Novel exocyclic nucleoside related to clitocine: A convergent synthesis of 3-azido-2,3-dideoxy clitocine

Article abstract of DOI:10.1055/s-0030-1258503

The synthesis of a new clitocine derivative was achieved through a convergent strategy. A protected 4,6-diamino-5-nitropyrimidine was condensed with p-chlorobenzoyl (PCB)-protected methyl 3'-azido-2',3'- dideoxyribofuranoside, followed by subsequently deprotection to give the desired product. Georg Thieme Verlag Stuttgart.

Full text of DOI:10.1055/s-0030-1258503

LETTER
1959
Novel Exocyclic Nucleoside Related to Clitocine: A Convergent Synthesis of
3¢-Azido-2¢,3¢-dideoxy Clitocine
S
a
ynthesis of
3¢
-A
z
i
ido-2
¢
,3
a
¢
-dideoxy
n
Key Laboratory of Systems Bioengineering, Ministry of Education and Department of Pharmaceutical Engineering,
School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, P. R. of China
E-mail: Guoxh@tju.edu.cn
School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, P. R. of China
E-mail: sjiang@tju.edu.cn
b
Received 17 March 2010
3¢-amino, a characteristic group of oligonucleotide N3¢–
P5¢ phosphoramidates that had been developed as anti-
sense drugs.12 Based on above considerations, 3¢-azido-
substituted clitocine could be considered as a potential an-
titumor and antiviral target. We report herein the synthesis
of the new 3¢-azido-2¢,3¢-dideoxy clitocine [6, 6-amino-5-
nitro-4-(3¢-azido-2¢,3¢-dideoxy-b-D-ribofuranosylamino)-
pyrimidine].
Abstract: The synthesis of a new clitocine derivative was achieved
through a convergent strategy. A protected 4,6-diamino-5-nitro-
pyrimidine was condensed with p-chlorobenzoyl (PCB)-protected
methyl 3¢-azido-2¢,3¢-dideoxyribofuranoside, followed by subse-
quently deprotection to give the desired product.
Key words: nucleoside analogues, exocyclic nucleosides, conver-
gent synthesis, clitocine, antiviral drug
NH2
O
O
Clitocine (1, Figure 1), 6-amino-5-nitro-4-(b-D-ribofura-
nosylamino) pyrimidine, is a naturally occurring amino
exocyclic nucleoside isolated from the mushroom, Clito-
cybe inversa,1 whose syntheses have been reported.2 Cli-
tocine has already been demonstrated to exhibit strong
insecticidal activity against the pink bollworm Pectino-
phora gossypiella1 and cytotoxic activities against some
cancer cell lines [L1210, WI-L2, 3LL, DU145, K-562,
MCF7, U251, human cervical cancer cells (HeLa) and
CCRF-CEM].2a,3 It is structurally similar to adenosine and
this makes it to be a potential inhibitor for adenosine ki-
nase.4 The successful applications of clitocine as a thera-
peutic composite to treat diseases associated with HepG2
liver cancer cells,5 P-glycoprotein tumor cells,6 and non-
sense mutations7 have been disclosed. Because of these
interesting pharmacological activities, several research
groups have synthesized various acyclic,8 carbocyclic,9 4-
substituted amino,10 5¢-deoxy,4a,b and 2¢-deoxy11 ana-
logues of clitocine.
NO2
NH
N
N
N
N
N
HN
O
HN
N
O
H2N
N
H2N
HO
N
H2N
HO
O
O
O
OH OH
2
3
1
O
O
N
NH2
NO2
NH
N
N
HN
HN
O
N
H2N
HO
N
O
N
O
HO
HO
O
OH
N3
N3
6
4
5
Figure 1 Some nucleoside structures
Two synthetic building blocks were required, a protected
base and a sugar. The base 4,6-diamino-5-nitro-pyrimi-
dine (7) was prepared from 4,6-dihydroxy-pyrimidine
employing a three-step method,13 and then silylated to
give TMS protected 8.2a
Following many successful nucleoside drugs related to
acyclovir (2), such as valaciclovir (3), and penciclovir (4),
which can be seen as acyclic nucleosides; we believe that
it is worthwhile to explore some exocyclic structures. In
continuation of our interest in the synthesis of novel nu-
cleosides, we wished to investigate the synthesis and bio-
logical activities of compounds containing the clitocine
aglycon, which might be regarded as an exocyclic nucle-
oside structure.
We initially used TBDPS-protected methyl 3-azido-2,3-
dideoxy-D-erythro-pentofuranoside as a sugar source,
which was easily prepared from 2-deoxy-D-ribose (9).14
But further coupling failed to meet our expectation. The
protected base 8 was glycosylated with silylated sugar in
1,2-dichloroethane with trimethylsilyl trifluoromethane-
sulfonate (TMSOTf) as the Lewis acid catalyst at room
temperature for 72 hours, but no detectable product was
observed. The lability of silylated sugar under acidic con-
dition might be responsible for this failure.
Zidovudine (AZT, 5) is the first approved drug for treat-
ment of AIDS, and is characterized by a 3¢-azido substit-
uent. 3¢-Azido functionality can also be easily reduced to
SYNLETT 2010, No. 13, pp 1959–1962
x
x
.x
x
.2
0
1
0
Advanced online publication: 16.07.2010
DOI: 10.1055/s-0030-1258503; Art ID: W04510ST
© Georg Thieme Verlag Stuttgart · New York

1960
X. Guo et al.
LETTER
O
OH
HO
A second route was designed to overcome tedious workup
of Mitsunobu reaction and improve productivity of 3b-
OH sugar 12 (Scheme 2). Two additional steps were used
to realize the inversion of 3-OH. First, 3a-OH was mesy-
lated to give 14 in a yield of 90%. Then a Walden inver-
sion was performed in the next step with substitution of
the methanesulfonate group in position 3. Sodium nitrite
was then used as O-nucleophile, and the compound 15
with free hydroxy groups was isolated in 62% yield. Sub-
sequent mesylation of 15 gave 12 (1:1 ratio of a/b) in 92%
yield.
i
ii
OMe
O
HO
OH
10
OH
9
PCBO
PCBO
PCBO
OMs
O
iv
iii
OMe
O
OMe
OH
12α
11
O
OMe
N3
13
Scheme 1 Synthesis of PCB protected sugar. Reagents and conditi-
ons: (i) HCl, MeOH, r.t.; (ii) p-chlorobenzoyl chloride, Et3N, CH2Cl2,
ice bath (90% for two steps); (iii) Ph3P, DEAD, MsOH, toluene, 60–
70 °C (86%); (iv) NaN3, DMF, 110 °C (70%).
To address the above-mentioned protecting problem, we
changed the tert-butyldiphenylsilyl (TBDPS) protecting
group to p-chlorobenzoyl (PCB) group. Two routes were
used to provide PCB protected sugar starting from 2-
deoxy-D-ribose (9). The first route (Scheme 1) employed
a Mitsunobu reaction as a key step to achieve inversion of
the configuration at 3-OH. The starting 9 was first quanti-
tatively methylated at position 1 with hydrogen chloride
in methanol.15 The obtained methyl glycoside 10 was se-
lectively 5-O-benzoylated using p-chlorobenzoyl chloride
in dichloromethane and triethylamine, afforded 11 as an
a/b mixture in a yield of 90%. The mixture of anomers
could be used in the next step without separation, which
was treated with triphenylphosphine, diethyl azodicar-
boxylate (DEAD), and methanesulfonic acid in toluene at
60–70 °C to give 12a in 86% yield.16 It is of interest to
note that 1a-anomer of 12 was found as the only main
product after Mitsunobu reaction, whose structure was un-
ambiguously determined by X-ray analysis of a single
crystal (Figure 2)17. The 12a were then heated in DMF
with an excess of sodium azide at 110 °C to give the cor-
responding azido compounds 13 in 70% yield. Pure com-
pound 12a is very stable after recrystallization, but slow
racemization at C-1 of 13 was observed after prolonged
storage at room temperature.
Figure 2 ORTEP plot of compound 12a
Finally, the silylated base 8 was directly glycosylated with
azide substituted sugar 13 in 1,2-dichloroethane with
TMSOTf as the Lewis acid catalyst to give 6-amino-5-
NHTMS
PCBO
O2N
i
N
O
+
OMe
TMSHN
N
N3
13
NH2
8
PCBO
PCBO
i
ii
OMe
OMe
NH2
O
O
NO2
NH
NO2
NH
N
N
OH
11
OMs
ii
14
N
N
O
PCBO
HO
O
PCBO
PCBO
OMs
O
iii
OH
OMe
OMe
O
N3
16
N3
6
12
15
Scheme
3
Synthesis of 3¢-azido-2¢,3¢-dideoxy clitocine (6).
Scheme 2 Synthesis of 3b-OH sugar. Reagents and conditions: (i)
MsCl, Et3N, CH2Cl2, ice bath (90%); (ii) NaNO2, DMF, 120 °C
(62%); (iii) MsCl, Et3N, CH2Cl2, ice bath (92%).
Reagents and conditions: (i) TMSOTf, DCE, r.t. (16%); (ii) NaOMe,
MeOH, r.t. (65%).
Synlett 2010, No. 13, 1959–1962 © Thieme Stuttgart · New York

LETTER
Synthesis of 3¢-Azido-2¢,3¢-dideoxy Clitocine
1961
R.; Weir, N. G.; Woods, J. M. Nucleosides Nucleotides
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ribo-furanosylamino) pyrimidine (16) as a white solid in
16% yield after chromatography.18 No significant amount
of a-anomer was isolated. Treatment of 16 with a solution
of NaOMe in methanol gave nucleoside 6 in 65% yield19
(Scheme 3).
(10) Varaprasad, C. V.; Habib, Q.; Li, D. Y.; Huang, J. F.; Abt,
J. W.; Rong, F.; Hong, Z.; An, H. Y. Tetrahedron 2003, 59,
2297.
In conclusion, we have developed an efficient method to
prepare the novel 3¢-azido-2¢,3¢-dideoxy clitocine ana-
logue. The synthesis was accomplished via convergent
route, which should be applicable to the synthesis of sim-
ilarly functionalized analogues of other pyrimidine as
well as purine nucleosides.
(11) Sharkin, Y. A.; Semizarov, D. G.; Viktorova, L. S.;
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(4) (a) Lee, C. H.; Daanen, J. F.; Jiang, M.; Yu, H.; Kohlhaas,
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(17) The CCDC number of compound 12a is 777653.
(18) 6-Amino-5-nitro-4-(3¢-azido-5¢-O-p-chloro-benzoyl-2¢,3¢-
dideoxy-b-D-ribofuranosylamino) Pyrimidine (16)
TMS-protected 4,6-diamino-5-nitropyrimidine 8 (0.86 g, 2.9
mmol) was dissolved in DCE (10 mL). To this solution,
methyl 3¢-azido-5¢-O-p-chlorobenzoyl-2¢,3¢-dideoxy-b-D-
ribofuranoside (13, 0.75 g, 2.4 mmol) and TMSOTf (0.72
mL, 4.0 mmol) were added, the mixture was stirred for 48 h
at r.t., and 10% NaHCO3 (15 mL) was added. After 20 min
stirring, CH2Cl2 (20 mL) was added to the resulting
suspension; the mixture was filtered through Hyflo Super
Cel; the organic layer was separated, washed with H2O (10
mL), and dried with Na2SO4. Nucleoside 16 (0.11 g) and
recovered sugar 13 (0.27 g) were isolated by silica gel
chromatography (elution with EtOAc–PE = 1:2). The yield
was 16% based on recovered starting material. A white solid
was afforded after recrystallizaion in EtOAc; mp 178–180
°C. IR (KBr): n = 3440, 3332, 2109, 1389, 1344, 1290, 1245
cm–1. 1H NMR (500 MHz, DMSO-d6): d = 9.57 (1 , d, JNH–
H1¢ = 8.51 Hz, NH), 8.61 (2 H, d, JNH2 = 15.10 Hz, NH2), 8.00
(1 H, s, C2-H), 7.98 (2 H, m, ArH), 7.61 (2 H, m, ArH), 6.32
(1 H, m, C1¢-H), 4.56 (1 H, m, C4¢-H), 4.36 (3 H, m, C5¢-H,
C3¢-H), 2.62 (1 H, dd, J = 5.69, 12.80 Hz, C2¢-H), 2.20 (1 H,
m, C2¢-H) ppm. 13C NMR (500 MHz, DMSO-d6): d = 164.66
(C=O), 159.29 (C-2), 158.58 (C-6), 156.02 (C-4), 138.46
(CCl), 131.11 (2 C, Ar), 128.98 (2 C, Ar), 128.17 (CC=O),
112.03 (C-5), 81.11 (C-1¢), 80.62 (C-4¢), 64.83 (C-5¢), 61.68
(C-3¢), 36.77 (C-2¢) ppm.
(5) Liu, F. Y.; Ren, G.; Fu, C. X.; Wu, P. CN 101333236, 2008;
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1994, 37, 3057. (b) Franchetti, P.; Cappellacci, L.;
Abu Sheikha, G.; Grifantini, M.; Loi, A. G.; De Montis, A.;
Spiga, M. G.; La Colla, P. Nucleosides Nucleotides 1995,
14, 607. (c) Bacchelli, C.; Condom, R.; Patino, N.; Aubertin,
A. M. Nucleosides, Nucleotides Nucleic Acids 2000, 19, 567.
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(19) 6-Amino-5-nitro-4-(3¢-azido-2¢,3¢-dideoxy-b-D-
ribofuranosylamino) Pyrimidine 6
To a solution of nucleoside 16 (90 mg, 0.2 mmol) in MeOH
(10 mL) cooled to 0 °C was added 0.1 M NaOMe in MeOH
Synlett 2010, No. 13, 1959–1962 © Thieme Stuttgart · New York

1962
X. Guo et al.
LETTER
(0.64 mL), and the mixture was stirred at r.t. for 18 h in the
argon atmosphere. The reaction mixture was neutralized
with Dowex 50 (H+), and the resin was rapidly filtered. After
evaporation under vacuum to dry, a light yellow solid
product 6 was isolated from the residue by silica gel
chromatography, elution with an EtOAc–PE (3:2). The yield
was 40 mg (65%). 1H NMR (500 MHz, DMSO-d6): d = 9.39
(1 H, d, JNH–H1¢ = 8.2 Hz, NH), 8.56 (2 H, br s, NH2), 8.00 (1
H, s, C2-H), 6.22 (1 H, td, J = 6.0 Hz, JNH–H1¢ = 8.2 Hz, C1¢-
H), 5.23 (1 H, t, J = 5.0 Hz, OH), 4.33 (1 H, td, J = 4.2 Hz,
J
H2a¢–H3¢ = 7.0 Hz, C3¢-H), 3.88 (1 H, q, J = 3.58, 3.58, 3.60
Hz, C4¢-H), 3.51 (2 H, t, J = 4.2 Hz, C5¢-H), 2.39 (1 H, ddd,
H2a¢–H1¢ = 6.0 Hz, JH2a¢–H3¢ = 7.0 Hz, JH2b¢–H2a¢ = 13.0 Hz, C2¢-
Ha), 2.27 (1 H, ddd, JH2b¢–H3¢ = 4.2 Hz, JH2b¢–H1¢ = 6.0 Hz,
H2b¢–H2a¢ = 13.0 Hz, C2¢-Hb) ppm. 13C NMR (500 MHz,
J
J
DMSO-d6): d = 159.98 (C-2), 159.29 (C-6), 156.49 (C-4),
109.99 (C-5), 84.62 (C-1¢), 82.21 (C-4¢), 62.14 (C-5¢), 62.08
(C-3¢), 38.40 (C-2¢) ppm.
Synlett 2010, No. 13, 1959–1962 © Thieme Stuttgart · New York

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