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Synlett 2006(6): 845-848  
DOI: 10.1055/s-2006-933147
LETTER
© Georg Thieme Verlag Stuttgart · New York

2-(Phenylthio)ethyl as a Novel Two-Stage Base Protecting Group for Thymidine Analogues

Jennifer D’Onofrio, Lorenzo De Napoli, Giovanni Di Fabio*, Daniela Montesarchio
Dipartimento di Chimica Organica e Biochimica, Università degli Studi di Napoli ‘Federico II’, Complesso Universitario di Monte S. Angelo, via Cynthia 4, 80126 Napoli, Italy
e-Mail: difabio@unina.it;
Further Information

Publication History

Received 6 December 2005
Publication Date:
14 March 2006 (online)

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Abstract

2-(Phenylthio)ethyl is here proposed for temporary masking the thymine residue in the synthesis of sugar modified thymidine derivatives. This protection has been devised as a ‘two-stage’ system. The 2-(phenylthio)ethyl residue can be easily and regiospecifically inserted at the N3-position of the pyrimidine by a Mitsunobu reaction with 2-(phenylthio)ethanol and is perfectly stable also to strongly basic conditions. This allowed us to selectively achieve O-alkylation of the ribose moieties in satisfactory yields, avoiding undesired base alkylations. After oxidation of the thioether to sulfone, the thymine protecting group can be totally removed, by a β-elimination mechanism, upon the same basic treatment required for the final deprotection and detachment of oligonucleotides from the support in solid-phase synthesis protocols.

Key words

protecting groups - Mitsunobu reactions - thymidine - oligonucleotides - solid-phase synthesis

13

Selected Data for Compound 2.
1H NMR (400 MHz, CDCl3): δ = 7.61-6.82 (13 H, complex signals, arom. protons), 6.38 (1 H, dd, H-1′, J = 6.2, 6.8 Hz), 4.49 (1 H, m, H-3′), 4.01-3.96 (3 H, overlapped signals, CH2N and H-4′), 3.79 (6 H, s, OCH3), 3.45 (1 H, dd, H-5′a, J = 4.0, 12.0 Hz), 3.25 (1 H, dd, H-5′b, J = 4.0, 12.0 Hz), 2.33-2.17 (2 H, complex signal, H2-2′), 1.54 (3 H, s, CH3 T), 0.97 (2 H, m, CH2Si), 0.83 {9 H, s, [(CH3)3C]Si of TBDMS group}, 0.07 [9 H, s, (CH3)3Si], -0.02 and -0.04 [3 H each, s, Si(CH3)2 of TBDMS group]. 13C NMR (100 MHz, CDCl3): δ = 163.22 (C-4), 150.57 (C-2), 135.40 (C-6), 158.61, 144.28, 133.19, 129.95, 126.98, 113.15 (arom. carbons), 110.18 (C-5), 86.81 (quat. C of DMT group), 86.56 (C-1′), 85.35 (C-4′), 71.97 (C-3′), 62.82 (C-5′), 55.14 (OCH3), 41.53 (C-2′), 37.96 [(CH3)3SiCH2 CH2N], 25.59 {[(CH3)3C]Si of TBDMS group}, 17.81 [(CH3)3 C of TBDMS group], 15.87 [(CH3)3SiCH2CH2N], 12.54 (CH3 T), -1.89 [(CH3)3SiCH2CH2N], -4.98 [Si(CH3)2 of TBDMS group]. MS: m/z calcd for C42H58N2O7Si2: 758.38. ESI-MS found: m/z = 759.61 [M + H+]; m/z = 781.53 [M + Na+]; m/z = 797.50 [M + K+].

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Typical Procedure for the Insertion of 2-(Trimethyl-silyl)ethyl Group: Synthesis of 2
The amount of 1.0 g (1.52 mmol) of 5′-O-(4,4′-dimethoxy-triphenylmethyl)-3′-O-(tert-butyldimethylsilyl)thymidine was dissolved in 10 mL of benzene at 0 °C and treated with 160 µL (1.14 mmol) of 2-(trimethylsilyl)ethanol and 470 µL (1.90 mmol) of tributylphosphine. After 10 min the reaction mixture was taken to r.t. and treated with 480 mg (1.90 mmol) of 1,1′-(azodicarbonyl)dipiperidine (ADDP).
After 18 h, the crude was taken to dryness, redissolved in 100 mL of EtOAc and washed twice with H2O. The organic layer was concentrated under reduced pressure and purified by silica gel chromatography [eluent system: 2% MeOH in CHCl3-pyridine (1:0.05)], affording 745 mg (0.98 mmol, 65%) of pure 2.

17

Selected Data for Compound 3.
1H NMR (400 MHz, CDCl3): δ = 7.47-6.85 (18 H, complex signals, arom. protons), 6.48 (1 H, dd, H-1′, J = 5.6, 9.6 Hz), 4.27 (1 H, d, H-3′, J 3 ′,2 ′b = 12.0 Hz), 4.22 (2 H, m, CH2N), 4.01 (1 H, br s, H-4′), 3.82 (6 H, s, OCH3), 3.68 (1 H, dd, H-5′a, J = 4.0, 12.0 Hz), 3.29 (1 H, dd, H-5′b, J = 4.0, 12.0 Hz), 3.19 (2 H, t, CH2S, J = 8.0, 8.0 Hz), 1.87 (3 H, s, CH3 T), 1.76 (1 H, dd, H-2′a, J = 4.0, 12.0 Hz), 1.57 (1 H, complex signal, H-2′b), 0.83 {9 H, s, [(CH3)3C]Si}, -0.02 and -0.08 [3 H each, s, Si(CH3)2]. 13C NMR (100 MHz, CDCl3): δ = 162.83 (C-4), 150.37 (C-2), 135.86 (C-6), 158.29, 150.37, 144.70, 135.95, 135.28, 133.27, 129.87, 129.75, 128.51, 127.99, 127.86, 127.51, 126.63, 125.35, 112.83 (arom. carbons), 109.62 (C-5), 86.81 (C of DMT group), 86.16 (C-1′), 85.12 (C-4′), 74.55 (C-3′), 63.12 (C-5′), 54.80 (OCH3), 40.59 (CH2N), 39.55 (C-2′), 29.22 (CH2S), 25.34 {[(CH3)3C]Si}, 17.77 [(CH3)3 C], 12.68 (CH3 T), -5.86 and -6.18 [Si(CH3)2]. MS: m/z calcd for C45H54N2O7SSi: 794.34. ESI-MS (positive ions) found: m/z 833.75 [M + K+].

18

Typical Procedure for the Insertion of 2-(Phenylthio)-ethyl Group: Synthesis of 3 The amount of 900 mg (1.37 mmol) of 5′-O-tert-butyl-dimethylsilyl-3′-O-(4,4′-dimethoxytriphenylmethyl)thy-midine was dissolved in 10 mL of benzene at 0 °C and treated with 38 µL (1.02 mmol) of 2-(phenylthio)ethanol and 422 µL (1.71 mmol) of tributylphosphine. After 10 min the reaction mixture was taken to r.t., treated with 431 mg (1.71 mmol) of ADDP and left at r.t. for 18 h. The crude was then taken to dryness, redissolved in 100 mL of EtOAc and washed twice with H2O. The organic layer was concentrated under reduced pressure and purified by silica gel chromatography [eluent system: 2% acetone in CHCl3-pyridine (1:0.05)], affording 980 mg (1.23 mmol, 90%) of pure 3.

19

Selected Data for Compound 5.
31P NMR (161.98 MHz, CDCl3): 149.3. MS: calcd for C48H57N4O10PS: 912.35. ESI-MS (positive ions) found: m/z = 935.89 [M + Na+]; m/z = 952.90 [M + K+].

20

Removal of the 2-(phenylsulfonyl)ethyl group by aq NH3 at 55 °C after an overnight treatment was only partial, requiring longer reaction times to go to completion (ca.
72 h). On the other hand, a 0.1 M NaOH solution ensured complete thymine deprotection after an overnight treatment at 50 °C, i.e. conditions usually adopted also for oligo-nucleotide deprotection and detachment from the solid support.

21

Data for 5 ′DBB TGGGAG ³ ′OH
MS: m/z calcd for C81H92N27O36P5: 2173.49; MALDI-TOF (negative ions) found: 2171.76 [M - H]-.