Nucleoside H-Phosphonates, XXII: Synthesis and Properties of New Nucleotide Analogues - H-Phosphonothiolate Diesters

Abstract

Condensation of nucleoside 3′-H-phosphonate mono­esters with various thiols, promoted by condensing agents, provides a convenient access to a new class of H-phosphonate analogues, H-phosphonothiolate diesters. Chemical properties, relevant to possible applications of these compounds as a new type of synthetic ­intermediates in the preparation of nucleotide analogues bearing a sulfur atom at the bridging position of a phosphate group, were ­investigated.

H-phosphonates - H-phosphonothiolates - phosphate analogues - nucleotide analogues

References and Notes

<A NAME="RG24907ST-1">1</A> Wilson C. Keefe AD. Curr. Opin. Chem. Biol.  2006,  10:  607 

<A NAME="RG24907ST-2A">2a</A> Tuschl T. Thomson JB. Eckstein F. Curr. Opin. Struct. Biol.  1995,  5:  296 

<A NAME="RG24907ST-2B">2b</A> Eckstein F. Antisense Nucleic Acid Drug Dev.  2000,  10:  117 

<A NAME="RG24907ST-3">3</A> Eckstein F. Gish G. Trends Biochem. Sci.  1989,  14:  97 

<A NAME="RG24907ST-4">4</A> Beaton G. Brill WK.-D. Grandas A. Ma Y.-X. Nielsen J. Yau E. Caruthers M. Tetrahedron  1991,  47:  2377 

<A NAME="RG24907ST-5">5</A> Stawinski J. In Handbook of Organophosphorus Chemistry   Engel R. Marcel Dekker; New York: 1992.  p.377 

<A NAME="RG24907ST-6">6</A> Beaucage SL. Iyer RP. Tetrahedron  1993,  49:  10441 

<A NAME="RG24907ST-7">7</A> Horner L. J. Prakt. Chem.  1992,  334:  645 

<A NAME="RG24907ST-8">8</A> Åkerfeldt S. Acta Chem. Scand.  1959,  13:  1479 

<A NAME="RG24907ST-9">9</A> Åkerfeldt S. Acta Chem. Scand.  1962,  16:  1897 

<A NAME="RG24907ST-10">10</A> Xu Y. Kool ET. Nucleic Acids Res.  1998,  26:  3159 

<A NAME="RG24907ST-11A">11a</A> Cosstick R. Vyle JS. J. Chem. Soc., Chem. Commun.  1988,  992 

<A NAME="RG24907ST-11B">11b</A> Cosstick R. Vyle JS. Nucleic Acids Res.  1990,  18:  829 

<A NAME="RG24907ST-11C">11c</A> Mag M. Lüking S. Engels JW. Nucleic Acids Res.  1991,  19:  1437 

<A NAME="RG24907ST-12A">12a</A> Garegg PJ. Regberg T. Stawinski J. Strömberg R. J. Chem. Soc., Perkin Trans. 1  1987,  1269 

<A NAME="RG24907ST-12B">12b</A> Liu XH. Reese CB. Tetrahedron Lett.  1995,  36:  3413 

<A NAME="RG24907ST-12C">12c</A> Weinstein LB. Earnshaw DJ. Cosstick R. Cech TR. J. Am. Chem. Soc.  1996,  118:  10341 

<A NAME="RG24907ST-13">13</A> Cook AF. J. Am. Chem. Soc.  1970,  92:  190 

<A NAME="RG24907ST-14">14</A> Beevers APG. Fettes KJ. O’Neil IA. Roberts SM. Arnold JRP. Cosstick R. Fisher J. Chem. Commun.  2002,  1458 

<A NAME="RG24907ST-15">15</A> Cook AF. Holman MJ. Nussbaum AL. J. Am. Chem. Soc.  1969,  91:  6479 

<A NAME="RG24907ST-16">16</A> Åkerfeldt S. Fagerlind L. J. Med. Chem.  1967,  10:  115 

<A NAME="RG24907ST-17">17</A> Padmanabhan S. Coughlin JE. Zhang GR. Kirk CJ. Iyer RP. Bioorg. Med. Chem. Lett.  2006,  16:  1491 

<A NAME="RG24907ST-18A">18a</A> Kuimelis RG. Mclaughlin LW. J. Am. Chem. Soc.  1995,  117:  11019 

<A NAME="RG24907ST-18B">18b</A> Kuimelis RG. McLaughlin LW. Nucleic Acids Res.  1995,  23:  4753 

<A NAME="RG24907ST-18C">18c</A> Kuimelis RG. McLaughlin LW. Biochemistry  1996,  35:  5308 

<A NAME="RG24907ST-19A">19a</A> Stawinski J. Kraszewski A. Acc. Chem. Res.  2002,  35:  952 

<A NAME="RG24907ST-19B">19b</A> Kraszewski A. Stawinski J. Trends Org. Chem.  2003,  10:  1 

<A NAME="RG24907ST-20A">20a</A> Stawinski J. Zain R. Nucleosides Nucleotides  1995,  14:  711 

<A NAME="RG24907ST-20B">20b</A> Cieslak J. Jankowska J. Sobkowski M. Kers A. Kers I. Stawinski J. Kraszewski A. Collect. Symp. Ser.  1999,  2:  63 

<A NAME="RG24907ST-21">21</A> Cieslak J. Jankowska J. Stawinski J. Kraszewski A. J. Org. Chem.  2000,  65:  7049 

<A NAME="RG24907ST-22">22</A>

Compound 3 was obtained on independent way by reacting H-phosphonothiolate 2a with pivaloyl chloride in MeCN-pyridine (4:1). The signals of two P-diastereomers were not resolved in the ³¹P NMR spectrum.

<A NAME="RG24907ST-23">23</A>

Ethyl H-phosphonate reacted with ethanethiol analogously to that of 1, producing compound of type 4 (R = Et) that resonated at δ _P = 157.8 ppm (³ J _PH = 9.4 Hz, hept). This compound was prepared independently by reacting ethyl phosphorodichloridite with 2 equiv of ethanethiol in MeCN-pyridine (4:1).

<A NAME="RG24907ST-24">24</A> Comparison with original sample obtained by reaction of 1 with phenol in the presence of pivaloyl chloride, followed by the addition of n-butylamine. See: Kers A. Stawinski J. Kraszewski A. Tetrahedron  1999,  55:  11579 

<A NAME="RG24907ST-25">25</A>

Comparison with original sample obtained by condensation of 1 with ethanol in the presence of pivaloyl chloride. The P-diastereomers were not resolved.

<A NAME="RG24907ST-26">26</A> Atherton FR. Openshaw HT. Todd AR. J. Chem. Soc.  1945,  660 

<A NAME="RG24907ST-27">27</A> Sekine M. Satoh M. Yamagata H. Hata T. J. Org. Chem.  1980,  45:  4162 

<A NAME="RG24907ST-28">28</A>

General Procedure for Synthesis and Oxidative Transformations of H-Phosphonothiolates 2a-d Nucleoside H-phosphonate monoester 1 (0.15 mmol) was rendered anhydrous by evaporation of added pyridine, and the residue was dissolved in MeCN-pyridine (4:1; 2 mL) or in CH₂Cl₂-pyridine (4:1; 2 mL, for thiols c and d). To this solution, the appropriate thiol a-d (2 equiv) and a condensing agent (diphenyl phosphorochloridate; 1 equiv) were added. The reactions were complete within 5 min (³¹P NMR analysis) producing the expected nucleoside H-phosphonothiolates 2.
^³¹ P NMR Data for Compounds 2
Compound 2a: δ = 33.75 and 34.08 ppm (¹ J _PH = 658.2 Hz, ³ J _PH = 11.1 Hz, dq); 2b: δ = 33.96 and 34.23 ppm (¹ J _PH = 659.9 Hz, ³ J _PH = 10.7 Hz, dq); 2c: δ = 32.66 and 32.79 ppm (¹ J _PH = 672.2 Hz, ³ J _PH = 10.7 Hz, dq); 2d: δ = 33.01 and 33.37 ppm (¹ J _PH = 652.0 Hz, ³ J _PH = 11.4 Hz, dt).
To the solution containing 2a-d, a mixture of CCl₄ (10 equiv), H₂O (50 equiv), and Et₃N (2 equiv) was added. The reactions were complete within 5 min (³¹P NMR analyses), producing quantitatively the corresponding phosphorothiolates 7a-d, that were isolated by silica gel column chromatography (purity >98%, ¹H NMR).
^³¹ P NMR Data for Compounds 7 Compound 7a (82%): δ = 18.76 ppm (³ J _PH = 11.1 Hz, q); 7b (72%): δ = 18.99 ppm (³ J _PH = 11.1 Hz, q); 7c (64%): δ = 16.64 ppm (³ J _PH = 10.2 Hz, q); 7d (56%): δ = 19.86 ppm (³ J _PH = 10.1 Hz, t).
Sulfurization of the in situ generated H-phosphonothiolates 2a-d was performed by the addition of elemental sulfur (3 equiv) and Et₃N (2 equiv) to the corresponding reaction mixtures. The reactions were complete within 5 min (³¹P NMR analyses), affording quantitatively the corresponding phosphorodithioates 8a-d, that were isolated by silica gel column chromatography (purity >98%, ¹H NMR).


^³¹ P NMR Data for Compounds 8 Compound 8a (67%): δ = 74.22 and 75.26 ppm (³ J _PH = 12.6 Hz, q); 8b (61%): δ = 74.39 and 75.26 ppm (³ J _PH = 12.7 Hz, q); 8c (65%): δ = 73.85 and 74.17 ppm (³ J _PH = 12.6 Hz, q); 8d (59%): δ = 74.54 and 76.35 ppm (³ J _PH = 12.9 Hz, t).

<A NAME="RG24907ST-29A">29a</A> Gallagher MJ. Garbutt R. Liu YH. Gum HL. Phosphorus, Sulfur Silicon Relat. Elem.  1993,  75:  201 

<A NAME="RG24907ST-29B">29b</A> Kers A. Kers I. Stawinski J. Sobkowski M. Kraszewski A. Tetrahedron  1996,  52:  9931 

<A NAME="RG24907ST-30">30</A> Cieslak J. Szymczak M. Wenska M. Stawinski J. Kraszewski A. J. Chem. Soc., Perkin Trans. 1  1999,  3327 

<A NAME="RG24907ST-31A">31a</A> Stawinski J. Strömberg R. In Current Protocols in Nucleic Acid Chemistry   Beaucage SL. Bergstrom DE. Glick GD. Jones RA. John Wiley and Sons, Inc.; New York: 2001.  Chap. 2.6.1.

<A NAME="RG24907ST-31B">31b</A> Stawinski J. Strömberg R. In Oligonucleotide Synthesis: Methods and Applications   Vol. 288:  Herdewijn P. Humana Press; Totowa NJ: 2004.  p.81