Deoxythreosyl phosphonate nucleosides as selective anti-HIV agents

Article abstract of DOI:10.1021/ja043045z

Out of a series of eight new phosphonate nucleosides with an L-threose and an L-2-deoxythreose sugar moiety, two new compounds were identified (PMDTA and PMDTT) that showed potent anti-HIV-1 (HIV-2) activity [EC₅₀ = 2.53 μM (PMDTA) and 6.59 μM (PMDTT)], while no cytoxicity was observed at the highest concentration tested [CC₅₀ > 316 μM (PMDTA) and > 343 μM (PMDTT)]. The kinetics of incorporation of PMDTA into DNA (using the diphosphate of PMDTA as substrate and HIV-1 reverse transcriptase as catalyst) was similar to the kinetics observed for dATP, while the diphosphate of PMDTA was a very poor substrate for DNA polymerase α. The incorporated PMDTA fits very well in the active site pocket of HIV-1 reverse transcriptase.

Full text of DOI:10.1021/ja043045z

Published on Web 03/19/2005
Deoxythreosyl Phosphonate Nucleosides as Selective
Anti-HIV Agents
Tongfei Wu,† Matheus Froeyen,† Veerle Kempeneers,† Christophe Pannecouque,‡
Jing Wang,† Roger Busson,† Erik De Clercq,‡ and Piet Herdewijn*,†
Contribution from the Laboratories of Medicinal Chemistry and Virology,
Rega Institute for Medical Research, Minderbroedersstraat 10, LeuVen, Belgium
Received November 18, 2004; E-mail: Piet.Herdewijn@rega.kuleuven.ac.be
Abstract: Out of a series of eight new phosphonate nucleosides with an L-threose and an L-2-deoxythreose
sugar moiety, two new compounds were identified (PMDTA and PMDTT) that showed potent anti-HIV-1
(HIV-2) activity [EC50 ) 2.53 µM (PMDTA) and 6.59 µM (PMDTT)], while no cytoxicity was observed at the
highest concentration tested [CC50 > 316 µM (PMDTA) and > 343 µM (PMDTT)]. The kinetics of
incorporation of PMDTA into DNA (using the diphosphate of PMDTA as substrate and HIV-1 reverse
transcriptase as catalyst) was similar to the kinetics observed for dATP, while the diphosphate of PMDTA
was a very poor substrate for DNA polymerase R. The incorporated PMDTA fits very well in the active site
pocket of HIV-1 reverse transcriptase.
Introduction
Pioneering work on the chemistry of phosphonate nucleosides
has been carried out by A. Burger,1,2 while the work of D.
Rammler,3,4 A. Holy´,5 and J. Moffatt6 has led to important new
reaction schemes to synthesize phosphonate nucleosides. This
research has opened the way to biological applications of
phosphonate nucleosides.
A first category of phosphonate nucleosides (1; Figure 1) are
real nucleoside analogues as they contain a nucleobase and a
sugar moiety.3-6 A second series of phosphonate nucleosides
represented by PMEA (2a; Figure 1) and PMPA (2b; Figure 1)
can better be considered as alkylated nucleobases as the sugar
moiety is replaced by an alkoxyalkyl moiety.7
Up to now, potent antiviral activity (HSV, CMV, HBV, HIV)
has been associated with phosphonoalkoxyalkyl nucleobases and
exceptionally with sugar containing phosphonate nucleosides.
Several attempts to discover antiviral nucleoside phosphonates
† Laboratory of Medicinal Chemistry.
Figure 1. Structure of a phosphonate nucleoside 1, phosphonomethoxy-
ethyladenine (PMEA) and phosphonylmethoxypropyladenine (PMPA) 2,
threosyl nucleoside phosphonates 3, and phosphonomethoxydihydrofuranyl
nucleosides 4.
‡ Laboratory of Virology.
(1) Parikh, J. R.; Wolff, M. E.; Burger, A. J. Am. Chem. Soc. 1957, 79, 2778-
2781.
(2) Wolff, M. E.; Burger, A. J. Am. Pharm. Assoc. 1959, 48, 56-59.
(3) Yengoyan, L.; Rammler, D. H. Biochemistry 1966, 5, 3629-3638.
(4) Rammler, D. H.; Yengoyan, L.; Paul, A. V.; Bax, P. C. Biochemistry 1967,
6, 1828-1837.
have led to synthetic schemes for the preparation of furanose,8
pyranose,9 and carbocyclic phosphonate nucleosides,10 lacking,
however, potent antiviral activity. Exceptions are the isosteric
d4T and d4A analogues11 and a 3,4-disubstituted tetrahydrofuran
derived cytosine nucleoside. These compounds do not have a
4′-hydroxymethyl substituent (as in regular nucleosides), and
the phosphonoalkoxy moiety is connected directly to the five-
membered ring.
(5) Holy´, A. Tetrahedron Lett. 1967, 10, 881-884.
(6) Jones, G. H.; Moffatt, J. G. J. Am. Chem. Soc. 1968, 90, 5337-5338.
(7) Holy´, A.; Votruba, I.; Merta, A.; Cerny, J.; Vesely, J.; Vlach, J.; Sediva,
K.; Rosenberg, I.; Otmar, M.; Hrebabecky, H.; Tra´vn´ıekb, M.; Vonkac,
V.; Snoeck, R.; De Clercq, E. Antibiral Res. 1990, 13, 295-311.
(8) See, for example: (a) Montgomery, J. A.; Hewson, K. Chem. Commun.
1969, 15-16. (b) Hampton, A.; Perini, F.; Harper, P.-J. Biochemistry 1973,
12, 1730-1736. (c) Fuertes, M.; Witkowski, J. T.; Streeter, D. G.; Robins,
R. K. J. Med. Chem. 1974, 17, 642-645. (d) Hol’y, A.; Rosenberg, I.
Collect. Czech Chem. Commun. 1982, 47, 3447-3463. (e) Morr, M.; Ernst,
L.; Grotjahn, L. Z. Naturforsch. 1983, 38B, 1665-1668. (f) Hollmann, H.;
Schlimme, E. Liebigs Ann. Chem. 1984, 98-107. (g) Barton, D. H. R.;
Ge´ro, S. D.; Quiclet-Sire, B.; Samadi, M. J. Chem. Soc., Chem. Commun.
1989, 1000-1001. (h) Liu, J.; Van Aerschot, A.; Balzarini, J.; Janssen,
G.; Busson, R.; Hoogmartens, J.; De Clercq, E.; Herdewijn, P. J. Med.
Chem. 1990, 33, 2481-2487.
(9) (a) Pe´rez-Pe´rez, M.-J.; Rozenski, J.; Herdewijn, P. Bioorg. Med. Chem.
Lett. 1994, 4, 1199-1202. (b) Pe´rez-Pe´rez, M.-J.; Doboszewski, B.;
Rozenski, J.; Herdewijn, P. Tetrahedron: Asymmetry 1995, 6, 973-
984.
9
5056
J. AM. CHEM. SOC. 2005, 127, 5056-5065
10.1021/ja043045z CCC: $30.25 © 2005 American Chemical Society

Anti-HIV Phosphonate Nucleosides
A R T I C L E S
Phosphorylation by kinases and incorporation into nucleic
acids (eventually leading to chain termination) is considered as
an important mechanism to explain the antiviral activity of
nucleosides. The lack of antiviral activity of nucleoside phos-
phonates is generally explained by their poor substrate properties
for cellular and viral kinases. On the other hand, the potent
antiviral activity of phosphonylated alkylated nucleobases is
ascribed to their intracellular phosphorylation to their diphos-
phates and to a refractory incorporation of the modified
nucleosides in nucleic acids.12 The enzymatic incorporation of
phosphonate nucleosides in nucleic acids is almost irreversible,
which is not so for regular nucleotides. A disadvantage of the
acyclic nucleoside phosphonates is their low selectivity index
in cellular screening systems.7,13 However, this drawback is
compensated by their long half-life in the cell, resulting in a
once a day (or even once a week) treatment schedule at low
drug concentrations. The selectivity for HIV reverse transcriptase
versus mitochondrial DNA polymerases of the triphosphates of
anti-HIV nucleosides is an important factor determining in vivo
toxicity.14 In search for potent and selective anti-HIV nucleoside
phosphonates, we decided to synthesize and evaluate nucleosides
with a threose sugar moiety and a phosphonalkoxy substituent
(3a-h).
Threose nucleosides have been previously synthesized be-
cause they can be assembled from natural precursor molecules.15
It has been demonstrated that threose nucleic acids (TNA) form
duplexes with DNA and RNA of thermal stability, similar to
that of the natural nucleic acid association.15 Triphosphates of
threose nucleosides are accepted as substrates by several
polymerases, and they can be enzymatically incorporated into
DNA.16,17 These nucleosides are accepted as substitutes for
ribonucleosides in the catalytic site of a hammerhead ribozyme,
although the catalytic efficiency of the ribozyme is significantly
reduced.18
sis), and the absence of a hydroxymethyl substituent in the 4′-
position of the proposed molecules 3a-h (Figure 1) may avoid
steric hindrance during enzymatic phosphorylation reaction (to
obtain the diphosphate). The structure of the proposed com-
pounds resembles somewhat the structure of the 5-phospho-
nomethoxy-2,5-dihydrofuranyl nucleosides 4a and 4b (Figure
1), previously synthesized by Kim et al.,11 and of the apiose
family of nucleoside analogues.19
Here, we describe the synthesis and selective anti-HIV activity
of two series of threosyl nucleoside phosphonates, abbreviated
as PMT (phosphonomethoxythreosyl) and PMDT (phospho-
nomethoxydeoxythreosyl), with an adenine, a thymine, a uracil,
and a cytosine base moiety.
Chemistry
The nucleosides 3a-h were synthesized starting from (R,S)-
2,3-dihydroxy-dihydrofuran-1-one (5) (Scheme 1).15 The hy-
droxyl group at C-2 of compound 5 can be selectively protected
with a TBDMS group. The free hydroxyl group of 6 is then
protected by benzoylation, and the lactone is reduced to the
hemiketal using Dibal-H in THF. The anomeric hydroxyl group
is protected with a TBDMS group, and the O-benzoyl group is
removed with ammonia in methanol. At the stage of 9, the
phosphonate function is introduced using the triflate of diiso-
propylphosphonomethyl alcohol and NaH in THF. The two silyl
protecting groups of 10 are removed and replaced by benzoyl
protecting groups. The presence of a 2-O-benzoyl group allows
selective introduction of the base moiety in the R-configuration.
The nucleobases uracil, thymine, and N4-acetylcytosine are
introduced after silylation and using SnCl4 as Lewis catalyst.
Deprotection of 12-15 is done in two steps, first, removal of
the benzoyl protecting groups with ammonia in methanol
(yielding 16-19) and, second, hydrolysis of the diisopropyl
protecting groups with (TMS)Br at room temperature (giving
3a-d). To obtain the 2′-deoxygenated analogues, the 2′-OH
group of 16-18 is removed by Barton deoxygenation,20,21 giving
20-22. Compound 23 is obtained from 22. Hydrolysis of the
phosphonate ester function of 20 was carried out with (TMS)-
Br at room temperature. However, for compounds 21-23,
(TMS)Br rapidly cleaved the nucleobase from the sugar even
at 0 °C. For this reason, (TMS)I was used for hydrolysis of the
diisopropyl esters of 21-23. After purification by silica gel
chromatography, Sephadex-DEAE A-25 resin and Dowex-
sodium ion-exchange resin, nucleoside phosphonate acids 3e-h
were obtained.
The phosphonoalkoxy group of the proposed threose nucleo-
side phosphonates 3a-h (Figure 1) is bound at the 3′-position,
bringing the phosphorus atom and the nucleobase closer to each
other than in previously synthesized nucleoside phosphonates
where the phosphonate group is bound to the primary hydroxyl
group of the nucleoside.8h The presence of an anomeric center
in threose nucleoside phosphonates gives them stereoelectronic
properties similar to those of natural nucleosides. The phos-
phonate group is stable against enzymatic degradation (hydroly-
(10) See, for example: (a) Wollf-Kugel, D.; Halazy, S. Tetrahedron Lett. 1991,
32, 6341-6344. (b) Bronson, J. J.; Ferrara, L. M.; Martin, J. C.; Mansuri,
M. M. Bioorg. Med. Chem. Lett. 1992, 2, 685-690. (c) Ja¨hne, G.; Mu¨ller,
A.; Kroha, H.; Ro¨sner, M.; Holzha¨user, O.; Meichsner, C.; Helsberg, M.;
Winkler, I.; Riess, G. Tetrahedron Lett. 1992, 33, 5335-5338. (d) Coe,
D. M.; Garofalo, A.; Roberts, S. M.; Storer, R.; Thorpe, A. J. J. Chem.
Soc., Perkin Trans. 1 1994, 3061-3063. (e) Pe´rez-Pe´rez, M. J.; Rozenski,
J.; Busson, R.; Herdewijn, P. J. Org. Chem. 1995, 60, 1531-1537. (f)
Liboska, R.; Masojidkova, M.; Rosenberg, I. Collect. Czech. Chem.
Commun. 1996, 61, 313-332.
The most active congener 3e was converted to its diphosphate
24 to be able to study its interaction with reverse transcriptase
and DNA polymerase R. Therefore, the amino group of PMDTA
(3e, as triethylammonium salt) was protected with a dimethyl-
aminomethylene group, and the free hydroxyl group was reacted
with pyrophosphate in the presence of carbonyldiimidazole
(Scheme 2). Deprotection with ammonia yielded the diphosphate
24, which was isolated by ion-exchange chromatography and
reversed-phase HPLC.
(11) Kim, C. U.; Luh, B. Y.; Martin, J. C. J. Org. Chem. 1991, 56, 2642-
2647.
(12) Wang, W.; Jin, H.; Fuselli, N.; Mansour, T. S. Bioorg. Med. Chem. Lett.
1997, 7, 2567-2572.
(13) For a review on the chemistry and biology of isopolar phosphorus-modified
nucleotide analogues, see: Holy´, A. In AdVances in AntiViral Drug Design;
De Clercq, E., Ed.; JAI Press: London, 1993; Vol. 1, pp 179-231.
(14) Lee, H.; Hanes, J.; Johnson, K. A. Biochemistry 2003, 42, 14711-14719.
(15) Scho¨ning, K.-U.; Scholz, P.; Guntha, S.; WU, X.; Krishnamurthy, R.;
Eschenmoser, A. Science 2000, 290, 1347-1351.
(19) Nair, V.; Jahnke, S. T. AntiViral Chem. Chemother. 1995, 39, 1017-
(16) Kempeneers, V.; Vastmans, K.; Rozenski, J.; Herdewijn, P. Nucleic Acids
Res. 2003, 31, 6221-6226.
(17) Chaput, J. C.; Szostack, J. W. J. Am. Chem. Soc. 2003, 125, 9274-9275.
(18) Kempeneers, V.; Froeyen, M.; Vastmans, K.; Herdewijn, P. Chem.
BiodiVersity 2004, 1, 112-123.
1029.
(20) Barton, D. H.; Subramanian, R. J. Chem. Soc., Perkin Trans. 1 1977, 15,
1718-1723.
(21) Barton, D. H.; McCombie, S. W. J. Chem. Soc., Perkin Trans. 1 1975,
1574-1585.
9
J. AM. CHEM. SOC. VOL. 127, NO. 14, 2005 5057

A R T I C L E S
Scheme 1 a
Wu et al.
a Conditions and reagents: (a) (TBDMS)Cl, imidazole, MeCN; (b) BzCl, pyridine; (c) Dibal-H, THF; (d) saturated NH3 in MeOH; (e) trifluoromethane-
sulfonate of diisopropylphosphonylmethanol, NaH, THF; (f) TFA/H2O; (g) SnCl4, MeCN; (h) (1) PhOC(S)Cl, DMAP, MeCN; (2) Bu3SnH, AIBN; (i) (1)
P(O)Cl3, 1,2,4-triazole, DCM; (2) NH3; (j) (1) (TMS)Br, DCM; (2) Sephadex-DEAE, Dowex-Na+; (k) (1) (TMS)I, DCM; (2) Sephadex-DEAE, Dowex-
Na+.
Scheme 2 a
(Table 1). The cytotoxicity of the compounds was determined
in parallel. The origin of the HIV-1 (IIIB) virus stock22 and the
HIV-2 (ROD)23 stock has been described. They were obtained
from the culture supernatant of HIV-1- or HIV-2-infected MT-4
cells, respectively. The inhibitory effect of the compounds on
HIV-1 and HIV-2 replication were monitored by measuring the
viability of MT-4 cells 5 days after infection.24 The cytotoxicity
of the compounds was determined in parallel by measuring the
a Conditions and reagents: (a) dimethylformamide dimethyl acetal, DMF,
viability of mock-infected cells on day 5, using a tetrazolium-
room temperature, 16 h; (b) (Im)2CO, DMF, 12 h, dibutylammonium
pyrophosphate, DMF, 2 h; (c) NH3, H2O, 1 h; (d) DEAE cellulose,
LiChroprep C-18.
(22) Popovic, M.; Sarngadharan, M. G.; Read, E.; Gallo, R. C. Science 1984,
224, 497-500.
(23) Barre´-Sinoussi, F.; Chermann, J. C.; Rey, F.; Nugeyre, M. T.; Chamaret,
S.; Gruest, J.; Dauguet, C.; Axler-Blin, C.; Vezinet-Brun, F.; Rouzioux,
C.; Rozenbaum, W.; Montagnier, L. Science 1983, 220, 868-871.
(24) Pauwels, R.; Balzarini, J.; Baba, M.; Snoeck, R.; Schols, D.; Herdewijn,
P.; Desmyter, J.; De Clercq, E. J. Virol. Methods 1988, 20, 309-321.
Antiviral Activity
Compounds 3a-h were evaluated for their potential to inhibit
the replication of HIV in a cell culture model for acute infection
9
5058 J. AM. CHEM. SOC. VOL. 127, NO. 14, 2005

Anti-HIV Phosphonate Nucleosides
A R T I C L E S
Table 1. Anti-HIV-1 Activity and Cytotoxicity of the Phosphonate
Nucleosides 3a-h
Table 2. Kinetic Parameters for dATP and PMDTApp
Incorporation into a DNA Hybrid for HIV Reverse Transcriptasea
a
b
EC50
M)
CC50
M)
compd (base)
(
µ
(
µ
SI
PMTA, 3a
PMTT, 3b
PMTU, 3c
PMTC, 3d
PMDTA, 3e
PMDTT, 3f
PMDTU, 3g
PMDTC, 3h
PMEA
>268
>328
>155
>308
>268
>328
155
>308
>316
>343
>336
>321
246
K
cat/km
<1
1
1
Km
(
µ
M)
K
cat (min-
)
(min-1 M-
)
dATP
PMDTApp
0.10 ( 0.018
0.29 ( 0.026
0.66 ( 0.019
0.79 ( 0.016
6.6
2.72
2.53
6.59
>125
>51
>336
>321
5.50 (a)
a For the assay conditions, see the Experimental Section.
44.9
17.6
>104
>100
14.00 (b)
3.35 (a)
3.48 (b)
246
>350
>350
incorporation of PMDTApp by the HIV reverse transcriptase a
small increase in the Km value, but also a slight increase in the
kcat value, compared to those for dATP. This indicates that,
although the affinity of the enzyme for the phosphonate
nucleotide might be a little lower, the overall catalytic efficiency
differs only by a factor of 2.5.
Since PMDTApp was such a poor substrate for the DNA
polymerase R, kinetic parameters could not be determined under
steady-state conditions.
PMPA
a EC50 ) 50% effective concentration, or concentration required to protect
50% of the cells against viral cytopathicity [HIV-1(IIIB), HIV-2(ROD)] in
MT-4 cells. For PMEA and PMPA, (a) data for HIV-1, (b) data for HIV-2.
b CC50 ) 50% cytotoxic concentration, or concentration reducing the number
of viable cells by 50%.
based colorimetric method to determine the number of viable
cells.
Now that we proved that PMDTA can be incorporated into
DNA, functioning as a chain terminator, a model was built to
analyze the interactions between the incorporated nucleotide and
reverse transcriptase. Therefore, the adenine phosphonate
nucleoside was built at the 3′-end of the primer and paired with
a thymidine nucleotide in the template strand (Figure 2). This
model revealed that the sugar ring is puckered in the C3′-endo
conformation. Hydrophobic interactions between the phospho-
nate nucleotide and reverse transcriptase are occurring at Leu74,
Tyr115, and Gln151, while no steric hindrance with Met184 is
expected to occur during translocation. This model visualizes
the experimental results of the incorporation study of PMDTA
into DNA using the reverse transcriptase.
PMDTA showed an EC50 value of 2.53 µM against both
HIV-1 and HIV-2. PMDTT had an EC50 value of 6.59 µM
against HIV-1 and HIV-2. No cytotoxicity was observed for
PMDTA or PMDTT at the highest concentration tested (316
and 343 µM, respectively), giving the compounds an SI of >125
(PMDTA) and >51 (PMDTT) in these cellular systems. In this
cellular test system, the anti-HIV activity of both compounds
is in the same range as the activity of PMEA and PMPA, while
no cellular toxicity has been observed (Table 1).
Incorporation of PMDTA into DNA Using Reverse
Transcriptase
The antiviral activity of phosphonate nucleosides is mostly
explained by their intracellular metabolism to their diphosphates
followed by incorporation into the viral genome and chain
termination.7 We used a primer/extension assay to compare the
ability of the HIV reverse transcriptase and the human DNA
polymerase R to accept PMDTApp as a substrate in comparison
to dATP. This should give us an idea about the selectivity of
the anti-HIV compound since the human DNA polymerase R
is mainly involved in replication of the nuclear genome while
the HIV reverse transcriptase plays a key role in the replication
of the viral genome. The incorporation studies were done with
a DNA template and a DNA primer, as DNA polymerase R
and reverse transcriptase are both able to synthesize double-
stranded DNA (although reverse transcriptase is also able to
synthesize a DNA strand using RNA as template). Both enzymes
were able to extend a DNA primer with the phosphonate
nucleotide, but the modified nucleotide was only a very poor
substrate for the human DNA polymerase R. Only a high
enzyme concentration (0.4 U/µL) resulted in the incorporation
of PMDTApp, a concentration more than 100 times higher than
the concentration used to incorporate the natural dATP substrate
(data not shown).
Conclusion
A new series of phosphonate nucleosides have been discov-
ered with a deoxythreosyl sugar moiety. The compounds with
a thymine and adenine base moiety showed potent anti-HIV-
1,2 activity while showing no cellular toxicity at the highest
concentration tested. These data demonstrate that considerable
improvement in the anti-HIV phosphonate field is an attainable
goal. The diphosphate of the adenine congener is an efficient
substrate for HIV-1 reverse transcriptase and a very poor
substrate for human DNA polymerase R. A 100-fold higher
DNA polymerase R concentration was needed to observe
incorporation of PMDTA into DNA. This makes PMDTA a
good candidate for further evaluation as an anti-HIV-1 com-
pound. It also shows that the TNA-scaffold15 is a useful handle
to develop new antiviral compounds.
Experimental Section
For all reactions, analytical grade solvents were used. All moisture-
sensitive reactions were carried out in oven-dried glassware (135 °C)
under a nitrogen atmosphere. Anhydrous THF was refluxed over
sodium/benzophenone and distilled. A Varian Unity 500 MHz spec-
1
The HIV reverse transcriptase, on the other hand, accepted
PMDTApp as easily as the natural building block. These results
from primer/extension assays were confirmed by our kinetic
data. Using a steady-state method, values for Km and Kcat were
determined for dATP and PMDTApp insertion opposite a single
T in the DNA template (Table 2). These data show for the
trometer and a 200 MHz Varian Gemini apparatus were used for H
NMR and 13C NMR. Exact mass measurements were performed on a
quadrupole time-of-flight mass spectrometer (Q-Tof-2, Micromass,
(25) Esnouf, R. M. Acta Crystallogr. 1999, D55, 938-940.
(26) Kraulis, P. J. J. Appl. Crystallogr. 1991, 24, 946-950.
(27) Merritt, E. A.; Bacon, D. J. Methods Enzymol. 1997, 277, 505-524.
9
J. AM. CHEM. SOC. VOL. 127, NO. 14, 2005 5059

A R T I C L E S
Wu et al.
Figure 2. Close-up of the adenine phosphonate molecule (at the right) built in at the 3′-side of the primer and pairing with base T5 of the template (at the
left). The reverse transcriptase domains are colored as blue (fingers, A2-A88, A121-A146), yellow (palm, A89-A120, A147-A242), red (thumb, A234-
A311), and white (rest, A312-A539, B6-B433). The picture was generated using Bobscript, Molscript, and Raster3d.25-27
Manchester, U.K.) equipped with a standard electrospray-ionization
(ESI) interface; samples were infused in i-PrOH/H2O (1:1) at 3 µL/
min. Precoated aluminum sheets (Fluka Silica gel/TLC-cards, 254 nm)
were used for TLC; the spots were examined with UV light. Column
chromatography was performed on ICN silica gel 63-200, 60 Å. For
sake of clarity, NMR signals of sugar protons and carbons are indicated
with a prime, and signals of base protons and carbons are given without
a prime.
) 13.0 Hz, 1H, C(3′)H), 7.57-8.01 (m, 5H, Ar H); 13C NMR (500
MHz, DMSO-d6) δC -5.16 (SiCH3 ), -4.84 (SiCH3), 17.84 (C(CH3)3),
25.42 (C(CH3)3), 67.20 (C-4′), 71.67 (C-2′), 75.46 (C-3′), 128.65
(aroma-C), 128.90 (aroma-C), 129.36 (aroma-C), 133.94 (aroma-C),
165.08 (Bz CO), 172.76 (C-1′); exact mass calcd for C17H25O5Si1 [M
+ H]+ 337.1471, found 337.1465.
2-O-Tertbutyldimethylsilyl-3-O-benzoyl-L-threose (8). To a solu-
tion of 7 (10.0 g, 29.7 mmol) in 100 mL of dry THF was slowly added
dropwise 1.0 M diisopropyl aluminum hydride (37.1 mL, 37.1 mmol)
in toluene at -78 °C. The reaction mixture was stirred at -78 °C, and
as soon as the starting material was completely consumed (TLC, 4-10
h), methanol (10 mL) was added over a period of 5 min to quench the
reaction. The cooling bath was removed, 100 mL of a saturated aqueous
sodium potassium tartrate solution and 200 mL of EtOAc were added,
and the mixture was stirred vigorously for 3 h. The organic layer was
washed with water and brine, dried over Na2SO4, and concentrated in
vacuo. The residue was purified by chromatography on a silica gel
column (n-hexane:EtOAc ) 8:1) to afford 8 (7.40 g, 21.8 mmol) as a
colorless solid in 73% yield: mp 70-71 °C; 1H NMR (200 MHz,
DMSO-d6) δH 0.10 (s, 6H, SiCH3), 0.87 (s, 9H, CH3), 3.93 (dd, J1 )
9.89 Hz, J2 ) 3.66 Hz, 1H, C(4′)Ha), 4.16 (br s, 1H, OH), 4.24 (dd, J1
) 10.26 Hz, J2 ) 5.86 Hz, 1H, C(4′)Hb), 5.02-5.07 (m, 2H, C(2′)H,
C(3′)H), 6.54 (d, J ) 4.76 Hz, 1H, C(1′)H), 7.51-8.00 (m, 5H, Ar H);
13C NMR (200 MHz, DMSO-d6) δC -7.39 (SiCH3), -7.30 (SiCH3),
15.41 (C(CH3)3), 23.27 (C(CH3)3), 67.06 (C-4′), 77.14 (C-2′), 78.87
(C-3′), 100.23 (C-1′), 126.58 (aroma-C), 127.09 (aroma-C), 131.40
(aroma-C), 163.18 (Bz CO); exact mass calcd for C17H26O5Si1Na1 [M
+ Na]+ 361.1447, found 361.1452.
1r,2-Di-O-tertbutyldimethylsilyl-L-threose (9a) and 1â,2-Di-O-
tertbutyldimethylsilyl-L-threose (9b). To a solution of 8 (7.30 g, 21.6
mmol) and imidazole (2.94 g, 43.1 mmol) in 100 mL of MeCN was
added (TBDMS)Cl (0.98 g, 23.8 mmol) at 0 °C in one portion. The
reaction mixture was slowly warmed to room temperature and stirred
overnight. The reaction mixture was concentrated. The residue was
partitioned between H2O and EtOAc. The organic layer was washed
with water and brine, dried over Na2SO4, and concentrated in vacuo.
The residue was dissolved in MeOH saturated with ammonia (100 mL),
and the reaction mixture was stirred at room temperature overnight.
The mixture was concentrated, and the residue was purified by column
2-O-Tertbutyldimethylsilyl-L-threosolactone (6). To a solution of
(R,S)-2,3-dihydroxydihydrofuran-1-one (5) (10.8 g, 92 mmol) and
imidazole (12.5 g, 184 mmol) in 250 mL of MeCN was added
(TBDMS)Cl (16.6 g, 110 mmol) at 0 °C in one portion. The reaction
mixture was slowly warmed to room temperature and stirred overnight.
The reaction mixture was concentrated. The residue was partitioned
between H2O and EtOAc. The organic layer was washed with water
and brine, dried over Na2SO4, and concentrated in vacuo. The residue
was purified by chromatography on a silica gel column (n-hexane:
EtOAC ) 6:1) to afford 6 (15.2 g, 65.4 mmol, 71%) as a colorless
1
solid: mp 99-100 °C; H NMR (200 MHz, DMSO-d6) δH 0.12 (s,
6H, SiCH3), 0.90 (s, 9H, CH3), 3.86 (dd, J1 ) 6.96 Hz, J2 ) 7.70 Hz,
1H, C(4′)Ha), 4.11-4.36 (m, 3H, OH, C(3′)H, C(4′)Hb), 5.82 (d, J )
5.13 Hz, 1H, C(2′)H); 13C NMR (200 MHz, DMSO-d6) δC -4.93
(SiCH3), 17.99 (C(CH3)3), 25.61 (C(CH3)3), 69.62 (C-4′), 72.62 (C-
2′), 74.59 (C-3′), 174.60 (C-1′); exact mass calcd for C10H20O4Si1Na1
[M + Na]+ 255.1028, found 255.1010.
2-O-Tertbutyldimethylsilyl-3-O-benzoyl-L-threosolactone (7). To
a solution of 6 (18.00 g, 77.5 mmol) in 200 mL of pyridine was added
dropwise BzCl (11.2 mL, 96.9 mmol) at 0 °C. The reaction mixture
was warmed to room temperature and stirred overnight. The reaction
mixture was concentrated and coevaporated with 20 mL of toluene
two times in vacuo. The residue was partitioned between H2O (100
mL) and EtOAc (350 mL). The organic layer was washed with water
and brine, dried over Na2SO4, and concentrated in vacuo. The residue
was purified by chromatography on a silica gel column (n-hexane:
EtOAc ) 8:1) to afford 7 (25.9 g, 77.0 mmol) as a colorless solid in
1
99% yield: mp 52-53 °C; H NMR (500 MHz, DMSO-d6) δH 0.14
(d, J1 ) 13.2 Hz, 6H, SiCH3), 0.87 (s, 9H, CH3), 4.23 (dd, J1 ) 6.8
Hz, J2 ) 9.3 Hz, 1H, C(4′)Ha), 4.68 (dd, J1 ) 7.3 Hz, J2 ) 9.3 Hz, 1H,
C(4′)Hb), 4.96 (d, J ) 6.8 Hz, 1H, C(2′)H), 5.48 (dd, J1 ) 7.3 Hz, J2
9
5060 J. AM. CHEM. SOC. VOL. 127, NO. 14, 2005

Anti-HIV Phosphonate Nucleosides
A R T I C L E S
chromatography (n-hexane:EtOAc ) 20:1, 10:1) to give compound 9a
(3.15 g, 9.06 mmol) as a colorless oil in 42% yield and 9b (1.43 g,
4.10 mmol) as a colorless oil in 19% yield. The stereochemistry at
position 1′ is tentatively assigned using 1H NMR. The compound with
the small coupling constant of H-1′ (J ) 1.1 Hz) was characterized as
9a, while the compound with a coupling constant of 3.6 Hz was char-
acterized as 9b. Data for 9a: 1H NMR (200 MHz, DMSO-d6) δH 0.06-
0.08 (m, 12H, SiCH3), 0.87 (s, 18H, CH3), 3.59-3.65 (m, 1H, C(2′)H),
3.87-3.99 (m, 3H, C(4′), C(3′), C(4′)Hb), 5.00 (d, J ) 1.1 Hz, 1H
C(1′)H), 5.07-5.10 (m, 1H, OH); 13C NMR (200 MHz, DMSO-d6) δC
-5.14 (SiCH3 ), -4.92 (SiCH3), -4.65 (SiCH3), -4.38 (SiCH3), 17.66
(C(CH3)3), 17.81 (C(CH3)3), 25.61 (C(CH3)3), 25.73 (C(CH3)3), 71.92
(C-4′), 76.66 (C-2′), 85.58 (C-3′), 103.91 (C-1′); exact mass calcd for
C16H36O4Si2Na1 371.2050, found 371.2059. Data for 9b: 1H NMR (200
MHz, DMSO-d6) δH 0.05 (s, 6H, SiCH3), 0.06 (d, J1 ) 5.2 Hz, 6H,
SiCH3), 0.86 (s, 9H, CH3), 0.87 (s, 9H, CH3), 3.41 (dd, J1 ) 8.0 Hz,
J2 ) 3.7 Hz, 1H, C(2′)H); 3.81 (dd, J1 ) 5.2 Hz, J2 ) 3.7 Hz, C(3′)H),
3.94-4.07 (m, 2H, C(4′)Ha, C(4′)Hb), 5.12-5.15 (m, 2H, OH, C(1′)H);
1H NMR 200 MHz (DMSO-d6 + 1D D2O) δH 0.02 (s, 6H, SiCH3),
0.04 (d, J2 ) 4.4 Hz, 6H, SiCH3), 0.84 (s, 18H, CH3), 3.39 (dd, J1 )
7.7 Hz, J2 ) 3.6 Hz, 1H, C(2′)H); 3.79 (dd, J1 ) 4.4 Hz, J2 ) 4.4 Hz,
1H, C(3′)H), 3.92-4.07 (m, 2H, C(4′)Ha C(4′)Hb) 5.10 (d, 1H, J2 )
3.6 Hz, C(1′)H); 13C NMR (200 MHz, DMSO-d6) δC -4.95 (SiCH3),
-4.74 (SiCH3 ), -4.67 (SiCH3), 17.45 (C(CH3)3), 25.64 (C(CH3)3),
25.79 (C(CH3)3), 70.80 (C-4′), 74.17 (C-2′), 79.45 (C-3′), 97.11 (C-
1′); exact mass calcd for C16H36O4Si2Na1 371.2050, found 371.2052.
C-3′), 97.3 (C-1′); exact mass calcd for C23H52O7P1Si2 [M + H]+
527.2989, found 527.2972.
1r,2-O-Benzoyl-3-O-(diisopropylphosphonomethyl)-L-threose (11a)
and 1â,2-O-Benzoyl-3-O-(diisopropylphosphonomethyl)-L-threose
(11b). A solution of 10a (4.25 g, 8.1 mmol) in TFA-H2O (3:1, 20
mL) was allowed to stand at room temperature for 2 h. The reaction
mixture was neutralized with saturated NaHCO3 solution. Then the
mixture was partitioned between DCM (400 mL) and water (20 mL).
The organic layer was washed with water and brine, dried over Na2-
SO4, and then concentrated in vacuo. The residue was purified by
chromatography on silica gel (DCM:MeOH ) 20:1) to give 3-O-
diisopropylphosphonomethyl-L-threose (2.20 g, 7.3 mmol) as a colorless
amorphous solid in 92% yield. To the solution of 3-O-(diisopropyl-
phosphonomethyl)-L-threose (687 mg, 2.3 mmol) in 100 mL of pyridine
was added dropwise BzCl (0.67 mL, 5.8 mmol) at 0 °C. The reaction
mixture was warmed to room temperature and stirred overnight. The
reaction mixture was concentrated and coevaporated with 20 mL of
toluene two times in vacuo. The residue was partitioned between H2O
(20 mL) and EtOAc (150 mL). The organic layer was washed with
water and brine, dried over Na2SO4, and concentrated in vacuo. The
residue was purified by chromatography on a silica gel column (n-
hexane:EtOAc ) 1:1) to afford 11a and 11b (1.0 g, 2.0 mmol) as a
colorless oil in 87% yield. The H-1′ proton of 11a appeared as a singlet,
while the H-1′ proton of 11b appeared as a doublet (J ) 4.4 Hz). Data
for 11a: 1H NMR (200 MHz, DMSO-d6) δH 1.20-1.26 (m, 12H,
C(CH3)2), 3.40-4.11 (m, 3H, PCH2, C(4′)Ha), 4.40-4.54 (m, 2H,
C(3′)H, C(4′)Hb), 4.56-4.71 (m, 2H, OCH(CH3)2), 5.51 (s, 1H, C(2′)H),
6.47 (s, 1H, C(1′)H), 7.43-8.07 (m, 10H, Ar H); 13C NMR (200 MHz,
DMSO-d6) δC 23.82 (CH3), 64.45 (d, J ) 155.4 Hz, PCH2), 70.59 (CH-
(CH3)), 73.23 (C-4′), 80.12 (C-2′), 80.30 (C-3′), 99.78 (C-1′), 129.04
(aroma-C), 129.83 (aroma-C), 134.14 (aroma-C), 164.61 (Bz CO),
165.07 (Bz CO); exact mass calcd for C25H31O9P1Na1 [M + Na]+
529.1603, found 529.1601. Data for 11b: 1H NMR (200 MHz, CDCl3)
δH 1.30-1.36 (m, 12H, C(CH3)2), 3.84 (dAB, J ) 13.9 Hz, JP,H ) 8.8
Hz, 1H, PCHa), 3.96 (dAB, J ) 13.9 Hz, JP,H ) 8.8 Hz, PCHb), 4.09
(dd, J ) 3.5 and 9.9 Hz, 1H, C(4′)Ha), 4.43 (dd, J ) 6.2 and 9.9 Hz,
1H, C(4′)Hb), 4.67-4.86 (m, 3H, C(3′)H, POCH), 5.56 (t, J ) 4.4,
1H, C(2′)H), 6.76 (d, J ) 4.4, 1H, C(1′)H), 7.31-7.61 (m, 6H, Bz H),
7.89-8.02 (m, 4H, Bz H); 13C NMR (200 MHz, CDCl3) δC 23.94
(CH3), 64.66 (d, J ) 169.4 Hz, PCH2), 70.72 (C-4′), 71.42 (POCH),
82.83 (C-3′), 95.67 (C-1′) 128.39 (aroma-C), 128.51 (aroma-C), 128.90
(aroma-C), 129.51 (aroma-C), 129.78 (aroma-C), 133.39 (Bz CO),
133.61 (Bz CO); C-2′ was hidden by the peak of CDCl3; exact mass
calcd for C25H31O9PNa [M + Na]+ 529.1603, found 529.1594.
1-(N6-Benzoyladenin-9-yl)-2-O-benzoyl-3-O-(diisopropylphospho-
nomethyl)-L-threose (12). To a mixture of 11a and 11b (425 mg, 0.83
mmol) and silylated N6-benzoyladenine (401 mg, 1.6 mmol) in dry
MeCN (30 mL) was dropwise added SnCl4 (0.3 mL, 2.5 mmol) under
N2 at room temperature. The reaction mixture was stirred at room
temperature for 4-5 h. Then the reaction was quenched with saturated
NaHCO3 and concentrated. The residue was partitioned between H2O
(20 mL) and EtOAc (100 mL). The organic layer was washed with
water and brine, dried over Na2SO4, and concentrated in vacuo. The
residue was purified by chromatography on a silica gel column (DCM:
MeOH ) 40:1) to afford 12 (431 mg, 0.69 mmol) as a colorless
amorphous solid in 83% yield: 1H NMR (500 MHz, CDCl3) δH 1.31-
1.36 (m, 12H, CH3), 3.94 (dd, J1 ) 14.0 Hz, J2 ) 8.6 Hz, 1H, PCHa),
4.01 (dd, J1 ) 14.0 Hz, J2 ) 8.6 Hz, 1H, PCHb), 4.38 (dd, J1 ) 11.0
Hz, J2 ) 4.6 Hz, 1H, C(4′)Ha), 4.50-4.52 (m, 2H, C(3′)H, C(4′)Hb),
4.73-4.80 (m, 2H, OCH), 5.08 (s, 1H, C(2′)H), 6.56 (s, 1H, C(1′)H),
7.48-7.65 (m, 6H, Ar H), 8.02-8.08 (m, 4H, Ar H), 8.50 (s, 1H, A
C(8)H), 8.82 (s, 1H, A C(2)H), 9.07 (br s, 1H, NH); 13C NMR (500
MHz, CDCl3) δC 23.97 (CH3), 24.01 (CH3), 24.03 (CH3), 24.06 (CH3),
65.36 (d, JP,C ) 168.9 Hz, PCH2), 71.45 (POCH), 71.51(POCH), 73.55-
(C-4′), 80.27 (C-2′), 83.74 (JP,C ) 9.8 Hz, C-3′), 87.86 (C-1′), 122.72
(A C(5)), 127.80 (aroma-C), 128.65 (aroma-C), 128.67 (aroma-C),
1r,2-Di-O-tertbutyldimethylsilyl-3-O-(diisopropylphosphono-
methyl)-L-threose (10a) and 1â,2-Di-O-tertbutyldimethylsilyl-3-O-
(diisopropylphosphonomethyl)-L-threose (10b). To a solution of 9a
(3.41 g, 9.8 mmol) in dried THF (25 mL) was added sodium hydride
(80% dispersion in mineral oil, 0.56 mg, 19.6 mmol) at -78 °C. Then
the solution of the triflate of diisopropylphosphonomethanol (5.80 g,
19.6 mmol) in dried THF (10 mL) was dropwise added, and the reaction
mixture was slowly warmed to room temperature. The reaction was
quenched with saturated NaHCO3 and concentrated. The residue was
partitioned between H2O and EtOAc. The organic layer was washed
with water and brine, dried over Na2SO4, and concentrated in vacuo.
The residue was purified by chromatography on a silica gel column
(n-hexane:EtOAC ) 2:1) to afford 10a (4.75 g, 9.0 mmol, 92%) as a
colorless oil: 1H NMR (200 MHz, DMSO-d6) δH 0.06-0.10 (m, 12H,
SiCH3), 0.86 (s, 9H, C(CH3)3), 0.87 (s, 9H, C(CH3)3), 1.22-1.26 (m,
12H, C(CH3)2), 3.75 (d, J ) 9.2 Hz, 2H, CH2), 3.78 (d, J ) 9.2 Hz,
1H, C(4′)Ha), 3.88-3.95 (m, 1H, C(3′)H), 3.99 (s, 1H, C(2′)H), 4.10
(dd, J1 ) 9.2 Hz, J2 ) 8.6 Hz, 1H, C(4′)Hb), 4.52-4.68 (m, 2H, CH),
5.02(s, 1H, C(1′)H); 13C NMR (200 MHz, DMSO-d6) δC -4.92
(SiCH3), -4.80 (SiCH3), -4.40 (SiCH3), -4.26 (SiCH3), 17.90 (SiC),
23.94 (OCH(CH3)2), 25.73 (C(CH3)3), 64.07 (d, JP,C ) 165.5 Hz, PCH2),
69.71 (C-4′), 70.43 (POCH), 83.12 (C-2′), 87.03 (d, JP,C ) 12.0 Hz,
C-3′), 103.8 (C-1′); exact mass calcd for C23H52O7P1Si2 [M + H]+
527.2989, found 527.2988.
The synthesis of 10b started from 9b (2.00 g, 5.7 mmol), followed
the same procedure as for the synthesis of 10a from 9a, and offered
10b (2.70 g, 5.1 mmol, 90%) as a colorless oil: 1H NMR (200 MHz,
CDCl3) δH 0.08-0.11 (m, 12H, SiCH3), 0.93 (br s, 18H, C(CH3)3),
1.33 (d, J ) 6.2 Hz, 12H, C(CH3)2), 3.66-3.94 (m, 3H, C(4′)Ha, PCH2),
4.02-4.22 (m, 3H, C(2′)H, C(3′)H, C(4′)Hb), 4.67-4.83 (m, 2H,
1
CH(CH3)2), 5.13 (d, J ) 3.7 Hz, 1H, C(1′)H); H NMR (200 MHz,
DMSO-d6) δH 0.06-0.93 (m, 12H, SiCH3), 0.87 (s, 18H, C(CH3)3),
1.22-1.26 (m, 12H, C(CH3)2), 3.58-3.65 (m, 1H, C(4′)Ha), 3.78 (d, J
) 9.2 Hz, PCH2), 3.96-4.08 (m, 3H, C(2′)H, C(3′)H, C(4′)Hb), 4.51-
4.67 (m, 2H, CH(CH3)2), 5.15 (d, J ) 3.7 Hz, 1H, C(1′)H); 13C NMR
(200 MHz, DMSO-d6) δC -5.22 (SiCH3 ), -5.07 (SiCH3 ), -4.58
(SiCH3 ), 17.88 (C(CH3)3), 23.98 (OCH(CH3)2), 25.62 (C(CH3)3), 25.71
(C(CH3)3), 65.12 (d, JP,C ) 173.6 Hz, PCH2), 68.38 (C-4′), 70.87 (OCH-
(CH3)2), 70.96 (OCH(CH3)2), 78.88 (C-2′), 85.68 (d, JP,C ) 12.0 Hz,
9
J. AM. CHEM. SOC. VOL. 127, NO. 14, 2005 5061

A R T I C L E S
Wu et al.
128.86 (aroma-C), 129.93 (aroma-C), 132.31 (aroma-C), 133.99 (aroma-
C), 141.98 (A C(8)), 149.45 (A C(6), 151.59 (A C(4)), 152.93 (A C(2)),
164.44 (OBz CO), 165.17 (NBz CO); exact mass calcd for C30H35N5O8P1
[M + H]+ 624.2223, found 624.2222.
residue was partitioned between H2O (30 mL) and EtOAc (150 mL).
The organic layer was washed with water and brine, and concentrated
in vacuo. The residue was purified by chromatography on a silica gel
column (n-hexane:EtOAc ) 2:1) to afford 15 (0.51 g, 0.94 mmol) as
a colorless amorphous solid in 52% yield: 1H NMR (200 MHz, DMSO-
d6) δH 1.17-1.23 (m, 12H, CH(CH3)2), 2.10 (s, 3H, CH3), 3.80-4.00
(m, 2H, PCH2), 4.24-4.36 (m, 2H, C(4′)Ha, C(3′)H), 4.48-4.63 (m,
3H, C(4′)Hb, OCH(CH3)2), 5.44 (s, 1H, C(2′)H), 6.04 (s, 1H, C(1′)H),
7.27 (d, J ) 7.7 Hz, 1H, C C(5)H), 7.54-7.77 (m, 3H, Ar H), 8.03-
8.07 (m, 3H, Aro H, C C(6)H), 10.95 (s, 1H, NH); 13C NMR (200
MHz, DMSO-d6) δC 23.76 (CH(CH3)3), 24.39 (Ac CH3), 63.77 (d, JP,C
) 166.4 Hz, PCH2), 70.44 (CH(CH3)3), 70.59 (CH(CH3)3), 73.56 (C-
4′), 79.75 (C-3′) 82.83 (d, JP,C ) 13.7 Hz,C-3′), 90.74 (C-1′), 94.74 (C
C(5)), 128.86 (aroma-C), 129.14 (aroma-C), 134.07 (aroma-C), 129.77
(aroma-C), 134.23 (aroma-C), 145.40 (C C(6)), 154.69 (C C(2)), 162.95
(Bz CO), 164.77 (C C(4)), 171.26 (Ac CO); exact mass calcd for
C24H33N3O9P1 [M + H]+ 538.1954, found 538.1956.
1-(Adenin-9-yl)-3-O-(diisopropylphosphonomethyl)-L-threose (16).
A solution of 12 (431 mg, 0.80 mmol) in MeOH saturated with
ammonia (100 mL) was stirred at room temperature overnight. The
mixture was concentrated, and the residue was purified by column
chromatography (CH2Cl2:MeOH ) 9:1) to give compound 16 (278 mg,
0.67 mmol) as a white powder in 84% yield: 1H NMR (500 MHz,
DMSO-d6) δH 1.21-1.26 (m, 12H, CH3), 3.85-3.94 (m, 2H, PCH2),
4.10-4.13 (m, 2H, C(4′)Ha, C(3′)H), 4.24-4.27 (m, 1H, C(4′)Hb),
4.57-4.63 (m, 3H, CH(CH)3, C(2′)H), 5.93 (d, J ) 2.1 Hz, 1H, C(1′)H),
6.05 (br s, 1H, OH), 7.24 (s, 2H, NH2), 8.15 (s, 1H, C(2)H), 8.18 (s,
1H, C(8)H); 13C NMR (200 MHz, DMSO-d6): δC 23.82 (CH3), 63.5
(JP,C ) 164.6 Hz, PCH2), 70.41 (OCH), 70.53 (OCH), 71.65 (C-4′),
78.27 (C-2′), 85.62 (JP,C ) 13.6 Hz, C-3′), 89.53 (C-1′), 118.79 (A
C(5)), 139.39 (A C(8)), 149.47 (A C(6)), 152.90 (A C(4)), 156.24 (A
C(2)); exact mass calcd for C16H27N5O6P1 [M + H]+ 416.1699, found
416.1681.
1-(Thymin-1-yl)-2-O-benzoyl-3-O-(diisopropylphosphonomethyl)-
L-threose (13). Thymine (0.34 g, 2.7 mmol), ammonia sulfate (10 mg,
0.07 mmol), and 6 mL of HMDS were added to a dried flask. The
mixture was refluxed overnight under nitrogen. HDMS was removed
in vacuo. To the flask with the residue was added the solution of
compound 11a,b (0.92 g, 1.8 mmol) in 10 mL of dry MeCN followed
by dropwise addition of SnCl4 (640 µL 5.4 mmol) under N2 at room
temperature. The reaction mixture was stirred for 4 h. The reaction
was quenched with saturated aqueous NaHCO3 and concentrated to a
small volume. The residue was partitioned between H2O (30 mL) and
EtOAc (150 mL). The organic layer was washed with water and brine,
dried over Na2SO4, and concentrated in vacuo. The residue was purified
by chromatography on a silica gel column (n-hexane:EtOAc ) 1:1) to
afford 13 (0.76 g, 1.4 mmol) as a colorless amorphous solid in 78%
yield: 1H NMR (200 MHz, CDCl3) δH 1.35 (d, J ) 6.2 Hz, 12H, CH3),
1.99 (d, J ) 1.5 Hz, 3H, T CH3), 3.86-4.05 (m, 2H, PCH2), 4.11-
4.16 (m, 1H, C(4′)Ha), 4.26 (br t, 1H, C(3′)H), 4.40 (d, J ) 10.6 Hz,
1H, C(4′)Hb), 4.70-4.86 (m, 2H, OCH(CH3)2), 5.38 (s, 1H, C(2′)H),
6.29 (t, J ) 2.2 Hz, 1H, C(1′)H), 7.43-7.66 (m, 4H, Ar H, T C(6)H),
8.02-8.07 (m, 2H, Ar H), 9.13 (s, 1H, NH); 13C NMR (200 MHz,
CDCl3) δC 12.42 (T CH3), 23.83 (CH(CH3)3), 23.92 (CH(CH3)3), 64.48
(d, JP,C ) 168.5 Hz, PCH2), 71.29 (CH(CH3)3), 71.45 (CH(CH3)3), 72.72
(C-4′), 80.28 (C-2′), 83.70 (JP,C ) 10.6 Hz, C-3′), 89.02 (C-1′), 111.39
(T C(5)), 128.60 (aroma-C), 129.90 (aroma-C), 133.84 (T C(6)), 136.12
(aroma-C), 150.42 (T C(2)), 163.86 (T C(4)), 165.32 (Bz CO); exact
mass calcd for C23H31N2O9P1 [M + H]+ 511.1845, found 511.1831.
1-(Uracil-1-yl)-2-O-benzoyl-3-O-(diisopropylphosphonomethyl)-
L-threose (14). Uracil (0.81 g, 7.2 mmol), ammonia sulfate (10 mg,
0.07 mmol), and 20 mL of HMDS were added to a dried flask. The
mixture was refluxed overnight under nitrogen. HDMS was removed
in vacuo. To the residue was added the solution of compound 11a,b
(2.43 g, 4.8 mmol) in 50 mL of dry MeCN followed by a dropwise
addition of SnCl4 (1.7 mL, 14.4 mmol). The reaction mixture was stirred
for 4 h. The reaction was quenched with saturated aqueous NaHCO3
and concentrated to a small volume. The residue was partitioned
between H2O (30 mL) and EtOAc (100 mL). The organic layer was
washed with water and brine, dried over Na2SO4, and concentrated in
vacuo. The residue was purified by chromatography on a silica gel
column (DCM:MeOH ) 25:1) to afford 14 (2.09 g, 4.2 mmol) as a
colorless amorphous solid in 84%: 1H NMR (500 MHz, DMSO-d6)
δH 1.23-1.26 (m, 12H, CH3), 3.97 (d, J ) 9.0 Hz, 2H, PCH2), 4.16
(dd, J1 ) 10.7 Hz, J2 ) 4.2 Hz, 1H, C(4′)Ha), 4.36 (d, J ) 10.7 Hz,
1H, C(4′)Hb), 4.39-4.40 (m, 1H, C(3′)H), 4.58-4.64 (m, 2H,
OCH(CH3)2), 5.41 (s, 1H, C(2′)H), 5.61 (d, J ) 8.1 Hz, 1H, U C(5)H),
6.02 (d, J ) 2.0 Hz, 1H, C(1′)H), 7.55-7.60 (m, 2H, Ar H), 7.63 (d,
J ) 8.1 Hz, 1H, U C(5)H), 7.70-7.73 (m, 1H, Ar H), 8.02-8.04 (m,
2H, Ar H), 11.4 (s, 1H, NH); 13C NMR (500 MHz, DMSO-d6) δC 23.74
(CH(CH3)3), 23.84 (CH(CH3)3), 63.10 (d, JP,C ) 168.5 Hz, PCH2), 70.53
(CH(CH3)3), 72.32 (C-4′), 79.83 (C-2′), 82.78 (C-3′), 89.06 (C-1′),
101.91 (U C(5)), 128.95 (aroma-C), 129.63 (aroma-C), 134.07 (aroma-
C), 140.72 (U C(6)), 150.39 (U C(2)), 163.19 (U C(4)), 164.73 (Bz
CO); exact mass calcd for C22H29N2O9P1Na1 [M + Na]+ 519.1508,
found 519.1506.
1-(Thymin-1-yl)-3-O-(diisopropylphosphonomethyl)-L-threose (17).
A solution of 13 (715 mg, 1.7 mmol) in MeOH saturated with ammonia
(100 mL) was stirred at room temperature overnight. The mixture was
concentrated, and the residue was purified by column chromatography
(CH2Cl2:MeOH ) 10:1) to give compound 17 (515 mg, 1.2 mmol) as
a white powder in 71% yield: 1H NMR (200 MHz, CDCl3) δH 1.27-
1.33 (m, 12H, CH3), 1.93 (d, J ) 1.7 Hz, 3H, T CH3), 3.75 (d, J ) 8.8
Hz, 2H, PCH2), 4.13 (br t, 1H, C(3′)H), 4.24-4.31 (m, 2H, C(4′)H2),
4.38 (s, 1H, C(2′)H), 4.61-4.80 (m, 2H, OCH(CH3)2), 5.81 (s, 1H,
C(1′)H), 7.41 (d, J ) 1.46 Hz, 1H, T C(6)H), 10.27 (br s, 1H, NH);
13C NMR (200 MHz, CDCl3) δC 2.42 (T CH3), 23.89 (CH(CH3)3), 64.46
(d, JP,C ) 168.5 Hz, PCH2), 71.26 (CH(CH3)3), 73.54 (C-4′), 78.94
(C-2′), 85.33 (d, JP,C ) 10.6 Hz, C-3′), 93.12 (C-1′), 110.12 (T C(5)),
136.40 (T C(6)), 151.08 (T C(2)), 164.56 (T C(4)); exact mass calcd
for C16H28N2O8P1 [M + H]+ 407.1583, found 407.1568.
1-(Uracil-1-yl)-3-O-(diisopropylphosphonomethyl)-L-threose (18).
A solution of 14 (2.03 g, 4.0 mmol) in MeOH saturated with ammonia
(300 mL) was stirred at room temperature overnight. The mixture was
concentrated, and the residue was purified by column chromatography
(CH2Cl2:MeOH ) 20:1) to give compound 18 (1.52 g, 3.8 mmol) as a
white powder in 96% yield: 1H NMR (200 MHz, DMSO-d6) δH 1.19-
1.25 (m, 12H, CH3), 3.78 (dd, J1 ) 13.9 Hz, J2 ) 9.2 Hz, 1H, PCHa)
3.85 (dd, J1 ) 13.9 Hz, J2 ) 9.2 Hz, 1H, PCHb), 3.98-4.28 (m, 4H,
C(2′)H, C(3′)H, C(4′)H2), 4.50-4.66 (m, 2H, CH(CH3), 5.50 (d, J )
8.0 Hz, 1H, U C(5)H), 5.66 (d, J ) 1.5 Hz, 1H, OH), 5.93 (d, J ) 4.4
Hz, 1H, C(1′)H), 7.54(d, J ) 8.0 Hz, 1H, U C(6)H); 13C NMR (200
MHz, DMSO-d6) δc 23.70 (CH(CH3)3), 23.79 (CH(CH3)3), 63.29 (d,
JP,C ) 166.3 Hz, PCH2), 70.34 (CH(CH3)3), 70.47 (CH(CH3)3), 72.29
(C-4′), 77.84 (C-2′), 85.23 (JP,C ) 10.7 Hz, C-3′), 91.68 (C-1′), 101.12
(U C(5)), 141.12 (U C(6)), 150.72 (U C(2)), 163.46 (U C(4)); exact
mass calcd for C15H26N2O8P1 [M + H]+ 393.1427, found 393.1425.
1-(N4-Acetylcytosin-1-yl)-2-O-benzoyl-3-O-(diisopropylphospho-
nomethyl)-L-threose (15). N4-Acetylcytosine (0.41 g, 2.7 mmol),
ammonia sulfate (10 mg, 0.07 mmol), and 6 mL of HMDS were added
to a dried flask. The mixture was refluxed overnight under nitrogen.
HDMS was removed in vacuo. To the residue was added a solution of
compound 11a,b (0.92 g, 1.8 mmol) in 10 mL of dry MeCN followed
by a dropwise addition of stannic chloride (640 µL 5.4 mmol). The
reaction mixture was stirred for 4 h. The reaction was quenched with
saturated aqueous NaHCO3 and concentrated to a small volume. The
1-(Cytosin-1-yl)-3-O-(diisopropylphosphonomethyl)-L-threose (19).
A solution of 15 (450 mg, 0.84 mmol) in MeOH saturated with
9
5062 J. AM. CHEM. SOC. VOL. 127, NO. 14, 2005

Anti-HIV Phosphonate Nucleosides
A R T I C L E S
ammonia (100 mL) was stirred at room temperature overnight. The
mixture was concentrated, and the residue was purified by column
chromatography (CH2Cl2:MeOH ) 20:1) to give compound 19 (281
mg, 0.72 mmol) as a white powder in 86% yield. 1H NMR (200 MHz,
DMSO-d6) δH 1.18-1.25 (m, 12H, CH3 ), 3.72 (dd, J1 ) 13.6 Hz, J2
) 8.8 Hz, 1H, PCHa) 3.84 (dd, J1 ) 13.6 Hz, J2 ) 8.8 Hz, 1H, PCHb),
3.95-4.05 (m, 3H, C(2′)H, C(3′)H, C(4′)Ha), 4.25 (d, J ) 9.5 Hz, 1H,
C(4′)Hb), 4.48-4.64 (m, 2H, CH(CH3), 5.65 (d, J ) 7.6 Hz, 1H, C
C(5)H), 5.70 (d, J ) 1.5 Hz, 1H, OH), 5.85 (d, J ) 15.4 Hz, 1H,
C(1′)H), 7.04 (br s, 1H, NaH), 7.14(br s, 1H, NbH), 7.50 (d, J ) 7.6
Hz, 1H, C C(6)H); 13C NMR (200 MHz, DMSO-d6) δC 23.68 (CH-
(CH3)3), 23.78 (CH(CH3)3), 64.46 (d, JP,C ) 164.8 Hz, PCH2), 70.30
(CH(CH3)3), 70.42 (CH(CH3)3), 72.00 (C-4′), 78.19 (C-2′), 85.66 (d,
JP,C ) 12.2 Hz, C-3′), 92.30 (C-1′), 93.46 (C C(5)), 141.63 (C C(6)),
155.47 (C C(2)), 165.94 (C C(4)); exact mass calcd for C15H27N3O7P1
[M + H]+ 392.1586, found 392.1577.
C(5)H), 6.21 (dd, J1 ) 8.0 Hz, J2 ) 2.0 Hz, 1H, C(1′)H), 7.71 (d, J )
8.0 Hz, 1H, U C(6)H), 9.16 (s, 1H, NH); 13C NMR (200 MHz, CDCl3)
δP 23.98 (CH(CH3)3)), 38.42 (C-2′), 63.86 (d, JP,C ) 170.7 Hz, PCH2),
71.26 (CH(CH3)3), 71.36 (CH(CH3)3), 73.94 (C-4′), 80.11 (d, JP,C
)
11.2 Hz, C-3′), 85.44 (C-1′), 101.95 (U C(5)), 140.92 (U C(6)), 150.63
(U C(2)), 163.47 (U C(4)); exact mass calcd for C15H26N2O7P1 [M +
H]+ 377.1478, found 377.1479.
1-(Cytosin-1-yl)-2-deoxy-3-O-(diisopropylphosphonomethyl)-L-
threose (23). To a solution of 1,2,4-triazole (662 mg, 9.6 mmol) in 15
mL of pyridine was added phosphorus oxychloride (223 µL, 2.4 mmol)
at room temperature. The mixture was stirred for 10 min. Then the
solution of 22 (289 mg, 0.80 mmol) was added to the mixture. The
reaction mixture was stirred for 4 h. Then ammonia gas was bubbled
into the reaction mixture for 1-3 h, and the reaction mixture was
concentrated in vacuo. The residue was purified by column chroma-
tography (CH2Cl2:MeOH ) 12:1) to give compound 23 (220 mg, 0.58
mmol) as a colorless foam in 73% yield: 1H NMR (200 MHz, CDCl3)
1-(Adenin-9-yl)-2-deoxy-3-O-(diisopropylphosphonomethyl)-L-
threose (20). To a solution of phenyl(chloro)thiocarbonate (0.25 mL,
1.8 mmol) and DMAP (426 mg, 3.5 mmol) in dried MeCN (25 mL)
was added compound 16 (483 mg, 1.2 mmol) at room temperature.
The reaction mixture was stirred for 12 h. The mixture was concen-
trated, and the residue was purified by column chromatography (CH2-
Cl2:MeOH ) 10:1) to give 1-(adenin-9-yl)-2-O-phenoxythiocarbonyl-
3-O-diisopropylphosphonomethyl-L-threose as a colorless oil. To a
solution of 1-(adenin-9-yl)-2-O-phenoxythiocarbonyl-3-O-diisopropyl-
phosphonomethyl-L-threose in dried toluene (50 mL) were added
tributytin hydride (339 µL, 1.2 mmol) and AIBN (48 mg, 0.3 mmol).
The reaction mixture was refluxed for 6 h and concentrated in vacuo.
The residue was purified by column chromatography (CH2Cl2:MeOH
) 10:1) to give compound 20 (110 mg, 0.27 mmol) as a colorless oil
in 23% yield: 1H NMR (200 MHz, CDCl3) δH 1.27-1.34 (m, 12H,
CH3), 2.54-2.75 (m, 2H, C(2′)H2), 3.62-3.82 (m, 2H, PCH2), 4.04
(dd, J1 ) 10.3 Hz, J2 ) 4.0 Hz, 1H, C(4′)Ha), 4.35 (d, J ) 10.3 Hz,
1H, C(4′)Hb), 4.43-4.48 (m, 1H, C(3′)H), 4.62-4.84 (m, 2H,
OCH(CH3)2), 6.21 (br s, 2H, NH2), 6.47 (dd, J1 ) 7.2 Hz, J2 ) 2.7 Hz,
1H, C(1′)H), 8.31(s, 1H, A C(2)H), 8.33(s, 1H, A C(8)H); 13C NMR
(200 MHz, CDCl3) δC 23.89 (CH(CH3)3), 38.05 (C-2′), 64.10 (d, JP,C
) 169.4 Hz, PCH2), 71.31 (CH(CH3)3), 71.46 (CH(CH3)3), 73.68 (C-
4′), 80.49 (d, JP,C ) 10.7 Hz, C-3′), 83.42 (C-1′), 119.50 (A C(5)),
136.63 (A C(8)), 149.73 (A C(6)), 153.07 (A C(4)), 155.62 (A C(2));
exact mass calcd for C16H27N5O5P1 [M + H]+ 400.1750, found
400.1740.
1-(Thymin-1-yl)-2-deoxy-3-O-(diisopropylphosphonomethyl)-L-
threose (21). This compound was prepared as described for 20, using
17 (450 mg, 1.1 mmol) as starting material. Column chromatographic
purification (CH2Cl2:MeOH ) 10:1) gave compound 21 (275 mg, 0.70
mmol) as a colorless oil in 64% yield: 1H NMR (200 MHz, CDCl3)
δH 1.31 (s, 6H, CH3), 1.34 (s, 6H, CH3), 1.97 (d, J ) 1.1 Hz, 3H, T
CH3), 2.16 (d, J ) 15.0 Hz, 1H, C(2′)Ha), 2.46-2.62 (m, 1H, C(2′)-
Hb), 3.72(d, J ) 9.2 Hz, 2H, PCH2), 3.84 (dd, J1 ) 10.6 Hz, J2 ) 3.7
Hz, 1H, C(4′)Ha), 4.29-4.37(m, 2H, C(4′)Hb, C(3′)H), 4.66-4.84 (m,
2H, OCH(CH3)2), 6.24 (dd, J1 ) 8.0 Hz, J2 ) 2.6 Hz, 1H, C(1′)H),
7.55 (d, J ) 1.1 Hz, 1H, T C(6)H), 8.48 (s, 1H, NH); 13C NMR (200
MHz, CDCl3) δC 12.45 (T CH3), 23.92 (CH(CH3)3), 38.27 (C-2′), 63.99
(d, J ) 169.2 Hz, PCH2), 71.26 (CH(CH3)3, 73.36 (C-4′), 80.23 (d, J
) 10.5 Hz, C-3′), 84.83 (C-1′), 110.72 (T C(5)), 136.55 (T C(6)), 150.57
(T C(2)), 163.80 (T C(4)); exact mass calcd for C16H27N2O7P1Na1 [M
+ Na]+ 413.1454, found 413.1447.
δ
H 1.22-1.30 (m, 12H, CH3), 2.27 (d, J ) 15.0, 1H, C(2′)Ha), 2.41-
2.55 (m, 1H, C(2′)Hb), 3.63 (d, J ) 9.5 Hz, 2H, PCH2), 3.91 (dd, J1 )
10.3, J2 ) 3.5, 1H, C(4′)Ha), 4.22-4.36 (m, 2H, C(4′)Hb, C(3′)H),
4.56-4.76 (m, 2H, OCH(CH3)2), 5.77 (d, J ) 7.3 Hz, 1H, C C(5)H),
6.17 (dd, J1 ) 7.3, J2 ) 1.8, 1H, C(1′)H), 7.67 (d, J ) 7.3 Hz, 1H, C
C(6)H), 8.18 (s, 2H, NH2); 13C NMR (200 MHz, CDCl3) δC 23.80
(CH(CH3)3), 38.46 (C-2′), 63.66 (d, JP,C ) 172.2 Hz, PCH2), 71.48 (CH-
(CH3)3), 71.60 (CH(CH3)3), 71.75 (CH(CH3)3), 74.12 (C-4′), 80.40 (d,
JP,C ) 11.2 Hz, C-3′), 86.68 (C-1′), 94.21 (C C(5)), 141.9 (C C(6)),
156.58 (C C(2)), 165.83 (C C(1)); exact mass calcd for C15H26N3O6P1-
Na1 [M + H]+ 376.1637, found 376.1638.
1-(Adenin-9-yl)-3-O-(phosphonomethyl)-L-threose Sodium Salt
(3a). To a solution of 16 (220 mg, 0.55 mmol) and Et3N (1 mL) in
DCM (9 mL) was added bromotrimethylsilane (290 µL, 2.2 mmol) at
room temperature. The reaction mixture was stirred for 48 h. The
reaction was quenched with 1.0 M TEAB solution. The mixture was
concentrated, and the residue was purified by column chromatography
(CH2Cl2:MeOH ) 2:1, 1:1, 1:2) to give the crude title compound.
Purification using Sephadex-DEAE A-25 with gradient TEAB solution
from 0.01 to 0.5 M and ion exchanges by the Dowex-Na+ resin offered
3a (96 mg, 0.25 mmol) as a colorless solid after precipitation from
diethyl ether in 45% yield: 1H NMR (500 MHz, D2O) δH 3.54-3.62
(m, 2H, PCH2), 4.32-4.39 (m, 3H, C(4′)H2, C(3′)H), 4.82 (dd, J1 )
2.4 Hz, J2 ) 2.0 Hz, 1H, C(2′)H), 6.09 (d, J ) 2.4 Hz, 1H, C(1′)H),
8.23 (s, 1H, A C(8)H), 8.45 (s, 1H, A C(2)H); 13C NMR (500 MHz,
D2O) δC 70.1 (d, JP,C ) 164.6 Hz, PCH2), 75.38 (C-4′), 80.70 (C-2′),
87.56 (JP,C ) 9.8 Hz, C-3′), 91.93 (C-1′), 121.21 (A C(5)), 143.74 (A
C(8)), 151.49 (A C(6)), 155.48 (A C(4)), 158.30 (A C(2)); 31P NMR
(500 MHz, D2O) δP 13.64; exact mass calcd for C10H13N5O6P1 [M -
H]- 330.0603, found 330.0602.
1-(Thymin-1-yl)-3-O-(phosphonomethyl)-L-threose Sodium Salt
(3b). This compound was prepared as described for 3a, using 17 (220
mg, 0.58 mmol) as starting material. Compound 3b (90 mg, 0.24 mmol)
was obtained as a colorless solid after precipitation from diethyl ether
in 42% yield: 1H NMR (500 MHz, D2O) δH 1.89 (s, 3H, T CH3), 3.60-
3.68 (m, 2H, PCH2), 4.16 (d, J ) 4.1 Hz, 1H, C(3′)H), 4.24 (dd, J1 )
10.7 Hz, J2 ) 4.1 Hz, 1H, C(4′)Ha), 4.42 (d, J ) 10.7 Hz, 1H, C(4′)-
Hb), 4.45 (s, 1H, C(2′)H), 5.85 (d, J ) 1.2 Hz,1H, C(1′)H), 7.59-7.60
(m, 1H, T C(6)H); 13C NMR (500 MHz, D2O) δC 14.28 (T CH3), 67.95
(d, JP,C ) 157.2 Hz, PCH2), 75.78 (C-4′), 80.17 (C-2′), 87.27 (d, JP,C
) 11.7 Hz, C-3′), 94.22 (C-1′), 113.36 (T C(5)), 140.66 (T C(6)), 154.30
(T C(2)), 169.39 (T C(4)); 31P NMR (500 MHz, D2O) δP 15.68; exact
mass calcd for C10H14N2O8P1 [M - H]- 321.0488, found 321.0474.
1-(Uracil-1-yl)-3-O-(phosphonomethyl)-L-threose Sodium Salt
(3c). This compound was prepared as described for 3a, using 18 (200
mg, 0.53 mmol) as starting material and (TBMS)Br (200 mL, 2.1
mmol). Compound 3c (93 mg, 0.26 mmol) was obtained as a colorless
solid after precipitation from diethyl ether in 49% yield: 1H NMR (500
MHz, D2O) δH 3.58-3.67 (m, 2H, PCH2), 4.16 (d, J ) 3.3 Hz, 1H,
1-(Uracil-1-yl)-2-deoxy-3-O-(diisopropylphosphonomethyl)-L-
threose (22). This compound was prepared as described for 20, using
18 (1.1 g, 2.8 mmol) as starting material. Column chromatographic
purification (CH2Cl2:MeOH ) 40:1) gave compound 22 (500 mg, 1.3
mmol) as a colorless oil in 46% yield: 1H NMR (200 MHz, CDCl3)
δH 1.29-1.34 (m, 12H, CH3), 2.21 (d, J ) 15.4, 1H, C(2′)Ha), 2.44-
2.60 (m, 1H, C(2′)Hb), 3.69 (d, J ) 9.2 Hz, 2H, PCH2), 3.86 (dd, J1 )
10.6 Hz, J2 ) 3.3 Hz, 1H, C(4′)Ha), 4.30-4.38 (m, 2H, C(4′)Hb,
C(3′)H), 4.65-4.81 (m, 2H, OCH(CH3)2), 5.74 (d, J ) 8.1 Hz, 1H, U
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A R T I C L E S
Wu et al.
C(3′)H), 4.26 (dd, J1 ) 10.7 Hz, J2 ) 3.9 Hz, 1H, C(4′)Ha), 4.45 (d, J
) 10.7 Hz, 1H, C(4′)Hb), 4.47 (s, 1H, C(2′)H), 5.85 (d, J ) 8.0 Hz,
1H, U C(5)H), 5.85 (s, 1H, C(1′)H), 7.80 (d, J ) 8.1 Hz, 1H, U C(6)H);
13C NMR (500 MHz, D2O) δC 67.98 (d, J ) 156.2 Hz, PCH2), 76.22
(C-4′), 80.09 (C-2′), 87.15 (d, J ) 11.7 Hz, C-3′), 94.63 (C-1′), 104.09
(U C(5)), 145.23 (U C(6)), 154.26 (U C(2)), 169.22 (U C(4)); 31P NMR
(500 MHz, D2O) δ 15.37; exact mass calcd for C9H12N2O8P1 [M -
H]- 307.0331, found 307.0325.
J2 ) 3.7 Hz, 1H, C(4′)Ha), 4.38-4.40 (m, 1H, C(3′)H), 4.42 (dd, J1 )
10.5 Hz, J2 ) 2.0 Hz, 1H, C(4′)Hb), 5.88 (d, J ) 8.3 Hz, 1H, U C(5)H),
6.21 (dd, J1 ) 8.2 Hz, J2 ) 2.0 Hz, 1H, C(1′)H), 7.99 (d, J ) 8.2 Hz,
1H, U C(6)H); 13C NMR (500 MHz, D2O) δC 39.46 (C-2′), 67.56 (d,
J ) 156.9 Hz, PCH2), 76.77 (C-4′), 82.31 (d, J ) 13.8 Hz, C-3′), 88.57
(C-1′), 101.45 (U C(5)), 145.81 (U C(6), 169.23 (U C(4)); 31P NMR
(500 MHz, D2O) δP 15.72; exact mass calcd for C9H12N2O7P1 [M -
H]- 291.0382, found 291.0391.
1-(Cytosin-1-yl)-3-O-(phosphonomethyl)-L-threose Sodium Salt
(3d). This compound was prepared as described for 3a, using 19 (150
mg, 0.38 mmol) as starting material. Compound 3d (58 mg, 0.16 mmol)
was obtained as a colorless solid after precipitation from diethyl ether
in 43% yield: 1H NMR (500 MHz, D2O) δH 3.53-3.62 (m, 2H, PCH2),
4.15 (d, J ) 3.7 Hz, 1H, C(3′)H), 4.27 (dd, J1 ) 10.7 Hz, J2 ) 3.7 Hz,
1H, C(4′)Ha), 4.42 (s, 1H, C(2′)H), 4.44 (d, J ) 10.7 Hz, 1H, C(4′)-
Hb), 5.86 (s, 1H, C(1′)H), 6.01 (d, J ) 7.6 Hz, 1H, C C(5)H), 7.77 (d,
J ) 7.6 Hz, 1H, C C(6)H); 13C NMR (500 MHz, D2O) δC 68.0 (d, JP,C
) 156.2 Hz, PCH2), 76.17 (C-4′), 80.13 (C-2′), 87.27 (d, JP,C ) 11.8
Hz, C-3′), 95.16 (C-1′), 98.23 (C C(5)), 145.04 (C C(6)), 160.06 (C
C(2)), 168.84 (C C(4)); 31P NMR (500 MHz, D2O) δP 15.28; exact
mass calcd for C9H13N3O7P1 [M - H]- 306.0491, found 306.0481.
1-(Adenin-1-yl)-2-deoxy-3-O-(phosphonomethyl)-L-threose So-
dium Salt (3e). This compound was prepared as described for 3a, using
20 (70 mg, 0.23 mmol) as starting material. Compound 3e (38 mg,
0.11 mmol) was obtained as a colorless solid after precipitation from
diethyl ether in 43% yield: 1H NMR (500 MHz, D2O, 60 °C) δH 2.63-
(dd, J1 ) 15.5 Hz, J2 ) 1.3 Hz, 1H, C(2′)Ha), 2.75-2.81 (m, 1H, C(2′)-
Hb), 3.55-3.64 (m, 2H, PCH2), 4.09 (dd, J1 ) 10.0 Hz, J2 ) 4.0 Hz,
1H, C(4′)Ha), 4.33 (d, J ) 10.0 Hz, 1H, C(4′)Hb), 4.51 (dd, J1 ) 5.5
Hz, J2 ) 4.5 Hz, 1H, C(3′)H), 6.39 (dd, J1 ) 8.0 Hz, J2 ) 2.0 Hz, 1H,
C(1′)H), 8.22 (s, 1H, A C(2)H), 8.49 (s, 1H, A C(8)H); 13C NMR (500
MHz, D2O) δC 39.78 (C-2′), 68.34 (d, JP,C ) 155.2 Hz, PCH2), 76.53
(C-4′), 82.79 (d, JP,C ) 11.9 Hz, C-3′), 86.32 (C-1′), 121.13 (A C(5)),
143.89 (A C(8)), 151.33 (A C(6)), 155.25 (A C(4)), 158.18 (A C(2));
31P NMR (500 MHz, D2O) δP 154.46; exact mass calcd for C10H13N5O5P1
[M - H]- 314.0654, found 314.0632. Anal. Calcd for C10H12N5Na2O5P‚
2H2O: C, 30.39; H, 4.08; N, 17.72. Found: C, 30.39; H, 4.77; N, 17.42.
1-(Cytidin-1-yl)-2-deoxy-3-O-(phosphonomethyl)-L-threose So-
dium Salt (3h). This compound was prepared as described for 3f, using
23 (200 mg, 0.53 mmol) as starting material and iodotrimethylsilane
(0.6 mL, 4.2 mmol). Compound 3h (130 mg, 0.38 mmol) was obtained
as a colorless solid after precipitation from diethyl ether in 73% yield:
1H NMR (500 MHz, D2O) δH 2.32 (d, J ) 15.3, 1H, C(2′)Ha), 2.56-
2.61 (m, 1H, C(2′)Hb), 3.52-3.61 (m, 2H, PCH2), 4.01 (dd, J1 ) 10.5
Hz, J2 ) 3.6 Hz, 1H, C(4′)Ha), 4.39-4.40 (m, 1H, C(3′)H), 4.44 (dd,
J1 ) 10.7 Hz, J2 ) 1.7 Hz, 1H, C(4′)Hb), 6.06 (d, J ) 7.6 Hz, 1H, C
C(5)H), 6.20 (dd, J1 ) 7.8 Hz, J2 ) 2.0 Hz,1H, C(1′)H), 7.95 (d, J )
7.6 Hz, 1H, C C(6)H); 13C NMR (500 MHz, D2O) δC 37.22 (C-2′),
64.88 (d, J ) 157.2 Hz, PCH2), 74.37 (C-4′), 79.99 (d, J ) 11.7 Hz,
C-3′), 86.71 (C-1′), 95.99 (C C(5)), 143.02 (C C(6), 157.56 (C C(2)),
169.23 (C C(4)); 31P NMR (500 MHz, D2O) δP 15.96; exact mass calcd
for C9H13N3O6P1 [M - H]- 290.0535, found 290.0542.
1-(Adenin-9-yl)-2-deoxy-3-O-(diphosphorylphosphonomethyl)-L-
threose (24). A solution of the phosphonate triethylamine salt 3e (52
mg, 0.12 mmol) in DMF (12 mL) was treated with dimethylformamide
dimethyl acetal (0.72 mL) and kept at room temperature overnight.
After evaporation of the solvent, the residue was dissolved in DMF
(7.2 mL) and treated with N,N′-carbonyldiimidazole (58 mg, 0.36
mmol). After 12 h a 1 M solution of dibutylammonium pyrophosphate
in DMF (2.0 mL) was added, and the mixture was kept at room
temperature for 2 h. Then the mixture was treated with NH4OH (2.4
mL) and subsequently concentrated under reduced pressure for 1 h.
The residue was purified by chromatography on DEAE with a linear
gradient of triethylammonium bicarbonate (0-0.8 M) as eluent. Further
purification was carried out by reversed-phase chromatography on a
LiChroprep C-18 column (2 × 30 cm). 3e (5 mg, 0.01 mmol) as
1
colorless oil was obtained in 8% yield. The H NMR spectrum of 24
1-(Thymin-1-yl)-2-deoxy-3-O-(phosphonomethyl)-L-threose So-
dium Salt (3f). To a solution of 21 (260 mg, 0.67 mmol) and Et3N (1
mL) in DCM (25 mL) was added iodotrimethylsilane (0.73 mL, 5.36
mmol) at 0 °C. The reaction mixture was stirred for 2 h. The reaction
was quenched with 1.0 M TEAB solution. The mixture was concen-
trated, and the residue was purified by column chromatography (CH2-
Cl2:MeOH ) 2:1, 1:1, 1:2) to give crude 3f. Purification using
Sephadex-DEAE A-25 with gradient TEAB solution from 0.01 to 0.5
M and ion exchanges by the Dowex-Na+ resin offered 3f (95 mg, 0.27
mmol) as a colorless solid after precipitation from diethyl ether in 40%
yield: 1H NMR (500 MHz, D2O) δH 1.91 (s, 3H, T CH3), 2.29 (d, J )
15.4 Hz, 1H, C(2′)Ha), 2.58-2.64 (m, 1H, C(2′)Ha), 3.57-3.65 (m,
2H, PCH2), 3.95 (dd, J1 ) 10.5 Hz, J2 ) 3.4 Hz, 1H, C(4′)Ha), 4.38-
4.41 (m, 2H, C(4′)Hb, C(3′)H), 6.20 (dd, J1 ) 8.3 Hz, J2 ) 2.4 Hz, 1H,
C(1′)H), 7.78 (d, J ) 1.0 Hz, 1H, T C(6)H); 13C NMR (500 MHz,
D2O) δC 14.50 (T CH3), 39.62 (C-2′), 67.81 (d, J ) 158.1 Hz, PCH2),
76.63 (C-4′), 82.66 (d, J ) 11.3 Hz, C-3′), 88.41 (C-1′), 113.94 (T
(C(5)), 141.32 (T (C(6)), 154.68 (T (C(2)), 169.51 (T C(4)); 31P NMR
(500 MHz, D2O) δP 16.02; exact mass calcd for C10H14N2O7P1 [M -
H]- 305.0538, found 305.0537. Anal. Calcd for C10H14N2Na1O7P‚
2H2O: C, 32.98; H, 4.98; N, 7.69. Found: C, 32.84; H, 4.94; N, 7.80.
was identical to that of 3e. Other data: 31P NMR (D2O) δP -22.73
(P-â), -10.28 (P-γ), 9.05 (P-R); exact mass calcd for C10H15N5O11P3
[M - H]- 473.9950.
Kinetic Measurements. Determination of Km and kcat values for the
incorporation of dATP and PMDTApp into a DNA hybrid was carried
out under steady-state conditions as described by Creighton et al.28 For
each Km and kcat determination eight different substrate concentrations
in the range of 0.1-12.5 µM were used. Results are the average of
three independent determinations. The reaction mixture contained 250
nM primer/template complex and 0.025 U/µL HIV reverse transcriptase.
The reaction was quenched after 1, 2, and 3 min by adding a double
volume of stop solution (90% formamide, 0.05% bromophenol blue,
0.05% xylene cyanol, and 50 mM EDTA). Samples were analyzed by
gel electrophoresis on a 16% polyacrylamide ureum gel in TBE buffer
(89 mM Tris-borate, 2 mM EDTA buffer, pH 8.3) after they were
heated for 5 min at 70 °C. Products were visualized by phosphorim-
aging. The amount of radioactivity in the bands corresponding to the
products of the enzymatic reactions was determined using the Optiquant
image analysis software (Packard). Rate profiles were determined using
GraphPad Prism software.
1-(Uracil-1-yl)-2-deoxy-3-O-(phosphonomethyl)-L-threose Sodium
Salt (3g). This compound was prepared as described for 3f, using 22
(154 mg, 0.41 mmol) as starting material and iodotrimethylsilane (0.47
mL, 3.3 mmol). Compound 3g (50 mg, 0.14 mmol) was obtained as a
colorless solid after precipitation from diethyl ether in 34% yield: 1H
NMR (500 MHz, D2O) δH 2.31-2.35 (m, 1H, C(2′)Ha), 2.57-2.62
(m, 1H, C(2′)Hb), 3.54-3.62 (m, 2H, PCH2), 3.97 (dd, J1 ) 10.5 Hz,
Construction of a Model. 1. Electrostatic Charges. Atomic
electrostatic charges to be used in the Amber software package were
calculated from the electrostatic potential at the 6-31G* level using
the package Gamess29 and the two-stage RESP fitting procedure keeping
(28) Creighton, S.; Bloom, L. B.; Goodman, M. F. Methods Enzymol. 1995,
262, 232-256.
9
5064 J. AM. CHEM. SOC. VOL. 127, NO. 14, 2005

Anti-HIV Phosphonate Nucleosides
A R T I C L E S
account of the phosphate linkages.30 Also, the adenine base atomic
charges were kept the same as those of DNA adenine in the Amber 94
topology files.31
this modeling work the variable angles were the ø angle and the angles
in the 3′-phosphonate linker. The molecule in the resulting conformation
was then brought into the enzyme. The base was modified to an adenine
(by fitting onto an adenine base nucleotide by Quatfit (Quatfit, CCL).
The complementary adenine base (E5) was changed into a thymine by
a similar procedure.
A phosphodiester bond was created between the terminal residue of
the primer and the introduced phosphonate nucleotide. The Amber
molecular mechanics energy of the system was minimized in the sander
module of Amber 7 for 5000 steps.38
4. Analysis. The phosphonate nucleotide fits into the enzyme. The
puckering of the sugar ring is between O4′-endo and C3′-endo. A
combined Ligplot/HBPlus analysis39,40 reveals hydrophobic contact with
Asp185, Tyr115, and Gln151. However, no sterical hindrance with
Met184 or Asp185 is to be expected to occur during translocation (the
closest contact is for Asp185 OD2 999.O1P, 2.5 Å).
2. Amber Parameters. The force field parameters used in the Amber
simulations are those from the parm99 dataset.32 However, they were
modified for polyphosphate by contributions developed by H. A.
Carlson33 and for P-C linkage by M. Baaden.34
3. Model Building. The modeling is based on the PDB structure
file 1rtd.35 An initial model of the phosphonate nucleotide with a
thymine base was constructed in Macromodel.36 The geometry was
optimized in Gamess in the AM1 force field.29
A locally developed software (Dancer) was used to fit the structure
on the entering triphosphate in the 1rtd structure. This software performs
a flexible fit by optimizing some defined dihedral angles and using a
fitting procedure similar to the one used in the SEAL package.37 In
Acknowledgment. We thank Chantal Biernaux for excellent
editorial help. We are indebted to Dr. William A. Lee (Gilead
Sciences) for a generous gift of human DNA polymerase R,
and Marleen Renders for performing the DNA polymerase R
assay. Luk Baudemprez is acknowledged for running the NMR
spectra.
(29) Schmidt, M. W.; Baldridge, K. K.; Boatz, J. A.; Elbert, S. T.; Gordon, M.
S.; Jensen, J. H.; Koseki, S.; Matsunaga, N.; Nguyen, K. A.; Su, S.; Windus,
T. L.; Dupuis, M.; Montgomery, J. A. J. Comput. Chem. 1993, 14, 1347-
1363.
(30) Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem.
1993, 97, 10269-10280.
(31) Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.;
Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P.
A. J. Am. Chem. Soc. 1995, 117, 5179-5197.
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(33) Meagher, K. L.; Redman, L. T.; Carlson, H. A. J. Comput. Chem. 2003,
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(37) Kearsley, S. K.; Smith, G. M. Tetrahedron Comput. Methodol. 1990, 3,
615-633.
(34) Baaden, M.; Wipff, G.; Yaftian, M. R.; Burgard, M.; Matt, D. J. Chem.
Soc., Perkin Trans. 2 2000, 1315-1321.
(38) Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. R.; Cheatham, T.
E.; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. Comput. Phys.
Commun. 1995, 91, 1-41.
(35) Huang, H.; Chopra, R.; Verdine, G. L.; Harrison, S. C. Science 1998, 282,
1669-1675.
(36) Mohamadi, F.; Richards, N. G. J.; Guida, W. C.; Liskamp, R.; Lipton, M.;
Caufield, C.; Chang, G.; Hendrickson, T.; Still, W. C. J. Comput. Chem.
1990, 11, 440-467.
(39) Wallace, A. C.; Laskowski, R. A.; Thornton, J. M. Protein Eng. 1995, 8,
127-134.
(40) McDonald, I. K.; Thornton, J. M. J. Mol. Biol. 1994, 238, 777-793.
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