Discovery of a 2′-fluoro-2′-C-methyl C-nucleotide HCV polymerase inhibitor and a phosphoramidate prodrug with favorable properties

Article abstract of DOI:10.1016/j.bmcl.2017.02.037

A series of 2′-fluorinated C-nucleosides were prepared and tested for anti-HCV activity. Among them, the triphosphate of 2′-fluoro-2′-C-methyl adenosine C-nucleoside (15) was a potent and selective inhibitor of the NS5B polymerase and maintained activity

Full text of DOI:10.1016/j.bmcl.2017.02.037

Accepted Manuscript
Discovery of a 2’-Fluoro-2’-C-Methyl C-Nucleotide HCV Polymerase Inhibitor
and a Phosphoramidate Prodrug with Favorable Properties
Thorsten A. Kirschberg, Sammy Metobo, Michael O. Clarke, Vangelis
Aktoudianakis, Darius Babusis, Ona Barauskas, Gabriel Birkus, Thomas Butler,
Daniel Byun, Gregory Chin, Edward Doerffler, Thomas E. Edwards, Martijn
Fenaux, Rick Lee, Willard Lew, Michael R. Mish, Eisuke Murakami, Yeojin
Park, Neil H. Squires, Neeraj Tirunagari, Ting Wang, Mark Whitcomb, Jie Xu,
Huiling Yang, Hong Ye, Lijun Zhang, Todd C. Appleby, Joy Y. Feng, Adrian
S. Ray, Aesop Cho, Choung U. Kim
PII:
S0960-894X(17)30170-1
DOI:
http://dx.doi.org/10.1016/j.bmcl.2017.02.037
BMCL 24709
Reference:
Bioorganic & Medicinal Chemistry Letters
To appear in:
Received Date:
Revised Date:
Accepted Date:
17 January 2017
15 February 2017
16 February 2017
Please cite this article as: Kirschberg, T.A., Metobo, S., Clarke, M.O., Aktoudianakis, V., Babusis, D., Barauskas,
O., Birkus, G., Butler, T., Byun, D., Chin, G., Doerffler, E., Edwards, T.E., Fenaux, M., Lee, R., Lew, W., Mish,
M.R., Murakami, E., Park, Y., Squires, N.H., Tirunagari, N., Wang, T., Whitcomb, M., Xu, J., Yang, H., Ye, H.,
Zhang, L., Appleby, T.C., Feng, J.Y., Ray, A.S., Cho, A., Kim, C.U., Discovery of a 2’-Fluoro-2’-C-Methyl C-
Nucleotide HCV Polymerase Inhibitor and a Phosphoramidate Prodrug with Favorable Properties, Bioorganic &
Medicinal Chemistry Letters (2017), doi: http://dx.doi.org/10.1016/j.bmcl.2017.02.037
This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers
we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and
review of the resulting proof before it is published in its final form. Please note that during the production process
errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.

Discovery of a 2’-Fluoro-2’-C-Methyl C-Nucleotide HCV Polymerase Inhibitor and a
Phosphoramidate Prodrug with Favorable Properties
Thorsten A. Kirschberga*, Sammy Metoboa, Michael O. Clarkea, Vangelis Aktoudianakisa, Darius Babusisa,
Ona Barauskasa, Gabriel Birkusa, Thomas Butlera, Daniel Byuna, Gregory China, Edward Doerfflera,
Thomas E. Edwardsb, Martijn Fenauxa, Rick Leea, Willard Lewa, Michael R. Misha, Eisuke Murakamia,
Yeojin Parka, Neil H. Squiresa, Neeraj Tirunagaria, Ting Wanga, Mark Whitcomba, Jie Xua, Huiling Yanga,
Hong Yea, Lijun Zhanga, Todd C. Applebya, Joy Y. Fenga, Adrian S. Raya, Aesop Choa, Choung U. Kima.
a)Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA
b)Berylium, 7869 NE Day Road West, Bainbridge Island, WA 98110, USA
ABSTRACT
A series of 2’-fluorinated C-nucleosides were prepared and tested for anti-HCV activity. Among
them, the triphosphate of 2’-fluoro-2’-C-methyl adenosine C-nucleoside (15) was a potent and
selective inhibitor of the NS5B polymerase and maintained activity against the S282T resistance
mutant. A number of phosphoramidate prodrugs were then prepared and evaluated leading to the
identification of the 1-aminocyclobutane-1-carboxylic acid isopropyl ester variant (53) with
favorable pharmacokinetic properties including efficient liver delivery in animals.
Keywords: Hepatitis C; Antiviral; C-nucleoside; NS5B polymerase
Hepatitis C Virus (HCV) infection is a major cause of chronic liver disease worldwide.
When left untreated, it can lead to end stage liver diseases including cirrhosis and hepatocellular
carcinoma. [1] Until 2011, the standard of care for patients with HCV infection was a regimen
consisting of pegylated interferon-α and ribavarin, which has only limited efficacy. [2] More
recently several direct-acting antivirals (DAAs) have been developed and licensed for use,
resulting in combination regimens with markedly improved clinical outcomes. [3] A notable
advance in this context was the discovery of the nucleotide prodrug sofosbuvir (1) (Figure 1).
Combined with other DAAs, sofosbuvir affords high cure rates for infections across all
genotypes of HCV. [4]

Nucleotide inhibitors are an important class of DAA as they have pan-genotype activity
and a high barrier to emergence of resistant mutations. These inhibitors are phosphorylated
within host cells to the bioactive nucleoside triphosphates (NTPs) that are then used as substrates
by the HCV RNA-dependent RNA polymerase (non-structural protein 5B, NS5B) and
incorporated into the growing RNA genome. Once integrated, the nucleotide analogs prevent
incoming NTP substrates from further incorporation, thus stopping RNA elongation. [5]
We have recently reported a series of C-nucleosides such as compounds 2 and 3 as anti-
HCV agents, and the discovery of a clinical candidate GS-6620 (4) through extensive exploration
of phosphoramidate prodrugs of 3 (Figure 1). [6] GS-6620 displayed potent and selective
inhibition of HCV replicons derived from genotypes 1 to 6 (EC50 of 0.048 to 0.68 M), but
selected for the S282T mutant that was highly resistant in both enzymatic and cellular assays
(>30 fold). In Phase 1 clinical studies, reductions in plasma viral load to below the limit of
quantification (>4 logs) were observed in some individuals, but high doses were required and
intersubject variability was unacceptable as a result of poor oral absorption. GS-6620 is a double
prodrug with an isobutyryl ester masking the 3’-hydroxyl of phosphoramidate prodrug 5 (Figure
1). Blocking the polar hydroxyl group in this way was important for achieving the desired level
of permeability in both in vitro assays and in vivo animal PK studies. However, follow-up
studies suggested that intestinal metabolism of the isobutyryl pro-moiety was the likely cause for
poor absorption and variability in humans. [7]

Figure 1: Structures of nucleoside derivatives targeting HCV
We sought to extend our initial clinical proof of concept in the C-nucleoside series by
identifying a new agent with improved oral delivery and activity against the S282T resistance
mutant. Toward this end, a series of nucleosides in which the 2’-hydroxyl group is replaced with
a 2’-fluoro group was targeted; elimination of one hydrogen bond donor may affect intestinal
permeability,[8] and purine analogs with this ribose modification had been reported to be
relatively insensitive to the S282T resistance mutation. [9] Furthermore, we wanted to broaden
our exploration of phosphoramidate promoieties in the hope that we might discover further
motifs for cell-type specific prodrug activation. [10] Here, we present syntheses and
characteristics of new 2’-fluoro-2’-C-methyl C-nucleosides, resulting in the discovery of orally
bioavailable phosphoramidate prodrugs that are efficiently activated in the liver.
The new compounds were prepared by synthetic routes analogous to those of 2’-hydroxy-
2’-C-methyl C-nucleosides recently reported (Scheme 1). [11] Transient silyl protection of the
amino group and lithium-halogen exchange of the bromo heteroaromatics 7 and 8 in one pot
were e o t t - C, and reaction with the lactone 9 furnished the hemiacetals 10 and 11 in
moderate yields. Reduction to compounds 12 and 13 was achieved with high diastereoselectivity

(~95/5 t o of β/α- some s), s n the e l e 2’-hydroxy-2’-C-methyl series, using triethylsilane
in the presence of boron trifluoride etherate.[11] The target nucleosides 14 and 15 were then
obtained by hydrolysis of the benzoyl ester groups using aqueous ammonium hydroxide solution
or ammonia in methanol.
To prepare the 1’-cyano substituted nucleoside 17, the 1’-hydroxy intermediate 10 was
treated with trimethylsilyl cyanide in the presence of indium trifluoromethanesulfonate, again
providing ~95/5 t o of β/α-isomers. The resulting product 16 was de-benzoylated using
aqueous ammonium hydroxide solution to afford the desired product, while monitoring carefully
to minimize cyanide hydrolysis.
Scheme 1. Synthesis of C-Nucleosides

Reagents and conditions: (a) (i) 7 or 8, (ClSiMe2CH2)2, THF, - ˚C, B L (ii) then 9; for 10,
.
40%; for 11, 59%. (b) BF3 OEt2, triethylsilane, CH2Cl2, 91% (12); 64% (13) (~95/5 t o of β/α-
anomers) (c) conc. NH3(aq), MeOH, 66% (14); 60% (17). (d) NH3 MeOH, 54% (15). (e)
TMSCN, In(OTf)3, DCE, 58% (~95/5 t o of β/α-anomers).
Nucleoside triphosphates and representative (L)-alanine ethyl ester phosphoramidate prodrugs
were also prepared according to previously reported methods (Scheme 2). [12]
Scheme 2. Synthesis of nucleoside triphosphates and phosphoramidate prodrugs.

Reagents and conditions: (a) (i) POCl3, (MeO)3PO (ii) Bu3N.pyrophosphate (average yields
~10%) (b) N-methyl imidazole (NMI), 18, , C to rt., (average yields ~ 30%).
Data for these compounds elucidated the impact of key structural elements on intrinsic
potency of the triphosphate against both the genotype 1b wild-type (WT) and the S282T mutant
NS5B enzymes. Furthermore, the potency differential for the nucleoside / prodrug pair in the
cellular replicon assay established the need for a prodrug strategy in order to bypass the first
phosphorylation step (Table 1).
Table 1. Enzymatic activity (IC50) against WT and S282T NS5B and antiviral activity (EC50) in
the genotype 1b replicon (GT 1b)
Compound
(triphosphate) IC50 [µM]
NS5B, WT NS5B, S282T
Compound
(Nuc/PD)
GT1b, EC50
[µM]a
Fold
(Nuc / PD)
>89 / >89
>89 / 0.59
>89 / 3.24
>89 / 1.45
0.046
0.15
0.42
0.29
2.8
5.9
6.0
>30
14 / 14-PD
15 / 15-PD
17 / 17-PD
3 / 6
14-TP
15-TP
17-TP
3-TP
aTP = Triphosphate ; PD = Prodrug as in Scheme 2. b Effective concentration at which 50% inhibition occurs as
determined by a luciferase-based genotype 1b replicon assay in huh-7 cells. All values reported are the averages of
at least three repeats.

All three 2’-fluoro triphosphates displayed inhibitory potency in the wild-type NS5B
biochemical assay th t w s s m l to o bette th n the 2’-hydroxy analog (3-TP). A particular
benefit was the much smaller differences in inhibitory potency between WT and S282T mutant.
To understand this better, an X-ray structure of the elongation phase ternary complex of NS5B
and 15 diphosphate (15-DP) was obtained (Figure 2B). [13] The bound conformations of 15-DP
and adenosine diphosphate (ADP) (Figure 2A) were almost identical in the structures of these
two ternary complexes. he 2’-fluoro atom in 15-DP forms a hydrogen bond with N291 that is
analogous to that seen with the natural 2’-hydroxyl group in ADP, and the modified base in 15-
DP forms a Watson-Crick pairing with the template base, demonstrating that the non-natural
carbon-carbon replacement of the glycosidic bond does not alter the ability of C-nucleotides to
adopt the necessary conformation for incorporation into the elongating RNA strand. However, in
contrast to ADP, in which the 2′-OH g o p nte ts e tly w th the S2 2 Oγ tom, the 2′-
fluoro-2′-C-methyl motif in 15-DP engenders a conformational change in the side chain of S282,
moving it away from the inhibitor. A similar S282 conformation was observed previously in the
ternary complex of NS5B with 2′-fluoro-2′-C-methyl uridine diphosphate as the incoming
nucleotide [14]. The altered S282 conformation provides a rationale for why the loss in activity
against the S282T is reduced, as the ste l sh between the 2’-C-Me group and this residue may
be alleviated.
S282
S282
N291
N291
D225
D225
A
B

Figure 2: Hydrogen bonding networks involved in the recognition at the 2′-position observed for
(2A) the NS5B/ADP ternary elongation complex (PDB ID: 4WTD) and (2B) the NS5B/15-DP
ternary elongation complex (PDB ID: 5UJ2).
While the C-nucleosides 14-17 were inactive in the replicon assay (Table 1), two of the
monophosphate prodrugs (15-PD and 17-PD) showed activity that was similar to the 2’-hydroxyl
containing C-nucleoside comparator 6 with no apparent cellular toxicity (data not shown). Given
the exceptional potency of 14-TP in the enzyme assay, the lack of cellular activity of 14-PD is
notable.
Cellular antiviral activity is a function of intracellular levels of the triphosphate. To
address the SAR apparent in Table 1, intracellular triphosphate levels after continuous prodrug
incubation in huh-7 replicon cells were measured (Table 2). [15] The lack of formation of any
quantifiable levels of 14-TP from 14-PD over the course of 24 hours explains the lack of
replicon activity. The corresponding monophosphate of 14 was detected, yet the diphosphate of
14 was not seen. Incubation with 15-PD and 17-PD resulted in formation of high levels of 15-
TP and 17-TP. The 6-fold higher antiviral activity of 15-PD over 17-PD can be qualitatively
explained by both a higher intrinsic potency in biochemical assays and the higher triphosphate
level. Notably, the 2’-hydroxy-containing nucleoside prodrug 6 (Figure 1) produced much
higher levels of the corresponding triphosphate, suggesting some limitation of the 2′-F-2′-C-Me
motif for intracellular activation.
Table 2. Nucleoside triphosphate levels after prodrug incubation in huh-7 replicon cells
TP Concentration [pmol / million cells]
Timea
[h]
14-PD
15-PD
17-PD
6
2
BLQb
2.4
1.6
26

6
BLQ
BLQ
13.0
20.5
5.8
3.3
117
83
24
a Continuous 24 h incubation with 10 µM of prodrug. Results are the average of duplicate wells from a single side-
by-side experiment. b Below lower limit of quantification (0.137 pmol / million cells).
The clinical development of ribonucleoside analogs has been hampered by toxicity.
Insufficient selectivity for viral over host polymerases has been implicated for many analogs. In
particular, the incorporation efficiency by human RNA polymerases needs to be monitored
carefully. [16] The potential for toxicity with 15-TP was studied, with no inhibition of the
human DNA or RNA polymerases tested evident (Table 3). Furthermore, incorporation of 15-TP
by the mitochondrial RNA polymerase was minimal (0.04% relative to the rate of incorporation
of natural adenosine triphosphate) – a result that stands in contrast to the 2’-hydroxyl series, in
which 1’-substituent was important for limiting incorporation. [6]. The control compo n 4’-
azido cytidine triphosphate used in this assay showed an incorporation efficiency equivalent to
that of the natural substrate (cytidine triphosphate).
Table 3: Inhibition of human polymerases for 15-TP and control compoundsa,b
RNA Pol II
>200
DNA Pol 
DNA Pol 
DNA Pol 
>200
>200
>200
15-TP
0.0024
7.3
1.4
0.74
Control agent
Aphidicolin
3’-dTTP
3’-dTTP
-Amanitin
a IC50 in [M]. b Values represent the average of two independent experiments.
Encouraged by these results, we embarked on a prodrug campaign for nucleoside 15 in
which the aminoacid and ester substituents were varied, while the phenol substituent was kept
constant. In general, the compounds were tested as stereoisomeric mixtures at phosphorus [17]
To monitor for activity beyond genotype 1, and to assess prodrug cleavage and phosphorylation

beyond huh-7 cells, a genotype 4a replicon assay constructed in 1C cells was also employed
(Table 4).[18]
Table 4: Potency of phosphoramidate prodrugs in replicon systems for HCV genotypes
1a, 1b, and 4a.a
Compoundb
Ester (R)
Amino Acid
EC50 GT1a
[M]
EC50 GT1b EC50 GT4a
[M]
[M]
0.37
0.58
0.10
15-PD
14.7
0.39
35.2
>88
26.4
0.65
37.6
>88
5.7
19
20
21
22
0.27
11.2
>88
1.7
2.2
-
23

1.2
3.3
3.4
8.6
0.83
2.3
24
25
>88
>88
>88
62.5
86.2
26
27
60.5
0.59
0.33
0.80
0.66
0.15
0.14
28
29
1.0
2.0
0.38
30
31c
32
33
0.51
>88
2.6
0.67
>88
5.6
0.11
58.1
2.0
>88
>88
>88
34

0.74
0.69
0.59
35
5.0
2.3
41.8
18.8
1.1
36
37
0.38
11.3
68.3
51.6
83.7
3.9
-
38
39
14.4
29.1
7.0
40
0.81
7.9
0.67
7.3
0.46
2.1
41
42
43
44
0.53
>88
0.56
>88
0.37
>88
36.0
18.8
>88
3.6
2.1
45
46
16.1
47b
28.7
>88
1.1

6.4
>88
0.35
48
6.2
20.3
>88
4.3
49
50
72.4
77.8
4.3
3.4
6.2
6.1
0.82
1.5
51
52
a Shaded rows for compounds further described in tables 5, 6, and 7. b Synthesized as
c
described in footnote [23] using stereoisomeric mixtures of the phosphoramidate reagents.
Single isomer at phosphorus (SP).
Across the ethyl esters (15PD – 30), those of small, unbranched (L)-amino acids were
preferred for activity, and the incorporation of a (D)-amino acid (19) was detrimental. Branching
t the m no β position (21, 22) or the introduction of side-chain polarity (e.g., 24-27)
reduced activity. Conversely, small , disubstituted derivatives (28, 29) were particularly
potent.
Branching at the ester in the form of the isopropyl derivatives led to a general decrease in
cellular activity that was magnified in the sec-butyl analogs (compare, for example, 29, 36, 46
and 48). In the latter, the chiral center at the alkyl ester exerted little influence on activity except
in the interesting quartet of alaninyl derivatives 41 – 44. Here the two (L)-alaninyl analogs 41
and 43 were of similar potency, whereas one of the (D)-alaninyl pair (42) was markedly more
active than the other (44). The activity of 42 in the face of the lack of activity of 44 and its lower
alkyl homologs is suggestive of the involvement of a different and specific esterase. Neopentyl
and methoxyethyl esters were also less active.
In general, these analogs were slightly more active in the genotype 4A replicon assay
than in the genotype 1 systems. However, for the prodrugs containing amino acids with small

,disubstitutions and secondary alkyl esters (36, 37, 47, 48), activity in the 4a replicon was 5-
20 fold greater. This increased selectivity is likely due to higher expression of carboxyl esterase
1 (CES1) and cathepsin A, hydrolases known to activate phosphoramidate prodrugs. [19] A
heightened dependence on CES1, an enzyme known to be highly expressed in the liver [20] and
implicated in cleavage of phosphoramidate prodrugs in vivo, was intriguing and stimulated
further assessment; for a successful prodrug strategy we envisioned high plasma and intestinal
stability coupled with high liver extraction leading to efficient and selective prodrug activation in
the target tissue. Toward that end, several selected analogs were compared in hepatic subcellular
fraction (S9), intestinal S9 and plasma stability assays in vitro (Table 5). [21]
Table 5: Stability assessment of selected prodrugs
Compound
Plasma stab.
human / hamster
t1/2 [min]
Intestinal S9 stab.
human/ hamster
t1/2 [min]
Liver extraction
human / hamster
[%]
454 / >789
683 / 316
461/ 498
134 / 24
>789 / 192
129 / 100
175 / 70
83 / 76
28 / 84
62 / 83
88 / 91
65 / 97
17 / 85
65 / 86
79 / 93
15-PD
19
28
668 / 420
>789 / >789
380 / 673
155 / 124
534 / >789
29
31a
590 / 11
>789 / 415
>789 / 106
>789 / 48
32
36
37
a Single isomer at phosphorus (SP).
Sufficient plasma stability was observed across the series. The (D)-alanine derived
prodrugs 19 and 32 failed to activate efficiently in human liver S9 fraction and were not pursued
further. Given the clinical experience with GS-6620, particular attention was paid to maximizing
intestinal stability while retaining rapid liver activation. While the ethyl esters showed promise,

the isopropyl congeners exhibited the greatest stability differential, as desired, especially in
combination with a disubstituted amino acid as in 36 and 37.
Based on these promising results, liver triphosphate levels following oral dosing of 31,
36, and 37 at 5 mg-eq/kg in hamster were compared with those for the 2’-hydroxyl nucleoside
prodrug 5 (Table 6). [22] (High instability in rat plasma limited the relevance of this species for
pre-clinical assessment.)
Table 6: In-vivo triphosphate levels in hamster liver after oral dosing, solubility and
permeability
Compound
TP-levels hamster livera
Solubility pH 7.4b
Caco-2 permeabilityc
[x10-6cm/s]
[]
[g/mL]
0.34
1.29
1.89
0.53
642
657
538
306
0.94 / 16.6
4.2 / 17.6
2.4 / 9.7
31
36
37
5
0.2 / 8.9
a) Determined at t = 1h post dose. b) Amorphous material . c) Measured in the apical (A) to basolateral (B)
and B/A directions at 10 M.
In these experiments, the disubstituted amino acid prodrugs 36, and 37 out-performed the
(L)-alanine example 31 as well as 5. The Caco-2 data for this compound set suggests that higher
permeability (and therefore reduced prodrug residence time in enterocytes upon absorption) may
contribute to the overall outcome. In a follow-up experiment, 37 was dosed orally in male beagle
dogs at 5 mg/kg and >70% fraction absorbed was determined via portal vein sampling. In stark
contrast, only 10% of an oral dose of the 2’-hydroxyl nucleoside prodrug 5 was absorbed in
comparative studies. [6]
In order to support further development, the two individual phosphorous stereoisomers of
37 were synthesized and tested separately. [23] Key data from these studies are reported in Table
7.
Table 7: Isomer comparison for compound 37

EC50: 1a EC50: 1b EC50: 4a Plasma
stab.
Intestinal Liver
Caco-2
S9 stab.
extractiona permeabilityb
[M]
[M]
[M]
human / human/
human /
hamster
[x10-6 cm/s]
hamster
hamster
t1/2 [min] t1/2 [min] [%]
0.80
7.3
3.0
0.44
0.74
546 / 218 >789 / 99 76 / 90
1.7 / 9.3
1.3 / 9.2
53
54
31.2
>789 /
430
>789 / 18 78 / 96
a Human / hamster liver S9 fraction used. b Measured in the apical (A) to basolateral (B) and B/A
directions at 10 M compound concentration.
Although 53 exhibited greater potency in both genotype 1 replicons, the activity of the
two isomers was within 2-fold in the more optimal enzymatic background of the 4a replicon
assay. Overall, the profile of 53 was slightly better than that of 54 in terms of potency, oral
absorption potential and hamster liver triphosphate levels (~30% increase).
The favorable characteristics of 53 led to its progression into toxicology studies in rats
and monkeys. Following 28 days of dosing, 53 appeared well tolerated at 1,000 and 30
mg/kg/day in rats and monkeys, respectively. However, closer inspection during histopathology
found vacuolization in the brains of rats treated with 53 in two independent studies in a
somewhat dose dependent manner. This unexpected effect may have been associated with the
unnatural amino acid but the exact mechanism remains to be investigated.
In summary, we discovered the 2’-fluoro-2’-C-methyl adenosine C-nucleoside 15 as a
potent and selective inhibitor of HCV polymerase and a series of effective phosphoramidate
prodrugs of it. Repl ement of the 2’-hy oxyl to the 2’-fluoro afforded increased activity
against WT enzyme, reduced S282T resistance, and resulted in high oral absorption potential.
Importantly, efficient delivery of the triphosphate into liver tissue was achieved with prodrugs
containing a matched combination of branched alkyl ester and disubstituted amino acid.

References and Notes
[1] Lavanchy, D., Clin. Microbiol. Infect. 2011, 17, 107-115
[2] Zeuzem, S.; Berg, T.; Moeller, B.; Hinrichsen, H.; Mauss, S.; Wedemeyer, H.;
Sarrazin, C.; Hueppe, D.; Zehnter, E.; Manns, M. P., J. Viral Hepatitis 2009, 16, 75-90
[3] http://hepatitiscnewdrugresearch.com/approved-treatments-for-hepatitis-c.html
[4] Sofia, M. J., Antiviral Chem. Chemother., 2011, 22, 23-49.
[5] Migliaccio, G.; Tomassini, J. E.; Bosserman, M. R.; Ceccacci, A.; Colwell, L. F.;
Cortese, R.; Francesco R. D.; Eldrup, A. B.; Getty, K. L.; Hou, Z. S.; LaFemina, R. L.;
Ludmerer, S. W.; MacCoss, M.; MacMasters, D. R.; Stahlhut, M. W.; Olsen, D. B.; Hazuda, D.
J.; Flores, O. A., J. Biol. Chem., 2003, 278, 49164-49170
[6] Cho, A.; Zhang, L.; Xu, J.; Lee, R.; Butler, T.; Matebo, S.; Aktoudianakis, V.; Lew,
W.; Ye, H.; Clarke, M.; Doerffler, E.; Byun, D.; Wang, T.; Babusis, D,; Carey, A. C.; German,
P.; Sauer, D.; Zhong, W.; Rossi, S.; Fenaux, M.; McHutchison, J. G.; Perry, J.; Feng, J.; Ray, A.
S.; Kim, C.U. J. Med. Chem., 2014, 57, 1812-1825.
[7] Feng, J. Y.; Cheng, G.; Perry, J.; Barauskas, O.; Xu, Y.; Fenaux, M.; Eng, S.;
Tirunagari, N.; Peng, B.; Yu, M.; Tian, Y.; Lee, Y.-J.; Stepan, G.; Lagpacan, L. L.; Jin, D.;
Hung, M.; Ku, K. S.; Han, B.; Kitrinos, K.; Perron, M.; Birkus, G.; Wong, K. A.; Zhong, W.;
Kim, C-U.; Carey, A.; Cho, A.; Ray, A. S. Antimicrob. Agents Chemother., 2014, 58, 1930-1942.
Murakami, E.; Wang, T.; Babusis, D.; Lepist E.-I.; Sauer, D.; Park, Y.; Vela, J. E.; Shih, R.;
Birkus, G.; Stefanidis, D.; Kim, C.U.; Cho, A. Ray, A. S., Antimicrob. Agents Chemother., 2014,
58, 943-1951.
[8] Lipinski, C. A.; Lombardo, F.; Dominy, B. W., Feeney P. J., Adv. Drug Delivery Rev.,
1997, 23, 3-25.
[9] Chang, W.; Bao, D.; Chun, B.-K.; Naduthambi, D.; Nagaranatham, D.; Rachakonda,
S.; Reddy, P. G.; Ross, B. S.; Zhang, H.-R.; Bansal, S.; Espiritu, C. L.; Keilman, M.; Lam, A.
M.; Niu, C.; Micolochick Steuer, H.; Furman, P. A.; Otto, M. J.; Sofia, M. J. ACS Med. Chem.
Letters 2011, 2, 130-135.

[10] McGuigan, C.; Mehellou, Y.; Balzarini, J. ChemMedChem., 2009, 4, 1779-1791.
Sofia, M. J., Antiviral Chem. Chemother., 2011, 22, 23-49. McGuigan, C.; Gilles, A.; Madela,
K.; Aljarah, M.; Holl, S.; Jones, S.; Vernachio, J.; Hutchins, J.; Ames, B.; Bryant, K. D.;
Gorovits, E.; Ganguly, B.; Hunley, D.; Hall, A.; Kolykhalov, A.; Liu, Y.; Muhammed, J.; Raja,
N.; Walters, R.; Wang, J.; Chamberlain, S.; Henson, G. J. Med. Chem., 2010, 53, 4949-4957.
[11] Cho, A.; Saunders, O. L.; Butler, T.; Zhang, L.; Xu, J.; Vela, J. E.; Feng, J. Y.; Ray,
A. S.; Kim, C. U. Bioorg. Med. Chem. Letters, 2012, 22, 2705-2707. Cho, A. ; Zhang, L.; Xu,
J.; Babusis, D,; Butler, T.; Lee, R.; Saunders, O. L.; Wang, T.; Parrish, J.; Perry, J.; Feng, J. Y.;
Ray, A. S.; Kim, C. U. Bioorg. Med. Chem. Letters, 2012, 22, 4127-4132. For additional work
en bl ng the eff ent synthes s of 2’-C-Methyl C-Nucleosides please also see: Tokarenko, A.;
Slavetinska, L. P.; Klepetarova, B.; Hocek, M. Eur. J. Org. Chem., 2015, 7962-7983. Draffan, A.
G.; Frey, B.; Pool, B.; Gannon, C.; Tyndall, E. M.; Lilly, M.; Francon, P.; Hufton, R.; Halim, R.;
Jahangiri, S.; Bond, S.; Nguyen, V. T. T.; Jeynes, T. P.; Wirth, V.; Luttick, A.; Tilmanis, D.;
Thomas, J. D.; Pryor, M.; Porter, K.; Morton, C. J.; Lin, B.; Duan, J.; Kukolj, G.; Simoneau, B.;
McKercher, G.; Lagace, L.; Amad, M.; Bethell, R. C.; Tucker, S. P. ACS Med Chem Letters
2014, 5, 679-684.
[12] McGuigan C.; Cahard, D.; Sheeka, H. M.; De Clercq, E.; Balzarini, J., J. Med.
Chem., 1996, 39, 1748-1753
[13] Brief description of crystallization conditions: Crystals were grown at 4 °C using the
sitting drop vapor diffusion method with 0.4 L of NS5B (2a JFH-1 C-te m n l Δ21 w th S15G,
C223 , V321I m t t ons n Δ β-hairpin loop deletion) at 5 mg/mL (~70 M) in 5 mM Tris
pH 7.5, 200 mM ammonium acetate, 1 mM EDTA, 1 mM DTT and an equal volume of
precipitant against 80 L of reservoir (25% PEG 550 MME, 50 mM MgCl2, 0.1 M Hepes pH
7.5) over weeks to months. To obtain the ternary complex, crystals were soaked at 4 °C over
three days in a modified reservoir (28% PEG 550 MME, 8% ethylene glycol, 0.2 M ammonium
acetate, 50 mM BisTris propane pH 6.0, 50 mM Tris pH 7.2), 15-DP (10 mM), MnCl2 (6 mM),
n the symmet l RNA p me templ te p , 5′-AUAAAUUU, (2 mM). For more details
please see [14]. The diphosphate (15-DP) was synthesized in a way similar to that of the
triphosphate, except that Bu4N phosphate was used instead of Bu4N pyrophosphate.

[14] Appleby, T. C.; Perry J. K.; Murakami, E.; Barauskas, O.; Feng, J.; Cho, A.; Fox III,
D.; Wetmore, D. R.; McGrath, M. E.; Ray, A. S.; Sofia, M. J.; Swaminathan, S.; Edwards, T. E.
Science, 2015, 347, 771-775.
[15] Measurements of Triphosphate Levels in Replicon Cells. Replicon cells (Huh-7
ells) we e m nt ne n D lbe o’s mo f e e gle me m ont n ng glutaMAX
supplemented with 10% heat inactivated fetal bovine serum, penicillin-streptomycin, and G418
disulfate salt solution. The cells were transferred to 12-well tissue culture plates treated by
trypsonization and grown to confluency (0.88 x 106 cells/well). The cells were then treated for
24 hours with a test compound (10 µM), and then washed twice with 2.0 mL ice cold 0.9%
sodium chloride saline, scraped into 0.5 mL 70% methanol, and frozen overnight to facilitate the
extraction of nucleotide metabolites. The extract was transferred into tubes, dried, and re-
suspended in 1 mM ammonium phosphate (pH 8.5). TP levels were quantified using liquid
chromatography coupled to triple quadrapole mass spectrometry (LC-MS/MS) 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.
[16] Feng, J. Y.; Xu, Y.; Barauskas, O.; Perry, J.; Ahmadyar, S.; Stepan, G.; Yu, H.;
Babusis, D.; Park, Y.; McCutcheon, K.; Perron, M.; Schultz, B. E.; Sakowicz, R.; Ray, A. S.,
Antimicrob Agents Chemother., 2016, 60, 806-817.
[17] Tyndall, E. M.; Draffan, A. G.; Frey, B.; Pool, B.; Halim, R.; Jahangiri, S.; Bond, S.;
Wirth, V.; Luttick, A.; Tilmanis, D.; Thomas, J.; Porter, K.; Tucker, S. P., Bioorg. Med. Chem.
Letters, 2015, 25, 869-873.
[18] Peng, B.; Yu, M.; Lee, Y.-J.; Tian, Y.; Yang, H.; Chan, K.; Mo, H.; McHutchison,
J.; Delaney IV, W.; Cheng, G. Gastroenterology, 2013, 144, 59-61.
[19] Murakami, E.; Tolstykh, T.; Bao, H.; Niu, C.; Micolochick-Steuer, H. M.; Bao, D.;
Chang, W.; Espiritu, C.; Bansai, S.; Lam, A. M.; Otto, M. J.; Sofia, M. J.; Furman, P. A., J. Biol.
Chem., 2010, 285, 34337-34347. Murakami, E.; Wang, T.; Park, Y.; Hao, J.; Lepist, E.-I.;
Babusis, D,; Ray, A. S., Antimicrob. Agents Chemother., 2015, 59, 3563-3569.

[20] Imai, T.; Taketani, M.; Shii, M.; Hosokawa, M.; Chiba, K. Drug Metab. Disp., 2006,
34, 1734-1741. Imai, T. Drug Metab. Pharmacokinet., 2006, 21, 173-185.
[21] Stability in blood plasma: Test compounds were incubated at 2 µM in hamster, rat, or
human plasma samples for up to 4 hours at 37 °C. At the desired time points, aliquots from the
incubation were quenched by adding 9 volumes of 100% acetonitrile supplemented with an
internal standard. The samples were centrifuged at 3,000g for 30 minutes and the supernatants
were transferred to new plates containing an equal volume of water for analysis by LC-MS/MS.
Intestinal and Hepatic S9 Stability. Test ompo n s we e n b te t 2 μM n h m n
intestinal and hepatic S9 fractions (obtained from In Vitro Technologies, Baltimore, MD) for 90
min at 37 °C in the presence of NADPH and UDPGA (Phase I and Phase II cofactor, Sigma-
Aldrich). At specified time points following compound addition, the samples were quenched
with 9 volumes of an aqueous solution containing an internal standard, 50% acetonitrile and 25%
methanol. The sample plates were centrifuged at 3000g fo 3 m n, n 1 μL of the es lt ng
solutions were analyzed by LC/MS/MS. The data (ratio of the sample to the internal standard
peak area) were plotted on a semi log scale and fitted using an exponential fit. Assuming the
first order kinetics, half-life and rate of metabolism were determined. Predicted hepatic
extraction was calculated from the half-life by reported methods using the well-stirred model for
hepatic clearance. LC/MS/MS Instrumentation.: Liquid chromatography was performed using an
Agilent 1200-series quaternary pump system (Agilent Technologies, Santa Clara, CA) with a 2
μm 2 × 2.1 mm Me y RP C18 (Phenomenex, Torrance, CA). HPLC system was coupled to a
Quattro Premier triple-quadrupole mass spectrometer (Waters, Milford, MA).
Mass
spectrometry was performed in positive-ion mode and multiple reaction monitoring modes using
a Quattro Premier (Waters, Milford, MA). The test compound was eluted with a mobile phase
consisting of 0.2% formic acid and a linear gradient from 0 to 95% acetonitrile over 2 minutes.
[22] Hamster Liver Triphosphate Analysis. Groups of 12 Golden Syrian hamsters
were administered a test compound orally at 5 mg-eq/kg. The formulation consisted of EtOH,
PEG400 and water, and buffered with 50 mM pH 4 citrate (2.5 mg-eq/mL) for oral dosing. At 1,
4, 8 and 12 hr, livers were harvested under isoflurane anesthesia. Collected livers were wrapped
in aluminum foil and snap-frozen in liquid nitrogen immediately following removal to avoid
sample dephosphorylation. Livers were processed by sectioning into smaller pieces with a razor
blade and collecting into pre-weighed 15 mL conical tubes kept on dry ice. Four volumes of ice-

cold extraction buffer (0.1% KOH and 67 mM EDTA in 70% MeOH, containing 0.25 µM Cl-
ATP) were added and samples were promptly homogenized using an Omni-Tip THTM with
disposable, hard tissue homogenizer probes (Omni International). Aliquots of homogenate were
then centrifuged (20,000xg at 4oC for 10 min). Aliquots of supernatant were transferred to clean
tubes, evaporated to dryness in a heated centrifugal evaporator, and reconstituted with an equal
volume of 1 mM ammonium phosphate (pH 7.0). Intracellular triphosphate levels were
measured by LC/MS/MS. The levels of endogenous adenosine triphosphate were also
determined to assure the sample stability.
[23] Synthesis: Nucleoside 15 (500 mg, 1.8 mmol) was dissolved in NMP (5 mL) and THF (5
mL), and the solution was cooled to 0 °C. A solution of tert-butylMgCl (1.0M in THF, 2.6 mL)
was added dropwise. The cooling was removed and stirring was continued for 30 minutes. A
solution of isopropyl 1-(((4-nitrophenoxy)(phenoxy)phosphoryl)amino)cyclobutane-1-
carboxylate (1.3 g 1.6 eq.) in THF (13 mL) was added. The reaction mixture was stirred at room
temperature for 18 hours, which was diluted with EtOAc and quenched with aqueous saturated
ammonium chloride solution. The organic layer was washed sequentially with aqueous sodium
hydroxide (0.1M), water, and brine, and dried over sodium sulfate. After filtration and
evaporation of solvents, the residue was purified via flash silica gel chromatography (eluent: A:
20%MeOH in EtOAc and B: hexanes). The product was isolated in 65% yield. Compound 53:
1H NMR (400 MHz, MeOH –d4)  = 8.04 (s, 1H), 7.61 (s, 1H), 7.35-7.28 (m, 2H), 7.25 (m, 2H),
7.15 (t, J = 6.8 Hz, 1H), 5.64 (d, J = 25.0 Hz, 1H), 5.03-4.96 (m, 1H), 4.57 (dd, J = 10.7/4.8 Hz,
1H), 4.47-4.33 (m, 1H), 4.12 (m, 2H), 2.48 (m, 2H), 2.30 (m, 2H), 1.96-1.80 (m, 2H), 1.24 (m,
6H), 1.16 (d, J = 22 Hz, 3H) ppm. 19F NMR (376MHz, MeOH-d4)  = -156ppm. 31P NMR
(162MHz, MeOH –d4):  = 2.58 ppm.
The phosphoramidate reagent (isopropyl 1-(((4-nitrophenoxy) (phenoxy)phosphoryl) amino)
cyclobutane-1-carboxylate) was prepared as the racemic mixture according to [6]. The isomers
were then separated via chiral chromatography [Chiralpak AY 20 m; mobile phase EtOH; 40
°C]. The earlier eluding fraction was taken and crystalized from EtOAc and heptane, which was
used for preparation of 53.

Graphical abstract