A total synthesis of mycalisine A

Article abstract of DOI:10.1016/j.cclet.2013.03.014

In this paper, we report a total synthesis of a naturally occurring pyrrolo[2,3-d]pyrimidine nucleoside, mycalisine A. Our synthetic strategy uses d-xylose as the starting material and Vorbrüggen glycosylation as the key step. Mycalisine A was synthesized in 11 steps with a 15% overall yield.

Full text of DOI:10.1016/j.cclet.2013.03.014

Chinese Chemical Letters 24 (2013) 379–382
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Chinese Chemical Letters
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Original article
A total synthesis of mycalisine A
*
Yan-Hui Dou, Hai-Xin Ding, Ru-Chun Yang, Wei Li, Qiang Xiao
Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science & Technology Normal University, Nanchang 330013, China
A R T I C L E I N F O
A B S T R A C T
Article history:
In this paper, we report a total synthesis of a naturally occurring pyrrolo[2,3-d]pyrimidine nucleoside,
Received 26 November 2012
Received in revised form 24 January 2013
Accepted 27 February 2013
Available online 11 April 2013
mycalisine A. Our synthetic strategy uses D-xylose as the starting material and Vorbru¨ggen glycosylation
as the key step. Mycalisine A was synthesized in 11 steps with a 15% overall yield.
ß 2013 Qiang Xiao. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved.
Keywords:
Naturally occurring nucleoside
Total synthesis
Vorbru¨ggen glycosylation
Mycalisines A
Pyrrolo[2,3-d]pyrimidine
1. Introduction
2. Experimental
All reagents and catalysts were purchased from commercial
sources and used without purification. MeCN, pyridine and DCM
were dried with CaH2 and distilled prior to use. THF was dried with
LiAlH4 and distilled prior to use. Thin layer chromatography was
performed using silica gel GF-254 plates (Qingdao Chemical
Company, China) detected by UV (254 nm) or charting with 10%
sulfuric acid in ethanol. Column chromatography was performed
on silica gel (200–300 mesh, Qingdao Chemical Company, China).
NMR spectra were recorded on a Bruker AV400 spectrometer, and
In 1985, two novel nucleosides, mycalisines A and B (Fig. 1),
were isolated from a marine sponge Mycale sp., collected in the
Gulf of Sagami, Japan [1]. They have the characteristic pyrrolo[2,3-
d]pyrimidine base moiety, which has been found in many naturally
occurring and biologically significant nucleosides, such as cade-
guomycin [2], sangivamycin [3], and toyocamicin [4]. Both
mycalisines A and B showed inhibitive activity in cell division of
fertilized starfish eggs. However, mycalisine A was found to be 400
times more active than mycalisine B [1]. As part of our continuing
effort in the synthesis of bioactive marine nucleosides [5–8], we
report an efficient total synthesis mycalisine A in the present
paper.
Until now, only one synthesis of mycalisine A has been
reported, which used regioselective methylation of toyocamicin
2 as the key step (Fig. 1 route a) [9]. This poor regioselective
methylation of the extraordinarily expensive toyocamicin makes
this strategy impracticable. Our retrosynthetic analysis of myca-
lisine A is shown in Fig. 1 (route b). We reasoned that ribose acetate
3 would be a logical precursor for the late-stage Vorbru¨ggen
glycosylation with nucleobase 4. This intermediate 3 could be
chemical shifts (d
) are reported in ppm. 1H NMR and 13C NMR
spectra were calibrated with TMS as an internal standard, and
coupling constants (J) are reported in Hz. The ESI-MS were
obtained on a Bruker Dalton microTOFQ II spectrometer in the
positive ion mode.
2.1. 5-O-Benzoyl-1,2-O-diacetyl-3-O-methyl-
D
-ribofuranose 9 (3)
-ribofura-
5-O-Benzoyl-1,2-O-isopropylidene-3-O-methyl-
a
-D
nose (10) (500 mg, 1.62 mmol) was dissolved in HOAc (15 mL) and
Ac2O (1.5 mL). Concentrated H2SO4 (0.75 mL) was added to the
above mixture slowly. Then, the obtained solution was stirred at
room temperature overnight and poured into ice water (100 mL).
After extraction with DCM (50 mL ꢀ 3), the organic layer was
washed with saturated NaHCO3 and dried with anhydrous Na2SO4.
After filtration and removal of solvent in vacuo, the obtained
residue was purified by flash column to give compound 3 as a
ultimately derived from commercially available D-xylose 5.
mixture (
8.06 (m, 2H), 7.56 (m, 1H), 7.43 (m, 2H), 6.14 (s, 1H), 5.32 (d, 1H,
a:b d
= 2:3, 500 mg, 88%). 1H NMR (400 MHz, CDCl3):
* Corresponding author.
E-mail address: xiaoqiang@tsinghua.org.cn (Q. Xiao).
1001-8417/$ – see front matter ß 2013 Qiang Xiao. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved.
http://dx.doi.org/10.1016/j.cclet.2013.03.014

[
Y.-H. Dou et al. / Chinese Chemical Letters 24 (2013) 379–382
NH2
N
NH2
N
O
N
NC
NC
NH2
N
NC
NC
NH
N
N
N
N
N
N
HO
N
HO
NC
a
O
O
O
O
O
OH
O
OH
b
CH3
CH3 O
OH
CH3
OH OH
1
mycalisine B
2
mycalisine A
NH2
BzO
HO
O
O
N
OAc
OH
Br
OH
N
H
N
O
OAc
CH3
OH
4
3
5
Fig. 1. Structures of mycalisines A and B and their retrosynthetic analysis.
J = 4.4 Hz), 4.65 (m, 1H), 4.40 (m, 1H), 4.30 (m, 1H), 4.06 (m, 1H),
3.40 (s, 3H), 2.14 (s, 3H), 1.91 (s, 3H); 13C NMR (100 MHz, CDCl3):
169.7, 168.9, 166.1, 133.2, 129.8, 128.7, 128.4, 98.4, 79.7, 78.9, 73.0,
63.6, 59.3, 20.8, 20.6; ESI-MS: m/z 353.2 [M+H]+.
(100 MHz, CDCl3): d 169.7, 166.1, 156.5, 153.9, 149.9, 133.6, 130.2,
129.5, 129.3, 128.7, 114.9, 102.8, 88.3, 84.7, 80.1, 78.1, 73.8, 63.0,
59.4, 20.7; ESI-MS: m/z 452.3 [M+H]+.
d
2.4. 4-Amino-5-cyano-7-(3-O-methyl-b-D-ribofuranosyl)-7H-
2.2. 4-Amino-6-bromo-5-cyano-7-(2-O-acetyl-3-O-methyl-5-O-
pyrrolo[2,3-d]pyrimidine (1)
benzoyl-b-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine (11)
Compound 12 (200 mg, 0.443 mmol) was suspended in freshly
prepared saturated methanolic ammonia (20 mL). After stirred at
room temperature for 12 h, the solvent was removed in vacuo. The
residue was purified using silica gel chromatography to give
compound 1 (146 mg, 95%) as a white solid. Rf = 0.17 (DCM:
4-Amino-6-bromo-5-cyano-7H-pyrrolo[2,3-d]pyrimidine (4)
(525 mg, 2.20 mmol) was suspended in freshly distilled CH3CN
(5 mL). N,O-Bis(trimethylsilyl)acetamide (2.2 mL, 8.80 mmol)
was added and the mixture was stirred for 15 min. Then 5-O-
benzoyl-1,2-O-diacetyl-3-O-methyl-
2.0 mmol) and trimethylsilyl
D
-ribofuranose (3) (704 mg,
trifluoromethanesulfonate
MeOH = 30:1); 1H NMR (400 MHz, DMSO-d6):
d 8.45 (s, 1H), 8.22
(s, 1H), 6.04 (d, 1H, J = 4.4 Hz), 5.57 (d, 1H, J = 5.6 Hz), 5.29 (m, 1H),
(2.20 mL, 3.3 mmol) were added. After 10 min at room
temperature, the reaction flask was placed in a preheated
(80 8C) oil bath for 3 h. The reaction mixture was cooled to room
temperature. Ice water (10 mL) was added carefully to quench
the reaction. After extraction with EtOAc (50 mL ꢀ 3), the
combined organic extracts were washed sequentially with
saturated aqueous NaHCO3, H2O and brine. The obtained organic
layer was dried over anhydrous Na2SO4, filtered and evaporated
to dryness in vacuo. The residue was chromatographed on silica
gel column developed with DCM/MeOH (50:1) to give
compound 11 (790 mg, 58%) as a white solid. Rf 0.42 (CH2Cl2:
4.53 (m, 1H), 4.02 (s, 1H), 3.83 (s, 1H), 3.66 (m, 1H), 3.57 (m, 1H),
3.39 (s, 3H); 13C NMR (100 MHz, DMSO-d6):
d 157.5, 154.0, 150.5,
132.7, 115.7, 101.7, 88.4, 83.4, 79.7, 73.8, 61.5, 58.0; ESI-MS: m/z
306.1 [M+H]+, 304.1 [MꢁH]ꢁ.
2.5. 4-Amino-5-cyano-7-(3-O-methyl-5-(O-nitrophenylselenide)-
-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine (13)
b-
D
O-Nitrophenylselenocyanate (204 mg, 0.9 mmol) and Bu3P
(0.225 mL, 0.9 mmol) were added to compound (100 mg,
1
0.32 mmol) in freshly distilled pyridine (5 mL). The obtained
mixture was stirred at room temperature for 4 h. After the solvent
was removed in vacuo, the residue was purified using silica gel to
give selenide 1 (143 mg, 87%) as a white solid. Rf = 0.42 (DCM:
EtOAc = 8:1). 1H NMR (400 MHz, CDCl3):
d 8.45 (s, 1H), 8.06
(m, 2H), 7.57 (m, 1H), 7.45 (m, 2H), 6.58 (m, 1H), 5.40 (m, 1H),
4.50 (m, 2H), 4.45 (m, 1H), 4.11 (m, 1H), 3.53 (s, 3H), 2.23
(s, 3H); 13C NMR (100 MHz, CDCl3):
d
170.1, 166.2, 154.1,
MeOH = 20:1); 1H NMR (400 MHz, DMSO-d6):
d 8.46 (s, 1H), 8.26–
151.9, 150.2, 133.3, 129.7, 129.5, 128.5, 118.0, 114.0, 104.6, 86.4,
80.2, 79.5, 79.3, 70.9, 64.5, 59.1, 21.5; ESI-MS: m/z 530.3
[M+H]+.
8.22 (m, 2H), 7.78 (d, 1H, J = 8.0 Hz), 7.64 (t, 1H, J = 7.6 Hz), 7.44 (t,
1H, J = 7.6 Hz), 6.09 (d, 1H, J = 5.2 Hz), 5.72 (d, 1H, J = 6.4 Hz), 4.77–
4.72 (m, 1H), 4.25–4.21 (m, 1H), 3.93–3.91 (m, 1H), 3.45 (d, 2H,
J = 6.8 Hz), 3.39 (s, 3H); 13C NMR (100 MHz, DMSO-d6):
d 157.5,
2.3. 4-Amino-5-cyano-7-(2-O-acetyl-3-O-methyl-5-O-benzoyl-
b
-
D
-
154.1, 150.8, 147.0, 134.7, 132.9, 131.9, 130.5, 126.8, 126.7, 115.6,
101.6, 88.4, 84.0, 82.9, 80.8, 72.9, 58.1, 23.9; ESI-MS: m/z 491.1
[M+H]+, 489.4 [MꢁH]ꢁ.
ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine (12)
Compound 11 (200 mg, 0.377 mmol) was dissolved in THF
(10 mL) and CH3OH (5 mL). Pd(OH)2 (50 mg) and Et3N (0.1 mL)
were added to the above solution. The resulted solution was
hydrogenated for 5 h. After filtration through celite and evapora-
tion of the mother liquor, the residue was chromatographed on a
silica gel column to give compound 12 (148 mg, 93%) as a white
solid. Rf 0.17 (CH2Cl2: EtOAc = 8:1). 1H NMR (400 MHz, CDCl3):
8.28 (s, 1H), 8.03 (m, 2H), 7.67 (m, 1H), 7.63 (m, 1H), 7.49 (m, 2H),
6.22 (d, 1H, J = 3.2 Hz), 6.07 (s, 1H), 5.79 (m, 1H), 4.74–4.71 (m, 2H),
4.41 (m, 1H), 4.28 (m, 1H), 3.44 (s, 3H), 2.18 (s, 3H); 13C NMR
2.6. Mycalisine A
Selenide 13 (100 mg, 0.20 mmol) was dissolved in THF (5 mL).
30% H2O2 (0.172 mL, 2 mmol) was added and the resulted solution
was stirred for 2 h at room temperature. Pyridine (2 mL) and Et3N
(0.4 mL, 0.3 mmol) were added. The obtained mixture was heated
at 50 8C overnight. After the removal of the solvent in vacuo, the
residue was purified using silica gel to give mycalisine A (52 mg,
87%) as a white solid. Rf = 0.14 (DCM: MeOH = 50:1); 1H NMR
d

[
Y.-H. Dou et al. / Chinese Chemical Letters 24 (2013) 379–382
381
BzO
HO
BzO
BzO
HO
O
d
O
O
O
c
b
a
O
OH
OH
O
OH
OH
O
O
O
OH
O
O
O
O
O
OH
9
8
5
7
6
NH2
NH2
N
NC
NC
N
BzO
Br
BzO
BzO
h
f
N
BzO
O
N
e
N
g
O
N
O
O
OAc
O
O
O
CH3
CH3O
OAc
O
OAc
CH3
O
OAc
11
CH3
10
3
12
NH2
N
NC
NH2
N
NC
NH2
NC
NO2
Se
k
N
N
N
j
O
HO
i
N
N
N
O
N
O
O
CH3
OH
O
OH
CH3
CH
3O
OH
mycalisine A
1
13
Scheme 1. Reagents and conditions: (a) Acetone, H2SO4, Na2CO3, r.t., 3 h, 73%; (b) BzCl, Py, r.t., 4 h, 75%; (c) Dess-Marton, DCM, r.t., 5 h, 97%; (d) NaBH4, CH3OH, r.t., 3 h, 97%; (e)
NaH, DMF, CH3I, 0 8C, 92%; (f) AcOH, Ac2O, H2SO4, 24 h, 88%; (g) i. 4, BSA, CH3CN; ii. 3, TMSOTf, CH3CN, 58%; (h) 5% Pd/C, Et3N, THF, CH3OH, r.t., 4 h, 93%; (i) sat. NH3 in MeOH,
r.t., 3 h, 95%; (j) O-nitrophenylselenocyanate, Bu3P, Py, r.t., 4 h, 87%; (k) i. H2O2, THF, r.t., 2 h; ii. Et3N, THF, 50 8C, overnight, 87%.
(400 MHz, DMSO-d6):
6.32 (d, 1H, J = 6.8 Hz), 5.83 (d, 1H, J = 6.8 Hz), 4.92–4.89 (m, 1H),
4.44 (s, 1H), 4.30 (s, 1H), 4.22 (d, 1H, J = 4.8 Hz), 3.39 (s, 3H); 13C
d
8.53 (s, 1H), 8.25 (s, 1H), 7.01 (brs, 2H),
data were in accordance with those of the reported natural
product.
NMR (100 MHz, DMSO-d6):
d 157.8, 157.5, 154.4, 151.3, 133.0,
4. Conclusion
115.4, 101.6, 87.8, 87.7, 84.6, 78.9, 72.5, 56.5; ESI-MS: m/z 288.2
[M+H]+, 286.5 [MꢁH]ꢁ.
In summary, we have achieved an efficient total synthesis of
mycalisine A from
strategy integrates
D
-xylose in 11 steps with a 15% overall yield. Our
stereo- and regioselective Vorbru¨ggen
a
3. Results and discussion
glycosylation and a new versatile nucleoside donor 3 for the
preparation of the related nucleoside derivatives. Investigations in
this transformation are well underway and will be reported in due
course.
In the forward direction (Scheme 1), crystalline 1,2-O-
isopropylidene-a-D-xylofuranose 6 was prepared in 73% yield
with a modification of a reported procedure on 100 g scale [10].
Then 5-OH in 6 was selectively protected as the corresponding
benzoate to give 7 in 75% yield. Dess-Martin oxidation of the 3-OH
in 7 afforded ketone 8 in 97% yield [11]. Subsequently stereo-
selective reduction with NaBH4 gave ribose 9 exclusively in 97%
yield [12]. Next, compound 9 was subjected to methylation with
CH3I and NaH in DMF to provide 10 in excellent yield. Final
cleavage of the acetonide with acetic acid/acetic anhydride/H2SO4
provided the key intermediate 3 in 88% yield as a mixture
Acknowledgments
We thank NSFC (Nos. 20962009 and 21062006), NCET (No. 11-
1000), the Training Project of Jiangxi Youth Scientists, Education
Department of Jiangxi Province (Nos. GJJ11223 and GJJ12583), and
Bureau of Science & Technology of Nanchang City for financial
support.
(
a:
b
= 2:3) [13].
With compound 3 in hand, we proceeded to investigate the
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yield. The correct stereo- and regiochemical outcome of the
glycosylation was confirmed by NMR analysis. Then debromina-
tion was conducted under hydrogenation conditions using 5% Pd/C
as the catalyst to give 12 in 93% yield. Global deprotection under
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