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Zn Inhibits Coronavirus and Arterivirus RNA Polymerase Activity In Vitro and Zinc Ionophores Block the Replication of These Viruses in Cell Culture

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Increasing the intracellular Zn(2+) concentration with zinc-ionophores like pyrithione (PT) can efficiently impair the replication of a variety of RNA viruses, including poliovirus and influenza virus. For some viruses this effect has been attributed to interference with viral polyprotein processing. In this study we demonstrate that the combination of Zn(2+) and PT at low concentrations (2 µM Zn(2+) and 2 µM PT) inhibits the replication of SARS-coronavirus (SARS-CoV) and equine arteritis virus (EAV) in cell culture. The RNA synthesis of these two distantly related nidoviruses is catalyzed by an RNA-dependent RNA polymerase (RdRp), which is the core enzyme of their multiprotein replication and transcription complex (RTC). Using an activity assay for RTCs isolated from cells infected with SARS-CoV or EAV--thus eliminating the need for PT to transport Zn(2+) across the plasma membrane--we show that Zn(2+) efficiently inhibits the RNA-synthesizing activity of the RTCs of both viruses. Enzymatic studies using recombinant RdRps (SARS-CoV nsp12 and EAV nsp9) purified from E. coli subsequently revealed that Zn(2+) directly inhibited the in vitro activity of both nidovirus polymerases. More specifically, Zn(2+) was found to block the initiation step of EAV RNA synthesis, whereas in the case of the SARS-CoV RdRp elongation was inhibited and template binding reduced. By chelating Zn(2+) with MgEDTA, the inhibitory effect of the divalent cation could be reversed, which provides a novel experimental tool for in vitro studies of the molecular details of nidovirus replication and transcription.
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Zn
2+
Inhibits Coronavirus and Arterivirus RNA
Polymerase Activity
In Vitro
and Zinc Ionophores Block
the Replication of These Viruses in Cell Culture
Aartjan J. W. te Velthuis
1
, Sjoerd H. E. van den Worm
1
, Amy C. Sims
2
, Ralph S. Baric
2
, Eric J. Snijder
1
*,
Martijn J. van Hemert
1
*
1Molecular Virology Laboratory, Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands,
2Departments of Epidemiology and Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
Abstract
Increasing the intracellular Zn
2+
concentration with zinc-ionophores like pyrithione (PT) can efficiently impair the replication
of a variety of RNA viruses, including poliovirus and influenza virus. For some viruses this effect has been attributed to
interference with viral polyprotein processing. In this study we demonstrate that the combination of Zn
2+
and PT at low
concentrations (2 mMZn
2+
and 2 mM PT) inhibits the replication of SARS-coronavirus (SARS-CoV) and equine arteritis virus
(EAV) in cell culture. The RNA synthesis of these two distantly related nidoviruses is catalyzed by an RNA-dependent RNA
polymerase (RdRp), which is the core enzyme of their multiprotein replication and transcription complex (RTC). Using an
activity assay for RTCs isolated from cells infected with SARS-CoV or EAV—thus eliminating the need for PT to transport Zn
2+
across the plasma membrane—we show that Zn
2+
efficiently inhibits the RNA-synthesizing activity of the RTCs of both
viruses. Enzymatic studies using recombinant RdRps (SARS-CoV nsp12 and EAV nsp9) purified from E. coli subsequently
revealed that Zn
2+
directly inhibited the in vitro activity of both nidovirus polymerases. More specifically, Zn
2+
was found to
block the initiation step of EAV RNA synthesis, whereas in the case of the SARS-CoV RdRp elongation was inhibited and
template binding reduced. By chelating Zn
2+
with MgEDTA, the inhibitory effect of the divalent cation could be reversed,
which provides a novel experimental tool for in vitro studies of the molecular details of nidovirus replication and
transcription.
Citation: te Velthuis AJW, van den Worm SHE, Sims AC, Baric RS, Snijder EJ, et al. (2010) Zn
2+
Inhibits Coronavirus and Arterivirus RNA Polymerase Activity In Vitro
and Zinc Ionophores Block the Replication of These Viruses in Cell Culture. PLoS Pathog 6(11): e1001176. doi:10.1371/journal.ppat.1001176
Editor: Raul Andino, University of California San Francisco, United States of America
Received May 17, 2010; Accepted October 1, 2010; Published November 4, 2010
Copyright: ß2010 te Velthuis et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported by the Netherlands Organization for Scientific Research (NWO) with grants from the Council for Chemical Sciences (NWO-CW
grant 700.55.002 and 700.57.301) and an NWO Toptalent grant (021.001.037). The funders had no role in study design, data collection and analysis, decision to
publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests exist.
* E-mail: e.j.snijder@lumc.nl (ES); m.j.van_hemert@lumc.nl (MJvH)
Introduction
Zinc ions are involved in many different cellular processes and
have proven crucial for the proper folding and activity of various
cellular enzymes and transcription factors. Zn
2+
is probably an
important cofactor for numerous viral proteins as well. Neverthe-
less, the intracellular concentration of free Zn
2+
is maintained at a
relatively low level by metallothioneins, likely due to the fact that
Zn
2+
can serve as intracellular second messenger and may trigger
apoptosis or a decrease in protein synthesis at elevated
concentrations [1,2,3]. Interestingly, in cell culture studies, high
Zn
2+
concentrations and the addition of compounds that stimulate
cellular import of Zn
2+
, such as hinokitol (HK), pyrrolidine
dithiocarbamate (PDTC) and pyrithione (PT), were found to
inhibit the replication of various RNA viruses, including influenza
virus [4], respiratory syncytial virus [5] and several picornaviruses
[6,7,8,9,10,11]. Although these previous studies provided limited
mechanistic information, this suggests that intracellular Zn
2+
levels
affect a common step in the replicative cycle of these viruses.
In cell culture, PT stimulates Zn
2+
uptake within minutes and
inhibits RNA virus replication through a mechanism that has
only been studied in reasonable detail for picornaviruses [11,12].
In vitro studies with purified rhinovirus and poliovirus 3C proteases
revealed that protease activity was inhibited by Zn
2+
[13,14],
which is in line with the inhibition of polyprotein processing by
zinc ions that was observed in cells infected with human rhinovirus
and coxsackievirus B3 [11]. The replication of segmented
negative-strand RNA viruses such as influenza virus, however,
does not depend on polyprotein processing and the effect of
PDTC-mediated Zn
2+
import was therefore hypothesized to result
from inhibition of the viral RNA-dependent RNA polymerase
(RdRp) and cellular cofactors [4]. Moreover, an inhibitory effect of
Zn
2+
on the activity of purified RdRps from rhinoviruses and
hepatitis C virus was noted, but not investigated in any detail
[15,16].
Details on the effect of zinc ions are currently largely unknown
for nidoviruses. This large group of positive-strand RNA (+RNA)
viruses includes major pathogens of humans and livestock, such as
severe acute respiratory syndrome coronavirus (SARS-CoV), other
human coronaviruses, the arteriviruses equine arteritis virus
(EAV), and porcine reproductive and respiratory syndrome virus
(PRRSV) [17,18]. The common ancestry of nidoviruses is reflected
in their similar genome organization and expression strategy, and
in the conservation of a number of key enzymatic functions in their
PLoS Pathogens | www.plospathogens.org 1 November 2010 | Volume 6 | Issue 11 | e1001176
large replicase polyproteins [19]. A hallmark of the corona- and
arterivirus replicative cycle is the transcription of a 59- and 39-
coterminal nested set of subgenomic (sg) mRNAs from which the
viral structural and accessory protein genes are expressed [20,21].
Analogous to picornaviruses [13,22], zinc ions were demon-
strated to inhibit certain proteolytic cleavages in the processing of
the coronavirus replicase polyproteins in infected cells and cell-free
systems [23,24]. In this study we report that the zinc-ionophore
pyrithione (PT) in combination with Zn
2+
is a potent inhibitor of
the replication of SARS-coronavirus (SARS-CoV) and equine
arteritis virus (EAV) in cell culture. To assess whether - besides a
possible effect on proteolytic processing - nidovirus RTC subunits
and RNA synthesis are directly affected by Zn
2+
, we employed in
vitro systems for SARS-CoV and EAV RNA synthesis that are
based on membrane-associated RTCs isolated from infected cells
(from here on referred to as RTC assays) [25,26]. In addition, we
used in vitro recombinant RdRp assays to directly study the effect of
zinc ions on the RdRps of SARS-CoV and EAV [27,28].
Using these independent in vitro approaches, we were able to
demonstrate that Zn
2+
directly impairs nidovirus RNA synthesis,
since it had a strong inhibitory effect in both RTC and RdRp
assays. Interestingly, the Zn
2+
-mediated inhibition could be
reversed through the addition of a Zn
2+
chelator (MgEDTA).
We therefore applied this compound to stop and restart the in vitro
RNA-synthesizing activity at will. This convenient tool allowed us
to study various mechanistic aspects of arteri- and coronavirus
RNA synthesis in more detail. Additionally, the zinc-mediated
inhibition of nidovirus RNA synthesis described here may provide
an interesting basis to further explore the use of zinc-ionophores in
antiviral therapy.
Results
Zinc and pyrithione inhibit nidovirus replication in vivo
Zinc ions are involved in many different cellular processes, but
the concentration of free Zn
2+
is maintained at a relatively low
level by metallothioneins [1]. Zn
2+
and compounds that stimulate
import of Zn
2+
into cells, such as PT, were previously found to
inhibit replication of several picornaviruses, including rhinovirus-
es, foot-and-mouth disease virus, coxsackievirus, and mengovirus
in cell culture [6,7,8,9,10,11]. To determine whether Zn
2+
has a
similar effect on nidoviruses, we investigated the effect of PT and
Zn
2+
on the replication of EAV and SARS-CoV in Vero-E6 cells,
using reporter viruses that express green fluorescent proteins
(GFP), i.e., EAV-GFP [29] and SARS-CoV-GFP [30]. EAV-GFP
encodes an N-terminal fusion of GFP to the viral nonstructural
protein 2 (nsp2), one of the cleavage products of the replicase
polyproteins, and thus provides a direct readout for translation of
the replicase gene. In SARS-CoV-GFP, reporter expression occurs
from sg mRNA 7, following the replacement of two accessory
protein-coding genes (ORFs 7a and 7b) that are dispensable for
replication in cell culture.
We first assessed the cytotoxicity of a range of PT concentrations
(0–32 mM) in the presence of 0 to 8 mMZnOAc
2
.TreatmentwithPT
of concentrations up to 32 mM in combination with ,4mMZnOAc
2
did not reduce the viability of mock-infected cells after 18 h (Fig. 1A),
as measured by the colorimetric MTS (3-(4,5-dimethylthiazol-2-yl)-5-
(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) viabili-
ty assay. As elevated Zn
2+
concentrations are known to inhibit cellular
translation, we also used metabolic labeling with
35
S-methionine to
assess the effect of PT and Zn
2+
on cellular protein synthesis.
Incubation of Vero-E6 cells for 18 h with the combinations of PT and
Zn
2+
mentioned above, followed by a 2-h metabolic labeling,
revealed no change in overall cellular protein synthesis when the
concentration of ZnOAc
2
was ,4mM (data not shown).
Using these non-cytotoxic conditions we subsequently tested the
effect of PT and ZnOAc
2
on EAV-GFP and SARS-CoV-GFP
replication. To this end, Vero-E6 cells in 96-well plates were
infected with a multiplicity of infection (m.o.i.) of 4. One hour post
infection (h p.i.), between 0 and 32 mM of PT and 0, 1, or 2 mM
ZnOAc
2
were added to the culture medium. At 17 h p.i., a time
point at which GFP expression in untreated infected cells reaches
its maximum for both viruses, cells were fixed, and GFP
fluorescence was quantified.
The reporter gene expression of both SARS-CoV-GFP and
EAV-GFP was already significantly inhibited in a dose-dependent
manner by the addition of PT alone (Fig. 1B and C). This effect
was significantly enhanced when 2 mMofZn
2+
was added to the
medium. We found that addition of ZnOAc
2
alone also reduced
virus replication, but only at levels that were close to the 50%
cytotoxicity concentration (CC
50
) of ZnOAc
2
in Vero-E6 cells
(,70 mM, data not shown). This is likely due to the poor solubility
of Zn
2+
in phosphate-containing medium and the inefficient
uptake of Zn
2+
by cells in the absence of zinc-ionophores. The
combination of 2 mM PT and 2 mM ZnOAc
2
resulted in a 9861%
and 8563% reduction of the GFP signal for EAV-GFP and
SARS-CoV-GFP, respectively. No cytotoxicity was observed for
this combination of PT and ZnOAc
2
concentrations. From the
dose-response curves in Fig. 1, a CC
50
value of 82 mM was
calculated for PT in the presence of 2 mM zinc. Half maximal
inhibitory concentrations (IC
50
) of 1.4 mM and 0.5 mM and
selectivity indices of 59 and 164 were calculated for SARS-CoV
and EAV, respectively.
Zn
2+
reversibly inhibits the RNA-synthesizing activity of
isolated nidovirus RTCs
We previously developed assays to study the in vitro RNA-
synthesizing activity of RTCs isolated from cells infected with
SARS-CoV or EAV [25,26]. In these RTC assays [a-
32
P]CMP is
incorporated into both genomic (replication) and sg mRNA
(transcription) (Fig. 2). This allowed us to monitor the synthesis of
the same viral RNA molecules that can be detected by
hybridization of RNA from nidovirus-infected cells. A benefit of
these assays is that the activity does not depend on continued
protein synthesis and that it allows us to study viral RNA synthesis
Author Summary
Positive-stranded RNA (+RNA) viruses include many
important pathogens. They have evolved a variety of
replication strategies, but are unified in the fact that an
RNA-dependent RNA polymerase (RdRp) functions as the
core enzyme of their RNA-synthesizing machinery. The
RdRp is commonly embedded in a membrane-associated
replication complex that is assembled from viral RNA, and
viral and host proteins. Given their crucial function in the
viral replicative cycle, RdRps are key targets for antiviral
research. Increased intracellular Zn
2+
concentrations are
known to efficiently impair replication of a number of RNA
viruses, e.g. by interfering with correct proteolytic pro-
cessing of viral polyproteins. Here, we not only show that
corona- and arterivirus replication can be inhibited by
increased Zn
2+
levels, but also use both isolated replication
complexes and purified recombinant RdRps to demon-
strate that this effect may be based on direct inhibition of
nidovirus RdRps. The combination of protocols described
here will be valuable for future studies into the function of
nidoviral enzyme complexes.
Zn
2+
Inhibits Nidovirus Replication
PLoS Pathogens | www.plospathogens.org 2 November 2010 | Volume 6 | Issue 11 | e1001176
independent of other aspects of the viral replicative cycle [26]. To
investigate whether the inhibitory effect of PT and zinc ions on
nidovirus replication in cell culture is reflected in a direct effect of
Zn
2+
on viral RNA synthesis, we tested the effect of Zn
2+
addition
on RTC activity. For both EAV (Fig. 2A) and SARS-CoV
(Fig. 2B), a dose-dependent decrease in the amount of RNA
synthesized was observed when ZnOAc
2
was present. For both
viruses, a more than 50% reduction of overall RNA-synthesis was
observed at a Zn
2+
concentration of 50 mM, while less than 5%
activity remained at a Zn
2+
concentration of 500 mM. Both
genome synthesis and sg mRNA production were equally affected.
To test whether the inhibition of RTC activity by Zn
2+
was
reversible, RTC reactions were started in the presence or absence
of 500 mMZn
2+
. After 30 min, these reactions were split into two
aliquots and magnesium-saturated EDTA (MgEDTA) was added
to one of the tubes to a final concentration of 1 mM (Fig. 3A). We
used MgEDTA as Zn
2+
chelator in these in vitro assays, because it
specifically chelates Zn
2+
while releasing Mg
2+
, due to the higher
stability constant of the ZnEDTA complex. Uncomplexed EDTA
inhibited RTC activity in all reactions (data not shown), most
likely by chelating the Mg
2+
that is crucial for RdRp activity
[27,28], whereas MgEDTA had no effects on control reactions
without Zn
2+
(Fig. 3B, compare lane 1 and 2). As shown in Fig. 2,
the EAV RTC activity that was inhibited by Zn
2+
(Fig. 3B&C,
lane 3) could be restored by the addition of MgEDTA (Fig. 3B,
lane 4) to a level observed for control reactions without Zn
2+
(Fig. 3B, lane 1). Compared to the untreated control, the EAV
RTC assay produced approximately 30% less RNA, which was
consistent with the 30% shorter reaction time after the addition of
the MgEDTA (100 versus 70 min for lanes 1 and 4, respectively).
Surprisingly, SARS-CoV RTC assays that were consecutively
supplemented with Zn
2+
and MgEDTA incorporated slightly
more [a-
32
P]CMP compared to untreated control reactions
(Fig. 3C; compare lane 1 and 4). This effect was not due to
chelation of the Zn
2+
already present in the post-nuclear
supernatant (PNS) of SARS-CoV-infected cells, as this increase
was not observed when MgEDTA was added to a control reaction
without additional Zn
2+
(Fig. 3C, lane 2).
Figure 1. The zinc ionophore pyrithione inhibits nidovirus
replication in cell culture. (A) Cytotoxicity of PT in Vero-E6 cells in
the absence (blue circles) or presence of 2 (black squares), 4 (red
triangles), or 8 mM (gray diamonds) ZnOAc
2
as determined by the MTS
assay after 18 hours of exposure. (B) Dose-response curves showing the
effect of PT and Zn
2+
on the GFP fluorescence in Vero-E6 cells infected
with a GFP-expressing EAV reporter strain at 17 h p.i. Data were
normalized to GFP expression in infected, untreated control cultures
(100%). The different Zn
2+
concentrations added to the medium were 0
(blue circles), 1 (green triangles), or 2 mM ZnOAc
2
(black squares).
(C) Effect of PT and Zn
2+
on the GFP fluorescence in Vero-E6 cells
infected with a GFP-expressing SARS-CoV reporter strain at 17 h p.i.
Data were normalized to GFP expression in infected untreated control
cells (100%). Colors for different Zn
2+
concentrations as in Fig. 1B. Error
bars indicate the standard deviation (n = 4).
doi:10.1371/journal.ppat.1001176.g001
Figure 2. Inhibition of the
in vitro
RNA-synthesizing activity of
isolated RTCs by Zn
2
+
.Incorporation of [a-
32
P]CMP into viral RNA by
EAV (A) and SARS-CoV (B) in RTC assays in the presence of various Zn
2+
concentrations, as indicated above each lane.
doi:10.1371/journal.ppat.1001176.g002
Zn
2+
Inhibits Nidovirus Replication
PLoS Pathogens | www.plospathogens.org 3 November 2010 | Volume 6 | Issue 11 | e1001176
Zinc ions affect the in vitro activity of recombinant
nidovirus RdRps
To establish whether inhibition of RTC activity might be due to
a direct effect of Zn
2+
on nidovirus RdRp activity, we tested the
effect of Zn
2+
on the activity of the purified recombinant RdRps of
SARS-CoV (nsp12) and EAV (nsp9) using previously developed
RdRp assays [27,28]. Using an 18-mer polyU template, the EAV
RdRp incorporated [a-
32
P]AMP into RNA products of up to 18
nt in length (Fig. 4A). Initiation was de novo, which is in line with
previous observations and the presence of a conserved priming
loop in the nsp9 sequence [28]. Unlike the EAV RdRp nsp9, the in
vitro activity of the SARS-CoV RdRp nsp12 - which lacks a
priming loop - was shown to be strictly primer-dependent [27].
Thus, to study the RdRp activity of SARS-CoV nsp12, a primed
polyU template was used (Fig. 4B), thereby allowing us to sample
[a-
32
P]AMP incorporation as described previously [27]. As
specificity controls, we used the previously described SARS-CoV
nsp12 mutant D618A [27], which contains an aspartate to alanine
substitution in motif A of the RdRp active site, and EAV nsp9-
D445A, in which we engineered an aspartate to alanine
substitution at the corresponding site of EAV nsp9 [28,31]. Both
mutant RdRps showed greatly reduced [a-
32
P]AMP incorporation
in our assays (Fig. 4), confirming once again that the radiolabeled
RNA products derived from nidovirus RdRp activity.
Addition of ZnOAc
2
to RdRp assays resulted in a strong, dose-
dependent inhibition of enzymatic activity for both the EAV and
SARS-CoV enzyme (Fig. 5A and B, respectively), similar to what
was observed in RTC assays. In fact, compared to other divalent
metal ions such Co
2+
and Ca
2+
, which typically bind to amino acid
side chains containing oxygen atoms rather than sulfur groups, Zn
2+
was the most efficient inhibitor of SARS-CoV nsp12 RdRp activity
(Supplemental Fig. S1). To test whether, as in the RTC assay, the
RdRp inhibition by zinc ions was reversible, RdRp assays were pre-
incubated with 6 mM Zn
2+
, a concentration that consistently gave
.95% inhibition. After 30 min, 8 mM MgEDTA was added to
both a control reaction and the reaction inhibited with ZnOAc
2
,
and samples were incubated for another 30 min (Fig. 5C). As shown
in Fig. 5D, the inhibition of EAV RdRp activity by Zn
2+
could be
reversed by chelation of Zn
2+
(Fig. 5D; compare lanes 3 and 4). The
amount of product synthesized was consistently 6065% of that
synthesized in a 60-min control reaction (Fig. 5D; compare lanes 1
and 4), which was within the expected range given the shorter
Figure 3. Inhibition of nidovirus RTC activity by Zn
2
+
can be
reversed by chelation. (A) Schematic representation of the in vitro
assays with isolated RTCs, which were initiated with [a-
32
P]CTP, either in
the absence (sample 1 and 2) or presence of 500 mMZn
2+
. After a 30-
min incubation at 30uC, both the untreated and Zn
2+
-treated samples
were split into two aliquots, and 1 mM of the Zn
2+
chelator MgEDTA
was added to samples 2 and 4. All reactions were subsequently
incubated for another 70 min before termination. (B) Analysis of RNA
products synthesized in assays with EAV RTCs. Numbers above the
lanes refer to the sample numbers described under (A). (C)In vitro
activity assay with SARS-CoV RTCs.
doi:10.1371/journal.ppat.1001176.g003
Figure 4. EAV and SARS-CoV RdRp assays with wild-type
enzyme and active-site mutants. (A) The EAV polymerase was
incapable of primer extension and required a free 39end and poly(U)
residues to initiate. Nucleotide incorporating activity of the wild-type
enzyme and D445A mutant of nsp9 on an 18-mer poly(U) template
confirmed the specificity of our assay. (B) SARS-CoV nsp12 RdRp assays
were performed with an RNA duplex with a 59U
10
overhang as
template. The bar graph shows the nucleotide incorporating activities
of wild-type and D618A nsp12. Error bars represent standard error of
the mean (n = 3).
doi:10.1371/journal.ppat.1001176.g004
Zn
2+
Inhibits Nidovirus Replication
PLoS Pathogens | www.plospathogens.org 4 November 2010 | Volume 6 | Issue 11 | e1001176
reaction time. The inhibition of the SARS-CoV RdRp was
reversible as well. During the 30-min incubation after the addition
of MgEDTA, SARS-CoV nsp12 incorporated 4065% of the label
incorporated during a standard 60-min reaction (Fig. 5E). This was
slightly lower than the expected yield and may be caused by the
elevated Mg
2+
concentration, which was shown to be suboptimal for
nsp12 activity [27] and results from the release of Mg
2+
from
MgEDTA upon chelation of Zn
2+
.
Differential effect of Zn
2+
on the initiation and elongation
phase of nidovirus RNA synthesis
For EAV, close inspection of the RdRp assays revealed a less
pronounced effect of Zn
2+
on the generation of full-length 18-nt
products than on the synthesis of smaller reaction intermediates
(Fig. 5A). This suggested that Zn
2+
specifically inhibited the
initiation step of EAV RNA synthesis. To test this hypothesis, an
RTC assay was incubated for 30 min with unlabeled CTP
(initiation), after which the reaction was split in two. Then,
[a-
32
P]CTP was added to both tubes (pulse), 500 mMZn
2+
was
added to one of the tubes, and samples were taken at different time
points during the reaction (Fig. 6A). Fig. 6B shows that in the
presence of Zn
2+
[a-
32
P]CMP was predominantly incorporated
into nascent RNA molecules that were already past the initiation
phase at the moment that Zn
2+
was added to the reaction. No new
initiation occurred, as was indicated by the smear of short
radiolabeled products that progressively shifted up towards the
position of full-length genomic RNA. This suggested that Zn
2+
does not affect the elongation phase of EAV RNA synthesis and
that it specifically inhibits initiation. This also explains the
relatively weak signal intensity of the smaller sg mRNA bands
(e.g., compare the relative change in signal of RNA2 to RNA7)
produced in the presence of Zn
2+
, since multiple initiation events
are required on these short molecules to obtain signal intensities
similar to those resulting from a single initiation event on the long
genomic RNA, e.g., 16 times more in the case of RNA7. In
contrast to EAV, the effect of Zn
2+
on RNA synthesis by SARS-
CoV RTCs was not limited to initiation, but appeared to impair
the elongation phase as well, given that the addition of Zn
2+
completely blocked further incorporation of [a-
32
P]CMP when
added 40 min after the start of the reaction (Fig. 6C).
In the RdRp assays, the short templates used made it technically
impossible to do experiments similar to those performed with
complete RTCs. However, we previously noticed that at low
concentrations of [a-
32
P]ATP (,0.17 mM) SARS-CoV nsp12
RdRp activity was restricted to the addition of only a single
nucleotide to the primer [27]. EAV nsp9 mainly produced very
short (2–3 nt long) abortive RNA products and only a fraction of
full length products, as is common for de novo initiating RdRps
[28]. This allowed us to separately study the effect of Zn
2+
on
initiation and elongation by performing an experiment in which a
pulse with a low concentration of [a-
32
P]ATP was followed by a
chase in the presence of 50 mM of unlabeled ATP, which
increased processivity and allowed us to study elongation (Fig. 7A
and C) as described previously [27]. The results of these
experiments were in agreement with those obtained with isolated
RTCs. For EAV, with initiation and dinucleotide synthesis
completely inhibited by the presence of 6 mM Zn
2+
(Supplemental
Fig. S2A), the amount of reaction intermediates shorter than 18 nt
diminished with time, while products from templates on which the
RdRp had already initiated were elongated to full-length 18-nt
molecules (Fig. 7B, right panel). This was consistent with the
observation that the EAV RdRp remained capable of extending
the synthetic dinucleotide ApA to trinucleotides in the presence of
Zn
2+
(Supplemental Fig. S2B). Likely due to the absence of
reinitiation in the reactions shown in Fig. 7B, the low processivity
of the EAV RdRp, and the substrate competition between the
remaining [a-
32
P]ATP and the .200 fold excess of unlabeled
ATP, the differences between the 5- and 30-min time points were
small. In the absence of Zn
2+
, the RdRp continued to initiate as
indicated by the ladder of smaller-sized RNA molecules below the
full-length product (Fig. 7B, left panel) and the time course shown
in Supplemental Fig. S2A. In contrast, the addition of Zn
2+
to a
SARS-CoV RdRp reaction also blocked elongation, since
Figure 5. The activity of the RdRps of EAV and SARS-CoV is
reversibly inhibited by Zn
2
+
.RdRp activity of purified EAV nsp9 (A)
and SARS-CoV nsp12 (B) in the presence of various Zn
2+
concentrations,
as indicated above the lanes. (C) Schematic representation of the
experiment to test whether Zn
2+
-mediated inhibition of RdRp activity
could be reversed with MgEDTA. RdRp reactions, either untreated controls
(sample 1 and 2) or reactions containing 6 mM Zn
2+
(samples 3 and 4)
were incubated for 30 min. Both Zn
2+
-containing and control samples
were split into two aliquots and 6 mM MgEDTA was added to sample 2
and 4. All reactions were incubated for an additional 30 min and then
terminated. Reaction products of the RdRp assays with EAV nsp9 and
SARS-CoV nsp12 are shown in (D)and(E), respectively. Numbers above
the lanes refer to the sample numbers described under (C).
doi:10.1371/journal.ppat.1001176.g005
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2+
Inhibits Nidovirus Replication
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extension of the radiolabeled primer as observed in the absence of
Zn
2+
(Fig. 7D, left panel) no longer occurred (Fig. 7D, right panel).
Zinc affects SARS-CoV RdRp template binding
To assess whether Zn
2+
affects the interaction of recombinant
SARS-CoV nsp12 with the template used in our assays, we
performed electromobility shift assays (EMSA) in the presence and
absence of Zn
2+
(Fig. 8A). To measure the binding affinity of the
RdRp for the template, we determined the fraction of bound
template at various protein concentrations and observed a 3–4 fold
reduction in RNA binding when Zn
2+
was present in the assay
(Fig. 8B). We also assessed whether pre-incubation of the RdRp or
RNA with Zn
2+
was a requirement for this drop in binding
affinity, but found no significant difference with experiments not
involving such a preincubation (data not shown).
No binding was observed when a similar RNA binding assay
was performed with purified EAV RdRp. Likewise, nsp9 did not
bind RNA in pull-down experiments with Talon-beads, His
6
-
tagged nsp9, and radiolabeled EAV genomic RNA or various
short RNA templates including polyU, whereas we were able to
detect binding of a control protein (SARS-CoV nsp8, which has
demonstrated RNA and DNA binding activity [32]) using this
assay. It presently remains unclear why we are not able to detect
the binding of recombinant EAV nsp9 to an RNA template.
Discussion
Although a variety of compounds have been studied, registered
antivirals are currently still lacking for the effective treatment of
SARS and other nidovirus-related diseases [33]. RdRps are
suitable targets for antiviral drug development as their activity is
strictly virus-specific and may be blocked without severely affecting
key cellular functions. Several inhibitors developed against the
polymerases of e.g. human immunodeficiency virus (HIV) and
hepatitis C virus are currently being used in antiviral therapy or
clinical trials [34,35,36]. Therefore, advancing our molecular
knowledge of nidovirus RdRps and the larger enzyme complexes
that they are part of, and utilizing the potential of recently
developed in vitro RdRp assays [25,26,27,28] could ultimately aid
in the development of effective antiviral strategies.
Zinc ions and zinc-ionophores, such as PT and PDTC, have
previously been described as potent inhibitors of various RNA
viruses. We therefore investigated whether PT-stimulated import
of zinc ions into cells also inhibited the replication of nidoviruses in
cell culture. Using GFP-expressing EAV and SARS-CoV [29,30],
we found that the combination of 2 mM PT and 2 mMZn
2+
efficiently inhibited their replication, while not causing detectable
cytoxicity (Fig. 1). Inhibition of replication by PT and Zn
2+
at
similar concentrations (2–10 mM) was previously observed for
several picornaviruses such as rhinoviruses, foot-and-mouth
disease virus, coxsackievirus, and mengovirus [6,7,8,9,10,11].
The inhibitory effect of Zn
2+
on the replication of picornaviruses
appeared to be due to interference with viralpolyprotein processing.
In infections with the coronavirus mouse hepatitis virus (MHV),
Zn
2+
also interfered with some of the replicase polyproteins
cleavages [24], albeit at a much higher concentration (100 mM
Zn
2+
) than used in our studies. Since impaired replicase processing
will indirectly affect viral RNA synthesis in the infected cell, we used
two recently developed in vitro assays to investigate whether Zn
2+
also affects nidovirus RNA synthesis directly. Our in vitro studies
revealed a strong inhibitory effect of zinc ions on the RNA-
synthesizing activity of isolated EAV and SARS-CoV RTCs. Assays
with recombinant enzymes subsequently demonstrated that this was
likely due to direct inhibition of RdRp function. The inhibitory
effect could be reversed by chelating the zinc ions, which provides
an interesting experimental (on/off) approach to study nidovirus
RNA synthesis. Addition of Zn
2+
following initiation of EAV RNA
synthesis had little or no effect on NTP incorporation in molecules
whose synthesis had already been initiated in the absence of Zn
2+
(Fig. 6 and 7), indicating that Zn
2+
does not affect elongation and
does not increase the termination frequency, as was previously
found for Mn
2+
[25]. Therefore, Zn
2+
appears to be a specific
inhibitor of the initiation phase of EAV RNA synthesis. In contrast,
Zn
2+
inhibited SARS-CoV RdRp activity also during the
elongation phase of RNA synthesis, probably by directly affecting
template binding (Fig. 8). In coronaviruses, zinc ions thus appear to
inhibit both the proper proteolytic processing of replicase
polyproteins [23,24] and RdRp activity (this study). Contrary to
the RTC assays, millimolar instead of micromolar concentrations of
ZnOAc
2
were required for a nearly complete inhibition of
nucleotide incorporation in RdRp assays.
It has been well established that DNA and RNA polymerases use a
triad of conserved aspartate residues in motifs A and C to bind
Figure 6. Effect of Zn
2
+
on initiation and elongation in
in vitro
assays with isolated EAV and SARS-CoV RTCs. (A)Anin vitro RTC
assay with isolated EAV RTCs was allowed to initiate with unlabeled
NTPs (initiation). After 30 min, [a-
32
P]CTP was added (pulse), the
reaction was split into two equal volumes, and Zn
2+
was added to a
final concentration of 0.5 mM to one of the tubes. At the time points
indicated, samples were taken and incorporation of [a-
32
P]CMP into
viral RNA was analyzed. (B) Radiolabeled EAV RNA synthesized at the
time points indicated above the lanes in the presence and absence of
Zn
2+
.(C) Radiolabeled RNA synthesized by isolated SARS-CoV RTCs in
reactions terminated after 100 (lane 1) and 40 (lane 2) min. Reaction
products of a reaction to which 500 mMZn
2+
was added after 40 min,
and that was terminated at t = 100 are shown in lane 3.
doi:10.1371/journal.ppat.1001176.g006
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divalent metal ions like Mg
2+
, which subsequently coordinate
incoming nucleotides during the polymerization reaction [37,38].
Mg
2+
is also the divalent metal ion that is required for the in vitro
activity of isolated SARS-CoV and EAV RTCs and recombinant
RdRps [25,26,27,28], although de novo initiation of EAV nsp9 is
primarily Mn
2+
-dependent. Zn
2+
could not substitute for Mg
2+
or
Mn
2+
as cofactor as it was incapable of supporting the polymerase
activityofnidovirusRTCsandRdRpsintheabsenceofMg
2+
(data
not shown), as was also reported for the poliovirus RdRp [39].
Moreover, inhibition of nidovirus RdRp activity by Zn
2+
was even
observed at low concentrations and in the presence of a more than
25-fold excess of Mg
2+
, suggesting that either the affinity of the active
site for Zn
2+
is much higher or that Zn
2+
does not compete for Mg
2+
-
binding and binds to another zinc(-specific) binding site in the protein.
Specific protein domains or pockets that contain zinc ions may
be involved in protein-protein interactions, protein-RNA/DNA
interactions, or conformational changes in enzyme structures.
Zinc-binding domains commonly consist of at least three
conserved cysteine and/or histidine residues within a stretch of
,10–30 amino acids, such as in zinc-finger motifs and
metalloproteases [2,40,41]. However, in RdRps there are only
few precedents for the presence of zinc-binding pockets, such as
those identified in the crystal structure of the Dengue RdRp [42].
Sequence analysis of the EAV nsp9 amino acid sequence revealed
that it lacks patches rich in conserved cysteines and/or histidines.
In contrast, inspection of the SARS-CoV nsp12 amino acid
sequence revealed two such patches, namely H295-C301-C306-
H309-C310 and C799-H810-C813-H816. A crystal structure for
nsp12 is presently unavailable, but a predicted structure that
represents the C-terminal two-thirds of the enzyme has been
published [31]. Interestingly, in this model, C799, H810, C813
and H816 are in a spatial arrangement resembling that of the Zn
2+
Figure 7. The effect of Zn
2
+
on initiation and elongation activity of purified EAV and SARS-CoV RdRps. (A) An EAV RdRp reaction was
initiated in the presence of [a-
32
P]ATP under conditions that do not allow elongation, i.e., low ATP concentration. After 20 min, the reaction was split
into two equal volumes, and Zn
2+
was added to one of the tubes. A chase with 50 mM unlabeled ATP, which allows elongation, was performed on
both reactions and samples were taken after 5 and 30 min. (B) EAV RdRp reaction products that accumulated in the presence and absence of Zn
2+
(indicated above the lanes) after a 5- and 30-min chase with unlabeled ATP. The length of the reaction products in nt is indicated next to the gel.
(C) A SARS-CoV RdRp reaction was initiated in the presence of 0.17 mM[a-
32
P]ATP, which limits elongation. After 10 min, the reaction was split into
two equal volumes, and Zn
2+
was added to one of the tubes. A chase with 50 mM unlabeled ATP was performed on both reactions and samples were
taken after 5, 10, 15, and 30 min. (D) SARS-CoV RdRp reaction products formed at the chase times indicated above the lanes in the presence and
absence of Zn
2+
. The length of the reaction products in nt is indicated next to the gel (p is the primer length).
doi:10.1371/journal.ppat.1001176.g007
Zn
2+
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PLoS Pathogens | www.plospathogens.org 7 November 2010 | Volume 6 | Issue 11 | e1001176
coordinating residues in the Zn2 zinc-binding pocket found in
motif E of the Dengue virus RdRp (see Supplemental Fig. S3).
Clearly, an in-depth analysis of nidovirus RdRps, e.g. through
structural analysis and subsequent mutational studies targeting
aforementioned cysteines and histidines, is required to provide
further insight into and a structural basis for the Zn
2+
-induced
inhibitory effects on RdRp activity documented in this study. Such
studies may, however, be complicated when Zn
2+
binding proves
to be very transient in nature and not detectable with currently
available methods.
In summary, the combination of zinc ions and the zinc-ionophore
PT efficiently inhibits nidovirus replication in cell culture. This
provides an interesting basis for further studies into the use of zinc-
ionophores as antiviral compounds, although systemic effects have
to be considered [43,44] and a water-soluble zinc-ionophore may be
better suited, given the apparent lack of systemic toxicity of such a
compound at concentrations that were effective against tumors in a
mouse xenograft model [45]. In vitro, the reversible inhibition of the
RdRp by Zn
2+
has also provided us with a convenient research tool
to gain more insight into the molecular details of (nido)viral RNA
synthesis, and revealed novel mechanistic differences between the
RdRps of SARS-CoV and EAV.
Materials and Methods
Cells and viruses
Vero-E6 cells were cultured and infected with SARS-CoV
(strain Frankfurt-1; accession nr. AY291315) or SARS-CoV-GFP
as described previously [46]. All procedures involving live SARS-
CoV were performed in the biosafety level 3 facility at Leiden
University Medical Center. BHK-21 or Vero-E6 cells were
cultured and infected with EAV (Bucyrus strain; accession nr.
NC_002532) or EAV-GFP [29] as described elsewhere [25].
Effect of zinc ions on nidovirus replication in cell culture
One day prior to infection, Vero-E6 cells were seeded in
transparent or black (low fluorescence) 96-well clusters at 10,000
cells per well. The next day, cells were infected with SARS-CoV-GFP
or EAV-GFP with an m.o.i. of 4, and 1 h p.i. the inoculum was
removed and 100 ml of medium containing 2% fetal calf serum (FCS)
was added to each well. In some experiments 0–32 mMofpyrithione
(Sigma) was added in addition to 0–2 mMZnOAc
2
. Infected cells
were fixed at 17 h p.i. by aspirating the medium and adding 3%
paraformaldehyde in PBS. After washing with PBS, GFP expression
was quantified by measuring fluorescence with a LB940 Mithras plate
reader (Berthold) at 485 nm. To determine toxicity of ZnOAc
2
and
PT, cells were exposed to 0–32 mM PT and 0–8 mMZnOAc
2
.After
18 h incubation, cell viability was determined with the Cell Titer 96
AQ MTS assay (Promega). EC
50
and CC
50
values were calculated
with Graphpad Prism 5 using the nonlinear regression model.
RNA templates and oligonucleotides
RNA oligonucleotides SAV557R (59-GCUAUGUGAGAU-
UAAGUUAU-39), SAV481R (59-UUUUUUUUUUAUAACUU-
AAUCUCACAUAGC-39) and poly(U)
18
(59-UUUUUUUUU-
UUUUUUUUU-39) were purchased from Eurogentec, purified
from 7 M Urea/15% PAGE gels and desalted through NAP-10
columns (GE healthcare). To anneal the RNA duplex SAV557R/
SAV481R, oligonucleotides were mixed at equimolar ratios in
annealing buffer (20 mM Tris-HCl pH 8.0, 50 mM NaCl and
5 mM EDTA), denatured by heating to 90uC and allowed to
slowly cool to room temperature after which they were purified
from 15% non-denaturing PAGE gels.
In vitro viral RNA synthesis assay with isolated RTCs
SARS-CoV and EAV RTCs were isolated from infected cells and
assayed for activity in vitro as described previously [25,26]. To assess
the effect of Zn
2+
,1ml of a ZnOAc
2
stock solution was added to
standard 28-ml reactions, resulting in final Zn
2+
concentrations of
10–500 mM. When Zn
2+
had to be chelated in the course of the
reaction, magnesium-saturated EDTA (MgEDTA) was added to a
final concentration of 1 mM. After RNA isolation, the
32
P-labeled
reaction products were separated on denaturing 1% (SARS-CoV)
or 1.5% (EAV) agarose formaldehyde gels. The incorporation of
[a-
32
P]CMP into viral RNA was quantified by phosphorimaging of
the dried gels using a Typhoon scanner (GE Healthcare) and the
ImageQuant TL 7 software (GE Healthcare).
Expression and purification of nidovirus RdRps
SARS-CoV nsp12 and EAV nsp9 were purified essentially as
described elsewhere [27,28], but with modifications for nsp9. In
short, E. coli BL21(DE3) with plasmid pDEST14-nsp9-CH was
grown in auto-induction medium ZYM-5052 [47] for 6 hours at
37uC and a further 16 hours at 20uC. After lysis in buffer A
(20 mM HEPES pH 7.4, 200 mM NaCl, 20 mM imidazole, and
0.05% Tween-20) the supernatant was applied to a HisTrap
column (GE Healthcare). Elution was performed with a gradient
of 20–250 mM imidazole in buffer A. The nsp9-containing
fraction was further purified by gel filtration in 20 mM HEPES,
300 mM NaCl and 0.1% Tween-20 on a Superdex 200 column
(GE Healthcare). The fractions containing nsp9-CH were pooled,
dialyzed against 1000 volumes of buffer B (20 mM HEPES,
100 mM NaCl, 1 mM DTT and 50% glycerol) and stored at
220uC. RdRps with a D618A (SARS-CoV) or D445A (EAV)
mutation were obtained by site-directed mutagenesis of the wild-
type (wt) plasmid pDEST14-nsp9-CH [28] with oligonucleotides
59-TACTGCCTTGAAACAGCCCTGGAGAGTTGTGAT-39
and 59-ATCACAACTCTCCAGGGCTGTTTCAAGGCAGTA
-39, and plasmid pASK3-Ub-nsp12-CHis
6
with oligonucleotides
59-CCTTATGGGTTGGGCTTATCCAAAATGTG-39and 59-
CACATTTTGGATAAGCCCAACCCATAAGGA-39, as de-
scribed elsewhere [27]. Mutant proteins were purified parallel to
the wt enzymes.
Figure 8. The effect of Zn
2
+
on SARS-CoV nsp12 template
binding. (A) Electrophoretic mobility shift assay with radiolabeled
dsRNA and nsp12 in the presence and absence of Zn
2+
(indicated above
the lanes). The position of unbound and nsp12-bound RNA in the gel is
marked on the left of the panel. (B) Determination of the nsp12 affinity
for RNA in the presence and absence of Zn
2+
. A fixed amount of RNA
was incubated with an increasing amount of nsp12. This revealed a 3–4
fold reduction in the percentage of bound RNA in the presence of zinc
ions (grey) relative to the percentage of bound RNA in the absence of
zinc ions (black). Error bars represent standard error of the mean (n = 3).
doi:10.1371/journal.ppat.1001176.g008
Zn
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PLoS Pathogens | www.plospathogens.org 8 November 2010 | Volume 6 | Issue 11 | e1001176
RdRp assays with purified enzymes
Standard reaction conditions for the RdRp assay with 0.1 mMof
purified SARS-CoV nsp12 are described elsewhere [27]. To study
the effect of Zn
2+
in this assay, 0.5 ml of a dilution series of
0–80 mM ZnOAc
2
was added to the 5 ml reaction mixture, yielding
final Zn
2+
concentrations of 0–8 mM. The EAV RdRp assay
contained 1 mM nsp9, 1 mM RNA template poly(U)
18
, 0.17 mM
[a-
32
P]ATP (0.5 mCi/ml; Perkin-Elmer), 50 mM ATP, 20 mM Tris-
HCl (pH 8.0), 10 mM NaCl, 10 mM KCl, 1 mM MnCl
2
,4mM
MgOAc
2
, 5% glycerol, 0.1% Triton-X100, 1 mM DTT and 0.5
units RNaseOUT. ZnOAc
2
was added to the reaction to give a final
concentration of 0–6 mM. To chelate Zn
2+
during reactions,
MgEDTA was added to a final concentration of 8 mM. Reactions
were terminated after 1 hour and analyzed as described [27].
SARS-CoV nsp12 electrophoretic mobility shift assay
SARS-CoV RdRp was incubated with 0.2 nM 59
32
P-labeled
SAV557R/SAV481R RNA duplex, for 10 minutes at 30uC either
in presence or absence of 6 mM ZnOAc
2
. Reactions were
analyzed as described previously [27].
Supporting Information
Figure S1 Effect of various divalent cations on the RdRp
activity of SARS-CoV nsp12. Purified recombinant SARS-
CoV nsp12 was incubated with a primed template, ATP, and
[a-
32
P]ATP in the presence of either 6 mM Mg
2+
only (lane 1),
and with increasing concentrations of a second divalent metal
(M
2+
), specifically: 2–6 mM Ca
2+
(lane 2–4), 2–6 mM Co
2+
(lane
5–7), 2–6 mM Zn
2+
(lane 8–10), or 2–6 mM Mn
2+
(lane 11–13).
The strongest inhibition was observed for Zn
2+
. For more details
on the SARS-CoV nsp12 RdRp assay, see the main text.
Found at: doi:10.1371/journal.ppat.1001176.s001 (1.55 MB TIF)
Figure S2 Effect of Zn
2
+
on the dinucleotide extension
activity of EAV nsp9. Purified recombinant EAV nsp9 was
incubated with a U
18
template in the presence of [a-
32
P]ATP,
ATP, 4 mM Mg
2+
, 1 mM Mn
2+
, and 1 mM ApA. (A) Reaction
mixtures were split into two aliquots, one of which was
supplemented with 6 mM Zn
2+
, and samples were taken at the
time points (minutes) indicated above the lanes. In the absence of
Zn
2+
, EAV nsp9 initiates de novo and produces di- and
trinucleotides, indicated with A2 and A3, respectively. A non-
specific band, unrelated to RdRp activity, between A2 and A3 is
indicated with an asterisk. In the presence of 6 mM Zn
2+
, the
synthesis of dinucleotides and trinucleotides was blocked. (B) When
performing the assay described under (A) in the absence of Zn
2+
,a
full-length product of 18 nucleotides is formed. This product is not
observed when the assay is performed in the presence of 6 mM
Zn
2+
, but nsp9 was capable of elongating the provided dinucleotide
primer ApA into tri- (ApA*pA) and tetranucleotide ((ApA*pA*pA)
products (the asterisk indicates radiolabeled phosphates). Due to the
absence of a 59triphosphate group, these reaction products migrate
much slower in the 20% acrylamide and 7 M urea gel used for this
analysis. See the main text for additional experimental details on the
EAV nsp9 RdRp assay.
Found at: doi:10.1371/journal.ppat.1001176.s002 (2.16 MB TIF)
Figure S3 Putative zinc-binding residues in the predict-
ed structure of SARS-CoV nsp12 and comparison with
the structure of the zinc-containing Dengue virus RdRp
domain. (A) Sequence alignment of coronavirus RdRps showing
conservation of four potential zinc-binding residues amino acids
(C799-H810-C813-H816 in SARS-CoV; indicated with asterisks)
in the C-terminal region of coronavirus nsp12. Black shading
indicates complete conservation among coronaviruses. The
coronavirus RdRp sequences were aligned with Muscle 3.6. The
aligned sequences and NCBI accession numbers are the following:
mouse hepatitis virus strain A59 (MHV_A59; NP_068668),
human CoV 229E (HCoV_229E; NP_068668), infectious bron-
chitis virus strain Beaudette (IBV_B; P0C6Y1), bovine coronavirus
(BCoV; NP_742138.1), feline coronavirus (FeCoV; YP_239353.1),
and SARS-CoV strain Frankfurt-1 (SARS_Fr1; AAP33696).
(B) Crystal structure of the Dengue virus RdRp domain showing
the position of four cysteine and histidine residues that form Zn
2+
-binding pocket Zn2, located close to motif E (depicted in red). A
second Zn
2+
-binding pocket (Zn1) and the two zinc ions identified
in the crystal structure are indicated in blue-gray. (C) Predicted
three-dimensional structure model of SARS-CoV nsp12 (Xu et al.,
Nucl. Acids Res. 31: 7117–7130), based on PDB code 1O5S,
rendered with Swiss-PdbViewer 4.01 and POV-Ray 3.6. The
positions of the conserved cysteine and histidine residues indicated
in panel A (C799-H810-C813-H816) close to motif E (depicted in
red) and RdRp active-site residues (D618, D760 and D761) are
indicated. The spatial arrangement of these cysteines and
histidines in this model strikingly resembles the positioning of
the metal ion-coordinating residues of Zn-binding pocket Zn2 in
the Dengue virus RdRp domain (see panel B).
Found at: doi:10.1371/journal.ppat.1001176.s003 (0.86 MB TIF)
Author Contributions
Conceived and designed the experiments: AJWtV SHEvdW EJS MJvH.
Performed the experiments: AJWtV SHEvdW MJvH. Analyzed the data:
AJWtV SHEvdW ACS RSB EJS MJvH. Contributed reagents/materials/
analysis tools: ACS RSB. Wrote the paper: AJWtV EJS MJvH.
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Zn
2+
Inhibits Nidovirus Replication
PLoS Pathogens | www.plospathogens.org 10 November 2010 | Volume 6 | Issue 11 | e1001176
... 6 One of zinc's mechanisms of action is its ability to chelate ions essential for the function of transmembrane proteins. These proteins, responsible for substance transport and maintaining membrane potential, lose their functionality in the presence of zinc, preventing microorganisms from effectively adapting to environmental conditions [12]. In vitro studies have shown that zinc acts as an inhibitor of certain metalloproteins that are important for the metabolic processes of pathogens. ...
... Additionally, zinc disrupts the functions of viral capsids, which are essential for protecting the virus's genetic material and its integration with the host genome. This mechanism has been described in the context of RNA viruses, such as coronaviruses, where zinc supplementation significantly reduced the virus's ability to replicate [12]. ...
... Clinical studies have shown that zinc supplementation combined with vitamins D and C enables more effective support for the treatment of viral infections, shortening the duration of illness 9 and reducing its severity [12]. Patients using such supplementation reported a faster recovery and lower risk of complications [16]. ...
Article
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Introduction Zinc plays a vital role in immune function, enhancing defense mechanisms and reducing infection duration and severity. Purpose of Research:This study aimed to assess the impact of zinc on immune function, its role in preventing and treating infections, particularly in vulnerable populations such as the elderly, and its interactions with vitamins D and C. Additionally, the research explored zinc’s effects on microbial cell membranes, gut microbiome balance, and immune modulation, focusing on age-related immune decline and infection susceptibility. Materials and Methods:The study utilized a comprehensive approach, combining literature reviews, clinical trials, experimental studies, and microbiota analyses to investigate zinc's role in immune function, infection management, and antimicrobial resistance. Results: Zinc was found to modulate the immune system, influencing T lymphocytes, B lymphocytes, macrophages, and natural killer cells. Deficiency weakened immune responses, increasing infection risk. Zinc supplementation, especially with vitamins D and C, improved immune function, shortened infection duration, and alleviated symptoms. Zinc and vitamin D enhanced antimicrobial peptide production and epithelial barrier function, while zinc and vitamin C reduced oxidative stress and enhanced neutrophil activity. Zinc also destabilized microbial membranes, inhibiting bacterial and viral replication, including multi-drug-resistant strains. Furthermore, zinc supplementation improved gut microbiome composition, promoting beneficial bacteria and reducing pathogenic growth. Clinical studies confirmed its effectiveness in reducing respiratory infections, improving vaccine responses, and decreasing complications in vulnerable individuals.
... Zinc supplementation has been a part of a number of therapies, as zinc has been found to have antiviral properties [9]. Furthermore, Barnard et al. as well as Pormohammad et al. showed that increased intracellular zinc concentrations decrease SARS-CoV-2 replication [10][11][12]. ...
Article
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The exact role of zinc in COVID-19-infected patients is not well understood. We examined the effects and outcomes of zinc deficiency on COVID-19-infected patients. We focused on patient outcomes: severity, symptomatology, and mortality. The meta-analysis was performed to examine whether COVID-19-infected individuals suffered greater symptomology and mortality. Secondary outcomes explored included severity and hospital length of stay. For mortality, we found that COVID-19-infected individuals with zinc deficiency had a greater risk of mortality than individuals without zinc deficiency (risk ratio (RR)=5.77; 95% confidence interval (CI): 3.48, 9.54; p=0.004). For symptomology, we found that COVID-19-infected individuals with zinc deficiency had a greater risk of symptomatology than individuals without a zinc deficiency (RR=1.39; 95% CI: 1.13, 1.70; p=0.020). Zinc-deficient individuals are at a greater risk for mortality and symptomatology. Our findings further reinforce the importance of supplementation as a prophylactic agent against viral infections such as COVID-19.
... It has also been documented that zinc, along with pyrithione, inhibited the viral replication in the COVID-19 infections. Zinc efficiently subdued the multi-protein replication of RNA viruses and SARS-CoV RdRp elongation, resulting in the reduction of template binding [35]. It is also documented that the incinerated zinc nanoparticle compound, i.e., Yashada bhasma, which is a component of the Svarnvir tablet, has a mean particle size in the range of 49-80 nm [16]. ...
Article
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Aim Traditional Ayurvedic herbo-mineral medicines have proven their potential in managing COVID-19. Cell-based assays of the Svarnvir-IV tablet demonstrated the virucidal activity against SARS-CoV-2 and its therapeutic action, along with safety in cytotoxicity, has been proved. In the present study, in vivo, safety profile and compositional analysis of the Svarnvir-IV tablet were performed. Methods The safety and potency of the Svarnvir tablet were evaluated comprehensively through in vivo drug screening on Drosophila, along with elemental composition analysis of Svarnvir tablets using atomic absorption spectroscopy (AAS), inductively coupled plasma-mass spectroscopy (ICP-MS), X-ray diffraction (XRD), and scanning electron microscopy energy dispersive spectroscopy (SEM-EDS). Results The Svarnvir tablet was found safe in Drosophila and their larvae up to the dosage of 1 mg/ml. In comparison to the control, morphologically and physiologically healthy and active flies were observed without any change in circadian locomotor activity rhythms or activity patterns. In addition, the elemental composition of Svarnvir tablets was evaluated using AAS, ICP-MS, and SEM-EDS, and the microstructure was examined by means of XRD and SEM. Conclusions Overall, these findings will contribute to an accessible and safe therapeutic approach for traditional age-old Ayurvedic medication to combat SARS-CoV-2 variants.
... Specifically, manganese activates antiviral innate immunity via the cGAS-STING pathway against DNA virus infection (38). Zinc restricts coronavirus replication and arterivirus RNA polymerase activity (39) and was even used as a drug for asymptomatic or mild coronavirus disease 2019 infection in a randomized controlled trial (40). Furthermore, silver nanoparticles were also indicated to be antiviral materials against nonenveloped and enveloped viruses (41). ...
Article
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Swine enteric coronaviruses pose a significant challenge to the global pig industry, inflicting severe diarrhea and high mortality rates among piglets, and resulting in substantial economic losses. In our clinical practice, we observed that the addition of potassium molybdate (PM) to the feed could dramatically reduce diarrhea and diarrhea-related mortality in piglets. However, the underlying mechanisms remain elusive and merit further investigation. In this study, we revealed that PM effectively inhibited the infection of both aminopeptidase N (APN)-dependent coronaviruses, transmissible gastroenteritis virus (TGEV), and porcine respiratory coronavirus (PRCV), both in vitro and ex vivo. Specifically, PM was found to block TGEV and PRCV penetration by degrading the cell receptor APN through the upregulation of phosphatidylinositol 3-kinase catalytic subunit type 3 (PIK3C3) expression. In addition, knockdown and knockout of PIK3C3 resulted in the attenuation of PM-induced autophagy, thereby rescuing APN expression and viral infection. Correspondingly, replenishment of PIK3C3 in PIK3C3-null ST cells restored PM-mediated APN degradation and successfully blocked viral entry. Furthermore, our findings demonstrated that PM promoted the assembly of the PIK3C3-BECN1-ATG14 complex, leading to induced autophagic degradation by upregulating PIK3C3 Ser249 phosphorylation. In vivo experiments further confirmed that PM-induced PIK3C3-mediated autophagic degradation of APN, thereby limiting the pathogenicity of TGEV. In summary, our study for the first time identified the mechanism by which PM blocked TGEV and PRCV internalization by degrading the cell receptor APN via PIK3C3-mediated autophagy. This study provides valuable insights and potential strategies for preventing APN-restricted coronavirus infection. IMPORTANCE Aminopeptidase N (APN) is one of the most important host receptors of coronavirus. Modulating APN expression can represent a novel approach for controlling APN-dependent coronaviruses and their variants infection. Here we found that a chemical compound potassium molybdate (PM) negatively regulates APN expression by inducing phosphatidylinositol 3-kinase catalytic subunit type 3 (PIK3C3)-mediated autophagy against APN-dependent coronavirus internalization, including transmissible gastroenteritis virus (TGEV) and porcine respiratory coronavirus (PRCV). Furthermore, PM can promote PIK3C3-BECN1-ATG14 complex assembly to induce autophagic degradation of APN by upregulating PIK3C3 Ser249 phosphorylation. Lastly, results from pig experiments also confirmed that PM can trigger PIK3C3-mediated autophagic degradation of APN to restrict TGEV pathogenicity in vivo without toxicity. Our findings underscore the promising potential of PM as an effective agent against APN-dependent coronavirus and potentially emerging viral disease entry.
... Zn also decreases the activity of ACE2, preventing the attachment of COVID-19 to the host's cells [74]. In an in vitro study, Zn salts reduced Hepatitis C virus (HCV) replication in E. coli by 50% by impairing the HCV RNA polymerase [75]. In addition, Zn supplementation (50 mg/day) for three months prevents COVID-19 complications in cancer patients [76]. ...
Article
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There is currently no particular cure for coronavirus disease-19 (COVID-19). However, studies suggest that certain medicinal plants, fruits, and vegetables possess bioactive substances capable of ameliorating the disease. This review aims to articulate fruits, vegetables, and medicinal plants that have anti-coronavirus properties. Relevant articles were collected from reputable academic repositories, namely SpringerLink, PubMed, Google Scholar, and Scopus. Available information shows that alkaline-rich fruits and vegetables, such as mango, cabbage, lemon, onion, okra, carrot, cucumber, pepper, spinach, and avocado, have anti-coronavirus properties. The mentioned fruits and vegetables stimulate an unfavorable pH for the replication of the virus and normalize the acid-base imbalance induced in the lungs and kidneys of the infected. Fruits and vegetables also contain health-boosting substances such as proteins, amino acids, glycosides, vitamins, and minerals. Medicinal plants, including Clitoria ternatea L., Vitex trifolia L., Sphaeranthus indicus L., Clerodendrum inerme L. Gaertn., Glycyrrhiza glabra L., Strobilanthes cusia (Nees) Kuntze, Vitis vinifera var. aestivalis (Michx.) Kuntze, Hyoscyamus niger L., and Cedrela Sinensis Juss., also possess anti-coronavirus properties. Clitoria ternatea and Cedrela sinensis reduce the virus’s replication by shredding its receptor, called the angiotensin-converting enzyme 2 (ACE2). Vitex trifolia and Sphaeranthus indicus prevent hyper-inflammatory responses and cytokine storms. Glycyrrhiza glabra induces nitrous oxide synthase and blocks the virus’s replication. Clerodendrum inerme and Strobilanthes cusia inhibit the virus’s ribosome and protein translation. Vitis vinifera represses nucleocapsid protein and lowers apoptosis. Hyoscyamus niger inhibits Ca2+ channels and lessens breathing difficulties induced by the coronavirus. Thus, dietary supplements and drugs formulated with these medicinal plants, fruits, and vegetables may lessen the effects of COVID-19.
... Evidence indicates that Zn2+ treatment leads to a decrease in ACE2 activity in rat lungs. Additionally, in vitro studies show that Zn2+ ions can inhibit SARS-coronavirus RNA polymerase, thereby suppressing viral replication (Te Velthuis et al., 2010), as summarized in Table 2. Vit: C Boosts interferon-alpha production, modulates cytokines, reduces inflammation, improves endothelial function, and acts as an antioxidant, with potential therapeutic use in COVID-19. Vit: D Enhances immune cell growth and maturity, modulates immune responses, and is linked to reduced severity of COVID-19 infections through its immunomodulatory effects. ...
Chapter
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Amidst the relentless battle against Coronaviridae, vaccines stand as our beacon of hope, illuminating a path towards an eventual triumph over the pandemic. Through tireless collaboration and scientific ingenuity, researchers have forged ahead, developing a diverse array of vaccines to combat COVID-19 and its variants. Yet, alongside these remarkable achievements, formidable challenges persist. Vaccine hesitancy, fueled by misinformation and cultural complexities, threatens to impede progress, underscoring the need for comprehensive strategies to foster trust and understanding. Moreover, the imperative of global cooperation looms large, demanding equitable vaccine distribution to ensure that no community is left behind in our shared pursuit of health and resilience. As we navigate these uncharted waters, let us draw inspiration from the resilience and compassion that define our collective humanity, forging ahead with determination and unity to overcome this unprecedented crisis.
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With the onset of the COVID-19 pandemic, coupled with the low availability of medicines and vaccines with proven efficacy, there was a growing impact on public health, followed by inconsistencies from both an economic and social perspective, due to the declaration of the "State of Emergency" and the adoption of strict sanitary control measures, which also contributed to the progression of food insecurity. In this context, the search for natural methods for the prevention and control of symptoms gained prominence, with functional foods and bee products being highlighted due to their bioactive compounds, which are capable of modulating metabolic processes and acting as antioxidants, anti-inflammatories, anti-infectives, and antivirals. The aim of this study was to review natural strategies with antiviral and anti-COVID properties across various databases. A comprehensive review of functional foods, bee products, and biotechnology was conducted in scientific article and patent databases, with no time constraints. Among the findings, several functional foods, natural products, and bee products exhibited significant antiviral, anti-inflammatory, and immunomodulatory activities against coronaviruses, highlighting the critical role of food in human health. Additionally, these findings represent a promising strategy for the food industry in the development of biopreservatives, functional foods, and organic products for both human and animal health.
Article
Context: The problem of correcting immune system function and compensating for co-morbidities becomes particularly clinically significant in the post-COVID period. There is evidence that certain trace elements in the human body, particularly zinc ions, play a critical role in restoring the function of the immune system and internal organs. Objective: To analyze the mechanisms of zinc action maintaining the body homeostasis in order to justify pathogenetically the inclusion of zinc drugs in the therapy of patients in the post-COVID period. Methods: Data from Elsevier, Global Health, PubMed-NCBI, Embase, MEDLINE, Scopus, Research gate, RSCI Scopus, Cochrane Library, Google Academy, e-LIBRARY.RU and CyberLeninka were used. Results: This review showed that the importance of zinc in maintaining body homeostasis in the post-COVID period is determined by its multifaceted effect on all parts of the immune system, its anti-inflammatory activity, antimicrobial properties and participation in the restoration of internal organ function. Elimination of zinc deficiency in the post-COVID period is essential to support immunity, compensate for comorbidities and reduce the risk of complications. The impossibility of synthesizing zinc in the body requires its constant intake in sufficient quantities. Zinc levels are significantly reduced after infectious diseases, as this element is specifically distributed to organs and tissues to maintain immunological and metabolic functions. The degree of zinc deficiency is associated with the severity of COVID-19 and the post-COVID period. It is pathogenetically justified to prescribe zinc drugs in the post-COVID period, the choice of which should take into account comorbidities and severity of hypozincemia. Conclusion: Regularly administered therapy with zinc drugs in the post-COVID period will help correct the population immunity and restore public health.
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An RNA-dependent RNA polymerase (RdRp) is the central catalytic subunit of the RNA-synthesizing machinery of all positive-strand RNA viruses. Usually, RdRp domains are readily identifiable by comparative sequence analysis, but biochemical confirmation and characterization can be hampered by intrinsic protein properties and technical complications. It is presumed that replication and transcription of the ∼30-kb severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) RNA genome are catalyzed by an RdRp domain in the C-terminal part of nonstructural protein 12 (nsp12), one of 16 replicase subunits. However, thus far full-length nsp12 has proven refractory to expression in bacterial systems, which has hindered both the biochemical characterization of coronavirus RNA synthesis and RdRp-targeted antiviral drug design. Here, we describe a combined strategy involving bacterial expression of an nsp12 fusion protein and its in vivo cleavage to generate and purify stable SARS-CoV nsp12 (106 kDa) with a natural N-terminus and C-terminal hexahistidine tag. This recombinant protein possesses robust in vitro RdRp activity, as well as a significant DNA-dependent activity that may facilitate future inhibitor studies. The SARS-CoV nsp12 is primer dependent on both homo- and heteropolymeric templates, supporting the likeliness of a close enzymatic collaboration with the intriguing RNA primase activity that was recently proposed for coronavirus nsp8.
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