One-pot synthesis of nucleoside 3'-O-(S-phenyl methanephosphonothioates)

Article abstract of DOI:10.1016/S0040-4039(99)02248-0

The one-pot reaction of nucleosides with McP(O)Cl₂ and thiophenol, providing nucleoside 3'-O-(S-phenyl methanephosphonothioate), potential monomers for the synthesis of oligonucleoside methanephosphonate, is described. (C) 2000 Elsevier Science Ltd.

Full text of DOI:10.1016/S0040-4039(99)02248-0

TETRAHEDRON
LETTERS
Pergamon
Tetrahedron Letters 41 (2000) 1223–1226
One-pot synthesis of nucleoside 30-O-(S-phenyl
methanephosphonothioates)
Jaroslaw Pyzowski, Arkadiusz Chworos, Lucyna A. Wozniak and Wojciech J. Stec ∗
Polish Academy of Sciences, Centre of Molecular and Macromolecular Studies, Department of Bioorganic Chemistry,
Sienkiewicza 112, 90-363 Lodz, Poland
Received 22 September 1999; accepted 3 December 1999
Abstract
The one-pot reaction of nucleosides with MeP(O)Cl2 and thiophenol, providing nucleoside 30-O-(S-phenyl
methanephosphonothioate), potential monomers for the synthesis of oligonucleoside methanephosphonate, is
described. © 2000 Elsevier Science Ltd. All rights reserved.
Keywords: nucleoside; methanephosphonothioates; S-aryl esters.
Former reports from this laboratory presented a one-pot reaction of appropriately protected 30-OH-
nucleosides (1) with methanephosphonodichloridate (2) and aniline. This provided in satisfactory yields
0
the corresponding nucleoside 30-O-methanephosphonanilidates [RO3 -PMe(O)NHPh, R=50-O-DMT-
nucleoside, 3].1 Under treatment with sodium hydride/carbon disulfide, anilidates 3 were converted into
0
sodium nucleoside 30-O-methanephosphonothioates [RO3 -PMe(O)SNa, R=50-O-DMT-nucleoside, 4].2
Regioselective S-alkylation of 4 with alkyl halides afforded nucleoside 30-O-(S-alkyl methanephospho-
0
nothioates) [RO3 -PMe(O)SAlk, R=50-O-DMT-nucleoside, 5], convenient substrates for the stereocon-
trolled synthesis of dinucleoside (30,50)-methanephosphonates (6).3 Since the PN→PS conversion 3→4,
as well as the S-alkylation of 4, are stereospecific reactions, diastereomerically pure methanephospho-
nothioates 5 are available either via separation of the diastereomeric mixture of anilidates 3 followed
by their regioselective and stereospecific conversion into S-alkyl esters 5, or by a separation of the
diastereomeric mixture of 5 into individual diastereomeric species. We have also demonstrated that the
reaction of diastereomerically pure esters 5 with 50-OH nucleosi(ti)des in the presence of DBU/LiCl is
stereospecific, and affords dinucleoside (30,50)-methanephosphonates (6) with a predetermined sense of
chirality at the phosphorus centre.4
During the studies we conducted for further development of this methodology, it was tempting to
prepare the corresponding nucleoside 30-O-(S-aryl methanephosphonothioate)s (7), and to compare
their reactivity with the previously studied3 S-alkyl substrates 5. In spite of a report on the successful
∗
Corresponding author. Tel: (48 42) 681 97 44; fax: (48 42) 681 54 83; e-mail: wjstec@bio.cbmm.lodz.pl (W. J. Stec)
0040-4039/00/$ - see front matter © 2000 Elsevier Science Ltd. All rights reserved.
PII: S0040-4039(99)02248-0
tetl 16176

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S-arylation of O-alkyl alkanephosphonothioates with benzenediazonium chloride, providing in 50%
yield O-ethyl S-phenyl ethanephosphonothioate,5 our efforts at the S-arylation of methanephospho-
nothioates 4 with benzenediazonium chloride have failed.6,7Although nucleoside 30-O-(S-aryl metha-
nephosphonothioate)s were described by Brill and Caruthers,8 their preparation involved either 30-O-
methanephosphonylimidazolidates and oxybenzotriazolidates,9 or P(III) derivatives,10 and required the
use of highly reactive phosphonylating agents.
Therefore, we decided to adapt the methodology developed previously for preparation of anilidates 3,
and apply it to the synthesis of nucleoside 30-methanephosphonothioates 7 (Scheme 1a).
Scheme 1. Reaction conditions: (i) MeP(O)Cl2 (2), pyridine, rt, 15 min (ii) thiophenol, 30 min; (iii) separation into diastereo-
mers; (iv) single diastereomer 7, 30-O-acetyl thymidine, DBU/LiCl
We have found that the one-pot reaction of an appropriately protected nucleoside 1 with methanephos-
phonodichloridate and thiophenol can be used as a fast and effective route to the diastereomeric mixture
of 7, easily separable into pure diastereomers via silica gel column chromatography.
The typical procedure is as follows: Into a stirred solution of N-protected (except thymine) nucleoside
1 (1 mmol) in dry pyridine (10 mL) at ambient temperature was added in one portion a solution of
methanephosphonodichloridate (2 mmol) in pyridine (2 mL). After 15 min an excess of thiophenol (1
mL) was added in one portion, and stirring was continued for additional 30 min. The reaction mixture was
partially concentrated to a total volume of ca. 5 mL, diluted with chloroform (50 mL), washed twice with
H2O, and dried over MgSO4. After concentration of the organic fraction under reduced pressure the crude
product was purified by flash column chromatography (230–400 mesh, chloroform–ethanol, 98:2 v/v).
Purified and separated diastereomers FAST 7 and SLOW 7 (quantitative separation of diastereomers)
were dissolved in CH2Cl2, precipitated from hexane (petroleum ether) and stored as stable, white
powders.11 The yields of compounds 7 and selected spectroscopic characteristics are given in Table 1.
The absolute configuration at the P-chiral centre in 7 was not assigned directly. However, one can
assume it is based upon the relative mobility/NMR relationship.12 As reported by Caruthers et al.13 the
X-ray data for FAST thymidine 30-(S-phenyl methanephosphonothioate)13 demonstrates that FAST 7 has
(SP) configuration, while SLOW 7 possesses the (RP) configuration.
Both the FAST 7 and SLOW 7 (B=Thy) diastereomers were condensed in the presence DBU/LiCl
with 30-O-acetylthymidine under conditions comparable with those used in earlier experiments with 5
(alkyl_CH3−, C6H5CH2−).3 End-protected dithymidylyl (30,50)-methanephosphonates 6 were obtained
in moderate yields (53% and 42%, respectively), but the process of condensation was accompanied by
partial P-epimerisation.14 That loss of stereospecificity can be explained by enhanced P-epimerisation of
7 in the presence of DBU. Such an effect of DBU was previously observed in the DBU-promoted tran-
sesterification of nucleoside 30-O-p-nitrophenyl methanephosphonates15 and the DBU-assisted solvolysis
reactions of nucleoside 30-O-(O-2,4,6-trimethylbenzoyl methanephosphonates).16 Studies involving the

1225
Table 1
search for conditions for the condensation of 7 with 50-OH nucleosides in the presence of catalysts other
than DBU are presently in progress.
Acknowledgements
This paper is dedicated to Professor Aleksander Zamojski on the occasion of his 70th birthday. This
work was financially assisted by the State Committee for Scientific Research (KBN), grant no. 3T09A
061 17 (to W.J.S) and, in part, by Genta Inc., Lexington, MA, USA.
References
1. Pyzowski, J.; Wozniak, L. A.; Stec, W. J. Collect. Czech. Chem. Commun. 1996, 61, S152–153.
2. Stec, W. J. Acc. Chem. Res. 1983, 16, 411–417 and references cited therein.
3. Stec, W. J.; Wozniak, L. A.; Pyzowski, J.; Niewiarowski, W. Antisense Nucleic Acid Drug Dev. 1997, 7, 381–395.
4. Wozniak, L. A. In Reviews on Heteroatom Chemistry; Oae, S., Ed.; Myu: Tokyo, Japan, 1999; pp. 173–202.
5. Allahyari, R., Lee, P. W.; Lin, G. H. Y.; Wing, R. M.; Fukuto, T. R. J. Agric. Food Chem. 1977, 25, 471–478.
6. The yields of S-arylation of the 50-O-DMT-protected nucleoside 30-O-methanephosphonothioates 4 were negligible when
benzenediazonium chloride in water was used as the S-arylating agent. However, the utilization of benzenediazonium
tetrafluoroborate under anhydrous conditions afforded the expected 7, albeit in low yields. The process of S-arylation was
accompanied by rapid 50-O-detritylation. Higher activity of benzenediazonium tetrafluoroborate was observed in the case of
Se-arylation of thymidine 30-O-methanephosphonoselenoate (mixture of 1:1 diastereomers) under anhydrous conditions,
1
yielding thymidine 30-O-(Se-phenyl methanephosphonoselenolate)s [31P NMR 51.12 ppm, JP–Se=414 Hz; 50.96 ppm,
1JP–Se=415 Hz] with efficiency >60%.
7. Modifications of the purines, which further decrease the yields of 7, could be expected, as indicated by Hiramoto, K.; Kaku,
M.; Sueyoshi. A.; Fujise, M.; Kikugawa, K. Chem. Res. Toxicol. 1997, 8, 356–362 and references cited therein.
8. Brill, W. K. D.; Caruthers, M. H. Tetrahedron Lett. 1988, 29, 1227–1230.
9. Miller, P. S.; Reddy, M. P.; Murakami, A.; Blake, K. R.; Lin, S.-B.; Agris, C. H. Biochemistry 1986, 25, 5092–5095.
10. Brill, W. K.-D.; Caruthers, M. H. Tetrahedron Lett. 1987, 28, 3205–3208.
11. 50-O-DMT-N4-Benzoyl-20-deoxycytidine 30-O-(S-phenyl methanephosphonothioate) (7, B=CBz) was obtained from N4-
benzoyl-20-deoxycytidine (1 mmol). Total yield: 60%. SLOW (Rp): 31P NMR (CDCl3): 54.17, 1H NMR (CDCl3): 1.75 (d,
J=15.6, 3H, P-CH3), 2.4 (m, 1H, H20), 2.71 (m, 1H, H200), 3.33 (m, 2H, H50, H500), 4.18 (d, J=3.2, 1H, H30), 5.13 (d,
J=3.2, 1H, H40), 6.14 (dd, J=6.4, 6.5, 1H, H10); C44H41O8N3P1S1, HR FAB MS [M−H]: 802.235 (calcd 802.243); FAB
1
analyses were performed at 1:1 diastereomeric mixtures). FAST (SP): 31P NMR (CDCl3): 54.92, H NMR (CDCl3): 1.71
(d, J=15.58, 3H, P-CH3), 2.42 (m, 1H, H20), 2.60 (m, 1H, H200), 3.07 (m, 2H, H50, H500), 4.3 (d, J=3.3, 1H, H30), 5.16 (m,

1226
1H, H40), 6.12 (dd, J=6.4, 6.5, 1H, H10); C44H41O8N3P1S1, HR FAB MS [M−H]: 802.235. 50-O-DMT-Thymidine 30-O-(S-
phenyl methanephosphonothioate (7, B=Thy) was obtained from 50-O-DMT-thymidine (1 mmol). Yield 63% (FAST:SLOW
1
3:2). SLOW (RP). 31P NMR (CDCl3): 55.0, H NMR (CDCl3): 1.76 (d, J=15.6, 3H, P-CH3), 2.47 (m, 1H, H20), 2.71 (m,
1H, H200), 3.48 (m, 2H, H50, H500), 4.16 (m, 1H, H30), 5.43 (dd, J=5.8, 10.0, 1H, H40), 6.46 (dd, J=5.4, 9.0, 1H, H10);
C38H38O8N2P1S1, HR FAB MS [M−H]: 713.212, calcd 713.216. FAST (SP): 31P NMR (CDCl3): 54.73, 1H NMR (CDCl3):
1.72 (d, J=15.6, 3H, P-CH3), 2.54 (m, 2H, H20, H200), 3.49 (m, 2H, H50, H500), 4.34 (m, 1H, H30), 5.40 (m, 1H, H40), 6.43
(dd, J=5.6, 8.9, 1H, H10); C38H38O8N2P1S1, FAB MS [M−H]: 713.2. 50-O-DMT-N6-Benzoyl-20-deoxyadenosine 30-O-(S-
phenyl methanephosphonothioate) (7, B=ABz) was obtained from N6-benzoyl-20-deoxyadenosine (1 mmol). Yield 53%.
1
SLOW (RP): 31P NMR (CDCl3): 54.43, H NMR (CDCl3): 1.79 (d, J=15.6, 3H, P-CH3) 2.90 (m, 1H, H20), 3.12 (m, 1H,
H200), 3.5 (m, 2H, H50, H500), 4.35 (m, 1H, H40), 5.55 (m, 1H, H30), 6.53 (dd, 1H, J=5.5, 5.8, H10); C45H41O7N5P1S1, HR
FAB MS [M−H]: 826.234, calcd 827.237. FAST (SP): 31P NMR (CDCl3): 54.26, 1H NMR (CDCl3): 1.77 (d, J=15.5, 3H,
P-CH3), 2.69 (m, 1H, H20), 3.03 (m, 1H, H200), 3.6 (m, 2H, H50, H500), 4.54 (m, 1H, H30), 5.45 (m, 1H, H40), 6.52 (dd,
1H, J=5.4, 5.7, H10); C45H41O7N5P1S1, HR FAB MS [M−H]: 826.234. 50-O-DMT-N4-Isobutyryl-20-deoxyguanosine 30-O-
(S-phenyl methanephosphonothioate) (7, B=Gibu) was obtained from N4-isobutyryl-20-deoxyguanosine (1 mmol). Purified
by a column chromatography (twice) (CHCl3-3% EtOH), followed by precipitation from petroleum ether. Total yield: 57%.
1
SLOW (RP): 31P NMR (CDCl3): 55.00, H NMR (CDCl3): 1.76 (d, J=15.6, 3H, P-CH3), 2.80 (m, 2H, H20, H200), 3.25
(m, 1H, H500), 3.47 (dd, J=3.1, 10.6, 1H, H500), 4.16 (m, 1H, H40), 5.80 (m, 1H, H30), 6.14 (dd, J=5.9, 6.9, 1H, H10);
C42H43N5O8P1S1, HR FAB MS [M−H]: 808.253, calcd 808.257. FAST (SP): 31P NMR (CDCl3): 54.74, 1H NMR (CDCl3):
1.69 (d, J=15.2, 3H, P-CH3), 2.13 (m, 1H, H20), 2.55 (m, 1H, H200), 3.20 (dd, J=3.1, 10.7, 1H, H50), 3.42 (dd, 1H, J=2.9,
10.9, H500), 4.21 (m, 1H, H40), 6.76 (m, 2H, H30, H10); C42H43N5O8P1S1, HR FAB MS [M−H]: 808.253.
12. Wozniak, L. A.; Pyzowski, J.; Wieczorek, M.; Majzner, W.; Stec, W. J. J. Org. Chem. 1998, 61, 5395–5402.
13. Caruthers, M. H.; Haltiwanger, R. C. Acta Crystallogr. 1989, C45, 1639–1641.
14. (RP)-50-O-DMT-Thymidylyl-(30,50)-30-O-acetylthymidine 30-methanephosphonate (6) was obtained from (RP)-7 (B=Thy)
and 30-O-acetylthymidine. Reaction time 2 h; yield 42%; 31P NMR (CDCl3): 33.00 (89%), 34.55 (11%); 1H NMR (CDCl3):
1.58 (d, J=17.6, 3H, P-CH3); C44H48O14N4P1, FAB MS [M−H]: 887.3, calcd 887.87. (SP)-50-O-DMT-Thymidylyl-(30,50)-
30-O-acetylthymidine 30-methanephosphonate (6) was obtained from (SP)-7 (B=Thy) and 30-O-acetylthymidine. Reaction
time 2 h; yield 53%; 31P NMR (CDCl3): 33.05 (7%) 34.14 (93%); 1H NMR (CDCl3): 1.57 (d, J=17.6, 3H, P-CH3);
C44H48O14N4P1, FAB MS [M−H]: 887.3.
15. Lesnikowski, Z.; Zabawska, D.; Jaworska-Maslanka, M. M.; Schinazi, R. F.; Stec, W. J. New J. Chem. 1994, 18, 1197–1204.
16. Wozniak, L. A.; Chworos, A.; Pyzowski, J.; Stec, W. J. J. Org. Chem. 1998, 63, 9109–9112.