Synthesis of 4′‐Selenoribonucleosides, the Building Blocks of 4′‐SelenoRNA, Using a Hypervalent Iodine

Noriko Saito‐Tarashima1, Masashi Ota1, Noriaki Minakawa1

1 Graduate School of Pharmaceutical Science, Tokushima University, Shomachi, Tokushima
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 1.40
DOI:  10.1002/cpnc.34
Online Posting Date:  September, 2017
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Abstract

Herein is described a detailed protocol for the synthesis of 4′‐selenoribonucleoside derivatives that involves the use of a hypervalent iodine species. These derivatives are versatile units for the preparation of 4′‐selenoRNA. Large‐scale synthesis of a 4‐selenosugar starting from D‐ribose is achieved in eight steps, including a final chromatographic purification. The resulting 4‐selenosugar is then subjected to the one‐pot Pummerer‐like reaction using hypervalent iodine in the presence of silylated nucleobases. The reaction with silylated uracil affords the desired 4′‐selenouridine derivatives with excellent β‐selectivity and in good yield. Conversely, when purine nucleobases are used in the Pummerer‐like reaction, N7 4′‐selenoribonucleoside isomers are obtained alongside the desired N9 isomers. However, the undesired N7 isomers can be converted to the desired N9 ones under acidic conditions. © 2017 by John Wiley & Sons, Inc.

Keywords: “armed” 4‐selenosugar; hypervalent iodine; Pummerer‐like reaction; 4′‐selenoribonucleoside

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Preparation of “Armed” 4‐Selenosugar
  • Basic Protocol 2: Preparation of 4′‐Selenopyrimidine Nucleosides
  • Basic Protocol 3: Preparation of 4′‐Selenopurine Nucleosides
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

Basic Protocol 1: Preparation of “Armed” 4‐Selenosugar

  Materials
  • D‐Ribose, 98% (TCI) dried well with P 2O 5 at 50°C using a vacuum oil pump
  • Potassium carbonate (K 2CO 3), 99.5% (Wako Pure Chemical)
  • Bromine (Br 2), 99% (Wako Pure Chemical)
  • Sodium bisulfite (NaHSO 3), 60% to 69% (Kishida Chemical)
  • Toluene, 99% (Kishida Chemical)
  • Methanol (MeOH), 99.5% (Wako Pure Chemical)
  • Celite pad (Kanto Chemical)
  • Anhydrous acetone, 99% (Wako Pure Chemical) distilled and stored with 4‐Å molecular sieves (Wako Pure Chemical)
  • Argon gas
  • Sulfuric acid, 96% (Kanto Chemical)
  • Sodium bicarbonate (NaHCO 3), 99% (Junsei Chemical)
  • Chloroform (CHCl 3), 99% (Junsei Chemical)
  • Brine: saturated aqueous NaCl
  • Anhydrous sodium sulfate (Na 2SO 4), 99% (Kanto Chemical)
  • Anhydrous pyridine, 99% (Wako Pure Chemical) distilled from KOH and stored with 4‐Å molecular sieves (Wako Pure Chemical)
  • Methanesulfonyl chloride (MsCl), 99% (TCI)
  • Ethyl acetate (AcOEt), 99% (Wako Pure Chemical)
  • Potassium hydroxide (KOH), 85% (Kishida Chemical)
  • Acetone, 99% (Wako Pure Chemical)
  • Hydrochloric acid (HCl), 35% to 37% (Kanto Chemical)
  • Dichloromethane, super dehydrated (CH 2Cl 2), 99.5% (Wako Pure Chemical)
  • Imidazole, 99% (Kishida Chemical)
  • tert‐Butylchlorodiphenylsilane (TBDPSCl), 97% (Wako Pure Chemical)
  • Tetrahydrofuran (THF), super dehydrated, 99.5% (Wako Pure Chemical)
  • Sodium borohydride (NaBH 4), 95% (TCI)
  • Potassium sodium tartrate tetrahydrate, 95% (Wako Pure Chemical)
  • Saturated aqueous sodium bicarbonate (NaHCO 3; Junsei Chemical)
  • Selenium (Se) powder
  • Ethanol (EtOH), 95% (Wako Pure Chemical)
  • Silica gel 60, 0.063 to 0.2 mm (Kanto Chemical)
  • Hexane, 95% (Kanto Chemical)
  • 1‐ and 2‐L round‐bottom flasks
  • Magnetic stir plate and stir bar
  • Disposable syringes
  • Vacuum evaporator
  • Vacuum oil pump
  • TLC plate, Merck silica gel 60 F254
  • Balloon for applying argon atmosphere
  • pH test paper
  • 5‐L separatory funnel
  • Cannula
  • Dropping funnel
  • Reflux condenser
  • Sintered glass filter
  • Additional reagents and equipment for thin‐layer chromatography [TLC; appendix 3D (Meyers & Meyers, )] and column chromatography ( appendix 3E; Meyers, )

Basic Protocol 2: Preparation of 4′‐Selenopyrimidine Nucleosides

  Materials
  • Uracil, 98% (TCI) dried well with P 2O 5 at 50°C using a vacuum oil pump
  • Anhydrous 1,2‐dichloroethane, 99.5% (Kishida Chemical) distilled from P 2O 5 and stored with 4‐Å molecular sieves
  • Trimethylsilyl trifluoromethanesulfonate (TMSOTf), 98% (TCI)
  • Argon gas
  • Anhydrous 2,6‐lutidine, 97.5% (Wako Pure Chemical) distilled from KOH and stored with KOH
  • Iodosyl benzene, 95% (TCI)
  • S.10 ( protocol 1)
  • Hexane, 95% (Kanto Chemical)
  • Ethyl acetate (AcOEt), 99% (Wako Pure Chemical)
  • Anhydrous sodium sulfate (Na 2SO 4), 99% (Kanto Chemical)
  • 2,4,6‐Triisopropylbenzenesulfonyl chloride (TPSCl), 95% (TCI)
  • 4‐Dimethylaminopyridine (DMAP), 99% (Wako Pure Chemical)
  • Triethylamine (Et 3N), 99% (Kishida Chemical)
  • Anhydrous acetonitrile (CH 3CN), 99.5% (Wako Pure Chemical) distilled from P 2O 5 and stored with 4‐Å molecular sieves
  • NH 4OH, 28% (Nacalai Tesque)
  • Methanol (MeOH), 99.5% (Wako Pure Chemical)
  • Chloroform (CH 3Cl), 99% (Junsei Chemical)
  • Silica gel 60, 0.063 to 0.2 mm (Kanto Chemical)
  • Balloon for applying argon atmosphere
  • 200‐mL round‐bottom flask
  • 500 mL round‐bottom two‐neck flask
  • Magnetic stirrer and stir bar
  • Cannula
  • TLC plate, Merck silica gel 60 F254
  • Vacuum evaporator
  • Vacuum oil pump
  • 1‐ and 2‐L separatory funnel
  • 300‐mL round‐bottom flask
  • Additional reagents and equipment for thin‐layer chromatography [TLC; appendix 3D (Meyers & Meyers, )] and column chromatography ( appendix 3E; Meyers, )

Basic Protocol 3: Preparation of 4′‐Selenopurine Nucleosides

  Materials
  • 6‐Chloropurine, 98% (TCI) dried well with P 2O 5 at 50°C using a vacuum oil pump
  • Anhydrous 1,2‐dichloroethane, 99.5% (Kishida Chemical) distilled from P 2O 5 and stored with 4‐Å molecular sieves
  • Argon gas
  • Anhydrous 2,6‐lutidine, 97.5% (Wako Pure Chemical) distilled from KOH and stored with KOH
  • Trimethylsilyl trifluoromethanesulfonate (TMSOTf), 98% (TCI)
  • S.10 ( protocol 1)
  • Iodosyl benzene, 95% (TCI)
  • Ethyl acetate (AcOEt), 99% (Wako Pure Chemical)
  • Saturated aqueous sodium bicarbonate (NaHCO 3; Junsei Chemical)
  • Brine: saturated aqueous NaCl
  • Anhydrous sodium sulfate (Na 2SO 4), 99% (Kanto Chemical)
  • Silica gel 60, 0.063 to 0.2 mm, 70 to 230 mesh (Kanto Chemical)
  • Hexane, 95% (Kanto Chemical)
  • Dry toluene, 99.5% (Wako Pure Chemical)
  • Methanolic ammonia (NH 3/methanol), methanol saturated with NH 3 gas at 0°C:
  •  Methanol (MeOH), 99.5% (Wako Pure Chemical)
  •  Ammonia (NH 3) gas, 99.9% (Shikoku Acetylene)
  • Chloroform (CHCl 3), 99% (Junsei Chemical)
  • 2,6‐Dichloropurine, 97% (TCI) dried well with P 2O 5 at 50°C using a vacuum oil pump
  • Acetic acid, 99.7% (Wako Pure Chemical)
  • Sodium nitrite (NaNO 2), 99.5% (Kanto Chemical)
  • 200‐mL round‐bottom flask
  • Balloon for applying argon atmosphere
  • 500‐mL round‐bottom two‐neck flask
  • Magnetic stirrer and stir bar
  • Cannula
  • 2‐L, 500‐mL, and 300‐mL separatory funnels
  • Vacuum oil pump
  • TLC plate, Merck silica gel 60 F254
  • 100‐mL round‐bottom two‐neck flask
  • 150‐ and 300‐mL steel containers
  • Vacuum evaporator
  • Additional reagents and equipment for thin‐layer chromatography [TLC; appendix 3D (Meyers & Meyers, )] and column chromatography ( appendix 3E; Meyers, )
NOTE: All glassware and equipment should be well‐dried prior to especially the Pummerer‐like reaction.NOTE: “Dry” solvent refers to a commercially available anhydrous solvent, whereas “anhydrous” solvent refers to a solvent distilled from an appropriate drying agent and stored with 4‐Å molecular sieves.NOTE: “Stir” means stir with a stir bar and magnetic plate.
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Figures

Videos

Literature Cited

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