New Nucleoside-Based Polymeric Supports for the Solid Phase Synthesis of Ribose-Modified Nucleoside Analogues

Abstract

New solid supports, linking protected pyrimidine and purine nucleoside derivatives through the nucleobase, have been prepared. The support, incorporating a suitable derivative of 2′-azido, 2′-deoxyuridine, allowed the simple and efficient solid-phase synthesis of ribose-modified nucleoside and nucleic acid analogues, particularly of aminoacyl derivatives of 2′-deoxy, 2′-amino-uridine, following methodologies well established in peptide and oligonucleotide chemistry.

combinatorial chemistry - Mitsunobu reaction - nucleosides - nucleotides - solid phase synthesis

References

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8

Sharma et al. (Sharma, R. A.; Bobek, M.; Bloch, A. J. Med. Chem. 1975, 18, 955-957) can be acknowledged for the pioneering synthesis of some aminoacyl and peptidyl derivatives of 2′-amino-2′-deoxyuridine but, to the best of our knowledge, these nucleoside hybrids have not been further investigated in their biological potential.

9

Reagents and conditions for route A: a: 0.35 M Bu₃P, THF-H₂O-EtOH (4.5:1.4:6), r.t., 5 h; b: HATU, HOBt, DIPEA, Fmoc-a.a.-OH, DMF, r.t., 1 h.; c: 20% piperidine-DMF, r.t., 5 min; d: Ac₂O-pyridine (1:1, v/v), r.t., 30 min; e: 0.5 M MCPBA, CH₂Cl₂, r.t., 1 h; f: Et₃N·3HF, THF, r.t., 18 h; g: 1% DCA, CH₂Cl₂, r.t., 10 min; h: 17 M NH₄OH, 60 °C, 18 h.

10 Silva DJ. Wang H. Allanson NM. Jain RK. Sofia MJ. J. Org. Chem.  1999,  64:  5926 

11

In the synthesis of short oligomers 17-20, better crudes were obtained if the oxidation of the support was carried out before the coupling with the phosphoramidite building block.

12

Reagents and conditions for route B: a: 0.35 M Bu₃P, THF-H₂O-EtOH (4.5:1.4:6), r.t., 5 h; b: Ac₂O-pyridine (1:1, v/v), r.t., 30 min; c: 0.5 M MCPBA, CH₂Cl₂, r.t., 1 h; d: Et₃N·3HF, THF, r.t., 18 h; e: coupling with DMT-phosphoramidite (5′-DMT-dC-3′-phosphoramidite for 17; 5′-DMT-T-3′-phosphoramidite for 18); f: 1% DCA, CH₂Cl₂, r.t., 10 min; g: 17 M NH₄OH, 60 °C, 18 h.

13

Reagents and conditions for route C: a: 0.35 M Bu₃P, THF-H₂O-EtOH (4.5:1.4:6), r.t., 5 h; b: HATU, HOBt, DIPEA, Fmoc-a.a.-OH, DMF, r.t., 1 h.; c: 1% DCA, CH₂Cl₂, r.t., 10 min; d: Ac₂O-pyridine (1:1, v/v), r.t., 30 min; e: 0.5 M MCPBA, CH₂Cl₂, r.t., 1 h; f: Et₃N·3HF, THF, r.t., 18 h; g: coupling with 3′-DMT-T-5′-phosphoramidite; h: 1% DCA, CH₂Cl₂, r.t., 10 min; i: 20% piperidine/DMF, r.t., 5 min; l: 17 M NH₄OH, 60 °C, 18 h.

14

Reagents and conditions for route D: a: 0.35 M Bu₃P, THF-H₂O-EtOH (4.5:1.4:6), r.t., 5 h; b: HATU, HOBt, DIPEA, Fmoc-a.a.-OH, DMF, r.t., 1 h.; c: Ac₂O-pyridine (1:1, v/v), r.t., 30 min; d: 0.5 M MCPBA, CH₂Cl₂, r.t., 1 h; e 1% DCA, CH₂Cl₂, r.t., 10 min; f: coupling with 5′-DMT-dA-3′-phosphoramidite; g: 1% DCA, CH₂Cl₂, r.t., 10 min; h: Ac₂O-pyridine (1:1, v/v), r.t., 30 min; i: Et₃N·3HF, THF, r.t., 18 h; l: coupling with 3′-DMT-T-5′-phosphoramidite; m: 1% DCA, CH₂Cl₂, r.t., 10 min; n: 20% piperidine-DMF, r.t., 5 min; o: 17 M NH₄OH, 60 °C, 18 h.

15

Selected data for compound 13: ¹H NMR (500 MHz, D₂O): δ = 7.78 (1 H, d, J = 7.5 Hz, H-6), 6.06 (1 H, d, J = 8.0 Hz, H-1′), 5.89 (1 H, d, J = 7.5 Hz, H-5), 4.60 (1 H, m, H-2′), 4.33-4.22 (2 H, overlapped signals, H-3′ and CH α Leu), 4.20 (1 H, m, H-4′), 3.85 (2 H, m, H₂-5′), 2.00 (3 H, s, acetyl protons), 1.60-1.57 (3 H, overlapped signals, CH and CH₂ Leu), 0.90 and 0.86 (3 H each, 2 d, CH₃ Leu). Compound 14: ¹H NMR (500 MHz, D₂O): δ = 7.86 (1 H, d, J = 8.0 Hz, H-6), 7.42-7.26 (5 H, complex signals, aromatic protons), 6.01 (1 H, d, J = 7.0 Hz, H-1′), 5.93 (1 H, d, J = 8.0 Hz, H-5); H-2′ signal is buried under the residual HDO signal; 4.21 (1 H, dd, J = 2.5 and 2.0 Hz, CH α of Phe), 4.16 (1 H, m, H-4′), 3.93-3.84 (2 H, m, H₂-5′), 3.81 (1 H, m, H-3′), 3.73 (2 H, m, CH₂ of Phe), 1.97 (3 H, s, acetyl protons). Compound 15: ¹H NMR (500 MHz, D₂O): δ = 7.75 (1 H, d, J = 8.0 Hz, H-6), 6.07 (1 H, d, J = 8.0 Hz, H-1′), 5.89 (1 H, d, J = 8.0 Hz, H-5), 4.72-4.64 (1 H, m, H-2′), 4.34 (1 H, dd, J = 5.5 and 2.5 Hz, H-3′), 4.20 (1 H, m, H-4′), 4.12 (1 H, d, J = 6.5 Hz, CH α Val), 3.85 (2 H, m, H₂-5′), 2.18-2.12 [1 H, m, CH(CH₃)₂], 1.83 (3 H, s, acetyl protons), 0.92 and 0.89 [3 H each, 2 d, J = 7.0 Hz, CH(CH₃)₂]. Compound 16: ¹H NMR (500 MHz, D₂O): δ = 7.85 (1 H, d, J = 8.5 Hz, H-6), 6.05 (1 H, d, J = 8.5 Hz, H-1′), 5.92 (1 H, d, J = 8.5 Hz, H-5), 4.65 (1 H, m, H-2′), 4.35 (1 H, m, H-3′), 4.30 (1 H, m, CH α Lys), 4.25 (1 H, m, H-4′), 3.85 (2 H, m, H₂-5′), 3.25 (2 H, t, CH₂ ε Lys), 2.08 and 2.04 (3 H each, 2 s, acetyl protons), 1.75 (2 H, m, CH₂ β Lys), 1.55 (2 H, m, CH₂ δ Lys), 1.35 (2 H, m, CH₂ γ Lys). Compound 17: ¹H NMR (500 MHz, D₂O), significant signals: δ = 7.86 (1 H, d, J = 7.5 Hz, H-6 U), 7.78 (1 H, d, J = 7.5 Hz, H-6 C), 6.31 (1 H, dd, J = 6.5 and 7.0 Hz, H-1′ C), 6.14 (1 H, d, J = 7.5 Hz, H-5 C), 6.07 (1 H, d, J = 7.5 Hz, H-5 U), 5.88 (1 H, d, J = 8.0 Hz, H-1′ U), 3.89-3.76 (4 H, overlapped signals, H₂-5′ U and C), 2.62-2.30 (2 H, m, H-2′ C), 2.15 (1 H, m, H-2′ U), 1.93 (3 H, s, acetyl protons). Compound 18: ¹H NMR (500 MHz, D₂O) significant signals at: δ = 7.40 (1 H, d, J = 8.0 Hz, H-6 U), 7.67 (1 H, s, H-6 T), 6.35 (1 H, dd, J = 6.5 and 6.5 Hz, H-1′ T), 6.09 (1 H, d, J = 8.5 Hz, H-1′ U), 5.91 (1 H, d, J = 8.0 Hz, H-5 U); H-3′, H-2′ U and H-3′ T are buried under the residual HDO signal; 4.15 (5 H, overlapped signals, H-4′ U, H-4′ T, CH α Lys and H₂-5′ T), 3.85 (2 H, m, H₂-5′ U), 3.28 (2 H, m, CH₂ ε Lys), 2.36 (2 H, m, H₂-2′ T), 1.93 (3 H, s, CH₃ T), 1.85 (2 H, m, CH₂ β Lys), 1.79 (2 H, m, CH₂ δ Lys), 1.22 (2 H, m, CH₂ γ Lys). Compound 19: ¹H NMR (500 MHz, D₂O) significant signals at: δ = 7.91 (1 H, d, J = 8.0 Hz, H-6 U), 7.68 (1 H, s, H-6 T), 6.32 (1 H, dd, J = 6.5 and 6.5 Hz, H-1′ T), 6.10 (1 H, d, J = 8.0 Hz, H-1′ U), 5.94 (1 H, d, J = 8.0 Hz, H-5 U); H-3′, H-2′ U and H-3′ T are buried under the residual HDO signal; 4.47 (2 H, overlapped signals, H-4′ U, H-4′ T and H-4′ U), 4.19 (5 H, overlapped signals, H₂-5′ U, H₂-5′ T and CH α Lys), 3.24 (2 H, m, CH₂ ε Lys), 2.33 (2 H, m, H₂-2′ T), 1.93 (3 H, s, CH₃ T), 1.80 (2 H, m, CH₂ β Lys), 1.72 (2 H, m, CH₂ δ Lys), 1.18 (2 H, m, CH₂ γ Lys). ³¹P NMR (161.98 MHz, D₂O): δ = 1.75. Compound 20: ¹H NMR (500 MHz, D₂O), significant signals at: δ = 8.33 (1 H, s, H-2 A), 8.29 (1 H, s, H-8 A), 7.78 (1 H, d, J = 9.5 Hz, H-6 U), 7.53 (1 H, s, H-6 T), 6.44 (1 H, dd, J = 7.0 and 7.5 Hz, H-1′ A), 6.19 (1 H, dd, J = 8.0 and 8.5 Hz, H-1′ T), 6.11 (1 H, d, J = 11.0 Hz, H-1′ U), 5.80 (1 H, d, J = 9.5 Hz, H-5 U), 3.35 (2 H, m, CH₂ ε Lys); H-3′, H-2′ U and H-3′ A are buried under the residual HDO signal; 2.55 (2 H, m, H₂-2′ A), 2.32 (2 H, m, H₂-2′ T), 1.84 (3 H, s, CH₃ T), 1.68-1.49 (4 H, overlapped signals, CH₂ β and CH₂ δ Lys), 1.19 (2 H, m, CH₂ γ Lys). ³¹P NMR (161.98 MHz, D₂O): δ = 2.20, 1.92.