key: cord-266104-xqvwht7c
authors: Mu, Chenglin; Sheng, Yifan; Wang, Qian; Amin, Amr; Li, Xugang; Xie, Yingqiu
title: Potential compound from herbal food of rhizoma polygonati for treatment of COVID-19 analyzed by network pharmacology and molecular docking technology
date: 2020-08-14
journal: Journal of functional foods
DOI: 10.1016/j.jff.2020.104149
sha: 
doc_id: 266104
cord_uid: xqvwht7c

Abstract Rhizoma Polygonati (huangjing in Chinese, 黄精) is an herb-homology-food used as a component of alternative medicine treating COVID-19 in the current pandemic emergency in China but the mechanisms remain elusive. Here using TCMSP and Swiss Target Prediction databases to sort out the potential targets of the main chemical components and GenCLiP3, NCBI, and GeneCard databases to search for COVID-19 related targets, the chemical compound-target-pathway network was analyzed. Each component was molecularly docked with host cell target angiotensin converting enzyme II, SARS-CoV-2 targets Spike protein, RNA-dependent RNA polymerase, or 3CL hydrolase. Our results showed a higher affinity of the compound diosgenin and (+)-Syringaresinol-O-beta-D-glucoside binding to the three SARS-CoV-2 proteins compared to the other compounds tested. Thus, our data suggest that potential compounds in Rhizoma Polygonati may act on different targets and have a great potential in treatment of COVID-19.

New coronavirus (SARS-CoV-2) has been spreading more than 200 countries, causing huge mortalities. According to World Health Organization, the disease induced Rhizoma Polygonati, also named as huangjing, which rhizome is used as medicine, is one of herb-homology-food from plant belonging to the family Liliaceae Polygonatum. According to the "Flora of China", there are about 40 species of the RP plant in the global northern temperate zone, with 31 species in China, distributed throughout the country, and some species are unique to specific regions. In ancient times, Rhizoma Polygonati has been used as alternative food for shortage of food as it contains polysaccharide. It has been recorded in the ancient pharmacology books that other unknown nutrition could help weight loss, anti-fatigue, and reduce hair whiten.

Moreover, modern and ancient pharmacological records showed that Rhizoma Polygonati has a wide pharmacological function in antibacterial, antiviral, immunity enhancement, anti-ageing, anti-cancer, anti-diabetes, anti-fatigue, and anti-heart Network pharmacology in TCM combines with multidisciplinary technologies, such as systems biology, and computational biology in order to build a complex network between drug-target-diseases, and elucidate the mechanism of drugs in treatment (Luo et al., 2020) . Molecular docking in TCM is also a computer-based drug design technology that simulates the geometric structure of molecules and the interaction force between molecules through stoichiometric calculation methods . The aim is to seek for the best binding mode of small molecule drugs and large molecules (proteins) with known structures. Using both techniques, some Chinese 

The potential targets are used to construct through STRING database (Szklarczyk et al., 2019) to obtain the targets-PPI network. Cytoscape 3.7.2 (Shannon et al., 2003) software was applied to construct the drug-compound-target-pathway network.

The disease-related targets obtained from screening were input into the DAVID database (Huang et al., 2009 ) by entering the list of target gene names and selecting the species as "homo sapiens ". All target gene was named to their official gene symbol.

To perform GO enrichment, threshold was set to the P <0.01 and the WeChat online mapping website was used to visualize the analysis results. Further, the core target was imported into the KOBAS3.0 database (Wu et al., 2006) , and use the KEGG function to do pathway analysis. Taking P <0.01was used to sort out pathways and the top 20 KEGG pathways that meet the conditions were selected.

The 3D structure of the active substance of Rhizoma Polygonati was searched 

From TCMSP, a total of 38 compound components in Rhizoma Polygonati were obtained. Further, 12 compounds was selected to meet parameter which was set as an OB at least 30% and DL at least 0.18 as threshold. From these 12 potential active ingredients, 10 compounds were finally identified as the active chemical compound of Rhizoma Polygonati (Table 1 and Figure 1 ). Then, a total of 129 targets corresponding to the above active compound were identified from the TCMSP database and the Swiss-TargetPrediction database.

The 48, 346, 33 targets of COVID-19 were obtained after sorting from NCBI, GeneCards, and GenCLiP3 databases respectively. After removing duplicated targets, 363 treatment targets were found for COVID-19 or the virus. Further, by using Venny 2.1 drawing software, the 129 druggable targets of corresponding active ingredients of Rhizoma Polygonati were mapped to 363 COVID-19-related disease targets. Then finally 23 druggable targets of corresponding active ingredients of Rhizoma Polygonati was identified to be potential Rhizoma Polygonati targets in treatment of COVID-19

( Figure 2 ).

The 23 intersection targets obtained above were further analyzed on the STRING platform by PPI network, then the data was input into Cytoscape 3.7.2 to obtain the PPI map, which contains 23 nodes and 122 edges ( Figure 3 ). The nodes in the network graph represent proteins, and the degree value was represented by the number of lines connected to the same node, meaning the importance of each node in the network. The larger, and the darker color were in the PPI network, the greater the value was. Each edge represents the interaction between proteins in the PPT network. The more lines there were in the PPI, the greater association were found in the drug and the virus. The thickness of the line represents combine-score in the PPI network. In our result, the average node value of the target protein is 11.09, and there were 11 target proteins which had more than the average degree value. For example, CASP3, TP53, MAPK14, PTGS2, CAT, FOS, PPARG, CASP8, BCL2L1, IL2, RELA, whose value were significantly higher than that of the other targets, suggesting essential roles in the PPI map. Among them, CASP3 and TP53 had the largest nodes and the darkest colors, indicating they were probably the most important potential targets in COVID-19 which Rhizoma Polygonati could work on.

The data obtained from TCMSP website were input into the DAVID database for GO analysis. Total 84 GO term were selected according to p-value parameter (p≤0.01).

Among them, 64 GO term are biological processes (BP), 6 GO term are cellular components (CC), and 14 are molecular functions (MF). From those GO term, it suggests that Rhizoma Polygonati compounds are involved in regulating the activities of peroxidase, prostaglandin-endoperoxide synthase, channel protein in host-virus interaction. They may function in regulation of apoptosis, DNA damage repair, redox, cell metabolism, and inflammatory response (Figure 4) .

To perform KEGG pathway enrichment, the key targets of the intersection of diseases and drugs were imported into the KOBAS 3.0 database. From data analysis, a total of 188 pathways were enriched. By setting up parameter, p ≤0.05, 179 channels was selected, and the top 20 channels were displayed (See Table 2 ). Data analysis shows that targets were significantly enriched in multiple pathways such as tuberculosis, 

Polygonati. In figure 5 , the docking results of diosgenin with the four proteins are displayed. As far as the binding mode between the compound diosgenin small molecule and the receptor protein 3CL is concerned, the amino acid residue Met276 forms a hydrogen bond interaction with the ligand small molecule, the amino acid residues of Arg131, Lys137, Asp289, Leu287, Leu286, Ala285, Gly275, Tyr239 form a hydrophobic interactions with the diosgenin (Figure 6A ). For the binding mode between the small molecule of diosgenin and the receptor protein ACE2 (Figure 6B ), amino acid residues of Phe40, Asp350, Asp382, Ala348, His378, His401, Asn394, Arg393, Tyr385, Phe390 , Trp69 form hydrophobic interactions with the small molecule diosgenin. Figure 6C shows the binding mode between the small molecule of diosgenin ligand and Spike protein S1. Spike protein S1 amino acid residue Asn437 forms a hydrogen bond interaction with diosgenin, and amino acid residues Phe334, Lys333, Ile428, Thr431, Asn435, Tyr438, Ser336, Ala339 form a hydrophobic interaction with diosgenin. Figure 6D shows the binding mode between the small molecule of diosgenin ligand and RdRp. The amino acid residue Lys267 and diosgenin form a hydrogen bond interaction, while the amino acid residues Pro461, Thr319, Val320, Phe321, Pro322, Trp268, Ile266, Tyr265, Ser255 and diosgenin form a hydrophobic interaction.

In addition, we found binding mode between the small molecule of baicalein with 3CL. In details, amino acid residues Glu166, Ser144, Gly143, Cys145, Leu141, His163 form hydrogen bond interactions, amino acid residues Gln189, Arg188, Met165, Phe140, Asn142 form hydrophobic interactions ( Figure 7A ). For the binding mode between (+)-Syringaresinol-O-beta-D-glucoside small molecule and receptor protein ACE2, amino acid residues Glu564, Asn210, Lys94, Glu208, Asp206, Gly205, Trp203, (Zhang et al., 2013) . Moreover, Rhizoma Polygonati could also eliminate cytokine storm of COVID-19 during treatment of lung inflammation by enhanced immune response in the mice [5] . Therefore, to explore the active ingredients and mechanism of different species of Rhizoma Polygonati based on their active compounds concentration in the treatment of pulmonary symptoms caused by the new coronavirus will help to precisely apply TCM for anti-virus. In a recent news report, Rhizoma Polygonati has been widely applied among more than 60% of anti-SARS-CoV-2 formula of TCM based on recommendation (Patent, google). However, Rhizoma Polygonati potential compound need further be investigated by basic, translational research on specific targeting such as viral entry, replication, or host response. Moreover, clinical trials will also be needed to be warrant to develop Rhizoma Polygonati drugs.

In our study, diosgenin is among the top selective candidate to interact with drug targets.

Diosgenin is identified as a precursor for some hormones, such as progesterone, cortisone, and also is used for oral contraceptive pills and starting materials of steroidal 

Qian Wang works on Rhizoma Polygonati. The project is supported in part by Mount Tai Rhizoma Polygonati research and development project.

All data is presented here. 

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 Molecular docking identified high affinity binding of diosgenin and (+)-Syringaresinol-O-beta-D-glucoside to the target proteins of SARS-CoV-2

RP may act on multiple target-signaling for potential treatment of COVID-19

Yifan Sheng: Writing-Part of original draft preparation

Qian Wang works on Rhizoma Polygonati. The project is supported in part by Mount Tai Rhizoma Polygonati research and development project