Synthesis of Fluorinated Nucleosides

Satoshi Katayama1, Satoshi Takamatsu1, Naoko Hirose1, Kunisuke Izawa1, Tokumi Maruyama2

1 AminoScience Laboratories, Ajinomoto Co., Kanagawa, 2 Tokushima Bunri University, Kagawa
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 1.12
DOI:  10.1002/0471142700.nc0112s25
Online Posting Date:  July, 2006
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Abstract

Two practical synthetic approaches to the production of lodenosine [FddA, 9‐(2,3‐dideoxy‐2‐fluoro‐β‐D‐threo‐pentofuranosyl)adenine] via 6‐chloropurine riboside or 6‐chloropurine 3′‐deoxyriboside are described. The reaction sequence contains new fluorination methods and new applications of radical reduction. The reagents and reaction conditions of each step have been carefully selected to ensure robustness and safety.

Keywords: Lodenosine; FddA); adenine 2′‐deoxy‐2′‐fluoroarabinoside; FdaraA; 6‐chloropurine 3′‐deoxyriboside; fluorination; radical reduction

     
 
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Table of Contents

  • Basic Protocol 1: Preparation of 6‐Chloropurine 3′‐O‐Benzoyl‐5′‐O‐ Tritylriboside
  • Basic Protocol 2: Synthesis of FddA from 6‐Chloropurine 3′‐O‐Benzoyl‐5′‐O‐Tritylriboside
  • Alternate Protocol 1: Synthesis of FdaraA from 6‐Chloropurine 3′‐O‐Benzoyl‐5′‐O‐Tritylriboside
  • Basic Protocol 3: Preparation of 6‐Chloropurine 3′‐Deoxyriboside
  • Basic Protocol 4: Preparation of FddA from 6‐Chloropurine 3′‐Deoxyriboside
  • Commentary
  • Literature Cited
  • Figures
  • Tables
     
 
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Materials

Basic Protocol 1: Preparation of 6‐Chloropurine 3′‐O‐Benzoyl‐5′‐O‐ Tritylriboside

  Materials
  • 6‐Chloropurine riboside ( S.1), 99% pure (Aldrich)
  • Di‐n‐butyltin(IV) oxide, 95+%
  • Methanol (MeOH), 99.8+%
  • Triethylamine, 99+%
  • Benzoyl chloride, 99+%
  • Diethyl ether, 99.5+%
  • Magnesium sulfate (MgSO 4), anhydrous, 99.5+%
  • Dichloromethane (CH 2Cl 2), 99+%
  • Ethanol (EtOH), 99.5%
  • N,N‐Dimethylformamide (DMF), anhydrous, 99.8+%
  • Benzene, 99.5+%
  • 4‐Dimethylaminopyridine (DMAP), 99+%
  • Trityl chloride, 98+%
  • Chloroform (CHCl 3), 99+%
  • Pyridine, dehydrated for organic synthesis, 99+%
  • Dimethylsulfoxide (DMSO)
  • 3:2 and 1:4 (v/v) 10 mM phosphoric acid/MeOH
  • Reflux condenser
  • Vacuum filtration unit with glass filter
  • Rotary evaporator equipped with vacuum oil pump
  • 3.5 × 50–cm and 6.5 × 35–cm sintered glass chromatography columns packed with silica gel G
  • TLC plates: silica‐coated aluminum plate with fluorescent indicator (Merck silica gel 60 F 254)
  • 254‐nm UV lamp
  • HPLC apparatus with:
    • Cosmosil guard column 5C18‐MS (4.6 × 10–mm, Nacalai Tesque)
    • Cosmosil packed column 5C18‐MS (4.6 × 150–mm, Nacalai Tesque)
    • CCPD pump (Toso)
    • SPD‐M10A photo diode array UV‐VIS detector (Shimadzu)

Basic Protocol 2: Synthesis of FddA from 6‐Chloropurine 3′‐O‐Benzoyl‐5′‐O‐Tritylriboside

  Materials
  • 6‐Chloro‐9‐(3‐O‐benzoyl‐5‐O‐trityl‐β‐D‐ribofuranosyl)purine ( S.3; see protocol 1)
  • Dichloromethane (CH 2Cl 2), anhydrous, 99.8%
  • Pyridine, dehydrated for organic synthesis, 99+%
  • Diethylaminosulfur trifluoride (DAST), 95+%
  • 5% (w/v) and saturated sodium hydrogen carbonate (NaHCO 3), 99.5+%
  • Chloroform (CHCl 3), 99+%
  • Magnesium sulfate (MgSO 4), anhydrous, 99.5+%
  • Ethyl acetate (EtOAc), 99+%
  • n‐Hexane, 95+%
  • Sulfuryl chloride, 99+%
  • Imidazole, 99+%
  • Sodium sulfate (Na 2SO 4), anhydrous, 99+%
  • Toluene, anhydrous, 99.8+%
  • Triethylamine trihydorofluoride (Et 3N·3HF), 98%
  • Acetonitrile (CH 3CN), 99.5+%
  • 70:30 and 50:50 (v/v) 0.02 M aq. KH 2PO 4 (pH 3.2) in CH 3CN
  • 4‐Dimethylaminopyridine (DMAP), 99+%
  • Trifluoromethanesulfonyl chloride, 99+%
  • Saturated aq. ammonium chloride (NH 4Cl), 99+%
  • Saturated aq. sodium chloride (NaCl), 99+%
  • Triethylamine, 99+%
  • Methanol (MeOH), 99.8+%
  • Ammonia, anhydrous, 99.99+%
  • Phenyl chlorothionoformate, 98+%
  • 2,2′‐Azobis(isobutyronitrile) (AIBN), 98+%
  • Tris(trimethylsilyl)silane, 96+%
  • Nitrogen, 99.998+%
  • Dimethylsulfoxide (DMSO), anhydrous, 99.9+%
  • 5 M aq. sodium hydroxide (NaOH)
  • Carbon disulfide, 99.9+%
  • Iodomethane, 99.5+%
  • 1,2‐Dimethoxyethane, 99+%
  • 50% (v/v) aq. hypophosphorous acid (H 3PO 2)
  • 35% to 37% (v/v) hydrochloric acid (conc. HCl)
  • Amberlite IRA‐900 (OAc form; ICN)
  • Reflux condenser
  • Rotary evaporator equipped with a vacuum oil pump
  • 3.5 × 50–cm and 2.5 × 32–cm chromatography columns packed with silica gel G
  • Vacuum filtration unit with glass filter
  • 22 × 3–cm, 230‐ to 400‐mesh silica gel column
  • TLC plates: silica‐coated aluminum plate with fluorescent indicator (Merck silica gel 60 F 254)
  • HPLC with Inertsil ODS 2 4.6 × 150–mm column (GL Science)
  • Glass filter with aspirator
  • Vacuum oil pump
  • 40‐mm‐diameter Kiriyama filter funnel (glass Büchner‐type funnel) and no. 5B filter paper
  • 50°C vacuum oven
CAUTION: DAST should be handled with gloves. This material can cause burns.

Alternate Protocol 1: Synthesis of FdaraA from 6‐Chloropurine 3′‐O‐Benzoyl‐5′‐O‐Tritylriboside

  • 9‐(5‐O‐Trityl‐2‐deoxy‐2‐fluoro‐β‐D‐arabinofuranosyl)adenine ( S.5; see protocol 2)
  • Trifluoroacetic acid, 98+%
  • Aspirator

Basic Protocol 3: Preparation of 6‐Chloropurine 3′‐Deoxyriboside

  Materials
  • Inosine ( S.11), 98+%
  • Acetic acid, 99.5+%
  • Trimethyl orthoacetate, 99+%
  • Acetonitrile (CH 3CN), 99.8+%
  • Acetyl bromide, 97+%
  • 85:15 and 80:20 (v/v) 0.02 M aq. KH 2PO 4 (pH 3.2) in CH 3CN
  • 25% (w/v) aq. sodium hydroxide (NaOH)
  • 50% (v/v) aq. hypophosphorous acid (H 3PO 2)
  • Triethylamine, 99+%
  • 6 M hydrochloric acid (HCl)
  • 2,2′‐Azobis[2‐(2‐imidazolin‐2‐yl)propane]dihydrochloride, 97+% (VA‐044; Wako Pure Chemical Industries)
  • Dichloromethane (CH 2Cl 2), 99+%
  • Dimethylformamide (DMF), 99.5+%
  • Thionyl chloride, 98+%
  • Saturated aq. sodium hydrogen carbonate (NaHCO 3), 99.5+%
  • Saturated aq. sodium chloride (NaCl), 99+%
  • Sodium sulfate (Na 2SO 4), anhydrous, 98+%
  • Methanol (MeOH), 99.8+%
  • 28% (w/w) sodium methoxide solution in methanol
  • 1‐ and 2‐L four‐neck round‐bottom flasks
  • Mechanical stirrer
  • Thermometers
  • Reflux condensers
  • Vacuum oil pump
  • HPLC with Inertsil ODS 2 4.6 × 150–mm column (GL Science)
  • Dropping funnel
  • Separatory funnel
  • Rotary evaporator with vacuum pump or water aspirator
  • 1‐L one‐neck round‐bottom flask
  • 60‐mm‐diameter Kiriyama filter funnel (glass Büchner‐type funnel) and no. 5B filter paper
  • 50°C vacuum oven
  • 300‐mL three‐neck round‐bottom flask

Basic Protocol 4: Preparation of FddA from 6‐Chloropurine 3′‐Deoxyriboside

  Materials
  • 6‐Chloro‐9‐(3‐deoxy‐β‐D‐erythro‐pentofuranosyl)‐9H‐purine ( S.15)
  • Acetonitrile (CH 3CN), 99.8+%
  • Nitrogen
  • 2,4,6‐Collidine, 99+%
  • Trityl chloride, 98+%
  • Mobile phase: HPLC‐grade MeOH, far‐UV‐grade CH 3CN, and 0.1% H 3PO 4 (see Tables and for gradients)
  • Methanol (MeOH), 99.8+%
  • Dichloromethane (CH 2Cl 2), 99+%
  • 6 M hydrochloric acid (HCl)
  • Saturated aq. sodium hydrogencarbonate (NaHCO 3), 99.5+%
  • Sodium sulfate (Na 2SO 4), anhydrous, 98+%
  • Benzotrifluoride, 98+%
  • n‐Hexane, 95+%
  • Toluene, 99.5+%
  • Perfluorobutanesulfonyl fluoride, 90+%
  • N,N‐Dimethylcyclohexylamine, 98+%
  • 5.0% aq. ammonium chloride (NH 4Cl), 99.5+%
  • 80% aq. acetic acid, 99.7+%
  • Cyclohexane, 99.5+%
  • Tetrahydrofuran, 99.5+%
  • Ammonia (NH 3), anhydrous, 99.99+%
  • 35% to 37% hydrochloric acid (conc. HCl)
  • 25% aq. ammonia (NH 3)
  • Ethyl acetate (EtOAc), 99.5+%
  • 500‐mL and 1‐L round‐bottom flasks
  • Reflux condensers
  • HPLC with Zorbax SB‐phenyl 4.6 × 250–mm column (Chrompack)
  • Rotary evaporator with vacuum pump and water aspirator
  • Separatory funnel
  • 60‐ and 40‐mm Kiriyama filter funnels (glass Büchner‐type funnel) with no. 5A and 5B filter papers
  • 50°C vacuum oven
  • 500‐mL four‐neck round‐bottom flasks
  • 1‐L stainless steel pressure vessel equipped with a pressure gauge
  • Water trap unit
  • Glass filter holder with PTFE membrane filter
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Literature Cited

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