# Network Pharmacology Reveals Polyphyllin II as One Hit of Nano Chinese Medicine Monomers against Nasopharyngeal Carcinoma

Authors: Meng-Zhe Yang; Bei-Bei Zhang; Jian-Chun Huang; Xian-Yu Bai; Zhen-Qiang Liang; Xiang Yi; Ning Xu; Yuan-Jiao Huang; Ai-Jun Jiao
Journal: Bioinorganic Chemistry and Applications
 (2021)

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## Abstract

Nasopharyngeal carcinoma (NPC) is a malignant tumor in southern China, and nano Traditional Chinese Medicine (TCM) represents great potential to cancer therapy. To predict the potential targets and mechanism of polyphyllin II against NPC and explore its possibility for the future nano-pharmaceutics of Chinese medicine monomers, network pharmacology was included in the present study. Totally, ninety-four common potential targets for NPC and polyphyllin II were discovered. Gene Ontology (GO) function enrichment analysis showed that biological processes and functions mainly concentrated on apoptotic process, protein phosphorylation, cytosol, protein binding, and ATP binding. In addition, the anti-NPC effects of polyphyllin II mainly involved in the pathways related to cancer, especially in the PI3K-Akt signaling indicated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The “drug-target-disease” network diagram indicated that the key genes were SRC, MAPK1, MAPK14, and AKT1. Taken together, this study revealed the potential drug targets and underlying mechanisms of polyphyllin II against NPC through modern network pharmacology, which provided a certain theoretical basis for the future nano TCM research.


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## Body

## 1. Introduction

Nasopharyngeal carcinoma (NPC) is a malignant tumor in the upper and side walls of the nasopharyngeal cavity [1]. It is a common disease in southern China [2]. Currently, the preferred treatment option for nasopharyngeal carcinoma is radiotherapy, especially in the early stages of patients [3]. However, many patients are already at an advanced stage when they are diagnosed. Due to radio resistance, it can cause local recurrence and distant metastasis [4]. This is still a difficult problem in clinical therapy. In order to minimize the adverse effects of traditional therapies, Chinese herbal medicine treatment, as a combination or alternative therapy, has a good effect on cancer treatment [5].Paris polyphylla var. yunnanensis has a variety of pharmacological effects, including analgesic, anti-inflammatory, immunomodulatory, and anti-tumor effects [6–8]. Polyphyllin II (PP2) is an active ingredient isolated from rhizomes. Many studies have shown that PP2 induces apoptosis of human lung cancer cells, inhibits the invasion and migration of liver cancer cells, and induces apoptosis of ovarian cancer [9–11]. These studies suggest that PP2 has a broad application prospect in anti-tumor effect. However, PP2 has not been reported on NPC.Network pharmacology explains the development process of diseases from the perspectives of systems biology, pharmacology, and biological networks [12]. This method can predict the connection between drugs and diseases from a network perspective and visualize and analyze complex biological systems. In addition, more and more researchers focused on nano-drug studies. Several evidences indicated that drug loading into nanomaterials can improve the bioavailability and targeted drug delivery [13].This study aims to explore the possible targets and mechanism of action of PP2 against NPC using network pharmacology. Moreover, we hope to obtain some novel evidences of the PP2 nano-drug delivery system for targeted treatment of NPC.


## 2. Materials and Methods

### 2.1. The Collection of Potential Targets of PP2

The structure of PP2 was obtained from PubChem database (https://pubchem.ncbi.nlm.nih.gov/) and saved in SDF format. Import the molecular structure into the PharmMapper database (http://www.swisstargetprediction.ch/), set the parameters, select “Human Protein Targets Only,” and get the PDB ID. Next, the target protein and gene information are corrected using the Uniprot database (https://www.uniprot.org/uploadlists/) to obtain more reliable targets.


### 2.2. The Collection of Gene Targets Related to NPC

The GeneCards website (https://www.genecards.org/) can provide all known and predicted human genes in genome, proteome, transcription, inheritance, and function. The gene targets related to NPC were searched using this database, with “nasopharyngeal carcinoma” as the key word, to obtain gene targets related to NPC.


### 2.3. Screening of Potential Targets

Through Venny 2.1.0, the collected NPC-related targets and the targets of PP2 (https://bioinfogp.cnb.csic.es/tools/venny/) were used as Venn diagrams to screen out common target genes. This is the potential target of PP2 against NPC.


### 2.4. Construction of a Protein-Protein Interaction (PPI) Network

The STRING database (https://string-db.org/, version 11.0) can search the existing PPI online. Import the potential targets of PP2 for NPC into the STRING database, set the species (Human sapiens), and construct the PPI.


### 2.5. Biological Function Annotation and Pathway Analysis

GO enrichment analysis and KEGG analysis are done using the DAVID database (https://david.ncifcrf.gov/) and R software (3.6.2). GO enrichment analysis includes biological process (BP), molecular function (MF), and cellular component (CC). We selected the top ten items and drew a bar chart. In addition, the significantly enriched pathways are screened and bubble graphs are drawn.


### 2.6. Establishment of Biological Network Model

The biological network model is constructed with Cytoscape-v3.6.1 software. Import drugs, targets and disease, draw a “drug-target-disease” network model, and analyze the relationship between each node.


## 2.1. The Collection of Potential Targets of PP2

The structure of PP2 was obtained from PubChem database (https://pubchem.ncbi.nlm.nih.gov/) and saved in SDF format. Import the molecular structure into the PharmMapper database (http://www.swisstargetprediction.ch/), set the parameters, select “Human Protein Targets Only,” and get the PDB ID. Next, the target protein and gene information are corrected using the Uniprot database (https://www.uniprot.org/uploadlists/) to obtain more reliable targets.


## 2.2. The Collection of Gene Targets Related to NPC

The GeneCards website (https://www.genecards.org/) can provide all known and predicted human genes in genome, proteome, transcription, inheritance, and function. The gene targets related to NPC were searched using this database, with “nasopharyngeal carcinoma” as the key word, to obtain gene targets related to NPC.


## 2.3. Screening of Potential Targets

Through Venny 2.1.0, the collected NPC-related targets and the targets of PP2 (https://bioinfogp.cnb.csic.es/tools/venny/) were used as Venn diagrams to screen out common target genes. This is the potential target of PP2 against NPC.


## 2.4. Construction of a Protein-Protein Interaction (PPI) Network

The STRING database (https://string-db.org/, version 11.0) can search the existing PPI online. Import the potential targets of PP2 for NPC into the STRING database, set the species (Human sapiens), and construct the PPI.


## 2.5. Biological Function Annotation and Pathway Analysis

GO enrichment analysis and KEGG analysis are done using the DAVID database (https://david.ncifcrf.gov/) and R software (3.6.2). GO enrichment analysis includes biological process (BP), molecular function (MF), and cellular component (CC). We selected the top ten items and drew a bar chart. In addition, the significantly enriched pathways are screened and bubble graphs are drawn.


## 2.6. Establishment of Biological Network Model

The biological network model is constructed with Cytoscape-v3.6.1 software. Import drugs, targets and disease, draw a “drug-target-disease” network model, and analyze the relationship between each node.


## 3. Results

### 3.1. The Collection of Potential Targets of PP2

The 2D molecular structure of PP2 was obtained from the PubChem database, as shown in Figure1. First, we import the structure into PharmMapper database to obtain PDB ID. Then, we use the Uniprot database for correction and normalization. The PP2 target was finally screened out, and the top 10 gene names are listed in Table S1 (Supplementary Table S1).Figure 1
The molecular structure of PP2.


### 3.2. The Common Targets of PP2 and NPC

GeneCards database showed a total of 1786 gene targets related to NPC. 1786 NPC-related genes and 283 drug target genes were screened through Venny 2.1.0 mapping to screen out 94 common targets. Figure2 shows potential target genes for PP2 treatment of NPC.Figure 2
The Venn diagram of potential targets.


### 3.3. PPI Network of PP2 and NPC

The PPI network can study the molecular mechanisms and drug targets of complex diseases from a systematic perspective. Figure3 represents a PPI network of PP2 and NPC-related targets. The circles represented proteins, and the lines represented interactions. Figure 4 shows that SRC, MAPK1, and AKT1 have more interactions in 64 circles.Figure 3
The PPI network model of PP2 against NPC.Figure 4
The intersection targets in PPI network diagram.


### 3.4. GO Function Enrichment Analysis

GO enrichment analysis showed the anti-tumor effect of PP2 in biological processes. The abscissa is the generation (%), and the ordinate is the enrichment result. The results are shown in bubble charts. The results show that BP has more negative regulation of apoptotic process and protein phosphorylation (Figure5). The enrichment target in CC is mostly cytosol (Figure 6). The enrichment targets in MF are mostly protein binding and ATP binding (Figure 7).Figure 5
BP in GO enrichment analysis.Figure 6
CC in GO enrichment analysis.Figure 7
MF in GO enrichment analysis.


### 3.5. KEGG Function Analysis

KEGG analysis revealed that key targets were mainly enriched in 15 signal pathways, as shown in Figure8, including pathways in cancer, PI3K-Akt signaling pathway, prolactin signaling pathway, progesterone-mediated oocyte maturation, prostate cancer, proteoglycans in cancer, estrogen signaling pathway, Chagas disease (American trypanosomiasis), osteoclast differentiation, Ras signaling pathway, TNF signaling pathway, colorectal cancer, hepatitis B, and epithelial cell signaling in Helicobacter pylori infection. Among them, pathways in cancer, PI3K-Akt signaling pathway, and FoxO signaling pathway are most enriched. Pathways in cancer have 29 target genes; PI3K-Akt signaling pathway has 21 target genes; FoxO signaling pathway has 14 target genes. The results suggest that PP2 may play a role in the treatment of NPC through the aforementioned ways.Figure 8
KEGG bubble chart.


### 3.6. Biological Network Model

The construction of a “drug-target-disease” visual network model is shown in Figure9. The yellow node in the figure is the treatment target, the red node is NPC, and the blue node is PP2. The result showed that multitarget of PP2 was against NPC. The key genes involved are mainly SRC, MAPK1, AKT1, MAPK14, GRB2, and HSP90AA1.Figure 9
“Drug-target-disease” network diagram.


## 3.1. The Collection of Potential Targets of PP2

The 2D molecular structure of PP2 was obtained from the PubChem database, as shown in Figure1. First, we import the structure into PharmMapper database to obtain PDB ID. Then, we use the Uniprot database for correction and normalization. The PP2 target was finally screened out, and the top 10 gene names are listed in Table S1 (Supplementary Table S1).Figure 1
The molecular structure of PP2.


## 3.2. The Common Targets of PP2 and NPC

GeneCards database showed a total of 1786 gene targets related to NPC. 1786 NPC-related genes and 283 drug target genes were screened through Venny 2.1.0 mapping to screen out 94 common targets. Figure2 shows potential target genes for PP2 treatment of NPC.Figure 2
The Venn diagram of potential targets.


## 3.3. PPI Network of PP2 and NPC

The PPI network can study the molecular mechanisms and drug targets of complex diseases from a systematic perspective. Figure3 represents a PPI network of PP2 and NPC-related targets. The circles represented proteins, and the lines represented interactions. Figure 4 shows that SRC, MAPK1, and AKT1 have more interactions in 64 circles.Figure 3
The PPI network model of PP2 against NPC.Figure 4
The intersection targets in PPI network diagram.


## 3.4. GO Function Enrichment Analysis

GO enrichment analysis showed the anti-tumor effect of PP2 in biological processes. The abscissa is the generation (%), and the ordinate is the enrichment result. The results are shown in bubble charts. The results show that BP has more negative regulation of apoptotic process and protein phosphorylation (Figure5). The enrichment target in CC is mostly cytosol (Figure 6). The enrichment targets in MF are mostly protein binding and ATP binding (Figure 7).Figure 5
BP in GO enrichment analysis.Figure 6
CC in GO enrichment analysis.Figure 7
MF in GO enrichment analysis.


## 3.5. KEGG Function Analysis

KEGG analysis revealed that key targets were mainly enriched in 15 signal pathways, as shown in Figure8, including pathways in cancer, PI3K-Akt signaling pathway, prolactin signaling pathway, progesterone-mediated oocyte maturation, prostate cancer, proteoglycans in cancer, estrogen signaling pathway, Chagas disease (American trypanosomiasis), osteoclast differentiation, Ras signaling pathway, TNF signaling pathway, colorectal cancer, hepatitis B, and epithelial cell signaling in Helicobacter pylori infection. Among them, pathways in cancer, PI3K-Akt signaling pathway, and FoxO signaling pathway are most enriched. Pathways in cancer have 29 target genes; PI3K-Akt signaling pathway has 21 target genes; FoxO signaling pathway has 14 target genes. The results suggest that PP2 may play a role in the treatment of NPC through the aforementioned ways.Figure 8
KEGG bubble chart.


## 3.6. Biological Network Model

The construction of a “drug-target-disease” visual network model is shown in Figure9. The yellow node in the figure is the treatment target, the red node is NPC, and the blue node is PP2. The result showed that multitarget of PP2 was against NPC. The key genes involved are mainly SRC, MAPK1, AKT1, MAPK14, GRB2, and HSP90AA1.Figure 9
“Drug-target-disease” network diagram.


## 4. Discussion

Patients with advanced NPC or patients with metastases are usually treated with a combination of radiotherapy and chemotherapy [14]. However, this therapy has relatively large side effects, drug resistance, and poor efficacy. Therefore, it is more and more important to seek new and effective treatments. In recent years, Chinese herbal medicine has attracted more and more attention because of its good curative effect and low toxicity. The medicinal value of Paris polyphylla var. yunnanensis is extremely high. PP2 has shown significant anti-cancer activity on a variety of cancers [15, 16].Network pharmacology provides a new method for modern drug research and development, which greatly saves time and cost [17]. In this study, we used network pharmacology to screen out a total of 94 potential targets for PP2 in the treatment of NPC. GO enrichment analysis shows that biological processes and functions are mainly enriched in negative regulation of apoptotic process, protein phosphorylation, cytosol, protein binding, and ATP binding. Apoptosis is a process necessary for normal development [18]. Cancer cells will evade apoptosis to maintain continuous proliferation and form tumors [19]. The anti-apoptotic protein Bcl-2 is a key regulator of the endogenous apoptosis pathway, which regulates cell apoptosis by blocking the mitochondrial membrane [20]. The research on inhibitors of Bcl-2 family members is constantly developing [21, 22]. In addition to the more researched BH3 compounds, recent studies have shown that BDA-366 targeting small molecules have been found to be an effective BH4 domain antagonist of Bcl-2, which can effectively inhibit the growth of lung cancer cells [23]. Protein phosphorylation can coordinate a variety of cell functions, such as cell growth, differentiation, and apoptosis. Studies have shown that inhibiting the phosphorylation of ERK and p38 induces apoptosis in cisplatin-resistant nasopharyngeal carcinoma cells [24]. Protein phosphorylation may occur at multiple sites in the protein [25].KEGG analysis indicated that the anti-NPC effect of PP2 may be through pathways in cancer and PI3K-Akt signaling pathway. Wnt/beta-catenin pathway is a cancer-related signaling pathway. Wnt signal inhibits the degradation ofβ-catenin when activated, thereby regulating the transcription of a variety of genes. The Wnt pathway is upregulated in colorectal cancer [26]. The enhanced expression of activated β-catenin protein leads to an increase in Wnt signaling in breast cancer stem cells [27]. Therefore, inhibiting the expression of Wnt can eliminate tumor-resistant stem cells, thereby overcoming resistance to conventional treatments. The tumor suppressor gene p53 regulates the stress response of cells and is called the “guardian of the genome” [28]. Studies have shown that the overexpression of microRNA-372 enhances the radiosensitivity of nasopharyngeal carcinoma by inhibiting the negative regulation of PBK and activating the p53 signaling pathway [29]. Many potential compounds are being developed that can restore or activate p53-dependent tumor cell apoptosis [30]. PI3K-Akt signaling pathway is the most frequently activated pathway in cancer [31]. PI3K produces PIP3 and PIP2, interacts with Akt, and is phosphorylated and activated by PDK1 and PDK2. The PI3K signaling pathway is one of the most frequently altered pathways in malignant tumors, controlling cancer cell proliferation, survival, and metabolism [32].The “drug-target-disease” network diagram shows that the key genes are mainly SRC, MAPK1, AKT1, and MAPK14. The SRC family of non-receptor protein tyrosine kinases plays a vital role in cell signal transduction pathways and is expressed in many tumors. Studies have reported that the activation of SRC promotes the expression of YAP/TAZ in tumor cells and plays an important role in tumor growth and metastasis [33]. It is worth mentioning that SRC mutations rarely occur in human tumors [34]. Therefore, the increased activity may be due to abnormal regulation. The MAPK signaling pathway is closely related to tumor biology, regulating normal cell proliferation, differentiation, and apoptosis [35]. Studies have shown that MAPK1 is an important gene that promotes cell proliferation, migration, and invasion in the process of gastric cancer [36]. After its gene knockout, it inhibits the proliferation, invasion, and migration of gastric cancer cells and induces cell apoptosis [37]. MAPK14 is also called P38α, and its significance in the mechanism of action of several anti-cancer drugs has been extensively studied [38]. The AKT/mTOR pathway is one of the classic signaling pathways, which maintains energy homeostasis, which is conducive to tumor growth and metastasis [39].As we all know, cancer treatment will gradually become more precise and more personalized. The rapid development of research on nano-drug delivery system allows drugs to reach the treatment site directly, reducing side effects. Especially for traditional Chinese medicine, the use of such a technology can improve treatment effect and reduce damage to healthy tissues and cells [40]. Currently, liposomes, nanomicelles, and silica nanoparticles are the most popular nano-drug delivery systems in cancer research. Curcumin-loaded nanostructured lipid carrier system (CRM-NLCs) is found to have anti-tumor properties [41]. The study showed that CRM-NLCs is beneficial to the treatment of cancer. A review mainly mentioned the application of ZnO nanomaterials in biomedicine. ZnO nanoparticles may also be highly toxic to cancer cells [42]. In addition, there is another review which also mainly mentioned that ZnO nanoparticles have good anti-tumor effects on lung cancer, ovarian cancer, cervical cancer, gastric cancer, and other cancers [43]. Nano-drug delivery system is good for Chinese medicine targeted therapy.


## 5. Conclusion

This study successfully realized the construction of the pharmacodynamic relationship between PP2 and NPC from the perspective of network pharmacology, as well as the visualization of the target network, and predicted the key targets of PP2 against NPC. It provided a good theoretical basis for subsequent experimental verification and nano-drug design.



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