Studies directed toward the development of amide-linked RNA mimics: Synthesis of the monomeric building blocks

Article abstract of DOI:10.1021/jo801156a

(Chemical Equation Presented) A general approach toward the synthesis of all four monomeric building blocks of the ribonucleoside amino acids 3′-amino-5′-carboxymethyl-3′,5′-dideoxy nucleosides in their protected forms is described that will facilitate the development of amide-linked RNA mimics.

Full text of DOI:10.1021/jo801156a

Studies Directed toward the Development of
Amide-Linked RNA Mimics: Synthesis of the
Monomeric Building Blocks
Tushar Kanti Chakraborty,* Praveen Kumar Gajula, and
Dipankar Koley
Indian Institute of Chemical Technology,
Hyderabad 500 007, India
chakraborty@iict.res.in
ReceiVed May 28, 2008
FIGURE 1. Structures of ribonucleoside amino acids 1-4.
for potential therapeutic applications involving antisense strat-
egy.6 The advantages of this approach are that it not only
facilitates the assembly of such substrates using standard solid-
or solution-phase peptide synthesis methods but also would help
to enhance the stabilities of these analogues toward nucleases.
However, the success of this strategy will depend on the easy
availability of the monomeric building blocks,7 which warrants
the development of a robust synthetic strategy for the synthesis
of all of the members of the nucleoside amino acids. We have
earlier reported the synthesis of a thymidine-based deoxyribo-
nucleoside amino acid that was then cyclooligomerized.8 Herein,
we report the synthesis of four ribonucleoside amino acids, 3′-
amino-5′-carboxymethyl-3′,5′-dideoxy nucleosides 1-4, in the
protected forms (Figure 1).
A general approach toward the synthesis of all four mono-
meric building blocks of the ribonucleoside amino acids 3′-
amino-5′-carboxymethyl-3′,5′-dideoxy nucleosides in their
protected forms is described that will facilitate the develop-
ment of amide-linked RNA mimics.
For the synthesis of 1-4, we started from the known
compound 7 (Scheme 1), which was prepared from glucose
diacetonide 59 via 610 according to the reported procedure.11
Compound 7 was converted to the azido intermediate 8 in two
steps, involving formation of a triflate intermediate with Tf2O
The recent developments in the area of RNA interference
(RNAi)1 have renewed interest in oligonucleotide-based anti-
sense therapeutics.2 That gene expression can be regulated by
short interfering RNAs (siRNAs) guiding the degradation of
the mRNA before it can be translated into protein by the cells’
ribosomes is conceptually similar to the antisense oligonucle-
otide therapy.3 Whereas traditional small-molecule drugs attack
the aberrant proteins, antisense therapy targets the RNAs that
control their production.4 However, use of siRNAs as thera-
peutics is bogged down by their poor enzymatic stabilities,
cellular uptakes, biodistribution, and pharmacokinetics. Chemi-
cal modifications can not only address these shortcomings but
can also be fine-tuned to reduce toxicity and other side-effects
of siRNAs. Various types of chemically modified RNA ana-
logues have been prepared by many groups, and their properties
have been studied in details.5 Replacement of the phosphodiester
linkages with amide bonds has also been extensively studied
(6) (a) Lebreton, J.; Mesmaeker, A. D.; Waldner, A.; Fritsch, V.; Wolf, R. M.;
Freiser, S. M. Tetrahedron Lett. 1993, 34, 6383–6386. (b) Lebreton, J.; Waldner,
A.; Fritsch, V.; Wolf, R. M.; Mesmaeker, A. D. Tetrahedron Lett. 1994, 35,
5225–5228. (c) Mesmaeker, A. D.; Lebreton, J.; Waldner, A.; Fritsch, V.; Wolf,
R. M. Bioorg. Med. Chem. Lett. 1994, 4, 873–878. (d) Mesmaeker, A. D.;
Waldner, A.; Lebreton, J.; Hoffmann, P.; Fritsch, V.; Wolf, R. M.; Freier, S. M.
Angew. Chem., Int. Ed. Engl. 1994, 33, 226–229. (e) Bergmann, F.; Bannwarth,
W.; Tam, S. Tetrahedron Lett. 1995, 36, 6823–6826. (f) Waldner, A.; Mesmaeker,
A. D.; Wendenborn, S. Bioorg. Med. Chem. Lett. 1996, 6, 2363–2366. (g)
Mesmaeker, A. D.; Lesueur, C.; Bevierre, M.-O.; Fritsch, V.; Wolf, R. M. Angew.
Chem., Int. Ed. Engl. 1996, 35, 2790–2794. (h) Mesmaeker, A. D.; Leberton,
J.; Jouanno, C.; Fritsch, V.; Wolf, R. M.; Wendeborn, S. Synlett 1997, 1287–
1290. (i) Goodnow, R. A., Jr.; Richou, A.-R.; Tam, S. Tetrahedron Lett. 1997,
38, 3195–3198. (j) Goodnow, R. A., Jr.; Tam, S.; Pruess, D. L.; McComas,
W. W. Tetrahedron Lett. 1997, 38, 3199–3202. (k) Robins, M.; Doboszewski,
B.; Nilsson, B. L.; Peterson, M. A. Nucleosides, Nucleotides Nucleic Acids 2000,
19, 69–86. (l) Wilds, C. J.; Minasov, G.; Natt, F.; von Matt, P.; Altmann, K.-H.;
Egli, M. Nucleosides, Nucleotides Nucleic Acids 2001, 20, 991–994. (m) Li, X.;
Zhan, Z.-Y. J.; Knipe, R.; Lynn, D. G. J. Am. Chem. Soc. 2002, 124, 746–747.
(n) Li, X.; Lynn, D. G. Angew. Chem., Int. Ed. 2002, 41, 4567–4569. (o) Pallan,
P. S.; von Matt, P.; Wilds, C. J.; Altmann, K.-H.; Egli, M. Biochemistry 2006,
45, 8048–8057. (p) Threlfall, R.; Davies, A.; Howarth, N. M.; Fisher, J.; Cosstick,
R. Chem. Commun. 2008, 585–587. (q) Gogoi, K.; Kumar, V. A. Chem. Commun.
2008, 706–708.
(1) Fire, A.; Xu, S.; Montgomery, M. K.; Kostas, S. A.; Driver, S. E.; Mellow,
C. C. Nature 1998, 391, 806–811.
(2) (a) Hannon, G. J. Nature 2002, 418, 244–251. (b) Meister, G.; Tuschl,
T. Nature 2004, 431, 343–349.
(3) (a) Egli, M. Angew. Chem., Int. Ed. Engl. 1996, 35, 1894–1909. (b)
Antisense Drug Technology: Principles, Strategies, and Applications; Crooke,
S. T., Ed.; Dekker: New York, 2001; p 929. (c) Cobb, A. J. A. Org. Biomol.
Chem. 2007, 5, 3260–3275.
(4) (a) Manoharan, M. Curr. Opin. Chem. Biol. 2004, 8, 570–579. (b)
Rozners, E. Curr. Org. Chem. 2006, 10, 675–692.
(7) For earlier synthesis of some nucleoside amino acids, see. (a) Fujii, M.;
Yamamoto, K.; Hidaka, J. Tetrahedron Lett. 1997, 38, 417–420. (b) Rozners,
E.; Xu, Q. Org. Lett. 2003, 5, 3999–4001. (c) Rozners, E.; Liu, Y. J. Org. Chem.
2005, 70, 9841–9848. (d) Xu, Q.; Katkevica, D.; Rozners, E. J. Org. Chem.
2006, 71, 5906–5913.
(5) (a) Kumar, V. A. Eur. J. Org. Chem. 2002, 2021–2032. (b) Kaur, H.;
Babu, B. R.; Maiti, S. Chem. ReV. 2007, 107, 4672–4697. (c) Mathe´, C.; Pe´rigaud,
C. Eur. J. Org. Chem. 2008, 1489–1505.
(8) Chakraborty, T. K.; Koley, D.; Prabhakar, S.; Ravi, R.; Kunwar, A. C.
Tetrahedron 2005, 61, 9506–9512.
(9) Stevens, J. D. Methods Carbohydr. Chem. 1972, 6, 1230–1282.
6916 J. Org. Chem. 2008, 73, 6916–6919
10.1021/jo801156a CCC: $40.75 2008 American Chemical Society
Published on Web 08/02/2008

SCHEME 1. Synthesis of Ribonucleoside Amino Acids 1-4a
added dropwise via syringe. Then the reaction mixture was brought
to 0 °C, and stirring was continued for 1 h at 0 °C. It was quenched
carefully with aqueous NaHCO3 solution, extracted with EtOAc,
washed with CuSO4 solution and brine, dried (Na2SO4), and
concentrated in vacuo. The mixture was applied directly to flash
chromatography (ethyl acetate-hexane 1:9) to give the triflate,
which was directly used for the next step without any characteriza-
tion.
The triflate was dissolved in dry DMF (30 mL), and lithium azide
(1.43 g, 29.23 mmol) was added at 0 °C. The reaction mixture was
stirred at room temperature for 6 h. It was quenched by addition
of water (5 mL) at 0 °C, and the mixture was extracted with ether,
washed with water and brine, dried (Na2SO4), and concentrated in
vacuo. Purification by column chromatography (SiO2, 8% to 10%
EtOAc in petroleum ether eluant) furnished 8 (2.04 g, 49%) as
colorless oil. Rf ) 0.4 (SiO2, 15% EtOAc in petroleum ether); [R]25
D
) +90.14 (c 1.41, CHCl3); IR (neat) νmax 3446, 2926, 2854, 2107,
1733, 1377, 1257, 1167, 1022, 875, 760 cm-1; 1H NMR (300 MHz,
CDCl3) δ 5.67 (d, J ) 3.7 Hz, 1H), 4.62 (t, J ) 4.5 Hz, 1H), 4.07
(q, J ) 7.5 Hz, 2H), 3.99 (m, 1H), 2.90 (m, 1H), 2.52-2.32 (m,
2H), 2.06 (m, 1H), 1.77 (dt, J ) 14.3, 8.3 Hz, 1H), 1.50 (s, 3H),
1.29 (s, 3H), 1.21 (t, J ) 7.5 Hz, 3H); 13C NMR (75 MHz, CDCl3)
δ 172.8, 112.9, 103.9, 80.2, 76.3, 64.3, 60.5, 30.2, 27.4, 26.4, 26.2,
14.2; MS (ESIMS) m/z (%) 308 (100) [M + Na]+; HRMS (ESIMS)
calcd for C12H19N3O5Na [M + Na]+ 308.1222, found 308.1226.
Synthesis of 9. An ice-cold solution of 8 (2.0 g, 7 mmol) in
TFA:H2O (16.8 mL, 1:1) was stirred for 15 min at 0 °C and at
room temperature for 4 h. The reaction was then cooled to 0 °C
and slowly quenched with solid NaHCO3 until the effervescence
ceased. The reaction mixture was then diluted with water and
extracted with CH2Cl2, washed with brine, dried (Na2SO4), and
concentrated in vacuo to give lactol as a thick liquid. The crude
product was directly subjected to acetylation.
and pyridine in CH2Cl2, followed by displacement of the triflate
with azide, to give 8 in 49% overall yield.12
Acetonide deprotection of 8 with 50% aqueous TFA at 0 °C
furnished lactol,13 which on acetylation with acetic anhydride
afforded compound 9 in 85% over two steps. Next, compounds
10a, 10b, 10c, and 10d were synthesized from 9 under different
conditions. The modified nucleoside 10a was obtained from 9
via SnCl4-mediated glycosylation of unprotected adenine,7d,14
whereas 10b was synthesized from 9 using a protocol developed
by Zou and Robins.7d,15 For the synthesis of 10c7b and 10d,7c
compound 9 was coupled with bis(trimethylsilyl)uracil and
bis(trimethylsilyl)cytosine in the presence of TMSOTf to give
10c in 65% and 10d in 70% yields, respectively. Finally,
reduction of the azide functionality and methanolysis using Ph3P
in methanol followed by in situ protection of the resulting amine
with (Boc)2O afforded compounds 1-4 in good yields.
In summary, we have devised a common strategy for the
synthesis of all four nucleoside amino acids, starting from 5, in
moderate overall yields (1, 10.4%; 2, 13.6%; 3, 11.5%; 4,
12.2%). Synthesis of the RNA-mimics with these monomeric
building blocks for biological interest is under progress and will
be reported in due course.
To a stirred solution of the lactol in CH2Cl2 (20 mL) at 0 °C
under nitrogen atmosphere was added Et3N (2.92 mL, 21 mmol).
After 10 min, Ac2O (1.58 mL, 16.8 mmol) followed by DMAP
(342 mg, 2.8 mmol) were added at 0 °C. The reaction mixture was
warmed to room temperature and stirred for 1 h at the same
temperature. It was quenched with saturated aqueous NH4Cl
solution, extracted with EtOAc, washed with brine, dried (Na2SO4),
and concentrated in vacuo. Purification by column chromatography
(SiO2, 15% to 20% EtOAc in petroleum ether eluant) afforded an
anomeric mixture 9 (1.95 g, 85%) as colorless oil. Rf ) 0.45 (SiO2,
40% EtOAc in petroleum ether); [R]25D ) +17.16 (c 2.72, CHCl3);
IR (neat) νmax 3445, 2931, 2111, 1750, 1440, 1372, 1215, 1102,
1
1016, 957, 893, 762, 600 cm-1; H NMR (200 MHz, CDCl3) δ
6.05 (s, 1H), 5.27 (d, J ) 4.4 Hz, 1H), 4.14 (q, J ) 7.3 Hz, 2H),
4.04 (dt, J ) 8.0, 4.4 Hz, 1H), 3.79 (dd, J ) 8.0, 4.4 Hz, 1H), 2.45
(dd, J ) 13.2, 7.3 Hz, 2H), 2.18 (s, 3H), 2.08 (s, 3H), 2.13-1.81
(m, 2H), 1.28 (t, J ) 7.3, 3H); 13C NMR (75 MHz, CDCl3) δ172.6,
172.4, 169.5, 168.8, 97.9, 93.6, 81.8, 80.8, 76.1, 71.8, 63.2, 61.4,
60.6, 30.1, 29.8, 29.5, 28.9, 21.0, 20.5, 20.2, 14.1; MS (ESIMS)
m/z (%) 352 (100) [M + Na]+; HRMS (ESIMS) calcd for
C13H19N3O7Na [M + Na]+ 352.1120, found 352.1116.
Experimental Section
Synthesis of 8. Dry pyridine (2.0 mL, 24.84 mmol) was added
to a solution of 7 (3.8 g, 14.61 mmol) in dry CH2Cl2 (30 mL) at
-78 °C, followed by triflic anhydride (3.68 mL, 21.92 mmol),
Synthesis of 10a. Adenine (98.5 mg, 0.73 mmol) was added to
a solution of 9 (200 mg, 0.6 mmol) in dry CH3CN (2 mL) under
nitrogen atmosphere. The reaction mixture was cooled to 0 °C, and
SnCl4 (0.14 mL, 1.2 mmol) in dry CH3CN (1 mL) was added. The
reaction mixture was warmed to room temperature and stirred for
15 min till the cloudy solution turned clear. The reaction mixture
was again cooled to 0 °C, and CH2Cl2 (10 mL) and saturated
aqueous NaHCO3 (5 mL) were added. The organic layer was
separated, and the aqueous layer was extracted with CH2Cl2. The
combined organic layers were washed with brine, dried (Na2SO4),
and concentrated under reduced pressure, and the residue was
purified by silica gel chromatography (SiO2, 1% to 2% MeOH in
CHCl3 eluant) to afford 10a (140 mg, 57%) as colorless oil. Rf )
0.45 (SiO2, 5% MeOH in CHCl3); [R]25D ) -2.89 (c 0.405, CHCl3);
(10) (a) Brimacombe, J. S.; Ching, O. A. Carbohydr. Res. 1968, 8, 82–88.
(b) Tsui, H. C.; Paquette, L. A. J. Org. Chem. 1998, 63, 9968–9977. (c) Arun,
M.; Joshi, S. N.; Puranik, V. G.; Bhawal, B. M.; Deshmukh, A. R. A. S.
Tetrahedron 2003, 59, 2309–2316.
(11) Tulshian, D.; Doll, R. J.; Stansberry, M. F. J. Org. Chem. 1991, 56,
6819–6822.
(12) (a) Gruner, S. A. W.; Truffault, V.; Voll, G.; Locardi, E.; Stockle, M.;
Kessler, H. Chem. Eur. J. 2002, 8, 4365–4376. (b) Hungerford, N. L.; Fleet,
G. W. J. J. Chem. Soc., Perkin Trans. 1 2000, 3680–3685. For the preparation
of LiN3 see: (c) Hofman-Bang, N. Acta Chem. Scand. 1957, 11, 581–582.
(13) Ghosh, S.; Shahsidhar, J.; Dutta, S. K. Tetrahedron Lett. 2006, 47, 6041–
6044.
(14) Robins, M. J.; Doboszewski, B.; Timoshchuk, V. A.; and Peterson, M. A.
J. Org. Chem. 2000, 65, 2939–2945.
(15) Zou, R.; Robins, M. J. Can. J. Chem. 1987, 65, 1436–1437.
IR (neat) νmax 3430, 2925, 2112, 1741, 1638, 1216, 761, 669 cm-1
;
J. Org. Chem. Vol. 73, No. 17, 2008 6917

1H NMR (300 MHz, CDCl3) δ 8.34 (s, 1H), 7.84 (s, 1H), 5.97 (d,
J ) 3.0 Hz, 1H), 5.94 (q, J ) 3.0 Hz, 1H), 5.71 (br s, 2H),
4.65-4.59 (m, 2H), 4.13 (q, J ) 6.7 Hz, 2H), 4.09 (m, 1H), 2.48
(dt, J ) 16.6, 8.3 Hz, 2H), 2.27-2.05 (m, 2H), 2.19 (s, 3H), 1.22
(t, J ) 6.7 Hz, 2H); 13C NMR (75 MHz, CDCl3) δ 172.7, 169.8,
155.6, 153.1, 149.3, 139.7, 120.4, 87.9, 80.8, 75.7, 62.9, 60.6, 29.9,
28.0, 20.5, 14.1; MS (ESIMS) m/z (%) 405 (50) [M + H]+; HRMS
(ESIMS) calcd for C16H21O5N8 [M + H]+ 405.1634, found
405.1651.
Synthesis of 10d. Procedure A was followed with 9 (200 mg,
0.6 mmol), cytosine (153 mg, 1.38 mmol), and trimethylsilyl
trifluoromethanesulfonate (0.21 mL, 1.2 mmol) in ClCH2CH2Cl (5
mL). Chromatographic purification (SiO2, 5% to 6% MeOH in
CHCl3 eluant) afforded 10d (161 mg, 70%) as colorless oil. Rf )
0.40 (SiO2, 10% MeOH in CHCl3); [R]25 ) +51.73 (c 0.75,
D
CHCl3); IR (neat) νmax 3426, 2924, 2112, 1729, 1641, 1375, 1216,
760, 669 cm-1;1H NMR (300 MHz, CDCl3) δ 7.30 (d, J ) 7.5 Hz,
1H), 5.81 (d, J ) 7.5 Hz, 1H), 5.59 (dd, J ) 6.0, 2.2 Hz, 1H), 5.54
(d, J ) 2.2 Hz, 1H), 4.15 (q, J ) 6.7 Hz, 2H), 4.07 (dd, J ) 9.0,
6.0 Hz, 1H), 3.93 (dt, J ) 9.0, 4.5 Hz, 1H), 2.52 (dt, J ) 18.1, 9.8
Hz, 2H), 2.18 (s, 3H), 1.98-2.12 (m, 2H), 1.26 (t, J ) 6.7 Hz,
3H); 13C NMR (75 MHz, CDCl3) δ 172.8, 169.9, 166.0, 155.2,
142.3, 95.3, 92.7, 80.2, 76.0, 63.1, 60.7, 30.2, 28.0, 20.6, 14.2;
MS (ESIMS) m/z (%) 403 (60) [M + Na]+; HRMS (ESIMS) calcd
for C15H20N6O6Na [M + Na]+ 403.1342, found 403.1358.
General Procedure (B). Triphenylphosphine (2 equiv) was
added to the carbohydrate derivative (1 equiv) in dry MeOH under
nitrogen atmosphere at 0 °C. The reaction mixture was brought to
room temperature and stirred at the same temperature for 1 h. To
the same reaction mixture (Boc)2O (1.2 eq) was added at room
temperature and the reaction mixture was stirred for 1 h. Solvent
was removed under reduced pressure and the residue was purified
by silica gel chromatography.
Synthesis of 10b. N,O-Bis(trimethylsilyl)acetamide (0.59 mL,
2.4 mmol) was added to a solution of 2-N-acetyl-6-O-diphenyl-
carbamoylguanine (465 mg, 1.2 mmol) in ClCH2CH2Cl (4 mL).
The mixture was refluxed for 10 min, cooled to room temperature,
and added to a solution of 9 (200 mg, 0.6 mmol) in ClCH2CH2Cl
(2 mL) at 0 °C. Trimethylsilyl trifluoro-methanesulfonate (0.21 mL,
1.2 mmol) was added dropwise at 0 °C. The brown solution was
refluxed for 1 h. The reaction mixture was cooled to 0 °C, and
CH2Cl2 (10 mL) and saturated aqueous NaHCO3 (5 mL) were
added. The organic layer was separated, and the aqueous layer was
extracted with CH2Cl2. The combined organic layers were washed
with brine, dried (Na2SO4), and concentrated under reduced
pressure, and the residue was purified by silica gel chromatography
(SiO2, 1% to 2% MeOH in CHCl3 eluant) to afford 10b (315 mg,
79%) as colorless oil. Rf ) 0.5 (SiO2, 5% MeOH in CHCl3); [R]25
D
Synthesis of 1. Procedure B was followed with 10a (100 mg,
0.24 mmol), Ph3P (130 mg, 0.49 mmol), and (Boc)2O (0.068 mL,
0.29 mmol) in MeOH (3 mL). Chromatographic purification (SiO2,
3% to 4% MeOH in CHCl3 eluant) afforded 1 (90.6 mg, 84%) as
white solid (mp ) 135 °C). Rf ) 0.3 (SiO2, 5% MeOH in CHCl3);
[R]25D ) +20.42 (c 0.93, CHCl3); IR (neat) νmax 3348, 3177, 2977,
) -22.75 (c 1.9, CHCl3); IR (neat) νmax 3428, 2657, 2111, 1736,
1630, 1593, 1383, 1214, 1062, 758, 696 cm-1; 1H NMR (200 MHz,
CDCl3) 8.58 (s, 1H), 7.86 (s, 1H), 7.45-7.18 (m, 10H), 5.86 (dd,
J ) 5.2, 2.2 Hz, 1H), 5.82 (d, J ) 1.5 Hz, 1H), 5.26 (m, 1H), 4.08
(m, 1H), 4.09 (q, J ) 3.0 Hz, 2H), 2.55-2.35 (m, 2H), 2.31 (s,
3H), 2.22-2.03 (m, 2H), 2.18 (s, 3H), 1.19 (t, J ) 7.5, 3H); 13C
NMR (75 MHz, CDCl3) 172.9, 169.9, 168.3, 156.2, 153.8, 151.8,
150.1, 143.3, 141.6, 129.2, 127.7, 121.6, 126.5, 88.4, 81.0, 76.2,
62.1, 60.5, 29.7, 27.6, 25.0, 20.5, 14.1; MS (ESIMS) m/z (%) 680
(65) [M + Na]+; HRMS (ESIMS) calcd for C31H31N9O8Na [M +
Na]+ 680.2193, found 680.2189.
2931, 1673, 1610, 1520, 1482, 1370, 1249, 1169, 1099, 1040 cm-1
;
1H NMR (200 MHz, DMSO-d6) δ 8.29 (s, 1H), 8.14 (s, 1H), 7.31
(br s, 2H), 6.6 (d, J ) 8.3 Hz, 1H), 5.92 (d, J ) 5.2 Hz, 1H), 5.84
(d, J ) 2.2 Hz, 1H), 4.54 (m, 1H), 4.18 (dd, J ) 15.1, 8.3 Hz,
1H), 3.99 (q, J ) 6.7 Hz, 2H), 3.85 (dt, J ) 7.5, 3.7 Hz, 1H), 2.36
(dt, J ) 18.1, 9.0 Hz, 2H), 2.00-1.79 (m, 2H), 1.40 (s, 9H), 1.23
(br s, 1H), 1.12 (t, J ) 6.7 Hz, 2H); 13C NMR (50 MHz, DMSO-
d6) δ 172.4, 169.6, 155.2, 151.5, 151.1, 140.0, 139.9, 89.3, 80.3,
79.1, 78.1, 72.7, 59.7, 55.2, 29.8, 28.1, 13.9; MS (ESIMS) m/z (%)
437 (60) [M + H]+; HRMS (ESIMS) calcd for C19H29 N6O6 [M +
H]+ 437.2143, found 437.2159.
General Procedure (A) (Coupling of Uracil and Cytosine
with 9). A suspension of the nucleobase and (NH4)2SO4 (trace) in
HMDS (2 mL/mmol) was stirred at reflux (with exclusion of
moisture) until a clear solution was formed. Volatiles were
evaporated, and toluene was added and coevaporated several times.
The residue was dried in vacuum, and a solution of the carbohydrate
derivative in 1,2-dichloroethane (under N2) was added. TMSOTf
(1.2 equiv) was added at 0 °C, and the solution was brought to
room temperature and stirred for 3 h at same temperature for 10c,
being refluxed for 50 min in case of 10d. The reaction mixture
was cooled to 0 °C, and CH2Cl2 (10 mL) and saturated aqueous
NaHCO3 (5 mL) were added. The organic layer was separated, and
the aqueous layer was extracted with CH2Cl2. The combined organic
layers were washed with brine and dried (Na2SO4). Solvent was
removed under reduced pressure, and the residue was purified by
silica gel chromatography.
Synthesis of 2. Procedure B was followed with 10b (100 mg,
0.15 mmol), Ph3P (79.8 mg, 0.30 mmol), and (Boc)2O (0.042 mL,
0.18 mmol) in MeOH (3 mL). Chromatographic purification (SiO2,
2% to 3% MeOH in CHCl3 eluant) afforded 2 (82.8 mg, 79%) as
colorless oil. Rf ) 0.4 (SiO2, 5% MeOH in CHCl3); [R]25D ) +9.68
(c 0.63, CHCl3); IR (neat) νmax 3398, 3305, 3109, 3071, 2926, 2856,
1708, 1620, 1589, 1449, 1285, 1165, 1061, 910, 862, 730, 696
1
cm-1; H NMR (200 MHz, CDCl3) 8.50 (br s, 1H), 8.11 (s, 1H),
7.22-7.48 (m, 10H), 6.64 (m, 1H), 5.75 (d, J ) 5.8 Hz, 1H), 5.70
(m, 1H), 4.67 (m, 1H), 4.12 (q, J ) 7.3, 2H), 3.98 (m, 1H), 3.29
(m, 1H), 2.45-2.56 (m, 2H), 2.19 (s, 3H), 1.82-2.02 (m, 2H),
1.46 (s, 9H), 1.23 (t, J ) 7.3 Hz, 3H); 13C NMR (75 MHz, CDCl3)
δ 172.8, 168.6, 156.2, 153.5, 151.1, 150.3, 141.9, 141.6, 129.2,
127.2, 127.1, 126.4, 126.1, 125.9, 121.5, 92.1, 85.9, 79.8, 74.2,
60.5, 55.9, 30.6, 29.7, 29.1, 28.3, 24.9, 14.2; MS (ESIMS) m/z (%)
712 (100) [M + Na]+; HRMS (ESIMS) calcd for C34H39N7O9Na
[M + Na]+ 712.2701, found 712.2699.
Synthesis of 10c. Procedure A was followed with 9 (200 mg,
0.6 mmol), uracil (201 mg, 1.8 mmol), and trimethylsilyl trifluo-
romethanesulfonate (0.21 mL, 1.2 mmol) in CH2Cl2 (5 mL).
Chromatographic purification (SiO2, 2% to 3% MeOH in CHCl3
eluant) afforded 10c (150 mg, 65%) as colorless oil. Rf ) 0.42
(SiO2, 5% MeOH in CHCl3); [R]25 ) +50.15 (c 0.75, CHCl3);
D
IR (neat) νmax 3429, 2939, 2871, 2112, 1694, 1450, 1377, 1265,
1120, 1023, 901, 868, 810, 573 cm-1; 1H NMR (200 MHz, CDCl3)
δ 8.88 (br s, 1H), 7.2 (d, J ) 8.2, 1H), 5.77 (dd, J ) 8.2, 2.0 Hz,
1H), 5.57 (d, J ) 3.4 Hz, 1H), 5.49 (dd, J ) 6.1, 3.4 Hz, 1H), 4.15
(q, J ) 6.8 Hz, 2H), 3.96 (dt, J ) 8.2, 4.1 Hz, 1H), 4.05 (m, 1H),
2.50 (dt, J ) 6.8, 3.4 Hz, 2H), 2.2 (s, 3H), 2.18-1.94 (m, 2H),
1.26 (t, J ) 6.8 Hz, 3H); 13C NMR (75 MHz, CDCl3) δ172.6, 169.9,
162.7, 149.7, 141.2, 103.0, 91.4, 80.5, 75.4, 62.9, 60.7, 30.0, 28.0,
20.5, 14.2; MS (ESIMS) m/z (%) 404 (40) [M + Na]+; HRMS
(ESIMS) calcd for C15H19N5O7Na [M + Na]+ 404.1182, found
404.1182.
Synthesis of 3. Procedure B was followed with 10c (100 mg,
0.26 mmol), Ph3P (137 mg, 0.52 mmol), and (Boc)2O (0.072 mL,
0.31 mmol) in MeOH (3 mL). Chromatographic purification (SiO2,
3% to 4% MeOH in CHCl3 eluant) afforded 3 (87.8 mg, 81%) as
colorless oil. Rf ) 0.45 (SiO2, 5% MeOH in CHCl3); [R]25
)
D
+74.83 (c 0.77, CHCl3); IR (neat) νmax 3430, 3363, 3316, 3211,
2978, 2931, 1676, 1508, 1459, 1372, 1255, 1163, 1097, 912, 857,
1
816, 771, 730 cm-1; H NMR (500 MHz, CDCl3) δ 10.23 (br s,
1H), 7.61 (d, J ) 8.5 Hz, 1H), 5.80 (d, J ) 8.5 Hz, 1H), 5.71 (s,
1H), 5.39 (d, J ) 8.5 Hz, 1H), 4.26 (m, 1H), 4.14 (q, J ) 7.5 Hz,
2H), 4.04 (m, 1H), 3.82 (m, 1H), 2.57-2.48 (dt, J ) 16.1, 8.5,
6918 J. Org. Chem. Vol. 73, No. 17, 2008

2H), 2.19 (m, 1H), 2.04 (m, 1H), 1.44 (s, 9H), 1.26 (t, J ) 7.5 Hz,
3H); 13C NMR (50 MHz, CDCl3) δ 172.9, 164.0, 155.6, 150.6,
139.3, 102.2, 92.5, 82.2, 80.1, 75.0, 60.6, 54.9, 31.0, 29.6, 28.2,
14.2; MS (ESIMS) m/z (%) 436 (100) [M + Na]+; HRMS (ESIMS)
calcd for C18H27N3O8Na [M + Na]+ 436.1690, found 436.1676.
Synthesis of 4. Procedure B was followed with 10d (100 mg,
0.26 mmol), Ph3P (137 mg, 0.52 mmol), and (Boc)2O (0.072 mL,
0.31 mmol) in MeOH (3 mL). Chromatographic purification (SiO2,
5% to 6% MeOH in CHCl3 eluant) afforded 4 (86.6 mg, 80%) as
white solid (mp ) 98 °C). Rf ) 0.4 (SiO2, 10% MeOH in CHCl3);
[R]25D ) +99.65 (c 0.87, CHCl3); IR (neat) νmax 3754, 3454, 2925,
(s, 1H), 1.16 (t, J ) 6.9 Hz, 3H); 13C NMR (50 MHz, DMSO-d6)
δ 172.4, 165.4, 155.2, 154.7, 147.5, 141.5, 94.0, 91.9, 79.5, 78.1,
73.0, 59.8, 30.1, 28.9, 28.1, 14.0; MS (ESIMS) m/z (%) 435 (60)
[M + Na]+; HRMS (ESIMS) calcd for C18H28N4O7Na [M + Na]+
435.1850, found 435.1831.
Acknowledgment. The authors wish to thank DST, New
Delhi for financial support (SR/S1/OC-01/2007); UGC and
CSIR, New Delhi for research fellowships (PKG and D.K.).
Supporting Information Available: General experimental
1
2854, 1638, 1458, 1093 cm-1; H NMR (200 MHz, DMSO-d6) δ
1
procedures and the copies of H and 13C NMR spectra for
7.55 (d, J ) 7.7 Hz, 1H), 7.31-7.14 (m, 2H), 6.48 (d, J ) 7.7 Hz,
1H), 5.79 (d, J ) 5.4 Hz, 1H), 5.74 (d, J ) 7.7 Hz, 1H), 5.6 (d, J
) 1.5 Hz, 1H), 4.03 (q, J ) 6.9 Hz, 2H), 3.98 (m, 1H), 3.72 (m,
1H), 2.47-2.31 (m, 2H), 1.97-1.77 (m, 2H), 1.38 (s, 9H), 1.23
compounds 1-4, 8, 9, and 10a-d. This material is available
free of charge via the Internet at http://pubs.acs.org.
JO801156A
J. Org. Chem. Vol. 73, No. 17, 2008 6919