Coronaviruses are positive-stranded RNA viruses with a crown-like appearance under an electron microscope due to the presence of spike glycoproteins (S protein) (Yan et al., 2020). The subfamily of orthocoronavirinae in the Coronaviridae family is subdivided into four CoVs genera, i.e., alphacoronavirus (alphaCoV), betacoronavirus (betaCoV), deltacoronavirus (deltaCoV), and gammacoronavirus (gammaCoV) (Chan et al., 2013). Genomic evaluation showed that bats and rodents are the gene sources of alphaCoVs and betaCoVs, respectively, while the avian species are sources of deltaCoVs and gammaCoVs (Su et al., 2016). The virus can cause respiratory, enteric, hepatic, and neurological diseases (Kahn and McIntosh, 2005). HCoV-OC43 and HCoV-HKU1 (lineage A betaCoVs); HCoV-229E, and HCoV-NL63 (alphaCoVs) have been identified as the human CoVs. Most of them are associated with mild immune responses such as common colds and upper respiratory tract infections, especially in immunocompromised people. However, SARS-CoV, SARS-CoV-2, and MERS-CoV (lineage B and C betaCoVs, respectively) are epidemic causing variables associated with adverse outcomes in subjects of all ages. Exposing the virus to heat treatment at a temperature above 75°C for 3 min results in its inactivation (Abraham et al., 2020; Raeiszadeh and Adeli, 2020). Exposure to higher temperatures causes a decrease in the replication rate. It is also inactivated by lipid solubilizing solvents, such as ether, ethanol, chlorine-containing disinfectants, peroxyacetic acid, and etc (Jing et al., 2020).

SARS-CoV-2 has a single-stranded RNA envelope. For its characterization, a metagenomic next-generation sequencing approach was applied, which is 29881 bp in length and encodes 9,860 amino acids (Chen L. et al., 2020). Two types of proteins are expressed as structural and non-structural using gene fragmentation (Mousavizadeh and Ghasemi, 2020). The S, E, M, and N gene codes are for structural proteins, whereas non-structural 3-chymotrypsin-like protease, papain-like protease, and RNA-dependent RNA polymerase are encoded by the ORF region. The S glycoproteins are present in the surface of SARS-CoV-2 that binds to the ACE2 host cell receptor and potentiates the penetration of the virus to the cell. As the S protein binds to the receptor, the TM protease Serine 2, positioned at the host cell membrane, helps in entering into the cell and activating the S protein. As the virus gets cell entry, the viral RNA is released in the process of RNA replication. Then, transcription takes place through protein cleavage and the assembly of the replicase-transcriptase complex (Chen L. et al., 2020). Structural proteins are synthesized, assembled, and packaged in the host cell and viral particles are released further.

The transmission routes of SARS-CoV-2 are shown in Figure 1. The first case was identified in a seafood market in Wuhan, China; however, other cases were not linked with it. Human to human transmission occurred later and people acted as hosts and carriers of the virus (Riou and Althaus, 2020). The presentation of the infection included fever, dry cough, tiredness, arthralgia, anosmia (loss of smell) and loss of taste. Symptomatic individuals were isolated and kept in quarantine for a certain period of time. Viral transmission was associated with respiratory droplets from coughing and sneezing (Dhand and Li, 2020). Asymptomatic individuals can also transmit the infection. Given that they are not quarantined, they may spread the infection up to 80% more than symptomatic individuals, who are diagnosed and isolated on time (Ford et al., 2020). There is some evidence that the transmission of the virus is more prevalent in intensive care units (ICUs), compared with general wards, perhaps due to the abundance of devices producing aerosols. This applies to COVID-19 patients hospitalized in such departments among non—COVID-19 patients. Such a comparison is not applicable to COVID-19 wards, where all the patients are infected. Additionally, the virus can be found on floors, computer mice, trash bins, and door handles and people can be infected through hand contact with the contaminated surfaces (Guo et al., 2020). Based on data from China CDC and local CDCs, it has been found that the virus can remain incubated for about three to 7 days and the time from infection to symptoms takes 12.5 days (Li Q. et al., 2020). The data showed that the virus gets doubly replicated every 7 days (T.K and G, 2020).

With a particle size lower than 100 μm, airborne transmission is primarily suspected of transmitting SARS-CoV-2 (Jayaweera et al., 2020). Aerosols may originate from dental activities and various medical surgeries and procedures, such as endotracheal intubation, bronchoscopy, open suctioning, nebulized treatment administration, manual ventilation before intubation, turning the patient into the prone position, disconnecting the patient from the ventilator, non-invasive positive-pressure ventilation, tracheostomy, and cardiopulmonary resuscitation. Furthermore, aerosols may be produced by a droplet oozed during a normal conversation or an infected subject coughing and sneezing (Tran et al., 2012). These findings have also been corroborated by many studies. In a study by Lai et al., many healthcare workers were infected while they were treating the patients in Tongji Hospital in Wuhan, China (Lai X. et al., 2020). The study shows that 9,684 healthcare workers were undertaken and 110 of them had COVID-19 with an infection rate of 1.1%. A major infection rate of about 71.8% was found in nurses (70 nurses), with a median age of 36.5 years. However, no surfaces were tested positive for COVID. The commonly observed symptoms were fever, myalgia or fatigue, cough, sore throat, and muscle ache. For taking precautions, the World Health Organization (WHO) recommended a set of protocols to be followed.

Another mode of SARS-CoV-2 transmission is self-inoculation. It may occur through poor hand hygiene or poorly following the disease-controlling etiquettes (Przekwas and Chen, 2020). Viral transmission has been increased due to frequently touching contaminated fomites.

Besides airborne transmission, the fecal route has also a discernible effect on the transmission of the virus (Heller et al., 2020). A study conducted in China showed that out of 1,070 specimens collected from 205 COVID patients from three different hospitals, the virus in 29% of the positive COVID cases was transmitted through fecal route after they observed live infectious agents in the patients’ stools (Wang W. et al., 2020). Xing et al., examined three patients for the continually shredding of the virus through stools, even after the nasopharynx samples showed negative results (Xing et al., 2020). Consequently, there is a strong need for the inclusion of feces or anal swab tests before discharging patients after recovering from COVID-19.

Earlier studies showed that about 66% of COVID cases in China were due to the seafood market in which various living wild animals, including bats, marmots, and poultry, were on sale (Chen N. et al., 2020; Huang et al., 2020). This has been linked to the sudden outbreak of COVID in Wuhan city. The WHO investigation reports showed that the Huanan seafood market samples were tested positive for COVID, but linking it to specific animals was not established.

Until October 11, 2021, a total of 238,664,271 positive cases and 4,867,551 deaths have been reported around the world according to Worldometer. info (Worldometer, 2020). 215,862,052 cases out of them have recovered, with an average recovery rate of 90.45%. About 100,751,486 positive cases (42.21%) of the total cases have been reported in the United States, India, and Brazil only. Apart from these three countries, the other top ten countries included UK, Russia, Turkey, France, Iran, Argentina, and Spain. All these countries contributed to more than 60% of the total reported cases. While Seychelles topped in total cases per million people, with 218,297counts, Peru topped in deaths per million people in the list of around 220 countries.

The human gastrointestinal tract hosts around 1,014 resident microorganisms such as bacteria, archaea, viruses, and fungi (Gill et al., 2006). The prevailing gut bacteria in healthy individuals include the phyla of Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. The bacterial families Bacteroidaceae, Prevotellaceae, Rikenellaceae, Lachnospiraceae, and Ruminococcaceae reside in the colon in large numbers (van der Lelie et al., 2020). The gut microbiota populations consist of at least one trillion microorganisms and weigh up to 3 kg (Rooks and Garrett, 2016; Nagpal et al., 2018). The microbiota’s genetic material inherently regulates their population dynamics and the expression of a wide range of biomolecules.

During pathogen infection, the gut microbiota will act as competitors in the antivirus combat. Meanwhile, the myeloid cells will be activated and cytokines such as IL-6, IL-1, and TNF will be released. Then, it will be followed by an increased expression of cytokine-related receptors (e.g., IFN-α/β receptor). Cytokine activated genes (CAGs) will be transcribed and then proteins with antiviral functions will be coded. Combined with Th17 cells, released cytokines will induce inflammation through NF-κβ or JAK-STAT signaling pathway. The gut microbiota also play a role in reducing inflammation in case of hypersensitivity.

Constant crosstalk between the microbiome and the human body provides them with habitat and nourishment. In return, the microbiome contributes to the regulation of the host’s physiological functions in terms of digestion and immunity (Figure 2). Digestion is co-facilitated by substances produced by microorganisms (Singh et al., 2017; Anand and Mande, 2018). At the same time, microorganisms serve as competitors against intruding pathogens. The gastrointestinal immune tissue maintains a balance between Th17 lymphocytes and T-regulatory cells (Tregs) to supervise the microorganisms’ population growth. This balanced coexistence is known as symbiosis (Li et al., 2020b; Lee and Shin, 2020). When internal or external factors induce alterations in the microbiome, a temporary status of dysbiosis occurs. Dysbiosis pertains to the depletion or excessive proliferation of intestinal microbial populations and/or the disruption of their physiological functions. A dysbiotic microbiome has been detected in several diseases from inflammatory bowel diseases (IBDs) to cardiovascular diseases and depression (Tang et al., 2017; Khan et al., 2019).

Various pro-inflammatory markers have been detected and investigated within the last years (Vandeputte et al., 2016). Although their association with diseases that are systematic or that affect different body systems remains obscure, the “leaky gut” theory provides a formidable explanation (Obrenovich, 2018). According to this theory, alterations in the gut microbiota composition can lead to a leakage of endotoxins into the circulation that promotes systemic inflammation in addition to the development of obesity, metabolic diseases, asthma, and multiple sclerosis among others (Singh et al., 2017; Tang et al., 2017).

Localized or circulated toxins are perceived as pathogen- and microorganism-associated molecular patterns (PAMPs, MAMPs) by cellular pattern recognition receptors (PRRs). These toxins induce the production of pro-inflammatory cytokines (Negi et al., 2019). Cytokines are signaling biomolecules secreted by immune cells to affect numerous endogenous processes, including immunomodulation (Schirmer et al., 2016). Detected pro-inflammatory markers are presented in Table 1.

The role of the microbiome in infectious diseases has been extensively studied. Despite the advances in the field, many aspects of this topic remain unknown (Negi et al., 2019; Dhar and Mohanty, 2020). Briefly, the mainstay of treatment for infections, especially antibiotics, affects the gut microbiota by decreasing the population of microorganisms that are sensitive to the prescribed medicines. In most cases, this dysbiotic condition leads to temporary gastrointestinal distress (Bernstein, 2014; He et al., 2020). At the same time, the interaction between the microorganisms and the host immune system can affect the immune response against pathogens (Rooks and Garrett, 2016; Nagpal et al., 2018).

COVID-19 seems to affect the digestive system as well, taking into account that many patients have gastrointestinal symptoms, including but not limited to vomiting and diarrhea (Xiao et al., 2020). Moreover, enterocytes express ACE-2 inhibitors and can be infected by SARS-CoV-2 (Wang J. et al., 2020; He et al., 2020). Stool diagnosis has been one of the most sensitive and specific methods for detecting SARS-CoV-2 although it is not widely used for practical reasons (Xiao et al., 2020; Zuo et al., 2020). Accumulating evidence concerns the implications of the gut microbiota in the prognosis, diagnosis, and treatment of COVID-19.

The non-cannabinoid metabolites of Cannabis sativa L., caflanone (Figure 3A), were employed to establish the potential against COVID-19 and associated with the virus entry factors. Ngwa and colleagues investigated the in silico and in vitro effect of caflanone. Caflanone was docked with the ACE2 receptor (PDB ID: 1R4L) while in vitro antiviral activity was evaluated against the OC43 human coronavirus (hCoV-OC43). The results indicated that caflanone has a high affinity with the CoV-2 spike glycoprotein-binding sites towards the angiotensin-converting enzyme 2 (ACE2), which could inhibit the viral entry of SARS-CoV-2. Binding energy is much lower than chloroquine (CLQ) that was initially considered as prophylactics or a therapeutic anti-COVID-19 compound. Key amino acid residues in the ACE2 receptor interacting with caflanone were Arg273, Phe274, Glu375, and Zn coordinated to Glu402. In vitro results suggested that caflanone could inhibit hCoV-OC43 with an IC₅₀ value of 0.42 µM. Moreover, they found that caflanone could decrease the expression of the viral entry-related factors, such as AXL-2, ABL-2, cathepsin L, PI4Kiiiβ, and various cytokines, viz. IL-1β, IL-6, IL-8, Mip-1α, and TNF-α (Ngwa et al., 2020).

Ngwa and colleagues investigated the in silico effect of hesperetin (Figure 3B) while it was docked with the ACE2 receptor (PDB ID: 1R4L) and compared with chloroquine. Hesperetin has a higher binding affinity than chloroquine towards the ACE2 receptor, which suggested its potential against COVID-19 (Ngwa et al., 2020). Hesperetin is a commonly available flavonoid found in citrus fruits, as reported by Cordia sebestena L. (Prakash et al., 2020) and Origanum majorana L. (Erenler et al., 2016).

Furthermore, Ngwa and colleagues investigated the in silico effect of myricetin while it was docked with the ACE2 receptor (PDB ID: 1R4L) compared with chloroquine. In a docking study, Myricetin (Figure 3C) showed better binding affinity than chloroquine (Ngwa et al., 2020). Myricetin can be isolated from many sources, including Myrica rubra (Lour.) Siebold and Zucc. (Wang et al., 2010), Hypericum afrum Lam. (Larit et al., 2021), Abelmoschus moschatus Medik. (Liu et al., 2005), Tecomaria capensis (Thunb.) Spach var. aurea (Elshamy et al., 2020), and Moringa oleifera Lam. (Shervington et al., 2018).

In addition, Ngwa and colleagues investigated the in silico effect of the linebacker while it was docked with the ACE2 receptor (PDB ID: 1R4L) and compared with chloroquine. Linebacker presented the potential of having a higher affinity with the infection-related proteins of SARS-CoV-2, which is regarded as novel prophylactics and a therapeutic natural product. It can be isolated from Cannabis sativa L. (Ngwa et al., 2020).

Chymotrypsin-like protease (3CLpro), papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), and Spike (S) protein are the crucial proteins of SARS-CoV-2 that infect the host cell. Luteolin was reported to have anti-SARS-CoV activity before (Wu et al., 2004; Prasad et al., 2020). Yu et al., performed the docking simulation to investigate the binding efficiency of luteolin (Figure 3D) on these proteins (PDB IDs: 6LU7 for 3CLpro; 4OVZ for PLpro; 6NUS for RdRp and 6VSB for S glycoprotein). Luteolin is the main flavonoid constituent of honeysuckle, which is the important antiviral ingredient used in traditional Chinese medicines (TCM), including Lianhuaqingwen (LH). Their results suggested that luteolin has lower binding energy and stronger interactions with the key amino acid residues than the co-crystallized ligand found in the crystal structure of these test proteins of SARS-CoV-2. Thus, it can be suggested that luteolin exhibits a potential antiviral activity (Yu et al., 2020). Luteolin can be isolated from many sources such as Martynia annua L. (Lodhi and Singhai, 2013), Lonicera japonica Thunb. (Kang et al., 2010), Vitex negundo L. (Rooban et al., 2012), Colchicum ricthii R. Br. (Abdalla et al., 1994), and Elsholtzia rugulosa Hemsl. (Liu R. et al., 2011).

Pectolinarin (Figure 3E) indicated its inhibitor activity with the reduction of the fluorescent intensity of 3CLpro. Its measured IC₅₀ value was 51.64 µM from the curves of the concentration in the fluorescence experiment. In a docking study, Seri Jo et al. found that the L-mannopyranosyl β-D-glucopyranoside moiety and the chromen-4-one moiety of pectolinarin could capture the space of S1, S2, and S3’ sites (Aanouz et al., 2020). Pectolinarin can be isolated from Cirsium subcoriaceum (Less.) Sch. Bip. (Martínez-Vázquez et al., 2007), C. chanroenicum Nakai (Lim et al., 2008), and C. setidens (Dunn) Nakai (Yoo et al., 2008).

Baicalin (Figure 3F) could significantly reduce the fluorescent intensity of 3CLpro as the IC₅₀ value was 34.71 µM. Baicalin binds in silico to Glu166, Gly143, and Asn142 by forming hydrogen bonds and His41 by pi-pi stacking (Jo et al., 2020; Mu et al., 2020). Quyuan Tao et al. screened all the compounds in the Huashi Baidu formula and studied the herb-compound-targets network. Consequently, they found that baicalin was the most stable active part in the docking study with 3CLpro (Tao Q. et al., 2020). Baicalin has been isolated from Scutellaria baicalensis Georgi (Ohkoshi et al., 2009; Peng-fei et al., 2012). Baicalein (Figure 3G), a phytoconstituent of Polygonatum sibiricum Redouté, could bind to the acid residues of 3CLpro, Glu166, Ser144, Gly143, Cys145, Leu141, and His163 by forming hydrogen bonds, and Gln189, Arg188, Met165, Phe140, and Asn142 by forming hydrophobic interactions (Mu et al., 2020). Baicalein can also be isolated from Scutellariae baicalensis Georgi Radix (Kimura et al., 2001), and Scutellaria baicalensis Georgi (Kimura et al., 1997). Zandi et al. had studied the anti-SARS-CoV-2 activity of baicalin and baicalein in Vero and Calu-3 cell lines and compared it with remdesivir. They found EC₅₀ (µM) of baicalin, baicalein and remdesivir as 4.5, 9.0, and 1.0 respectively (in Vero cell line), and 1.2, 8.0, and 0.14 respectively (in Calu-3 cell line). Further, they had reported strong binding of baicalin and baicalein with SARS-CoV-2 RdRp, when checked by in silico tools. In the thermal shift assay, they found that baicalein caused a ΔTm of 3.9°C of nsp12, which suggested that baicalein is a strong and specific binder for nsp12 component of RdRp (Zandi et al., 2021).

In the fluorescence experiment, herbacetin (Figure 3H) could attenuate the intensity of the fluorescence of 3CLpro. In a docking study, the phenyl moiety of herbacetin could occupy the S1 site while the chromen-4-one moiety is located in the S2 site with hydrogen bonds (Jo et al., 2020). Herbacetin can be isolated from Linum usitatissimum L. (Veeramani et al., 2018), Rhodiola rosea L. (Péter Zomborszki et al., 2019), and Ephedra sinica Stapf (Hyuga et al., 2013).

In a previous study, quercetin (Figure 3I) and its 7-O-Arylmethylquercetin derivatives exerted their anti-SARS-CoV and anti-HCV in vitro effects (Park et al., 2012; Prasad et al., 2020). Now, a docking study indicated that quercetin could bind to ACE2 by forming hydrogen bonds with the amino acid residues Lys745, Tyr613, His493, and Asp609 (Tao Q. et al., 2020). It could also reveal a strong interaction between the main protease of SARS-CoV-2 and Glu290 and Asp289 (Vijayakumar et al., 2020). As part of the molecular mechanism exploration of Respiratory Detox Shot, Zhang and the team had performed molecular docking studies of quercetin with the 3CLpro of SARS-CoV-2 (PDB ID: 6LU7) and found that quercetin can form hydrogen bonds with His163A, Ser144A, and Cys145A (Zhang ZJ. et al., 2020). These results indicated that a novel natural product requires in vitro and in vivo further study since the molecule is effective against both the viral target and the host receptor target. Quercetin has been isolated from multiple sources, including Euonymus alatus (Thunb.) Siebold (Fang et al., 2008), Rosa canina L. (Fujii and Saito, 2014), Diospyros kaki L. f. (Cho et al., 2016), and Toona sinensis (Juss.) M. Roem. (Zhang et al., 2016). Quercetin is also readily available in various foods like onion (Allium cepa L.), apple (Malus domestica (Suckow) Borkh.), and Broccoli (Brassica cretica Lam.), etc (Boyer and Liu, 2004; Lombard et al., 2005; Wu et al., 2019).

The protein-ligand docking suggested that cyanidin (Figure 3J) could downregulate the RNA-dependent RNA polymerase and prevent the replication of SARS-CoV-2 by binding to the Asp761 catalytic residue (Vijayakumar et al., 2020). Cyanidin can be isolated from sources like Prunus cerasus L. (Wang et al., 1999) and Oryza sativa L. cv. Heugjinjubyeo (Hyun and Chung, 2004). There are plenty of sources where cyanidin has been isolated in its glycosidic form, though.

In a docking study, diosgenin (Figure 3K) is one of the most active components in Polygonatum sibiricum Redouté. A small molecule of diosgenin could form a hydrogen bond with Met276, form hydrophobic interactions between Arg131, Lys137, Asp289, Leu287, Leu286, Ala285, Gly275, or Tyr239, and 3CLpro, and form hydrophobic interactions between Phe40, Asp350, Asp382, Ala348, His378, His401, Asn394, Arg393, Tyr385, Phe390, or Trp69, and ACE2. In addition, it could form a hydrogen bond with Asn437, form hydrophobic interactions between Phe334, Lys333, Ile428, Thr431, Asn435, Tyr438, Ser336, or Ala339, and the S protein, form a hydrogen bond with Lys267, and form hydrophobic interactions between Pro461, Thr319, Val320, Phe321, Pro322, Trp268, Ile266, Tyr265, or Ser255, and the RdRp. This molecule possesses the potential against the infection of SARS-CoV-2 (Mu et al., 2020). Diosgenin has also been isolated from other sources like Hellenia speciosa (J.Koenig) S.R.Dutta (Selim and Al Jaouni, 2015), Solanum virginianum L. (Sato and Latham, 2002), Dioscorea bulbifera L. (Pietropaolo et al., 2014), and Dioscorea nipponica Makino (Kang et al., 2011).

(+)-Syringaresinol-O-beta-D-glucoside (SBG) exerts its antiviral effect through forming hydrogen bonding interactions with Glu564, Asn210, Lys94, Glu208, Asp206, Gly205, Trp203, Tyr202, and Gln102 and hydrophobic interactions with Leu91, Lys94, Ser563, Leu95, Lys562, Val212, Pro565, Val209, Trp566, and Gln98 of the ACE2 receptor (Mu et al., 2020). SBG (Figure 3L) can be isolated from Viscum album L. (Nazaruk and Orlikowski, 2015).

Narcissoside (Figure 4M) has a higher affinity with the protein complex 6W63 of SARS-CoV-2 causing COVID-19 and the standard inhibitor X77. In a docking study, it could bind to Arg188, Glu166, His 164, Cys145, Asn14, Cys44, His 41, Gln192, and Thr190 by forming hydrogen bonds and exerting its potent to inhibit the activity of the COVID-19 proteins (Dubey and Dubey, 2020). Narcissoside has been reported to be found in Azima tetracantha Lam. (Duraipandiyan et al., 2016), Morinda citrifolia L. (Su et al., 2005), Polygonatum odoratum (Mill.) Druce (Ganbaatar et al., 2015), and Lolium multiflorum Lam. (Kuppusamy et al., 2018).

In docking the non-structural polypeptide, NSP25 (GVITHDVSSAINRPQIGVVREFLTR) study, kaempferol (Figure 4N) could distinctly perform interactions with Gly1 and Arg25 through forming hydrogen bonds, with Val18 through pi-sigma, and with Phe22 through the pi-pi stacked bonds (Hamza et al., 2020). TMPRSS2, a key receptor for the entry of SARS-CoV-2, is reportedly being downregulated after the treatment of the LNCaP cells with kaempferol using qPCR data as detected by Da and the team (Da et al., 2019). Kaempferol is observed in many plant sources and is even found in propolis, a resinous production by honeybees (Berretta et al., 2020). This suggested that kaempferol could serve as a potential candidate since it can act on the host receptor target as well as the viral target. Kaempferol has been isolated from multiple sources, including Euonymus alatus (Thunb.) Siebold (Fang et al., 2008), Vachellia nilotica (L.) P.J.H.Hurter and Mabb.(Singh et al., 2008), Persicaria tinctoria (Aiton) Spach. (Kataoka et al., 2001), Eruca vesicaria (L.) Cav. (Kishore et al., 2017), Lagenaria siceraria (Molina) Standl. (Rajput et al., 2011), and Nelumbo nucifera Gaertn. (Lee B. et al., 2015).

In a docking study, rutin (Figure 4O) showed the highest affinity with Mpro, which binds to Ser144, His163, Asn142, Cys145, Gly143, His41, Phe140, Thr25, Thr26, Thr190, Arg188, Met165, Glu166, His164, Leu141, and Gln189 residue sites. In addition, it possesses the potential to combat COVID-19 (Das et al., 2020). In a docking study of Felipe Moura A da Silva, rutin formed hydrogen bonds with His41, Thr25, Cys44, Met165, Gln189, and Thr190 (da Silva et al., 2020). Rutin is again a very common phytoconstituent which is widely available in a large number of resources, including but not limited to Dendropanax morbifer H. Lev. (Choi et al., 2015), Schinus molle L. (Machado et al., 2008), Triticum aestivum L. (Dixit, 2014), Chrozophora tinctoria (L.) A. Juss. (Abdel-Naim et al., 2018), Spermacoce hispida L. (Sundaram.R et al., 2018), Calendula officinalis L. (Das et al., 2020), Edgeworthia chrysantha Lindl. (Shengqiang et al., 2009), Caragana spinosa (L.) Hornem., and Memecylon edule Roxb. (Srinivasan et al., 2015).

Isorhamnetin-3-O-b-D-glucoside (IRG) (Figure 4P) showed high affinity, good stability, and flexibility with Mpro by binding to Cys145, Gly143, Asn142, Ser144, His163, Phe140, Gln189, Asp187, Arg188, Met165, His41, Thr26, and Met49 (Das et al., 2020). It has been reported that it is found in Calendula officinalis L. (Das et al., 2020), Chrysanthemum morifolium (Ramat.) Hemsl (Jun Hu et al., 2017), and Salvadora persica L.(Ali et al., 1997).

Calendoflaside (Figure 4Q) showed its inhibiting function to Mpro by binding to major amino acid residues as Arg188, Asp187, Met165, His163, Ser144, Glu166, Phe140, Leu141, Cys145, Gly143, Asn142, Leu27, Met49, Gln189, and His41 (Das et al., 2020). It has been reported that it is found in Calendula officinalis L. (Das et al., 2020).

Procyanidin B2 revealed the lowest binding energy to 3CLpro, which has been isolated from Uncaria tomentosa (Willd. ex Schult.) DC. It also showed low barriers to bind in the ligand pathway simulations, that predicted inhibitory effect against SARS-CoV-2 (Yepes-Perez et al., 2020). Procyanidin B2 (Figure 4R) can also be obtained from Malus domestica (Suckow) Borkh. (Shoji et al., 2003), Vitis sp. (Yin et al., 2017), Litchi chinensis Sonn. (Li and Jiang, 2007), Adansonia digitata L. (Shahat, 2008), Malus domestica (Suckow) Borkh. (Hibasami et al., 2004), and Hypericum perforatum L. (Butterweck et al., 1998).

The special structure of procyanidin has strong interactions with the proteins of SARS-CoV-2 which could inhibit the functions and the process of infection. The binding results revealed that procyanidin in ACE2 could bind to Ser44, Ser47, Asp350, Asp382, Tyr385, Arg393, Asn394, and His401 by forming hydrogen bonds, to Phe40 and Phe390 through hydrophobic interactions, and to Asn394, Gly395, Ser43, Leu351, His378, Ala348, Trp69, Leu391, Met62, Ser47, and Asn51 through VDW interactions. In Mpro, procyanidin forms hydrogen bonds with Ser44, Ser47, Asp350, Asp382, Tyr385, Arg393, Asn394, and His401, hydrophobic interactions with Phe40 and Phe390, pi-sulfur bonds with Met49, and pi-alky interactions between the benzene ring and Cys145. In regard to the S protein, procyanidin shows that there are hydrogen bonds with Ser375, Thr376, Gly404, Asp405, Arg408, and Ile410 residues hydrophobic interactions with Thr376, Val407, and Arg408, and pi-cation and pi-anion interactions with Lys378 and Asp405, respectively. The blocking of procyanidin could effectively prevent the infection and replication of the virus (Maroli et al., 2020). Procyanidin can be isolated from Sclerocarya birrea (A.Rich.) Hochst. (Galvez et al., 1993), Machaerium floribundum Benth. (Waage et al., 1984), and Phaseolus vulgaris L. (Silverstein et al., 1996). Furthermore, there are numerous sources where procyanidin oligomers and their derivatives are abundantly available.

Nicotiflorin (kaempferol-3-O-rutinoside) could bind to the catalytic dyad of 3CL pro, His41, and Cys145. Furthermore, it could form hydrogen bonds with Met49, Glu166, and Thr190, form pi-pi and pi-sigma interactions with His41, and form pi-sulfur interactions with Cys145. It possesses an inhibitory effect on SARS-CoV-2 (da Silva et al., 2020). Nicotiflorin (Figure 4S) can be obtained from Caragana spinosa (L.) Hornem. (Olennikov and Partilkhaev, 2012), Zeravschania aucheri (Boiss.) Pimenov (Zahra Ahmadian et al., 2017), Nymphaea candida C. Presl (Zhao J. et al., 2017), Edgeworthia chrysantha Lindl. (Shengqiang et al., 2009), and Brickellia cavanillesii A. Gray (Avila-Villarreal et al., 2016).

Broussochalcone A (Figure 4T) is a kind of key polyphenol obtained from Broussonetia papyrifera (L.) L'Hér. ex Vent. It possesses higher affinity, higher stability, and less conformational fluctuations in the Mpro of SARS-CoV-2 than darunavir and lopinavir which are anti-HIV drugs. In a docking study, it bound to the key catalytic residues, His41 and Cys145. Furthermore, it formed hydrogen bonds with Thr26, Gly143, Ser144, Cys145, and Glu166, pi-sigma interactions with His41, pi-alkyl with Met165, and pi-sulfur interactions with Met49 to exert its potential to combat COVID-19 (Ghosh et al., 2020).

As the main content of Broussonetia papyrifera (L.) L'Hér. ex Vent., papyriflavonol A showed better binding energy and higher stability when it was docked with Mpro than darunavir and lopinavir as it formed hydrogen bonds with Leu141, Cys145, and Arg188, and formed pi-alkyl interactions with His41, Leu27, and Met165 (Ghosh et al., 2020). Papyriflavonol A (Figure 4U) can also be isolated from Macaranga pruinosa (Miq.) Müll.Arg. (Syah and Ghisalberti, 2010).

Broussoflavan A (Figure 4V) could be extracted from Broussonetia papyrifera (L.) L'Hér. ex Vent. The Broussoflavan A-Mpro complex showed better stability than darunavir and lopinavir due to the formation of hydrogen bonds with the residues Gly143, Glu166, and Asn143, the formation of pi-alkyl interactions with His41, Met165, and Cys145, and the formation of pi-sulfur interactions with Met49. The results predicted the promising potential of Broussoflavan A against COVID-19 (Ghosh et al., 2020).

Fisetin (Figure 4W) is a 7-hydroxyflavonol that can be obtained from various pigmented fruits and vegetables, like Elaeagnus indica Servett. (Srinivasan et al., 2016), Hymenaea courbaril L. (jatoba) (da Costa et al., 2014), and Toxicodendron vernicifluum (Stokes) F.A.Barkley (Lee JH. et al., 2015). In their respiratory detox shot, which is a Chinese Herbal Medicine analysis, Zhang and the team found that fisetin could make hydrogen bonds with the Cys145A amino acid residues of SARS-CoV-2 3CLpro (PDB ID: 6LU7). Therefore, fisetin can act as a potential inhibitor for this target enzyme. It is also one of the components in this Chinese Herbal Medicine (Zhang ZJ. et al., 2020).

Isolicoflavonol (Figure 4X), a flavonol analog, can be isolated from various sources, such as Glycyrrhiza uralensis Fisch. ex DC. (Han et al., 2012), Broussonetia papyrifera (L.) L'Hér. ex Vent.(Zheng et al., 2008), Macaranga indica Wight (Yang et al., 2015), and Macaranga conifera (Rchb.f. and Zoll.) Müll.Arg. (Jang et al., 2002). Besides kaempferol and fisetin, Zhang and the team have also performed a docking study on isolicoflavonol. They found that isolicoflavonol exerted a significant hydrogen bonding effect on the Ser144A, Cys145A, and His163A amino acid residues of SARS-CoV-2 3CLpro (PDB ID: 6LU7) (Zhang ZJ. et al., 2020). Therefore, isolicoflavonol can act as a potential inhibitor for this target enzyme.

Licoisoflavone B (Figure 4Y) can be traced in many plants, such as Lupinus albus L. (Tahara et al., 1984), Lupinus angustifolius L. ( Lane et al., 1987 ), Sophora moorcroftiana (Benth.) Benth. ex Baker (Shirataki et al., 1988), and Sinkiang licorice root (Saitoh et al., 1978). Zhang and the team have performed a docking study on licoisoflavone B, along with the abovementioned natural products, viz. kaempferol, fisetin, and isolicoflavonol. They found that licoisoflavone B could make hydrogen bonds with Asn142A and Gln189A amino acid residues of SARS-CoV-2 3CLpro (PDB ID: 6LU7). This finding suggested that licoisoflavone B could serve as a potential candidate as this viral enzyme inhibitor (Zhang ZJ. et al., 2020).

Crocin (Figure 5A) could be extracted from Crocus sativus L. With its prominent effect on anti-HSV and anti-HIV drugs, crocin indicated a more promising binding energy value (−8.2 kcal/mol) with the main protease of SARS-CoV-2 than most natural products in the docking study (Aanouz et al., 2020). Another reported source for crocin is Gardenia jasminoides J. Ellis (Lee et al., 2005).

Even rarely isolated from Laurus nobilis L., β-eudesmol (Figure 5B) has antibacterial and antiviral functions. In a docking study, the β-Eudesmol binding energy value is −7.1 kcal/mol while the CLQ value is −6.0 kcal/mol against the main protease of SARS-CoV-2 (Aanouz et al., 2020). β-eudesmol can be isolated from Zingiber zerumbet (L.) Roscoe ex Sm. (Yu et al., 2008), Magnolia obovata Thunb. (Tachikawa et al., 2000), Dioscorea japonica Thunb. (Miyazawa et al., 1996), and Teucrium ramosissimum Desf. (Ben Sghaier et al., 2016).

Sarsasapogenin (Figure 5C) could be a potential inhibitor for the Nsp15 of SARS-CoV-2 by forming a strong hydrogen bond with Lys290. Its binding energy is much lower than hydroxychloroquine and chloroquine (Kumar S. et al., 2020). Sarsasapogenin can be found in Anemarrhena asphodeloides Bunge (Bao et al., 2007), Asparagus officinalis L. (Wang et al., 2011), and Yucca glauca Nutt. (El-Olemy et al., 1974) while glycosidic and other derivatives have been isolated from numerous other sources.

Ursonic acid (Figure 5D) also showed lower binding energy with Nsp15 than hydroxychloroquine and chloroquine. Besides, the ursonic acid and Nsp15 complex got a stable result after the MD, radius of gyration, RMSD, and RMSF studies (Kumar S. et al., 2020). Ursonic acid has been reportedly found in various sources, including Piper betle L. (Saeed et al., 1993), Ziziphus jujuba Mill. (Kawabata et al., 2017), Ficus carica L. (Chiang et al., 2005), Lantana camara L. (Begum et al., 2004), and Catharanthus roseus (L.) G. Don (Thanh Tam et al., 2016).

Carvacrol (Figure 5E) could form hydrogen bonds with Ser459, residue bind domain of S protein (Kulkarni et al., 2020). Carvacrol has been isolated from multiple sources, some of which are Lippia multiflora Moldenke (Kunle et al., 2003), Origanum acutidens (Hand.-Mazz.) Ietsw. (Kordali et al., 2008), Origanum dictamnus L. (Liolios et al., 2009), Lippia origanoides Kunth (Games et al., 2016), and Thymus vulgaris L. (Fachini-Queiroz et al., 2012).

The structure of hydroxyl with a phenyl ring indicated the activity and antiviral property of geraniol (Figure 5F). In a docking study, it could bind to Lys458 and Ser459 of the S protein by forming hydrogen bonds (Kulkarni et al., 2020). Even geraniol has been reported in numerous medicinal plants, for instance, Pelargonium graveolens L'Hér. (Gupta et al., 2001), Camellia sinensis (L.) Kuntze (Zhou et al., 2019), Rosa × damascena Herrm. (Sadraei et al., 2013), Cymbopogon flexuosus (Nees ex Steud.) W. Watson (Ganjewala and Luthra, 2009), and Cymbopogon martini (Roxb.) W. Watson (Kamble et al., 2020).

Glycyrrhizic acid is one of the important constituents of Glycyrrhiza glabra L. Previous studies on glycyrrhizic acid (glycyrrhizin) indicated that it has capability to induce interferon to prevent the replications of the MERS-CoV virus (Omrani et al., 2014; Luo et al., 2020). Maddah et al. had performed the high throughput virtual ligand screening using the dataset of 56 licorice compounds. Based on the docking studies, SAR between docking energy and ADMET properties, and MD simulations, glycyrrhizic acid was found to have highest affinity against various targets such as “spike receptor-binding domain, main protease, papain-like protease, RNA-dependent RNA polymerase, or endoribonuclease non-structural protein, as well as human angiotensin-converting enzyme 2”. This suggest that glycyrrhizic acid can be tested further to check its potential as anti-SARS-CoV-2 agent (Maddah et al., 2021).

Quinadoline B (Figure 5G) could be extracted from the mangrove-derived fungus Cladosporium sp. PJX-41 that possesses anti-SARS-CoV-2 potency by binding to the Lys711 and Arg355 sites of PLpro through H-bonds and Leu557, Ala579, and Ile580 through pi-alkyl interactions. In regard to RdRp, quinadoline B showed the highest affinity with the binding sites, by binding to Gln73 through H-bonds, to Arg569 through pi-cation, to Ala686 through pi-alkyl interactions, and to Tyr689, Ala580, and Ala688 sites through pi-pi stacking and pi-alkyl interactions. Concerning nsp15, it could be bound to His235 and His250 through van der Waals (VDW) affinity, to Lys290 through the pi-cation intermolecular bonding, to Tyr343, Lys345, and Leu346 through pi-pi stacking/pi-alkyl interactions. In addition, nsp15 exerts an H-bonding effect on the Val292 site. Regarding the S protein, it interacted with binding sites through pi-sulfur bonding to Cys454, pi-anion to Asp441, pi-alkyl to Ala444, and pi-pi stacking to Phe430. With the ADMET results, quinadoline B indicated high gastrointestinal (GI) absorption, low blood-brain barrier penetrability, and high drug-likeness (Quimque et al., 2020). Quinadoline B has also been extracted from Aspergillus giganteus Wehmer, 1901 NTU967 which was isolated from the marine alga, Ulva lactuca (Chen JJ. et al., 2020), and Aspergillus sp. FKI-1746 (Koyama et al., 2008).

In the compounds of fungal secondary metabolites, scedapin C (Figure 5H) could be isolated from the marine-derived fungus Scedosporium apiospermum (Sacc.) Sacc. ex Castell. and Chalm., 1919 F41-1, exerting the highest affinity with PLpro through various interactions, viz. hydrogen bonding with Arg712, pi-cation interactions with Lys711, pi-pi stacking interactions with His342, and pi-alkyl interactions with Ala579. Concerning 3CLpro, scedapin C could bind to Cys145 through pi-sulfur interactions, Met165 through pi-pi stacking interactions, His41 through pi-pi stacking interactions, and Met49 through pi-alkyl interactions. Compared with favipiravir, RdRp has higher binding energy by binding to Lys593 and Cys813 through hydrogen bonds, Ile589 and Leu758 through pi-alkyl interactions, and Cys813 through pi-sulfur interactions. In regard to nsp15, scedapin C hinged itself on His235 through pi-pi stacking interactions, His250 and Lys290 through VDW affinity, Thr341 through H-bonds, and Tyr343 through pi-pi stacking interactions (Quimque et al., 2020).

Berberine (Figure 5I) could be extracted from the root, rhizomes, stems, and the bark of Hydrastis canadensis L. (Berberidaceae). After the viral screening and the docking study of the potential inhibition against 3CLpro, the main protease in SARS-CoV-2, it showed much lower binding energy to 3CLpro, compared with other compounds isolated from Tinospora cordifolia (Willd.) Hook. f. and Thomson. In addition, the berberine:3CLpro structure possesses higher stability than other inhibitors according to the MD simulation and exerts a potent effect against COVID-19 by preventing the activity of 3CLpro (Chowdhury, 2020). Other reported biological sources, where berberine is one of the important phytoconstituents, are Berberis vulgaris L. (Freile et al., 2003), Berberis aquifolium Pursh (Čerňáková and Košťálová, 2008), Berberis vulgaris L. (Imanshahidi and Hosseinzadeh, 2008), and Corydalis chaerophylla DC. (Basha et al., 2002).

Nigellidine is a bioactive component obtained from the seeds of Nigella sativa L., which was reported before for its anti-oxidative, anti-inflammatory, anti-bacterial, anti-hypertensive, and immunomodulatory functions. In the docking study of Maiti and workers, nigellidine (Figure 5J) could interdict the function of the Nucleocapsid (N) protein of SARS-CoV-2 by binding to Ala55 (through hydrogen bonds), Gln306 (through N-O bonds), and ARG203, ARG209, Leu230, Gln241, Gln242, Ala308, Ala305, and Phe307 residue sites. In regard to the Nsp2 of SARS-CoV-2, which could concern the integrity of mitochondria and the resistance to the diverse stresses of the host cell, nigellidine could block it by binding to Cys240 through rigid bonds, and Leu169, Val126, Trp243, Ala127, Cys132, The256, Gly257, Tyr242, Val157, and other positions with Ala 241 through hydrogen bonds. Concerning Mpro, nigellidine could form a stable bond with Glu166 (Maiti et al., 2020).

Noscapine (Figure 5K) has a higher affinity and a much lower binding score to the pocket-3 of Mpro, compared with chloroquine, ribavirin, and favipiravir. It formed hydrogen bonds with Thr199 and Asn238, and hydrophobic interactions with Asp197, Thr198, Thr199, Leu237, Asn238, Tyr239, and Leu271 in silico. Furthermore, the results of the molecular dynamic simulation revealed that noscapine possessed good stability and conformational change. Additionally, it was a potential natural product against SARS-CoV-2 (Kumar N. et al., 2020). Apart from the natural source Papaver somniferum L. (Dang and Facchini, 2012) from which it is abundantly isolated, there is enough literature available on noscapine and the synthesis of its derivatives (Zhou et al., 2003; Ni et al., 2011; Devine et al., 2018).

Transmembrane protease Serine 2 (TMPRSS2) is the essential receptor of the host cell that could modulate the entry of SARS-CoV-2. Vivek-Ananth et al. studied the affinity of qingdainone (Figure 5L) to TMPRSS2. With the lowest binding energy, qingdainone could form hydrogen bonds with D440 and A399 as well as hydrophobic interactions with I381, S382, T387, E388, N398, A400, D440, C465, and A466 (Vivek-Ananth et al., 2020). Qingdainone is also well known as candidine. It can be isolated from sources such as Yarrowia lipolytica (Jahng, 2013), Isatis tinctoria L. (Zou and Huang, 1985; Wu et al., 2007), and Strobilanthes cusia (Nees) Kuntze (Zou and Huang, 1985).

(+)-Oxoturkiyenine has lower binding energy to cathepsin L which is an essential receptor of the host cell for the entry of SARS-CoV-2. The residues of cathepsin L, such as Q19 and W189, could form hydrogen bonds with (+)-oxoturkiyenine (Figure 5M), pi-pi interactions with W189, and hydrophobic interactions with G139, H140, H163, and W189 (Vivek-Ananth et al., 2020) (+)-Oxoturkiyenine can be isolated from Hypecoum pendulum L. (Kadan et al., 2004; Mete and Gözler, 2004).

3α,17α-Cinchophylline could be extracted from Cinchona calisaya Wedd., the herb that possesses antiviral and anti-inflammatory activities. In regard to cathepsin L, the receptor of the host cell which plays the key role in the process of SARS-CoV-2 entry, 3α,17α-cinchophylline (Figure 5N) formed hydrogen bonds with C25, H163, G23, and M70, and hydrophobic interactions with Q21, C22, L69, M70, A135 and W189 to reveal its potential function for COVID-19 (Vivek-Ananth et al., 2020).

Speciophylline could be extracted from Uncaria tomentosa (Willd. ex Schult.) DC. It exerts a higher affinity with 3CLpro compared with N3, the inhibitor of 3CLpro as it is known. To the S1 cleavage site, speciophylline (Figure 5O) performs its affinity without obviously energetic expend (Yepes-Perez et al., 2020). It has also been reported that it is isolated from Mitragyna speciosa Korth. (Beckett et al., 1965), Uncaria lanosa f. philippinensis (Elmer) Ridsdale (Olivar et al., 2018), Uncaria bernaysii F. Muell. (Phillipson and Hemingway, 1973), and Uncaria attenuata Korth. (David Phillipson and Hemingway, 1975).

Cadambine comes from Uncaria tomentosa (Willd. ex Schult.) DC. It possesses a significant affinity with 3CLpro. Furthermore, the ligand-pathway simulation study showed low barriers to bind in the case of this test molecule. Thus, cadambine (Figure 5P) could be a potent inhibitor of SARS-CoV-2 (Yepes-Perez et al., 2020). It can be isolated from Neolamarckia cadamba (Roxb.) Bosser (Kumar et al., 2015), Neonauclea purpurea (Roxb.) Merr. (Handa et al., 2004), and Uncaria rhynchophylla (Miq.) Miq. (Qi et al., 2014).

As an anthocyanin derivative, delphinidin 3,3′-di-glucoside-5-(6-p-coumarylglucoside) (DGCG) (Figure 6A), displayed a potential function to interdict the main protease of SARS-CoV-2 according to the molecular dynamic simulation, the radius of gyration analysis, and the binding of free energy results (Fakhar et al., 2020). DGCG has been reportedly isolated from Gentiana cv. Albireo (Hosokawa et al., 1997).

Pelargonidin 3-O-[β-D-Glucopyranosyl-(1->2)-[4-hydroxycinnamoyl-(->6)]-β-D-glucopyranoside](E-) 5-O-(6-O-malonyl-β-D-glucopyranoside), PGHGM (Figure 6B) is another derivative of anthocyanin with activity against the main protease of SARS-CoV-2 as per the results obtained by the radius of gyration, the binding of free energy, the molecule stability, and the flexibility studies (Fakhar et al., 2020). PGHGM can be isolated from Pomacea maculata Perry, 1810 (KHALIL et al., 2020).

From the Nerium oleander L., digitoxigenin (Figure 6C) and its derivatives exert antiviral and anti-cancer properties. It has a binding energy value of −7.2 kcal/mol and is proposed to be an effective inhibitor to the coronavirus against the main protease of SARS-CoV-2 (Aanouz et al., 2020). Another important and main source where digitoxigenin can be isolated is Digitalis lanata Ehrh. (Caspi and Hornby, 1968).

In the screening study of the DrugBank dataset, digitoxin (Figure 6D) revealed the lowest binding energy with Site 2 of the S protein of SARS-CoV-2. It formed hydrogen bonds with Lys458, Ser459, Asp467, and Glu471, and carbon-hydrogen bonds with Lys458 and Glu471. Furthermore, it formed alkyl hydrophobic interactions with Lys458 and Pro491 (Wei TZ. et al., 2020). Clinically relevant, digitoxin can be isolated from Digitalis purpurea L. (Hagimori et al., 1984).

The results of the docking study by Hamza et al., suggested that anthraquinone (Figure 6E) may have an inhibitory effect against COVID-19 by being bound to non-structural polypeptides (GVITHDVSSAINRPQIGVVREFLTR) amino acid residues, such as Val2 (through hydrogen bonds), Ile3 (through hydrogen bonds), and Gly1 (through pi-cation interactions) (Hamza et al., 2020). Anthraquinone is such an important scaffold with many natural derivatives. Consequently, it becomes a separate class of compounds.

Anethole (Figure 6F) could bind to Ser459 of the S protein by forming hydrogen bonds, which are rich in some plant families such as Apiaceae, Myrtaceae, and Fabaceae (Kulkarni et al., 2020). Some of the biological sources of anethole are Foeniculum vulgare Mill. (Dongare et al., 2012), Pimpinella anisum L. (Kubo et al., 2008), Illicium verum Hook. f. (Liu, 1996), Croton grewioides Baill. (de Siqueira et al., 2006), and Vepris madagascarica (Baillon) H. Perier (Rabehaja et al., 2013).

Cinnamaldehyde has a high ability to fight against inflammation, viruses and cancer. In a docking study, cinnamaldehyde could form hydrogen bonds with Glu471 and Arg454 and the key residues of the S protein. It also displays the capacity for preventing the infection process of SARS-CoV-2 (Kulkarni et al., 2020). Cinnamaldehyde (Figure 6G) has been tracked in multiple sources, including but not limited to Cinnamomum verum J. Presl (Kakinuma et al., 1984; Al-Bayati and Mohammed, 2009; Liu et al., 2014).

Previous studies indicated that curcumin (Figure 6H) which is the most important phytoconstituent in turmeric (Curcuma longa L.) (Anderson et al., 2000) has a potential effect against AIDS inhibiting the HIV protease and integrase enzymes, along with having a synergistic action with antiretroviral drugs (Prasad and Tyagi, 2015; Gupta et al., 2020). In the case of the influenza A virus, curcumin reportedly reduces inflammatory cytokines (Ciavarella et al., 2020; Gupta et al., 2020). In the case of H1N1, it was found that it decreases the nucleoprotein expression, thereby preventing the infection of the influenza virus (Richart et al., 2018; Lai Y. et al., 2020; Gupta et al., 2020). All these findings strongly suggested the potent antiviral activity inherently possessed by curcumin. This has led Oso and the team to check the affinity of curcumin against COVID-19-associated proteases, such as cathepsin K, COVID-19 main protease, and SARS-CoV 3C-like protease, by performing in silico studies. Their results suggested that curcumin has strong binding affinities towards all the target proteins, with the best against the SARS-CoV 3C-like protease. Interaction analysis performed by Oso and the team further suggested that curcumin could form hydrogen bonding with the Trp188 of cathepsin K while it could form hydrogen bonding with Gly143 and Ser144 of the COVID-19 main protease. Furthermore, curcumin was found to form hydrogen bonding with Gly109, Gln110, Thr111, and Phe294 of the SARS-CoV 3C-like protease as per their analysis (Oso et al., 2020).

Syn-16 is the coumarin derivative that exhibited the potential for combating COVID-19. After the structure-based virtual screening, molecular dynamics simulation, and the binding of free energy calculation, Khan and workers found that Syn-16 could form three different hydroxyl groups of hydrogen bonds and have stable interactions with the S1, S2, and S5 pocket residues. Thus, Syn-16 displayed the promising potential that it could bind to 3CLpro and prevent the replication and maturation of SARS-CoV-2 (Khan et al., 2020).

Gallocatechin gallate (Figure 6I), a derivative obtained from Saxifraga spinulosa Adams, 1817, non Royle, 1835, was reported about its function in inactivating the influenza A virus and norovirus. Takeda and the team studied its capacity for fighting against SARS-CoV-2. The results suggested that a pyrogallol-enriched fraction (Fr 1C) inactivated 99.53% of SARS-CoV-2 with 10s of exposure, decreased the S2 subunit of the S protein, interdicted the cDNA reverse transcription more rapidly than any other fractions (Takeda et al., 2020). Gallocatechin gallate is available in Camellia sinensis (L.) Kuntze (Sugita-Konishi et al., 1999), and Diospyros kaki L. f. (Matsuo and Ito, 2014).

Ararobinol showed the highest affinity towards cathepsin L in the docking study. Earlier studies indicated that ararobinol (Figure 6J) has antiviral properties. Ararobinol can build hydrogen bonds with cathepsin L residues, such as Q19 and A138, pi-pi interactions with W189, and hydrophobic interactions with C25, G139, L144, H163, and W189 (Vivek-Ananth et al., 2020). Ararobinol could be found in Senna occidentalis (L.) Link. It can also be isolated from sources like Frangula caroliniana (Walter) A. Gray (Mekala et al., 2017) and Senna siamea (Lam.) H.S.Irwin and Barneby (Kumar et al., 2017).

Gingerol (Figure 7A), which is an important phytoconstituent of Zingiber officinale Roscoe (Guh et al., 1995), has also been investigated by means of cheminformatics by Oso and the team for its binding affinity and potential against COVID-19-associated proteases, like cathepsin K, COVID-19 main protease, and SARS-CoV 3C-like protease. Their results suggested that gingerol also had a good binding affinity with all these target enzymes, especially Cathepsin K. Their further performed studies indicated that gingerol could form hydrogen bonding with Asn18, Gln19, His162, Trp184, and Trp188 amino acid residues of Cathepsin K. It also has the potential to form hydrogen bonding with Thr199, Leu272, and Leu287 amino acid residues of the COVID-19 main protease. Additionally, they found it has the potential to form hydrogen bonding with Thr111 and Thr292 of the SARS-CoV 3C-like protease (Oso et al., 2020). Gingerol has found in Aframomum melegueta K. Schum. (Mohammed et al., 2017).

In the simulation, Nat-1 (coumarin analog) had a pi-alkyl interaction with Gln189, which is in the S5 pocket residues with different hydroxyl groups. The binding model indicated that there are interactions between Nat-1 and 3CLpro, which could contribute to the new treatments of the SARS-COV-2 infection (Khan et al., 2020).

Isochaetochromin D1 is a kind of Fusarium sp. metabolites that has an interfering function in viral enzymes. In regard to the non-structural protein 15 (nsp15) of SARS-CoV-2, it could bind to Val292 and His250 through H-bonding, His235, and Lys290 through VDW interactions, and other sites through pi interactions to interdict the activity of nsp15 (Quimque et al., 2020).

Bisindigotin (Figure 7B) can be extracted from Isatis tinctoria L. (Mohn et al., 2009) and Persicaria tinctoria (Aiton) Spach. In the screening study of the Traditional Chinese Medicine Systems Pharmacology (TCMSP), bisindigotin exerted the lowest binding energy with the S protein that binds to Arg457, Ser469, and Glu471 through hydrogen bonds, Lys458 through carbon-hydrogen bonds, Asp467 and Glu471 through pi-anion interactions, and Arg457 through pi-alkyl interactions, which increased the stability of the binding (Wei TZ. et al., 2020).

Edgeworoside C could be isolated from Edgeworthia gardneri (Wall.) Meisn. and widely used for the treatment of metabolic diseases. In a docking study, edgeworoside C (Figure 7C) could form hydrogen bonds with A386, N398, A399, V434, D435, D440, D435, V434, A386, N398, and D440 of TMPRSS2, and bind to E260, I381, A400, N433, and A466 through hydrophobic interactions to exhibit its antiviral properties (Vivek-Ananth et al., 2020). Edgeworoside C has been isolated from Edgeworthia chrysantha Lindl. (Yan et al., 2004).

Adlumidine (Figure 7D) is the main constituent of Fumaria indica (Hausskn.) Pugsley (Blaskó et al., 2004) which could treat cough, fever, and skin and urinary-related diseases. The study suggested that adlumidine has a high affinity with the TMPRSS2 which is the key target for the entry of SARS-CoV-2. The complex has hydrogen bonds between adlumidine and E388, E389, S436, C465, C437, and A466 while it has hydrophobic interactions with E260, I381, S382, T387, N398, A399, and A400 (Vivek-Ananth et al., 2020). Previous literature suggested that adlumidine can be obtained from Pseudofumaria lutea (L.) Borkh. (Yang et al., 1993), and Dactylicapnos torulosa (Hook.f. and Thomson) Hutch. (Rücker et al., 1994).

Asparagoside-C (Figure 7E) has a higher affinity with the S protein of SARS-CoV-2. It could be extracted from Asparagus racemosus Willd. The molecular dynamic simulation results suggested that asparagoside-C and S protein possess a stable conformation, caused by hydrogen bonds with Gly496, Gln414, Ser494, Thr415, and Tyr453. Concerning the nucleocapsid protein (N protein), it is also observed that it forms hydrogen bonds with Glu234, Gly230, Val292, His235, and Asp240 (Chikhale et al., 2020).

Asparagoside-D (Figure 7F) is also an important phytoconstituent obtained from Asparagus racemosus Willd. It has a better binding energy result than the standard drug Remdesivir and this is indicated in the treatment regimen for COVID-19 right now. Asparagoside-D could form hydrogen bonds with Gly502, Ser494, Lys417, Asp420 Tyr449, and Gln498 of the S protein and with Glu340, His243, Gln245, Asp240, Asn278, and Leu346 of the N protein in SARS-CoV-2. Thus, it has a major potential for acting against COVID-19 (Chikhale et al., 2020).

Asparagoside-F (Figure 7G) is another important phytoconstituent obtained from Asparagus racemosus Willd. It has better affinity and stability because of hydrogen bonds formed between the N and Glu234, Gly230, Ala232, Hip235, Asp240, Glu340, and Val339. This displays the capacity for blocking the key protein of SARS-CoV-2 (Chikhale et al., 2020).

3-(3-Methylbut-2-enyl)-3,4,7-trihydroxyflavane (MTHF) (Figure 7H), could be isolated from Broussonetia papyrifera (L.) L'Hér. ex Vent.. It possesses a better blocking capacity for the Mpro of SARS-CoV-2 than darunavir and lopinavir. The docking study indicated that it could form a highly stable and less fluctuated complex with Mpro, by binding to Leu141, Asn142, Gly143, Cys145, and Glu166 through forming hydrogen bonds, Met49 through pi-sulfur and pi-alkyl interactions, and His41 through pi-sigma and pi-alkyl interactions (Ghosh et al., 2020).

Kazinol F (Figure 7I) revealed that it has the lowest binding energy value among all the constituents of Broussonetia papyrifera (L.) L'Hér. ex Vent. by forming hydrogen bonds with Leu141, Gly143, and Met165 amino acid residues in Mpro, pi-alkyl interactions with Cys145 and Met49, pi-pi T-shaped interactions with His41, and the key catalytic residue of Mpro (Ghosh et al., 2020). Another source for isolating Kazinol F is Broussonetia × kazinoki Siebold (Baek et al., 2009).

Kazinol J (Figure 7J) has been isolated from Broussonetia papyrifera (L.) L'Hér. ex Vent. It showed a lower binding energy value, higher affinity, higher stability, and less fluctuation when it bound with Mpro compared with darunavir and lopinavir. kazinol J occupied the in silico residues, such as Ser144, His163, and Thr190 through forming hydrogen bonds, Met49, Met165, Pro168, and Cys145 through pi-alkyl interactions, and His41 through pi-sigma interactions (Ghosh et al., 2020).

Cinnamyl acetate (Figure 7K) showed its anti-SARS-CoV-2 potential by binding with Glu471, Arg454, and Ser459 of the S protein through H-bond interactions (Kulkarni et al., 2020). Cinnamyl acetate is mainly obtained from Cinnamomum verum J. Presl (Choi et al., 2001; Kaul et al., 2003), and Cinnamomum osmophloeum Kaneh. (Cheng SS. et al., 2006).

L-4-terpineol (Figure 7L) could be extracted from the essential oil of tea tree and lavender. It can bind to the S protein by forming hydrogen bonds with Leu492 and Tyr505 (Kulkarni et al., 2020). Some of the other reported biological sources are Artemisia herba-alba Asso (Nezhadali et al., 2008), Pistacia chinensis subsp. integerrima (J.L.Stewart) Rech. f. (Shirole et al., 2015), Artemisia nanschanica Krasch. (Shang et al., 2012), and Nigella sativa L. (Liu et al., 2013).

Allicin (Figure 7M) is a sulfoxide derivative that is categorized under sulfinic acids. It is one of the very important phytoconstituent found in Allium sativum L. (garlic). Oso and the team performed simulation studies to assess the binding potential of allicin to various targets of SARS-COV-2, viz. cathepsin K, COVID-19 main protease, and SARS-CoV 3C-like protease. Their results suggested that allicin elicited a similar sort of binding affinity towards all these tested proteins. Allicin could form hydrogen bonding with Gly66 of cathepsin K or Gly143 and Ser144 of the COVID-19 main protease, and Thr190 of the SARS-CoV 3C-like protease (Oso et al., 2020).

Lianhua Qingwen (LHQW) capsule contains so many different kinds of natural product extracts, such as “Forsythia suspensa (Thunb.) Vahl. (Lianqiao), Lonicera japonica Thunb. (Jinyinhua), Ephedra sinica Stapf (Mahuang), Prunus armeniaca L (Kuxingren), Gypsum fibrosuum (Shigao), Isatis tinctoria L. (Banlangen), Dryopteris crassirhizoma Nakai (Mianmaguanzhong), Houttuynia cordata Thunb (Yuxingcao), Pogostemon cablin (Blanco) Benth. (Guanghuoxiang), Rheum palmatum L. (Dahuang), Rhodiola rosea Linn. (Hongjingtian), Mentha canadensis L. (Bohe), Glycyrrhiza uralensis Fisch. ex DC. (Gancao)”, which reportedly affect COVID-19 (Li L.-C. et al., 2020). Zheng et al., studied the mechanism of action of LHQW in COVID-19. Their analysis indicated that most of the constituents are modulating the expression of the lung proteins and having a relationship with more than 2,000 targets, 160,000 protein-protein interactions, and 30 functional modules. LHQW is modulating 189 proteins that are related to the co-expression of ACE2, thus concerning its ability to repair lung damage, attenuate the cytokine storm, and alleviate the symptoms caused by the ACE2-expression disease (Zheng et al., 2020). In a clinical study of efficacy and safety from Hu and the workers, they found that the treatment group has a higher recovery rate, improvement in chest, computed tomography manifestations rate, and clinical cure rate, but it has a shorter recovery time from symptoms like fever, cough, and fatigue. In this study, the results suggested a natural-product-combination-based capsule contributes to attenuating the symptoms of COVID-19 in clinical environments (Hu et al., 2020).

The formula of pudilan (PLD) contains dandelion, Isatis root, Scutellaria baicalensis Georgi, and Corydalis bungeana Turcz. herb. This polyherbal formulation is used in clinical settings as anti-SARS CoV-2 in China. Kong and the workers studied its efficacy against COVID-19. The ingredients’ data analysis results indicated that PLD could prevent the entry of SARS-CoV-2 by blocking ACE2, modulating the immune-related factors and proteins to relieve the cytokine storm, and attenuating the inflammation. Thus, PLD can alleviate the symptoms and exert its potency for the treatment of COVID-19 (Kong et al., 2020).

In one patient infected with COVID-19, Lan-ting Tao and his co-workers performed a form of Traditional Chinese Therapy including a combination of acupuncture and a preparation consisting of Chinese herbs were used for the treatment. Regarding the introduction, the formula contains Aconitum carmichaeli Debeaux lateralis praeparata, Radix et Glycyrrhiza glabra L. praeparata cum Melle, Lonicera japonica Thunb., Gleditsia sinensis Lam., Ipomoea cairica (L.) Sweet, Citrus × aurantium L., and Agastache rugosa (Fisch. and C.A.Mey.) Kuntze that could enhance immune mechanism as anti-pathogenic qi and rejuvenate the functionality of the lung. The results of the treatment indicated that the therapy attenuated symptoms to less cough and sputum, relieved shortness of breath on exertion, and decreased shadows of CT images. Furthermore, the patient felt much better and returned to their previous condition. According to their analysis, the formula alleviated the lung by modulating the kidney qi and the toned spleen and stomach, promoting immunity, preventing transmission of the pathogen, and recovering the host system and turning it back to the normal level (Tao LT. et al., 2020).

One 23-year-old infected male was studied by Qian Liu and the team. Before the intervention, the patient presented with diarrhoea (2-days history), pneumonia, and liver damage, but there were no fever and cough. The prescription contained almond, Lophatherum gracile Brongn., tuckahoe (Wolfiporia aff. extensa), forsythia (Forsythia suspensa (Thunb.) Vahl.), Wurfbainia villosa (Lour.) Skornick. and A.D.Poulsen, hawthorn (Crataegus sp.), medicated leaven (Massa Fermentata Medicinalis), malt (Hordeum vulgare L.), and Pueraria montana var. lobata (Willd.) Maesen and S.M.Almeida ex Sanjappa & Predeep. Following treatment, CT imaging was cleared of the typical signs of pneumonia. Recovery was also documented by means of a negative nucleic acid test, the positive IgG, and the IgM results (Liu Q. et al., 2020).

QFDY is the granular formulation under traditional Chinese medicines. It is used by the clinical experts of Hubei Province for COVID-19 patients under the emergency response mechanism. Hong and the team performed the network pharmacology and molecular docking studies with the key components of this formulation and the COVID-19 targets. They hypothesized that QFDY acts multimodally by regulating ACE2’s co-expressing genes, inflammation, and affecting immune-associated signalling pathways associated with 3CL hydrolase and ACE2 (Hong et al., 2020).

Coronil is an ayurvedic triherbal formulation, that is clinically used as an immunomodulator in patients with COVID-19. Coronil contains extracts from Withania somnifera (L.) Dunal, Tinospora cordifolia (Willd.) Hook. f. and Thomson, and Ocimum tenuiflorum L (Balkrishna et al., 2021a). Balkrishna et al., reported the anti-SARS-CoV-2 activity of coronil using the zebrafish model. They found that coronil potentially inhibited SARS-CoV-2 spike protein, and reducing the behavioural fever. Coronil also attenuates and modulates the cytokines production viz. IL-6 and TNF-alpha when tested in A549 cell lines (Balkrishna et al., 2020). Balkrishna et al., also reported the ACE-2 inhibitory potential of coronil (Balkrishna et al., 2021a). In a cross-sectional satisfaction covid survey, which Balkrishna et al., had conducted on 367 patients participants, they found treatment satisfaction in patients when using Divya-Swasari-Coronil-Kit (Balkrishna et al., 2021b).

KSK is a polyherbal formulation of India’s Siddha System of Medicine, well known to be traditionally used in diseases similar to that of COVID-19. Natarajan et al., had conducted a single centre, randomized controlled trial in Chennai, India on RT-PCR confirmed COVID-19 cases. Their trial results suggested that KSK could significantly reduce the viral load of SARS-CoV-2 in patients, and did not report any clinically diagnosed, serious adverse effect (Natarajan et al., 2021).

Withania somnifera (L.) Dunal, commonly known as ashwagandha, is a well-known medicinal plant having multiple therapeutic effects. Chopra et al., had conducted a randomized, multicentre study on 400 participants to assess the efficacy and safety when using ashwagandha in place of hydroxychloroquine. Their efficacy and safety assessment suggested that ashwagandha has similar effects to hydroxychloroquine, although the therapeutic efficacy of the latter has been heavily criticized until then (Chopra et al., 2021).

Devpura et al., had conducted a placebo controlled randomized double blind trial on 100 COVID-19 patients. The ayurvedic treatment covered different natural products like 1 gm of Tinospora cordifolia (Willd.) Hook. f. and Thomson, 2 gm of Swasari Ras which is a traditional herbo-mineral formulation, 0.5 gm of Withania somnifera (L.) Dunal, and 0.5 g of Ocimum tenuiflorum L., along with a traditional nasal drop, Anu Taila. Tinospora cordifolia (Willd.) Hook. f. and Thomson, Withania somnifera (L.), and Ocimum tenuiflorum L. were combined in the form of a 500 mg tablet, Coronil. With 71% recovery on Day 3 and 100% recovery on day 7 when treated with this Patanjali Divya Coronil Kit, in comparison to 60% recovery in placebo group. On day 7, significant fold change reduction was also marked when checked for serum levels of hs-CRP, IL-6 and TNF-alpha in comparison to placebo group, with no clinically observed adverse effects (Devpura et al., 2021).

Karimi and the team had performed multicenter, randomized and controlled clinical trial on 358 COVID-19 patients in Iran, to assess the potential of three herbal formulations based on Persian Medicine System. The treatment consists of two herbal capsules and one herbal decoction, where capsule 1 contains extracts prepared from the root of Rheum palmatum L., rhizome of Glycyrrhiza glabra L., and fruit peel of Punica granatum L.; capsule 2 contains seeds of Nigella sativa L. in powdered form; while herbal decoction contains powdered herbs of “Matricaria chamomilla L., Zataria multiflora Boiss., G. glabra L., Ziziphus jujuba Mill., Ficus carica L., Urtica dioica L., Althaea officinalis L., and Nepeta bracteata Benth.”. 174 patients received standard treatment as per the government protocols, while 184 received these herbal remedies along with standard treatment for a period of 7 days. The results clearly suggested that the combination of herbal remedies along with standard treatment has not accelerated the clinical improvement and decrease in symptoms, but it has also significantly reduced the hospital stay duration. Further, patients have well accepted the herbal treatment (Karimi et al., 2021).