Concise total synthesis of two marine natural nucleosides: Trachycladines A and B

Article abstract of DOI:10.3762/bjoc.10.176

We report the first total synthesis of trachycladines A (10 steps, 34.2% overall yield) and B (11 steps, 35.0% overall yield) by using 5-deoxy-1,2,3-tri-O-acetyl-β-D-ribofuranose as the starting material. The critical step was the SnCl₄ assisted regio- and steroselective deprotection of perbenzylated 1-O-methyl-5-deoxyribofuranose. The enzyme adenylate deaminase (EC 3.5.4.6) was successfully applied to the chemoenzymatic synthesis of trachycladines B.

Full text of DOI:10.3762/bjoc.10.176

Concise total synthesis of two marine natural nucleosides:
trachycladines A and B
Haixin Ding1, Wei Li1, Zhizhong Ruan1, Ruchun Yang1, Zhijie Mao1, Qiang Xiao*1
and Jun Wu*1,2
Full Research Paper
Open Access
Address:
Beilstein J. Org. Chem. 2014, 10, 1681–1685.
1Jiangxi Key Laboratory of Organic Chemistry, Jiangxi Science &
Technology Normal University, Nanchang 330013, China and 2Marine
Drugs Research Center, College of Pharmacy,Jinan University,
Guangzhou 510632, China
doi:10.3762/bjoc.10.176
Received: 17 April 2014
Accepted: 26 June 2014
Published: 24 July 2014
Email:
Qiang Xiao* - xiaoqiang@tsinghua.org.cn; Jun Wu* -
wwujun2003@yahoo.com
Associate Editor: S. Flitsch
© 2014 Ding et al; licensee Beilstein-Institut.
License and terms: see end of document.
* Corresponding author
Keywords:
marine nucleosides; natural products; total synthesis; trachycladines
A and B; Vorbrüggen glycosylation
Abstract
We report the first total synthesis of trachycladines A (10 steps, 34.2% overall yield) and B (11 steps, 35.0% overall yield) by using
5-deoxy-1,2,3-tri-O-acetyl-β-D-ribofuranose as the starting material. The critical step was the SnCl4 assisted regio- and steroselec-
tive deprotection of perbenzylated 1-O-methyl-5-deoxyribofuranose. The enzyme adenylate deaminase (EC 3.5.4.6) was success-
fully applied to the chemoenzymatic synthesis of trachycladines B.
Introduction
Marine organisms are a main source for the great diversity of As a key class of marine natural nucleosides, trachycladines A
naturally occurring nucleosides [1], which play an important and B (Figure 1) hold an important position in drug develop-
role in medical research and pharmaceutical development, espe- ment. Both trachycladines A and B contain a rare naturally
cially for the clinical treatment against malignant proliferation occurring 2′-C-methyl-5′-deoxy-D-ribose sugar moiety. The
and infections by fungi, bacteria and viruses [2-7]. The initial biological activity of trachycladine B has not been reported yet
discovery of marine nucleosides can be traced back to the iden- due to its insufficient availability in natural resources. Trachy-
tifications of spongothymidine and spongouridine in the early cladines A, which was isolated from the same sponge natural
1950s from the Caribbean sponge Tethyacrypta [8,9], which product Trachycladus laevispirulifer (and also from the sponges
subsqeuently led to the commercialization of arabinofuranosyl- Theonella cupola and Theonella sp) in 1995 [13,14], exhibits
cytosine (Ara-C) [10], arabinofuranosyladenine (Ara-A) [11], significant cytotoxicity in vitro against several human cell lines
and azidothymidine (AZT) [12] for clinical use.
such as leukaemia (CCRF-CEM, IC50 0.4 µg/mL), colon
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Beilstein J. Org. Chem. 2014, 10, 1681–1685.
tumour (HCT-116, IC50 0.9 µg/mL), and breast tumour cells
(MCF-7, IC50 0.2 µg/mL) [13]. Furthermore, such 2′-C-
branched ribonucleosides are also potential agonists for adeno-
sine kinase receptors and play an important role in related drug
discovery [15].
Figure 1: Structures of trachycladine A and B.
To facilitate the discovery of lead compounds as anticancer
reagents from marine nucleosides [16-18], the total synthesis of
trachycladines A and trachycladines B are reported herein
Figure 2: Retrosynthetic analysis of trachycladines A and B.
allowing to assemble their unique chemical structure for the the C-5′ hydroxy group was accompanied by several undesired
first time.
side reactions.
Results and Discussion
Then we turned to synthetic route (B), which utilizes carbohy-
Until now, there is only one publication about the total syn- drate 4 as a Vorbrüggen glycosylation donor. Firstly, without
thesis of analogues of trachycladines A and B. In 2005, Enders the deoxygenation of the C-5′ hydroxy group at the late syn-
et al. reported the first asymmetric synthesis of 4′-epi-trachy- thetic stage, carbohydrate 4 is a versatile intermediate for the
cladines A and B in 14 steps. They used 2,2-dimethyl-1,3- diversity-oriented synthesis of the related 2′-C-β-methyl-5′-
dioxan-5-one as a starting material and employed the SAMP-/ deoxyribonucleosides. As the key intermediate for the prepar-
RAMP-hydrazone methodology to obtain an overall yield of ation of the antitumor drug capecitabine [24,25], 5-deoxy-1,2,3-
18–21% [19,20]. Due to the formation of the opposite configur- tri-O-acetyl-β-D-ribofuranose (6) is commercially available
ation at C-4′ and a lengthy synthetic route this strategy is not with a cheap market price. In addition, the regioselective
suitable for the total synthesis of trachycladine A and B.
cleavage of the 2-O-benzyl protection group of perbenzylated
1-O-methyl ribofuranoside by using SnCl4 has been widely
From a synthetic point of view, the target nucleosides could be used for the synthesis of 2-O-substituted nucleosides [26-30].
synthesized from either 1,2,3,5-tetra-O-benzoyl-2-C-β-methyl- To the best of our knowledge, an application for 5-deoxyribo-
D-ribofuranose (5) (route A) or 5-deoxy-1,2,3-tri-O-acetyl-β-D- furanoside is not published. This step would be vital for the
ribofuranose (6) (route B). The corresponding retrosynthetic introduction of the corresponding 2′-C-β-methyl group in our
analysis is shown in Figure 2.
synthetic strategy.
In synthetic route (A), nucleoside 3 could be synthesized by Our synthetic route to 5-deoxy-1-O-acetyl-2,3-di-O-benzoyl-2-
using 1,2,3,5-tetra-O-benzoyl-2-C-methyl-D-ribofuranose (5) as C-β-methyl-D-ribofuranose (4) is shown in Scheme 1. Treat-
a carbohydrate acceptor by a Vorbrüggen glycosylation with the ment of 5-deoxy-1,2,3-tri-O-acetyl-β-D-ribofuranose (6) with
corresponding silylated nucleobases and a Lewis acid as a cata- catalytic NaOMe in MeOH gave 5-deoxy-D-ribose in quantitat-
lyst. As the key intermediate for the preparation of the anti- ive yield. Without further work-up, an excess of freshly
HCV nucleoside valopicitabine (NM-283) [21,22] and related prepared Dowex-50 H+ resin was added to the mixture until pH
nucleosides, there are suitable methodologies for the synthesis 5 was reached. After stirred overnight, 5-deoxy-1-O-methylri-
of carbohydrate 5 [23]. After the selective deoxygenation of the bofuranose 7 was obtained as a mixture of anomers (α:β = 2:3,
C-5′ hydroxy group of nucleosides 3, trachycladine A and B 93% for two steps). Then, the other two hydroxy groups were
could be afforded. According to the preliminary results from protected as 2,4-dichlorobenzyl ether. Compound 8 was isolated
our lab (unpublished results), the deoxygenation procedure of in 95% yield after reacting compound 7 with NaH and 2,4-
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Beilstein J. Org. Chem. 2014, 10, 1681–1685.
dichlorobenzyl chloride in anhydrous DMF. 2,4-Dichlorobenzyl
chloride was used because it is less irritant than the usually used
benzyl bromide.
Figure 3: The X-ray crystal structural of 1-O-methyl-3-O-(2,4-
dichlorobenzyl)-5-deoxy-α-D-ribofuranose (9).
H-1, H-3, 5-CH3 and 2-β-methyl. Then, the remaining 3-(O-2,4-
dichlorobenzyl) group was removed under hydrogenation with
20% Pd(OH)2/C as a catalyst to give 12 in 91% yield. As the
anomerization of the 1-O-α-methyl glycoside may occur under
acidic conditions, the structural characterization may be much
more complex. The addition of triethylamine is necessary to
neutralize the possibly formed hydrogen chloride due to the
reduction of the aromatic chloro substitutes during hydrogena-
tion. The protection of all free hydroxy groups of 12 as
benzoates afforded 13 in 92% yield. Due to the steric environ-
ment of 2-OH the benzoylation with benzoyl chloride required
an extended reaction time (48 h) and 2 equiv DMAP as base
and catalyst. At last, the 1-O-methyl group was transformed to
1-O-acetate glycosylation acceptor 4 as an anomeric mixture
(α:β = 2:3) in 84% yield. Therefore, the key intermediate 4 was
synthesized from commercial available 5-deoxy-1,2,3-tri-O-
Scheme 1: Synthesis of 5-deoxy-1-O-acetyl-2,3-di-O-benzoyl-2-C-β-
methyl-D-ribofuranose (4). Reagents and conditions: (a) i. CH3ONa
(cat.), CH3OH, 0 °C; ii. Dowex-50 H+ resin, pH 5, rt, overall 93% yield
in two steps; (b) NaH, 2,4-dichlorobenzyl chloride, DMF, 0 °C, 95%;
(c) SnCl4, DCM, 0 °C, 87%; (d) Dess–Martin oxidation, DCM, reflux,
92%; (e) CH3MgBr, ether, −10 °C, 87%; (f) H2, 20% Pd(OH)2/C, Et3N,
THF/EtOAc 1:1, rt, 91%; (g) Benzoyl chloride, DMAP (2 equiv), DCM,
rt, 92%; (h) Ac2O/AcOH 1:1, H2SO4, rt, 84%.
Regioselective cleavage of the 2-O-(2,4-dichlorobenzyl) group acetyl-β-D-ribofuranose (6) in 8 steps in 43.2% overall yield.
was attempted with anhydrous SnCl4 in DCM by the method
reported by Brown [31,32] and our group [16]. To our delight, Unfortunately, the Vorbrüggen glycosylation of carbohydrate 4
this approach can afford 3-O-(2,4-dichlorobenzyl)-1-O-methyl- with bis(trimethylsilyl)hypoxanthine with TMSOTf as a cata-
α-D-ribofuranose (9). After extensive optimization, compound lyst afforded a mixture of inseparable N9 and N7 isomers with
9 was obtained as an α-anomer only in 87% yield with exclu- 40% yield. To further improve the yield and add to the molec-
sive regio- and stereoselectivity (Scheme 1). The anomeric ular diversity, N6-benzoyladenine 17 was used as a base to give
hydrogen atom of 9 shows a characteristic doublet with a nucleoside 14 in 87% yield (Scheme 2). All benzoyl protecting
coupling constant of J = 4.8 Hz at 4.87 ppm. The structure of 9 groups were removed simultaneously by using ammonia satu-
was further unambiguously confirmed by X-ray diffraction rated methanol in a sealed press tube to give 15 in 96% yield. In
analysis (Figure 3). This is the first report on the usage of SnCl4 the next transformation to trachycladine B the classic proce-
as a regio- and stereoselective deprotection reagent in perbenzy- dure with sodium nitrite in acetic acid proved to be inefficient
lated 5-deoxy-1-O-methylribofuranose. Based on these find- as it gave complicated mixtures. Therefore, we applied an alter-
ings SnCl4 may prove useful for the regio- and stereoselective native method.
cleavage of the 2-O-benzyl group at perbenzylated 1-O-methyl-
ribofuranose analogues.
In the past decades, adenosine deaminase (adenosine aminohy-
drolase, ADA, EC 3.5.4.4) and adenylate deaminase (5′-
Dess–Martin oxidation of compound 9 provided ketone 10 in adenylic acid deaminase, AMP deaminase, AMPDA, EC
92% yield. Next, the addition reaction with CH3MgBr in dry 3.5.4.6) have been widely used in enzymatic hydrolysis [33-36].
ether gave 11 exclusively with the requisite β-methyl configur- In our experiment, ADA failed to give trachycladine A due to
ation at C-2. NOE experiments showed correct correlations of its lack of the 5′-hydroxy group, which plays a crucial role for
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Beilstein J. Org. Chem. 2014, 10, 1681–1685.
Scheme 3: Synthesis of trachycladine A (1). Reagents and conditions:
(a) DBU, TMSOTf, CH3CN, 86%; (b) NH3 sat. methanol, sealed press
tube, 92%.
Conclusion
In conclusion, the total synthesis of trachycladine A and B have
been successfully accomplished for the first time with 34.8%
and 35.6% overall yield, respectively. All spectral data of syn-
thetic trachycladine A and B are in accordance with those of the
natural products. We would like to particularly emphasize three
Scheme 2: Synthesis of trachycladine B (2). Reagents and conditions:
(a) i. N,O-Bis(trimethylsilyl)acetamide (BSA), MeCN; ii. TMSOTf,
MeCN, 87%; (b) NH3 sat. methanol, 96%; (c) AMPDA, phosphate
buffer at pH 5.6 and 40 °C, 97%.
the activity of the enzyme [35]. AMPDA is commercially avail- aspects of this work : (1) this is the first report using SnCl4 as a
able as a practical lyophilate powder and was widely used in the regio- and stereoselective deprotection reagent in perbenzylated
food industry for the production of inosine 5′-phosphate. 1-O-methyl-5-deoxyribofuranosides, (2) adenylate deaminase
AMPDA is a more versatile biocatalyst compared to ADA, (EC 3.5.4.6) facilitated chemoenzymatic hydrolysis was used
since it can convert a larger number of adenosine derivatives for the synthesis of trachycladine B, and (3) the reported carbo-
into the corresponding inosine derivatives.
hydrate 4 (1-O-acetyl-2,3-O-dibenzoyl-2-β-C-methyl-5-deoxy-
D-ribofuranose) can be used as a common intermediate for the
AMPDA was used as a biocatalyst in the enzymatic hydrolysis synthesis of versatile 5′-deoxy-2′-C-branched nucleosides.
of adenosine 15. The reaction proceeded smoothly in the pres-
ence of AMPDA in phosphate buffer at pH 5.6 and 40 °C with
Supporting Information
3% DMSO as a co-solvent. Adenosine 15 was enzymatically
deaminated to give trachycladine B in almost quantitative yield.
Supporting Information File 1
The reaction is a novel instance of the broad substrate tolerance
of AMPDA and extends its usage in nucleoside chemistry.
Therefore, trachycladine B was synthesized in 35.0% overall
yield from 5-deoxy-1,2,3-tri-O-acetyl-β-D-ribofuranose (6).
Detailed experimental procedures, characterization data of
compounds, and copies of 1H and 13C NMR spectra.
[http://www.beilstein-journals.org/bjoc/content/
supplementary/1860-5397-10-176-S1.pdf]
Supporting Information File 2
Next, the coupling of carbohydrate 4 with 2,6-dichloropurine
(18) afforded nucleoside 16 in 86% yield with DBU as a base
and TMSOTf as a Lewis acid (Scheme 3). After heated in a
pressure tube with ammonia saturated methanol, the benzoyl
protecting groups were removed and the chlorine atom at pos-
ition C6 was substituted at the same time to afford trachycla-
X-ray crystal structural of compound 9.
[http://www.beilstein-journals.org/bjoc/content/
supplementary/1860-5397-10-176-S2.cif]
dine A in 92% yield. Therefore, trachycladine A was synthe- Acknowledgements
sized in 34.2% overall yield from 5-deoxy-1,2,3-tri-O-acetyl-β- We thank the NSFC (No. 20962009, 21062006), the NCET (11-
D-ribofuranose (6).
1000), the Education Department of the Jiangxi Province (GJJ
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25.Shimma, N.; Umeda, I.; Arasaki, M.; Murasaki, C.; Masubuchi, K.;
Kohchi, Y.; Miwa, M.; Ura, M.; Sawada, N.; Tahara, H.; Kuruma, I.;
Horii, I.; Ishitsuka, H. Bioorg. Med. Chem. 2000, 8, 1697–1706.
doi:10.1016/S0968-0896(00)00087-0
11223, GJJGJJ12583), the Training Program of Jiangxi Youth
Scientists, and the Bureau of Science & Technology of
Nanchang City for financial support.
26.Li, N.-S.; Piccirilli, J. A. J. Org. Chem. 2004, 69, 4751–4759.
doi:10.1021/jo0495337
References
27.Jeannot, F.; Gosselin, G.; Mathé, C. Org. Biomol. Chem. 2003, 1,
2096–2102. doi:10.1039/b303093h
1. Bhakuni, D. S.; Rawat, D. S. Bioactive marine natural products;
Co-published by Springer with Anamaya Publishers: New Delhi, New
York, 2005.
28.Martin, P. Helv. Chim. Acta 1995, 78, 486–504.
doi:10.1002/hlca.19950780219
2. Md, S. H.; Fareed, S.; Ansari, S.; Khan, M. S. Indian J. Mar. Sci. 2012,
41, 27–39.
29.Hori, H.; Nishida, Y.; Ohrui, H.; Meguro, H. J. Org. Chem. 1989, 54,
1346–1353. doi:10.1021/jo00267a022
3. Vo, T.-S.; Ngo, D.-H.; Ta, Q. V.; Kim, S.-K. Eur. J. Pharm. Sci. 2011,
44, 11–20. doi:10.1016/j.ejps.2011.07.005
30.Martin, O. R.; Kurz, K. G.; Rao, S. P. J. Org. Chem. 1987, 52,
2922–2925. doi:10.1021/jo00389a049
4. Sagar, S.; Kaur, M.; Minneman, K. P. Mar. Drugs 2010, 8, 2619–2638.
doi:10.3390/md8102619
31.Lou, C.; Xiao, Q.; Tailor, R. R.; Ben Gaied, N.; Gale, N.; Light, M. E.;
Fox, K. R.; Brown, T. Med. Chem. Commun. 2011, 2, 550–558.
doi:10.1039/c1md00068c
5. Newman, D. J.; Cragg, G. M. Curr. Med. Chem. 2004, 11, 1693–1713.
doi:10.2174/0929867043364982
32.Lou, C.; Xiao, Q.; Brennan, L.; Light, M. E.; Vergara-Irigaray, N.;
Atkinson, E. M.; Holden-Dye, L. M.; Fox, K. R.; Brown, T.
Bioorg. Med. Chem. 2010, 18, 6389–6397.
6. Newman, D. J.; Cragg, G. M. J. Nat. Prod. 2004, 67, 1216–1238.
doi:10.1021/np040031y
7. Müller, W. E. G.; Grebenjuk, V. A.; Pennec, G. L.; Schröder, H.-C.;
Brümmer, F.; Hentschel, U.; Müller, I. M.; Breter, H.-J. Mar. Biotechnol.
2004, 6, 105–117. doi:10.1007/s10126-002-0098-6
8. Bergmann, W.; Stempien, M. F., Jr. J. Org. Chem. 1957, 22,
1575–1577. doi:10.1021/jo01363a009
doi:10.1016/j.bmc.2010.07.005
33.Ferrero, M.; Gotor, V. Monatsh. Chem. 2000, 131, 585–616.
doi:10.1007/s007060070088
34.Ferrero, M.; Gotor, V. Chem. Rev. 2000, 100, 4319–4348.
doi:10.1021/cr000446y
9. Bergmann, W.; Feeney, R. J. J. Org. Chem. 1951, 16, 981–987.
doi:10.1021/jo01146a023
35.Santaniello, E.; Ciuffreda, P.; Alessandrini, L. Synthesis 2005,
509–526. doi:10.1055/s-2005-861821
10.Kern, W.; Estey, E. H. Cancer 2006, 107, 116–124.
doi:10.1002/cncr.21543
36.Gupta, M.; Nair, V. Collect. Czech. Chem. Commun. 2006, 71,
769–787. doi:10.1135/cccc20060769
11.Becher, H. J. Inn. Med. 1986, 13, 237–245.
12.Sachs, M. K. Arch. Intern. Med. 1992, 152, 485–501.
doi:10.1001/archinte.1992.00400150019005
13.Searle, P. A.; Molinski, T. F. J. Org. Chem. 1995, 60, 4296–4298.
doi:10.1021/jo00118a059
License and Terms
14.Ichiba, T.; Nakao, Y.; Scheuer, P. J.; Sata, N. U.; Kelly-Borges, M.
Tetrahedron Lett. 1995, 36, 3977–3980.
This is an Open Access article under the terms of the
Creative Commons Attribution License
doi:10.1016/0040-4039(95)00692-6
15.Li, N.-S.; Lu, J.; Piccirilli, J. A. Org. Prep. Proced. Int. 2010, 42,
191–283. doi:10.1080/00304948.2010.483657
(http://creativecommons.org/licenses/by/2.0), which
permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.
16.Song, Y.; Ding, H.; Dou, Y.; Yang, R.; Sun, Q.; Xiao, Q.; Ju, Y.
Synthesis 2011, 1442–1446. doi:10.1055/s-0030-1259975
17.Sun, J.; Dou, Y.; Ding, H.; Yang, R.; Sun, Q.; Xiao, Q. Mar. Drugs
2012, 10, 881–889. doi:10.3390/md10040881
The license is subject to the Beilstein Journal of Organic
Chemistry terms and conditions:
18.Dou, Y.-H.; Ding, H.-X.; Yang, R.-C.; Li, W.; Xiao, Q. Chin. Chem. Lett.
2013, 24, 379–382. doi:10.1016/j.cclet.2013.03.014
19.Enders, D.; Breuer, I.; Drosdow, E. Synthesis 2005, 3239–3244.
doi:10.1055/s-2005-918439
(http://www.beilstein-journals.org/bjoc)
The definitive version of this article is the electronic one
which can be found at:
20.Enders, D.; Nühring, A.; Runsink, J.; Raabe, G. Synthesis 2001,
1406–1414. doi:10.1055/s-2001-15236
doi:10.3762/bjoc.10.176
21.Toniutto, P.; Fabris, C.; Bitetto, D.; Fornasiere, E.; Rapetti, R.; Pirisi, M.
Curr. Opin. Invest. Drugs 2007, 8, 150–158.
22.Bichko, V.; Lallos, L.; Soubasakos, M.; LaColla, M.; Tausek, M. M.;
Gillum, J.; Standring, D. N. J. Hepatol. 2007, 46 (Suppl. 1),
S163–S164. doi:10.1016/S0168-8278(07)62025-X
23.Harry-O'kuru, R. E.; Smith, J. M.; Wolfe, M. S. J. Org. Chem. 1997, 62,
1754–1759. doi:10.1021/jo961893+
24.McGavin, J. K.; Goa, K. L. Drugs 2001, 61, 2309–2326.
doi:10.2165/00003495-200161150-00015
1685