Palladium‐Catalyzed Cross‐Coupling Reactions in C6 Modifications of Purine Nucleosides

Michal Hocek1, Peter Šilhár1

1 Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 1.16
DOI:  10.1002/0471142700.nc0116s28
Online Posting Date:  March, 2007
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Abstract

This unit describes the cross‐coupling methodology for introduction of diverse C‐substituents to position 6 of purine nucleosides. Protected 6‐chloropurine nucleosides undergo Pd‐catalyzed cross‐coupling reactions with trialkylaluminium, alkylzinc halides, aryl(tributyl)stannanes, and arylboronic acids to give the corresponding 6‐substituted intermediates, which can be deprotected by treatment with NaOMe. (Acetyloxy)methylzinc iodide is used for introduction of the hydroxymethyl group, which can further be transformed to fluoromethyl and difluoromethyl groups. Most of the title 6‐substituted purine ribonucleosides possess cytostatic and/or anti‐HCV activity.

Keywords: purines; nucleosides; cross‐coupling reactions; palladium

     
 
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Table of Contents

  • Basic Protocol 1: Cross‐Coupling of an Acetyl‐Protected 6‐Chloropurine Nucleoside
  • Basic Protocol 2: Cross‐Coupling of a Toluoyl‐Protected 6‐Chloropurine Nucleoside
  • Support Protocol 1: Preparation of (Acetyloxymethyl)Zinc Iodide
  • Basic Protocol 3: Preparation of 6‐(Fluoromethyl)Purine
  • Basic Protocol 4: Preparation Of 6‐(Difluoromethyl)Purine
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

Basic Protocol 1: Cross‐Coupling of an Acetyl‐Protected 6‐Chloropurine Nucleoside

  Materials
  • 6‐Chloro‐9‐(2,3,5‐tri‐O‐acetyl‐β‐D‐ribofuranosyl)purine (S.1; Buck and Reese, )
  • Cross‐coupling reagent (Sigma‐Aldrich):
    • Phenylboronic acid
    • 2‐(Tributylstannyl)thiophene
    • Trimethylaluminium (AlMe 3, 2 M solution in toluene)
    • Benzylzinc chloride (1 M solution in THF)
  • Potassium carbonate (K 2CO 3, anhydrous, Sigma‐Aldrich)
  • Palladium catalyst (Sigma‐Aldrich):
    • Tetrakis(triphenylphosphine)palladium (Pd(PPh 3) 4)
    • Bis(triphenylphosphine)palladium dichloride (PdCl 2(PPh 3) 2)
  • Argon
  • Toluene (dried, degassed, and flushed with argon)
  • Ethyl acetate
  • N,N‐Dimethylformamide (DMF, anhydrous under argon, Sigma‐Aldrich)
  • Tetrahydrofuran (THF, anhydrous, freshly distilled from Na/benzophenone under argon)
  • Ammonium chloride (NH 4Cl)
  • Anhydrous magnesium sulfate (MgSO 4)
  • Silica gel (200 to 400 mesh)
  • Hexanes
  • Chloroform
  • Anhydrous methanol
  • 1 M sodium methoxide (NaOMe) in methanol
  • Heptane
  • 50‐, 100‐, and 250‐mL round‐bottom flasks with 14/20 joints, flame dried
  • Rubber septa
  • 21‐G needles
  • Vacuum system (oil pump with manifold and cold trap)
  • Oil bath
  • Glass frit (10‐ to 20‐µm)
  • Rotary evaporator (Büchi) equipped with a vacuum system (membrane pump Vacuubrand)
  • Glass columns (3.5‐cm i.d., 40‐cm length)
  • Silica gel 60 F 254 aluminium TLC sheets (Merck)
  • UV lamp and heat gun
  • Vacuum pump
  • Additional reagents and equipment for column chromatography ( appendix 3E) and TLC ( appendix 3D)

Basic Protocol 2: Cross‐Coupling of a Toluoyl‐Protected 6‐Chloropurine Nucleoside

  Materials
  • 6‐Chloro‐9‐[2,3,5‐tri‐O‐(p‐toluoyl)‐β‐D‐ribofuranosyl]purine S.10 (Šilhár et al., )
  • Tetrakis(triphenylphosphine)palladium (Pd(PPh 3) 4)
  • Argon
  • Tetrahydrofuran (THF, anhydrous, freshly distilled from Na/benzophenone under argon)
  • 1 M (acetyloxymethyl)zinc iodide in THF (S.11, see protocol 3)
  • 1 M NaH 2PO 4
  • Chloroform
  • Anhydrous magnesium sulfate (MgSO 4)
  • Silica gel (200 to 400 mesh)
  • Hexanes
  • Ethyl acetate
  • Dichloromethane
  • Ethanol
  • Zinc chloride
  • Anhydrous methanol
  • 25%wt. aq. ammonia
  • 1 M sodium methoxide (NaOMe) in methanol
  • 25‐ and 250‐mL round‐bottom flasks with 14/20 joints, flame dried
  • Rubber septum
  • Vacuum system (oil pump with manifold and cold trap)
  • 21‐G needle
  • Rotary evaporator (Büchi) equipped with a vacuum system (membrane pump Vacuubrand)
  • Glass columns (3‐cm i.d., 20‐cm length)
  • Silica gel 60 F 254 aluminium TLC sheets (Merck)
  • UV lamp and heat gun
  • Vacuum pump
  • Additional reagents and equipment for column chromatography ( appendix 3E) and TLC ( appendix 3D)

Support Protocol 1: Preparation of (Acetyloxymethyl)Zinc Iodide

  Materials
  • Paraformaldehyde (Sigma‐Aldrich)
  • Zinc chloride (ZnCl 2, Sigma‐Aldrich)
  • Dichloromethane
  • Acetyl chloride (AcCl; Sigma‐Aldrich)
  • Sodium iodide (NaI; Sigma‐Aldrich)
  • Argon
  • Dry acetone
  • Hexanes
  • Zinc dust (Sigma‐Aldrich)
  • Dry tetrahydrofuran (THF)
  • 1,2‐Dibromoethane (Sigma‐Aldrich)
  • Chlorotrimethylsilane (Sigma‐Aldrich)
  • Iodomethyl acetate
  • 25‐mL, 250‐mL, and 1‐L round‐bottom flasks, flame dried
  • Reflux condenser
  • Dropping funnel with a by‐pass
  • Vacuum system (oil pump with manifold and cold trap)
  • Distillation head
  • Vacuum pump
  • Glass frit
  • Rotary evaporator (Büchi) equipped with a vacuum system (membrane pump Vacuubrand)
  • Rubber septum
  • 21‐G needles

Basic Protocol 3: Preparation of 6‐(Fluoromethyl)Purine

  Materials
  • 6‐(Hydroxymethyl)purine (S.13; see protocol 2)
  • Argon
  • Dry dichloromethane
  • Deoxo‐Fluor ([bis‐(2‐methoxyethyl)amino]sulfur trifluoride, Sigma‐Aldrich)
  • 5% aq. NaHCO 3
  • Chloroform
  • Anhydrous magnesium sulfate (MgSO 4)
  • Ethyl acetate
  • Methanol
  • 25‐mL round‐bottom flask
  • Rubber septum
  • 21‐G needles
  • Vacuum system (oil pump with manifold and cold trap)
  • Rotary evaporator (Büchi) equipped with a vacuum system (membrane pump Vacuubrand)
  • Additional reagents and equipment for deprotection and purification (see protocol 2)

Basic Protocol 4: Preparation Of 6‐(Difluoromethyl)Purine

  Materials
  • 6‐(Hydroxymethyl)purine (S.13; see protocol 2)
  • Dry dichloromethane
  • Dess‐Martin reagent [1,1,1‐Tris(acetyloxy)‐1,1‐dihydro‐1,2‐benziodoxol‐3‐(1H)‐one, Sigma‐Aldrich]
  • Saturated aq. NaHCO 3
  • Chloroform
  • Anhydrous magnesium sulfate (MgSO 4)
  • Silica gel (200 to 400 mesh)
  • Hexanes
  • Acetone
  • Argon
  • Deoxo‐Fluor ([bis‐(2‐methoxyethyl)amino]sulfur trifluoride, Sigma‐Aldrich)
  • Ethyl acetate
  • Methanol
  • 25‐, 50‐, and 250‐mL round‐bottom flasks
  • Vacuum system (oil pump with manifold and cold trap)
  • Rotary evaporator (Büchi) equipped with a vacuum system (membrane pump Vacuubrand)
  • 3 × 20–cm glass columns
  • Vacuum pump
  • TLC plates
  • Vacuum system (oil pump with manifold and cold trap)
  • 21‐G needles
  • Rubber septum
  • Additional reagents and equipment for column chromatography ( appendix 3E), TLC ( appendix 3D), and deprotection and purification (see protocol 2)
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Figures

Videos

Literature Cited

Literature Cited
   Buck, I.M. and Reese, C.B. 1990. An unambiguous synthesis of adenylosuccinic acid and its constituent nucleoside. J. Chem. Soc., Perkin Trans. 1, 2937‐2942.
   Hocek, M. 2003. Syntheses of purines bearing carbon substituents in positions 2, 6 or 8 by metal‐ or organometallics‐mediated C‐C bond forming reactions. Eur. J. Org. Chem. 245‐254.
   Hocek, M., Holý, A., Votruba, I., and Dvořáková, H. 2000. Synthesis and cytostatic activity of substituted 6‐phenylpurine bases and nucleosides: Application of the Suzuki‐Miyaura cross‐coupling reactions of 6‐chloropurine derivatives with phenylboronic acids. J. Med. Chem. 43:1817‐1825.
   Hocek, M., Holý, A., Votruba, I., and Dvořáková, H. 2001. Cytostatic 6‐arylpurine nucleosides III. Synthesis and structure‐activity relationship study in cytostatic activity of 6‐aryl‐, 6‐hetaryl‐ and 6‐benzylpurine ribonucleosides. Collect. Czech. Chem. Commun. 66:483‐499.
   Hocek, M., Nauš, P., Pohl, R., Votruba, I., Furman, P.A., Tharnish, P.M., and Otto, M.J. 2005. Cytostatic 6‐arylpurine nucleosides. 6. SAR in anti‐HCV and cytostatic activity of extended series of 6‐hetarylpurine ribonucleosides. J. Med. Chem. 48:5869‐5873.
   Hocek, M., Šilhár, P., Shih, I., Mabery, E., and Mackman, R. 2006. Cytostatic and antiviral 6‐arylpurine ribonucleosides. Part 7: Synthesis and evaluation of 6‐substituted purine L‐ribonucleosides. Bioorg. Med. Chem. Lett. 16:5290‐5293.
   Hocková, D., Hocek, M., Dvořáková, H., and Votruba, I. 1999. Synthesis and cytostatic activity of nucleosides and acyclic nucleoside analogues derived from 6‐(trifluoromethyl)purines. Tetrahedron 55:11109‐11118.
   Montgomery, J.A. and Hewson, K. 1968. Analogs of 6‐methyl‐9‐β‐D‐ribofuranosylpurine. J. Med. Chem. 11:48‐52.
   Parker, W.B., King, S.A., Allan, P.W., Bennett, L.L. Jr., Secrist, J.A. III, Montgomery, J.A., Gilbert, K.S., Waud, W.R., Wells, A.H., Gillespie, G.Y., and Sorscher, E.J. 1997. In vivo gene therapy of cancer with E. coli purine nucleoside phosphorylase. Hum. Gene Ther. 8:1637‐1644.
   Šilhár, P., Pohl, R., Votruba, I., and Hocek, M. 2004. Facile and efficient synthesis of 6‐(hydroxymethyl)purines. Org. Lett. 6:3225‐3228.
   Šilhár, P., Pohl, R., Votruba, I., and Hocek, M. 2005a. Synthesis of 2‐substituted 6‐(hydroxymethyl)purine bases and nucleosides. Collect. Czech. Chem. Commun. 70:1669‐1695.
   Šilhár, P., Pohl, R., Votruba, I., and Hocek, M. 2005b. The first synthesis and cytostatic activity of novel 6‐(fluoromethyl)purine bases and nucleosides. Org. Biomol. Chem. 3:3001‐3007.
   Šilhár, P., Pohl, R., Votruba, I., and Hocek, M. 2006. Synthesis and cytostatic activity of novel 6‐(difluoromethyl)purine bases and nucleosides. Synthesis 1848‐1852.
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