Rational modifications, synthesis and biological evaluation of new potential antivirals for RSV designed to target the M2-1 protein

Article abstract of DOI:10.1016/j.bmc.2020.115401

Respiratory syncytial virus (RSV) is the main cause of lower respiratory tract diseases in infants and young children, with potentially serious and fatal consequences associated with severe infections. Despite extensive research efforts invested in the identification of therapeutic measures, no vaccine is currently available, while treatment options are limited to ribavirin and palivizumab, which both present significant limitations. While clinical and pre-clinical candidates mainly target the viral fusion protein, the nucleocapsid protein or the viral polymerase, our focus has been the identification of new antiviral compounds targeting the viral M2-1 protein, thanks to the presence of a zinc-ejecting group in their chemical structure. Starting from an anti-RSV hit we had previously identified with an in silico structure-based approach, we have designed, synthesised and evaluated a new series of dithiocarbamate analogues, with which we have explored the antiviral activity of this scaffold. The findings presented in this work may provide the basis for the identification of a new antiviral lead to treat RSV infections.

Full text of DOI:10.1016/j.bmc.2020.115401

Journal Pre-proofs
Rational modifications, synthesis and biological evaluation of new potential
antivirals for RSV designed to target the M2-1 protein
Salvatore Ferla, Roberto Manganaro, Sara Benato, Jasmine Paulissen, Johan
Neyts, Dirk Jochmans, Andrea Brancale, Marcella Bassetto
PII:
S0968-0896(20)30206-6
https://doi.org/10.1016/j.bmc.2020.115401
BMC 115401
DOI:
Reference:
To appear in:
Bioorganic & Medicinal Chemistry
Received Date:
Accepted Date:
18 December 2019
21 February 2020
Please cite this article as: S. Ferla, R. Manganaro, S. Benato, J. Paulissen, J. Neyts, D. Jochmans, A. Brancale, M.
Bassetto, Rational modifications, synthesis and biological evaluation of new potential antivirals for RSV
designed to target the M2-1 protein, Bioorganic & Medicinal Chemistry (2020), doi: https://doi.org/10.1016/
j.bmc.2020.115401
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Rational modifications, synthesis and biological evaluation of new
potential antivirals for RSV designed to target the M2-1 protein
Salvatore Ferlaa*, Roberto Manganaroa, Sara Benatoa, Jasmine Paulissenb, Johan Neytsb, Dirk Jochmansb, Andrea
Brancalea, Marcella Bassettoa,c
aCardiff School of Pharmacy and Pharmaceutical Sciences, Cardiff, King Edward VII Avenue, Cardiff, CF103NB, UK
bKU Leuven – Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Virology and Chemotherapy,
Leuven, Belgium.
cDepartment of Chemistry, Swansea University, Swansea, UK
*Corresponding author
E-mail address: ferlas1@cardiff.ac.uk (Dr. S.Ferla)
Highlights




Rational modifications on a zinc-ejecting anti-RSV scaffold.
Synthesis of novel analogues to explore antiviral SARs.
New inhibitors of RSV replication identified.
Molecular dynamics and molecular docking studies on the RSV M2-1 protein.
Abstract
Respiratory syncytial virus (RSV) is the main cause of lower respiratory tract diseases in
infants and young children, with potentially serious and fatal consequences associated with
severe infections. Despite extensive research efforts invested in the identification of therapeutic
measures, no vaccine is currently available, while treatment options are limited to ribavirin and
palivizumab, which both present significant limitations. While clinical and pre-clinical
candidates mainly target the viral fusion, the nucleocapsid protein or the viral polymerase, our
focus has been the identification of new antiviral compounds targeting the viral M2-1 protein,
thanks to the presence of a zinc-ejecting group in their chemical structure. Starting from an
anti-RSV hit we had previously identified with an in silico structure-based approach, we have
designed, synthesised and evaluated a new series of dithiocarbamate analogues, with which we
have explored the antiviral activity of this scaffold. The findings presented in this work may
provide the basis for the identification of a new antiviral lead to treat RSV infections.
1. Introduction
Respiratory syncytial virus (RSV), a paramyxovirus,1 is the major responsible for acute lower
respiratory tract infections in infants, children, immunocompromised patients, and elderly
populations.2 Severe infections with this virus are often culminating in bronchiolitis and
pneumonia, with potentially fatal consequences:3 RSV is estimated to cause between 66000
and 199000 deaths every year in children under the age of five.4 Despite the fact that extensive

research efforts have been dedicated to elucidate epidemiology, diagnosis and
prevention/treatment since its discovery in 1956, no vaccine is currently available for this
virus.5 Two antiviral drugs are approved by the FDA to treat or prevent serious RSV infections:
ribavirin, a guanosine analogue with a broad-spectrum antiviral activity approved for treatment
in aerosolic form,6 and palivizumab, a humanised monoclonal antibody with strong RSV-
neutralising ability, which can be used for prophylactic purposes.7 Nonetheless, ribavirin is
non-specific for RSV, therefore not highly efficacious, and associated with toxicity issues and
high costs,8 while the use of palivizumab is limited to high-risk populations due to its elevated
cost.9 Different additional strategies to treat or prevent RSV infections are currently under
clinical evaluation, including recombinant antibodies, nanobodies and small molecules
targeting the viral life cycle.10 The most explored mechanism of action with small-molecule
antiviral candidates is the inhibition of RSV fusion, which accounts for different agents in
phase II clinical trials.11 Other candidates in clinical development include inhibitors of the viral
nucleoprotein and inhibitors of the viral polymerase, which accounts for one nucleoside
analogue, ALS-008176, in clinical evaluation, and various nucleoside and non-nucleoside
inhibitors currently at different stages of pre-clinical investigations.10-11 Despite these
advances, the development of safe and effective treatment options for RSV infections still
represents an unmet medical need.
RSV is classified into two main groups, RSV-A and RSV-B, according to the antigenic
sequence of the viral attachment glycoprotein, the G protein.12 Among the proteins encoded in
RSV non-segmented, single-stranded, negative-sense RNA genome, the matrix protein M2-1
is an essential transcription anti-termination co-factor of the viral polymerase,13 and currently
represents an underexploited target in the search for anti-RSV agents, with no candidate in pre-
clinical or clinical development. The M2-1 protein is functional in a tetrameric form,14 and
contains a zinc-binding domain (ZBD), whose proper functionality in coordinating a zinc ion
co-factor is crucial for the enzyme activity.15 The zinc-binding activity of the M2-1 protein has
been proven essential for viral replication and pathogenesis in vivo for related pneumoviruses,16
rendering its inhibition a promising strategy for developing new antivirals against RSV. In this
context, one appealing approach to inhibit zinc-binding enzymes is represented by metal
chelation with zinc-ejecting compounds, as is the case for example of zinc-ejecting HIV
nucleocapsid inhibitors, some of which have reached phase II clinical trials for the treatment
of AIDS.17 Starting from the identification of zinc-chelating small-molecule aldrithiol, AT-2,
as inactivator of RSV at millimolar concentrations,18 and thanks to the availability of crystal
structures of RSV M2-1 protein complexes,19-20 we have previously applied a structure-based

drug design approach to this protein, which guided the synthesis of different new structural
scaffolds.21 These novel small-molecules were characterised by the presence of a central zinc-
ejecting chemical group, functionalised with different lateral substituents to interact with the
protein sub-sites surrounding the ZBD. Among these structures, we had identified a new
dithiocarbamate scaffold (compound 1 in Figure 1), which inhibited RSV replication in vitro
with an EC50 in the low micromolar range, without causing significant cytotoxicity. Aiming at
further exploring the anti-RSV activity of this compound, the present study focusses on the
design, synthesis and evaluation of a preliminary series of structural derivatives of 1. Herein
we describe the identification of new potential anti-RSV agents with antiviral EC50 values in
the low micromolar range, and the evaluation of their predicted binding to RSV M2-1 protein
with a series of molecular dynamics and molecular docking simulations.
S
N
N
S
N
S
S
N
N
S
AT-2
1
Figure 1: Chemical structure of aldrithiol (AT-2) and hit 1.
2. Results and Discussion
In this manuscript, in an effort to further improve the RSV replication inhibitory activity and
to study the structure-activity relationships with new derivatives of our initial hit 1, we focussed
our attention on introducing various electron-donating (EDG)/ electron-withdrawing (EWG)
groups at different positions of the phenyl ring, and on replacing the original methylene bridge
between the piperazine central core and the phenyl ring itself (Figure 2). The dithiocarbamate
group, which is fundamental for its zinc-ejecting properties, the piperazine ring and the
benzothiazole system, which in our pervious work were both found to be essential for the
antiviral activity of 1, were kept unchanged, while their additional structural modifications is
the focus of present investigations.

Figure 2: Planned structural modifications on the scaffold of hit 1.
2.1 Chemistry
The newly designed derivatives were prepared following Scheme 1, which has been obtained
after several optimisations of reactions and routes. 2-Chloromethyl benzothiazole (5) was
prepared in two steps modifying a previously reported procedure for the preparation of
benzothiazinone compounds, by reacting 2-aminothiophenol (2) with chloroacetic acid (3), in
22, 23
dichloromethane (DCM) for 24 h, in the absence of any base.
The isolated amide salt 4
was then cyclised in acetonitrile (CH3CN) at reflux for 72 h, giving the desired product in a
better yield in comparison to a one-step synthesis method performed in parallel, in which
intermediate amid salt 4 was the major product, with the desired compound obtained in a very
low yield (6 %).24 Benzyl piperazine derivatives (22-36) were obtained in good yields by
reacting the corresponding commercially available benzyl chloride (7-21) with a large excess
of piperazine (6), in order to avoid a double nucleophilic attack and the formation of a di-
substituted piperazine molecule.25,26,27 Piperazine derivatives (34-36), in which the methylene
linker has been replaced, were prepared exploiting different reagents and conditions in order
to obtain the desired product in a good yield after column chromatography purification.25,28,29

Phenyl-piperazine 37 was purchased. Preparation of the final dithiocarbamate compounds 38-
46 was achieved through a nucleophilic displacement according to a reported one-step
reaction,30 in which benzyl piperazine derivatives (22-30) and carbon disulfide were reacted in
dimethylformamide (DMF), in the presence of sodium methoxyde (NaOMe) at 0 ˚C, followed
by the addition of 5 to give the desired product. Final compounds 47-53 were obtained
following a different two-step reaction, in which piperazine derivatives 31-37 and a large
excess of carbon disulfide were reacted for 2 h in a strong basic ethanolic solution of potassium
hydroxide (KOH), forming dithiocarbamate salts 31a-37a.31,32 The salts, recovered by
filtration, were then reacted with 5 for 24 h using methanol (MeOH) as solvent and
triethylamine (Et3N) as base, to afford the final products 47-53. Although both methods
produced a similar range of final yields, the use of EtOH or MeOH as solvent instead of DMF
and the absence of formation of side products, which makes the reaction purification much
easier, suggested that the 2-step reaction was the most efficient procedure to follow.
H
H
Cl
NH2
N
Cl
N
S
Cl
ii
i
O
O
SH
SH
4
Cl
Cl
2
3
5
iii
Cl
7-21
va
HN
NH
HN
N
R
31-37
R
iv
6
22-36
22-30
S
7, 22, 38 R= -CH2(4-OCH3-Ph)
8, 23, 39 R= -CH2(4-tBut-Ph)
15, 30, 46 R= -CH2(4-COOEt-Ph)
16, 31, 47 R= -CH2(4-F-Ph)
17, 32, 48 R= -CH2(3-CF3-Ph)
18, 33, 49 R= -CH2(4-CF3-Ph)
19, 34, 50 R= -CH2-CH2-Ph
20, 35, 51 R= -SO2-Ph
21, 36, 52 R= -CO-Ph
N
S
K
9, 24, 40 R= -CH2(4-COOMe)-Ph)
S
N
Cl
R
10, 25, 41 R= -CH2(4-CH3-Ph)
11, 26, 42 R= -CH2(2,4-CH3-Ph)
12, 27, 43 R= -CH2(2,4,6-CH3-Ph)
13, 28, 44 R= -CH2(2-CH3-Ph)
14, 29, 45 R= -CH2(3-CH3-Ph)
31a-37a
vb
N
N
S
N
S
N
S
R
37, 53 R= -Ph
38-53
5
Scheme 1: Reagents and conditions: (i). DCM, r.t.,24h; (ii). CH3CN, reflux, 72h, 59%; (iii). THF, reflux, 4h for 22-33, 49-
88%, OR THF, reflux, 48h for 34, 72%, OR DCM, 0˚C, 30 min. for 35, 84%, OR EtOH, r.t., 5h for 36, 75%; (iv). CS2, NaOMe,
DMF 0˚C 30 min, then o.n. for 38-46, 38-76%; (v). a) CS2, KOH, EtOH 0˚C then r.t., 2h; b) Et3N, MeOH, r.r., 24h for 47-53,
40-56%.
2.2 Antiviral evaluation
All the newly synthetised compounds were evaluated for their potential antiviral activity in a
cytophatic effect (CPE)-based in vitro assay in HEp-2 cells, in which the protective effect of
the tested compounds against the virus-induced CPE was measured. Two different viral RSV
strains, RSV-A and RSV-B, were used. Cells were treated with eight different concentrations

(0.7-100 µM) of the potential RSV inhibitors. The nucleoside viral polymerase inhibitor ALS-
8112 was used as positive control.33
Compound cytotoxicity (CC50) was also determined using uninfected Hep-2 cells in a MTS
assay. Results are reported in Table 1.
The activity of initial hit 1 is consistent with previously reported data,21 showing an antiviral
effect in the low µM range against both viral strains. Insertion of an electron donating
substituent in the para position of the phenyl ring, such as a mehtoxy (38), methyl (41) and t-
butyl (39) group, seems to be associated with antiviral activity retention against strain B-RSV,
having EC50 values similar to 1. On the contrary, these compounds show a different effect
against strain A, giving a slightly less potent and more variable activity profile. The same effect
against strain B is obtained when electron withdrawing groups, such as a methyl (40), a ethyl-
carboxylic ester (46), a trifluoromethyl (49) and a fluorine (47) in the para position. Notably,
while 40 and 46 are characterised by a reduction of antiviral effect against strain A, derivatives
47 and 49 present similar EC50 values against both strains. In general, these results indicate that
the para position of the phenyl ring can be substituted without affecting antiviral activity.
Importantly, the possibility to insert a fluorine atom or a trifluoromethyl group into the phenyl
ring without impairing the biological activity could be used as means to exploit the established
potential of fluorine atoms in enhancing the pharmacological profile and drug-like
physicochemical properties of molecules with pharmacological activities, for the potential
future development of this class of compounds.34 The presence of a substituent in meta position
of the phenyl ring (45, 48), regardless its EDG/EWG nature, is associated with a retained
antiviral effect, with 48 having an equivalent EC50 value against strain A and B, while the
introduction of a methyl group in ortho (44) is correlated with a reduction of activity, indicating
that there is enough space on the binding pocket to accommodate a phenyl ring differently
substituted in meta or in para position, but not in ortho position.
Introduction of a second methyl group at the ortho position of 41 (42) is associated with a
reduction of activity against strain B, while it seems not to affect antiviral activity against strain
A. A more consistent result against the two strains is obtained inserting a third methyl group
in ortho (43), which is associated with an almost 5-fold reduction in activity in both cases.
Extension of the methylene bridge to an ethyl linker (50) or its replacement with a -SO2- (51)
slightly affects antiviral activity, whereas a -CO- (52) linker led to a more marked drop of
activity against the two strains. The reduction in activity could be either caused by the different
polarity of the new linker, or by the different geometry conferred to the molecule. Interestingly,
53, in which the terminal phenyl ring is directly connected to the piperazine core, showed an

improved antiviral activity, revealing to be the best compound in this series, with an interesting
antiviral profile against both viral strains.
All the evaluated molecules, except 39 and 52, were found not to be cytotoxic at the test
concentrations in uninfected HEp-2 cells.
Table 1: EC50 and CC50 values of 1, 39-53 in the RSV CPE reduction assay.
Compound Structure
EC50 values EC50 values CC50 values
[μM]A,B
[μM]A,C
[μM]D
S
N
S
N
S
N
R
1
-CH2Ph
-CH2(4-OCH3-Ph)
8.3C
3.9±0.1
3.0±1.4
2.2±1.5
3.9±0.1
1.32
>100
38
12.9±13.8
28.7±29.0
14.8±9.0
17.9±19.6
4.97
>100
39
-CH2(4-C(CH3)3-Ph)
-CH2(4-COOCH3-Ph)
-CH2(4-CH3-Ph)
71.7±27.3
>100
40
41
>100
42
-CH2(2,4-CH3-Ph)
-CH2(2,4,6-CH3-Ph)
-CH2(2-CH3-Ph)
15.0±19.2
20.6
>100
43
42.2±40.7
10.4±3.2
11.8±8.9
40.8±13.3
4.4±1.9
3.3±0.1
3.31
>100
44
20.6
>100
45
-CH2(3-CH3-Ph)
3.0±1.5
4.0±0.1
2.5
>100
46
-CH2(4-COOCH2CH3-Ph)
-CH2(4-F-Ph)
-CH2(3-CF3-Ph)
-CH2(4-CF3-Ph)
- CH2CH2Ph
-SO2Ph
>100
47
>100
48
3.8±0.1
4.7±6.7
13.6±18.9
12.5±1.2
24.8
>100
49
>100
50
7.7±5.0
35.3±15.2
44.1±15.2
4.4±1.1
2.6±1.5
>100
51
>100
52
-COPh
45.0±30.8
>100
53
-Ph
1.3±0.2
2.6±1.5
ALS-8112
-
>100
A
EC50 and CC50 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). CPE scoring in RSV/Hep2 cell culture system. ALS-8112 was used as positive
control.

B RSV-A strain
C RSV-B strain
D Toxicity in Hep2 cell using viability staining with MTS.
E EC50 previously determined= 6 µM.21
2.3 Molecular modelling studies
In order to identify a likely binding mode for the new derivatives to the M2-1 protein and
rationalise the biological results obtained, a series of docking studies was performed on
selected compounds (1, 43, 48, 52, 53). The recently reported M2-1 protein complex crystal
structure (PDB ID: 6G0Y) was used, and docking studies were performed using Glide SP
scoring function.20,35 Compound 1 is predicted to lie in a large pocket formed by three
monomers immediately above the zinc-binding domain (ZBD) of one of them (Figure 3A).
The benzothiazole ring occupies the entrance of the binding site with its sulphur atom oriented
towards the oxygen atom of the GlyA18 backbone and it is involved in a π-interaction with
LysB113. The unsubstituted benzyl ring is placed in the inner portion of the pocket, involved
in a sandwich π-stacking interaction with HisA14, which probably holds in place this part of
the molecule. The central piperazine ring establishes multiple interactions with AspB109,
which locks 1 in a conformation that allows the sulphur atom of the thiocarbamate moiety to
be oriented towards the Zn-binding domain. Moreover, the piperazine ring interacts with
Cys15A, one of the three cysteine residues involved in the coordination of the Zn atom. A
similar occupation of the pocket and interactions were found for 48 (Figure 3B), with the only
difference in the benzyl ring positioning. In fact, the m-CF3 group, potentially due to steric
hindrance, forces the ring to occupy the pocket in a different position, with the sulphur atom
remaining close to the Zn-binding domain. Moreover, the piperazine ring forms a π-interaction
with HisA25, another residue involved in the Zn atom coordination. The shorter derivative 53
occupies the binding cavity similarly to 48 (Figure 3C). Interestingly, no docking results were
obtained for derivative 43. Potentially, the tri-substituted benzyl ring, due to steric hindrance,
does not fit into the inner part of the binding area, not allowing the rest of the molecule to
correctly bind to the active site, possibly explaining the large reduction in antiviral activity
found for this compound.
On the other hand, compound 52 occupies the pocket in a different orientation if compared
with the other active derivatives, placing the carbonyl group in correspondence of the Zn-

binding area, driven by its interaction with the backbone of GlyA18, therefore forcing the
thiocarbamate moiety to point away from this area, impeding its interaction with the Zn atom
and the surrounding residues (Figure 3D).
Figure 3: Proposed binding mode for compounds 1 (A), 48 (B), 53 (C), 52 (D) in the ZBD of
the M2-1 protein (PDB ID: 6G0Y). Compounds bind in a large pocket formed by three
monomers immediately above the zinc-binding domain (ZBD) of one of them. Importantly, the
sulphur atom of the thiocarbamate moiety is always oriented towards the ZBD except for 52.
The single monomers of M2-1 protein forming the functional tetramers are represented as
molecular surface and ribbons: monomer A in salmon, monomer B in turquoise, monomer C
in blue, monomer D in yellow. The residues of the different monomers are coloured
accordingly. Carbon atoms of compound 1 are shown in purple, in orange for 48, in pink for
53 and in green for 52. The ZBD of monomer A is labelled.
In order to validate the suggested binding mode, a series of 150 ns molecular dynamics (MD)
simulations on 1, 48 and 53 were performed, using the Desmond software package for MD
simulations.36 All the protein-ligand systems reached stability after an initial 70 ns of
equilibration, as showed by the C-alpha RMSD variation, therefore only the remaining 80 ns
of the simulation were considered in our analysis (Figure 4).

Figure 4: Plots of RMSD (Å) values against simulation frames for protein-inhibitor
complexes. After 70 ns of equilibration (red dotted line, corresponding to frame 1750), the
proteins reach stability (C-alpha RMSD variation). Only one replicate is shown for each
different protein-ligand complex. Color legend: 1-protein (purple), 48-protein (orange), 53-
protein (pink), 52-protein (green).
In general, all the three molecules tend to optimise their occupation of the binding site
maintaining then a stable pose during the entire MD simulation, with the thiocarbamate moiety
always oriented and placed nearby the Zn-binding domain. (Figure 5A, example of compound
1). In particular, the initial ligand-protein interactions with HisA14 (hydrophobic interactions)
and LysB113 (alternation between hydrophobic interaction and water bridges) are maintained
for most of the MD simulation (Figure 5B). The initial interactions between the piperazine
ring and AspB109 are then mediated by a water bridge, whereas an extra interaction between
the benzothiazole ring of all the tree derivatives and residue TyrC72 is formed (either as
hydrophobic contact or water bridge) and maintained during the entire simulation, potentially
contributing to the protein-ligand complex stability. As negative control, a MD simulation for
52 was also performed. The starting binding pose was maintained for the entire simulation,
with the thiocarbamate moiety always pointing away from the Zn-binding domain.

Figure 5: A) Proposed binding mode for 1 at the beginning of the MD simulation and after
150 ns. 1 tends to optimise its occupation of the binding site with the thiocarbamate moiety
always oriented and placed nearby the Zn-binding domain. Carbon atoms of 1 are shown in
purple, molecules of water as red spheres. The final pose shown is from the last frame of only
one replicate of the MD simulation for the 1-protein complex. B) Compound 1-protein contacts
monitored throughout the MD simulation. The stacked bar charts are normalised by the
program over the course of the trajectory: a value of 0.8 suggests that a specific interaction is
maintained for 80% of the simulation time. Only the simulation time between 80 ns and 150
ns (after equilibration of the system as discussed above) was considered in our analysis. The
analysis of only one MD replicate is shown.
To confirm the stability of these protein-ligand complexes, the compounds relative binding
free energies (∆Gbinding) were then calculated using the Prime/MM-GBSA based calculation
method for 1, 48 and 53.37,38 According to the ∆Gbinding values obtained, the three ligand-protein
complexes show similar results, in line with the similar biological activities found for these
three molecules (Table 2). In conclusion, molecular docking and MD studies have given
important elucidations on the potential binding mode for this family of compounds. The

information thus obtained will be used to perform further structural modifications on the
current scaffold.
Table 2: Calculated ligand-interaction energies for the compounds analysed after the
molecular dynamics simulations.
Compound
∆Gbinding (kJ/mol)a ±SD
-47.40±6.39
1
48
53
-42.80±8.40
-43.07±4.45
a Average values calculated as mean of three of ΔGbinding obtained from three indipendent MD
simulations (triplicate) for each compound. For each replicate, the average ΔGbinding value was
calculated excluding the first 70 ns of MD, in which the system protein-ligand reached stability.
Standard deviation (SD) is reported.
3. Conclusions
Starting from an anti-RSV hit we had previously identified with an in silico structure-based
approach and applying standard medicinal chemistry modifications, a family of 16 new
derivatives has been designed and synthesised. All newly prepared compounds were evaluated
for their potential antiviral activity in a cytophatic effect (CPE)-based in vitro assay in HEp-2
cells, using two different RSV strains, RSV-A and RSV-B. Among them, different displayed
retained activity, including the original hit 1, with no cytotoxic associated, confirming the anti-
RSV profile associated with this new scaffold. Most interestingly, 53, in which the terminal
phenyl ring is directly connected to the piperazine core, was found as the best compound in
this series, with an interesting antiviral profile against both viral strains, with EC50 values in
the low µM range. Molecular modelling studies revealed important information on the potential
binding mode of this family of compounds to their putative target, the viral M2-1 protein.
In conclusion, the antiviral activity associated with this chemical scaffold has been confirmed
and the phenyl derivative 53 was found to be an effective anti-RSV inhibitor with no toxicity
associated. The biological and in silico results obtained represent a promising starting point for

further structure-activity relationship enhancement, in order to improve potency in the quest
for an effective antiviral treatment for human RSV infections.
4. Experimental section
4.1 General Chemistry methods, general procedures and compound
characterisation examples
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
1
13
(UK). All reactions were performed under a nitrogen atmosphere. H and C-NMR spectra
1
were recorded with a Bruker Avance III HD spectrometer operating at 500 MHz for H and
13
125 MHz for C, with Me4Si as internal standard. Deuterated chloroform was used as the
1
solvent for NMR experiments, unless otherwise stated. H chemical shifts values (δ) are
referenced to the residual non-deuterated components of the NMR solvents (δ = 7.26 ppm for
CHCl3, etc.). The 13C chemical shifts (δ) are referenced to CDCl3 (central peak, δ = 77.0 ppm).
TLC was performed on silica gel 60 F254 plastic sheets. Flash column chromatography was
performed using silica on an Biotage Isolera 1 system. Melting points were determined on an
electro-thermal instrument, Griffin apparatus and are uncorrected. UPLC-MS analysis was
conducted on a Waters UPLC system with both Diode Array detection and Electrospray (+’ve
and –‘ve ion) MS detection. The stationary phase was a Waters Acquity UPLC BEH C18 1.7um
2.1x50mm column. The mobile phase was LC-MS grade H2O containing 0.1% formic acid (A)
and LC-MS grade MeCN containing 0.1% formic acid (B). Column temperature: 40 °C.
Sample diluent: MeCN. Sample concentration 1µg/mL. Injection volume 2 µL. Three
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.
All compounds tested in biological assays were >95% pure. Purity of intermediates was >90%,
unless otherwise stated. All intermediates were generally prepared according to literature
procedures, which are described in detail along with compound characterisation in the

Supporting Information. Details for the preparation and full characterisation of the new target
final compounds are given below.
4.1.1 General method A for the preparation of final compounds 38-46
To a solution of substituted benzyl-piperazine (2 mmol) in dimethylformamide (5 mL) was
added carbon disulphide (2 mmol) and sodium methoxide at 0 °C and it was stirred for 30 min.
2-Chloromethyl benzothiazole (5) (1 mmol) was added in one portion, the reaction mixture
was left to reach room temperature and stirring was continued until the reaction was complete
(monitoring by TLC). The reaction mixture was quenched by addition of ice-cold water and
then it was extracted with EtOAc (25 mL), dried over MgSO4 and evaporated to give the crude
product. Purification by flash column chromatography (n-hexane:EtOAc 100:0 v/v, increasing
to 80:20 v/v) gave the pure product.
4.1.2 Benzo[d]thiazol-2-ylmethyl 4-(4-methoxybenzyl)piperazine-1-carbodithioate (38)
1
Obtained in 75% yield as a white solid. H-NMR (CDCl3) δ: 2.52 (bs, 4H, CH2-piperazine),
3.48 (s, 2H, CH2), 3.78 (s, 3H, -OCH3), 3.93 (bs, 2H, CH2-piperazine), 4.35 (bs, 2H, CH2-
piperazine), 5.11 (s, 2H, CH2), 6.79 (d, J= 8.6 Hz, 2H, H-aromatic), 7.14 (d, J= 8.6 Hz, 2H, H-
aromatic), 7.35-7.38 (m, 1H, H-aromatic), 7.44-7.47 (m, 1H, H-aromatic), 7.81-7.84 (m, 1H,
13
H-aromatic), 7.97-8.00 (m, 1H, H-aromatic). C-NMR (CDCl3) δ: 38.9 (CH2), 52.2 (CH2),
55.2 (CH3), 61.8 (CH2), 113.7, 121.6, 122.9, 125.2, 126.0, (CH, C-aromatic), 129.2 (C), 130.3
(CH, C-aromatic), 135.7, 152.7, 159.0, 167.7, 194.2 (C). Melting point: 81-83° C. UPLC-MS
(Method C): Rt 1.67 min, MS [ESI, m/z]: 430.2 [M+H]. Anal. Calcd for C21H23N3OS3: C,
58.71; H, 5.40; N, 9.78. Found: C, 58.86; H, 5.20; N, 9.71.
4.1.3 Benzo[d]thiazol-2-ylmethyl4-(4-(tert-butyl)benzyl) piperazine-1-carbodithioate (39)
1
Obtained in 69% yield as a yellow waxy solid. H-NMR (CDCl3) δ: 1.31 (s, 9H, CH3 tert-
butyl), 2.54 (bs, 4H, CH2-piperazine), 3.51 (s, 2H, CH2), 3.95 (bs, 2H, CH2-piperazine), 4.37
(bs, 2H, CH2-piperazine), 5.11 (s, 2H, CH2), 7.23 (d, J= 8.3 Hz, 2H, H-aromatic), 7.33-7.38
(m, 3H, H-aromatic), 7.44-7.47 (m, 1H, H-aromatic), 7.81-7.84 (m, 1H, H-aromatic), 7.97-8.00
13
(m, 1H, H-aromatic). C-NMR (CDCl3) δ: 31.3 (CH3), 38.9 (CH2), 52.3 (CH2), 62.1 (CH2),
68.1 (C), 121.6, 122.9, 125.2, 125.3, 126.0, 128.8 (CH, C-aromatic), 130.8, 135.7, 150.4, 152.7,
167.7, 194.2 (C). Melting point: 73-75° C. UPLC-MS (Method C): Rt 1.89 min, MS [ESI, m/z]:
456.2 [M+H]. Anal. Calcd for C24H29N3S3: C, 63.26; H, 6.41; N, 9.22. Found: C, 63.22; H,
6.59; N, 9.05.

4.1.4 Methyl4-((4-(((benzo[d]thiazol-2-ylmethyl) thio) carbonothioyl) piperazin-1-yl)
methyl) benzoate (40)
Obtained in 76% yield as a yellow solid. 1H-NMR (CDCl3) δ: 2.55 (bs, 4H, CH2-piperazine),
3.58 (s, 2H, CH2), 3.91 (s, 3H, CH3 methyl ester), 3.95 (bs, 2H, CH2-piperazine), 4.37 (bs, 2H,
CH2-piperazine), 5.11 (s, 2H, CH2), 7.41-7.35 (m, 3H, H-aromatic), 7.44-7.47 (m, 1H, H-
aromatic), 7.81-7.83 (m, 1H, H-aromatic), 7.97-8.01 (m, 3H, H-aromatic). 13C-NMR (CDCl3)
δ: 39.0 (CH2), 51.9 (CH3), 52.4 (CH2), 62.0 (CH2), 121.6, 122.9, 125.2, 126.0, 128.8 (CH, C-
aromatic), 129.4 (C), 129.7 (CH, C-aromatic), 135.7, 142.7, 152.7, 166.9, 167.6, 194.4 (C).
Melting point: 83-85° C. UPLC-MS (Method C): Rt 1.79 min, MS [ESI, m/z]: 458.2 [M+H].
Anal. Calcd for C22H23N3O2S3: C, 57.74; H, 5.07; N, 9.18. Found: C, 57.89; H, 4.88; N, 8.93.
4.1.5 Benzo[d]thiazol-2-ylmethyl 4-(4-methylbenzyl)piperazine-1-carbodithioate (41)
Obtained in 49% yield as a yellow solid. 1H-NMR (CDCl3) δ: 2.33 (s, 3H, CH3), 2.54 (bs, 4H,
CH2-piperazine), 3.50 (s, 2H, CH2), 3.95 (bs, 2H, CH2-piperazine), 4.36 (bs, 2H, CH2-
piperazine), 5.12 (s, 2H, CH2), 7.16 (d, J= 7.8 Hz, 2H, H-aromatic), 7.21 (d, J= 7.8 Hz, 2H, H-
aromatic)7.35-7.38 (m, 1H, H-aromatic), 7.45-7.48 (m, 1H, H-aromatic), 7.82-7.84 (m, 1H, H-
aromatic), 7.97-7.99 (m, 1H, H-aromatic). 13C-NMR (CDCl3) δ: 21.1 (CH3), 38.9 (CH2), 52.3
(CH2), 62.1 (CH2), 121.6, 122.9, 125.2, 126.0, 129.1, 129.1 (CH, C-aromatic), 135.7, 137.1,
152.7, 159.1, 167.7, 194.2 (C). Melting point: 95-97° C. UPLC-MS (Method C): Rt 1.74 min,
MS [ESI, m/z]: 414.2 [M+H]. Anal. Calcd for C21H23N3S3: C, 60.98; H, 5.61; N, 10.16. Found:
C, 61.04; H, 5.34; N, 10.03.
4.1.6 Benzo[d]thiazol-2-ylmethyl4-(2,4-dimethylbenzyl) piperazine-1-carbodithioate (42)
Obtained in 38% yield as a yellow waxy solid. 1H-NMR (CDCl3): 2.30 (s, 3H, CH3), 2.33 (s,
3H, CH3), 2.53 (bs, 4H, CH2-piperazine), 3.46 (s, 2H, CH2), 3.91 (bs, 2H, CH2-piperazine),
4.34 (bs, 2H, CH2-piperazine), 5.11 (s, 2H, CH2), 6.95-7.00 (m, 2H, H-aromatic), 7.09 (d, J=
7.5 Hz, 2H, H-aromatic), 7.35-7.38 (m, 1H, H-aromatic), 7.44-7.47 (m, 1H, H-aromatic), 7.81-
13
7.83 (m, 1H, H-aromatic), 7.97-7.99 (m, 1H, H-aromatic). C-NMR (CDCl3) δ: 19.1 (CH3),
21.0 (CH3), 38.9 (CH2), 52.4 (CH2), 60.10(CH2), 121.6, 122.9, 125.23, 126.0, 126.2, 130.0,
131.3 (CH, C-aromatic), 135.7, 137.4, 150.4, 152.7, 166.9, 167.7, 194.2 (C). Melting point:
68-70° C. UPLC-MS (Method C): Rt 1.87 min, MS [ESI, m/z]: 428.2 [M+H]. Anal. Calcd for
C22H25N3S3: C, 61.79; H, 5.89; N, 9.83. Found: C, 61.56; H, 6.07; N, 9.65.
4.1.7 Benzo[d]thiazol-2-ylmethyl4-(2,4,6-trimethylbenzyl) piperazine-1-carbodithioate
(43)
Obtained in 68% yield as a yellow waxy solid. 1H-NMR (CDCl3): 2.26 (s, 3H, CH3), 2.33 (s,
6H, CH3), 2.54 (bs, 4H, CH2-piperazine), 3.49 (s, 2H, CH2), 3.88 (bs, 2H, CH2-piperazine),

4.31 (bs, 2H, CH2-piperazine), 5.29 (s, 2H, CH2), 6.84 (s, 2H, H-aromatic), 7.34-7.38 (m, 1H,
H-aromatic), 7.44-7.47 (m, 1H, H-aromatic), 7.81-7.83 (m, 1H, H-aromatic), 7.97-7.99 (m, 1H,
H-aromatic). 13C-NMR (CDCl3) δ: 20.0 (CH3), 20.9 (CH3), 38.9 (CH2), 52.0 (CH2), 55.2 (CH2),
121.6,122.9, 125.2, 126.0, 129.0 (CH, C-aromatic), 130.8, 135.7, 136.8, 138.0, 152.7, 167.8,
194.0 (C). Melting point: 82-84° C. UPLC-MS (Method C): Rt 2.10 min, MS [ESI, m/z]: 442.2
[M+H]. Anal. Calcd for C23H27N3S3: C, 62.55; H, 6.16; N, 9.51. Found: C, 62.29; H, 6.01; N,
9.75.
4.1.8 Benzo[d]thiazol-2-ylmethyl 4-(2-methylbenzyl)piperazine-1-carbodithioate (44)
Obtained in 72% yield as a light brown waxy solid. 1H-NMR (CDCl3): 2.37 (s, 3H, CH3), 2.54
(bs, 4H, CH2-piperazine), 3.49 (s, 2H, CH2), 3.92 (bs, 2H, CH2-piperazine), 4.35 (bs, 2H, CH2-
piperazine), 5.12 (s, 2H, CH2), 7.13-7.23 (m, 4H, H-aromatic), 7.35-7.38 (m, 1H, H-aromatic),
7.44-7.47 (m, 1H, H-aromatic), 7.81-7.83 (m, 1H, H-aromatic), 7.97-7.99 (m, 1H, H-aromatic).
13C-NMR (CDCl3) δ: 19.2 (CH3), 38.9 (CH2), 52.4 (CH2), 60.36 (CH2), 121.6, 122.9, 125.2,
125.6, 126.0, 127.5, 129.9, 130.4 (CH, C-aromatic), 135.7, 137.6, 152.7, 166.9, 167.7, 194.2
(C). Melting point: 98-100° C. UPLC-MS (Method C): Rt 1.79 min, MS [ESI, m/z]: 414.2
[M+H]. Anal. Calcd for C21H23N3S3: C, 60.98; H, 5.61; N, 10.16. Found: C, 61.16; H, 5.37; N,
10.09.
4.1.9 Benzo[d]thiazol-2-ylmethyl 4-(3-methylbenzyl)piperazine-1-carbodithioate (45)
Obtained in 45% yield as a yellow waxy solid. 1H-NMR (CDCl3): 2.35 (s, 3H, CH3), 2.55 (bs,
4H, CH2-piperazine), 3.51 (s, 2H, CH2), 3.96 (bs, 2H, CH2-piperazine), 4.36 (bs, 2H, CH2-
piperazine), 5.12 (s, 2H, CH2), 7.09-7.14 (m, 3H, H-aromatic), 7.20-7.23 (m, 1H, H-aromatic),
7.35-7.38 (m, 1H, H-aromatic), 7.44-7.48 (m, 1H, H-aromatic), 7.82-7.84 (m, 1H, H-aromatic),
7.98-8.00 (m, 1H, H-aromatic). 13C-NMR (CDCl3) δ: 21.3 (CH3), 39.0 (CH2), 52.2 (CH2), 62.3
(CH2), 121.6, 122.9, 125.2, 126.0, 126.4, 128.4, 128.5, 130.0 (CH, C-aromatic), 135.7, 138.2,
152.7, 167.6, 168.4 194.4 (C). Melting point: 48-50° C. UPLC-MS (Method C): Rt 1.75 min,
MS [ESI, m/z]: 414.2 [M+H]. Anal. Calcd for C21H23N3S3: C, 60.98; H, 5.61; N, 10.16. Found:
C, 61.09; H, 5.82; N, 10.02.
4.1.10 Benzo[d]thiazol-2-ylmethyl4-(4-propionylbenzyl) piperazine-1-carbodithioate (46)
Obtained in 43% yield as a light brown waxy solid. 1H-NMR (CDCl3): 1.39 (t, J=7.1, 3H, CH3),
2.54 (bs, 4H, CH2-piperazine), 3.58 (s, 2H, CH2), 3.96 (bs, 2H, CH2-piperazine), 4.42-4.33 (m,
4H, CH2 piperazine and CH2 ethyl ester), 5.10 (s, 2H, CH2), 7.35-7.39 (m, 1H, H-aromatic),
7.40 (d, J= 8.2 Hz, 2H, H-aromatic), 7.44-7.47 (m, 1H, H-aromatic), 7.81-7.83 (m, 1H, H-
aromatic), 7.97-8.00 (m, 1H, H-aromatic), 8.01 (d, J= 8.2 Hz, 2H, H-aromatic). 13C-NMR
(CDCl3) δ: 14.3 (CH3), 39.0 (CH2), 52.4 (CH2), 60.98 (CH2), 62.03 (CH2), 121.6, 122.9, 125.2,

126.0, 128.9, 129.7 (CH, C-aromatic), 133.9, 135.7, 138.2, 152.7, 166.4, 167.6, 194.5 (C).
Melting point: 70-72° C. UPLC-MS (Method C): Rt 1.89min, MS [ESI, m/z]: 472.1 [M+H].
Anal. Calcd for C23H25N3O2S3: C, 58.57; H, 5.34; N, 8.91. Found: C, 58.34; H, 5.19; N, 9.14.
4.1.11 General method B for the preparation of final compounds 47-53
To an ethanolic solution of potassium hydroxide (1mmol/100mL) a secondary amine (1 mmol)
was added. The mixture was cooled in an ice-bath and carbon disulphide (10 mmol) was added
drop-wise while stirring. The reaction mixture was stirred for 2 h at room temperature and then
the solvent volume was reduced by evaporation under reduced pressure. Addition of diethyl
ether until precipitation reached completion and filtration afforded the solid intermediate salt.
To a mixture of salt (1 mmol), methanol (5mL) and triethylamine (1.5 mmol) was added 2-
chloromethyl benzothiazole (5) (1mmol) and the reaction mixture was stirred at room
temperature for 24 h. The methanol from the reaction mixture was evaporated under reduce
pressure, EtOAc was added and the resulting solid was filtered off. The filtrate was washed
with H2O (3x15mL). The organic layers were collected, dried over MgSO4 and concentrated
under reduce pressure to give the crude product. Purification by flash column chromatography
gave the pure product.
4.1.12 Benzo[d]thiazol-2-ylmethyl 4-(4-fluorobenzyl)piperazine-1-carbodithioate (47)
Obtained in 45% yield as a yellow solid. Purification by flash column chromatography
(DCM:MeOH 100:0 v/v, increasing to 90:10 v/v). 1H-NMR (CDCl3): 2.47-2.60 (m, 4H, CH2-
piperazine), 3.49 (s, 2H, CH2), 3.94 (bs, 2H, CH2-piperazine), 4.37 (bs, 2H, CH2 piperazine),
5.11 (s, 2H, CH2), 7.00-7.04 (m, 2H, H-aromatic), 7.27-7.30 (m, 2H, H-aromatic), 7.34-7.41
(m, 1H, H-aromatic), 7.43-7.49 (m, 1H, H-aromatic), 7.80-7.86 (m, 1H, H-aromatic), 7.96-8.02
(m, 1H, H-aromatic). 13C-NMR (CDCl3) δ: 39.0 (CH2), 52.2 (CH2), 61.6 (CH2), 115.3 (CH, d,
J = 21 Hz), 121.6,122.9, 125.2, 125.8 (CH, C-aromatic), 130.6 (CH, d, J= 7 Hz), 135.7, 152.7,
161.2, 163.2, 167.7, 194.4 (C). 19F-NMR (CDCl3) δ: -115.15 (s, 1F). Melting point: 77-79° C.
UPLC-MS (Method C): Rt 1.75 min, MS [ESI, m/z]: 418.2 [M+H]. Anal. Calcd for
C20H20FN3S3: C, 57.53; H, 4.83; N, 10.06. Found: C, 57.60; H, 4.68; N, 9.92.
4.1.13
Benzo[d]thiazol-2-ylmethyl4-(3-(trifluoromethyl)benzyl)
piperazine-1-
carbodithioate (48)
Obtained in 54% yield as a yellow solid. Purification by flash column chromatography
1
(DCM:MeOH 100:0 v/v, increasing to 90:10 v/v). H-NMR (CDCl3): 2.55 (bs, 4H, CH2-
piperazine), 3.58 (s, 2H, CH2), 3.97 (bs, 2H, CH2-piperazine), 4.38 (m, 2H, CH2 piperazine),

5.11 (s, 2H, CH2), 7.35-7.38 (m, 1H, H-aromatic), 7.44-7.48 (m, 2H, H-aromatic),7.51-7.55
(m, 2H, H-aromatic), 7.59 (s, 1H, H-aromatic), 7.81-7.83 (m, 1H, H-aromatic), 7.97-7.99 (m,
13
1H, H-aromatic). C-NMR (CDCl3) δ: 39.0 (CH2), 52.4 (CH2), 61.8 (CH2,), 121.6, 122.9,
124.4 (m), 125.2, 125.6 (m), 126.0, 128.9, 132.3 (CH), 123.1 (m), 130.7 (C, q, J= 33 Hz),
135.7, 152.7, 161.2, 167.6, 194.5 (C). 19F-NMR (CDCl3) δ: -62.55 (s, 3F). Melting point: 71-
73°C. UPLC-MS (Method C): Rt 2.02 min, MS [ESI, m/z]: 468.1 [M+H]. Anal. Calcd for
C21H20F3N3S3: C, 53.94; H, 4.31; N, 8.99. Found: C, 54.15; H, 4.46; N, 8.86.
4.1.14
Benzo[d]thiazol-2-ylmethyl4-(4-(trifluoromethyl)benzyl)
piperazine-1-
carbodithioate (49)
Obtained in 56% yield as a white solid. Purification by co-precipitation from DCM/n-hexane.
1H-NMR (CDCl3): 2.59 (bs, 4H, CH2-piperazine), 3.63 (s, 2H, CH2), 4.00 (bs, 2H, CH2-
piperazine), 4.42 (bs, 2H, CH2 piperazine), 5.15 (s, 2H, CH2), 7.39-7.42 (m, 1H, H-aromatic),
7.48-7.51 (m, 3H, H-aromatic), 7.62-7.64 (m, 2H, H-aromatic), 7.85-7.87 (m, 1H, H-aromatic),
13
8.01-8.03 (m, 1H, H-aromatic). C-NMR (CDCl3) δ: 39.0 (CH2), 52.4 (CH2), 61.8 (CH2),
121.6, 122.9, 125.2, 125.4 (m), 126.1, 128.4 (CH, q, J= 130 Hz, C-aromatic), 131.8 (m), 135.7,
152.7, 161.2, 163.2, 167.7, 194.4 (C). 19F-NMR (CDCl3) δ: -63.00 (s, 3F). Melting point: 99-
101°C. UPLC-MS (Method C): Rt 2.03 min, MS [ESI, m/z]: 468.1 [M+H]. Anal. Calcd for
C21H20F3N3S3: C, 53.94; H, 4.31; N, 8.99. Found: C, 53.77; H, 4.57; N, 8.83.
4.1.15 Benzo[d]thiazol-2-ylmethyl4-phenethylpiperazine-1-carbodithioate (50)
Obtained in 41% yield as a white solid. Purification by co-precipitation from DCM/n-hexane.
1H-NMR (CDCl3): 2.62-2.70 (m, 6H, CH2), 2.85-2.82 (m, 2H, CH2), 4.01 (bs, 2H, CH2-
piperazine), 4.42 (bs, 2H, CH2-piperazine), 5.15 (s, 2H, CH2), 7.21-7.25 (m, 3H, H-aromatic),
7.29-7.34 (m, 2H, H-aromatic), 7.37-7.41 (m, 1H, H-aromatic), 7.47-7.50 (m, 1H, H-aromatic),
13
7.84-7.86 (m, 1H, H-aromatic), 8.00-8.02 (m, 1H, H-aromatic). C-NMR (CDCl3) δ: 33.1
(CH2), 39.0 (CH2), 52.4 (CH2), 59.6 (CH2), 121.6, 122.9, 125.2, 126.0, 126.4, 128.5, 128.6
(CH, C-aromatic), 135.7, 139.2, 152.7, 167.6, 194.5 (C). Melting point: 87-89°C. UPLC-MS
(Method C): Rt 1.70 min, MS [ESI, m/z]: 414.2 [M+H]. Anal. Calcd for C21H23N3S3: C, 60.98;
H, 5.61; N, 10.16. Found: C, 60.75; H, 5.42; N, 10.28.
4.1.16 Benzo[d]thiazol-2-ylmethyl 4-(phenylsulfonyl)piperazine-1-carbodithioate (51)
Obtained in 40% yield as a white solid. The crude product precipitated out from the reaction
mixture. Purification by co-precipitation from DCM/n-hexane followed by flash column
1
chromatography (DCM 100:0 v/v). H-NMR (CDCl3): 3.14-3.18 (m, 4H, CH2-piperazine),
4.27 (bs, 4H, CH2-piperazine), 5.05 (s, 2H, CH2), 7.37-7.40 (m, 1H, H-aromatic), 7.45-7.49
(m, 1H, H-aromatic), 7.56-7.60 (m, 2H, H-aromatic), 7.64-7.68 (m, 1H, H-aromatic), 7.76-7.78

(m, 2H, H-aromatic), 7.81-7.83 (m, 1H, H-aromatic), 7.97-7.99 (m, 1H, H-aromatic). 13C-NMR
(CDCl3) δ: 39.0 (CH2), 45.5 (CH2), 121.6, 122.8, 125.4, 126.2, 127.7, 129.4, 133.4 (CH, C-
aromatic), 135.2, 135.5, 152.4, 166.9, 195.5 (C). Melting point: 171-173°C. UPLC-MS
(Method C): Rt 2.03 min, MS [ESI, m/z]: 450.1 [M+H], 472.1 [M+Na]. Anal. Calcd for
C21H23N3S3: C, 60.98; H, 5.61; N, 10.16. Found: C, 60.75; H, 5.42; N, 10.28.
4.1.17 Benzo[d]thiazol-2-ylmethyl4-benzoylpiperazine-1-carbodithioate (52)
Obtained in 50% yield as a white solid. Purification by flash column chromatography (n-
hexane-EtOAc 100:0 v/v, increasing to 60:40 v/v). 1H-NMR (CDCl3): 3.31-4.57 (m, 8H, CH2-
piperazine), 5.11 (s, 2H, CH2), 7.36-7.39 (m, 1H, H-aromatic), 7.41-7.48 (m, 6H, H-aromatic),
13
7.82-7.84 (m, 1H, H-aromatic), 7.98-8.00 (m, 1H, H-aromatic). C-NMR (CDCl3) δ: 38.9
(CH2), 121.6, 122.9, 125.4, 126.2, 127.1, 128.7, 130.3 (CH), 134.7, 135.5, 152.5, 167.3, 170.7,
195.4 (C). Melting point: 125-127°C. UPLC-MS (Method C): Rt 1.93 min, MS [ESI, m/z]:
414.2 [M+H], 436.2 [M+Na]. Anal. Calcd for C20H19N3OS3: C, 58.08; H, 4.63; N, 10.16.
Found: C, 57.91; H, 4.51; N, 10.38.
4.1.18 Benzo[d]thiazol-2-ylmethyl4-phenylpiperazine-1-carbodithioate (53)
Obtained in 48% yield as a white solid. Purification by co-precipitation from DCM/n-hexane.
1H-NMR (CDCl3): 3.30 (bs, 4H, CH2-piperazine), 4.13 (bs, 2H, CH2-piperazine), 4.51 (bs, 2H,
CH2-piperazine) 5.14 (s, 2H, CH2), 6.91-6.94 (m, 3H, H-aromatic), 7.27-7.32 (m, 2H, H-
aromatic), 7.35-7.39 (m, 1H, H-aromatic), 7.44-7.48 (m, 1H, H-aromatic), 7.82-7.84 (m, 1H,
13
H-aromatic), 7.99-8.00 (m, 1H, H-aromatic). C-NMR (CDCl3) δ: 38.9 (CH2), 48.9 (CH2),
116.4, 120.8, 121.6, 122.9, 125.3, 126.1, 128.45 (CH, C-aromatic), 135.7, 149.9, 152.6, 167.5,
194.7 (C). Melting point: 110-112°C. UPLC-MS (Method C): Rt 2.18 min, MS [ESI, m/z]:
386.2 [M+H]. Anal. Calcd for C19H19N3S3: C, 59.19; H, 4.97; N, 10.90. Found: C, 59.34; H,
5.05; N, 10.75.
4.2 Molecular modelling
All molecular docking studies were performed on a Viglen Genie Intel®CoreTM i7-3770 vPro
CPU@ 3.40 GHz x 8 running Ubuntu 18.04. Molecular Operating Environment (MOE)
2019.1029 and Maestro (Schrödinger Release 2019-3)39 were used as molecular modelling
software. The ZBD of M2-1 protein was downloaded from the PDB data bank
(http://www.rcsb.org/; PDB code 6G0Y).20 The protein was pre-processed using the
Schrödinger Protein Preparation Wizard by assigning bond orders, adding hydrogens and
performing a restrained energy minimisation of the added hydrogens using the OPLS_2005

force field. Ligand structures were built with MOE and then prepared using the Maestro
LigPrep tool by energy minimising the structures (OPLS_2005 force filed), generating possible
ionization states at pH 7±2, generating tautomers and low-energy ring conformers. A 12 Å
docking grid (inner-box 10 Å and outer-box 21 Å) was prepared using as centroid the co-
crystallised Zn atom. Molecular docking studies were performed using Glide SP precision
keeping the default parameters and setting 5 as number of output poses per input ligand to
include in the solution. The output poses were saved as mol2 file. The docking results were
visually inspected for their ability to bind the active site.
Molecular dynamics simulations were performed on Viglen Genie Intel®Xeon® CPU ES-
2403 @ 1.80 GHz x 8 (graphic card: GeForce GTX 1080 Ti) running Ubuntu 18.04, using the
Desmond package for MD simulation: OPLS_2005 force field in explicit solvent, employing
the TIP3 water model. The initial coordinates for the MD simulation were taken from the best
docking experiment result for each single compound. A cubic water box was used for the
solvation of the system, ensuring a buffer distance of approximately 8 Å between each box side
and the complex atoms. The system was neutralized adding 27 chlorine counter ions. The
system was minimised and pre-equilibrated using the default relaxation routine implemented
in Desmond. A 150 ns MD simulation was performed, during which the equation of motion
were integrated using a 2 fs time step in the NPT ensemble, with temperature (300 K) and
pressure (1 atm) constant. All other parameters were set using the Desmond default values.
Data were collected every 10 ps (energy) and every 40 ps (trajectory). Each protein-ligand
complex simulation was performed in triplicate, using every time a random seed as starting
point. Visualisation of protein-ligand complex and MD trajectory analysis were carried out
using Maestro. RMSD, secondary structure and protein-ligand interactions analyses were
performed using the Simulation Event Analysis tool and the Simulation Interaction Diagram
of Desmond. The ∆Gbinding values of the protein-ligand complex were calculated using the
MM/GBSA method as implemented in the Prime module from Maestro using the default
settings and the Maestro script termal_mmgbsa.py. Briefly, the script takes in the MD
trajectory from the last 80 ns of simulation, splits it into individual frame snapshots (extracted
every 0.400 ns, for a total of 201 frames), and runs each one through MMGBSA (after deleting
waters and separating the ligand from the receptor). For each single simulation, an average
∆Gbinding values for the 80 ns is calculated.
4.3 Biological assays

4.3.1 Media, cells, virus and compounds
DMEM (catalogue no. 41965-039), PBS (catalogue no. 14190-094) and non-essential amino
acid solution (NEAA; catalogue no. 11140-035) were obtained from Thermo Fisher Scientific.
FBS was obtained from Hyclone (catalogue no. SV30160.03) and heat inactivated at 56°C for
30min. HEp-2 cells, RSV-A Long strain and RSV-B Wash strain were obtained from ATCC.
ALS-8112 was synthesized according to published procedures (purity >98%).40
4.3.2 Virus and cells for in vitro standard antiviral assay
HEp2 cells were seeded at 5x103 cells/well in a 96-well plate and were further cultured in
DMEM (supplemented with 2% FBS and 1% NEAA) at 37°C and 5% CO2. The day after,
medium was replaced by a serial dilution (1:2) of the antiviral test compounds in the same
medium and the cultures were infected with RSV-A Long strain or RVS-B wash strain at an
moi of 0.01 CCID50/cell (where CCID50 represents the 50% cell culture infectious dose in
HEp2 cells). After 5 days, the typical cytopathic effect (CPE) was scored microscopically in
all wells, on a scale of 0–5. The EC50 was calculated by logarithmic interpolation as the
concentration of compound that resulted in a 50% protective effect against virus-induced CPE.
Potential compound toxicity was evaluated in a similar set-up in treated, uninfected cultures
where metabolic activity was quantified at day 5 by using the 3-(4,5-dimethylthiazol-2-yl)-5-
(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) readout. The CC50 was
calculated by logarithmic interpolation as the concentration of compound that resulted in a 50%
decrease in the MTS signal.
Acknowledgements
M.B. and S.F. were supported by the Sêr Cymru II programme which is part-funded by Cardiff
University and the European Regional Development Fund through the Welsh Government.
Appendix A. Supplementary data
All experimental procedures and compound characterisation data for the reaction intermediates
are reported and described in detail in the Supporting Information.
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Declaration of interests
☒ The authors declare that they have no known competing financial interests or personal
relationships that could have appeared to influence the work reported in this paper.
☐The authors declare the following financial interests/personal relationships which may be
considered as potential competing interests: