Anti–SARS-CoV-2 Natural Products as Potentially Therapeutic Agents

Severe acute respiratory syndrome–related coronavirus-2 (SARS-CoV-2), a β-coronavirus, is the cause of the recently emerged pandemic and worldwide outbreak of respiratory disease. Researchers exchange information on COVID-19 to enable collaborative searches. Although there is as yet no effective antiviral agent, like tamiflu against influenza, to block SARS-CoV-2 infection to its host cells, various candidates to mitigate or treat the disease are currently being investigated. Several drugs are being screened for the ability to block virus entry on cell surfaces and/or block intracellular replication in host cells. Vaccine development is being pursued, invoking a better elucidation of the life cycle of the virus. SARS-CoV-2 recognizes O-acetylated neuraminic acids and also several membrane proteins, such as ACE2, as the result of evolutionary switches of O-Ac SA recognition specificities. To provide information related to the current development of possible anti–SARS-COV-2 viral agents, the current review deals with the known inhibitory compounds with low molecular weight. The molecules are mainly derived from natural products of plant sources by screening or chemical synthesis via molecular simulations. Artificial intelligence–based computational simulation for drug designation and large-scale inhibitor screening have recently been performed. Structure–activity relationship of the anti–SARS-CoV-2 natural compounds is discussed.


INTRODUCTION General Virology of Coronaviruses
The coronaviruses (CoVs) target humans and animals with exchangeable infectivity, causing a zoonotic outbreak. SARS-CoV-2 or 2019-nCoV spreads and causes the human life crisis of COVID-19 by infecting the human respiratory tract and causing pneumonia (Zhou et al., 2020). In addition, SARS-CoV-2 spreads by easy transmission among people, and COVID-19 patients exhibit flu-like symptoms such as fever and cough. Enveloped CoVs contain positive ssRNA genomes with relatively small RNAs (approximately 30 kb). They are classified into the Riboviria-Nidovirales-Cornidovirineae-Coronaviridae-Orthocoronavirinae-CoV genus (α-, β-, γ-, and δ-CoV). Most mammals are infected by α-CoV and β-CoV only, while avians and some mammals are infected by δ-CoV and c-CoV. SARS-CoV-2, belonging to the β-CoV genus, and bat SARS-like CoV-ZXC-21 are similar in their RNA genomes. The COVID-19-causing CoV isolates exhibit 79% identity with the previously named SARS-CoV and 50% identity with the Middle East respiratory syndrome (MERS) virus (Chan et al., 2020).
The current global COVID-19 pandemic is threatening the daily lives of human beings. The disease biology is a topic of interest. To overcome the disease, the academic society urgently needs to exchange the pandemic CoV-controlling drugs, but no truly effective agent has yet been discovered. In this review, antiviral candidate agents and the availability of natural compounds are discussed.

NATURAL PRODUCTS TO TARGET AND INHIBIT INFECTION OF CORONAVIRUSES
Recently, natural phytochemicals that exhibit anti-CoV activity have been extensively summarized (Li et al., 2005). LMW molecules exhibit antiviral activity. Recently, development of anti-CoV drugs has also been applied for molecular docking via simulation approaches. Computer-based artificial intelligence technology contributes to the development of anti-CoV agents. Human angiotensin-converting enzyme (ACE)-2, papain-like protease (PLpro), main 3C-like protease (3CLpro), RdRp, helicase, N7 methyltransferase, human DDP4, receptorbinding domain (RBD), cathepsin L, type II transmembrane (TM) Ser-protease, or transmembrane protease serine (TMPRSS)-2 is mainly targeted. CoV 3CLpro and PLpro are polyprotein-specific viral proteases. RdRp is a complementary RNA strand synthetic replicase. Remdesivir inhibits RdRp in the ssRNA genome of CoV, where the RdRp mediates RNA replication and remdesivir acts as an ATP analog and thus inhibits RdRp.
Currently, effective anti-CoV agents are not available, although several drugs have been prescribed and some natural compounds exhibit antiviral activity. Natural resources are a tremendous treasure trove of chemical compounds that are applicable for various viral infections. Natural products are produced by the metabolic pathways of a given organism, but humans utilize them for their benefits from the modern view of pharmacology. Therefore, phytochemicals have been screened to test their effectiveness against viruses, and some natural products inhibit the infection and amplification of viruses with a broad antiviral spectrum (Pour et al., 2019). Naturally occurring compounds such as artemisinin, baicalin, curcumin, rutin, glycyrrhizic acid, hesperidin, hesperetin, and quercetin have been examined for their anti-CoV activity by various assay based on the viral life cycle. However, none of the natural compounds have direct antiviral activity against CoVs or other RNA viruses. Only GA has been frequently described to be the most active component in several previous articles. Indeed, the molecular action mechanisms of the natural products are not specific because current candidates of natural antiviral agents are mainly examined by using in vitro cell-based assays or computer modeling through docking simulation before application to animal and clinical studies (Li et al., 2005;Packer and Cadenas, 2011). Conventional approaches to natural products were a mix of chemical analysis and structure-function relationship analysis. Recent AI-aided approaches combined with in silico computational simulation is cost-effective for the prediction of chemical compounds (Müller et al., 2018). Currently, new concepts of AI-aided in silico computational approaches have evolved for drug prediction based on drug candidate-ligand/receptor interaction. These approaches utilize known structures of the molecules to predict in silico docking molecules. Fundamental limitations of these AI in silico approaches have also been identified. In fact, in blocking or inhibiting viral proteases, S-glycoprotein, and the entry of SARS-CoV-2, several plant compounds have been suggested through computer simulation techniques (Li et al., 2005).
Natural compounds including chemoenzymatic modified molecules can be used in ethnopharmacology to modulate SARS-CoV-2/nCoV-19 infections due to current limited therapeutic options. The efficacy of natural products depends on the CoV strains. Several natural products inhibit viral replication (Müller et al., 2020), implying antiviral properties. (Kalhori et al., 2021) For example, several compounds exhibit promising prospects for CoV treatment in human patients, as described above for lycorine, scutellarein, silvestrol, tryptanthrin, saikosaponin B2, and polyphenolic compounds such as caffeic acid, isobavachalcone, myricetin, psoralidin, and quercetin, as well as lectins such as griffithsin. For example, Lycoris radiata (L'Hér.) Herb lycorine shows cytopathogenic and antiviral activities against SARS-associated CoV (Yu et al., 2012). Currently known natural products that are pharmacologically effective for SARS-CoV-2 inhibition are shown in Figure 2, with the synthetic compounds previously utilized for other targets in humans.
Natural products that show viral inhibitory activity are promising candidates as anti-CoV agents. Natural products to combat the CoVs are reviewed in this article, focusing on the general properties of CoVs and suggesting applicable drugs and natural compounds effective against several CoV species. Viral proteins such as 3CLpro, PLpro, N, S, and ACE2 have been targeted for antiviral replication or anti-infection. Some limited antiviral agents as inhibitors specific for proteases and RNA synthases are known to block viral replication (Häkkinen et al., 1999). CoV bioactive natural products can also enhance and strengthen host immunity. Vitamins A and C lower susceptibility to infections and help in the prevention of viral infections through host immune function (Häkkinen et al., 1999).

Inhibition of Ribonucleic Acid Helicase eIF4A and Protein Expression
SARS-CoV helicase, a virus replication enzyme, is involved in the unwinding of RNA. Helicases in protein sequences are commonly conserved during evolution in CoVs and other related nidoviruses. CoV helicase is an important therapeutic target because it hydrolyzes all deoxyribonucleotide and ribonucleotide triphosphates in SARS-CoV. Therefore, SARS-CoV-2 helicase has been targeted to screen for inhibitors. The 420-amino acid-long helicase is phylogenetically homologous to the helicases of other CoVs. Favipiravir or hydroxychloroquine, described later in further detail, recognizes SARS-CoV-2 helicase with weak affinities.
Aglaia sp. silvestrol inhibits the replication of MERS types with an EC50 value of 1.3 nM, acting as an inhibitor of RNA helicase eIF4A and protein expression via blocking replication/ transcription complex formation (Miean and Mohamed, 2001). Silvestrol inhibits HcoV-229E protein synthesis with an EC50 of 3 nM. Silvestrol also inhibits HCoV-229E ex vivo in bronchial epithelial cells via RNA helicase eIF4A inhibition (Lau et al., 2008). The polyphenolic compounds myricetin and scutellarein inhibit the helicase activity of SARS-CoVs. Phenolic compounds including myricetin and scutellarein of Isatis indigotica Fort. and Torreya nucifera L. inhibit SARS-CoV helicases including nsP13 helicase (Cho et al., 2013). Scutellaria baicalensis Georgi (Scutellaria radix) myricetin and scutellarein inhibit the ATPase activity of the SARS-CoV helicase Nsp-13 (Yu et al., 2012). Myricetin is enriched in fruits such as cranberry Vaccinium oxycoccos L. (Mikulic-Petkovsek et al., 2012) and in vegetables such as Calamus scipionum Lam. and garlic (Qing et al., 2016). Scutellarein from S. baicalensis is a strong inhibitor of SARS-CoV helicase because it inhibits SARS-CoV helicase Nsp13 via ATPase activity inhibition but not via direct inhibition of helicase activity. The flavonoid quercetin is structurally similar to other polyphenolics such as myricetin and scutellarein and shows similar inhibitory activity of SARS-CoV helicase . In addition, naturally occurring tomentins of Paulownia tomentosa (Thunb.) Steud., belonging to Scrophulariaceae, reversibly and allosterically inhibit the PLpro activity of SARS-CoV (Lung et al., 2020).
Artemisinin, isolated from Artemisia annua L. in 1972 by Dr. Tu Youyou, co-recipient of the 2015 Nobel Prize in Medicine, is an anti-Plasmodium falciparum malaria drug. It is a sesquiterpene lactone with an endoperoxide 1,2,4-trioxane ring, which is necessary to exert its activity. Artemisinin is a potential therapeutic candidate for certain RNA viruses (de Vries et al., 1997). Ferulic acid, as a hydroxycinnamic acid and a component of lignin, is a major metabolite of chlorogenic acid along with caffeic acid (CA) and isoferulic acid. Ferulic acid and its derivatives, including caffeoyltyramine, feruloyltyramine, and feruloyloctopamine, also inhibit SARS-CoV PLpro activity (Li, 2015). Recently, Adem et al. (2020) described that CA derivatives such as khainaosides, 6-O-caffeoyl-arbutin, and vitexfolin have been suggested to be inhibitory candidates with higher binding activities than that of nelfinavir against SARS CoV-2 S-protein as well as Nsp15 and Mpro enzymes by using molecular docking simulation via Web engines named Toxtree and www.swissadme. ch (Adem et al., 2021). Toosendanin (C₃₀H₃₈O₁₁), a triterpenoid isolated from the bark of Melia azedarach L., has analgesic, insecticidal, anti-botulinum, antimicrobial, and antiinflammatory activities, and antiviral RNA polymerase complex activities (Simmons et al., 2013). Matrine, an alkaloid of Sophora flavescens Aiton, inhibits IL-1β expression and MyD88/NF-κB and NLRP3 inflammasome in the inflammatory response in porcine respiratory syndrome virus-infected pigs (Hulswit et al., 2019). Using a structureand activity-based computational approach, natural products have been analyzed for the Nsp-9 (PDB ID-6W4B) enzyme inhibition of SARS-CoV-2 RNA replication and S-protein binding (Chandel et al., 2020). Baicalin exhibits binding affinity to both S-protein and Nsp9 enzyme.

Modulation of S-Glycoprotein
S-glycoprotein recognizes the host cell receptor to enter the cells through endosomal fusion, after which the S-glycoprotein is cleaved, endosomal membranes released, and RNA liberated into the cytosol (Langereis et al., 2012). S-glycoprotein interacts with its receptors via its RBD and plays a role in host tropism and pathogenicity, and in proposing some therapeutic clues (Xiong et al., 2013). Therefore, modulation of the S-glycoprotein is a potential target to control SARS-CoV-2 propagation. Tetrandrine, fangchinoline, and cepharanthine as bis-benzylisoquinoline alkaloids from Stephania tetrandra var. glabra Maxim. protect cells from virus-induced cell death. In addition, they inhibit viral replication, as well as CoV S-glycoprotein and N-protein synthesis. Also, they induce the virus-induced host response by the p38MAPK pathway. Terpenoid compounds such as αand β-pinene as well as cineole interact with the infectious bronchitis virus (IBV) N-protein to inhibit the N-protein-RNA interaction and block IBV replication. The terpenoids bind to the N-terminal active site of the N-protein.
The active site is composed of five amino acid residues Müller et al., 2020). These conserved amino acids in the active sites are commonly located in various IBVs. CA from Sambucus javanica subsp. chinensis Fukuoka (elderberry) extract inhibits the HCoV strain HCoV-NL63 (Weng et al., 2019). CA inhibits HCoV S-glycoprotein attachment to host cells. Chlorogenic acid and gallic acid (3,4,5-trihydroxybenzoic acid) also exhibit the same activities as CA. Gallic acid is a trihydroxybenzoic acid and forms dimeric ellagic acid. Tannins are hydrolyzed to glucose and gallic acid (gallotannin), or glucose and ellagic acid (ellagitannin). CA also inhibits the hepatitis B virus (Wang et al., 2009). Sambucus nigra L. extract (black elderberry) has been used for treating cold and flu symptoms. The adsorption, bioavailability, metabolism, and delivery mechanism of the extracts are documented for therapeutic plasma concentrations (Wittemer et al., 2005).
The NIH clinical collection of 727 tested antiviral compounds showed that the alkaloid omacetaxine (homoharringtonine) shows a nonomolar IC50 level (Cao et al., 2015). Two alkaloids of Tylophora indica (Burm. f.) Merr., tylophorine and 7-methoxycryptopleurine, inhibit transmissible gastroenteritis CoV replication . The T. indica alkaloids tylophorine and 7-methoxycryptopleurine block replication in CoV-infected cells of swine testicular tissues (Cho et al., 2006). 7-Methoxycryptopleurine (IC50 of 20 nM) is rather more efficient than tylophorine (IC50 of 58 nM). Tylophorine also blocks virus RNA replication and NF-κB activation mediated by cellular JAK phosphorylation in CoV . Tylophorine and 7methoxycryptopleurine inhibit N-and S-glycoprotein activity. Dihydrotanshinone recognizes the S-glycoprotein of SARS-CoV-2 to block its entry . Rhus chinensis Mill. luteolin and tetra-O-galloyl-β-D-glucose (TGG) specifically recognize the S2 subunit and prevent viral entry of SARS-CoV (Yi et al., 2004). Luteolin also binds to the S2 protein to exert its antiviral capacity by interfering with virus-cell attachment and consequent fusion. TGG and luteolin exhibit anti-SARS-CoV activities. Therefore, LMW natural products, which bind to the SARS-CoV S-glycoprotein, can block virus infection in its host cells.
For animal CoVs such as avian IBV, Alstonia scholaris (L.) R. Br. alstotide-1 and -3 interfere with membrane proteins and S-glycoproteins but not the nucleocapsid proteins of avian IBV (Nguyen et al., 2015). These peptide-derived drugs are potentially applicable for therapeutic characteristics, although they are poor in oral bioavailability. However, alstotides are suggested to be permeable to cells, stable, and nontoxic with anti-IBV activities. Alstotide-1 interacts with the IBV M-protein during the assembly and budding of virus particles. M-protein is a glycosylated and membrane-spanning protein. The alstotide-1 and M-protein interaction implicates that alstotide-1 inhibits the assembly and budding of virus particles. Punica granatum L. polyphenols also interact with the surface S-glycoprotein of murine CoV, MHV-A59 (Sundararajan et al., 2010).

Inhibition of Interaction of S-Glycoprotein With ACE2
The β-CoV SARS-CoV recognizes ACE2 in respiratory epithelial or type I and II alveolar epithelial cells of the lung in membranebound and soluble forms (Alifano et al., 2020). ACE2 is a type I membrane-anchored carboxypeptidase with an N-terminal signal peptide. The host SARS-CoV-2 receptor ACE2 in the renin-angiotensin system (RAS) plays a role in lung infection through removal of the barrier. The SARS-CoV-2 S-glycoprotein recognizes ACE2. ACE2 is necessary for a virus receptor. The receptor-binding motif (RBM) recognizes human ACE2 (Li, 2015;Gheblawi et al., 2020). The α-CoV HCoV-NL63 and the lineage B β-CoV SARS-CoV S-glycoproteins are well known to bind to ACE2, but β-CoV MERS virus is not specific for the ACE2 recognition, while the α-CoV HCoV-NL63 is specific for the ACE2 recognition. Thus, the S viral protein drives the first attachment step on respiratory cell surfaces. This is a therapeutic target. Host ACE2 is the known host site for the S-glycoprotein RBD. The RBD sequence of the SARS-CoV-2 S-glycoprotein is homologous to the RBD of the SARS-CoV S-glycoprotein. ACE2 is also a SARS-CoV-2 drug target. To date, the ACE2 protein can be recognized by the antidiabetic troglitazone, antihypertensive losartan, anti-analgesic ergotamine, antibacterial cefmenoxime, and hepatic-protective silybin. Phyllanthus emblica L. phyllaemblicin G7, the genus Swertia, Citrus aurantium L. xanthones, neohesperidin, and hesperidin bind to the ACE2 protein, but not to the ACE2-S-protein RBD interface. A flavonoid hesperidin isolated from citrus peel interacts with the SARS-CoV-2 receptors (Meneguzzo et al., 2020). In molecular docking analysis, flavonoids and anthraquinones exhibit binding capacities to ACE2. Their binding sites of ACE2 protein are different from that of the viral S-protein. For example, the flavone chrysin (CID: 5281607) isolated from the medicinal plant Oroxylum indicum binds to the ACE2 protein in silico (Basu et al., 2020).
In addition, 18β-glycyrrhetinic acid and licochalcone A bind to the ssRNA virus nucleoprotein (NP), a target candidate for therapeutic development, because these natural ligands influence the RNA-binding property of NP. The two agents specifically recognize the RNA-binding groove of NP (PDB code 4Z9P) and disrupt the NP-viral ssRNA interaction through a conformational shift of NP oligomers to impair ssRNA assembly. Glycyrrhizin and glycyrrhetinic acid also block SARS-CoV replication (Cinatl et al., 2003). In addition, glycyrrhizin inhibits H5N1 influenza A virus replication . Glycyrrhizin and glycyrrhetinic acid are also antiinflammatory, antiviral, and anti-allergic agents. Licochalcone A is a natural phenolic chalconoid found in the Glycyrrhiza species and exhibits antimalarial and antiviral activities. It inhibits influenza neuraminidases (NAs) of influenza subtypes such as H1N1, H9N2, and oseltamivir-resistant novel H1N1strains (Chen et al., 1994;Dao et al., 2011).

Inhibition of SARS-CoV Mpro, PLpro, 3CLpro, and Related Proteases
The CoV genomes encode a polypeptide which contains a protease region. Two cysteine proteases, PLpro and 3CLpro, are directly associated with RNA virus replication. PLpro and 3CLpro cleave the viral polyprotein and produce nonstructural proteins for viral replication at the commonly conserved 11 substrate-recognition sites. Structure-based information on PLpro from SARS-CoV or other CoVs is limited. 3CLpro is also called the CoV main protease (MPro) (MW 34 kDa). Thus, Mpro is used as a target for anti-CoV drugs. Mpro controls overall RNA replication and transcription. Therefore, it is a target protease, and computational in silico simulation enables the discovery of SARS-CoV-2 Mpro-specific inhibitors (Jin et al., 2020). 3CLpro has 100% identity with other SARS-CoV genomic RNA sequences. The 3CLpro of bat and human SARS-CoV-2 exhibits 99.02% amino acid sequence homology. The SARS-CoV-2 3CLpro protein is homologous with the known SARS-CoV, HCoV, MERS-CoV, and BCoV.
As described above, CoV proteases are considered antiviral targets for the reduction of virus replication and host pathogenicity. However, nM affinity-leveled compounds are not developed for the targets. Apart from the conventional discovery from natural products, computer-aided methods to design drugs have been applied by using chemical databases for the inhibitor screening of SARS-CoV 3CLpro activity. Moreover, the known crystal structure of HCoV-229E 3CLpro facilitates design of inhibitors (Anand et al., 2003). Currently, SARS-CoV 3CLpro (PDB: 1Q2W and 1UK4) and SARS-CoV 3CLpro are elucidated for their 3D structures (Yang et al., 2003).
SARS-CoV S-cellular TNF-α-converting enzyme activation facilitates virus entry, and thus this enzyme is an antiviral target. The inhibitor TAPI-2 inhibits virus entry of SARS-CoV into host cells. TAPI-2 inhibits SARS S-glycoprotein-mediated ACE2 shedding and TNF-α synthesis in the lung (Haga et al., 2010). ADAM17 inhibitors are widely beneficial for various diseases related to tumor immunosurveillance, cancer, and inflammatory diseases. As described previously, ADAM17 inhibitors reduce TNF-α-induced proinflammatory diseases and are attractive target candidates for the inflammatory diseases involved in SARS-CoVs. For example, a dual and selective small molecular inhibitor of ADAM17 and ADAM10, named INCB7839, is currently under combined usage with rituximab for B-cell non-Hodgkin lymphoma therapy (Witters et al., 2008). Although ADAM17 inhibitors such as matrix metalloproteinase (MMP) inhibitors marimastat and prinomastat inhibit ADAM17 activity (Packer and Cadenas, 2011), they are not clinically applicable due to ADAM17 sequence homology with the MMP enzymes and physiological problems. In this context, naturally occurring molecules have been used to attempt to develop selective ADAM17 inhibitors by using in silico approaches toward ligands and targets. Through the binding of ADAM17 to ligands, silymarin has been purified as an ADAM17-specific inhibitor that binds to the active amino acid residues in the ADAM17 protein. The inhibiting capacity has been compared with a previously known inhibitor, IK682. Silymarin is found in Silybum marianum (L.) Gaertn., known as milk thistle; and Cynara cardunculus L., known as wild artichokes; Curcuma longa L. turmeric rhizome; and Coriandrum sativum L. coriander seeds (Borah et al., 2016).
Cryptotanshinone, a natural compound isolated from S. miltiorrhiza, modulates androgen receptor (AR) transcriptional regulation and downregulates TMPRSS2 gene expression as an AR target gene in androgen-responsive tumor cells. Interestingly, cryptotanshinone selectively inhibits the AR gene and thus has potential as anti-AR or SARS-CoV therapy .

Inhibition of GRP78 (HSPA5) Interaction in Silico
MERS-CoV spikes also recognize a 78-kDa glucose-regulated protein (GRP78) known as Byun1, heat shock 70-kDa protein 5 (HSPA5), and binding immunoglobulin protein (BiP). HSP5A is an ER-resident unfolded protein response (UPR) protein and acts as an alternative entry site via S-protein interaction for human viruses including papillomavirus, Ebola virus, Zika virus, and HCoVs, as well as the fungus Rhizopus oryzae (Pujhari et al., 2019;Ibrahim et al., 2020). Viral infection increases HSPA5 translocation to the plasma membrane (PM) and forms a membrane protein complex. In addition, GRP78 regulates MERS-CoV entry in the presence of DPP4. Lineage D β-CoV and bat CoV HKU also recognize the GRP78 (Ho et al., 2007;, as simulated by molecular modeling and docking (Rao et al., 2002). Other ER molecules such as activating transcription factor 6 (ATF6), inositol-requiring enzyme 1 (IRE1), and protein kinase RNA (PKR)-like ER kinase (PERK) (Ibrahim et al., 2019) are involved. GRP78 releases IRE1, ATF6, and PERK activation, contributing to translation and refolding. GRP78 translocates to the membrane and recognizes the virus by its substrate-binding domain β (SBDβ), which is bound by the RBD. The binding region is molecularly targeted for COVID-19-specific drugs. Therefore, natural products can inhibit the HSPA5 binding to the S-glycoprotein. Small natural products prevent the S-glycoprotein-HSPA5 SBDβ interaction in silico. The effects of natural products that cause HSPA5 SDBβ dysfunction prevent SARS-CoV-2 S recognition because the HSPA5 SBDβ is the binding site for the SARS-CoV-2 S-glycoprotein. During viral infection, the HSPA5 (GRP78) translocated to the cell PM recognizes the SARS-CoV-2 S-protein. In in silico AI computer-aided simulation, several natural products recognize HSPA5 SBDβ. HSPA5 SBDβ-binding natural products can block virus attachment to the host cells if they are stressed. Thus, anti-COVID-19 agents specific for HSPA5 SBDβ recognition can be beneficial for elderly humans with cell stress. Therefore, approaches using AI computer-based molecular docking simulation yielded some natural products that bind to HSPA5 SBDβ . Four Cicer arietinum L. phytoestrogens, daidzein, genistein, formononetin, and biochanin A, recognize HSPA5 SBDβ. In addition, other natural compounds such as chlorogenic acid, linolenic acid, palmitic acid, CA, CA-phenethyl ester (CAPE), hydroxytyrosol, cis-p-coumaric acid, cinnamaldehyde, and thymoquinone showed moderate binding affinities to HSPA5 SBDβ. Phytoestrogens bear the same recognition affinity to HSPA5 SBDβ. Estrogenic hormones such as estrogens, progesterone, testosterone, and cholesterol have also binding affinities to HSPA5 SBDβ. From the binding affinity, phytoestrogens and estrogens are found to be the most feasible ligands to bind to HSPA5. Phytoestrogens such as daidzein, genistein, formononetin, and biochanin A also bind to estrogen receptors (ER) of humans and murines in silico and act like estrogen-like molecules (Sayed and Elfiky, 2018). Olive leaf hydroxytyrosol has moderate binding affinity to HSPA5 SBDβ. CA and p-coumaric acid also have average binding affinities to surface HSPA5 SBDβ and compete for recognition by the S-glycoprotein. The CAPE has a medium binding affinity to HSPA5 SBDβ. Cinnamaldehyde and thymoquinone have average binding affinity to HSPA5 SBDβ.

Carcinoembryonic Antigen Cell Adhesion Molecule Receptor
The N-terminal domain of S1 recognizes CEACAM1. S-glycoprotein-CEACAM receptor binding leads to S-glycoprotein-mediated fusion of membrane. For example, MHV recognizes the CEACAM expressed on BHK cell cultures (Heino et al., 2000). In MERS-CoV, CEACAM5 isoforms are associated with attachment (Naskalska et al., 2019). Therefore, MERS-CoV recognizes CEACAM5 as the attachment and entry site (Chan et al., 2016). In the structural aspect, the S1 N-terminal domain exhibits an identical tertiary structure compared with human galectins which recognize Galresidues. The S1 N-terminal domain of the MHV recognizes mouse CEACAM1a and that of BCoV recognizes carbohydrate residues (Peng et al., 2011;Peng et al., 2012;Walls et al., 2016). Because CEACAM1a mRNA is alternatively spliced, HCoVs have been suggested to be evolutionarily recombinant between the host galectin and the S1-glycoprotein genes. However, the BCoV S1glycoprotein gene is not subjected to such recombination but bears the glycan-binding lectin activity. MHV S1-glycoprotein has also been suggested to acquire mouse CEACAM1a-binding capacity (Peng et al., 2017), suggesting that CoVs receive evolutionary pressure to acquire the interaction capacity with host receptors over cross-species (Li, 2015;Li, 2016). Moreover, soluble forms of CEACAM directly involve in S-glycoprotein-mediated PM fusion, inducing conformational shifts Taguchi and Matsuyama, 2002). On the host side, host organisms have also evolved to escape the lethal pressure from coronavirus infections. The acquired geno-and phenotypes of such hosts are expressed for SA-recognizing proteins. For example, Siglecs are representatively expressed to utilize the innate responses of host immune cells.

Heparan Sulfate as Human Coronavirus Entry Site
MHV and HCoV-NL63 are known to interact with heparan sulfate (HS) (Watanabe et al., 2007;Milewska et al., 2014). The HS proteoglycans (HSPGs) are recognized by M-protein in the absence of the S-glycoprotein in the HCoV-NL63 entry into host cells. Then, the M-protein and S-glycoprotein enhance virus entry into the host cells (Milewska et al., 2014;Naskalska et al., 2019). In general, ACE2, APN, HSPA5, furin, O-Acneuraminic acid, and HSPGs are the CoV-binding molecules.
Apart from the precise targeting of the molecules, several medicinal plant resources also exhibit antiviral activities against respiratory and influenza virus diseases. For example, Panax ginseng can prevent viral respiratory diseases and influenza virus diseases . Pelargonium sidoides also prevents respiratory viral infections (Im et al., 2015). Astragalus mongholicus Bunge can treat common cold and upper respiratory infections and also prevent influenza virus infections (Kolodziej, 2011;Liang et al., 2019). Compounds and extracts with anti-CoV activities are summarized in Table 1.

Relationship Between Structures and Activities of Natural Products
The anti-SARS-CoV-2 natural compounds have been subjected to screening for understanding their structure-activity relationships (SARs). A possible approach to understand the SARs and inhibitory mechanism(s) is to resolve the inhibitor-target complex by using analytic tools. For example, crystallized complexes of the natural products and target proteins such as enzymes, surface proteins, and host receptors can be instrumentally analyzed. However, information on the successful SARs and the inhibitory mechanism(s) are currently limited. Instead, using molecular in silico ducking simulation and computational analysis, the SAR results have been reported. Using molecular modeling and docking techniques, potential binding abilities of the compounds to the pocket sites, interface sites, or catalytic sites of targets including proteases and the ACE2-S-glycoprotein complex have been suggested. The functional groups of the binding pocket interact with targets in van der Waals, hydrophilic, hydrophobic, and H-bond interactions.
As regards natural anthraquinones, rings and substituted glycosides differentially inhibit SARS-CoV-2 targets (Li and Jiang, 2018). For example, dihydroxyanthraquinone with C1 and C2−OH groups differently inhibit SARS-CoV-2 infection (Li and Jiang, 2018). Anthocyanins interact with the active site pockets of Mpro and human ACE2, where the active site of Mpro is polar in its chemical property, having affordable binding energies. Delphinidin, an anthocyanin derivative, forms H-bond in the binding site and π stacking with the hydrophobic pocket. A diglycosidic anthocyanin, delphinidin 3,5-diglucoside binds to the Mpro and ACE2 (Sharma and Shanavas, 2020), where it recognizes the flavylium nucleus ring and the Mpro catalytic site. In addition, the −OH groups of the phenyl ring recognize the Mpro S1 catalytic site through H-bonds (Sharma and Shanavas, 2020). The benzene ring and the Hie41 of the hydrophobic Mpro S2 domain form the p-π interaction. The −OH group of the flavylium nucleus binds to the Mpro S4, while the −OH groups of the benzoyl moiety of nonglycosidic 3,5-di-O-galloylshikimic acid form H-bonds with the Mpro cavity site. The OH-group and oxygen atoms of the benzoyl groups bind to the Mpro cavity site (Sharma and      Shanavas, 2020). In contrast, for ACE2, oxygen of the COOH of 5-di-O-galloylshikimic acid binds to the Mpro cavity site via H-bonds, and non-covalent and ionic interactions. The −OH groups of the benzoyl moiety form H-bonds with the Mpro cavity site, where the side chain groups bind to benzoyl rings via the p-π stacking interaction. Therefore, the −OH groups are crucial for the SAR. Flavones such as apigenin and quercetin inhibit 3CLpro activity, which coincides with the enzyme-inhibitory data. The 3CLpro inhibitory potential of biflavone with apigenin residue at the flavone C-3ʹ is enhanced, indicating that the 3CLpro inhibitory activity is upregulated by the additional apigenin residue at C-3′. In fact, the biflavonoid amentoflavone inhibits the 3CLpro activity. Quercetin recognizes the S-glycoprotein-ACE2 interface site (Smith and Smith, 2020;Williamson and Kerimi, 2020). A quercetin derivative, avicularin (Fukunaga et al., 1989) has also the Mpro-binding affinity. A similar scutellarein glucoside has the Mpro-and ACE2-binding affinities, where the −OH groups of glycoside form the H-bonds with the Mpro catalytic site. Another −OH group of the phenyl ring also forms H-bond with the Mpro. The phenyl ring also forms the π-π stacking interaction. The carbonyl oxygen and −OH group of the chromone nucleus form the H-bonds (Sharma and Shanavas, 2020). Similar to delphinidin diglucoside and scutellarein glucoside, L-arabinoside of avicularin binds to the catalytic site through H-bonds. The benzene ring involves in the π-π stacking with the hydrophobic subsite. Also, the −OH group of the chromone nucleus and benzene ring recognize the active site through H-bonds. The −OH groups of the arabinoside and phenyl ring recognize Mpro domain 1. Multiple π-π stacking interactions are formed between the chromone nucleus and the Mpro domain. The carbonyl group of the main nucleus forms the H-bonds with the Mpro. Likely, a flavanone glycoside, hesperidin, forms multiple H-bonds with the Mpro.
The flavonoid myricetin binds to both nsp13 and anti-3CLpro (Ananda Silva et al., 2020) as well as the TMPRSS2 active pocket through the 3 H-bonds, van der Waals forces, and π-anion (Pooja et al., 2021). Similarly, baicalein interacts with TMPRSS2 via 3 Hbonds, and van der Waals and π-stacking interactions. Aesculitannin B (Pooja et al., 2021) and proanthocyanidin bind to the TMPRSS2 active site via 5 H-bonds, and van der Waals and amide-π stacking interaction. Hydrocinnamic caffeic acid and ferulic acid recognize the Mpro active site via the H-bonds. Caffeic acid forms the H-bonds with both E-and N-proteins (Bhowmik et al., 2020). A bioflavonoid rutin also forms H-bonds with M-and N-proteins. Theaflavin interacts with the catalytic pocket groove near the RdRp active site through H-bonds and π-cation interaction, resulting in low docking score (Lung et al., 2020). Membrane binding of the alkyl gallates depends on alkyl chain lengths (Stefaniu et al., 2020) by high polarity-triggered reactivity. Therefore, the position of the −OH groups on the benzoic acid ring seems to be essential, compared with the number or type of ester, −OH, and methoxy groups. For the SAR of glycyrrhizin and glycyrrhetinic acid, the free −OH (C-3), carbonyl (C-11), and COOH (C-30) groups influence the antiviral activity, while esterification of the −OH group on C-3 or the COOH group on C-30 decreases the activity. In addition, the dual esterification in the C-3 and C-30 decreases the activity, while substitution of the C-30 increases the activity (Wang et al., 2012). Betulonic acid, a triterpenoid, has an anti-SARS-CoV activity through the ketoxime backbone (Kazakova et al., 2011). The betulonic acid has a −OH and a COOH with a double bond at position C-20, 3-OH and 28-COOH groups (Regueiro-Ren et al., 2018), and C-3 and C-17 positions are crucial for the activity. Polyphenolic tannins show different binding capacities to the 3CLpro due to their SAR activities. The tannins recognize the receptor-binding spot and putative catalytic dyad of the 3CLpro. Tannic acid is a specific polyphenolic form of tannin with weak acidic properties due to the grouped phenols, where −OH groups, ketone groups ( O), and phenolic rings involve in binding to the 3CLpro through H-bonds and other forces (Khalifa et al., 2020). For example, hydrolyzable tannins including pedunculagin directly recognize the catalytic dyads and 3CLpro receptor-binding site with 5 Hbonds. Similarly, castalin and tercatain recognize the 3CLpro receptor-binding site via H-bonds and arene-arene interactions, influencing the catalytic dyad residues. Other hydrolyzable tannins including punicalin and isoterchebin secondarily recognize the catalytic dyad residues of the 3CLpro. Thymoquinone also interacts with the catalytic site of the 3CLpro via multiple H-bonds and π-H interactions (Kadil. et al., 2020). The −OH and carbonyl groups interact with the targets via H-bonds. For example, the −OH group binds to the Mpro, Nsp15, and S-glycoprotein (Kodchakorn et al., 2020).

CONCLUSION
The COVID-19 outbreak is a global pandemic health problem. The SARS-CoV-2 RNA sequence has been known to be highly homologous with those of the CoVs. For the present crisis of pandemic SARS-CoV-2 infections, therapeutic and preventive approaches are simultaneously required to overcome the current life-threatening disease. Because development of blockers and inhibitors of viral entry and replication is urgent, computational AI has been incorporated to accelerate drug designation. Natural resources contain promising ligands for the development of therapeutic targets. Naturally occurring compounds are potentially promising resources for their antiviral properties. SARStargeting agents can be effective against related CoV strains due to their similar life cycles. LMW compounds can be generated, discovered, and simulated with AI assistance for target molecules. Chemical derivative modification of known structures by AI-based technologies can enhance such drug activities. Thus, natural products may be useful for use in medical therapy of SARS-CoV-2 infections.

AUTHOR CONTRIBUTIONS
Conceptualization, C-HK; writing-draft preparation, C-HK; review and editing, C-HK.