Synthesis and antiviral activity of a series of 1′-substituted 4-aza-7,9-dideazaadenosine C-nucleosides

Article abstract of DOI:10.1016/j.bmcl.2012.02.105

A series of 1′-substituted analogs of 4-aza-7,9-dideazaadenosine C-nucleoside were prepared and evaluated for the potential as antiviral agents. These compounds showed a broad range of inhibitory activity against various RNA viruses. In particular, the whole cell potency against HCV when R = CN was attributed to inhibition of HCV NS5B polymerase and intracellular concentration of the corresponding nucleoside triphosphate.

Full text of DOI:10.1016/j.bmcl.2012.02.105

Bioorganic & Medicinal Chemistry Letters 22 (2012) 2705–2707
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Bioorganic & Medicinal Chemistry Letters
journal homepage: www.elsevier.com/locate/bmcl
Synthesis and antiviral activity of a series of 10-substituted
4-aza-7,9-dideazaadenosine C-nucleosides
⇑
Aesop Cho , Oliver L. Saunders, Thomas Butler, Lijun Zhang, Jie Xu, Jennifer E. Vela, Joy Y. Feng,
Adrian S. Ray, Choung U. Kim
Gilead Sciences, 333 Lakeside Drive, Foster Cit, CA 94044, USA
a r t i c l e i n f o
a b s t r a c t
A series of 10-substituted analogs of 4-aza-7,9-dideazaadenosine C-nucleoside were prepared and evalu-
ated for the potential as antiviral agents. These compounds showed a broad range of inhibitory activity
against various RNA viruses. In particular, the whole cell potency against HCV when R = CN was attrib-
uted to inhibition of HCV NS5B polymerase and intracellular concentration of the corresponding nucle-
oside triphosphate.
Article history:
Received 27 January 2012
Revised 27 February 2012
Accepted 29 February 2012
Available online 8 March 2012
Ó 2012 Elsevier Ltd. All rights reserved.
Keywords:
C-nucleoside
Antiviral
Polymerase inhibitor
Structural modification of natural N-nucleosides on either the
sugar or the base has led to the discovery of a variety of therapeutic
agents, which includes antivirals and anticancer agents. This ap-
proach has been continuously employed to further identify agents
with improved efficacy and safety over existing drugs, overcome
issues associated with drug-resistance, and expand into new ther-
apeutic areas.1
Among all the conceivable modifications of the sugar moiety,
incorporation of a substitution at 10-position of the N-nucleosides
has been rarely exploited in drug discovery.2 This is partly due to
the chemical instability induced by the 10-substituent (i.e., ready
dissociation of the base and the sugar at lower pH). For example,
10-C-Me adenosine is rapidly degraded in aqueous solutions at
pH <7.3 However, C-nucleoside, in which the sugar and the base
are linked through the C–C bond, should be hydrolytically stable
even with a 10-substituent. Thus, we envisioned that C-nucleoside
could be an ideal scaffold to explore various 10-substituted nucleo-
sides for their therapeutic potential.
incorporated into RNA by host RNA polymerases, which is believed
to be the main mode of action for the observed cytotoxicity.4
A
C-nucleoside analog of 1, 4-aza-7.9-dideazaadenosine (2) has
shown equally potent cytotoxicity to cancer cell lines.5 The TP of
2 was also shown to be a substrate of host RNA polymerases and
incorporated into RNA (unpublished results). Thus, we chose com-
pound 2 as a template to investigate the effect of the 10-substituent
on antiviral activity and selectivity. Here, we report (1) preparation
of a series of novel 10-substituted analogs of compound 2, (2) their
antiviral activities against a panel of RNA viruses, and (3) correla-
tion of the observed anti-HCV potency with both intrinsic enzyme
(HCV NS5B) activity and intracellular level of the corresponding TP.
NH2
N
NH2
N
HO
HO
N
N
N
N
O
O
As part of an on-going effort to identify new antiviral agents, we
were interested in investigating 10-substiuted nucleosides as inhib-
itors of viral RNA-dependent RNA polymerases. Such nucleoside
inhibitors should be converted by intracellular kinases to the trip-
hosphorylated nucleosides, which then function as competitors of
the natural nucleoside triphosphates (TP) in RNA synthesis.
7-Deazaadenosine (1, Tubercidin) is a naturally occurring, cyto-
toxic N-nucleoside. It is triphosphorylated inside the cells and then
HO
OH
HO
OH
1
2
Compounds 3a–3d were prepared from a common intermediate 6,
which was obtained from coupling of the bromo heterocycle 46
with the ribonolactone 5 (Scheme 1).7 The resulting hemiketal 6
was reacted with TMSCN and AlMe3 in the presence of BF3–Et2O
affording compounds 7a (R = CN) and 7b (R = Me), respectively,7
while with vinyl magnesium bromide and ethynyl magnesium chlo-
ride followed by dehydrative ring closure with methanesulfonic
acid providing compounds 7c (R = vinyl) and 7d (R = ethynyl),
respectively.8 These products were obtained as mixtures of the
⇑
Corresponding author.
E-mail address: acho@gilead.com (A. Cho).
0960-894X/$ - see front matter Ó 2012 Elsevier Ltd. All rights reserved.
http://dx.doi.org/10.1016/j.bmcl.2012.02.105

2706
A. Cho et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2705–2707
Table 1
NH2
Antiviral activity of 10-substituted 4-aza-7,9-dideazaadenosine C-nucleosides
N
EC50/CC50 (lM)
NH2
N
BnO
N
O
O
BnO
N
(a)
3a
3b
3c
3d
O
+
N
HCV (1b)a
YFV
DENV-2
4.1/>89
11/>30
39/>45
ND
>89/>89
ND
>89/>89
ND
OH
BnO OBn
N
Br
BnO
OBn
9.46/>30
>30/>30
27.9/>30
1.71/>30
2.24/>30
>30/>30
>30/>30
>30/>30
>30/>30
5.23/>30
>30/>30
>30/>30
>30/>30
>30/>30
>30/>30
>30/>30
14.0/>30
>30/>30
>30/>30
>30/>30
>30/>30
>30/>30
>30/>30
>30/>30
4
5
6
WNV
Influenza A
Parainfluenza 3
SARS-CoV
Coxsackie A
NH2
N
NH2
N
(c)
(b)
N
N
N
HO
BnO
N
O
O
a
HCV subgenomic replicon.
R
R
OH
HO
BnO
OBn
7a-7d
3a R = CN
3b R = CH3
determine an enzyme inhibitory activity of TP 8a–8d. Under the
established protocol,12 the IC50 values were obtained (Table 2).
These studies revealed a good correlation between the intrinsic en-
zyme activity and the whole cell HCV potency. For example, com-
pound 3a showed the most potent anti-HCV activity (EC50 of
3c R = vinyl
3d R = ethynyl
Scheme 1. Reagents and conditions: (a) 1,1,4,4-tetramethyl-1,4-dichlorodisilyleth-
ylene (1.2 equiv), NaH (2.2 equiv, 60% mineral oil), n-BuLi, (3.3 equiv), THF, ꢀ78 °C
followed by addition of 5, 1 h, 60%; (b) TMSCN (4 equiv), BF3ꢁOEt2 (3 equiv), CH2Cl2,
4.1
l
M), and its TP derivative (8a) the most potent inhibitory activ-
M).
ꢀ78 °C, 5 h, 58% (85:15 b/
12 h, 45% (1:1 b/
then methanesulfonic acid (cat.), CH2Cl2, rt, 3 h, 85% (1:1 b/
magnesium chloride (6 equiv), THF, 0 °C to rt, 2 h, and then methanesulfonic acid
a
) 7a; AlMe3 (5 equiv), BF3ꢁOEt2 (4 equiv), CH2Cl2, 0 °C,
ity against the enzyme (IC50 of 5.6 l
a
) 7b; vinyl magnesium bromide (6 equiv), THF, 0 °C to rt, 2 h, and
7c; ethynyl
To gain further insights into the mode of the antiviral activity,
bis-(SATE) monophosphate prodrugs were tested in the HCV repli-
con assay. In addition, intracellular levels of the TPs were mea-
sured upon incubation of these prodrugs with replicon cells,13
and compared with those from the parent nucleosides. The results
are summarized in Table 2. The prodrugs 9a and 9b showed mark-
edly enhanced replicon activity when compared to the parent
nucleosides. These monophosphate prodrugs afforded >100-fold
higher levels of the TP species than the parent nucleosides.
Corresponding to the increased potency, an increase in cytotoxicity
was also observed for the 4 prepared prodrugs. The selectivity
a
)
(cat.), CH2Cl2, rt, 3 h, 65% (2:1 b/
a) 7d; (c) BCl3 or BBr3(4–8 equiv), CH2Cl2, ꢀ78 °C,
1 h.
two stereoisomers at the 10-position. Subsequent debenzylation
using BCl3 provided, after chromatographic separation of the two
isomers, the desired nucleosides 3a–3d.
In addition, the TP derivatives (8a–8d) and bis-(SATE) mono-
phosphate prodrugs (9a–9d) of these C-nucleosides were also pre-
pared according to published methods.9,10
NH2
N
NH2
N
O
S
O
P
O
P
O
P
O
P
N
N
N
N
HO
O
O
O
O
O
O
O
OH OH OH
O
R
R
O
OH
HO
OH
HO
S
8a R = CN
8b R = CH3
8c R = vinyl
9a R = CN
9b R = CH3
9c R = vinyl
8d R = ethynyl
9d R = ethynyl
The synthesized nucleosides 3a–3d were evaluated in cell-based as-
says against a panel of RNA viruses.11 Anti-HCV activity was obtained
using a subgenomic replicon. Viruses tested included representatives
of Flaviviridae (HCV, YFV, DENV-2, WNV), Orthomyxoviridae (influenza
A), Paramyxoviridae (parainfluenza 3), Picornaviridae (Coxsackie A),
and Coronaviridae (SARS-CoV). Antiviral activity (EC50) and cytotoxic-
ity (CC50 for host cells in each assay) are shown in Table 1. Compound
3a (R = CN) displayed broader spectrum activity (HCV, YFV, DENV-2,
Influenza A, Parainfluenza 3 and SARS-CoV). Compounds 3b and 3c
showed a reduced potency and a narrower spectrum of antiviral activ-
ity, and3d noactivity. Whileexhibitingvariouslevelsofantiviralactiv-
ities, these 10-substituted nucleosides exerted little or no cytotoxicity.
We then investigated to see if the observed antiviral activity
was derived from inhibition of viral RNA dependent RNA polymer-
ases (RdRp). Since readily available, the HCV RdRp was used to
indices (CC50/EC50) of 9b, 9c and 9d were less than 10-fold making
it difficult to differentiate HCV activity from cellular toxicity. The
greater potency and selectivity observed for 9a (EC50 of 0.085 lM
and selectivity of 40-fold) likely reflects a combination of the po-
tent enzyme activity and the high intracellular TP concentration
(4220 pmol/million cells when cells were incubated with 10 lM
of 9a). Further structural modification to improve the selectivity
of 3a and 9a is warranted.
In summary, a series of novel 10-substituted analogs of 4-aza-
7,9-dideazaadenosine C-nucleoside were prepared and tested in
in vitro antiviral assays. These compounds showed a broad range
of antiviral activity. In particular, the HCV potency of 3a and its
bis(SATE) prodrug 9a in the whole cell replicon assay were corre-
lated with the intrinsic enzyme activity and the intracellular levels
of the corresponding TP (8a), which suggests that the antiviral

A. Cho et al. / Bioorg. Med. Chem. Lett. 22 (2012) 2705–2707
2707
M)
Table 2
HCV replicon activity, TP formation of nucleosides and their SATE prodrugs, and inhibition of RdRp by respective TPs
Nucleoside
SATE prodrug
TP RdRp IC50 (l
EC50/CC50
(
lM)
TP concentrationa (pmol/million)
EC50/CC50
0.085/3.2
0.078/0.73
3.43/12
(
lM)
TP concentrationa (pmol/million)
3a/9a
3b/9b
3c/9c
3d/9d
4.1/>89
39/>89
>89/>89
>89/>89
17.6 (8a)
50.8 (8b)
2.0 (8c)
4,220 (8a)
ND
440 (8c)
150 (8d)
5.6
l
M (8a)
20
lM (8b)
178
232
l
l
M (8c)
M (8d)
0.66 (8d)
6.01/26
a
Cmax of intracellular TP (pmol/million cells) upon incubation of 10 l
M of nucleosides or prodrugs in Huh-7 cells for 24 h.13
Reagent, Promega, Madison WI) dye reduction. The West Nile virus CPE assay
uses Vero cells and WNV strain NY-99. The Dengue Virus CPE assay uses Vero
E6 cells and Dengue Virus Type 2 strain New Guinea C. The Yellow Fever CPE
assay uses HeLa cells and Yellow Fever Virus strain 17D. The Coxsackie A virus
activity is in part derived from inhibition of RdRp. The current
work establishes the potential of 10-substituted nucleosides as
antiviral agents.
CPE assay uses MRC-5 cells and Coxsackie
A strains A7 or A21. The
Parainfluenza CPE assay uses Vero cells and Parainfluenza 3 strain C 243. The
Influenza A CPE assay uses MDCK cells and H3N2 strain virus. The SARS-CoV
CPE assay uses Vero cells and SARS-CoV strain Toronto-2.
References and notes
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concentrations are final concentration. In a solution containing 50 mM Tris–
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HCl (pH 7.5), 10 mM KCl, 1 mM DTT, 5 mM MgCl2, 0.2 unit/
lL RNAsin
(Promega), and 0.01% BSA, 75 nM NS5B was pre-incubated with 4 ng/
lL
(50 nM) heteropolymer RNA template (sshRNA) at rt for 5 min, followed by the
addition and incubation of the inhibitors at RT for 5 min. The reaction was
started by addition of a mixture of ATP (3
(Perkin–Elmer, NEG603H, 3000 Ci/mmol, 3.3
l
M), 0.03
l
M
33-P-labeled ATP
lM for GTP, CTP,
l
M), and 500
and UTP. After 90 min incubation at 30 °C, the reaction mixture was spotted on
DE-81 filter paper and washed with 0.125 mM Na2HPO4 (3ꢂ), distilled water
(1ꢂ), and reagent ethanol (1ꢂ). The filter paper was air-dried and exposed to
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13. Replicon cells were maintained in Dulbecco’s modified Eagle medium
containing glutamax supplemented with 10% heat inactivated fetal bovine
serum, penicillin–streptomycin, and G418 disulphate salt solution. Cells were
transferred to 12-well tissue culture treated plates by trypsonization and
grown to confluency (0.88 ꢂ 106 cells/well). Cells were treated for 24 h with
10 lM compound. Following 24 h, cells were washed 2 times with 2.0 mL ice
cold 0.9% sodium chloride saline. Cells were then scraped into 0.5 mL 70%
methanol and frozen overnight to facilitate the extraction of nucleotide
metabolites. Extracted cell material in 70% methanol was transferred into
tubes and dried. After drying, samples were re-suspended in 1 mM ammonium
phosphate pH 8.5. TP levels were quantitated using liquid chromatography
coupled to triple quadrapole mass spectrometry by methods similar to those
previously reported in Durand-Gasselin, L.; Van Rompay, K. K.; Vela, J. E.;
Henne, I. N.; Lee, W. A.; Rhodes, G. R. Mol. Pharm. 2009, 6, 1145.
11. All virus EC50 values were measured in cytoprotection effect (CPE) assays.
Cytoprotection and compound cytotoxicity are assessed by MTS (CellTiterÒ96