, 1 H, H2).
13C NMR (100 MHz acetone-d6): δ = 176.1, 162.4, 156.3, 141.8,
128.0, 128.1, 128.2, 128.5, 128.6, 127.4, 110.2.
4-Amino-5-(tributylstannyl)pyrimidine (36)
To a mixture of 4-amino-5-iodopyrimidine (138 mg, 0.625 mmol)
and (Bu3Sn)2 (0.376 mL, 0.750 mmol) in anhyd DMF (5 mL) was
added Pd2dba3·CHCl3 (194 mg, 0.19 mmol) and the mixture was
heated at 65 °C. The mixture was filtered through Celite and diluted
with EtOAc (5 mL), washed with brine, and dried (MgSO4). The or-
ganic solvents were removed and the product was purified by col-
umn chromatography (hexanes–EtOAc (3:1) to give 36 (156 mg,
0.405 mmol, 65%) as a yellow oil.
1H NMR (400 MHz, acetone-d6): δ = 0.86–0.88 (m, 9 H, Bu), 1.12–
1.22 (m, 6 H, Bu), 1.31–1.38 (m, 6 H, Bu), 1.54–1.59 (m, 6 H, Bu),
5.72 (br s, 2 H, NH2), 8.08 (s, 1 H, H6), 8.33 (s, 1 H, H2).
HRMS (FAB): m/z [M + H] calcd for C11H10IN2O: 312.9838;
found: 312.9840.
13C NMR (100 MHz, acetone-d6): δ = 7.2, 8.9, 10.7, 13.1, 28.7,
28.8, 29.4, 113.5, 158.6, 161.9, 162.4, 162.5, 167.8.
4-(Benzyloxy)-5-(tributylstannyl)pyrimidine (41)
To a mixture of 40 (200 mg, 0.641 mmol) and (Bu3Sn)2 (0.41 mL,
0.769 mmol) in anhyd DMF (10 mL) was added Pd(PPh3)4 (220 mg,
0.192 mmol). The mixture was heated at 65 °C. The mixture was fil-
tered through Celite and diluted with EtOAc (5 mL), washed with
brine, and dried (MgSO4). The organic solvents were removed and
the product was purified by column chromatography (hexanes–
EtOAc, 3:1) to give 41 (183 mg, 0.384 mmol, 60%) as a yellow oil.
1H NMR (400 MHz, acetone-d6): δ = 0.83–0.86 (m, 9 H, Bu), 1.05–
1.07 (m, 6 H, Bu), 1.09–1.28 (m, 6 H, Bu), 1.29–1.31 (m, 6 H, Bu),
5.13 (s, 2 H, PhCH2), 7.32–7.36 (m, 5 H, HPh), 7.78 (s, 1 H, H6),
8.39 (s, 1 H, H2).
HRMS (FAB): m/z [M + H] calcd for C16H32N3Sn: 386.1618;
found: 386.1619.
5-[1-(3,5-Di-O-benzyl-2-deoxy-β-D-ribofuranosyl)-1H-imidaz-
ol-4-yl]pyrimidin-4-amine (37)
A mixture of 26 (302 mg, 0.616 mmol), 36 (355 mg, 0.924 mmol),
and Pd2dba3·CHCl3 (51 mg, 0.05 mmol) in anhyd DMF (10 mL)
was heated at 100 °C for 11 h. The mixture was filtered through
Celite and diluted with EtOAc (5 mL), washed with brine, and dried
(MgSO4). The organic solvents were removed and the product was
purified by column chromatography (CH2Cl2–MeOH, 3:1) to give
37 (183 mg, 0.400 mmol, 65%) as a yellow oil.
13C NMR (100 MHz, acetone-d6): δ = 7.2, 8.9, 10.7, 13.1, 28.7,
28.8, 29.4, 113.5, 127.6, 128.1, 128.5, 128.6, 128.8, 128.9.
1H NMR (400 MHz, DMSO-d6): δ = 3.61 (dd, J = 4.1, 10.1 Hz, 2 H,
H2′), 3.73 (dd, J = 1.9, 10.7 Hz, 1 H, H3′), 4.19 (br s, 2 H, H5′),
4.33–4.36 (m, 1 H, H4′), 4.49–4.69 (m, 4 H, PhCH2), 6.87 (t, J = 4.5
Hz, 1 H, H1′), 6.95 (br s, 2 H, NH2), 7.19–7.33 (m, 10 H, HPh), 7.43
(s, 1 H, H5im), 8.21 (s, 1 H, H2im), 8.39 (s, 1 H, H6pyr), 9.16 (s, 1 H,
H2pyr).
13C NMR (100 MHz, DMSO-d6): δ = 67.4, 72.5, 72.8, 73.2, 75.5,
81.7, 101.6, 127.7, 128.1, 128.2, 128.3, 128.6, 137.8, 137.9, 138.4,
158.3, 164.5.
HRMS (FAB): m/z [M + H] calcd for C23H37SnN2O: 477.1928;
found: 477.1929.
4-(Benzyloxy)-5-[1-(3,5-di-O-benzyl-2-deoxy-β-D-ribofurano-
syl)-1H-imidazol-4-yl]pyrimidine (42)
A mixture of 26 (85 mg, 0.173 mmol), 41 (123 mg, 0.259 mmol)
and Pd2dba3·CHCl3 (14 mg, 0.0137 mmol) in anhyd DMF (5 mL)
was heated at 100 °C for 11 h. The mixture was filtered through
Celite and diluted with EtOAc, washed with brine, and dried
(MgSO4). The organic solvents were removed and the product was
purified by column chromatography (hexanes–EtOAc (3:1) to give
42 (56 mg, 0.102 mmol, 60%) as a colorless oil.
HRMS (FAB): m/z [M + H] calcd for C26H28N5O3: 458.2192; found:
458.2195.
5-[1-(2-Deoxy-β-D-ribofuranosyl)-1H-imidazol-4-yl]pyrimidin-
4-amine (9)
1H NMR (400 MHz, CDCl3): δ = 3.54 (m, 2 H, H2′), 3.85 (m, 1 H,
H3′), 4.18–4.25 (m, 2 H, H5′), 4.36–4.39 (m, 1 H, H4′), 4.45–4.67
(m, 4 H, 2 PhCH2), 5.21–5.22 (m, 2 H, PhCH2), 6.76 (t, J = 4.5 Hz,
1 H, H1′), 7.33–7.34 (m, 10 H, HPh), 7.38–7.42 (m, 5 H, HPh), 7.94
(s, 1 H, H5im), 8.55 (s, 1 H, H2im), 8.64 (s, 1 H, H2pyr), 9.16 (s, 1 H,
H6pyr).
13C NMR (100 MHz, CDCl3): δ = 14.3, 21.2, 31.6, 36.6, 60.5, 68.5,
72.8, 72.4, 73.4, 75.7, 81.2, 81.5, 88.9, 110.5, 127.8, 127.7, 127.8,
127.9, 128.1, 133.3, 136.9, 137.6, 139.5, 148.6, 155.1, 163.6, 173.7.
Following the typical procedure for 4 using 37 (0.320 g, 0.699
mmol), 10% Pd/C (0.320 g), and ammonium formate (0.44 g, 6.99
mmol) in EtOH (50 mL). Purification by column chromatography
(EtOAc–EtOH–acetone–H2, 4:1:1:1) gave 9 (136 mg, 0.491 mmol,
70%) as hygroscopic white needles.
1H NMR (400 MHz, D2O): δ = 3.69 (m, 2 H, H2′), 3.84 (m, 1 H,
H3′), 4.00–4.13 (m, 2 H, H5′), 4.32 (m, 1 H, H4′), 6.40 (t, J = 4.5
Hz, 1 H, H1′), 7.22 (s, 1 H, H5im), 8.05 (s, 1 H, H2im), 8.48 (s, 1 H,
H2pyr), 9.46 (s, 1 H, H6pyr).
© Georg Thieme Verlag Stuttgart · New York
Synthesis 2012, 44, 3496–3504

3504
O. R. Wauchope et al.
PAPER
HRMS (FAB): m/z [M + H] calcd for C33H33N4O4: 549.2502; found:
549.2503.
Acknowledgment
The authors would like to thank Dr. Phil Mortimer at Johns Hopkins
University for his generous assistance with the HRMS as well as Dr.
David Yeh for his assistance with the 2D NMR.
5-[1-(2-Deoxy-β-D-ribofuranosyl)-1H-imidazol-4-yl]pyrimidin-
4-ol (10)
Following the typical procedure for 4 using 42 (0.662 g, 1.205
mmol), Pd/C (662 mg), ammonium formate (760 mg, 12.05 mmol),
and anhyd EtOH (20 mL); during the standard work up the Celite
pad was washed repeatedly with hot EtOH. Purification by column
chromatography (EtOAc–acetone–EtOH–H2, 8:1:1:0.5) gave 10
(200 mg, 0.719 mmol, 60%) as a white powder; mp >215 °C.
References
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1H NMR (400 MHz, CD3OD): δ = 3.65 (m, 2 H, H2′), 3.78 (m, 1 H,
H3′), 4.09–4.15 (m, 2 H, H5′), 4.32 (m, 1 H, H4′), 5.64 (t, J = 4.5
Hz, 1 H, H1′), 7.83 (s, 1 H, H5im), 7.92 (s, 1 H, H2im), 8.52 (br s, 1
H, H6pyr), 9.16 (s, 1 H, H6pyr).
13C NMR (100 MHz, CD3OD): δ = 61.2, 70.2, 76.1, 86.7, 89.5,
108.8, 131.6, 150.4, 151.7, 160.4.
HRMS (FAB): m/z [M + H] calcd for C12H15N4O4: 279.1093; found:
279.1094.
2,4-Bis(benzyloxy)-5-1-[(3,5-di-O-benzyl-2-deoxy-β-D-ribofu-
ranosyl)-1H-imidazol-4-yl]pyrimidine (44)
A mixture of 26 (200 mg, 0.408 mmol) and Pd(PPh3)4 (47 mg,
0.0406 mmol) in DME (5 mL) was stirred at r.t. under argon for 10
min. To this mixture was added 43 (0.449 mmol) in DME (5 mL).
Sat. aq NaHCO3 (30 mL) was added and the mixture refluxed under
argon for 4 h. The soln was cooled to r.t. and the DME layer sepa-
rated and set aside. The aqueous layer was then extracted with EtO-
Ac (3 × 50 mL), and the organic extracts were combined with the
DME layer, washed with brine (100 mL), and dried (MgSO4). The
solvent was removed to give a pale brown syrup. Column chroma-
tography (2% EtOH–CH2Cl2) gave 44 (170 mg, 0.260 mmol, 64%)
as a yellow oil.
1H NMR (400 MHz, CDCl3): δ = 2.33–2.35 (m, 2 H, H2′), 2.42–
2.45 (m, 1 H, H3′), 3.49 (m, 2 H, H5′), 4.40–4.49 (m, 1 H, H4′),
5.44–5.37 (m, 4 H, PhCH2), 4.56 (s, 2 H, PhCH2), 4.59 (s, 2 H,
PhCH2), 5.96 (t, J = 4.5 Hz, 1 H, H1′), 6.97 (s, 1 H, H5im), 7.34–7.67
(m, 20 H, HPh), 7.67 (s, 1 H, H2im), 9.13 (s, 1 H, H6pyr).
13C NMR (100 MHz, CDCl3): δ = 14.4, 22.9, 39.7, 53.3, 68.5, 68.7,
69.4, 72.4, 72.5, 73.3, 76.5, 81.5, 82.5, 88.7, 109.5, 115.7, 127.5,
127.6, 127.8, 127.9, 128.3, 134.0, 135.6, 136.1, 136.5, 136.8, 137.2,
137.3, 141.5.
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and Chemotherapy; Chu, C. K., Ed.; Elsevier Science:
Amsterdam, 2002, 299.
HRMS (FAB): m/z [M + H] calcd for C40H39N4O5: 655.2921; found:
655.2922.
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5-[1-(2-Deoxy-β-D-ribofuranosyl)-1H-imidazol-4-yl]uracil (11)
Following the typical procedure for 4 using 44 (479 mg, 0.73
mmol), 10% Pd/C (730 mg), and ammonium formate (461 mg, 7.30
mmol) in EtOH (20 mL). Purification by column chromatography
(EtOAc–acetone–EtOH–H2, 7:1:1:0.5) afforded 11 (200 mg, 0.680
mmol, 52%) as a white crystalline product; mp 245–247 °C.
1H NMR (400 MHz, DMSO-d6): δ = 3.44–3.47 (m, 2 H, H2′), 3.74–
3.75 (m, 1 H, H3′), 4.25–4.28 (m, 2 H, H5′), 5.23–5.24 (m, 1 H,
H4′), 5.98 (t, J = 4.5 Hz, 1 H, H1′), 7.62 (s, 1 H, H5pyr), 7.77 (s, 1 H,
H5im), 7.83 (s, 1 H, H2im), 10.9 (s, 1 H, NH), 11.2 (s, 1 H, NH).
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13C NMR (100 MHz, DMSO-d6): δ = 61.5, 71.3, 75.4, 85.4, 89.3,
106.3, 113.5, 133.7, 135.7, 136.8, 150.5, 162.4.
HRMS (FAB): m/z [M + H] calcd for C12H15N4O5: 295.1042; found:
295.1040.
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Synthesis 2012, 44, 3496–3504
© Georg Thieme Verlag Stuttgart · New York