Scalable Synthesis of 2,2′-Anhydro-arabinofuranosyl Imidazoles

Abstract

We report the efficient and scalable synthesis of 2,2′-anhydro-5-amino-1-β-arabinofuranosylimidazole-4-carboxamide and 2,2′-anhydro-5-amino-1-β-arabinofuranosylimidazole-4-carbonitrile from commercial arabino-adenosine. 2,2′-Anhydro-5-amino-1-β-arabinofuranosylimidazole-4-carboxamide is synthesised in only five steps with a single chromatographic purification. Additionally, we report a high-yielding, three-step conversion of 2,2′-anhydro-5-amino-1-β-arabinofuranosylimidazole-4-carboxamide into 2,2′-anhydro-5-amino-1-β-arabinofuranosylimidazole-4-carbonitrile. They are proposed key intermediates of the divergent prebiotic synthesis of ribonucleotides and this facile synthesis is anticipated to be instrumental in continued investigation of the origins of nucleotides.

Key words

AICAR - nucleosides - arabinosides - purines - prebiotic

• References and Notes

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• 12 2′,3′,5′-Trisacetoxy-9-β-arabinofuranosyl Hypoxanthine (ara-6) 9-β-Arabinofuranosyl adenine (ara- A; 23 g, 86 mmol) was suspended in AcOH_(aq) (1 L, 2 M), and NaNO₂ (29.7 g, 430 mmol) was added. The flask was fitted with a bubbler, and the mixture was stirred until evolution of gas ceased (approx. 18 h). Additional NaNO₂ (29.7 g) was added, and the solution was stirred for a further 18 h. The mixture was evaporated to dryness and the residue co-evaporated with toluene (4 × 200 mL). The residue was suspended in pyridine (750 mL) and cooled to 0 °C under argon, then Ac₂O (97.5 mL, 1.03 mol) was added in one portion. The mixture was stirred for 1 h at 0 °C and then overnight at r.t., EtOH (200 mL) was added at 0 °C, and the mixture was stirred for 1 h then concentrated to dryness. The residue was co-evaporated with toluene (4 × 200 mL), H₂O (300 mL) was added, and the mixture was stirred vigorously for 30 min. The solution was filtered and the filter cake was washed with H₂O (50 mL) and cold EtOAc (50 mL) and dried in vacuo to yield hypoxanthine ara- 6 as a fine white solid (25.0 g, 63.5 mmol, 74%); mp 220–222 °C. IR (solid): 3120 (CH), 3045 (CH), 1738 (OAc), 1691 (HNCO) cm^–1. ¹H NMR (600 MHz, CDCl₃): δ = 13.11 (1 H, br s, NH), 8.26 (1 H, s, H 2), 8.06 (1 H, s, H 8), 6.55 (1 H, d, J = 4.7 Hz, H 1′), 5.52 (1 H, dd, J = 4.7, 3.1 Hz, H 2′), 5.43 (1 H, dd, J = 4.3, 3.1 Hz, H 3′), 4.48 (1 H, ABX, J = 12.0, 4.3 Hz, H 5′), 4.44 (1 H, ABX, J = 12.0, 6.1 Hz, H 5′′), 4.29 (1 H, dt, J = 6.1, 4.3 Hz, H 4′), 2.17 (3 H, s, OAc), 2.15 (3 H, s, OAc), 1.92 (3 H, s, OAc). ¹³C NMR (151 MHz, CDCl₃): δ = 170.7, 169.7, 168.9, 159.1, 148.7, 145.7, 139.3, 124.3, 83.6, 80.2, 75.8, 75.0, 63.0, 20.9, 20.9, 20.4. HRMS: m/z calcd for C₁₆H₁₈N₄O₈ [M + H⁺]⁺: 395.1203; found: 395.1203. 2′,3′,5′-Trisacetoxy-β-furanosylarabino-1-(2-methoxyethoxymethyl) Hypoxanthine (ara-5) 2′,3′,5′-Trisacetoxy-β-furanosylarabino hypoxanthine (ara- 6; 23 g, 58.4 mmol) was dissolved in dry CH₂Cl₂ (250 mL) and activated 3 Å MS (5 g) were added. The mixture was cooled to 0 °C and ⁱ Pr₂EtNH₂ (20.4 mL, 117 mmol) was added, and the mixture was stirred for 1 h. MEMCl (9.9 mL, 87.6 mmol) was added at 0 °C, and the mixture was allowed to warm to r.t. and stirred overnight. The reaction was quenched with H₂O (500 mL) and the pH adjusted to 7 with HCl (1 M). The phases were separated, the aqueous phase was extracted with CHCl₃ (3 × 250 mL), and the combined organic phases were washed with phosphate buffer (2 × 250 mL, 100 mM, pH 7) and brine (250 mL), and dried over MgSO₄. The solvents were removed under reduced pressure, and the resulting residue was eluted through a short silica plug (5 cm × 5 cm, 5% MeOH/EtOAc) to yield hypoxanthine ara- 5 as a colourless oil (26.4 g, 54.7 mmol, 94%). IR (neat): 2962 (CH), 1742 (OAc), 1697 (HNCO) cm^–1. ¹H NMR (600 MHz, CDCl₃): δ = 8.11 (1 H, s, H 2), 7.89 (1 H, s, H 8), 6.44 (1 H, d, J = 4.8 Hz, H 1′), 5.52 (1 H, AB, J = 10.5 Hz, NCH₂O), 5.48 (1 H, AB, J = 10.5 Hz, NCH₂O), 5.43 (1 H, dd, J = 4.8, 3.4 Hz, H 2ʹ), 5.39 (1 H, dd, J = 4.3, 3.4 Hz, H 3′), 4.40 (1 H, ABX, J = 12.1, 4.3 Hz, H 5′), 4.36 (1 H, ABX, J = 12.1, 6.2 Hz, H 5′′), 4.22 (1 H, dt, J = 6.2, 4.3 Hz, H 4′), 3.74 (2 H, m, CH₂), 3.46 (2 H, m, CH₂), 3.27 (3 H, s, OCH₃), 2.10 (3 H, s, OAc), 2.06 (3 H, s, OAc), 1.84 (3 H, s, OAc). ¹³C NMR (151 MHz, CDCl₃): δ = 170.6, 169.7, 168.9, 156.7, 147.9, 147.2, 139.2, 124.0, 83.3, 79.9, 75.7, 75.3, 75.0, 71.6, 69.4, 62.9, 59.1, 20.9, 20.8, 20.4. HRMS: m/z calcd for C₂₀H₂₆N₄O₁₀ [M + H⁺]⁺: 483.1727; found: 483.1729. 2′,3′,5′-Trisacetoxy-β-furanosylarabino-5-aminoimidazole-4-carboxamide (8) 2′,3′,5′-Trisacetoxy-β-furanosylarabino-1-(2-methoxyethoxymethyl) hypoxanthine (ara- 5; 24.5 g, 50.8 mmol) was dissolved in MeOH/NH₃ (sat., 300 mL) and stirred for 30 min at r.t. The solvent was removed under reduced pressure, and the resulting residue was dissolved in NaOH_(aq) (0.2 M, 600 mL) and heated at reflux for 1 h. The solution was neutralised with Dowex 50W×8 (proton form), filtered, flash frozen with liquid nitrogen, and lyophilised. The residue was dissolved in pyridine (300 mL), cooled to 0 °C, and Ac₂O (130 mL) was added in one portion. The mixture was stirred at 0 °C for 1 h, quenched with EtOH (200 mL), and the solvents were removed under reduced pressure. The residue was partitioned between H₂O (500 mL) and CHCl₃ (250 mL) and the aqueous phase adjusted to pH 7 with sat. HNaCO_3(aq). The aqueous phase was further extracted with CHCl₃ (4 × 250 mL), and the combined organic phases were washed with brine (250 mL), dried over MgSO₄, and the solvents were removed under reduced pressure to yield crude 8 as a pale yellow foam which was sufficiently pure for continued synthesis (13.5 g, 35.2 mmol, 69%). Analytical material can be obtained by silica column chromatography (EtOAc/MeOH, 0–5%); mp 72–74 °C. IR (solid): 3326 (NH), 3173 (CH), 1742 (OAc), 1643 (HNCO) cm^–1. ¹H NMR (600 MHz, CDCl₃): δ = 7.16 (1 H, s, H 8), 6.66 (1 H, br s, NH), 5.99 (1 H, d, J = 5.3 Hz, H 1′), 5.70 (1 H, br s, NH), 5.47 (1 H, dd, J = 5.3, 4.0 Hz, H 2′), 5.37 (2 H, br s, NH₂), 5.39 (1 H, dd, J = 5.6, 4.0 Hz, H 3′), 4.41 (1 H, ABX, J = 12.3, 4.7 Hz, H 5′), 4.37 (1 H, ABX, J = 12.3, 3.5 Hz, H 5′), 4.17 (1 H, ddd, J = 5.6, 4.7, 3.5 Hz, H 4′), 2.13 (6 H, s, 2 × OAc), 1.94 (3 H, s, OAc). ¹³C NMR (151 MHz, CDCl₃): δ = 170.5, 169.8, 169.6, 167.1, 143.1, 129.1, 113.6, 84.1, 70.1, 75.6, 74.9, 62.2, 20.8, 20.8, 20.3. HRMS: m/z calcd for C₁₅H₂₀N₄O₈ [M + H⁺]⁺: 385.1359; found: 385.1361. 2′,3′,5′ -Trisacetoxy-β-furanosylarabino-2-bromo-5-aminoimidazole-4-carboxamide (9) 2′,3′,5′-Trisacetoxy-β-furanosylarabino-5-aminoimidazole-4-carboxamide (8; 3.5 g, 9.11 mmol) was dissolved in dry THF (200 mL) and N-bromoacetamide (1.32 g, 9.57 mmol) was added in a single portion. The mixture was stirred for 10 min at r.t. and then quenched by addition of sat. NaHSO_3(aq) (100 mL). The mixture was stirred for 15 min then NaCl was added until the mixture was fully saturated. The organic phase was separated, washed with brine (100 mL), dried (MgSO₄), and concentrated to dryness. The residue was purified by silica column chromatography, eluting with EtOAc/MeOH (1–4%) to give 2-bromo-5-aminoimidazole 9 as a white foam (3.52 g, 7.60 mmol, 83%); mp 123–126 °C. IR (solid): 3467 (NH), 3341 (NH), 1740 (OAc), 1646 (H₂NCO) cm^–1. ¹H NMR (600 MHz, MeOD): δ = 6.25 (1 H, d, J = 4.9 Hz, H 1′), 5.53 (1 H, d, J = 4.9, 2.8 Hz, H 2′), 5.35 (1 H, dd, J = 5.8, 2.8 Hz, H 3′), 4.59 (1 H, ABX, J = 12.4, 4.2 Hz, H 5′), 4.40 (1 H, ABX, J = 12.4, 2.8 Hz, H 5′), 4.27 (1 H, ddd, J = 5.8, 4.2, 2.8 Hz, H 4′), 2.13 (3 H, s, OAc), 2.13 (3 H, s, OAc), 1.92 (3 H, s, OAc). ¹³C NMR (151 MHz, MeOD): δ = 172.1, 171.6, 170.4, 168.3, 147.8, 113.8, 111.9, 88.6, 80.4, 77.4, 76.9, 63.2, 20.7, 20.6, 20.1. HRMS: m/z calcd for C₁₅H₂₀N₄O₈Br [M + H⁺]⁺: 463.0464; found: 463.0465. 2,2′-Anhydro-5-aminoimidazole-4-carboxamide-β-furanosylarabinoside (1) Sodium (75 mg, 3.24 mmol) was dissolved in dry MeOH (20 mL) and 2′,3′,5′-trisacetoxy-β-furanosylarabino-2-bromo-5-aminoimidazole-4-carboxamide (9; 1 g, 2.16 mmol) was added. The mixture was heated at reflux for 5 h, cooled to r.t. and NH₄Cl (69 mg, 1.1 mmol) was added. The mixture was allowed to stand at –20 °C for 1 h then filtered to give imidazole 1 as a fine white powder (300 mg, 1.17 mmol, 54%); mp 234–238 °C. IR (solid): 3493 (NH), 3359 (NH), 3210 (OH), 1638 (H₂NCO), 1581 (C=N), 1533 (C=C) cm^–1. ¹H NMR (600 MHz, D₂O): δ = 6.46 (1 H, d, J = 5.4 Hz, H 1′), 5.68 (1 H, d, J = 5.4 Hz, H 2′), 4.60 (1 H, br s, H 3′), 4.38 (1 H, ddd, J = 6.8, 4.9, 1.9 Hz, H 4′), 3.56 (1 H, ABX, J = 12.4, 4.9 Hz, H 5′), 3.42 (1 H, ABX, J = 12.4, 6.8 Hz, H 5′′). ¹³C NMR (151 MHz, D₂O): δ = 169.1, 152.6, 140.0, 109.9, 97.9, 89.3, 86.5, 75.3, 61.5. HRMS: m/z calcd for C₉H₁₂N₄O₅ [M + H⁺]⁺: 257.0880; found: 257.0882.^1e 3′,5′-Bisacetoxy-2,2′-anhydro-5-aminoimidazole-4-carboxamide-β-furanosylarabinoside (10) 2,2′-Anhydro-5-aminoimidazole-4-carboxamide-β-furanosylarabinoside (1; 256mg, 1 mmol) was suspended in H₂O (20 mL) at r.t., adjusted to pH 8 with 1 M NaOH_(aq), and N-acetylimidazole (220 mg, 2 mmol) was added. The reaction was stirred at r.t. for 10 min and during this time kept at pH 8 by manual dropwise addition of 1 M NaOH_(aq). N-Acetylimidazole (2 × 220 mg) was added and stirred at pH 8. After the third addition of reagent the reaction was stirred for 10 min, then the solution was adjusted to pH 5 with 1 M HCl_(aq). The reaction was extracted with CHCl₃ (20 × 20 mL), and the combined extracts were dried (MgSO₄) and evaporated to dryness to give 3′,5′-bisacetoxy-2,2′-anhydro-5-aminoimidazole-4-carboxamide-β-furanosylarabinoside (10) as a pale yellow powder (343 mg, 1 mmol, quant.); mp 163–166 °C. IR (solid): 3330, 1740, 1649, 1597 cm^–1. ¹H NMR (600 MHz, D₂O): δ = 6.52 (1 H, d, J = 5.7 Hz, H 1′), 5.91 (1 H, d, J = 5.7 Hz, H 2′), 5.52 (1 H, d, J = 1.9 Hz, H 3′), 4.75 (1 H, dt, J = 1.9, 4.1 Hz, H 4′), 4.20 (2 H, d, J = 4.1 Hz, H 5′), 2.20 (3 H, s, OAc), 1.98 (3 H, s, OAc). ¹³C NMR (151 MHz, D₂O): δ = 174.3, 173.5, 169.0, 152.2, 140.2, 109.7, 96.0, 87.3, 84.7, 78.7, 64.4, 20.8, 20.3. HRMS: m/z calcd for C₁₃H₁₆N₄O₇ [M + H⁺]⁺: 341.1092; found: 341.1090.