Practical Synthesis of 4′‐Thioribonucleosides Starting from D‐Ribose

Noriaki Minakawa1, Akira Matsuda2

1 Graduate School of Pharmaceutical Sciences, The University of Tokushima, Tokushima, 2 Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 14.12
DOI:  10.1002/0471142700.nc1412s59
Online Posting Date:  December, 2014
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Abstract

A practical synthesis of 4′‐thioribonucleosides, i.e., 4′‐thiouridine, ‐cytidine, ‐adenosine, and ‐guanosine, which are versatile units for nucleic acids–based therapeutics, is described. Large‐scale synthesis of 4‐thiosugar starting from D‐ribose was achieved (33%) in eight steps and with only three chromatographic purifications. After the appropriate chemical conversion of the 4‐thiosugar, the resulting sulfoxide was subjected to the Pummerer reaction in the presence of silylated nucleobases. In reactions with silylated pyrimidine bases, the desired 4′‐thioribonucleoside derivatives were obtained in good yield and β‐selectively. On the other hand, N‐7 isomers were obtained mainly in the Pummerer reaction with purine bases under the same conditions. However, the desired N‐9 isomers were obtained in moderate yields when the reaction mixtures were subsequently heated under reflux. As a result, effective synthesis of 4′‐thioribonucleosides was accomplished. © 2014 by John Wiley & Sons, Inc.

Keywords: D‐ribose; 4‐thiosugar; sulfoxide; Pummerer reaction; 4′‐thioribonucleoside

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Preparation of 4‐Thiosugar
  • Basic Protocol 2: Preparation of 4′‐Thiopyrimidine Nucleosides
  • Basic Protocol 3: Preparation of 4′‐Thiopurine Nucleosides
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

Basic Protocol 1: Preparation of 4‐Thiosugar

  Materials
  • D‐Ribose, 98% (TCI) dried well with P 2O 5 at 50°C using a vacuum oil pump
  • Allyl alcohol, 99% (Kanto Chemical)
  • Sulfuric acid (H 2SO 4), 96% (Kanto Chemical)
  • Sodium bicarbonate (NaHCO 3), 99% (Junsei Chemical)
  • Celite pad (Kanto Chemical)
  • Methanol (MeOH), 99.5% (Wako Pure Chemical)
  • Sodium hydride (NaH), 60% dispersion in mineral oil (Kanto Chemical)
  • Dry tetrahydrofuran (THF), 99.5% (Wako Pure Chemical), stored with 4 Å molecular sieves
  • Dry dimethylformamide (DMF), 99.5% (Wako Pure Chemical), stored with 4 Å molecular sieves
  • p‐Methoxybenzyl chloride (PMBCl), 95% (Wako Pure Chemical)
  • Ammoniun chloride (NH 4Cl), 98.5%, saturated aqueous (Wako Pure Chemical)
  • Ethyl acetate (AcOEt), 99% (Junsei Chemical)
  • Anhydrous sodium sulfite (Na 2SO 4), 99% (Kanto Chemical)
  • Chloroform, 99% (Junsei Chemical)
  • Palladium chloride (PdCl 2), 99% (Wako Pure Chemical)
  • Oxygen, 99.5%
  • Sodium borohydride (NaBH 4), 95% (Wako Pure Chemical)
  • Merck silica gel 60 F 254, 0.063 to 0.2 mm, 70 to 230 mesh (Kanto Chemical)
  • Anhydrous pyridine, 99% (Wako Pure Chemical) distilled from KOH and stored with 4 Å molecular sieves
  • Argon
  • Methanesulfonyl chloride (MsCl), 98% (Kanto Chemical)
  • Toluene
  • Dry methyl ethyl ketone, 99.5% (Kishida Chemical) stored with 4 Å molecular sieves
  • Lithium bromide, 95% (Kishida Chemical) dried well with P 2O 5 at 50°C using a vacuum oil pump
  • Sodium sulfide nonahydrate, 98% (Wako Pure Chemical)
  • Anhydrous dichloromethane, 98% (Junsei Chemical) distilled from P 2O 5 and stored with 4 Å molecular sieves
  • Trifluoroacetic acid, 99% (TCI)
  • 1,3‐Dichloro‐1,1,3,3‐tetraisopropyldisiloxane, 99.5% (Shin‐Etsu Chemical)
  • 2,4‐Dimethoxybenzoic acid, 98% (TCI)
  • Thionyl chloride, 95% (Wako Pure Chemical)
  • 4 Å molecular sieves (Wako Pure Chemical)
  • 500‐, 1‐, 2‐, and 5‐L round‐bottom flasks
  • Magnetic stir plate and magnetic stir bars
  • Vacuum oil pump
  • TLC plates
  • 3‐L three‐neck flask attached to a bubbler
  • 1‐L flasks
  • 150‐ and 500‐mL dropping funnels
  • Chromatography columns, 10 × 15–cm
  • Glass rods

Basic Protocol 2: Preparation of 4′‐Thiopyrimidine Nucleosides

  Materials
  • Anhydrous triethylamine, 99% (Et 3N, Kishida Chemical) distilled from CaH prior to the reaction
  • Trimethylsilyl trifluoromethanesulfonate (TMSOTf), 98% (TCI)
  • Uracil, 99% (Wako Pure Chemical) dried well with P 2O 5 at 50°C using a vacuum oil pump
  • Anhydrous toluene, 99% (Kishida Chemical) distilled from P 2O 5 and stored with 4 Å molecular sieves
  • Argon
  • Anhydrous dichloromethane (CH 2Cl 2), 98% (Junsei Chemical) distilled from P 2O 5 and stored with 4 Å molecular sieves
  • 1,4‐Anhydro‐2‐O‐(2,4‐dimethoxybenzoyl)‐3,5‐O‐(1,1,3,3‐tetraisopropyldisiloxane‐1,3‐diyl)‐4‐sulfinyl‐D‐ribitol (12, see Basic Protocol 1)
  • Ethyl acetate (AcOEt), 99% (Junsei Chemical)
  • Saturated aqueous sodium bicarbonate (NaHCO 3)
  • Anhydrous sodium sulfite (Na 2SO 4), 99% (Kanto Chemical)
  • Silica gel 60, 0.063 to 0.2 mm, 70 to 230 mesh (Kanto Chemical)
  • TLC plates with Merck silica gel 60 F 254
  • Hexane
  • Methanol (MeOH), 99.5% (Wako Pure Chemical)
  • Ammonium fluoride (NH 4F), 97% (Wako Pure Chemical)
  • Methanolic ammonia (NH 3/MeOH), saturated NH 3 at 0°C
  • Ammonia gas (NH 3), 99.9% (Shikoku Acetylene)
  • Chloroform (CHCl 3)
  • N4‐benzoylcytosine, 97% (TCI) dried well with P 2O 5 at 50°C using a vacuum oil pump
  • 30‐mL, 500‐mL and 1‐L round‐bottom flasks
  • Magnetic stir plate and magnetic bars
  • Cannula
  • Rotary evaporator
  • Chromatography columns (ϕ = 5 × 10, ϕ = 2 × 11, and ϕ = 5 × 18)
  • Vacuum oil pump

Basic Protocol 3: Preparation of 4′‐Thiopurine Nucleosides

  Materials
  • Anhydrous triethylamine, 99% (Et 3N, Kishida Chemical) distilled from CaH prior to the reaction
  • Trimethylsilyl trifluoromethanesulfonate (TMSOTf), 98% (TCI)
  • 6‐Chloropurine, 98% (TCI) dried well with P 2O 5 at 50°C using a vacuum oil pump
  • Anhydrous acetonitrile (CH 3CN), 98% (Wako Pure Chemical) distilled from P 2O 5 and stored with 4 Å molecular sieves
  • Anhydrous 1,2‐dichloroethane, 99.5% (ClCH 2CH 2Cl, Nacalai Tesque) distilled from P 2O 5 and stored with 4 Å molecular sieves
  • Argon
  • Ethyl acetate (AcOEt), 99% (Junsei Chemical)
  • Saturated aqueous sodium bicarbonate (NaHCO 3)
  • Brine
  • Anhydrous sodium sulfite (Na 2SO 4), 99% (Kanto Chemical)
  • Hexane
  • Silica gel 60, 0.063 to 0.2 mm, 70 to 230 mesh (Kanto Chemical)
  • Dry tetrahydrofuran (THF)
  • Acetic acid, 99.7% (AcOH, Wako Pure Chemical)
  • Tetrabutylammonium fluoride (TBAF), 1 M THF solution (TCI)
  • Acetone, 99.5% (Wako Pure Chemical)
  • Ethanolic ammonia (NH 3/EtOH), saturated NH 3 at 0°C
  • MeOH (Wako Pure Chemical)
  • Chloroform (CHCl 3)
  • 2‐Amino‐6‐chloropurine, 98% (Wako Pure Chemical) dried well with P 2O 5 at 50°C using a vacuum oil pump
  • TLC plates with Merck silica gel 60 F 254
  • 2‐Mercaptoethanol, 95% (Wako Pure Chemical)
  • Sodium methoxide (NaOMe), 28%
  • Hydrochloric acid, 37% (Kanto Chemical)
  • 20‐, 30‐, and 500‐mL round‐bottom flasks
  • Magnetic heat plate and bars
  • 1‐L two‐neck flasks
  • Cannula
  • Rotary evaporator
  • Chromatography columns (ϕ = 5 × 12−cm; ϕ = 1 × 6−cm; ϕ = 1 × 5−cm; ϕ = 5 × 10−cm)
  • Vacuum oil pump
  • 50‐mL steel container
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Figures

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Literature Cited

Literature Cited
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