Synthesis of β‐L‐2′‐Deoxythymidine (L‐dT)

Claire Pierra1, David Dukhan1, Gilles Gosselin1, Jean‐Pierre Sommadossi2

1 Université Montpellier II, Montpellier, 2 Idenix Pharmaceuticals, Inc., Cambridge, Massachusetts
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 14.3
DOI:  10.1002/0471142700.nc1403s24
Online Posting Date:  April, 2006
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The “unnatural” l‐nucleoside β‐l‐2′‐deoxythymidine (L‐dT) is a potent, specific, and selective inhibitor of the replication of hepatitis B virus (HBV), which is currently in Phase III clinical trials. This unit describes, in detail, a semi‐large‐scale synthesis of l‐dT. This convenient methodology produces l‐dT in six steps starting with l‐ribose and ending with a satisfactory overall yield of l‐dT, and may be applied to other 2′‐deoxynucleosides, incorporating different heterocyclic bases.

Keywords: anti‐HBV agent; semi‐large‐scale synthesis; l‐dT; l‐nucleosides; deoxygenation reaction

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Table of Contents

  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
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Basic Protocol 1:

  • Argon gas source
  • L‐Ribose (S.1; Interchim), dried over phosphorous pentoxide (P 2O 5)
  • Methanol and anhydrous methanol
  • 96% (v/v) sulfuric acid (H 2SO 4) in water
  • Chloroform and anhydrous chloroform
  • 10% (v/v) sulfuric acid (H 2SO 4) in 95% ethanol
  • Pyridine and dry pyridine
  • Benzoyl chloride, anhydrous (BzCl)
  • Dichloromethane (CH 2Cl 2)
  • Saturated aqueous sodium bicarbonate (aq. NaHCO 3)
  • Sodium sulfate, anhydrous (Na 2SO 4)
  • Toluene
  • Acetic acid (AcOH)
  • Acetic anhydride (Ac 2O)
  • Petroleum ether
  • Diethyl ether
  • Ethyl acetate (EtOAc)
  • 95% ethanol (EtOH)
  • Thymine
  • Ammonium sulfate [(NH 4) 2SO 4]
  • Hexamethyldisilazane (HMDS)
  • 1,2‐Dichloroethane, dry
  • Trimethylsilyl trifluoromethanesulfonate (TMSOTf)
  • Silica gel (Merck 60H)
  • Sand
  • Methanol saturated with ammonia (MeOH/NH 3, see recipe)
  • 1,3‐Dichloro‐1,1,3,3‐tetraisopropyldisiloxane (TIPSCl 2)
  • Acetonitrile, anhydrous
  • 4‐Dimethylaminopyridine (DMAP)
  • O‐Phenyl chlorothionoformate [PhOC(S)Cl]
  • 0.5 N hydrochloric acid (HCl) in water
  • Dioxane, dry
  • α,α′‐Azoisobutyronitrile (AIBN)
  • Tris(trimethylsilyl)silane (TTMSS)
  • Ammonium fluoride (NH 4F)
  • Absolute ethanol
  • 250‐, 500‐, 1000‐, and 2000‐mL round‐bottom flasks, oven dried
  • Magnetic stirrer and stir bars
  • Silica gel thin‐layer chromatography (TLC) plates (Merck, Kieselgel 60 F 254, 0.2‐mm thickness)
  • Heat gun
  • Rotary evaporator equipped with a vacuum pump
  • 200‐mL dropping funnels
  • 1‐, 2‐, and 3‐L separatory funnels
  • 500‐ and 1000‐mL Erlenmeyer flasks
  • Filter funnel
  • Vacuum desiccator with P 2O 5
  • 80° and 100°C oil baths
  • Reflux condensers
  • Glass chromatography columns: 8 × 50–cm, 6 × 30–cm, 7 × 15–cm
  • Steel cylinder
  • Splash head
  • Additional reagents and equipment for TLC ( appendix 3D) and column chromatography ( appendix 3E)
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Literature Cited

Literature Cited
   Bryant, M.L., Bridges, E.G., Placidi, L., Faraj, A., Loi, A.‐G., Pierra, C., Dukhan, D., Gosselin, G., Imbach, J.‐L., Hernandez, B., Juodawlkis, A., Tennant, B., Korba, B., Cote, P., Marion, P., Cretton‐Scott, E., Schinazi, R., and Sommadossi, J.‐P. 2001. Antiviral L‐nucleosides specific for Hepatitis B Virus infection. Antimicrob. Agents Chemother. 45:229‐235.
   Cimpoa, A.R., Hunter, P.J., and Evans, C.A. 1994. On the conversion of the arabino‐ and ribofuranosyl methyl glycosides to their 1‐O‐acetyl derivatives. J. Carbohydr. Chem. 13:1115‐1119.
   Gosselin, G., Pierra, C., Benzaria, S., Dukhan, D., Imbach, J.L., Loi, A.‐G., La Colla, P., Cretton‐Scott, E., Bridges, E.G., Standring, D.N., and Sommadossi, J.P. 2004. β‐L‐2′‐Deoxythymidine (L‐dT) and β‐L‐2′‐deoxycytidine (L‐dC): How simple structures can be potent, selective and specific anti‐HBV drugs. In Frontiers in Nucleosides and Nucleic Acids (R.F. Schinazi and D.C. Liotta, eds.), pp. 309‐317. IHL Press, Tucker, Georgia.
   Graciet, J.C.G. and Schinazi, R.F. 1999. From D‐ to L‐nucleoside analogs as antiviral agents. Adv. Antivir. Drug Design 3:1‐68.
   Gumina, G., Chong, Y., Choo, H., Song, G.‐Y., and Chu, C.K. 2002. L‐Nucleosides: Antiviral activity and molecular mechanism. Curr. Top. Med. Chem. 2:1065‐1086.
   Han, S.‐T.B. 2005. Telbivudine: A new nucleoside analogue for the treatment of chronic hepatitis B. Expert Opin. Investig. Drugs 14:511‐519.
   Holý, A. 1972. Nucleic acid components and their analogues. CLIII. Preparation of 2′‐deoxy‐L‐ribonucleosides of the pyrimidine series. Collect. Czech. Chem. Commun. 37:4072‐4087.
   Recondo, E.F. and Rinderknecht, H. 1959. Eine neue, einfache synthese des 1‐O‐acetyl‐2,3,5‐tri‐O‐β‐D‐ribofuranosides. Helv. Chim. Acta 42:1171‐1173.
   Smejkal, J. and Sorm, F. 1964. Nucleic acids components and their analogues. LIII. Preparation of 1‐2′‐deoxy‐β‐L‐ribofuranosylthymine, “L‐thymine”. Collect. Czech. Chem. Commun. 29:2809‐2813.
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