Synthesis and anti-HIV activity of 4′-cyano-2′,3′ -didehydro-3′-deoxythymidine

Article abstract of DOI:10.1081/NCN-120030721

A new anti-HIV agent 4′-cyano-2′,3′-didehydro-3′ -deoxythymidine (9) was synthesized by allylic substitution of the 3′,4′-unsaturated nucleoside 14, having a leaving group at the 2′-position, with cyanotrimethylsilane in the presence of SnCl4. Evaluation

Full text of DOI:10.1081/NCN-120030721

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Synthesis and Anti‐HIV Activity of
4′‐Cyano‐2′,3′‐didehydro‐3′‐deoxythymidine
Kazuhiro Haraguchi Ph.D. a , Yoshiharu Itoh a d , Shingo Takeda a , Yosuke Honma a
, Hiromichi Tanaka a , Takao Nitanda b , Masanori Baba b , Ginger E. Dutschman c &
Yung‐Chi Cheng c
a School of Pharmaceutical Sciences , Showa University , 1‐5‐8 Hatanodai, Shinagawa‐ku,
Tokyo, 142‐8555, Japan
b Center for Chronic Viral Diseases , Division of Human Retroviruses , Faculty of
Medicine , Kagoshima University , 8‐35‐1 Sakuragaoka, Kagoshima, 890‐8520, Japan
c Department of Pharmacology , School of Medicine , Yale University , 333 Cedar street,
New Haven, Connecticut, 06520, USA
d Central Pharmaceutical Research Institute , Japan Tobacco Inc. , Takatsuki, Osaka,
Japan
Published online: 07 Feb 2007.
To cite this article: Kazuhiro Haraguchi Ph.D. , Yoshiharu Itoh , Shingo Takeda , Yosuke Honma , Hiromichi Tanaka ,
Takao Nitanda , Masanori Baba , Ginger E. Dutschman & Yung‐Chi Cheng (2004) Synthesis and Anti‐HIV Activity of
4′‐Cyano‐2′,3′‐didehydro‐3′‐deoxythymidine, Nucleosides, Nucleotides and Nucleic Acids, 23:4, 647-654, DOI: 10.1081/
NCN-120030721
To link to this article: http://dx.doi.org/10.1081/NCN-120030721
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NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS
Vol. 23, No. 4, pp. 647–654, 2004
Synthesis and Anti-HIV Activity of
4’-Cyano-2’,3’-didehydro-3’-deoxythymidine
Kazuhiro Haraguchi,1, Yoshiharu Itoh,1,# Shingo Takeda,1
*
Yosuke Honma,1 Hiromichi Tanaka,1 Takao Nitanda,2 Masanori Baba,2
Ginger E. Dutschman,3 and Yung-Chi Cheng3
1School of Pharmaceutical Sciences, Showa University, Shinagawa-ku,
Tokyo, Japan
2Center for Chronic Viral Diseases, Division of Human Retroviruses,
Faculty of Medicine, Kagoshima University, Kagoshima, Japan
3Department of Pharmacology, School of Medicine, Yale University, New Haven,
Connecticut, USA
ABSTRACT
A new anti-HIV agent 4’-cyano-2’,3’-didehydro-3’-deoxythymidine (9) was synthe-
sized by allylic substitution of the 3’,4’-unsaturated nucleoside 14, having a leaving
group at the 2’-position, with cyanotrimethylsilane in the presence of SnCl4.
Evaluation of the anti-HIV activity of 9 showed that this compound is much less
potent than the recently reported 2’,3’-didehydro-3’-deoxy-4’-(ethynyl)thymidine (1).
Key Words: Anti-HIV; Cyano; Didehydro-3’-deoxythymidine; Unsaturated-sugar
nucleoside; Phenylselenide anion; Allylic substitution; Organosilicon reagent.
*
Correspondence: Kazuhiro Haraguchi, Ph.D., School of Pharmaceutical Sciences, Showa
University, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo 142-8555, Japan; E-mail: harakazu@pharm.
showa-u.ac.jp.
#Current address: Yoshiharu Itoh, Central Pharmaceutical Research Institute, Japan Tobacco Inc.,
Takatsuki, Osaka, Japan.
647
DOI: 10.1081/NCN-120030721
1525-7770 (Print); 1532-2335 (Online)
www.dekker.com
Copyright D 2004 by Marcel Dekker, Inc.

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INTRODUCTION
During our recent studies on the reaction of organometallic reagents with 4’,5’-
epoxy nucleosides,[1] 2’,3’-didehydro-3’-deoxy-4’-(ethynyl)thymidine (1) was synthe-
sized.[2] Biological evaluation of 1 revealed that this compound is a more potent anti-
HIV agent than the parent compound stavudine (2).[2–6] This finding was quite
unexpected, since it has been reported that removal of the 3’-hydroxyl group in the
anti-HIV active 4’-azidothymidine (3) leads to complete loss of the activity: compounds
4 and 5 are devoid of the activity.[7] An additional advantage of 1 is the fact that this
compound is less toxic to CEM cell growth and less inhibitory to mitochondrial DNA
synthesis than stavudine (2).
As a result of our brief examination of structure-activity relationship (SAR) of
4’-carbon-substituted 2’,3’-didehydro-3’-deoxythymidine derivatives, it became apparent
that the introduction of a methyl or vinyl group at the 4’-position leads to complete loss
of the activity (6[8] and 7),[2] and that alkylation of the ethynyl group of 1 is also
discouraging (for example, 8). From these results, one would readily expect that
suitable 4’-substituents should possess an sp-hybridized carbon atom, and its size should
be as small as possible. We describe here the synthesis and anti-HIV activity of
4’-cyano-2’,3’-didehydro-3’-deoxythymidine (9) motivated by the above considerations.
RESULTS AND DISCUSSION
Nucleosides having a cyano group at the 4’-position have mostly been synthesized
by manipulation of the respective 4’-hydroxymethyl precursors.[9] In 1996, an allylic
substitution of 3’,4’-unsaturated nucleosides having a leaving group at the 2’-position
was reported from our laboratory.[10] This method provides a new entry to the synthesis
of 4’-branched 2’,3’-didehydro-2’,3’-dideoxyribonucleosides. Also reported in this paper
is the fact that, irrespective of the stereochemistry (‘‘up’’ or ‘‘down’’) of the 2’-leaving
group, incoming nucleophiles attack the 4’-position from both the a- and b-faces,
presumably due to the intervention of an oxonium intermediate. Since organosilicon
reagents, including cyanotrimethylsilane, can be used as nucleophiles in combination
with SnCl4, this methodology was used for the present purpose.
Preparation of the 3’,4’-unsaturated thymine nucleoside 14, to be used as a sub-
strate for the allylic substitution, is shown in Scheme 1. Thus, 1-(b-D-ribofuranosyl)
thymine was converted to the 2’,3’-epoxide 10 according to the published procedure.[11]
Cleavage of the epoxide ring was conducted by reacting with a phenylselenide anion

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649
Scheme 1. Preparation of the 3’,4’-unsaturated thymine nucleoside.
[12]
prepared by reducing (PhSe)2 with LiAlH4
(in dioxane, for 2 h at room temperature)
to give the desired 3’-phenylseleno derivative (11, 56%) as well as its 2’-isomer (12,
42%). The 5’-O-trityl group of 11 was replaced with tert-butyldiphenylsilyl group from
the expectation that the anisotropic effect of this silyl protecting group would serve as a
stereochemical determinant of the 4’-substituted products at a later stage. Further
Scheme 2. 3’,4’-Unsaturated thymine nucleoside reacting with cyanotrimethylsilane.

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Haraguchi et al.
Table 1. Anti-HIV-1 activity in MT-2 cells.a
IC50 (mM)b
Compound
CC50 (mM)c
9
7.0 2.6
0.25 0.14
1.3 0.4
>100
>100
>100
1
Stavudine (2)
aData represent mean values for two separate experiments.
bInhibitory concentration required to achieve 50% protection of MT-2 cells
against the cytopathic effect of HIV-1.
cCytotoxic concentration required to reduce the viability of mock-infected
MT-2 cells by 50%.
acetylation of the 2’-hydroxyl group gave 13. Oxidation of 13 with m-CPBA gave the
corresponding selenoxide in 70% yield. Subsequent elimination of benzeneselenenic
acid was carried out in THF at 70°C for 1 h in the presence of i-Pr2NEt. Despite the
presence of two syn-hydrogens (H-2’ and H-4’) available for the elimination, exclusive
removal of the H-4’ was observed in this reaction to give the 3’,4’-unsaturated
derivative 14 as the sole product in 67% yield.
When 14 was reacted with cyanotrimethylsilane (10 equiv.) in the presence of
SnCl4 (5 equiv.) in CH2Cl2 at À70°C for 5 h, no SN2 product was formed. Instead two
isomeric products 15 (48%) and 16 (43%) resulting from allylic substitution were
isolated as shown in Scheme 2. The depicted stereochemistry of 15 at the 4’-position
was deduced from the 1H NMR observation that its 5-Me resonance appeared at a
significantly higher field of d 1.53 when compared with that of 16 (d 1.95) or 14
(d 1.92), due to the anisotropic effect of the phenyl ring in the 5’-O-protecting group.
Finally, removal of the 5’-O-silyl group in 15 was carried out with Bu4NF in THF to
give the desired 4’-cyano analogue 9 in almost quantitative yield.
Compound 9 thus synthesized was assayed for its ability to inhibit the replication
of HIV-1 in MT-2 cell culture by the reported procedure.[13] In Table 1 are shown the
assay results of 9 together with those of 1 and the parent compound stavudine (2).
Although the 4’-cyano analogue (9) was found to be active as we anticipated, its
activity is almost five times lower than that of stavudine (2). Further SAR studies on
this class of compounds are currently under investigation in our laboratory.
EXPERIMENTAL SECTION
1
Melting points are uncorrected. H NMR and 13C NMR were measured on a JEOL
JNM-LA 500 (500 MHz). Chemical shifts are reported relative to Me4Si. Mass spectra
(MS) were taken in FAB mode with m-nitrobenzyl alcohol as a matrix on a JEOL JMS-
700. Ultraviolet spectra (UV) were recorded on a JASCO V-530 spectrophotometer.
Column chromatography was carried out on silica gel (Micro Bead Silica Gel PSQ
100B, Fuji Silysia Chemical Ltd.). Thin layer chromatography (TLC) was performed on
silica gel (precoated silica gel plate F254, Merck). Where necessary, analytical samples
were purified by high-performance liquid chromatography (HPLC). HPLC was carried

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651
out on a Shimadzu LC-6AD with a Shim-pack PREP-SIL (H). KIT column (2 Â 25
cm). THF was distilled from benzophenone ketyl.
1-[2,3-Anhydro-5-O-trityl-b-D-lyxofuranosyl]thymine (10). To a pyridine
(30 mL) suspension of 1-(b-D-ribofuranosyl)thymine (5.16 g, 20 mmol) was added
TrCl (6.69 g, 24 mmol) at 0°C under Ar atmosphere, and the reaction mixture was
stirred at rt overnight. To this was added MsCl (4.6 mL, 60 mL), and the mixture was
stirred at 0°C for 5 h. The reaction mixture was quenched by adding ice chips and then
partitioned between CHCl3/H2O (200 mL Â 2/100 mL). Column chromatography (4%
MeOH in CH2Cl2) of the organic layer gave 1-(2,3-di-O-mesyl-5-O-trityl-b-D-
ribofuranosyl)thymine, which was dissolved in EtOH (200 mL). To the EtOH solution
of the product was added 1 M NaOH (200 mL), and the mixture was stirred at
refluxing temperature for 2 h. The reaction mixture was neutralized with 1 M HCl,
evaporated to dryness, and partitioned between EtOAc/H2O (200 mL/50 mL Â 4).
Column chromatography (hexane/EtOAc = 1/4) of the organic layer gave 10 (3.80 g,
1
39%) as a solid: mp 174–175°C; H NMR (CDCl3)d1.83 (3H, d, J5-Me,6 = 1.3 Hz,
5-Me), 3.39 (1H, dd, J5’a,5’b = 9.7 and J4’,5’a = 5.5 Hz, H-5’), 3.49 (1H, dd, J5’a,5’b
=
9.7 and J4’,5’b = 5.9 Hz, H-5’), 3.87 (1H, dd, J3’,4’ = 0.8 and J2’,3’ = 2.8 Hz, H-3’), 3.91
(1H, dd, J1’,2’ = 0.7 and J2’,3’ = 2.8 Hz, H-2’), 4.14–4.17 (1H, m, H-4’), 6.19 (1H, d,
J1’,2’ = 0.7 Hz, H-1’), 7.24–7.33 (9H, m, Tr), 6.98 (1H, d, J5-Me,6 = 1.3 Hz, H-6), 7.46–
7.49 (6H, m, Tr), 8.61 (1H, br NH); FAB-MS (m/z) 483 (M++ H).
1-(3-Deoxy-3-phenylseleno-5-O-trityl-b-D-arabinofuranosyl)thymine (11) and
1-(2-Deoxy-2-phenylseleno-5-O-trityl-b-D-xylofuranosyl)thymine (12). To a diox-
ane (20 mL) suspension of the phenylselenide anion,[12] prepared from (PhSe)2 (3.94 g,
12.61 mmol) and LiAlH4 (359 mg, 9.46 mmol), was added 10 (3.80 g, 7.88 mmol)
dissolved in dioxane (20 mL), and the mixture was stirred at rt for 2 h under Ar
atmosphere. Neutralization of the reaction mixture with AcOH followed by column
chromatography (hexane/EtOAc = 1/2) gave 11 (2.82 g, 56%, foam) and 12 (2.12 g,
42%, foam).
1
Physical data of 11: H NMR (CDCl3, after addition of D2O)d2.05 (3H, s, 5-Me),
3.43 (1H, dd, J5’a,5’b = 11.0 and J4’,5’a = 3.6 Hz, H-5’), 3.59–3.65 (2H, m, H-5’ and
H-3’), 3.97–4.01 (1H, m, H-4’), 4.48 (1H, dd, J2’,3’ = 5.4 and J1’,2’ = 5.2 Hz, H-2’), 6.05
(1H, d, J1’,2’ = 5.2 Hz, H-1’), 7.21–7.32, 7.32–7.38 and 7.46–7.53 (20H, each as m, Tr
and SePh), 7.71 (1H, s, H-6); FAB-MS (KI, m/z) 679 (M++ K).
Physical data of 12: 1H NMR (CDCl3, after addition of D2O)d1.65 (3H, d,
J5-Me,6 = 1.2 Hz, 5-Me), 3.51 (1H, dd, J5’a,5’b = 10.6 and J4’,5’a = 4.0 Hz, H-5’), 3.58 (1H,
dd, J5’a,5’b = 10.6 and J4’,5’b = 4.4 Hz, H-5’), 3.76 (1H, dd, J3’,4’ = 4.6 and J2’,3’ = 3.2 Hz,
H-3’), 4.23–4.25 (1H, m, H-4’), 4.29 (1H, dd, J2’,3’ = 3.2 and J1’,2’ = 4.4 Hz, H-2’), 6.01
(1H, d, J1’,2’ = 4.4 Hz, H-1’), 7.25–7.34, 7.41–7.44 and 7.61–7.63 (21H, each as m, Tr
and SePh), 6.98 (1H, d, J5-Me,6 = 1.3 Hz, H-6); FAB-MS (KI, m/z) 679 (M+ + K).
1-[2-O-Acetyl-5-O-(tert-butyldiphenylsilyl)-3-deoxy-3-phenylseleno-b-D-arabino-
furanosyl]thymine (13). An 80% AcOH (40 mL) solution of 11 (1.67 g, 2.61 mmol)
was stirred at 80°C for 1h. Evaporation of the reaction mixture followed by column
chromatography (3% MeOH in CH2Cl2) gave 1-(3-deoxy-3-phenylseleno-b-D-arabino-
furanosyl)thymine (0.57 g, 55%) as a syrup. To a pyridine (7 mL) solution of this

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Haraguchi et al.
product (563.9 mg, 1.42 mmol) was added t-butyldiphenylsilyl chloride (0.55 mL,
2.13 mmol). After stirring overnight at rt, the reaction mixture was quenched with
EtOH and evaporated to dryness. Column chromatography (hexane/AcOEt = 1/4) of the
residue gave 1-[5-O-(tert-butyldiphenylsilyl)-3-deoxy-3-phenylseleno-b-D-arabinofura-
nosyl]thymine (675.8 mg, 75%) as a syrup. A mixture of this product (633.4 mg,
1.0 mmol), i-Pr2NEt (0.52 mL, 3.0 mmol), Ac2O (0.19 mL, 2.0 mmmol), and DMAP
(24.4 mg, 0.2 mmol) in CH2Cl2 (10 mL) was stirred at rt for 1 h. The reaction mixture
was partitioned between CHCl3/sat. NaHCO3 (150 mLx2/50 mL). Column chromatog-
raphy (hexane/EtOAc = 1/1) of the organic layer gave 13 (599.3 mg, 88%) as a foam:
1H NMR (CDCl3)d1.09 (9H, s, t-Bu), 1.65 (3H, s, 5-Me), 1.89 (3H, s, Ac), 3.82 (1H,
dd, J3’,4’ = 8.6 and J2’,3’ = 6.0 Hz, H-3’), 3.89–3.95 (2H, m, H-5’), 4.01–4.04 (1H, m,
H-4’), 5.54 (1H, dd, J2’,3’ = 6.0 and J1’,2’ = 5.2 Hz, H-2’), 6.09 (1H, d, J1’,2’ = 5.2 Hz,
H-1’), 7.29–7.48, 7.59–7.67 (16H, each as m, SiPh, SePh, and H-6), 8.18 (1H, br, NH);
FAB-MS (m/z) 679 (M++ H), 621 (M+-t-Bu).
1-[2-O-Acetyl-5-O-(tert-butyldiphenylsilyl)-b-L-glycero-pent-3-enofuranosyl]
thymine (14). To a CH2Cl2 (8 mL) solution of 13 (563.8 mg, 0.83 mmol) was added
m-CPBA (172.6 mg, 1.0 mmol) in CH2Cl2 (4 mL) at 0°C, and the mixture was stirred
for 30 min. The reaction mixture was neutralized with Et3N and partitioned between
CHCl3/sat. NaHCO3 (150 mL Â 3/50 mL). Column chromatography (3% MeOH in
CH2Cl2) of the organic layer gave the corresponding selenoxide (403.4 mg, 70%) as a
foam. A mixture of this selenoxide (372.3 mg, 0.54 mmol) and i-Pr2NEt (0.74 mL,
1.61 mmol) in THF (7 mL) was stirred at 70°C under Ar atmosphere for 1 h.
Evaporation of the reaction mixture followed by column chromatography (hexane/
EtOAc = 2/1) gave 14 (188.4 mg, 67%) as a foam: 1H NMR (CDCl3)d1.09 (9H, s, t-Bu),
1.92 (3H, d, J5-Me,6 = 1.2 Hz, 5-Me), 1.95 (3H, s, Ac), 4.27 (1H, ddd, J5’a,5’b = 15.0 and
J2’,5’a = J3’,5’a = 1.6 Hz, H-5’), 4.32 (1H, ddd, J5’a,5’b = 15.0 and J2’,5’b = J3’,5’b = 1.2 Hz,
H-5’), 5.29–5.30 (1H, m, H-3’), 5.83 (1H, m, H-2’), 6.66 (1H, d, J1’,2’ = 7.2 Hz, H-1’),
7.01 (1H, q, J5-Me,6 = 1.2 Hz, H-6), 7.39–7.49 and 7.66–7.70 (10H, m, SiPh), 8.20 (1H,
br, NH); FAB-MS (m/z) 521 (M++ H) and 463 (M+-t-Bu).
5’-O-(tert-Butyldiphenylsilyl)-4’-cyano-2’,3’-didehydro-3’-deoxythymidine (15)
and Its 4’-epimer (16). To a CH2Cl2 (3.5 mL) solution of 14 (52.1 mg, 0.1 mmol)
was added Me3SiCN (0.13 mL, 1.0 mmol) and then SnCl4 (0.5 mL, 0.5 mmol) at
À70°C under Ar atmosphere. After being stirred at À70°C for 5 h, the reaction mixture
was partitioned between CHCl3/sat. NaHCO3 (60 mL Â 3/20 mL). Purification of the
organic layer by preparative TLC (hexane/AcOEt = 1/1) gave 15 (23.3 mg, 48%,
1
syrup) and 16 (20.8 mg, 43%, syrup). Physical data of 15: H NMR (CDCl3)d1.11 (9H,
s, t-Bu), 1.53 (3H, d, J5-Me,6 = 1.2 Hz, 5-Me), 3.94 (1H, d, J5’a,5’b = 11.2 Hz, H-5’),
4.04 (1H, d, J5’a,5’b = 11.2 Hz, H-5’), 6.15 (1H, dd, J1’,3’ = 1.2 and J2’,3’ = 6.0 Hz, H-3’),
6.39 (1H, dd, J1’,2’ = 2.0 and J2’,3’ = 6.0 Hz, H-2’), 6.80 (1H, d, J5-Me,6 = 1.2 Hz, H-6),
7.23 (1H, dd, J1’,3’ = 1.2 and J1’,2’ = 2.0 Hz, H-1’), 7.37–7.49 and 7.62–7.67 (10H,
each as m, SiPh), 8.87 (1H, br, NH); FAB-MS (m/z) 488 (M++ H). Physical data of 16:
1H NMR (CDCl3) d1.09 (9H, s, t-Bu), 1.95 (3H, d, J5-Me,6 = 1.2 Hz, 5-Me), 3.77 (1H,
d, J5’a,5’b = 10.0 Hz, H-5’), 3.93 (1H, d, J5’a,5’b = 10.0 Hz, H-5’), 6.13 (1H, dd,
J1’,3’ = 1.8 and J2’,3’ = 6.0 Hz, H-3’), 6.40 (1H, dd, J1’,2’ = 1.8 and J2’,3’ = 6.0 Hz, H-2’),

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6.99 (1H, d, J5-Me,6 = 1.2 Hz, H-6), 7.10 (1H, t, J1’,2’ = J1’,3’ = 1.8 Hz, H-1’), 7.40–7.49
and 7.63–7.67 (10H, each as m SiPh), 8.75(1H, br, NH); FAB-MS (m/z) 488 (M+ + H).
4’-Cyano-2’,3’-didehydro-3’-deoxythymidine (9). To a THF (4 mL) solution of
15 (48.1 mg, 0.099 mmol) was added Bu4NF.3H2O (39.2 mg, 0.15 mmol) at 0°C, and
the mixture was stirred at rt for 1 h. Evaporation of the reaction mixture followed by
column chromatography (3% MeOH in CH2Cl2) of the residue gave 9 (24.5 mg, 99%)
as a solid: mp 234–237°C; IR (KBr) 2260 cmÀ1 (CN); UV(MeOH)lmax 267 nm
(e12700),lmin 235 nm (e5900); 1H NMR (DMSO-d6 after addition of D2O) d1.74 (3H d,
J5-Me,6 = 1.2 Hz, 5-Me), 3.74 (1H, d, Jgem = 11.9 Hz, H-5’), 3.79 (1H, d, Jgem
=
11.9 Hz, H-5’), 6.33 (1H, dd, J1’,3’ = 1.3, J2’,3’ = 5.8 Hz, H-3’), 6.55 (1H, dd, J1’,2’ = 2.2,
J2’,3’ = 5.8 Hz, H-2’), 7.03 (1H, dd, J1’,2’ = 2.2, J2’,3’ = 1.3 Hz, H-1’), 7.33 (1H, d,
+
J5-Me,6 = 1.2 Hz, H-6); FAB-MS (m/z) 250 (M + H). Anal. Calcd for C11H11N3O4 1/
5CH2Cl2: C, 52.05; H, 4.44; N, 16.26. Found: C, 52.11; H, 3.90; N, 16.13.
Á
ACKNOWLEDGMENTS
This work was financially supported in part by grants from the Japan Health
Sciences Foundation (SA14718 to H. T.), Japan Society for the Promotion of Science
(KAKENHI No. 15590100 to K. H. and No. 15590020 to H. T.), the Research
Foundation of Pharmaceutical Sciences (to K. H.), and NIH USA (RO1 AI 38204 to
Y.-C. C.).
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deoxy-4’-ethynylthymidine. Bioorg. Med. Chem. Lett. 2003, 13, 3775–3777.
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Received November 25, 2003
Accepted December 1, 2003

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