Synthesis of a Deoxyxylopuromycin Analogue

Abstract

N⁶-Bis-demethylated deoxyxylopuromycin was synthesized over six steps in 56% overall yield. The key steps are Mitsunobu­ reaction with DPPA and a Staudinger-Vilarrasa coupling.

Key words

Antibiotic - ribosome - azide - Mitsunobu - Staudinger-Vilarrasa

References and Notes

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18

5′- O -( tert -Butyldiphenylsilyl)-2′-deoxyadenosine (6) TBDPSCl (1.6 g, 5.7 mmol) was added to 5 (1.2 g, 4.8 mmol) in dry pyridine (24 mL), and the solution was stirred for 18 h at r.t. under N₂. H₂O (2 mL) was added, stirring was continued for 30 min, and the volatiles were evaporated. The residue was partitioned (H₂O-EtOAc), and the organic phase was washed with H₂O (2 × 50 mL) and brine, then dried (Na₂SO₄). The volatiles were evaporated, and the residue was column chromatographed (step gradient from EtOAc-cyclohexane = 1:1 to 1:0 and then to EtOAc-MeOH = 95:5) to yield 6 (2.0 g, 88%). R _f = 0.33 (EtOAc-MeOH = 9:1). ^¹H NMR (300 MHz, CDCl₃): δ = 1.06 [s, 9 H, SiC(CH₃)₃], 2.53 (ddd, 1 H, J = 13.4, 6.2, 4.0 Hz, H_A2′), 2.75 (td, 1 H, J = 13.1, 6.4 Hz, H_B2′), 3.79-3.98 (m, 2 H, H5′5′′), 4.71-4.75 (m, 1 H, H3′), 5.84 (s, 2 H, NH₂), 6.46 (t, 1 H, J = 6.5 Hz, H1′), 7.31-7.45 (m, 6 H, ar), 7.62-7.65 (m, 4 H, ar), 8.02 (s, 1 H, H2), 8.29 (s, 1 H, H8). ^¹³C NMR (70 MHz, CDCl₃ + CD₃OD): δ = 18.7 (SiC), 26.3 [(CH₃)₃], 40.6 (C2′), 63.4 (C5′5′′), 70.6 (C3′), 84.0 (C1′), 87.1 (C4′), 118.8 (C5), 127.3 (p-ar), 129.4, 129.4 (o-ar), 132.1, 132.4 (i-ar), 134.9, 135.1 (m-ar), 138.2 (C2), 148.4 (C4), 152.1 (C6), 155.1 (C8). MS (ESI⁺): m/z = 490.1 [MH]⁺ 6- N -[(di- n -Butylamino)methylene]-5′- O -( tert -butyl-diphenylsilyl)-2′-deoxyadenosine (7) Compound 6 (600 mg, 1.3 mmol) was dissolved in MeOH (5 mL). N,N-Di-n-butylformamide dimethylacetal (600 mg, 2.6 mmol) was added, and the solution was stirred for 2 h at r.t. The volatiles were removed under reduced pressure, and the residue was purified using silica gel column chromatog-raphy (EtOAc-MeOH = 100:0 to 95:5 step gradient) to yield 7 (750 mg, 98%). R _f = 0.45 (CH₂Cl₂-MeOH = 9.5:0.5). ^¹H NMR (300 MHz, CDCl₃): δ = 0.82-0.88 (m, 6 H, 2 × NCH₂CH₂CH₂CH₃), 0.96 [(s, 9 H, SiC(CH₃)₃], 1.23-133 (m, 4 H, 2 × NCH₂CH₂CH₂CH₃), 1.49-1.62 (m, 4 H, 2 × NCH₂CH₂CH₂CH₃), 2.46 (ddd, J = 13.2, 6.0, 3.5 Hz, 1 H, H_A2′), 2.57-2.66 (m, 1 H, H_B2′), 3.28-3.34 (m, 2 H, NCH₂CH₂CH₂CH₃), 3.59-3.65 (m, 2 H, NCH₂CH₂CH₂CH₃), 3.72-3.85 (m, 2 H, H5′5′′), 4.05-4.09 (m, 1 H, H4′), 4.64-4.68 (m, 1 H, H3′), 6.44 (t, J = 6.6 Hz, 1 H, H1′), 7.25-7.32 (m, 6 H, ar), 7.53-7.58 (m, 4 H, ar), 8.02 (s, 1 H, H2), 8.41 (s, 1 H, H8), 8.91 (s, 1 H, CH=N). ^¹³C NMR (70 MHz, CDCl₃): δ = 13.6 (NCH₂CH₂CH₂CH₃), 13.8 (NCH₂CH₂CH₂CH₃), 19.1 (SiC), 19.6 (NCH₂CH₂CH₂CH₃), 20.1 (NCH₂CH₂CH₂CH₃), 26.8 [(CH₃)₃], 29.1 (NCH₂CH₂CH₂CH₃), 30.9 (NCH₂CH₂CH₂CH₃), 40.6 (C2′), 45.1 (NCH₂CH₂CH₂CH₃), 51.7 (NCH₂CH₂CH₂CH₃), 64.0 (C5′5′′), 71.7 (C3′), 84.01 (C1′), 87.0 (C4′), 126.1 (C5), 127.7, 129.7, 129.8, 132.7, 132.8, 135.4, 135.4 (Ar), 139.7 (C2), 151.0 (C4), 152.3 (C6), 158.3 (C8), 159.9 (CH=N). HRMS (ESI⁺): m/z calcd: 629.3635 [MH]⁺; found: 629.3636.
9-[3′-Azido-5′- O -( tert -butyldiphenylsilyl)-2′,3′-dideoxy-β- d -xylofuranosyl)-6- N -[(di- n -butylamino)methylene]-adenine (8)
To a THF (1.9 mL) solution of 7 (69 mg, 0.11 mmol) and Ph₃P (90 mg, 0.33 mmol), a mixture of DIAD (71 µL, 0.33 mmol) and DPPA (65 µL, 0.33 mmol) in THF (500 µL) was added dropwise at 0 ˚C under Ar. After 7 h of stirring at r.t., EtOH (1 mL) was added, and the solution was stirred for 30 min. After evaporation of all the volatiles, the oily residue was purified by silica gel column chromatography (EtOAc-cyclohexane = 3:7 to 8:2 step gradient). Ph₃PO contained in the chromatographed product was removed by precipitation from cold Et₂O (3 h, 4 ˚C). After the second precipitation the filtrate was evaporated to yield 8 (61 mg, 85%). R _f = 0.4 (CH₂Cl₂-MeOH = 9.5:0.5). ^¹H NMR (300 MHz, CDCl₃): δ = 0.94 (2 t, J = 7.3, 7.3 Hz, 6 H, 2 × NCH₂CH₂CH₂CH₃), 1.09 [s, 9 H, SiC(CH₃)₃], 1.21-1.45 (m, 4 H, 2 × NCH₂CH₂CH₂CH₃), 1.58-1.71 (m, 4 H, 2 × NCH₂CH₂CH₂CH₃), 2.54 (dd, J = 14.8, 0.9 Hz, 1 H, H_A2′), 2.83 (ddd, J = 14.0, 7.9, 6.0 Hz, 1 H, H_B2′′), 3.38 (t, J = 7.3 Hz, 2 H, NCH₂CH₂CH₂CH₃), 3.67-3.75 (m, 2 H, NCH₂CH₂CH₂CH₃), 3.96-4.07 (m, 2 H, H5′5′′), 4.19-4.24 (m, 1 H, H4′), 4.41-4.44 (m, 1 H, H3′), 6.41 (dd, J = 7.9, 2.1 Hz, 1 H, H1′), 7.42-7.70 (m, 10 H, ar), 8.19 (s, 1 H, H2), 8.52 (s, 1 H, H8), 9.02 (s, 1 H, CH=N). ^¹³C NMR (70 MHz, CDCl₃): δ = 13.6 (NCH₂CH₂CH₂CH₃), 13.9 (NCH₂CH₂CH₂CH₃), 19.1 (SiC), 19.7 (NCH₂CH₂CH₂CH₃), 20.1 (NCH₂CH₂CH₂CH₃), 26.8 [(CH₃)₃], 29.2 (NCH₂CH₂CH₂CH₃), 30.9 (NCH₂CH₂CH₂CH₃), 39.0 (C2′), 45.1 (NCH₂CH₂CH₂CH₃), 51.8 (NCH₂CH₂CH₂CH₃), 61.5 (C3′), 61.9 (C5′5′′), 83.1 (C1′), 83.1 (C4′), 125.8 (C5), 125.8, 127.8, 128.3, 131.8, 131.9, 132.0, 135.4 (ar), 139.8 (C2), 151.0 (C4), 156.6 (C6), 157.3 (C8), 158.4 (CH=N). HRMS (ESI⁺): m/z calcd: 654.3700 [MH]⁺; found: 654.3700.
9-[ 5 ′ -O- ( tert -Butyldiphenylsilyl)-3′-[ N -(9-fluorenyl)-methoxycarbonyl- O -methyl- l -tyrosyl]amido - 2′,3′-dideoxy-β- d -xylofuranosyl)-6- N -[(di- n -butylamino)-methylene]adenine (9)
N-Fmoc-O-Me-l-Tyr (45 mg, 0.11 mmol) and HOBt (18 mg, 0.11 mmol) were co-evaporated with anhyd THF (3 × 1 mL). The mixture was dissolved in anhyd THF (1 mL) and cooled down to 0 ˚C under N₂ for 10 min. Diisopropylcarbodiimide (16 µL, 0.10 mmol) was added, and the reaction mixture was stirred at the same temperature for 15 min and then 10 min at r.t. Me₃P (1 M in THF, 160 µL, 0.16 mmol) was added to 8 (52.6 mg, 0.08 mmol) in THF (1 mL) and stirred at r.t. for 5 min. The amino acid solution was added to the iminophosphorane solution and stirred for 4 h at r.t. The reaction mixture was concentrated under reduced pressure and dissolved in EtOAc (20 mL) and then washed with sat. aq NaHCO₃ solution (15 mL) and H₂O (2 × 20 mL). The organic layer was dried over Na₂SO₄, evaporated, and the residue was purified by silica gel column chromatog-raphy (CH₂Cl₂-MeOH = 99.5: 0.5 to 98:2 step gradient) to yield 9 (70 mg, 85%). R _f = 0.45 (CH₂Cl₂-MeOH = 9.5:0.5). ^¹H NMR (300 MHz, CDCl₃): δ = 0.81-0.91 (m, 6 H, 2 × NCH₂CH₂CH₂CH₃), 1.06, 1.07 [2 s, 9 H, SiC(CH₃)₃], 1.22-1.39 (m, 4 H, 2 × NCH₂CH₂CH₂CH₃), 1.52-1.72 (m, 4 H, 2 × NCH₂CH₂CH₂CH₃), 1.93 (dd, J = 15.0, 2.9 Hz, 1 H, H_A2′), 2.72-2.74 (m, 1 H, H_B2′), 1.88 (d, J = 6.1 Hz, 1 H, Hβ), 3.36 (t, J = 7.3 Hz, 2 H, NCH₂CH₂CH₂CH₃), 3.56-3.59 (m, 2 H, NCH₂CH₂CH₂CH₃), 3.66-3.71 (m, 2 H, H5′′), 3.89 (dd, J = 11.1, 3.9 Hz, 1 H, H5′), 4.01-4.02 (m, 1 H, H4′), 4.11-4.36 (m, 4 H, CH-Fmoc, Hα and CH₂-Fmoc), 4.73 (d, J = 7.4 Hz, 1 H, H3′), 5.37 (d, J = 7.3 Hz, 1 H, NH-Fmoc), 5.88 (dd, J = 8.9, 3.5 Hz, 1 H, H1′), 6.49, 6.91 [2 d, J = 8.5 Hz, 4 H, H-o-Ph(OMe)], 7.10-7.80 [m, 18 H, ar (Fmoc and TBDPS)], 8.39 (s, 1 H, H2), 8.94 (s, 1 H, H8), 9.56 (s, 1 H, CH=N). ^­¹³C NMR (70 MHz, CDCl₃): δ = 13.6 (NCH₂CH₂CH₂CH₃), 13.8 (NCH₂CH₂CH₂CH₃), 19.1 (SiC), 19.7 (NCH₂CH₂CH₂CH₃), 20.1 (NCH₂CH₂CH₂CH₃), 23.4, 26.7 [(CH₃)₃], 29.2 (NCH₂CH₂CH₂CH₃), 30.9 (NCH₂CH₂CH₂CH₃), 38.1 (C2′), 38.7 (Cβ), 45.2 (NCH₂CH₂CH₂CH₃), 47.1 (CH-Fmoc), 48.8 (C3′), 51.8 (NCH₂CH₂CH₂CH₃), 57.1 (C5′5′′), 62.6 (OCH₂ Fmoc), 66.8 (Cα), 82.7 (C4′), 84.5 (C1′), 113.6 [o-Ph(OMe)], 119.8, 125.0, 127.4, 127.5, 127.6, 128.3, 128.5, 130.2, 131.7, 131.8, 131.9, 131.9, 132.1, 133.1, 135.4, 135.5, 135.5, 141.2, 141.5, 143.7, 143.8 (Ar), 149.4 (C4), 151.8 (C2), 157.2 (C6), 157.2 (C=O), 158.3 (C8), 169.97 (CH=N). HRMS (ESI⁺): m/z calcd: 1049.5085 [M + Na]⁺; found: 1049.5084.
9-(3′- O -Methyl- l -tyrosyl)amido-2′,3′-dideoxy-β- d -xylofuranosyl)adenine (4)
Compound 9 (65 mg, 0.08 mmol) was dissolved in 33% MeNH₂-EtOH (8 mL), and the mixture was stirred overnight at r.t. in a closed vessel. The solution was concentrated under reduced pressure, and the residue was dissolved in MeOH (2 mL) and then NH₄F (16 mg, 0.43 mmol) was added. The reaction mixture was warmed to 50-55 ˚C for 4 h. The volatiles were evaporated, and the residue was washed with EtOAc (3×) and then purified by a preparative thin-layer column chromatography using i-PrOH-NH₃-H₂O (8:0.5:0.5) as the eluent to obtain 4 (24 mg, 90%). ^¹H NMR (300 MHz, CD₃OD): δ = 1.95-2.01 (m, 1 H, H_A2′), 2.67-2.77 (m, 2 H, H_B2′, Hβ), 3.44 (t, J = 7.2 Hz, 1 H, Hα), 3.49 (s, 3 H, OMe), 3.61-3.65 (m, 2 H, H5′5′′), 3.99 (dd, J = 9.7, 5.4 Hz, 1 H, H4′), 4.55-4.59 (m, 1 H, H3′), 6.03 (dd, J = 8.4, 5.1 Hz, 1 H, H1′), 6.58 [d, J = 8.6 Hz, 2 H, o-Ph(OMe)], 6.98 [d, J = 8.6 Hz, 2 H, m-Ph(OMe)], 8.05 (s, 1 H, H2), 8.11 (s, 1 H, H8). ^¹³C NMR (125 MHz, CD₃OD): δ = 39.4 (C2′), 39.9 (Cβ), 50.8 (C3′), 55.6 (OMe), 57.1 (Cα), 61.8 (C5′5′′), 83.3 (C4′), 86.0 (C1′), 115.1 [2 × C-o-Ph(OMe)], 122.4 (C5), 127.9 [C-p-Ph(OMe)], 131.7 [2 × C-m-Ph(OMe)], 142.6 (C2), 148.9 (C4), 153.5 (C8), 157.7 (C6), 160.5 [C-i-Ph(OMe)], 169.9 (C=O). HRMS (ESI⁺): m/z calcd: 428.2046 [MH]⁺; found: 428.2047.