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Review
Advances in the development of therapeutic strategies against COVID-19
and perspectives in the drug design for emerging SARS-CoV-2 variants
Jialing Yin
a,1
, Chengcheng Li
a,1
, Chunhong Ye
a
, Zhihui Ruan
a,b
, Yicong Liang
a
, Yongkui Li
a
, Jianguo Wu
a,b,
⇑
,
Zhen Luo
a,b,
⇑
a
Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, PR China
b
Foshan Institute of Medical Microbiology, Foshan 528315, PR China
article info
Article history:
Received 10 November 2021
Received in revised form 18 January 2022
Accepted 27 January 2022
Available online 31 January 2022
Keywords:
SARS-CoV-2
COVID-19 pandemic
Therapeutic strategies
Drug target
SARS-CoV-2 variants
abstract
Since Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was identified in late 2019, the
coronavirus disease 2019 (COVID-19) pandemic has challenged public health around the world.
Currently, there is an urgent need to explore antiviral therapeutic targets and effective clinical drugs.
In this study, we systematically summarized two main therapeutic strategies against COVID-19, namely
drugs targeting the SARS-CoV-2 life cycle and SARS-CoV-2-induced inflammation in host cells. The devel-
opment of above two strategies is implemented by repurposing drugs and exploring potential targets. A
comprehensive summary of promising drugs, especially cytokine inhibitors, and traditional Chinese med-
icine (TCM), provides recommendations for clinicians as evidence-based medicine in the actual clinical
COVID-19 treatment. Considering the emerging SARS-CoV-2 variants greatly impact the effectiveness
of drugs and vaccines, we reviewed the appearance and details of SARS-CoV-2 variants for further per-
spectives in drug design, which brings updating clues to develop therapeutical agents against the vari-
ants. Based on this, the development of broadly antiviral drugs, combined with immunomodulatory, or
holistic therapy in the host, is prior to being considered for therapeutic interventions on mutant strains
of SARS-CoV-2. Therefore, it is highly acclaimed the requirements of the concerted efforts from multi-
disciplinary basic studies and clinical trials, which improves the accurate treatment of COVID-19 and
optimizes the contingency measures to emerging SARS-CoV-2 variants.
Ó2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and
Structural Biotechnology. This is an open access article under the CC BY-NC-ND license (http://creative-
commons.org/licenses/by-nc-nd/4.0/).
Contents
1. Introduction . . . ...................................................................................................... 825
2. The structure of SARS-CoV-2 . . . . . . . . . ................................................................................... 825
3. Life cycle of SARS-CoV-2 . . . . . . . . . . . . ................................................................................... 825
4. Drugs targeting the SARS-CoV-2 life cycle . . . . . . . . . . . . . . . . . ................................................................ 827
4.1. Anti-viral entry . . . . . . . . ....... .................................................................................. 827
4.1.1. Inhibition of key enzymes in the binding process . . . ........................................................... 827
4.1.2. Competitive binding to ACE2 and SARS-CoV-2 S protein. . . . . . . . . . . . . . . . . ........................................ 828
4.2. Viral protease inhibitors . ....... .................................................................................. 828
https://doi.org/10.1016/j.csbj.2022.01.026
2001-0370/Ó2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
Abbreviations: SARS-CoV-2, Severe Acute Respiratory Syndrome Coronavirus 2; COVID-19, coronavirus disease 2019; ACE2, Angiotensin-converting enzyme 2; RBD,
receptor-binding domain; CTD, C-terminal domain; NTD, N-terminal domain; RdRp, RNA dependent RNA polymerase; ERGIC, endoplasmic reticulum-Golgi intermediate
compartment; ARDS, acute respiratory distress syndrome; CRS, cytokine release syndrome; MODS, multiple organ dysfunction syndrome; mAb, monoclonal antibody; Nbs,
nanobodies; JAK, Janus kinase; STAT, Signal Transducer and Activator of Transcription; TCZ, Tocilizumab;
a
1AT, alpha-1 antitrypsin; CEP, Cepharanthine; TCM, traditional
Chinese medicine; EMA, European Medicines Agency; FDA, U.S. Food and Drug Administration; NMPA, National Medical Products Administration; VOI, variants of interest;
VOC, variants of concern; VUM, variants under monitoring.
⇑
Corresponding authors at: Guangdong Provincial Key Laboratory of Virology, Institute of Medical Microbiology, Jinan University, Guangzhou 510632, PR China.
E-mail addresses: jwu898@jnu.edu.cn (J. Wu), zhluo18@jnu.edu.cn (Z. Luo).
1
Jialing Yin and Chengcheng Li contributed equally to the work.
Computational and Structural Biotechnology Journal 20 (2022) 824–837
journal homepage: www.elsevier.com/locate/csbj
4.3. Anti-viral RNA polymerase . . . . . . . . . . . . . . . ......................................................... ................ 829
4.4. Anti-viral release . . . . . . . ....... .................................................................................. 829
5. Drugs targeting SARS-CoV-2-induced inflammation in host cells . . . . . . . . . . . . . . . . . . ............................................. 829
5.1. Cytokine inhibitors . . . . . ....... .................................................................................. 829
5.2. Signaling pathway inhibitors . . . . . . . . . . . . . ......................................................................... 830
5.3. Steroids treatment. . . . . . ......................................................................................... 830
5.4. Holistic therapy and traditional Chinese medicine treatment . . . . . . .......... ............................................ 831
6. Emerging SARS-CoV-2 variants . . . . . . . ................................................................................... 832
6.1. Mutations in structural proteins . . . . . . . . . . ................................ ......................................... 832
6.2. Mutations in non-structural proteins. . . . . . . .... ..................................................................... 832
7. Perspectives in the drug design for SARS-CoV-2 variants . . . . . ................................................................ 833
8. Discussion. . . . . ...................................................................................................... 833
CRediT authorship contribution statement . . . . . . . . . . . . . . . . . . ................................................................ 833
Declaration of Competing Interest . . . . ................................................................................... 833
Acknowledgements . . . . . . . . . . . . . . . . ................................................................................... 833
References . . . . ...................................................................................................... 833
1. Introduction
The new coronavirus, namely 2019-nCoV, was first identified on
December 31, 2019. Due to being highly homologous to Severe
Acute Respiratory Syndrome Coronavirus (SARS-CoV), 2019-nCoV
was listed as Severe Acute Respiratory Syndrome Coronavirus 2
(SARS-CoV-2) by the International Commission for Classification
of Viruses (ICTV) on February 11, 2020 [1]. Among seven coron-
aviruses infecting humans, three coronaviruses can cause serious
diseases, including severe acute respiratory syndrome coronavirus
(SARS-CoV) emerging in 2003, Middle East respiratory syndrome
coronavirus (MERS-CoV) in 2012, and Severe Acute Respiratory
Syndrome Coronavirus 2 (SARS-CoV-2) in 2019 [2].
The outbreak of SARS-CoV-2 causes an acute respiratory disease
called coronavirus disease 2019 (COVID-19) and leads to a severe
epidemic worldwide. Typical symptoms of COVID-19 include fever,
sore throat, fatigue, cough, and difficulty breathing [3,4]. Some of
the clinical symptoms are similar to those of respiratory infections
and cannot be accurately diagnosed. The approach to quickly diag-
nose and develop related drugs and vaccines has become a top pri-
ority. At present, the WHO has approved the use of a variety of
vaccines [5]. As of January 9, 2022, the cumulative number of
reported cases worldwide has exceeded 304 million, and the
cumulative death toll has been more than 5.4 million [6]. As of Jan-
uary 13, 2022, a total of 9.2 billion doses of vaccine have been
administrated globally (Fig. 1).
Till now, there have been candidate drugs in COVID-19 treat-
ment at different stages and levels available for selection and fur-
ther research and development (Table 1). These small-molecule
drugs can exert therapeutic effects against COVID-19 by prevent-
ing SARS-CoV-2 from entering cells, inhibiting viral proteases or
RNA-dependent RNA polymerase activities, reducing virus-
induced inflammation, and balancing immunomodulatory effect
in host [7,8]. Fortunately, some antiviral drugs have been used
in clinical practice and play certain roles in the treatment of
COVID-19 patients, such as Remdesivir and Molnupinavir [9–11].
Currently, hundreds of clinical trials of COVID-19 drugs are under-
way to obtain satisfactory clinical results [12]. A large number of
promising clinical trials will determine which drugs or vaccines
are suitable for the treatment or prevention of COVID-19 (Table 2).
The effective medicine is expected to be approved for COVID-19
treatment, however, due to the rapid mutation of SARS-CoV-2 gen-
ome, the present drugs or vaccines may lose their control on SARS-
CoV-2 spread with the increased infectivity [13,14]. The emerging
SARS-CoV-2 variants bring severe challenges to COVID-19 surveil-
lance and control. In this review, we systematically summarized
the advances in the therapeutic strategies against COVID-19 tar-
geting the structure of SARS-CoV-2 in viral life cycle and immune
response in virus-host interaction. More importantly, we presented
the details and clues of SARS-CoV-2 variants for further perspec-
tives in drug design, which inspires follow-up researchers to
develop therapeutic agents against pandemic COVID-19 and
emerging SARS-CoV-2 variants.
2. The structure of SARS-CoV-2
SARS-CoV-2 is a kind of enveloped virus at a diameter ranging
from 80 to 220 nm with a positive single-stranded RNA inside its
shell, belonging to the b-CoV class of human coronaviruses [2].
The entire SARS-CoV-2 particle is mainly composed of 4 structural
proteins, a fragile lipid envelop, and genomic RNA. The four struc-
tural proteins are the membrane (M), nucleocapsid (N), envelop
(E), and spike (S) protein (Fig. 2A).
The M protein plays a central role in virus assembly. Its pres-
ence enables viruses and host factors to gather on the cell mem-
brane to form progeny virus particles [15]. The complex formed
by N protein and genomic RNA plays an important role in viral
transcription and assembly. The N protein is divided into N-
terminal domain, C-terminal domain, and disordered central
domain (NTD, CTD, and RNA binding domain) [16]. The E protein
is a small and complete membrane protein, and its functions run
through the life cycle of SARS-CoV-2, including assembly and
pathogenicity [17]. The S protein is the key to the invasion of cells
by SARS-CoV-2 and it exists on the surface of the virus membrane
in the form of trimers [18]. It is composed of S1 and S2 subunits
and the latter one is the most conserved region in spike protein
[19]. The E protein and the M protein are alternately arranged on
the surface of the virus membrane, together with the S protein
forming the virus shell, and the N protein interacts with the viral
RNA to form the core of the virus particle [2]. During viral replica-
tion, a polyprotein 1ab is translated through ORF1ab in viral gen-
ome, and subsequently cleaved into 16 non-structural proteins
by protease (Fig. 2B).
The proteins of SARS-CoV-2 are highly glycosylated [20]. For
example, about 40% surface of S protein is covered by glycans
[21], which helps the virus hide epitopes and avoid antibody recog-
nition [22]. SARS-CoV-2 S protein comprises 22 N-linked glycosyla-
tion sequons per protomer [23]. Because glycosylation is the key to
virus invasion, the glycosylation of S protein needs to be taken into
consideration when designing vaccines and antibodies [24].
3. Life cycle of SARS-CoV-2
SARS-CoV-2 can bind to Angiotensin-converting enzyme 2
(ACE2), a functional receptor of SARS-CoV [25], on the cell surface
with its S protein to enter the cell through membrane fusion and
J. Yin, C. Li, C. Ye et al. Computational and Structural Biotechnology Journal 20 (2022) 824–837
825
endocytosis [19] (Fig. 3A). Proteins from host cells, such as the
serine protease TMPRSS2 [26] and high-density lipoprotein
(HDL) scavenger receptor type B (SR-B1) [27], facilitate the
SARS-CoV-2 invasion processes (Fig. 3B). Transmembrane serine
protease 4 (TMPRSS4) is found to be most significantly related
to ACE2 [28]. SARS-CoV-2 has its unique Furin cleavage site never
found before in other coronaviruses, is required for the virus to
enter cells lacking cathepsin protease [29]. Furin can cleave the
SARS-CoV-2 spike protein at the S1/S2 site [2], resulting in active
S1 and S2 subunits. The cutting process occurs during the virus
packaging process [30].
Once entering the host cell, the virus particle releases the viral
genome, and utilizes host ribosome to translate the viral polypro-
teins pp1a and pp1ab [31]. Then the viral protease 3CLpro [32] and
PLpro [33] cleave the polyprotein into a variety of active proteins
(Fig. 3C). Viral replication is dominated by a replication/transcrip-
tion complex composed of non-structural proteins [34]. For exam-
ple, nsp7, nsp8, and nsp12 together form the virus-independent
RNA polymerase structure (RdRp) for viral genome replication
[35] (Fig. 3D). The translation of nsp14 can shut down the host pro-
tein synthesis and inhibit the innate immune response, while the
combination of nsp10 enhances this effect [36].
After four structural protein is produced by transcription, the N
protein binds to the genome, and the remaining three (S, E, and M)
are integrated into the endoplasm and then sent to the endoplas-
mic reticulum-Golgi intermediate compartment (ERGIC) for fur-
ther process, such as furin-mediated cleavage. Subsequently, the
assembled progeny virus was released by exocytosis or budding
[37,38] for the next round of invasion to host cell (Fig. 3E). In
ERGIC, E protein can form pores to cause Ca
2+
to leak and activate
NLRP3 inflammasome to achieve pro-inflammatory effects [39]
(Fig. 3F).
Fig. 1. Update of COVID-19 pandemic worldwide. As of January 9, 2022, the cumulative number of reported cases worldwide has exceeded 304 million, while the
cumulative death toll has exceeded 5.4 million. Till to January 13, 2022, 9.2 billion doses of vaccine have been administered globally.
Table 1
Summary of approved and developed drugs against COVID-19.
Approved drugs
Product Developer Therapeutic
class/drug type
Status Approving
Authority
Kineret (Anakinra) Sobi Immunomodulator Marketing authorization granted: 17/12/2021 EMA
Regkirona (Regdanvimab) Celltrion Healthcare Monoclonal antibody Marketing authorization granted: 12/11/2021 EMA
RoActemra Roche Immunomodulator Marketing authorization for COVID-19 indication
granted: 07/12/2021
EMA
Ronapreve (Casirivimab/
Imdevimab)
Roche & Regeneron Monoclonal antibody Marketing authorization granted: 12/11/2021 EMA
Veklury (Remdesivir) Gilead Sciences Nucleotide analogs Conditional marketing authorization granted: 03/07/
2020
EMA
Marketing authorization granted: 22/10/2020 FDA
Xevudy (Sotrovimab) GlaxoSmithKline & Vir
Biotechnology
Monoclonal antibody Marketing authorization granted: 17/12/2021 EMA
Developed drugs
Product Developer Therapeutic
class/drug type
Status Data source
Sarilumab Sanofi Aventis Immunomodulator Clinical phase EMA
Canakinumab Novartis Monoclonal antibody Clinical phase Clinical trials
Anakinra Swedish Orphan Biovitrum
AB (SOBI)
Immunomodulator Clinical phase EMA
Tocilizumab Roche Immunomodulator Clinical phase EMA
Pidotimod / Immunomodulator / /
Cepharanthine / Immunomodulator / /
The information is summarized from the available data online at sites https://www.fda.gov/drugs/emergency-preparedness-drugs/coronavirus-covid-19-drugs,https://www.
ema.europa.eu/en/human-regulatory/overview/public-health-threats/coronavirus-disease-covid-19/treatments-vaccines/treatments-covid-19/covid-19-treatments-
research-development, and https://clinicaltrials.gov/ct2/results?cond=COVID-19&term = anakinra&cntry=&state=&city=&dist=. EMA: European Medicines Agency; FDA: the
U.S. Food and Drug Administration.
J. Yin, C. Li, C. Ye et al. Computational and Structural Biotechnology Journal 20 (2022) 824–837
826
4. Drugs targeting the SARS-CoV-2 life cycle
The process of SARS-CoV-2 entering the human body and self-
replicating to release progeny virus can be divided into different
stages. According to the characteristics of each dynamic stage, dif-
ferent drug targets to these specialized processes are formulated to
block the life activities of the virus (Fig. 3).
4.1. Anti-viral entry
4.1.1. Inhibition of key enzymes in the binding process
Alpha-1 antitrypsin (
a
1AT) inhibits the protease activity of
TMPRSS2 at physiological concentrations to restrain the entry
and replication of SARS-CoV-2 in cell lines and primary cells [40].
A statistical study based on 500,000 people shows that mild
a
1-
Antitrypsin deficiency (AATD) genotypes were not associated with
increased SARS-CoV-2 infection rates or fatalities [41]. For the lack
of
a
1AT makes it easier to activate TMPRSS2, severe AATD patients
may be susceptible to SARS-CoV-2 [42,43]. There have been four
trials recruited or completed to test whether
a
1AT can be used
for the treatment of COVID-19 patients [44].
Halofuginone can reduce endogenous TMPRSS2 expression at
sub-micromolar concentrations, which showed significant resis-
tance to SARS-CoV-2 infection in vitro in both live- and pseudo-
virus models [45]. Halofuginone is an oral anti-fibrosis [46] and
anti-inflammatory [47] drug. A study in mice reveals that the dis-
tribution of halofuginone can be detected in various organs, includ-
ing kidneys and lungs [48]. ACE2 is widely expressed in these
organs [49], making these organs vulnerable to the SARS-CoV-2.
Therefore, the antiviral activity and wide distribution of halofugi-
none in vivo repurpose it as a promising anti-SARS-CoV-2 drug.
Platycodon grandiflorum D (PD), a natural component of Platy-
codon grandiflorum [50], and pan-coronavirus fusion inhibitor EK1
derived lipopeptide EK1C4 [51] can effectively block SARS-CoV2-
mediated membrane fusion to combat viral infections. Since
TMPRSS2 is induced by androgens (AR), the AR anti-caking agent
Table 2
Summary of approved COVID-19 vaccines.
Name of Vaccine NRA of
record
Type
Comirnaty (developed by Pfizer and
BioNTech)
EMA/FDA mRNA vaccine
COVID-19 Vaccine Janssen EMA Adenovirus vector
vaccine
Nuvaxovid EMA Recombinant protein
vaccine
Spikevax (previously COVID-19 Vaccine
Moderna)
EMA mRNA vaccine
Vaxzevria (previously COVID-19
Vaccine AstraZeneca)
EMA Adenovirus vector
vaccine
Moderna COVID-19 Vaccine FDA mRNA vaccine
Janssen COVID-19 Vaccine FDA Adenovirus vector
vaccine
SARS-CoV-2 Vaccine (Vero Cell),
Inactivated (InCoV)
NMPA Inactivated vaccine
COVID-19 Vaccine (Vero Cell),
Inactivated/Coronavac
TM
NMPA Inactivated vaccine
Ad5-nCoV NMPA Recombinant protein
vaccine
Recombinant Novel Coronavirus
Vaccine (CHO Cell)
NMPA Recombinant protein
vaccine
SARS-CoV-2 Vaccine, Inactivated (Vero
Cell)
NMPA Inactivated vaccine
NRA: National Regulatory Authority; EMA: European Medicines Agency; FDA: the U.
S. Food and Drug Administration; NMPA: National Medical Products
Administration.
Fig. 2. The morphologic and genomic structure of SARS-CoV-2. (A) SARS-CoV-2 is an enveloped virus consisting of spike protein (S), envelope protein (E), membrane
protein (M), nucleic acid protein (N), and single-stranded RNA in the virion. (B) The genomic RNA of SARS-CoV2 is linear, positive-sense, and single-stranded with the length
of approximately 30 kb, which contains a 5
0
cap and 5
0
UTR cap, open read frame (ORF), followed by 3
0
UTR and poly(A) tail. The largest gene, ORF1ab, encodes the pp1ab
protein containing 15 nsps (nsp1 to nsp10 and nsp12 to nsp16). The pp1a protein encoded by ORF1a gene also contains 10 nsps (nsp1 to nsp10). Structural protein is encoded
by 4 structural genes, including S protein, E protein, M protein, and N protein encoding genes. Accessory genes, encoding accessory proteins such as nsp3a and nsp6p, are
distributed in structural genes.
J. Yin, C. Li, C. Ye et al. Computational and Structural Biotechnology Journal 20 (2022) 824–837
827
Proxalutamide (GT0918) can significantly accelerate virus clear-
ance on day 7 in patients with mild to moderate COVID-19 [52].
4.1.2. Competitive binding to ACE2 and SARS-CoV-2 S protein
Catechin and curcumin have a strong binding affinity to the
virus S protein and host receptor ACE2 and its complex, which
can trigger local structural fluctuations of the protein through their
binding with RBD/ACE2 complex [53]. In a study, using protein
engineering technology, the self-assembled tetramerization
domain from p53 protein produces a super tetravalent form of
ACE2 coupled to the Fc region of human immunoglobulin
c
1, the
high-molecular-weight Quad protein (ACE2-Fc-TD) retains the
binding to the ACE2 and its binding SARS-CoV-2 S protein and
can form a complex with the S protein and antiviral antibodies
as a bait protein [54]. Similarly, antibodies that bind to viral RBD
epitopes (such as REGE-CoV) [55,56] or that target the ACE2 recep-
tor (such as h11B11) [57] can also effectively prevent and reduce
the symptoms of viral infections. The viral load in the SARS-CoV-
2 infected animals is significantly reduced after the single-dose
h11B11 treatment, while the animals showed less interstitial
pneumonia and limited pathological features under the preventive
treatment conditions [57], which makes it a potential therapeutical
agent in COVID-19.
4.2. Viral protease inhibitors
The organic selenium compound Ebselen and its structural ana-
logs can inhibit the activity of the SARS-CoV-2 protein PLpro in the
nanomolar range [45]. Two clinical trials of Ebselen are now
recruiting moderate and severe COVID-19 patients [44]. There is
also evidence that Catechin binds to the S1 ubiquitin-binding site
of PLpro, which may inhibit its protease function and cancel the
inhibitory function of SARS-CoV-2 on the ubiquitin–proteasome
system and the interferon-stimulated gene system [58].
The viral main protease Mpro is also a widely explored drug tar-
get. Two kinds of small molecule compounds with indole structure
named GRL-1720 and 5 h inhibit the main protein Mpro of the
SARS-CoV-2, which can effectively block viral infections in vitro
[59]. Another Mpro inhibitor, GC-376, is also a promising main
candidate for further development of the treatment of SARS-CoV-
2 infection [60]. GC-376 exhibits no toxicity in K18-hACE2 mice
experiment, showing moderate benefits in terms of clinical symp-
toms, weight change, and survival rate. Under low-dose virus
attack, GC-376 can prevent the virus from reaching the brain and
reduce inflammatory cell distribution and virus staining [60]. How-
ever, the potential anti-inflammatory effect needs to be further
developed.
Fig. 3. The life cycle of SARS-CoV-2. The entry of SARS-CoV-2 is initiated through that TMPRSS2 acts on the S protein to activate the S1 and S2 subunits. The S1 subunit binds
to the ACE2 receptor to occur endocytosis (A), and S2 mediates membrane fusion (B). Subsequently, the virus releases its genomic RNA, which is translated into viral
polyprotein by the ribosome of the host cell. Under the action of lysosomal cathepsin, the virus releases genomic RNA and then is translated into viral polyprotein,
subsequently cleaved into nonstructural proteins (nsp) with viral proteases including 3CLpro and PLpro (C). SARS-CoV-2 RdRp replicates and amplifies a large number of viral
genomes, and then are transcribed and translated into four structural proteins (D). The progeny genome and structural proteins are assembled on endoplasmic reticulum-
Golgi intermediate compartment (ERGIC), which are transported and released to the outside of host cell (E). The furin on the Golgi apparatus cleavages and pre-activates the S
protein. Infected cells can fuse with neighboring cells to form syncytia. In addition, E protein in ERGIC can form pores to cause Ca
2+
to leak to achieve pro-inflammatory effects
(F).
J. Yin, C. Li, C. Ye et al. Computational and Structural Biotechnology Journal 20 (2022) 824–837
828
4.3. Anti-viral RNA polymerase
The active form of Remdesivir, which has been approved for
COVID-19 treatment, acts as a nucleoside analog [61] and inhibits
RNA-dependent RNA polymerase (RdRp). Remdesivir is incorpo-
rated into the growing RNA product by RdRp [62], and the translo-
cation barrier causes RNA 3
0
-nucleotide to remain at the substrate
binding site of RdRp and interfere with the entry of the next nucle-
oside triphosphate, thereby stagnating RdRp [63]. Multiple trials
have confirmed the effectiveness of Remdesivir treatment
[64,65]. Through binding to viral RdRp, other nucleoside analogs
such as Ribavirin, Sofosbuvir, Galidesivir, Setrobuvir, and Tenofovir
behave as potent drugs against SARS-CoV-2[66,67]. Nevertheless, it
is still a long way for these FDA-approved RdRp inhibitors to apply
in COVID-19 from bench to bed.
So far, it has always been the top priority of scientists to find a
convenient, effective, and low-cost oral drug against COVID-19
because of the expensive monoclonal antibodies. On December
22, 2021, the FDA issued an emergency use authorization for Pfi-
zer’s Paxlovid, and on the following day, it urgently approved Mer-
ck’s Molnupiravir [68]. Paxlovid is composed of Nimarivir (PF-
07321332) and low-dose Ritonavir. Pfizer claims that compared
with placebo treatment group, the risk of hospitalization or death
in non-hospitalized adults at high risk of COVID-19 treated with
Paxlovid was reduced by 89%. Nimarivir is a SARS-CoV-2 3CLpro
inhibitor and can reduce virus replication [69]. Ritonavir can alle-
viate the degradation of Nimarivir and keep it at a higher concen-
tration for a long duration as possible [70]. Recently, the oral
antiviral drug Molnupiravir, an inhibitor of RdRp leading to viral
fatal mutations or premature termination of replication [71], has
attracted attention and expectation. Although Molnupirivir is
reported host mutation activity in animal cell culture experiments
[72], the safety of molnupiravir was confirmed in a drug safety
assessment [73].
4.4. Anti-viral release
The assembled progeny of SARS-CoV-2 is released by exocytosis
or budding [37,38]. Oseltamivir is a prodrug against neuraminidase
inhibitor, which has been approved for the treatment and prophy-
laxis of influenza A by inhibiting the release of progeny virion by
budding from the infected cells[74]. In both in vitro and in vivo
studies, Oseltamivir is ineffective against SARS-CoV-2 and fails to
improve the patients’ symptoms and signs in the clinic [75].
SARS-CoV-2 infected cells express Spike protein (S) on their sur-
face and fuse with ACE2-positive neighboring cells. The expression
of SARS-CoV-2 S protein in the absence of any other viral proteins
triggers the formation of syncytia [76] and determines syncytium-
mediated lymphocyte elimination [77]. The anti-helminth drug
Niclosamide was found to significantly reduce the calcium oscilla-
tion and membrane conductance in cells expressing spikes [78],
which interferes with the syncytial formation process induced by
S protein. A trial proved that Niclosamide has relatively safe clini-
cal benefits in COVID-19 management. Compared with the control
group, the cure rate of the Niclosamide treatment group increased
[79]. Niclosamide has poor oral bioavailability due to its limited
water solubility. Therefore, considering the economic issues of
treatment, it is necessary to explore its effective use.
5. Drugs targeting SARS-CoV-2-induced inflammation in host
cells
Inflammation is an early response triggered by harmful stimuli
and conditions to restore homeostasis. SARS-CoV-2 could evoke
the immune system and induce pro-inflammatory factors such as
IL-6, IL-1, TNF-
a
, and IFN [80–82] overproduction called a cytokine
storm, which brings catastrophic damage to cells and then causes
dysfunction and failure of tissues and organs [83]. The levels of
cytokines in critical COVID-19 patients are significantly higher
than those in mild conditions [84]. SARS-CoV-2 infection can cause
cytokine release syndrome (CRS) [85], which then produces a ser-
ies of consequences such as multiple organ dysfunction syndrome
(MODS), acute respiratory distress syndrome (ARDS), and even
death [86 87]. The intervention and treatment of cytokine storm
are necessary means to reduce COVID-19 mortality (Fig. 4).
5.1. Cytokine inhibitors
Overdose of interleukin-6 (IL-6) is one of the causes of cytokines
storm in COVID-19 [88]. Tocilizumab (TCZ) is the first IL-6 receptor
inhibitor discovered, which reduces the immune damage caused
by IL-6 to target cells by competitively binding to IL-6 receptors
[89]. Shreds of evidence have shown that in a limited number of
patients, symptoms, hypoxemia, and changes in chest tomography
(CT) opacity in patients treated with TCZ are immediately
improved [90]. Results from a primary intention-to-treat (ITT)
phase 2 population shows that TCZ may reduce lethality rates at
30 days [91]. In a meta-analysis, however, there was no difference
in mortality between the TCZ treatment group and the placebo
group. TCZ can reduce the length of hospital stay while the impact
on survival has not been statistically proven, but the combined use
of corticosteroids is found enable to optimize the proven effective-
ness of corticosteroids [92]. Hence, to better use TCZ in COVID-19
treatment, the combination of medication can be taken into
consideration.
Anakinra is a recombinant interleukin-1 (IL-1) receptor antago-
nist with anti-inflammatory and immunomodulatory effects [93].
A study has revealed that Anakinra significantly reduces the mor-
tality and the ICU invasive mechanical ventilation needs of
COVID-19 patients [94]. An updated meta-analysis shows that
Anakinra can reduce the 50% risk of death in hospitalized patients
with moderate to severe COVID-19 compared with patients
untreated with Anakinra [95]. Chloroquine owns an immunomod-
ulatory effect, inhibiting the production and release of TNF-
a
and
IL-6 [96], which may modulate cytokine storm in COVID-19
[97,98]. However, it has not been shown to benefit COVID-19
patients in randomized controlled trials [99].
Sarilumab is another IL-6 blocker [100,101], a fully human
immunoglobulin G1 monoclonal antibody with a high affinity for
membranes and IL-6 receptors [102]. A retrospective case from
an institution in southern Italy showed that 10 COVID-19 patients
(67%) observed rapid improvement in their respiratory parameters
after using Sarilumab [103]. In the results of the Sarilumab at a safe
dose of 400 mg and placebo groups, the COVID-19 patient mortal-
ity rates were 23% and 27%, while the hospital discharge rates were
53% and 41%, respectively [102].
Canakinumab is an IL-1 blocker developed by Novartis for the
treatment of inflammatory diseases [104]. In a study of 48 patients
with moderate COVID-19-related pneumonia, Canakinumab was
found to reduce the need for invasive mechanical ventilation.
63% of patients in the Canakinumab group were discharged within
21 days while the control group was 0% [105]. For mild or severe
COVID-19 pneumonia, a study has observed a decrease in the
inflammation index in the Canakinumab group, which can lead
to a rapid and lasting improvement in oxygenation levels [106].
With IL-12 or IL-15, IL-8 can be an effective inducer of IFN-
c
in
certain kinds of cells [107]. The combination of TNF-
a
and IFN-
c
can strongly induce cell death characterized by inflammatory cell
death [108]. In COVID-19 patients, these uncontrolled expressions
of cytokines can cause excessive damage to tissues and organs
[109]. As a result, inhibitors of abnormally increased levels of
J. Yin, C. Li, C. Ye et al. Computational and Structural Biotechnology Journal 20 (2022) 824–837
829
cytokines can be used as potential drugs for COVID-19 treatment.
Meanwhile, due to the existence of synergistic effects, combination
drugs or multi-targets can be considered view of drug develop-
ment. However, the combinate use of corticosteroids is still contro-
versial. While inhibiting inflammation, it also stops the elimination
of the virus and causes a series of side effects [110,111].
5.2. Signaling pathway inhibitors
Janus Kinase (JAK)-Signal Transducer and Activator of Tran-
scription (STAT) pathway is essential for the development and
function of the immune system [112], which are involved in the
various pro-inflammatory factors [113]. Therefore, the use of JAK
inhibitors is one of the ideas to reduce the cytokine storm in
COVID-19. Baricitinib and Ruxolitinib are potent and selective
JAK inhibitors approved for indications such as rheumatoid arthri-
tis and myelofibrosis [114], which are currently reused for the
treatment of SARS-CoV-2 infected patients. Studies have confirmed
the safety and effectiveness of these drugs in reducing cytokine
levels in the treatment of COVID-19 as antiviral drugs [115–117].
In addition, Baricitinib has the effect of reducing the endocytosis
of the SARS-CoV-2 [118]. The combined use of Baritinib and
Remdesivir can shorten the recovery time and accelerate the
improvement of clinical status, especially for patients receiving
high-flow oxygen or non-invasive ventilation [119].
The nuclear factor NF-
j
B pathway is a classic pro-inflammatory
signaling pathway [120]. The inhibition of NF-
j
B signaling has
therapeutic applications in cancer and inflammatory diseases
[121], as well as virus- and LPS- induced cytokine storms [122].
The use of NF-
j
B inhibitors Caffeic acid phenethyl ester (CAPE)
and Parthenolide can improve the survival rate of mice infected
with SARS-CoV [123]. Considering the spike protein of coronavirus
upregulates IL-6 and TNF-
a
in murine macrophages through the
NF-
j
B pathway [124], the exploration of NF-
j
B inhibitors may
be an effective measure to reduce the cytokine storm upon SARS-
CoV-2 infection. Although some studies have found potential
new drugs that can be used to inhibit NF-
j
B to inhibit SARS-
CoV-2 infection, [125,126], whether they can be applied to the
treatment of COVID-19 remains to be investigated.
In a trial to screen drugs with SARS-CoV-2-related pangolin
coronavirus model, the Cepharanthine (CEP) showed a significant
antiviral effect [127]. CEP inhibits viral replication by modulating
signaling pathways [128,129], among which it exhibits anti-
inflammatory effects through AMPK activation and NF-
j
B inhibi-
tion[130]. Another study also confirmed the antiviral effect of
CEP, and the combination of CEP and Nelfinavir can enhance their
efficacy [131]. Existing evidence shows that CEP has important
potential value in the treatment of COVID-19 [132], it still needs
further verification by in vivo experiments and clinical trials.
5.3. Steroids treatment
Pidotimod is a synthetic dipeptide molecule, which has biolog-
ical and immunological activity on both the adaptive and the
innate immune responses [133]. Pidotimod can increase the
expression of NF-
j
B protein without an increase of IL-8 expression
[134]. Pidotimod has been evaluated as an immunostimulant for
respiratory infections (RTIs) [135] and the treatment of many other
diseases [136]. A controlled experiment involving 20 COVID-19
patients showed that Pidotimod can effectively improve the fever
of patients and prevent the activation of the cytokine cascade
[137].
Viral infections usually cause excessive hyperinflammation
[138]. The anti-inflammatory effect of steroids can stabilize hemo-
dynamics and shorten the stay time of the intensive care unit (ICU)
and the duration of mechanical ventilation. The use of steroids has
always been controversial. Steroids can significantly reduce anti-
inflammatory factors and may also delay virus clearance [139].
Long-term use of steroids can cause many adverse events, such
as secondary infections [140]. In addition, The correlation between
steroids and mortality remains unclear [141]. Steroids are cur-
rently used in critically ill patients to reduce clinical deterioration.
One meta-analysis shows that the use of steroids is associated with
higher mortality [142], whereas another prospective meta-analysis
Fig. 4. Summary of therapeutic targets to SARS-CoV-2-induced inflammation in host cells. SARS-CoV-2 could evoke the immune system and trigger cytokine release
syndrome (CRS) and cytokine storm, leading to multiple organ dysfunction syndrome (MODS), acute respiratory distress syndrome (ARDS), and even death. The therapuetic
inventations are introduced to alleviate inflammation to reduce the severity of COVID-19.
J. Yin, C. Li, C. Ye et al. Computational and Structural Biotechnology Journal 20 (2022) 824–837
830
of seven randomized trials showed that the use of systemic corti-
costeroids was associated with lower all-cause mortality from
COVID-19 [143]. The contradictory results indicate that there is
still uncertainty in the role of corticosteroids, and more random-
ized controlled trials are needed to prove its effectiveness.
It is undeniable that corticosteroids have been widely used in
the treatment of severe COVID-19 cases [144]. A trial showed that
the 28-day mortality is reduced in COVID-19 patients receiving
respiratory support after receiving up to ten days of dexametha-
sone treatment, which is useless for patients who do not require
respiratory support [145]. The use of cedemethasone can reduce
lung damage in COVID-19 patients [146], which is recognized by
WHO in the clinical trial [147]. Whether other steroids have the
same effects as dexamethasone is still unknown [148]. The combi-
nation of other drugs may alleviate the side effects of steroid use.
An observational cohort study found that the combination of
Barectinib and corticosteroids in the COVID-19 treatment can sig-
nificantly improve lung function compared with corticosteroids
alone [149]. Nonetheless, how to maximize the drug effect with a
lower dose and shorter treatment time is another urgent problem
that needs to be solved.
5.4. Holistic therapy and traditional Chinese medicine treatment
Rehabilitation plasma therapy can be taken in the early stage of
COVID-19 by using antibodies in the convalescent serum to neu-
tralize the virus to reduce the body damage caused by the immune
system [150]. After the occurrence of cytokine storm, patients will
have a variety of symptoms, such as MODS and ARDS. At this stage,
anti-shock treatment is required to maintain the patient’s body
homeostasis and protect important organ functions.
In addition to conventional treatment, traditional Chinese med-
icine (TCM) plays an important role as an auxiliary method in clin-
ical COVID-19 treatment, which has been confirmed to have
antiviral activity against various coronavirus strains [151]. TCM
treatment can improve clinical efficacy and alleviate COVID-19
patients’ severe conditions [152,153]. Since TCM recipes were
according to the Diagnosis and Treatment Protocol for Novel
Coronavirus Pneumonia (Trial Version 7) [154], 92% of all of the
confirmed cases in China had taken TCM in COVID-19 treatment
[155]. Different recipes are recommended for different severity of
conditions in COVID-19 treatment. Namely, Lianhua Qingwen
(LHQW), Jinhua Qinggan (JHQG), Hua Shibaidu Granules (HSBD),
Xuanfeibaidu Granules (XFBD), Xuebijing Injection (XBJ), and Qing-
fei Paidu Decoction are common TCM recipes [155].
In Vero cells, LHQW reduced the mRNA expression of
pro-inflammatory cytokines TNF-
a
, IL-6, CCL-2/MCP-1, and
CXCL-10/IP-10 [156]. A comparative study of multiple combination
medications shows that the quadruple combination with LHQW
can be the first choice for the treatment of patients in critical
condition [157]. In detail, Rhein, forsythoside A, forsythoside I,
neochlorogenic acid and its isomers may be the effective active
ingredients of LHQW against SARS-CoV-2 [158]. A retrospective
analysis of JHQG treatment promotes the absorption of pneumonia
permeate with a higher 7-day viral clearance rate compared with
the control group [159]. HSBD is suitable for early COVID-19
treatment [160], while XBJ is mainly used for patients in critical
conditions [161]. The XBJ may relieve systemic inflammation by
inhibiting the secretion of pro-inflammatory cytokines mediated
by the HMGB1/RAGE axis to reduce mortality [162,163].
Traditional Chinese medicine has played a huge role in China’s
anti-COVID-19 epidemic battle. However, there are many
unsolved issues for Chinese scientists and researchers to precise
the administration of TCM in COVID-19 treatment in the future.
The concerning characteristics of TCM treatment are that the
types and dosages of medications often change due to the
different conditions of different patients. The molecular mecha-
nisms of most TCMs are unclear, which raises the limitations in
the global promotion of TCM against COVID-19 pandemic. Nota-
bly, the standardization behind different kinds of traditional Chi-
nese medicines with various functions is highlighted and needs to
be concerned.
Table 3
Detailed information on emerging SARS-CoV-2 variants.
VOC
WHO
Label
Pango lineage Earliest
Documented
Samples
Key Mutation Sites
Alpha B.1.1.7 United
Kingdom in
Sep-2020
DEL69/70; DEL144/145; N501Y;
A570D; D614G; P681H; T716I;
S982A; D1118H
Beta B.1.351 South Africa
in May-2020
D80A; D215G; DEL241/243;
K417N; E484K; N501Y; D614G;
A701V
B.1.351.2 L18F; D80A; D215G; DEL241/
243; K417N; E484K; N501Y;
D614G; A701V
B.1.351.3
Gamma P.1 Brazil in
Nov-2020
L18F; T20N; P26S; D138Y;
R190S; K417T; E484K; N501Y;
D614G; H655Y; T1027I; V1176F
Delta B.1.617.2 India in Oct-
2020
T19R; G142D; E156G; DEL157/
158; L452R; T478R; T478K;
D614G; P681R; D950N
AY.1 T19R; W258L; K417N; L452R;
T478K; D614G; P681R; D950N
AY.2 T19R; V70F; E156G; DEL157/
158; A222V; K417N; L452R;
T478K; D614G; P681R; D950N
AY.3 T19R; E156G; DEL157/158;
L452R; T478K; D614G; P681R;
D950N
Omicron B.1.1.529 South Africa
in Nov-2020
A67V; DEL69/70; T95I; G142D;
DEL143/145; T547K; D614G;
H655Y; N679K; P681H; D796Y;
N856K; Q954H; N969K; L981F
BA.1 A67V; DEL69/70; T95I; G142D;
DEL143/145; N211I; DEL212/
212; G339D; S371L; S373P;
S375F; S477N; T478K; E484A;
Q493R; G496S; Q498R; N501Y;
Y505H; T547K; D614G; H655Y;
N679K; P681H; D796Y; N856K;
Q954H; N969K; L981F
BA.2 T19I; L24S; DEL25/27; G142D;
V213G; G339D; S371F; S373P;
S375F; T376A; D405N; R408S;
K417N; N440K; S477N; T478K;
E484A; Q493R; Q498R; N501Y;
Y505H; D614G; H655Y; N679K;
P681H; N764K; D796Y; Q954H;
N969K
BA.3 A67V; DEL69/70; T95I; G142D;
DEL143/145; N211I; DEL212/
212; G339D; S371F; S373P;
S375F; D405N; S477N; T478K;
E484A; Q493R; Q498R; N501Y;
Y505H; D614G; H655Y; N679K;
P681H; N764K; D796Y; Q954H;
N969K
VOI
Lambda C.37 Peru in Dec-
2020
G75V; T76I; R246N; DEL247/
253; L452Q; F490S; D614G;
T859N
Mu B.1.621 Columbia
Oct-2020
T95I; Y144S; Y145N; R346K;
E484K; N501Y; D614G; P681H;
D950N
The mutations of amino acid in SARS-CoV-2 S protein are presented. The summa-
rized information represented in the table was derived from the public data
(https://outbreak.info/situation-reports#custom-report, as of 26 November 2021).
J. Yin, C. Li, C. Ye et al. Computational and Structural Biotechnology Journal 20 (2022) 824–837
831
6. Emerging SARS-CoV-2 variants
SARS-CoV-2 has been continuing to evolve, posing higher infec-
tivity efficiency and faster transmission, leading to a greater risk to
global public health. To better assess the consequences of different
variants and facilitate prevention measures or medical counter-
measures, WHO divides them into variants of interest (VOI) and
variants of concern (VOC) [164]. There are currently two VOIs:
Kappa and Mu; and five VOCs: Alpha, Beta, Gamma, Delta, and
Omicron (Table 3). On November 24, 2021, a new SARS-CoV-2 vari-
ant B.1.1.529 named Omicron was discovered in South Africa. Pre-
viously, the SARS-CoV-2 Delta variant has become the main
epidemic strain in many countries [165]. Now, the emergence of
omicron has aroused new attention and vigilance. The mutations
in Omicron are concentrated in the S protein, and there seems to
be a tendency to collect mutations that are beneficial to immune
escape [166,167]. A model predicts and calculates that Omicron’s
infectivity is about ten times that of the original virus or twice that
of the Delta variant. Omicron may greatly undermine the efficacy
of the Eli Lilly monoclonal antibody (mAb) approved by the FDA,
and may also reduce the efficacy of mAbs from Celltrion and Rock-
efeller University [168]. The main SARS-CoV-2 variants reported in
different places worldwide create new concerns about anti-viral
drugs and vaccinations against COVID-19 pandemic (Fig. 5). The
following critical mutation sites in SARS-CoV-2 genome determine
the virulence and spread of the SARS-CoV-2 (Table 4), which pro-
vides fresh ideas in the drug design for the main emerging variants.
6.1. Mutations in structural proteins
D614G mutation in S protein will not significantly change the
neutralizing properties of antibodies against SARS-CoV-2, and the
currently developed vaccine against wildtype is still effective
against the D614G strain [169]. The presence of the E484K muta-
tion located in the receptor-binding domain (RBD) of the S protein
will reduce the neutralizing power of a variety of effective mAbs
that change the receptor-binding motif on RBD [170]. The intro-
duction of E484K mutations into other variant strains will also lead
to a decrease in the neutralization of antibodies and monoclonal
antibodies caused by the vaccine [171]. N501Y mutation found in
the British variant strain B.1.1.7 has almost no effect on the neu-
tralizing effect of neutralizing nanobodies (Nbs) [172]. However,
the mutant strain often accompanies other key amino acid muta-
tions that affect the binding of S protein to ACE2. L18F mutation
occurs in the NTD region and can cancel the binding of S2L28 mon-
oclonal antibody to NTD [173] and the L18F mutation is positively
correlated with mortality [174]. K417N mutation, close to the ACE2
binding site, is slightly detrimental to ACE2 binding [171], but it
can promote the process of variants effectively avoiding antibodies
by eliminating the buried interface salt bridge between RBD and
neutralizing antibody CB6 [175]. L452R mutation locates in the
RBD hydrophobic plaques of the spike protein [176]. It will
increase the affinity of the spike protein to ACE2 and is kind of
destructive to NAb binding [177] and make the virus evade the
monoclonal antibody LY-CoV555 [178]. P681R is a mutation near
the furin-cleavage site [179], which enhances the cleavage of S1
and S2 by the full-length spike, resulting in increased infection
through the cell surface [180].
6.2. Mutations in non-structural proteins
Among the SARS-CoV-2 nonstructural proteins (nsp), virus-
associated enzymes such as RdRp and 3C are important drug tar-
gets [181]. Mutations at these sites may increase virus resistance
to related drugs [182,183]. Mutations in RdRp, for example, may
Fig. 5. The appearance of mutant strains of SARS-CoV-2 around the world. The
main emerging SARS-CoV-2 variant strains are classified as VOC (variants of
concern), VOI (variants of interest), and VUM (variants under monitoring). VOC
includes Alpha, Beta, Gamma, Delta, and Omicron; VOI contains Lambda and Mu,
while VUM includes Theta, Eta, Iota, and Kappa from the public data (https://
outbreak.info/situation-reports#custom-report, as of 26 November 2021). The time
of appearance is expressed as yy/mm.
Table 4
Mutations of concern and interest reports in SARS-CoV-2 variants.
Mutation of Concern Reports
Mutation Prominent in VOC Prominent in
VOI
E484K B.1.351; B.1.351.2; B.1.351.3; P.1 B.1.621
Mutation of Interest Reports
Mutation Prominent in VOC Prominent in
VOI
L18F B.1.351.2; B.1.351.3; P.1 /
K417N B.1.351; B.1.351.2; B.1.351.3; AY.1; AY.2; BA.2 /
K417T P.1 /
L452R B.1.617.2; AY.1; AY.2; AY.3 /
N501Y B.1.1.7; B.1.351; B.1.351.2; B.1.351.3; P.1; BA.1;
BA.2; BA.3
B.1.621
P681R B.1.617.2; AY.1; AY.2; AY.3 /
The mutations of amino acid in SARS-CoV-2 S protein are presented. The summa-
rized information represented in the table was derived from the public data
(https://outbreak.info/situation-reports#custom-report, as of 26 November 2021).
J. Yin, C. Li, C. Ye et al. Computational and Structural Biotechnology Journal 20 (2022) 824–837
832
reduce the effect of Remdesivir. Studies have shown that the
14,408 C>T mutation increases the viral mutation rate, while
15324 C>T has a reduced effect [184]. Mutations in nsp may corre-
late with the degree of symptoms caused by SARS-CoV-2. A study
found that mutations located in the nsp6 coding region were sig-
nificantly associated with asymptomatic COVID-19 [185], which
could make it difficult to initially screen COVID-19 patients. Differ-
ent nsps have their structures and functions, which can be changed
by the mutations [186]. For example, the V121D mutation in nsp1
may have a disruptive effect on it, and the G1691C in Nsp3 reduces
the flexibility of the protein [187]. Therefore, these mutations in
nsps should be taken into account in drug and vaccine develop-
ment or treatment against COVID-19.
7. Perspectives in the drug design for SARS-CoV-2 variants
The current SARS-CoV-2 genome site mutations are all subject
to natural selection and drug screening, which reflect the adapta-
tion of the virus to the treatments. Some mutations make the virus
increase the infectivity and transmission, however, in terms of
treatment, the previous drugs are still effective against SARS-
CoV-2 variants [188]. Other mutations render part of the antibody
ineffective against SARS-CoV-2 [189], and the virus escapes from
immunity, which brings new challenges to treatment. Therefore,
the exploration of broadly antiviral drugs is prior to being concen-
trated and developed. More importantly, the immunomodulatory
and holistic therapy in host, including anti-inflammatory strategies
and Chinese traditional medicine treatment, should be concerned
in the drug design for SARS-CoV-2 variants.
The binding of SARS-CoV-2 S protein to the ACE2 receptor is a
key activity for the virus to invade the human body, and most of
the mutation sites that are currently being studied are located in
the S protein [190]. Researchers need to test one by one to deter-
mine the impact of specific mutation sites on the life of the
SARS-CoV-2 and then test whether the previous treatments such
as monoclonal antibodies are still effective for the emerging vari-
ants. However, a SARS-CoV-2 variant often carries a combination
of different mutation sites and becomes a multiple mutant strain,
and the speed of mutation is rapid [177]. It is of high concern that
the effects from different combinations of mutation sites will have
on viral infection activities. As a result, the highly conservative
sites of the SARS-CoV-2 genome as drug targets could be paid more
attention to maintaining antiviral activities against variants.
8. Discussion
SARS-CoV-2 has caused a global pandemic since late 2019. With
the increase of experience and knowledge, defensive measures and
clinical treatment plans are adopted immediately according to
observation and management of COVID-19 pandemic. Meanwhile,
researchers are exploring more possibilities of repurposing drugs
against SARS-CoV-2 [191]. However, the development of specific
drugs and vaccines requires fundamental studies on SARS-CoV-2,
such as the interaction between the virus and the host, the epi-
demiology and molecular virology, the host immune responses to
viral infection, to uncover the mechanism underlying the infection,
transmission, and pathogenesis of the virus and explore effective
drugs.
Traditional Chinese medicine has played a huge role in China’s
anti-epidemic process [192]. Research on the mechanism of action
of traditional Chinese medicine may provide new ideas for the
development of anti-SARS-CoV-2 drugs. At the same time, it is nec-
essary to pullulate holistic treatments to deal with the systemic
pathological imbalance caused by the SARS-CoV-2.
Owing to the error-prone RNA replicase of SARS-CoV-2 [193],
the continuous emergence of mutant strains has undoubtedly
brought huge difficulties and challenges to the control of the global
COVID-19 epidemic. The appearance of SARS-CoV-2 variants
means that the virus adapts to manual interventions and natural
selection, which may eliminate the effectiveness of previous drugs
and vaccines. In this case, we must maintain epidemiological
surveillance of COVID-19 timely and focus on the evolution of
the virus, especially the emergence of drug-resistant strains.
The pathogenesis of COVID-19 can be mainly divided into two
phases [194]. In the early stage, the COVID-19 patients may begin
with a series of mild symptoms including fever, cough, fatigue,
hemoptysis, headache, or diarrhea, and then will develop pneumo-
nia [155,195]. Accordingly, antiviral drugs can be given to clear the
virus from the body of patients infected with SARS-CoV-2. Later on,
as the viral load increases and spreads in the human body, which
triggers excessive production of cytokines, a cytokine storm occurs
in the COVID-19 patients to deteriorate to moderate and severe
symptoms with respiratory distress syndrome and organ failure
[196,197]. It should be necessary to adopt antiviral drugs with
immunomodulatory treatment, and also encouraged to introduce
holistic therapy and traditional Chinese medicine treatment, and
even external mechanical equipment and maintain the normal
operation of the patient’s body [198].
In sum, SARS-CoV-2 mutation is an urgent issue that needs to be
explored and solved, which requires concerted efforts from the
fields of structural biology, medicine, virology, pharmacy, public
health, epidemiology, chemistry, and other disciplines, to jointly
deal with the treatment and control of COVID-19 pandemic.
CRediT authorship contribution statement
Jialing Yin: Conceptualization, Data curation, Investigation,
Writing – original draft. Chengcheng Li: Conceptualization, Data
curation, Investigation, Writing – original draft. Chunhong Ye:
Data curation, Investigation. Zhihui Ruan: Data curation, Formal
analysis, Investigation. Yicong Liang: Data curation, Formal analy-
sis, Methodology, Investigation. Yongkui Li: Formal analysis,
Methodology, Validation. Jianguo Wu: Conceptualization, Valida-
tion, Writing – review & editing. Zhen Luo: Conceptualization, Val-
idation, Funding acquisition, Supervision, Writing – original draft,
Writing – review & editing.
Declaration of Competing Interest
The authors declare that they have no known competing finan-
cial interests or personal relationships that could have appeared
to influence the work reported in this paper.
Acknowledgements
This study was supported by the National Natural Science Foun-
dation of China [32070148], the Guangdong Basic and Applied
Basic Research Foundation [2019A1515011073], and Guangzhou
Basic Research Program - Basic and Applied Basic Research Project
[202102020260].
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