Potential natural compounds for preventing SARS-CoV-2 (2019-nCoV) infection

Abstract

SARS-CoV-2 (2019-nCoV), a novel coronavirus, caused the pneumonia outbreak in China and continue to expand. The host receptor for 2019-nCoV Angiotensin-converting enzyme 2 (ACE2), is the same as the host receptor for SARS-CoV. Targeting ACE2 holds the promise for preventing and inhibiting 2019-nCoV infection. Chinese Medicine herbs could be a valuable pool for identifying active compounds for treating infection of 2019-nCoV. In this study, we summarize several active compounds including baicalin, Scutellarin, Hesperetin, Nicotianamine and glycyrrhizin that could have potential anti-2019-nCoV effects. We conduct molecular docking to predict their capacity for binding ACE2, which may prevent the 2019-nCoV infection. We propose that these selected compounds worth further investigation for preventing 2019-nCoV.

Full text

Potential natural compounds for preventing SARS-CoV-2 (2019-nCoV) infection
Hansen Chen 1 *, Qiaohui Du 2*
1. Department of Neurosurgery, School of Medicine, Stanford University
2. School of Chinese Medicine, The University of Hong Kong
*These two authors contributed equally to this study
Corresponding:
Dr. Hansen Chen: chenhs@stanford.edu
Or Mr. Qiaohui Du: elvisdu@hku.hk
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© 2020 by the author(s). Distributed under a Creative Commons CC BY license.
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© 2020 by the author(s). Distributed under a Creative Commons CC BY license.

Abstract
SARS-CoV-2 (2019-nCoV), a novel coronavirus, caused the pneumonia outbreak in
China and continue to expand. The host receptor for 2019-nCoV Angiotensin-
converting enzyme 2 (ACE2), is the same as the host receptor for SARS-CoV.
Targeting ACE2 holds the promise for preventing and inhibiting 2019-nCoV
infection. Chinese Medicine herbs could be a valuable pool for identifying active
compounds for treating infection of 2019-nCoV. In this study, we summarize
several active compounds, including baicalin, Scutellarin, Hesperetin,
Nicotianamine and glycyrrhizin that could have potential anti-2019-nCoV effects.
We conduct molecular docking to predict their capacity for binding ACE2, which
may prevent the 2019-nCoV infection. We propose that these selected compounds
worth further investigation for preventing 2019-nCoV.
Keywords: SARS-CoV-2 (2019-nCoV), Baicalin, Scutellarin, Hesperetin,
Nicotianamine, Glycyrrhizin
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Introduction
SARS-CoV-2 (2019-nCoV), a novel coronavirus, caused the pneumonia outbreak in
Wuhan city, Hubei Province, China and subsequently expands. The original
pneumonia cases were linked to a large seafood and animal market in Wuhan. This
is an emerging, rapidly evolving situation. One genome sequence (WH-Human_1)
of the 2019-nCoV was first released on Jan 10, 2020, and subsequently, five
additional Wuhan CoV genome sequences were released (Zhang, 2020; Shu and
McCauley, 2017). By comparing to the genomes of SARS-CoV and MERS-CoV, the
WH-human_1 genome has a better sequence homology toward the genomes of
SARS-CoV than that of MERS-CoV. By using structural modeling of its S-protein,
scientists suggest a strong interaction of human ACE2 molecules with 2019-nCoV
(Xu et al. 2020). ACE2 is a type I integral membrane protein, with its active site
domain exposed to the extracellular surface of cells. ACE2 has been demonstrated
to be a functional receptor for the SARS-coronavirus (CoV) (Kuhn et al., 2006).
Michael Letko et al. showed that the 2019-nCoV receptor-binding domain (RBD)
was capable of entering cells expressing human ACE2, but not any of the other
receptors, further confirming that human ACE2 is the receptor for the recently
emerging 2019-nCoV (Letko & Munster, 2020). As the host cell receptor is critical
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for the virus entry, targeting ACE2 holds the promise for preventing infection of
2019-nCoV infection.
The extracellular region of human ACE2 enzyme is composed of two domains, one
is zinc metallopeptidase domain and the other is C terminus. Zinc metallopeptidase
domain consists of ~42% residues (residues 19-611). While C terminus has ~48% to
human collectrin (residues 612-740) (Zhang, 2001 ). The metallopeptidase domain
divides into two subdomains. The residue from 19-102, 290-397, 417-430 are
composed of first subdomain. The other is consists of residue from 103-289, 398-
416, 431-615. One prominent α-helix connects the two subdomains and forms part
of the floor of the canyon. The main secondary structure of ACE2 is α-helical
segments, which is make up ~62% of metallopeptidase domain. Only six β-structure
segments in the ACE2. The zinc-binding site is located near the bottom and on one
side of the large active site cleft (subdomain I side), nearly midway along its length.
The zinc is coordinated by His374, His378, Glu402, and one water molecule. Proline and
leucine are two residues that preferred the P1 position with a partiality for
hydrophobic residues in P1’ position. Regarding to the hydropathy of ACE2, the side
chain of Phe274, Pro346, Thr371, Met360 and disulfide linkage of Cys344 and Cys361
provided a hydrophobic environment. The bioactive compound and functional
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peptide might interfere with viral spike protein binding to ACE2 through binding to
ACE2 active site and making large conformational change.
The development of drugs for targeting ACE2 and treating 2019-nCoV could be
time-consuming, and the safety of newly-developed drugs could be a major
concern, which needs time for testing. Therefore, it seems unrealistic to synthesize
new drugs and tests for safety and toxicity within such a limited time when the
infection is growing fast. Traditional Chinese Medicine has been practiced in China
for thousands of years, and Chinese medicine licorice was suggested to be
promising for treating SARS (Pilcher, 2003). Considering the low toxicity and
availability, screening active compounds from Chinese herbal medicine for
targeting the ACE2 receptor could be a potential strategy for treating 2019-nCoV.
In this mini-review, we summarize the potential natural compounds that could
target ACE2 for the potential treatment of 2019-nCoV. By using molecular docking,
we proposed that the five natural compounds, including baicalin, Scutellarin,
Hesperetin, glycyrrhizin and Nicotianamine (Figure 1) are potential compounds
that target the ACE2 receptor and exert anti-virus effects for preventing 2019-nCoV
infection.
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Figure 1, Chemical structure of baicalin, Scutellarin, Hesperetin, glycyrrhizin and
Nicotianamine.
Natural compounds candidates for 2019-nCoV treatment
In the following session, we will summarize these five natural compounds that may
have therapeutic effects against 2019-nCoV infection. To generate putative binding
poses, we used the AutoDock Vina software package with the default scoring
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function (Trott O, Olson AJ, 2010). In the AutoDock Vina configuration files, the
parameter num_modes was set to 1000 and exhaustiveness to 100. We identified
the receptor-binding pocket based on the structures of ACE2 proteins. We chose
all the rotatable bonds in ligands to be flexible during the docking procedure, and
we kept all the protein residues inside the binding pockets rigid. We assigned the
Gasteiger atomic partial charges and converted all receptors and ligands to the
PDBQT format using the AutoDockTools package. We did not use explicit hydrogens
either for the receptors or for the ligands.
Baicalin
Baicalin is extracted and purified from the Chinese medicinal plant Scutellaria
baicalensis Georgi (Chinese name: Huang Qin). Baicalin has broad therapeutic
effects, including anti-oxidative stress, anti-inflammation, anti-apoptosis (Chen et
al., 2017; Ishfaq et al., 2019). Scientists have been shown baicalin’s antiviral
activities for SARS coronavirus using the foetal rhesus kidney-4 (fRhK-4) cell line,
with an EC50 12.5 ug/ml at 48 hours, and selectivity index more 4 to 8 (Chen et al.,
2004). The plaque reduction assay showed that baicalin has an EC 50 of 11ug/ml
(Chen et al., 2004). Those results suggest that baicalin has anti-SARS effects. Since
the 2019-nCoV shared similarity with the SARS virus, we suspect that baicalin may
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also show anti-virus effects on 2019-nCoV. In addition, a study showed that baicalin
could inhibit ACE, with an IC50 value of 2.24 mM in vitro (Deng et al., 2012).
However, whether baicalin can bind to ACE2 is not yet studied. Therefore, we use
the molecular docking to test the possibility of baicalin binding to the ACE2
receptor, which may subsequently block the entry of 2019-nCoV. The docking
result shows that baicalin may have strong binding to the ACE2 enzyme (Figure 2),
with an estimated ΔG (kcal/mol) -8.46. , and the potential binding site at ASN-149,
ARG-273, HIS-505. The binding site is located on the hydrophobic region of ACE2.
Based on the anti-SARS activity and its potential binding to ACE2, we suggest that
baicalin is one of the potential candidates for 2019-nCoV treatment. Given the low
toxicity of baicalin, its efficacy on anti-2019nCoV worth further investigation.
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Figure 2, molecular docking result of baicalin to ACE2 enzyme.
Scutellarin
Scutellarin is another active compound from Chinese Medicine Erigeron
breviscapus (Vant.) Hand Mazz, which showed broad pharmacological effects,
including anti-oxidant, anti-inflammation, vascular relaxation, anti-platelet, anti-
coagulation (Wang and Ma, 2018). A study showed that scutellarin treatment could
reduce the expression and activity of ACE in brain tissue in vivo (Wang et al., 2016).
The IC50 value of scutellarin against ACE was 48.13 ± 4.98 μM (Wang et al., 2016).
However, whether scutellarin could inhibit ACE2 is not yet reported. Here we
conduct a molecular docking and find that scutellarin has the potential to bind to
ACE2, with estimated ΔG (kcal/mol) -14.9, with binding site GLU-495, UNK-957,
ARG-482 (Figure 3). Therefore, it’s worthwhile to test whether scutellarin could
inhibit ACE2 and block the infection of 2019-nCoV.
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Figure 3, molecular docking result of Scutellarin to ACE2 enzyme.
Hesperetin
Hesperetin is a bioflavonoid compound abundant in Chinese Medicine citrus
aurantium and Citri Reticulatae Pericarpium. Hesperetin dose-dependently
inhibited cleavage activity of the 3C-like protease (3CLpro) of SARS-coronavirus in
cell-free and cell-based assays, with an IC50 8.3 uM (Lin et al., 2005). Whether
Hesperetin could inhibit 2019-nCoV replication is not yet investigated. To
understand whether Hesperetin has the potential to inhibit ACE2, we conduct the
molecular docking of Hesperetin to the ACE2 enzyme. The results showed that
Hesperetin has the potential biding to ACE2 with an estimated ΔG (kcal/mol) -8.3,
with binding cites TYR-613, SER-611, ARG-482, GLU-479 (Figure 3). This result
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suggests that Hesperetin may bind to ACE2, therefore, block the infection of 2019-
nCoV.
Figure 4, molecular docking result of Hesperetin to ACE2 enzyme.
Nicotianamine
Nicotianamine is rich in soybean (Takenaka, 2009). Toshihiro et al. reported that
nicotianamine is a potent inhibitor of ACE2, with an IC50 value of 84 nM. The authors
screened ACE2 inhibitors from various foodstuffs and found that soybean
contained vigorous ACE2 inhibitory activity. They isolated the active compound
“soybean ACE2 inhibitor” (ACE2iSB), which was identical to nicotianamine by direct
comparison with a standard compound. We conducted the molecular docking of
Nicotianamine to the ACE2 enzyme, and the results showed that Nicotianamine has
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the potential biding to ACE2 with an estimated ΔG (kcal/mol) -5.1, with binding
cites ARG-518, GLU-406, SER-409, GLN-522, GLN-442 (Figure 4). Of which, ARG-518
is a residue located in the α-helix that might contribute to the conformational
change of ACE2. Since ACE2 is critical for the 2019-nCoV infection, we hypothesize
that nicotianamine may block the infection of 2019-nCoV through inhibiting ACE2,
which needs further investigation.
Figure 5, molecular docking result of Nicotianamine to ACE2 enzyme.
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Glycyrrhizin
Glycyrrhizin is another plant product isolated from Chinese Medicine herb licorice
root (Glycyrrhiza radix), a herb that is promising for SARS treatment (Pilcher, 2003).
Glycyrrhizin is used for treating chronic hepatitis and is relatively non-toxic. In vitro
study showed that glycyrrhizin has anti-SARS-CoV effects. It inhibited viral
adsorption and penetration and was most effective when administered both during
and after the viral adsorption period (Cinatl et al., 2003). Chemical modifications
increased the antiviral potency of glycyrrhizin, but also increased the cytotoxicity.
Thus the selectivity index was reduced as compared with that of glycyrrhizin
(selectivity index: ≥65) (Hoever et al., 2005). Whether glycyrrhizin has anti-2019-
nCoV effects need further investigation. Our docking results showed that
glycyrrhizin has the potential biding to ACE2 with an estimated ΔG (kcal/mol) - 9,
with the binding cites ARG-559, GLN-388, ARG-393, ASP-30 (Figure 5). Based on the
hydropathy of ACE2, the predict binding site of glycyrrhizin is located near the
hydrophobic site. GLN-388 and ARG-393 are close to the zinc metallopeptidase that
might regulate the activity of ACE2 in cells. Given the low toxicity of glycyrrhizin, its
anti-virus effects on SARS and its potential interaction with ACE2, it’s worthwhile
to test its efficacy against 2019-nCoV infection.
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Figure 6, molecular docking result of glycyrrhizin to ACE2 enzyme.
Summary
Drug development for treating 2019-nCoV is timely important due to its rapid
expansion. Vaccine development could take a long time to complete, and its safety
needs to be verified. Synthesized agents for blocking ACE2 also needs to test its
toxicity. Chinese Medicine is applied for anti-virus treatment for a long time, and
active compounds from Chinese Medicine may be applied for the 2019-nCoV. Due
to the low toxicity and availability of some active compounds from Chinese
Medicine, it is worthwhile to select potential candidates for 2019-nCoV treatment.
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Since 2019-nCoV share some common sequence with SARS-CoV, and used the
same host receptor ACE2, we review the potential active compounds for anti-SARS-
CoV, and at the same time, predict the binding affinity of those compounds to bind
ACE2. In this study, by using the molecular docking and reviewing the literature, we
propose for the first time that baicalin, Scutellarin, Hesperetin, Nicotianamine,
glycyrrhizin has the potential to bind to ACE2 and block the entry of 2019-nCoV.
Further studies are needed to verify our results and test the anti-2019-CoV effects
of these compounds.
Notes
Dr. Hansen Chen is a Postdoctoral Fellow in Department of Neurosurgery, School
of Medicine, Stanford University.
Mr. Qiaohui Du is a Ph.D. student in School of Chinese Medicine, The University of
Hong Kong
Funding
The authors did not receive grants for this study
Acknowledgment
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We thank Dr. Xingmiao Chen (From Shanghai, China) for her support and
suggestions
Conflict of interest
None
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