Novel nucleoside analogues as effective antiviral agents for Zika virus infections

Article abstract of DOI:10.3390/molecules25204813

Previously considered a neglected flavivirus, Zika virus has recently emerged as a public health concern due to its ability to spread rapidly and cause severe neurological disorders, such as microcephaly in newborn babies from infected mothers, and Guilla

Full text of DOI:10.3390/molecules25204813

molecules
Article
Novel Nucleoside Analogues as Effective Antiviral
Agents for Zika Virus Infections
Marcella Bassetto 1 , Cecilia M. Cima 2, Mattia Basso 2 , Martina Salerno 2, Frank Schwarze 3,
Daniela Friese 3, Joachim J. Bugert 3 and Andrea Brancale 2,
*
1
Department of Chemistry, Swansea University, Swansea SA2 8PP, UK; marcella.bassetto@swansea.ac.uk
School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff CF10 3NB, UK;
cimacm@cardiff.ac.uk (C.M.C.); bassomattia01@gmail.com (M.B.); m.salerno@bangor.ac.uk (M.S.)
Institut für Mikrobiologie der Bundeswehr, 80937 Munich, Germany;
Frank1Schwarze@bundeswehr.org (F.S.); danielafriese@bundeswehr.org (D.F.);
joachim1bugert@bundeswehr.org (J.J.B.)
2
3
*
Correspondence: brancalea@cardiff.ac.uk
ꢀꢁꢂꢀꢃꢄꢅꢆꢇ
ꢀꢁꢂꢃꢄꢅꢆ
Academic Editor: Katherine Seley-Radtke
Received: 26 September 2020; Accepted: 16 October 2020; Published: 20 October 2020
Abstract: Previously considered a neglected flavivirus, Zika virus has recently emerged as a public
health concern due to its ability to spread rapidly and cause severe neurological disorders, such as
microcephaly in newborn babies from infected mothers, and Guillain-Barré syndrome in adults.
Despite extensive efforts towards the identification of effective therapies, specific antivirals are still
not available. As part of ongoing medicinal chemistry studies to identify new antiviral agents,
we screened against Zika virus replication in vitro in a targeted internal library of small-molecule
agents, comprising both nucleoside and non-nucleoside agents. Among the compounds evaluated,
novel aryloxyphosphoramidate prodrugs of the nucleosides 20-C-methyl-adenosine, 2-CMA,
and 7-deaza-20C-methyl-adenosine, 7-DMA, were found to significantly inhibit the virus-induced
cytopathic effect in multiple relevant cell lines. In addition, one of these prodrugs exhibits a synergistic
antiviral effect against Zika virus when applied in combination with an indirect antiviral agent,
a l-dideoxy bicyclic pyrimidine nucleoside analogue, which potently inhibits vaccinia and measles
viruses in vitro by targeting a host pathway. Our findings provide a solid basis for further development
of an antiviral therapy for Zika virus infections, possibly exploiting a dual approach combining two
different agents, one targeting the viral polymerase (direct-acting antiviral), the second targeting a
host-directed autophagy mechanism.
Keywords: antiviral agents; aryloxyphosphoramidate prodrugs; Zika virus; in vitro screening
1. Introduction
Zika virus (ZIKV) belongs to the Flavivirus genus of the Flaviviridae family; it is closely related
to other arthropod-borne viruses of the same genus, such as Dengue (DENV), Yellow Fever (YFV),
and West Nile (WNV) viruses. First serologically surveyed in Uganda in 1952 [
Africa in 1954 and then spread to Indonesia, Micronesia, Thailand, the Philippines, French Polynesia,
and Easter Island-South Pacific [ ]. After a first report in Brazil in May 2015, ZIKV has spread
rapidly in several countries across the Americas, causing an epidemic which affected more than
850,000 patients [ ], and leading the World Health Organisation to declare it a public health emergency
of international concern in 2016 [ ]. ZIKV is transmitted to humans by mosquitos of the Aedes species,
mainly Aedes aegypti and Aedes albopictus [ ]. The number of new cases has lately diminished, but the
1], it was found in West
2
3
4
5
continuous increase in urbanisation and intercontinental travel, and the current climate changes,
which are predicted to lead to the adaptation of the main vector Aedes aegypti to new, expanded
Molecules 2020, 25, 4813; doi:10.3390/molecules25204813
www.mdpi.com/journal/molecules

Molecules 2020, 25, 4813
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geographic areas, pose the threat of future outbreaks [6]. ZIKV can also be transmitted through the
sexual route, blood transfusions, and the maternal–foetal route [7].
Although usually associated with a self-limiting and mild illness, either asymptomatic or
characterised by fever, skin rashes, conjunctivitis, headache, muscle and joint pain, during the recent
large outbreaks in French Polynesia and Brazil, different congenital malformations and an enhanced
risk of foetal loss have emerged as associated with ZIKV infections during pregnancy [
with ZIKV not only cause foetal abnormalities and congenital microcephaly [ ], but also a number of
neurological complications in adults, such as the Guillain Barr syndrome [ ]. This alarming evidence
8]. Infections
9
é
8
has prompted extensive efforts towards the development of both vaccines and specific therapeutic
measures [10], but to date, both options are still unavailable for human use, limiting the treatment of
infections to supporting care [11]. As a consequence, the identification of effective antiviral options is
highly needed and greatly significant to people’s health worldwide.
The ZIKV replication cycle is closely related to that of other flaviviruses [12], suggesting the
potential for antiflaviral agents to display therapeutic activity also in the case of Zika virus. In this
context, antiviral nucleoside analogues are a particularly interesting class of compounds, as they
currently represent the most important group of antiviral agents, with roughly 50% of all antiviral
drugs on the market belonging to this category [13,14]. With few exceptions, these agents exert their
mode of action at the viral polymerase level in their triphosphate form. Different prodrug approaches
have been developed to aid the metabolic activation of parent nucleosides into their active form,
with the McGuigan aryloxyphosphoramidate prodrug (ProTide) technology being the most effective
currently available, exploited, among others, in the blockbuster anti-HCV drug sofosbuvir [15]. To date,
different nucleoside analogues have shown antiviral effects against ZIKV replication in vitro and
in vivo [16], including sofosbuvir itself [17].
In this study, we focused on the in vitro evaluation, using multiple cellular systems relevant
to ZIKV replication, of a targeted small library of potential anti-ZIKV agents, focusing on diverse
compounds developed in our medicinal chemistry group as potential antivirals for different viruses,
including both nucleoside analogues and non-nucleoside small molecules. Within the compounds
evaluated in our assays, novel aryloxyphosphoramidate prodrugs of the nucleoside analogues 20-CMA
and 7-DMA were identified as inhibitors of ZIKV-induced cytopathic effect in multiple screening
systems, with antiviral EC50 values in the low micromolar range. In addition, one of these prodrugs
also displays a synergistic antiviral effect when applied in combination with a previously reported
antiviral L-nucleoside analogue, providing a solid basis for the further development of these agents
into a viable therapeutic option to treat ZIKV infections.
2. Results and Discussion
2.1. Compound Selection
With the aim to identify novel inhibitors of ZIKV-induced cytopathic effect in cells, we decided
to create a focused small library of in-house compounds, prioritising those ones which we had
identified, or which we are currently developing, as potential antivirals for related flaviviruses.
In particular, we decided to focus our efforts on five structural families in total. Two of these are
non-nucleosides, as summarised in Table 1. First, we included 13 diverse structural analogues of 1a
( –1o): these compounds have been previously identified in our group as potent inhibitors of the
1a
replication of hepatitis C virus, which is also a flavivirus [18]. In addition, we screened a second series
of 11 non-nucleoside compounds, 2a 2m 2a has been previously reported as a potent inhibitor of
–
:
ZIKV replication in Vero cells, with efficacy in reducing ZIKV viremia in vivo in an immunocompetent
mouse model, and a mechanism of action pointing towards inhibition of the viral RNA-dependent
RNA polymerase (RdRp) [19]. Different structural analogues of 2a, among which we selected 2b–2m,
have been recently explored in our research group for their inhibition of human norovirus (hNoV)
RdRp, and their ability to interfere with hNoV replication in a replicon system [20].

Molecules 2020, 25, 4813
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Table 1. Chemical structures of compounds 1a–1o and 2a–2m, previously reported non-nucleoside
antiviral agents, selected for evaluation against ZIKV-induced cytopathic effect in relevant cellular
models of the infection.
Cpd
R1
R2
X
R3
Ar
Ar1
Ar2
1a
1b
1c
1d
1e
1f
1g
1h
1i
C4H8
C4H8
C4H8
N=C
N=C
N=C
N=C
N=C
N=C
NHCO
NHCO
N=C
N=C
NHCO
NHCO
NHCO
C=O
C=O
C=O
C=O
C=O
C=O
C=O
C=O
C=O
Me
Me
Me
Me
Me
Me
-
-
2,5-OH-Ph
2-OH-Ph
Pyrazine
2,5-OH-Ph
2-Pyridine
2-OH-Ph
2,5-OH-Ph
2,5-OH-Ph
2-OH-Ph
2-OH-Ph
2-Pyridine
2-Pyridine
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
H
H
C4H8
C3H6
C4H8
C4H8
Me
Me
Me
Me
1l
C4H4
C4H4
1m
1n
1o
2a
2b
2c
2d
2e
2f
2g
2h
2i
2l
2m
-
-
-
-
-
-
-
-
-
-
-
-
-
-
H
Me
H
Cl
-
2-Pyridine
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
2-(3-Cl)-Benzo[b]thiophene
2-Benzo[b]thiophene
2-(3-CF3)-Benzo[b]thiophene
4-Me-Ph
2-(3-Cl)-Benzo[b]thiophene
2-(3-Cl)-Benzo[b]thiophene
Ph
2-Thiophene
2-Thiophene
2-Thiophene
2-Thiophene
2-Furan
Ph
Ph
2-Thiazole
Ph
-
-
-
-
-
-
-
-
2-(3-Cl)-Benzo[b]thiophene
4-Me-Ph
-
-
SO2
C=O
Ph
Ph
2-Thiophene
2-Thiazole
In parallel, we also tested three diverse structural families of nucleoside analogues. Figure 1
summarises the first two of these families.
Due to the anti-ZIKV activity previously found for 20-CMA (3a) and 7-DMA [21
,
22], we prepared
a small family of novel aryloxyphosphoramidate prodrugs of these two nucleosides (3b 3d) to evaluate
the effect of the application of this prodrug technology [23] on the activity of the parent compounds.
In addition, we prepared a series of nucleoside analogues (4b 4o) of the broad-spectrum antiviral agent
–
–
T-1105 (4a), which has also been reported to inhibit ZIKV replication in cell-based assays, along with its
close analogue T-705 (favipiravir), approved in Japan to treat influenza virus infections [24]. As T-1105
and T-705 exert their antiviral activity by inhibiting the viral polymerase after metabolic conversion
into their ribofuranosyl 50-triphosphate forms [24], a small series of ribofuranose analogues of T-1105
and their aryloxyphosphoramidate prodrugs was designed (4c–4i) to modify the sugar part of the
nucleoside with the insertion of a 20-C-methyl substituent, as present in 20-CMA and 7-DMA, and to
introduce the same replacement of the 20-hydroxy group with a fluorine atom, as present in sofosbuvir.
Since the corresponding α-anomers of nucleosides 4c and 4d were obtained during their synthetic
preparation (4g
prodrug of 4h
,
(
4h), these were also included in our assays, along with one aryloxyphosphoramidate
4i), and the unmodified ribofuranosyl analogue 4b. Finally, as our group is also
exploring the antiviral potential of acyclic analogues of T-1105 (unpublished data), acyclic compound
4l was also considered, along with acyclic aryloxyphosphoramidate prodrugs 4m, 4n, and 4o.

Molecules 2020, 25, 4813
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Figure 1. Chemical structures of nucleoside analogues 3a–3d and 4a–4o. The parent compounds 3a
and 4a have been previously found to inhibit ZIKV replication in cell-based assays.
Finally, an additional small series of nucleoside-based compounds, 5a
evaluation against ZIKV-induced cytopathic effect in our systems (Figure 2).
–
5e, was chosen for
Figure 2. Chemical structures of nucleoside analogues 5a–5e. These molecules are currently being
investigated in our group for their potential antiviral activity against different flaviviruses; the scaffold of
5a has been previously reported for its indirect antiviral properties against vaccinia and measles viruses.
This small series of l-dideoxy bicyclic pyrimidine nucleoside analogues 5a–5e was included
in our evaluation as among them; 5a has been previously found to potently inhibit the replication
of both measles and vaccinia viruses in vitro through an indirect mechanism that points towards
interference with one or more cellular targets involved with the viral life cycle, thus suggesting its
potential effect against other viruses [25]. Although 5a has previously been found to be inactive against

Molecules 2020, 25, 4813
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the replication of adenovirus and herpes viruses [25], early findings obtained in our group for its
potential in inhibiting DENV serotype 2 replication in cell systems (unpublished data) prompted
us to prepare a few additional analogues of this compound, and to evaluate them against other
flaviviruses, including ZIKV. In particular, our early findings in the case of DENV serotype 2 suggest
5a as an inhibitor of autophagy and micropinocytosis mechanisms, which are relevant to DENV and
other flaviviruses [26,27]. This inhibitory effect would likely affect the replication of other flaviviruses,
which enter host cells via multiple pathways, including micropinocytosis, as has been demonstrated
for ZIKV infections in glioblastoma cells [28].
2.2. Synthetic Chemistry
The preparation of 1a
4a are commercially available. T-1105 analogues 4b
summarised in Scheme 1, which also shows the preparation of novel aryloxyphosphoramidates 3b
Preparation of 4b, the ribofuranosyl form of 4a, has been previously described [29], and was
achieved by reacting commercially available 4a with tetra-O-acetyl- -d-ribofuranose , according to
, then deprotected in a
–
1o and 2a
–
2m has recently been reported by our group [17
4o were prepared according to the synthetic routes
3d
,19], while 3a and
–
–
.
β
6
a Vorbrüggen coupling procedure [30], which yields acetylated nucleoside
7
methanolic sodium methoxide solution. Synthesis of both anomers of the 20-C-methylated derivative,
4c and 4g, has also been previously described [31], and was carried out by coupling in Vorbrüggen
conditions 4a with commercial 2-C-methyl-β-d-ribofuranose tetrabenzoate 8. The coupling step of
the◦reaction had to be performed at room temperature, as attempts under reflux conditions or at
50 C led to the selective formation of the α-anomer only of protected product 9. Performing the
coupling step at room temperature allowed the obtainment of both anomers of
of 2/3. The two anomers were separated after removal of the benzoyl protecting groups in
out in methanolic ammonia, through a reverse-phase column chromatography purification of the
final reaction mixture containing 4c and 4g. 20-Deoxy-20- -fluoro-20-
-C-methyl analogues 4d and 4h
9, with an
α
/
β
ratio
9, carried
α
β
have not been previously described. Their preparation began with the reduction in and subsequent
acetylation of commercially available lactone 10, to obtain the acetylated corresponding alcohol 12 in
a 1/2
α/β anomeric mixture, following a reported procedure [32]. Coupling of 12 with pseudobase
4a was once again achieved in Vorbrüggen conditions. After chromatographic purification, a 1/1
α/β
anomeric mixture was isolated for 13. The two anomers 4d and 4h were separated after removal
of the benzoyl protecting groups, which was carried out in methanolic ammonia, through flash
column chromatography purification. Additionally, the preparation of novel acyclic analogues
4l and 21 has not been previously reported. Compound 4l was obtained by coupling 4a with
(2-acetoxyethoxy)methyl acetate 14 in Vorbrüggen conditions, as previously reported for the synthesis
of various acyclic nucleoside analogues [33], followed by deprotection of the residual acetyl group
in methanolic ammonia. Preparation of 21 was achieved following the same approach, by coupling
4a with 2-(acetoxymethoxy)propane-1,3-diyl dibenzoate 19 to obtain the protected final intermediate
20, which was treated in methanolic ammonia to achieve the removal of the benzoyl groups in
21. Then, 19 was prepared following a reported three-step synthetic procedure [34], starting from
1,3-dichloropropan-2-ol 16. Finally, novel aryloxyphosphoramide prodrugs 3b
4n, and 4o were prepared following a coupling reaction between the corresponding nucleoside
analogues 3a, commercial 7-DMA, 4c 4d 4g 4h 4l, and 21 and the appropriate aryl amino acid
–3d, 4e–4f, 4i, 4m,
,
,
,
,
phosphorochloridate 22 or 23, in the presence of N-methylimidazole (NMI), according to previously
validated procedures for the synthesis of ProTide pronucleotides [35]. Then, 22 and 23 were prepared
starting from the corresponding ester of L-alanine (either isopropryl or benzyl), and reacting it with
phenyl dichlorophosphate, as extensively reported in the literature [35].

Molecules 2020, 25, 4813
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Scheme 1. Preparation of nucleoside analogues 3b–3d and 4b–4o. Reagents and conditions: (i) a. BSA,
MeCN, reflux, 1 h; b. TMSOTf, MeCN, r.t., 2 h (66%); (ii) 25% MeONa/MeOH, 0 ◦C, 30 min (75%);
(iii) a. BSA, MeCN, reflux, 1h; b. SnCl4, r.t., 36 h (82%); (iv) 7N NH3/MeOH, r.t., o.n. (39% 4c, 25% 4g);
(v) LiAlH(tBuO)3, an. THF,
−
20 ◦C, 3 h; (vi) Ac2O, DMAP, 20 ◦C, 2 h (99% over two steps); (vii) a. 4a
,
−
BSA, MeCN, reflux, 1 h; b. SnCl4, 50 ◦C, 24 h (75%); (viii) 7N NH3/MeOH, r.t., o.n. (25% 4d, 46% 4h);
(ix) a. BSA, MeCN, reflux, 1 h; b. SnCl4, r.t., o.n. (81%); (x) 25% MeONa/MeOH, 0 ◦C, 30 min (78%);
(xi) dimethoxymethane, P2O5, CHCl3, 0 ◦C to r.t., 18 h (76%); (xii) PhCOONa, 15-Crown-5, DMF, reflux,
18 h (99%); (xiii) BF3*Et2O, Ac2O, 0 ◦C, 2 h (98%); (xiv) a. 4a, BSA, MeCN, reflux, 1 h; b. SnCl4, r.t., o.n.
(80%); (xv) 7N NH3/MeOH, r.t., o.n. (69%); (xvi) NMI, THF, Pyr, r.t., o.n. (36–57%).

Molecules 2020, 25, 4813
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Scheme 2 describes the preparation of the final family of tested compounds, 5a–5e.
Scheme 2. Preparation of nucleoside analogues 5a–5e. Reagents and conditions: (i) MsCl, Et3N, THF,
rt, 18 h (97%); (ii) n-pentanol, NaH, THF, 70 ◦C, 24 h (71%); (iii) NC-NH2, NH4OH, MeOH, rt, 3 days
(65%); (iv) methyl propiolate, EtOH, reflux, 3 h (70%); (v) AcBr, MeCN, reflux, 2 h (72%); (vi) Zn,
glacial AcOH, EtOH, reflux, 2 h (55%); (vii) H2, Pd/C, MeOH, rt, 18 h (95%); (viii) a. I2, CAN, MECN,
reflux, 6 h, b. MeONa, MeOH, rt, 18 h (56% over two steps); (ix) Pd(PPh3)4, CuI, DIPEA, DMF, rt, 18 h,
then addition of Et3N, CuI, 80 ◦C, 8 h (28–55%); (x) a. MeNH2, MeOH, 60 ◦C, 6 h, b. p-TsCl, 1,4-dioxane,
PhMe, reflux, 1 h (25% over two steps).
Preparation of 5a and 5d has been previously described [25], and the reported method
was followed also to obtain 5b and 5c. Briefly, commercial carbohydrate 27 was reacted with
cyanamide to afford the bicyclic oxazoline 28, which was treated with methyl propiolate in
methanol to provide the 2,20-anhydro-nucleoside 29. Following a bromoacetylation reaction with
acetyl bromide in acetonitrile, 29 was converted into nucleoside 30, which was subjected to a
reductive β-elimination with activated zinc powder in the presence of glacial acetic acid, to afford
50-O-acetyl-20,30-didehydro-20,30-dideoxyuridine 31. The dideoxy nucleoside 32 was then obtained
upon catalytic hydrogenation of 31, while preparation of L-5-iodo-20,30-dideoxyuridine 33 was achieved
after iodination at the C5-position of the nucleobase with iodine in the presence of ammonium cerium(IV)
nitrate (CAN), followed by deacetylation with sodium methoxide. A palladium-catalysed Sonogashira
coupling of 33 with acetylenes 26 and 34
which, after addition of copper (I) iodide in situ with heating, afforded the desired furanopyrimidine
products 5a , following an intramolecular cyclisation. While 34 36 are commercially available, 26 was
–36 provided the corresponding 5-alkynyl nucleosides,
–
d
–
prepared in two steps as previously described [29], starting from undec-10-yn-1-ol 24. Preparation of
the N-methyl-pyrrolo-pyrimidin-2-one analogue 5e has also been previously described [36], and was
obtained from 5a, which was treated with methylamine in methanol while heating, in order to achieve
the opening of the fused furane ring by the amine. This was then followed by refluxing the reaction in

Molecules 2020, 25, 4813
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a higher-boiling solvent mixture after treatment with p-TsCl, to promote a dehydration and cyclisation
of the system, with the formation of the target pyrro analogue 5e.
2.3. Antiviral Studies
The selected compounds were first evaluated at a fixed 10 µM concentration for their potential
inhibition of ZIKV-induced cytopathic effect in a MTS based TCID50 assay [37], using cell lines which
are physiologically relevant for ZIKV infection, including HUH7 hepatoma cells [38], dbtrg cells [28],
and A549 cells, which support Zika virus infection in vitro [39]. The cell lines used were chosen to
reflect the pathogenesis of ZIKV in liver (HUH7) and CNS tissues (dbtrg), in addition to a cell line
where the ZIKV strain originally isolated in Uganda in 1947 grows and forms plaques particularly well
(A549). The compounds’ cytotoxicity was also evaluated in the same assay. Ribavirin was used as a
positive control [40].
The results of this preliminary assay are summarised in Table 2.
Table 2. Reduction in ZIKV-induced cytopathic effect (CPE) and cytotoxicity data for the selected
compounds at a fixed 10 µM concentration in multiple cell lines 1.
% Cell
Viability,
ZIKV–Infected
HUH7
% Cell
Viability,
HUH7
% Cell
Viability,
ZIKV–Infected
Dbtrg
% Cell
Viability,
Dbtrg
% Cell
Viability,
ZIKV–Infected
A459
% Cell
Viability,
A459
Compound
(Cytotoxicity)
(Cytotoxicity)
(Cytotoxicity)
1a
1b
1c
1d
1e
1f
1g
1h
1i
1l
1m
1n
1o
2a
2b
2c
2d
2e
2f
2g
2h
2i
2l
13.5
3.4
8.8
8.3
0
4.9
6.1
5.4
5.7
12.1
7.9
5.1
5.2
23.5
14.5
32
20
11.1
15.3
46.2
26.1
16.1
22.0
25.2
37.9
30.6
0
0
0
0
0
0
0
0
0
0
0
0
0
15
17.3
18.4
24.9
14.1
19.3
24.3
21.8
15.5
18.2
12.6
14.8
8.9
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
40
33.6
n.d.
59.6
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
106.9
103.5
n.d.
112.3
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
n.d.
30.5 ± 15.9
25.5 ± 18.2
0.4 ± 0.7
4.5 ± 6.6
11.2 ± 9.9
3.9 ± 1.9
9.5 ± 7.1
9.8 ± 6.6
4.5 ± 3.3
1.6 ± 3.6
3.3 ± 2.7
31.4
117.9 ± 42.2
107.4 ± 35.9
108.6 ± 55.9
119.5 ± 47.3
117.8 ± 40.9
75.7 ± 54.3
160.6 ± 50.6
134.9 ± 51.6
106.4 ± 59.1
110.1 ± 63.5
99.9 ± 62.9
98.8
n.d.
n.d.
3.1 ± 3.9
4.1 ± 5.6
2.8 ± 2.8
0.25 ± 0.43
0.8 ± 1.4
0
2.5 ± 2.2
1.7 ± 1.7
9.2 ± 8.5
11 ± 7.5
5.2
94.9 ± 16.2
88.9 ± 18.5
76.9 ± 25.7
80.5 ± 27.2
76 ± 27.4
109.7 ± 4.8
114.7 ± 4.5
96.7 ± 15.2
91.8 ± 14.5
104.2 ± 10.7
107.3
2m
3a (20-CMA)
3b
3c
3d
4a
4b
4c
4d
4e
4f
48.2
98.2
10.2
100.5
120.4 ± 80.3
101.5
0.1
137.6 ± 35.6
53.3 ± 18.9
87.9 ± 18.7
107.9
8.1
115.5
100.6
106.8
118.5
105.6
90.8
97.8
117.5
106.5
4.6
4.6
7.3
0.4
0
6.6
0
0.1
97.4
99.2
105.6
98.7
85.9
82.3
104.9
99.3
0.1
0.6
0
0
0.1
0.1
0
0.2
4g
4h
4i
102.5
101.3
4.3
4.5
97.8
98.5
4l
0

Molecules 2020, 25, 4813
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Table 2. Cont.
% Cell
% Cell
Viability,
HUH7
% Cell
Viability,
ZIKV–Infected
Dbtrg
% Cell
Viability,
Dbtrg
% Cell
Viability,
ZIKV–Infected
A459
% Cell
Viability,
A459
Viability,
ZIKV–Infected
HUH7
Compound
(Cytotoxicity)
(Cytotoxicity)
(Cytotoxicity)
4m
4n
4o
5a
5b
5c
5d
5e
0.2
0.1
0.1
50.3
0
0
0.2
30.6
106.4
104.9
97.8
100.5
110.1
104.4
104.3
55.1
1.2
2.2
6.6
0
5.7
3.9
0.4
99.6
98
82.3
75.7
102.9
94.7
n.d.
n.d.
n.d.
0
8.2
0
28.6
2.7
n.d.
100
0
n.d.
n.d.
n.d.
84.8
91.6
87.6
104.7
81.6
n.d.
100
74.5
52
13.6
Ribavirin
Control-DMSO
Control-ZIKV
61.1 ± 26.4
158.7 ± 16.9
25.1 ± 10.1
94.8 ± 21.6
100
100
100
100
0
6 ± 1.4
0
14.4 ± 4.3
1
0
The most interesting antiviral results obtained are highlighted in bold. Reported values are the mean of at
least 2 independent experiments, with standard deviations of 10% of the value quoted unless otherwise stated
±
(mean value ± standard deviations).
From this evaluation, most of the structural families tested did not show a protective effect against
ZIKV-induced cytotoxicity in the cell lines considered. While analogues within the series of compounds
2a
the first structural scaffold (1a
Surprisingly and in contrast with what had been previously reported [19], 2a did not show a protective
effect against ZIKV-induced cytotoxicity in the cell lines used for our assays. Compounds 3a 3b 3d
5a 5d, and 5e reduced ZIKV-induced cytopathic effect in at least one cell line, showing a significant
–
2m and 4a
–
4o did not show antiviral activity nor relevant cytotoxic effects, several analogues of
–
1o) were found to show some significant cytotoxicity in this assay.
,
–
,
,
increase in cell viability in comparison with untreated, infected cells (control-ZIKV), with % values
indicating antiviral EC50s in the low micromolar range. The activity observed for 3a is in line with
previous literature, which highlights the anti-ZIKV properties of 20-CMA and 7-DMA [21
,22]: as 3b–3d
are novel ProTide prodrugs of either one of these two nucleoside analogues, their observed anti-ZIKV
effect suggests that application of this pronucleotide technology to 20-CMA and 7-DMA is associated
with an enhanced antiviral effect in comparison with the parent nucleosides. The effect observed for 5a
which is a known indirect antiviral agent [25], and to a lesser extent for 5d and 5e, suggests the very
promising potential to explore novel host pathways for the interference with ZIKV life cycle. Due to
their protective effect against ZIKV in multiple cell lines, dose–response curves were determined for
,
novel prodrugs 3b–3d and 5a in the HUH7 cell line, as reported in Table 3. Sofosbuvir was included
for this evaluation as a positive control. From this analysis, 3c and 3d emerged as the best antiviral hits
found in this study, and their antiviral dose–response curves were also determined in the U251 cell
line [41], which is an astrocytoma cell line susceptible to ZIKV infection, commonly used as an in vitro
model for ZIKV CNS infection.
Table 3. Antiviral EC50 and CC50 values calculated for selected hits in the HUH7 and U251 cell lines.
a,c
a,c
b,c
b,c
EC50
(µM),
EC50
(µM),
CC50
(µM),
CC50
(µM),
SI d, HUH7
SI d, U251
Compound
HUH7
U251
HUH7
U251
3b
3c
3d
5a
4 ± 0.2
11.6 ± 1.3
8.3 ± 0.9
10.2 ± 0.4
5.8 ± 0.8
>20
>5
18.2
15.4
>2
-
-
-
24.8
1.6
-
211.2 ± 4.6
128.2 ± 21.1
>20
133.5 ± 13.6
8.2 ± 1.1
8.6 ± 6.5
-
7.7 ± 4.5
203.7 ± 16.9
13.6 ± 1.7
-
139.1 ± 26.4
Sofosbuvir
23
18
a
EC50 = 50% effective concentration (concentration at which 50% inhibition of virus replication is observed).
b CC50 = 50% cytostatic/cytotoxic concentration (concentration at which 50% adverse effect is observed on the host cell).
c The EC50 and CC50 values are the mean of at least 3 independent experiments, with standard deviations of
10% of
±
the value quoted unless otherwise stated (mean value ± standard deviations). d SI = the ratio of CC50 to EC50
.

Molecules 2020, 25, 4813
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From this evaluation, 3c in particular emerges as a promising hit molecule for further development,
as it shows a low micromolar antiviral effect in both cell lines, and it is associated with the highest
selectivity index found in U251 cells, while it retains EC50 values comparable to the ones found for
sofosbuvir in our assay.
Finally, we also conducted a preliminary investigation to explore the possibility of combining the
effects of an anti-ZIKV nucleoside analogue, which most likely targets the viral polymerase, and of an
agent that likely targets a host pathway. For this evaluation, we tested the effect of the combination of
3b and 5a in the A-459 cell line, using an assay that measures cell adherence as an indication of cell
viability [42]. Our findings are summarised in Figure 3.
Figure 3. The effect of 3b (blue), 5a (purple), and a combination of both (light green) was tested
at a concentration of 20 µm against ZIKV in A-549 cells plated in a 16 well CIM-Plate 16 using the
xCELLigence RTCA DP Instrument. No compound (dark green; 0) and mock (no virus, pink) were
used as controls. Dpi: days postinfection.
In our assay, cells showed an increase in impedance up to a cell index (CI) of 3.5 in the first 24 h
after plating, representing increasing cell–cell contacts and adherence to the well bottom. At this
point, the medium was removed (spike; first dotted line in Figure 3) and antiviral compounds were
added for a 30-min pretreatment, then ZIKV was added. At the end of the first day of infection (1 day
postinfection (dpi)), CI varied, with CI values higher than mock in the combination (light green) and
with 5a alone. Virus without compounds (dark green) showed a beginning of loss of impedance,
reflecting ZIKV cytopathological effect of cells rounding, with loss of adherence and loss of electrical
resistance (impedance). Up to 2 days of infection, the CI values increased, except in the virus control,
whereas at 3 dpi (72 h), a significant separation of impedance was observed: the combination curve is
similar to the CI value of the uninfected control (mock), indicating full protection. The wells treated
with single compounds show less protection with lower CI values. CI value for uninfected cells (mock)
remains at the same level until the end of the experiment. All other CI values drop up to 88/96 h
postinfection, when the dropping of CI value for the virus only control flattens out, but does not
reach a plateau. Relative efficacy of compounds can be determined at any point between 72 and 96 h
postinfection. From 72 h postinfection, the effect of the combination of 3b and 5a was more effective
than the individual compounds. With the known mechanism of action of the active form of 3b being
viral polymerase inhibition, and the mechanism of action of 5a being most likely interference with
a host pathway, and with early data found in our lab indicating autophagy inhibition (unpublished
results), the observed increased efficacy suggesting synergy. In addition, the calculated EC50 of the

Molecules 2020, 25, 4813
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1:1 combination of 3b and 5a in HUH7 cells is 1
impedance/cell-adherence using thexCELLigence RTCA DP instrument.
±
0.2
µ
M, supporting the effects observed on cell
In conclusion, antiviral evaluation in multiple cell lines of a focused internal library of
small-molecule compounds led to the identification of multiple inhibitors of ZIKV-induced cytophatic
effect. While we identified three novel ProTide pronucleotides of 20-CMA and 7-DMA, 3b
, 3c, and 3d,
as potential leads for the treatment of ZIKV infections, we also found a highly interesting antiviral
activity for a l-dideoxy bicyclic pyrimidine nucleoside analogue, 5a, which had been previously
reported to potently inhibit the replication of vaccinia and measles viruses in cells, by interfering with
a host pathway. In addition to confirming the anti-ZIKV activity of 5a on its own, we also observed
a clear synergistic effect for its combination with our ProTide pronucleotide 3b, potentially paving
the way for a combination approach for the treatment of ZIKV infection, and also suggesting a novel,
host-directed approach for the development of new and improved antiflaviviral strategies. Further
exploration of both structural scaffolds and of the synergistic effect observed, along with the elucidation
of the precise mechanism of the anti-ZIKV activity of 5a, are currently ongoing.
3. Materials and Methods
3.1. Synthetic Chemistry
3.1.1. General Methodologies
All solvents and reagents were used as obtained from commercial sources unless otherwise
indicated. All solvents used for chromatography were HPLC grade from Fisher Scientific (UK).
1
All reactions were performed under a nitrogen atmosphere. H, 13C, 19F, and 31P-NMR spectra were
recorded with a Bruker Avance III HD spectrometer operating at 500 MHz for 1H and 125 MHz for 13C,
with Me4Si as internal standard. Deuterated chloroform was used as the solvent for NMR experiments,
1
unless otherwise stated. H chemical shift values (
δ
) are referenced to the residual non-deuterated
= 7.26 ppm for CHCl3, etc.). The 13C chemical shifts (
) are
= 77.0 ppm). TLC was performed on silica gel 60 F254 plastic
components of the NMR solvents (
referenced to CDCl3 (central peak,
δ
δ
δ
sheets. Normal-phase or reverse-phase automated flash column chromatography was performed
using a Biotage Isolera system. UPLC-MS analysis was conducted on a Waters UPLC system with both
Diode Array detection and Electrospray (+0ve and
Waters Acquity UPLC BEH C18 1.7 um 2.1
containing 0.1% formic acid (A) and LC-MS grade MeCN containing 0.1% formic acid (B). Column
temperature: 40 ◦C. Sample diluent: MeCN or H2O. Sample concentration 1
µg/mL. Injection volume
−
0ve ion) MS detection. The stationary phase was a
50 mm column. The mobile phase was LC-MS grade H2O
×
2 µL. Four alternative methods were used:
-
-
-
-
Linear gradient standard method (A): 90% A (0.1 min); 90–0% A (2.5 min); 0% A (0.3 min); 90% A
(0.1 min); flow rate 0.5 mL/min.
Linear gradient standard method (B): 90% A (0.1 min); 90–0% A (2.1 min); 0% A (0.8 min); 90% A
(0.1 min); flow rate 0.5 mL/min.
Linear gradient standard method (C): 90% A (0.1 min); 90–0% A (1.5 min); 0% A (1.4 min); 90% A
(0.1 min); flow rate 0.5 mL/min.
Linear gradient standard method (D): 99% A (0.1 min); 99–80% A (2.1 min); 0% A (0.8 min); 99% A
(0.1 min); flow rate 0.5 mL/min.
High resolution mass spectra (HRMS) were measured in positive mode electrospray ionisation
(ES+). All compounds tested in biological assays were >95% pure. Purity of intermediates was >90%,
unless otherwise stated. All known intermediates and known compounds were either purchased
(3a, 7–DMA, 4a), or prepared according to literature procedures (1a–1o, 2a–2m, 4b, 4c, 4g, 5a, 5d, 5e),
with their characterisation data in line with previously reported data. Details for the preparation and
full characterisation of novel compounds are given below.

Molecules 2020, 25, 4813
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3.1.2. General Method for the Preparation of Novel ProTides 3b–3d, 4e, 4f, 4i, 4m–4o
The appropriate nucleoside 3a, 7–DMA, 4c, 4d, 4g, 4h, 4l, or 21 (1 eq., 0.5 mmol) was suspended
in a mixture of anhydrous tetrahydrofuran/pyridine (1:2 v/v, 6 mL) at room temperature under a
nitrogen atmosphere. 1-Methylimidazole (6 eq., 3 mmol) was then added dropwise and the mixture
was stirred for 20 min. A solution of 23 or 24 (1.5 eq., 0.75 mmol) in anhydrous tetrahydrofuran (4 mL)
was then added dropwise and the reaction was stirred at room temperature overnight. The reaction
was concentrated under vacuum and the crude residue was purified twice by automated flash column
chromatography on silica gel (ethyl acetate to ethyl acetate/methanol 90:10 v/v) to afford the pure title
compounds as 1:1 diastereomeric mixtures.
20-C-Methyladenosine 50-O-[phenyl-(benzyloxy-l-alaninyl)] Phosphate 3b
1
Obtained in 36% yield as a white solid. H-NMR (CD3OD),
δ: 8.24–8.22 (m, 2H), 7.35–7.17 (m, 10H)
,
6.13, 6.11 (2s, 1H), 5.16–5.02 (m, 2H), 4.57–4.44 (m, 2H), 4.27–4.18 (m, 2H), 4.07–3.99 (m, 1H),
1.35–1.32 (m, 3H), 0.96, 0.93 (2s, 3H). 13C-NMR (CD3OD),
: 174.80, 174.61, 157.42, 157.41, 154.02,
δ
153.99, 152.19, 152.13, 150.44, 150.37, 140.73, 140.46, 137.24, 137.19, 130.81, 130.78, 129.56, 129.53,
129.35, 129.29, 129.24, 129.13, 128.27, 128.00, 126.15, 121.45, 121.44, 121.42, 121.40, 120.38, 93.37,
93.08, 82.26, 82.06, 80.02, 79.94, 74.46, 73.93, 67.95, 67.89, 67.31, 66.39, 51.77, 51.60, 20.51, 20.26, 20.16.
31P-NMR (202 MHz, CD3OD)
, δ: 4.01, 3.75. MS [ESI, m/z]: 621.2 [M + Na]. HRMS calculated for
C27H32N6O8P+: 599.2019; found 599.2037.
7-Deaza-20-C-methyladenosine 50-O-[phenyl-(benzyloxy-l-alaninyl)] Phosphate 3c
Obtained in 40% yield as a white solid. 1H-NMR (CDCl3),
7.24–7.22 (m, 2H), 7.15–7.03 (m, 2H), 6.39–6.29 (m, 2H), 5.68 (bs, 1H), 5.62 (bs, 1H), 5.38, 5.31 (2s, 2H),
4.54–4.42 (m, 2H), 4.23–4.21 (m, 1H), 4.14–4.01 (m, 2H), 3.45–3.39, 3.06–2.98 (2m, 1H), 1.37–1.31 (m, 3H)
0.82 (s, 3H). 13C-NMR (CDCl3),
: 176.60, 173.48, 173.42, 156.57, 156.55, 150.66, 150.58, 149.68, 149.55,
δ: 8.28 (s, 1H), 7.39–7.28 (m, 7H),
,
δ
135.19, 135.17, 129.79, 129.78, 128.63, 128.62, 128.49, 128.47, 128.20, 128.16, 125.13, 125.03, 122.17, 122.00,
120.16, 120.09, 99.21, 99.15, 91.44, 91.26, 81.13, 81.00, 78.97, 74.11, 73.79, 67.28, 65.92, 52.84, 50.44, 50.31,
29.70, 20.79, 20.05. 31P-NMR (202 MHz, CDCl3),
δ: 3.21, 2.69. UPLC-MS (Method B): Rt 1.68 min,
MS [ESI, m/z]: 598.3 [M + H]. HRMS calculated for C28H33N5O8P+: 598.2061; found 598.2073.
7-Deaza-20-C-methyladenosine 50-O-[phenyl-(isopropoxy-l-alaninyl)] Phosphate 3d
1
Obtained in 46% yield as a colourless waxy solid. H-NMR (CDCl3),
δ
: 8.19 (s, 1H), 7.22–7.13 (m, 4H)
,
7.05–6.93 (m, 2H), 6.32–6.22 (m, 2H), 5.81 (bs, 1H), 5.77 (bs, 1H), 4.93–4.83 (m, 1H), 4.62–4.32 (m, 3H),
4.18–4.12 (m, 1H), 3.98–3.89 (m, 2H), 1.26, 1.25 (2 s, 3H), 1.12–1.04 (m, 6H,), 0.71, 0.69 (2s, 3H). 13C-NMR
(CDCl3), δ: 173.24, 173.19, 173.14, 156.91, 156.89, 151.55, 151.48, 150.71, 150.66, 149.69, 149.58, 129.75, 125.04,
124.97, 121.84, 121.71, 120.13, 120.11, 120.09, 120.07, 103.43, 103.35, 99.16, 91.43, 91.27, 80.70, 80.64, 73.93,
73.58, 69.34, 69.28, 65.89, 65.85, 65.26, 65.23, 50.48, 50.36, 21.65, 21.57, 20.93, 20.89, 20.84, 20.80, 19.89, 19.86.
31P-NMR (202 MHz, CDCl3),
δ: 3.38, 3.11. MS [ESI, m/z]: 550.2 [M + H], 572.2 [M + Na]. HRMS calculated
for C24H33N5O8P+: 550.2061; found 550.2049.
4-(20-C-Methyl-β-d-ribofuranosyl)-3-oxo-3,4-dihydropyrazine-2-carboxamide
50-O-[phenyl-(benzyloxy-l-alaninyl)] Phosphate 4e
Obtained in 48% yield as a pale yellow waxy solid. 1H-NMR (CDCl3),
δ: 9.04 (bs, 1H),
7.86 (bs, 1H), 7.72–7.65 (m, 1H), 7.38–7.31 (m, 8H), 7.24–7.15 (m, 3H), 6.28–6.19 (m, 2H), 5.16, 5.15 (2s, 2H)
4.53–4.46 (m, 1H), 4.40–4.35 (m, 1H), 4.23–4.19 (m, 1H), 4.10–4.03 (m, 1H), 3.87 (d, J = 7.5 Hz, 1H),
3.75 (bs, 2H), 1.42–1.38 (m, 3H), 0.97, 0.96 (2s, 3H). 13C-NMR (CDCl3),
: 175.66, 168.82, 164.78, 163.92,
,
δ
157.46, 150.42, 143.64, 135.04, 129.93, 128.70, 128.62, 128.61, 128.24, 128.14, 127.42, 127.21, 125.43, 125.38,
119.98, 119.89, 99.98, 92.40, 90.00, 89.69, 81.63, 80.03, 75.27, 73.18, 72.92, 67.49, 64.49, 50.54, 50.41, 20.82,

Molecules 2020, 25, 4813
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20.78, 20.63, 20.61.31P-NMR (202 MHz, CDCl3),
δ
: 3.60, 3.19. UPLC-MS (Method B): Rt 1.71 min,
MS [ESI, m/z]: 625.2 [M + Na]. HRMS calculated for C27H32N4O10P+: 603.1851; found 603.1839.
4-[(2’-R)-2’-C-Deoxy-2’-C-fluoro-20-C-methyl-β-d-ribofuranosyl]-3-oxo-3,4-dihydropyrazine-2-
carboxamide 50-O-[phenyl-(benzyloxy-l-alaninyl)] Phosphate 4f
Obtained in 55% yield as a white glassy solid. 1H-NMR (CDCl3),
7.75–7.64 (m, 1H), 7.59–7.50 (m, 1H), 7.40–7.31 (m, 7H), 7.25–7.18 (m, 3H), 6.52, 6.47 (2d, JF = 18.2 Hz, 1H)
δ: 9.17–9.12 (bs, 1H),
,
6.27 (bs, 1H), 5.18–5.16 (m, 2H), 4.63–4.55 (m, 1H), 4.51–4.46 (m, 1H), 4.24–4.07 (m, 3H), 4.01,
3.96 (2d, J = 8.9 Hz, 1H), 3.85–3.74 (m, 1H), 1.45–1.42 (m, 3H), 1.35–1.30 (m, 3H). 13C-NMR (CDCl3),
δ: 173.87, 173.52, 163.21, 163.12, 155.40, 155.31, 150.43, 150.38, 143.94, 143.74, 134.98, 134.93, 130.05, 130.01,
128.72, 128.60, 126.89, 126.43, 125.58, 125.36, 120.61, 120.57, 119.69, 119.08, 101.18, 101.11, 99.70, 99.63,
89.38, 89.08, 80.34, 80.09, 70.83, 70.71, 67.57, 67.50, 63.57, 63.42, 50.61, 50.39, 30.19, 29.71, 20.82, 20.67,
16.59, 16.39. 19F-NMR (470 MHz, CDCl3),
δ:
−
163.21, δ: 4.26,
163.32. 31P-NMR (202 MHz, CDCl3),
−
3.52. UPLC-MS (Method B): Rt 1.80 min (diast. 1), 1.82 min (diast. 2), MS [ESI, m/z]: 605.2 [M + H].
HRMS calculated for C27H31FN4O9P+: 605.1807; found 605.1831.
4-[(2’-R)-2’-C-Deoxy-2’-C-fluoro-20-C-methyl-α
-d-ribofuranosyl]-3-oxo-3,4-dihydropyrazine-2-carboxamide 50-O-[phenyl-(benzyloxy-l-alaninyl)]
Phosphate 4i
1
Obtained in 57% yield as a white glassy solid. H-NMR (CDCl3),
δ
: 9.04, 9.02 (2d, J = 3.1 Hz, 1H)
,
7.72 (app. d, J = 4.2 Hz, 1H), 7.50–7.48 (m, 1H), 7.38–7.30 (m, 7 H), 7.24–7.15 (m, 3H), 6.38,
6.27 (2d, JF = 19.2 Hz, 1H), 6.28–6.14 (m, 1H), 5.19 (d, J = 5.7 Hz, 1H), 5.14 (s, 1H), 4.42–4.25 (m, 4H),
4.23–4.03 (m, 2H), 3.92–3.80 (m, 1H), 1.55, 1.42 (2d, JF = 22.5 Hz, 3H), 1.41–1.36 (m, 3H). 13C-NMR (CDCl3),
δ: 173.87, 173.40, 163.10, 155.55, 150.45, 150.33, 143.69, 143.58, 135.14, 135.06, 129.92, 129.86, 128.71,
128.69, 128.62, 128.55, 128.23, 127.93, 125.58, 125.35, 124.40, 124.33, 120.61, 120.16, 100.07, 99.93, 98.54,
98.40, 87.46, 87.32, 81.78, 81.66, 73.70, 73.56, 67.49, 67.39, 64.85, 64.25, 50.49, 50.30, 20.83, 20.62, 17.74,
17.54. 19F-NMR (470 MHz, CDCl3),
δ
:
−
176.77, δ: 3.68, 2.94.
176.84. 31P-NMR (202 MHz, CDCl3),
−
UPLC-MS (Method B): Rt 1.77 min, MS [ESI, m/z]: 605.2 [M + H]. HRMS calculated for C27H31FN4O9P+:
605.1807; found 605.1795.
Benzyl ((2-((3-carbamoyl-2-oxopyrazin-1(2H)-yl)methoxy)ethoxy)(phenoxy)phosphoryl)-l-alaninate 4m
Obtained in 51% yield as a pale yellow oil. 1H-NMR (CDCl3),
7.68 (2d, J = 4.1 Hz, 1H), 7.53, 7.48 (2d, J = 4.1 Hz, 1H), 7.37–7.29 (m, 7H), 7.21–7.14 (m, 3H), 6.24 (bs, 1H)
5.40 (d, J = 2.5 Hz, 1H), 5.35 (d, J = 5.3 Hz, 1H), 5.16 (s, 1H), 5.13 (s, 1H), 4.27–4.16 (m, 2H), 4.14–4.02 (m, 1H),
3.86–3.76 (m, 2H), 3.75–3.69 (m, 1H), 1.40, 1.38 (2d, J = 7.1 Hz, 3H). 13C-NMR (CDCl3),
: 173.48, 173.41,
δ: 9.07 (bs, 1H), 7.69,
,
δ
173.34, 162.98, 155.94, 155.92, 150.66, 150.63, 144.85, 144.81, 135.24, 135.21, 130.01, 129.97, 129.73, 129.71,
128.68, 128.66, 128.58, 128.53, 128.23, 128.19, 125.06, 124.87, 124.86, 120.22, 120.18, 120.12, 120.08, 77.90,
69.72, 69.67, 67.29, 67.27, 65.65, 65.61, 50.41, 50.31, 20.95, 20.91. 31P-NMR (202 MHz, CDCl3), δ: 2.68, 2.36.
UPLC-MS (Method B): Rt 1.81 min, MS [ESI, m/z]: 553.2 [M + Na]. HRMS calculated for C24H28N4O8P+:
531.1639; found 531.1645.
Isopropyl ((2-((3-carbamoyl-2-oxopyrazin-1(2H)-yl)methoxy)ethoxy)(phenoxy)
phosphoryl)-l-alaninate 4n
Obtained in 55% yield as an off-white waxy solid. 1H-NMR (CDCl3),
7.72 (d, J = 4.1 Hz, 1H), 7.57, 7.55 (2d, J = 4.1 Hz, 1H), 7.34–7.30 (m, 2H), 7.22–7.14 (m, 3H), 6.03 (bs, 1H)
5.43 (d, J = 2.4 Hz, 1H), 5.41 (d, J = 4.5 Hz, 1H), 5.02–4.96 (m, 1H), 4.30–4.23 (m, 2H), 4.03–3.92 (m, 1H)
3.88–3.83 (m, 1H), 3.61–3.52 (m, 1H), 1.37–1.34 (2d, J = 6.9 Hz, 3H), 1.24–1.20 (m, 6H). 13C-NMR (CDCl3),
: 173.51, 173.45, 173.30, 162.89, 155.90, 155.88, 150.59, 150.55, 144.90, 144.85, 130.01, 129.76, 129.74,
125.09, 124.98, 120.23, 120.19, 120.16, 120.12, 77.92, 69.80, 69.75, 69.42, 53.47, 50.40, 50.33, 21.72, 21.64,
δ: 9.11 (bs, 1H),
,
,
δ

Molecules 2020, 25, 4813
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21.09. 31P-NMR (202 MHz, CDCl3),
δ
: 2.80, 2.55. UPLC-MS (Method B): Rt 1.66min, MS [ESI, m/z]:
505.2 [M + Na]. HRMS calculated for C20H28N4O8P+: 483.1639; found 483.1651.
Benzyl ((2-((3-carbamoyl-2-oxopyrazin-1(2H)-yl)methoxy)-3-hydroxypropoxy)(phenoxy)
phosphoryl)-l-alaninate 4o
1
Obtained in 54% yield as a pale yellow solid. H-NMR (CDCl3),
δ
: 9.01 (bs, 1H), 7.65–7.61 (m, 2H)
,
,
7.32–7.27 (m, 7H), 7.17–7.10 (m, 3H), 6.60 (bs, 1H), 5.51–5.43 (m, 1H), 5.41–5.32 (m, 1H), 5.12, 5.09 (2s, 2H)
4.23–4.04 (m, 2H), 4.02–3.87 (m, 2H), 3.70—3.52 (m, 2H), 1.37–1.34 (m, 3H). 13C-NMR (CDCl3),
δ
: 173.58,
173.45, 163.58, 155.89, 150.54, 144.13, 135.22, 131.43, 129.76, 129.73, 128.68, 128.64, 128.56, 128.50, 128.21,
128.15, 127.87, 125.13, 124.73, 120.27, 120.23, 120.17, 120.14, 120.11, 79.83, 77.76, 67.27, 66.01, 61.17, 61.10,
50.42, 50.30, 20.79, 20.76. 31P-NMR (202 MHz, CDCl3),
δ: 3.34, 2.98. UPLC-MS (Method B): Rt 1.74 min,
MS [ESI, m/z]: 583.2 [M + Na]. HRMS calculated for C25H30N4O9P+: 561.1745; found 561.1763.
3.1.3. Preparation of Novel 20-Deoxy-20-α-fluoro-20-β-C-methyl-ribofuranosyl Analogues 4d and 4h
Commercially available 4a (20 mmol, 1.5 eq.) was suspended in anhydrous MeCN (50 mL) under a
nitrogen atmosphere. N,O-Bis(trimethylsilyl)acetamide (BSA, 40 mmol, 3 eq.) was then added, and the
mixture was stirred under reflux for 1 h. The resulting solution was then cooled to room temperature,
and acetylated alcohol 12, obtained in a 1/2 α/β anomeric mixture according to a previously reported
procedure [32] (13.5 mmol, 1 eq.), was dissolved in anhydrous MeCN (10 mL) and added to the reaction
mixture. Finally, the mixture was cooled in an ice-bath and SnCl4 (47 mmol, 3.5 eq.) was slowly added.
The reaction was allowed to warm to room temperature and then heated to 50 ◦C for 24 h. The mixture
was then cooled to 0 ◦C and a cold saturated NaHCO3 solution (100 mL) was added slowly while
stirring. The residue was then extracted with EtOAc (3
were washed with water and brine, dried over Na2SO4, and concentrated under vacuum. The crude
residue was purified twice by automated flash column chromatography on silica gel (ethyl acetate to
×
100 mL). The combined organic layers
ethyl acetate/methanol 90:10 v/v) to afford 13 as a 1/1 α/β anomeric mixture (pale yellow solid, 75%).
Compound 13 (1 mmol, 1 eq.) was then added to 7N methanolic ammonia (15 mL), and the mixture
was stirred at room temperature overnight. The reaction mixture was then dried under vacuum and
the crude residue was purified three times by automated flash column chromatography on silica gel
(dichloromethane to dichloromethane/methanol 90:10 v/v) to afford the pure nucleosides 4d and 4h.
4-[(2’-R)-2’-C-Deoxy-2’-C-fluoro-20-C-methyl-β-D-ribofuranosyl]-3-oxo-3,4-dihydropyrazine-2
-carboxamide 4d
Obtained in 25% yield as a pale yellow solid. 1H-NMR (DMSO-d6),
δ: 8.24 (d, J = 4.4 Hz, 1H),
8.23 (bs, 1H), 7.75 (bs, 1H), 7.56 (d, J = 4.4 Hz, 1H), 6.29 (d, JF = 18.3 Hz, 1H), 5.74 (d, J = 6.7 Hz,
1H), 5.43 (app. t, J = 4.5 Hz, 1H), 3.97–3.87 (m, 3H), 3.70 (ddd, J1 = 11.7 Hz, J2 = 3.7 Hz, J3 = 1.8 Hz,
1H), 1.21 (d, JF = 22.5 Hz, 3H). 13C-NMR (DMSO-d6),
δ
: 164.58, 154.23, 148.66, 126.66, 123.60, 101.59
(d, JF = 182.3 Hz), 82.65, 70.31 (d, JF = 17.1 Hz), 58.57, 49.07, 16.87 (d, JF = 24.9 Hz). 19F-NMR (470 MHz,
DMSO-d6),
δ
: 161.20. UPLC-MS (Method D): Rt 1.59 min, MS [ESI, m/z]: 288.2 [M + H]. HRMS calculated
−
for C11H15FN3O5+: 288.0990; found 288.0976.
4-[(2’-R)-2’-C-Deoxy-2’-C-fluoro-20-C-methyl-α-D-ribofuranosyl]-3-oxo-3,4-dihydropyrazine-2
-carboxamide 4h
Obtained in 46% yield as a white solid.
7.74–7.69 (m, 2H) 7.51 (d, J = 4.4 Hz, 1H), 6.38 (d, JF = 19.2 Hz, 1H), 5.78 (d, J = 7.2 Hz, 1H),
4.90 (app. t, J = 5.5 Hz, 1H), 4.21–4.18 (m, 1H), 4.06–4.01 (m, 1H), 3.75 (dd, J1 = 12.1 Hz, J2 = 3.5 Hz,
1H), 3.57–3.51 (m, 1H) 1.45 (d, JF = 22.4 Hz, 3H) : 164.83, 154.18, 148.77,
13C-NMR (DMSO-d6),
128.52, 122.75, 99.64 (d, JF = 191.2 Hz), 87.25 (d, JF = 14.5 Hz), 84.08, 73.21 (d, JF = 17.2 Hz), 60.68,
18.23 (d, JF = 25.1 Hz) 174.08. UPLC-MS (Method D): Rt 0.61 min,
19F-NMR (470 MHz, DMSO-d6),
MS [ESI, m/z]: 310.1 [M + Na]. HRMS calculated for C11H15FN3O5+: 288.0990; found 288.0998.
1H-NMR (DMSO-d6),
δ:
8.21 (bs, 1H),
,
,
.
δ
.
δ:
−

Molecules 2020, 25, 4813
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3.1.4. Preparation of 4-((2-Hydroxyethoxy)methyl)-3-oxo-3,4-dihydropyrazine-2-carboxamide 4l
Commercially available 4a (3.6 mmol, 1 eq.) was suspended in anhydrous MeCN (10 mL)
under a nitrogen atmosphere. N,O-Bis(trimethylsilyl)acetamide (BSA, 8.3 mmol, 2.3 eq.) was then
added, and the mixture was stirred under reflux for 1 h. The resulting solution was then cooled
to room temperature, and commercially available (2-acetoxyethoxy)methyl acetate 14 was added
(3.6 mmol, 1 eq.). The mixture was then cooled in an ice-bath and SnCl4 (8.3 mmol, 2.3 eq.) was slowly
added. The reaction was allowed to warm to room temperature and stirred overnight. The mixture
was then cooled to 0 ◦C, and a cold saturated NaHCO3 solution (40 mL) was added slowly while
stirring. The residue was then extracted with EtOAc (5
×
50 mL). The combined organic layers
were washed with water and brine, dried over Na2SO4, and concentrated under vacuum. The crude
residue was purified by automated flash column chromatography on silica gel (dichloromethane to
dichloromethane/methanol 90:10 v/v) to afford 15 as a yellow oil (81%). Compound 15 (2.5 mmol, 1 eq.)
was then dissolved in MeOH (10 mL) and the solution was cooled to 0 ◦C in an ice-bath. A 25% MeONa
solution in MeOH (0.9 mL, 1.5 eq.) was added and the reaction was stirred for 40 min at 0 ◦C. Glacial
acetic acid (3.6 mL) was then added dropwise to the reaction while stirring, and the mixture was dried
under vacuum. The crude residue was purified twice by automated flash column chromatography
on silica gel (ethyl acetate to ethyl acetate/methanol 85:15 v/v) to afford the pure title compound 4l
1
as a pale yellow oil in 78% yield. H-NMR (CD3OD),
δ
: 7.97 (d, J = 3.7 Hz, 1H), 7.70 (d, J = 3.7 Hz,
1H), 5.53 (s, 2H), 3.73–3.70 (m, 4H). 13C-NMR (CD3OD),
δ: 164.89, 156.04, 145.05, 132.14, 123.73, 78.32,
71.97, 60.51. UPLC-MS (Method D): Rt 0.65 min, MS [ESI, m/z]: 236.1 [M + Na]. HRMS calculated for
C8H12N3O4+: 214.0822; found 214.0810.
3.1.5. Preparation of
4-(((1,3-Dihydroxypropan-2-yl)oxy)methyl)-3-oxo-3,4-dihydropyrazine-2-carboxamide 21
Commercially available 4a (3.6 mmol, 1 eq.) was suspended in anhydrous MeCN (9 mL) under
a nitrogen atmosphere. N,O-Bis(trimethylsilyl)acetamide (BSA, 8.3 mmol, 2.3 eq.) was then added,
and the mixture was stirred under reflux for 1 h. The resulting solution was cooled to room temperature,
and 2-(acetoxymethoxy)propane-1,3-diyl dibenzoate 19 (3.6 mmol, 1 eq.), prepared following a reported
procedure [34], was added dissolved in MeCN (3 mL). The mixture was then cooled in an ice-bath,
and SnCl4 (8.3 mmol, 2.3 eq.) was slowly added. The reaction was allowed to warm to room temperature
and stirred overnight. The mixture was then cooled to 0 ◦C and a cold saturated NaHCO3 solution
(40 mL) was added slowly while stirring. The residue was then extracted with EtOAc (3
×
50 mL).
The combined organic layers were washed with water and brine, dried over Na2SO4 and concentrated
under vacuum. The crude residue was purified by automated flash column chromatography on
silica gel (dichloromethane to dichloromethane/methanol 90:10 v/v) to afford 20 as an orange oil
(80%). Compound 20 (2.8 mmol, 1 eq.) was then added to 7N methanolic ammonia (40 mL), and the
mixture was stirred at room temperature overnight. The reaction mixture was then dried under
vacuum, and the crude residue was purified by automated flash column chromatography on silica
gel (chloroform to chloroform/methanol 80:20 v/v) to afford the pure title compound 21 as a pale
1
yellow solid in 69% yield. H-NMR (DMSO-d6),
δ
: 8.38 (bs, 1H), 7.96 (d, J = 4.1 Hz, 1H), 7.73 (bs, 1H)
,
7.53 (d, J = 4.1 Hz, 1H), 5.46 (s, 2H), 4.69 (t, J = 5.5 Hz, 2H), 3.61–3.57 (m, 1H), 3.49–3.45 (m, 2H),
3.40–3.36 (m, 2H). 13C-NMR (DMSO-d6),
UPLC-MS (Method D): Rt 0.36 min, MS [ESI, m/z]: 266.1 [M + Na]. HRMS calculated for C9H14N3O5
δ
: 164.48, 155.00, 147.96, 131.63, 123.08, 82.40, 77.34, 61.37.
+
:
244.0928; found 244.0941.
3.1.6. General Procedure for the Preparation of Novel
3-(20,30-Dideoxy-ribo-β-l-furanosyl)-6-substituted-furo[2,3d]pyrimidin-2-(3H)one
Analogues 5b and 5c
l-5-iodo-20,30-dideoxyuridine 33 (0.35 mmol, 1 eq.), prepared as previously described [25],
was dissolved in anhydrous DMF (2 mL) under a nitrogen atmosphere. The appropriate alkyne

Molecules 2020, 25, 4813
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34 or 35 (1.05 mmol, 3 eq.) was then added, followed by tetrakis(triphenylphosphine)palladium
(0.03 mmol, 0.1 eq.), CuI (0.07 mmol, 0.2 eq.), and DIPEA (0.7 mmol, 2 eq.). The resulting mixture was
stirred at room temperature for 18 h. At this point, further CuI (0.07 mmol, 0.2 eq.) and Et3N (2 mL)
◦
were added, and the mixture was stirred at 80 C for 8 h. The residue was dried under vacuum
by co-evaporation with EtOAc, and the crude product was purified by automated flash column
chromatography on silica gel (dichloromethane to dichloromethane/methanol 92:8 v/v) to afford the
pure target compounds 5b and 5c.
3-(20,30-Dideoxy-ribo-β-l-furanosyl)-6-(1-nonanol) furo[2,3-d]pyrimidin- 2(3H)-one 5b
1
Obtained in 28% yield as an off-white solid. H-NMR (CDCl3),
δ
: 8.66 (s, 1H), 6.22 (dd, J1 = 4.1 Hz
4.01 (m, 1H), 3.79 (1H, dt, J1 = 12.1 Hz,
J2 = 4.2 Hz, 1H), 3.66 (m, 2H), 2.68–2.60 (m, 3H), 2.26–2.21 (m, 1H), 2.17 (t, J = 4.5Hz, 1H), 1.98 1.91
(m, 2H), 1.73–1.67 (m, 2H), 1.59–1.55 (m, 2H), 1.41 : 171.57,
1.32 (m, 11H). 13C-NMR (CDCl3),
,
J2 = 2.5 Hz, 1H), 6.13 (d, J = 7.5 Hz, 1H), 4.31 (m, 1H), 4.04
−
−
−
δ
159.75, 155.50, 137.21, 107.64, 99.29, 88.15, 83.55, 61.64, 61,59, 33.33, 32.23, 29.16, 29.10, 28.88, 28.64,
27.54, 26.61, 25.50, 23.31. MS [ESI, m/z]: 379.2 [M + H]. HRMS calculated for C20H31N2O5+: 379.2227;
found 379.2209.
3-(20,30-Dideoxy-ribo-β-l-furanosyl)-6-(n-butil)furo[2,3-d]pyrimidin- 2(3H)-one 5c
1
Obtained in 33% yield as a pale yellow solid. H-NMR (CDCl3),
δ
: 8.68 (s, 1H), 6.21 (d, J = 4.5 Hz, 1H)
2.61 (m, 3H), 2.33 (bs, 1H)
1.31 (m, 2H), 1.28(m, 1H), 0.91 (t, J = 7.2 Hz,
,
,
6.14 (s, 1H), 4.31 (m, 1H), 4.16 (d, J = 11.5 Hz, 1H), 3.89 (d, J = 11.5 Hz, 1H), 2.68
2.24 2.21 (m, 1H),1.97 1.93 (m, 2H),1.69 (m, 1H), 1.41
3H). 13C-NMR (CDCl3),
−
−
−
−
δ
: 171.72, 159.46, 155.02, 135.89, 107.24, 99.08, 88.99, 82.88, 62.85, 33.78, 28.87,
27.94, 23.89, 22.11, 13.70. MS [ESI, m/z]: 293.1 [M+H]. HRMS calculated for C15H21N2O4+: 293.1496;
found 293.1510.
3.2. Antiviral Studies
3.2.1. Antivirals
Lyophilized compounds were solubilized in DMSO (Sigma-Aldrich, St. Louis, MO, USA) to
◦
a stock concentration of 10 mM and kept frozen at
concentrations. Dissolved compounds were stored at
−
20 C and then were diluted to final assay
−
20 ◦C and brought to room temperature prior to
assay. All compounds were well dissolved in DMSO, and precipitates were not observed upon thawing.
3.2.2. Cell Culture
The human hepatoma cell line HUH7 was a gift of Ralf Bartenschlager, University of Heidelberg.
Human glioblastoma cell lines U138 and U251 were originally obtained from the American Tissue Type
Culture collection (ATCC) and European Collection of Authenticated Cell Cultures (ECACC)—with
the numbers U138 MG—ATCC® HTB16
™, U251MG ECACC catalogue number 09063001, respectively.
Cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) with 4.5 mg/mL glucose
(Gibco Life Technologies Thermo Fisher, Waltham, MA, USA) supplemented with 10% (v/v) heat
inactivated fetal bovine serum (FBS; Gibco Life Technologies) at 37 ◦C with 5% CO2 (DMEM/FC10).
3.2.3. Virus Culture
ZIKV-U (976 Uganda strain; isolated from a non-human primate in Uganda in 1947; strain form
the Stammsammlung (strain bank) of the Institut für Mikrobiologie der Bundeswehr) was grown to
high titer on Vero B4 cells, partially purified by centrifugation to remove cell debris and stored frozen
at −80 ◦C. Virus titer was determined by standard plaque assay.

Molecules 2020, 25, 4813
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3.2.4. Viability Assay
Cell viability was determined after seven days using CellTiter-Glo® (PROMEGA), (Madison,
WI, USA) following the manufacturer’s instructions. All experiments were performed in triplicate.
Briefly, cells were seeded into white 96 well plates (Greiner-Bio ONE; Kremsmünster, Austria) at a
density of 104 cells per well in a volume of 100
µ
L DMEM/FC10, then incubated for 16 h. Cells were
treated in triplicates with the antiviral compound, prediluted to a range of concentrations, and added
in a volume of 50 L DMEM, then immediately infected with ZIKV-U or DENV2, prediluted and added
in a volume of 50 L DMEM, at a multiplicity of infection of 0.3 to the final antiviral concentration
µ
µ
in 200
µ
L final assay volume. Uninfected/untreated controls were prepared in multiple triplicates
◦
in different locations on the 96 well plate. Cells were incubated for 4 days at 37 C with 5% CO2.
The reconstituted CellTiter-Glo® reagent was then added to the cells and luminescence was detected
within 60 min by the Victor X3 2030 Multilabel Reader (PerkinElmer, Waltham, MA, USA) according to
the manufacturer’s instructions. Data were analysed using Microsoft EXCEL and Graphpad PRISM
7.0 software.
3.2.5. Cell Adherence Assay
Cell adherence was determined using the xCELLigence assay in the 16 well format [42].
Briefly, cells were plated at a density of 104 cells per well in a 16 well CIM-Plate 16 for the xCELLigence
RTCA DP Instrument (ACEA Biosciences, Inc., San Diego, CA, USA). After plating, cells were observed
for one hour to confirm adherence and impedance. The monitoring was then suspended for a 30-min
pretreatment with compounds followed by infection with virus, after which monitoring was resumed.
The instrument recorded impedance over time in each well. The data shown represent averages of
duplicates. Data were analysed using the xCELLigence Real-Time Cell Analyzer (RTCA) software.
Author Contributions: Conceptualization, M.B. (Marcella Bassetto), A.B. and J.J.B.; methodology, M.B. (Marcella
Bassetto), C.M.C., M.B. (Mattia Basso), M.S., F.S. and D.F.; formal analysis, M.B. (Marcella Bassetto) and J.J.B.;
investigation, M.B. (Marcella Bassetto), A.B. and J.J.B.; resources, M.B. (Marcella Bassetto), A.B. and J.J.B.;
data curation, M.B. (Marcella Bassetto) and J.J.B.; writing—original draft preparation, M.B. (Marcella Bassetto);
writing—review and editing, M.B. (Marcella Bassetto), A.B. and J.J.B.; supervision, M.B. (Marcella Bassetto), A.B.
and J.J.B.; project administration, M.B. (Marcella Bassetto) and J.J.B.; funding acquisition, M.B. (Marcella Bassetto),
A.B. and J.J.B. All authors have read and agreed to the published version of the manuscript.
Funding: This research was funded by the Sêr Cymru II programme, part-funded by Cardiff University and the
European Regional Development Fund through the Welsh Government.
Acknowledgments: The authors would like to thank Ralf Bartenschlager, University of Heidelberg, for kindly
providing the human hepatoma cell line HUH7.
Conflicts of Interest: The authors declare no conflict of interest.
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Sample Availability: Samples of the compounds are not available from the authors.
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