Network pharmacology and bioinformatics analyses identify the intersection genes and mechanism of Huangbai for Recurrent Aphthous Stomatitis

doi:10.21203/rs.3.rs-1564426/v1

PDF

Research Article

Network pharmacology and bioinformatics analyses identify the intersection genes and mechanism of Huangbai for Recurrent Aphthous Stomatitis

https://doi.org/10.21203/rs.3.rs-1564426/v1

This work is licensed under a CC BY 4.0 License

Version 1

posted 27 Apr, 2022

You are reading this latest preprint version

Background: Recurrent aphthous stomatitis (RAS) are complex inflammatory diseases caused by multi-factors, which severely impact patient quality of life. However, there is still no effective treatment methods for RAS without side effects. Traditionally, Cortex Phellodendri has been known as “Huang Bai” for the treatment of gastroenteritis, abdominal pain, or diarrhea. Since “Huang Bai” is herb with antibacterial and anti-inflammatory functions. Our study aimed to explore the common genes and underlying mechanisms in “Huang Bai” for the treatment of RAS.

Methods: Network pharmacology methods and bioinformatics analyses were utilized by incorporating target searching and fishing. Network analysis and silico validation were used to discover the pharmacological mechanisms of “Huang Bai” for the treatment of recurrent aphthous stomatitis.

Results: Based on filtering criteria, 25 active ingredients in HB, 200 drug targets, and 578 differentially expressed genes (DEGs) between RAS and normal samples were obtained. The GO enrichment analysis revealed that the immune response was the most significantly enriched term within the DEGs. The KEGG pathway analysis identified 60 significant pathways, most of which involved in the inhibition of inflammation and regulation of immunological response. The functions are dependent on a multi-pathway, particularly the TNF signaling pathway and the HIF-1 signaling pathway. We identified six hub genes in the PPI network, most of which were validated as highly expressed in oral ulcers by DiseaseMeth databases. In addition, molecular docking displayed that the primary molecule combined well with the key targets.

Conclusions: This study reflects the multi-component multi-target multi-pathway action characteristics of HB. Our study provides potential biomarkers or treatment targets for further research.

active ingredients

Huangbai (HB)

Cortex Phellodendri

recurrent aphthous stomatitis

network pharmacology，computational biology

Recurrent aphthous stomatitis(RAS), also called recurrent oral ulcer(ROU) or recurrent aphthous ulcer(RAU), is a chronic inflammatory oral ulcer disease, which is the most principal clinical disease in the oral cavity(Ślebioda, Szponar, & Kowalska, 2014). The typical symptom is a single or several painful erosions that recur on the lips, the tip of the tongue, edge of the tongue, cheek, and other areas. The disease can affect people of all ages, races, and regions(Sánchez-Bernal, Conejero, & Conejero, 2020).RAS usually first appears in childhood or adolescence, frequently recurring and persistent lifetime morbidity, with incidence rates varying from 5 to 60% in different population(Akintoye & Greenberg, 2014). In children, the prevalence of the disease is significantly influenced by one or both parents with the presence of RAS(Miller, Garfunkel, Ram, & Ship, 1980). Children with parents with positive RAS have a 90% chance of developing RAS, while children with parents with negative RAS have a 20% chance(Ship, 1972). A study of genetic testing for single-gene disease indicates that children with RAS have Mutations in TNFAIP3, DNASE1L3, PTPN22, and STAT1(Girardelli et al., 2021). Therefore, researchers consider that individuals who are genetically predisposed to RAS are susceptible to RAS. In severe cases, RAS can lead to difficulty in eating and speech, causing pain to the patient. Scholars have explored multiple strategies to prevent RAS, including Laser therapy(Amorim Dos Santos et al., 2020), probiotics and vitamins(Aggour, Mahmoud, & Abdelwhab, 2021; B. Cheng, Zeng, Liu, Zou, & Wang, 2020; Lalla et al., 2012), mouthwash treatments(Dalessandri et al., 2019; Gorsky, Epstein, Rabenstein, Elishoov, & Yarom, 2007), and immunotherapy(Habibzadeh, Sheikh Rahimi, Edalatkhah, Piri, & Maleki, 2021). However, these therapies have side effects and high recurrence rates, Effective treatment options with few side effects are urgently needed to treat RAS.

“Huang Bai”(HB) is one of the most frequently used traditional Chinese medicine, also known as Cortex Phellodendri. It is originated from the dried bark of Phellodendron chinense Schneid. or Phellodendron amurense Rupr. HB is bitter, cold in nature, and functions on cleansing damp-heat and drying up the dampness, relieving fire and detoxification, remove swelling and decay(Schmidt, 1994). HB has a combination of immunomodulatory, anti-inflammatory, antibacterial, anti-hypertensive, antioxidant, and antipyretic therapeutic effects(Y. Cheng et al., 2021; Y. F. Xian et al., 2013; Y. F. Xian, Mao, Ip, Lin, & Che, 2011). Modern research has shown that HB contains numerous chemical components, including alkaloids and terpenoids. Both of these compounds are effective infections and neurological diseases(Lee et al., 2016). However, there are relatively few relevant studies on HB against RAS, and the mechanism is unclear(Hamedi et al., 2016; Shao et al., 2021).

Network pharmacology is a useful bioinformatics tool to discover all candidate targets, functions, and mechanisms of bioactive components to treat disease(Ge, Guo, Liang, Liu, & Wu, 2019; R. Li et al., 2019). In the research, we aimed to explore the potential therapeutic t argets and mechanisms of HB by utilizing a network pharmacology technology.

Composite ingredients of HB

A total of 140 active compounds were searched. Based on references and selection criteria (OB > 30% and DL > 0.18), HB mainly contained 39 active ingredients, including alkaloids, citrulline, phenolic acids, terpenoids, phenylpropanoids, etc. Fourteen of them were not found relevant targets. (Table 1)

Table 1

The details of active ingredients of HB

No.	TCMSP ID	Molecule Name	Oral bioavailability (%)	Drug likeness
HB1	MOL001454	berberine	36.86	0.78
HB2	MOL001458	coptisine	30.67	0.86
HB3	MOL002641	Phellavin_qt	35.86	0.44
HB4	MOL002643	delta 7-stigmastenol	37.42	0.75
HB5	MOL002644	Phellopterin	40.19	0.28
HB6	MOL002651	Dehydrotanshinone II A	43.76	0.4
HB7	MOL002662	rutaecarpine	40.3	0.6
HB8	MOL002663	Skimmianin	40.14	0.2
HB9	MOL002666	Chelerythrine	34.18	0.78
HB10	MOL000449	Stigmasterol	43.83	0.76
HB11	MOL002668	Worenine	45.83	0.87
HB12	MOL002670	Cavidine	35.64	0.81
HB13	MOL002672	Hericenone H	39	0.63
HB14	MOL000358	beta-sitosterol	36.91	0.75
HB15	MOL000622	Magnograndiolide	63.71	0.19
HB16	MOL000785	palmatine	64.6	0.65
HB17	MOL000787	Fumarine	59.26	0.83
HB18	MOL000790	Isocorypalmine	35.77	0.59
HB19	MOL000098	quercetin	46.43	0.28
HB20	MOL001131	phellamurin_qt	56.6	0.39
HB21	MOL001455	(S)-Canadine	53.83	0.77
HB22	MOL001771	poriferast-5-en-3beta-ol	36.91	0.75
HB23	MOL002894	berberrubine	35.74	0.73
HB24	MOL005438	campesterol	37.58	0.71
HB25	MOL006422	thalifendine	44.41	0.73

Identification of DEGs of RAS and HB-RAS intersection targets

The gene expression profiles GSE3726537(Baccaglini et al., 2010) were obtained from the GEO database. The platform for GSE37265 is GPL570, which includes fourteen samples of RAS patients, and fourteen samples from normal tissue. Data table header descriptions and series matrix files of GSE37265 were downloaded. The expression dataset is corrected as shown in Fig.1 with good consistency. Relative log expression (RLE) reflects the consistency of parallel experiments. Filtration based on principal component analysis did not exclude relevant samples. The first two principal components distinguished RAS and normal samples well, accounting for 23.36% (first component) and 18.65% (second component) of the observed difference (Fig. 2b). The gene expression profiles of these 28 samples were used in subsequent analyses. WGCNA analysis identified seven modules based on average hierarchical clustering and dynamic tree clipping (Fig. 2c, d). A total of 578 DEGs were extracted after standardization of the datasets based on the defined criteria. The DEGs are shown in the volcano plots and the heatmaps whose clustering was performed with Euclidean distance. GSE37265 includes 535 up-regulated genes and 43 down-regulated genes. (Fig.2, Supplementary Table 1)

We obtained 200 potential targets of active ingredients of HB. The co-expressed genes were integrated using the Venn Diagram online tool, including 23 up-regulated and 4 down-regulated genes in HB and RAS. (Fig.3 and Table 2)

Table 2

Differentially expressed genes in HB and RAS.

DEGs	Genes name
Up-regulated	CCL2 COL3A1 CXCL10 CXCL11 CXCL8 CYP1B1 HAS2 ICAM1 IL10 IL6 IRF1 MMP1 MMP3 PIK3CG PLAT SELE SERPINE1 SPP1 STAT1 TNF VCAM1 XDH NOS2
Down-regulated	FOS IFNG IL1B PTGS2

Construction of HB-RAS Interaction Networks

PPI network of common targets for HB and RAS

We obtain the network of intersection targets by the STRING database with 27 targets, saved them as TSV format files, used Cytoscape software to draw network diagrams for the core targets. The hub PPI network comprises 27 nodes and 215 edges with the maximum degree of freedom being 24, the minimum degree of freedom is 1. Eight nodes with higher value (“Degree” > 19, “Betweenness centrality” > 0.01595 and “Closeness centrality” > 0.73958) calculated by cytoHubba were screened as the key targets. The top ten degree-ranked targets in the net are PTGS2, IL6, TNF, IL1B, CCL2, ICAM1, CXCL8, IFNG, VCAM1, and CXCL10, indicating their essential roles for the network. We adjusted the color and size of each node according to the size of the "Combined" value of each node, as in Fig.4.

Network of drug-active components-key targets

The component-key target network including 73 nodes and 324 edges was constructed by using Cytoscape. We found that many targets are hit by different numbers of compounds and other targets, implying the multi-targets characteristics of HB as shown in Fig. 5. A network analysis showed that quercetin (HB19, degree = 142), and rutaecarpine (HB7, degree = 102) had the highest number of connections to different targets.

Pathway enrichment analysis for key targets

The results of GO analysis show that 1332 of 2015 biological processes, 19 of 53 cell components, 58 of 108 molecular functions enriched for these targets, and 29 target-related pathways were recognized as P value < 0.05. (Fig.6, Supplementary Table 2). Regarding BP, DEGs were significantly enriched in response to lipopolysaccharide, response to molecule of bacterial origin, cellular response to lipopolysaccharide, and cellular response to molecule of bacterial origin. This means lipopolysaccharide and bacterial production play key roles in RAS. For the CC, the DEGs were enriched in membrane raft, membrane microdomain, membrane region, and so on. MF analysis showed that the DEGs were significantly enriched in cytokine activity, cytokine receptor binding, receptor ligand activity, signaling receptor activator activity, and chemokine receptor binding. KEGG pathway-enrichment indicated that DEGs were mainly enriched in the TNF signaling pathway, AGE-RAGE signaling pathway in diabetic complications, Lipid and atherosclerosis, IL-17 signaling pathway, HIF-1 signaling pathway, Coronavirus disease - COVID-19, etc. The top 15 KEGG pathway enrichments are shown in Fig.7. Among these pathways, the HIF-1 signaling pathway and the TNF signaling pathway were associated with oral ulcer disease according to the CTD database. It is well known that a typical symptom of recurrent aphthous stomatitis is the inflammation of the oral cavity. Therefore, the mechanisms of HB’s anti-inflammatory function were investigated. Among the top 15 pathways, several pathways are associated with inflammation, and the TNF signaling pathway is the most distinct one.

Compound-Target Docking

The targets with the protein original ligand in both HIF-1 signaling pathway and TNF signaling pathway were selected to perform molecular docking, including TNF, IL6, IL1B, PTGS2, CCL2, NOS2, IFNG, MMP3, VCAM1, and IL10. The lowest Vina score value was chosen, which represents molecular docking with the best combining conformation(Tao et al., 2020) (Table 3). The results indicated that the active compounds had a good affinity to key targets and different components exhibited diversity towards the target proteins selected. quercetin and rutaecarpine showed strong interactions with TNF, PTGS2, IL10, and MMP3; moderate interactions with IL6, IL1B, CCL2, and NOS2; and no docking results to IFNG and VCAM1. Stigmasterol and Cavidine showed moderated interactions with TNF, PTGS2, and MMP3; weak interactions with IL6, IL1B, CCL2, IL10, and NOS2. Protein (TNF, MMP3) and compounds ( quercetin, rutaecarpine) with better binding affinities were shown in Fig.8.

Table 3

Vina score and RMSD of active chemical and key targets

Target	PDB ID	Ligand	Cavity size	Center			Size			Vina score	RMSD
Target	PDB ID	Ligand	Cavity size	x	y	z	x	y	z	Vina score	RMSD
TNF	1CA4	HB7	7177	-18	51	91	27	35	31	-9.6	0.000
		HB10	7177	-18	51	91	25	35	31	-8.9	0.000
		HB12	7177	-18	51	91	25	35	31	-8.8	0.000
		HB19	531	18	56	44	21	21	21	-9.1	0.000
IL6	4O9H	HB7	2579	0	6	42	30	21	21	-8	0.013
		HB10	2579	0	6	42	25	25	25	-7.1	0.000
		HB12	533	-20	17	27	22	22	22	-7.6	0.000
		HB19	2579	0	6	42	30	21	21	-7.5	0.000
IL1B	1T4Q	HB7	111	-19	4	5	21	21	21	-7.4	0.000
		HB10	130	-20	21	-16	25	25	25	-7	0.000
		HB12	168	-16	9	-14	22	22	22	-6.8	0.000
		HB19	158	-16	9	-14	21	21	21	-6.9	1.238
PTGS2	4DM6	HB7	4392	14	49	65	21	30	29	-10.3	2.913
		HB10	4392	14	49	65	25	25	25	-9.9	2.819
		HB12	16615	23	39	39	35	35	35	-9.4	2.394
		HB19	5179	12	53	17	33	21	29	-10	4.781
CCL2	4USP	HB7	102	7	3	45	21	21	21	-7.2	0.000
		HB10	102	17	0	50	25	25	25	-6.8	0.000
		HB12	102	7	3	45	22	22	22	-6.9	0.000
		HB19	102	7	3	45	21	21	21	-6.8	0.000
IL10	5IXI	HB7	453	93	-23	32	21	21	21	-9.3	0.000
		HB10	102	7	3	45	25	25	25	-6.9	0.000
		HB12	102	7	3	45	22	22	22	-6.9	0.000
		HB19	453	93	-23	32	21	21	21	-8.5	0.000
NOS2	5XN3	HB7	154	-6	0	23	21	21	21	-6.8	0.000
		HB10	154	-6	0	23	25	25	25	-6.6	0.000
		HB12	90	-3	-1	-2	22	22	22	-6.7	0.000
		HB19	154	-6	0	23	21	21	21	-6.6	0.000
MMP3	2D1O	HB7	4541	24	12	18	34	34	29	-10.3	0.000
		HB10	4541	24	12	18	34	34	25	-9.5	0.000
		HB12	4541	24	12	18	34	34	29	-8.7	0.000
		HB19	4541	24	12	18	34	34	29	-9.5	0.000

Recurrent aphthous stomatitis is a complex inflammatory disease caused by multiple factors, which severely influences the life of patients. The etiology of RAS lesions is unknown, but some local trauma, systemic, immune, genetic, allergic, nutritional, and microbiological factors are considered to be causative factors(Chiang et al., 2019). However, there are no effective drugs with low side effects against RAS.

HB has several biological activities against many Gram-positive and some Gram-negative bacteria(García-de-la-Mària et al., 2018; Higaki, Hasegawa, Morohashi, & Takayoshi, 1995). Besides its antibacterial activity, HB also acts as a well-established anti-inflammatory agent. Recent studies have shown that HB has both in vitro and in vivo anti-inflammatory effects(Mao et al., 2010; Park, Chung, Kim, Kwon, & Joh, 2007). Previous studies have shown the effectiveness of HB against RAS(Chen CH, 2009; L, 2021; Yang JM, 2013). Nevertheless, the mechanism is unclear. Presently, a comprehensive network pharmacology method was established to study the therapeutic targets and possible mechanisms of HB for treating RAS.

The chemical composition of HB mainly includes alkaloids, flavonoids, sterols, lactones, phenolic acids, terpenes, phenylpropanoids, and other chemical components using liquid chromatography-tandem mass spectrometry(Sun et al., 2016; H. Wang et al., 2013; X. Xian et al., 2014). Alkaloids are the main active ingredients in HB. About 42 alkaloids have been reported in the current studies. In the present study, quercetin and rutaecarpine were among the important active compounds of HB. Quercetin is a common flavonoid in Chinese herbs with therapeutic properties, including antioxidant and anti-inflammatory activities(Harwood et al., 2007). Quercetin has a long history of consumption as part of the normal human diet(Harwood et al., 2007). In a prospective active control trial, researchers confirmed the effectiveness of quercetin in reducing ulcer size and pain in patients with RAS(Pandya, Kalappanavar, Annigeri, & Rao, 2017). Quercetin was shown to be a safe and acceptable highly effective novel adjuvant therapy in two randomized controlled trials(Arafa, Ghalwash, El-Kersh, & Elmazar, 2018; Hamdy & Ibrahem, 2010). In addition, 90 percent of patients responded that they appreciated the ease of application when using the topical quercetin, and they did not object to its consistency or taste(Hamdy & Ibrahem, 2010). It may be promising to formulate a quercetin-based drug treatment for RAS in the future. Rutaecarpine is a major indolequinazoline alkaloid isolated from Evodiae fructus the dried fruit of Evodia rutaecarpa (Juss.) Benth(Nguyen et al., 2013). An increasing number of studies have revealed that rutaecarpine has extensive pharmacological actions, ranging from anti-inflammatory, anti-oxidant effects to vasodilatory effects(Cho, Shim, Lee, Mar, & Kim, 2005; Hibino, Yuzurihara, Kase, & Takeda, 2009; Ko et al., 2007). Mechanistic studies have shown evodiamine inhibits hypoxia induced inflammatory responses (COX-2 and iNOS expression) via suppressing the activation of hypoxia inducible factor-alpha (HIF-α) in macrophages(Y. N. Liu et al., 2009). Notably, many studies have shown that rutaecarpine can reduce pro-inflammatory mediators such as TNF-α, IL-1β, IL-6, and NF-κB to improve the symptoms of inflammation and oxidative stress(Han, Hu, & Chen, 2019; Jin et al., 2017; Y. Li et al., 2019). Taken together, we believe that these compounds play an important role in the healing process of RAS.

In the present study, integrated bioinformatics methods assisted in an analysis of how critical genes change in their expression to uncover potential RAS pathways based on GEO datasets “GSE37265”, and we identified 578 DEGs, including 535 up-regulated DEGs and 43 down-regulated DEG. Further, using the network pharmacology approach, we identified 27 intersection genes with HB treatment against RAS. The DGE-analysis identified 23 up-regulated DEGs and 4 down-regulated DEGs. PPI network analysis demonstrated that one active ingredient matches multiple targets and, in turn, one target matches multiple ingredients; reflecting the complex mechanism of action of multi-ingredient and multi-target against diseases in Chinese medicine. Gene pathway network analysis revealed that TNF, IL6, IL1B, PTGS2, CCL2, and IL10 were among the core targets of the HB in the treatment of RAS. Previous studies suggested that TNF-α plays a vital role in the pathological process of RAS, Oliveira(Oliveira et al., 2016) et al. found in their experiment that reducing TNF-α expression optimized the healing of traumatic oral ulcers in diabetic rats. TNF-α, as a pro-inflammatory factor, is involved in the development of RAS and can be used as an indicator of the severity of the disease. PTGS2 encoding cyclooxygenase-2(COX-2) has been documented to play a role in the development of RAS, Experiments in rats showed a decrease in PTGS2 activity and a decrease in COX-2 protein expression during the healing of oral ulcers(Slomiany & Slomiany, 2002).

GO enrichment analysis suggested that the HB regulates a variety of BPs and affects various CCs and MFs. GO functional enrichment analysis were mainly on biological processes, including response to lipopolysaccharide, response to molecule of bacterial origin, cellular response to lipopolysaccharide, and cellular response to molecule of bacterial origin. Cellular response to molecule of bacterial origin and reactive oxygen species metabolic process are important BPs involved in the development of RAS. wound healing and aging are key contributors that cause RAS. Reactive oxygen species metabolic process may trigger the stress response by regulating gene expression to shift redox homeostasis to a more oxidative state. This process facilitates the onset of RAS(Apel & Hirt, 2004; Liochev, 2013). Positive regulation of protein phosphorylation is a central signaling pathway that regulates cell survival, playing significant roles in the inhibition of RAS(Balasuriya et al., 2020; W. Yang, Zhang, & Wang, 2017).

The mechanisms of HB for treating RAS are fulfilled at least two function modules, including the inhibition of inflammation and the regulation of immunological response. The implementation of the functions relies on a smooth run of the complex multi-pathways network, particularly TNF signaling pathway and HIF-1 signaling pathway. CCL2, CXCL10, IL6, MMP3, TNF, IRF1, SELE, VCAM1, IL1B, PTGS2, ICAM1and FOS are involved in TNF-1 signaling pathway. Previous studies have been reported that excessive production of TNF-α, IL-6, and IL-1β was associated with an increased risk of RAS development(Bazrafshani, Hajeer, Ollier, & Thornhill, 2002; Guimarães et al., 2007; Scully & Porter, 2008). It has also been reported that matrix metalloproteinases play a negative role in mucosal pathology of the oral cavity(Karasneh, Bani-Hani, Alkhateeb, Hassan, & Thornhill, 2014; Skulason, Holbrook, & Kristmundsdottir, 2009). In summary, the anti-inflammatory effect is an important factor for HB contributing to the treatment of oral ulcers. Three targets are involved in HIF-1 signaling pathway which is an important regulator of the immune system, including IL6, NOS2, and IFNG. NOS2 is the isoforms of NOS, which produce high-level sustained NO synthesis and strongly affect adaptive immune responses(Bogdan, 2015). NO regulates the responses of many immune and inflammatory cell types like macrophages which are associated with some of the most important immune pathologies(Niedbala et al., 2014). Increased serum NO level is thought to take part in the pathogenesis of RAS(Gurel, Altinyazar, Unalacak, Armutcu, & Koca, 2007). Thus, NOS2 plays an important role in the HIF-1 signaling pathway for the regulation of anti-inflammation and immune protection functions of HB. Immunologic disturbances play a crucial role in the etiopathogenesis of oral ulcers. Hence, it is worthwhile to explore the impact of HB on immune function. According to the pathway enriched results, many target genes are enriched in the pathways related to immune inflammatory diseases. For example, nine targets are enriched in Toll-like receptor signaling pathway (P-value = 1.45 × 10 − 10). Six targets are enriched in NF-kappa B signaling pathway (P-value = 4.94× 10 − 6) and four targets in T cell receptor signaling pathway (P-value = 1.16 × 10 − 6). Therefore, it can be presumed that one pharmacological function of HB is related to the regulation of immune response for RAS treatment.

Molecular docking displayed components have good binding to core target genes. All selected core proteins had good affinity for the ligand (<-5 kcal/mol) and all effective docking fractions were > -7 kcal/mol, indicating that the compound has a strong binding affinity for the docked protein(Li, Fu, & Zhang, 2019). In silico validation of key targets for bioactive components offers an alternative path for the exploration of ligand-target interactions and action mechanisms. We could conclude that the different components display diverse interactions with these targets in the predicted pathways. The results demonstrated a synergistic effect mode of the HB in its oral ulcer treatment effects. PTGS2, which has the highest docking score, is a biomarker of iron death and inhibits the expression of inflammatory factors and apoptosis(H. Zhou et al., 2019; Y. Zhou et al., 2021). Future research directions can start from iron death mechanism pathway.

The limitation of this study is the lack of clinical or animal experiments. Further studies will combine molecular biology and pathophysiology to validate the predicted potential key targets and pathways, and explore the mechanism of action of the active ingredients.

In this study, we used network pharmacology and molecular docking methods to investigate the mechanism of HB against RAS. HB exhibited the therapeutic effects on oral ulcers probably by inhibiting inflammation, regulating immunological response, and suppressing oxidative stress. TNF signaling pathway and HIF-1 signaling pathway may play crucial roles in the protection of HB against recurrent aphthous stomatitis. This study is expected to be useful for the research and development of the drug and further elucidates its mechanism.

The data were obtained from public databases, so the ethics committee approval was unnecessary.

Active ingredients selection

Through the TCMSP(https://tcmspw.com/tcmsp.php), using “Huang Bai” as the keyword, we determined the oral bioavailability (OB) ≥30% and drug similarity (DL) ≥ 0.18 as the selection criteria. “Oral bioavailability” (OB) refers to the percentage of unmodified drugs that enter the circulatory system after oral administration(H. Liu, Wang, Zhou, Wang, & Yang, 2013; Xu et al., 2012). OB is a useful indicator for objective evaluation of the internal quality of drugs. The higher OB of an ingredient, the higher is the likelihood that it can be used clinically(Alam, Al-Jenoobi, Al-Mohizea, & Ali, 2015). The term“drug likeness” (DL) refers to the similarity between ingredients and known drugs(Walters & Murcko, 2002). Most ingredients in Chinese formulations have poor pharmacologic properties, so they cannot bind to specific protein targets on cells efficaciously. Several researchers(Huang et al., 2017; L. Yang et al., 2019) have recommended that molecules with OB ≥ 30% or DL ≥ 0.18 are considered to have better pharmacologic effects and are selected as candidate ingredients for further analyses. Protein sequences of these drug targets were normalized to official gene symbols using the UniProt database (https://www.uniprot.org/).

Acquisition of differentially expressed genes

GEO database(http://www.ncbi.nlm.nih.gov/geo), which is a publically available database of gene/microarray profiles, was used to screen relative targets of RAS. The search strategy (‘recurrent aphthous stomatitis’ [MeSH Terms] OR ‘recurrent aphthous stomatitis’ [All Fields]) AND (‘Homo sapiens’[Organism] was adopted to search differentially expressed genes (DEGs). The datasets were quantile-standardized by using R script. DEGs with the threshold criterion of |log FC| >1 and p < 0.05 in samples were screened using the limma V3.42.0 package of the R software program (version 4.1.2) (Ritchie et al., 2015). Then, the volcano plot and heatmap of DEGs were plotted by the Pheatmap V1.0.12 package(Khomtchouk, Van Booven, & Wahlestedt, 2014) again in the R analysis platform.

Construction of a network and analyses

We obtained the intersection of HB and RAS targets using the Venn diagram of Venny 2.1.0(https://bioinfogp.cnb.csic.es/tools/venny/). The shared target genes were then imported into the STRING database(Szklarczyk et al., 2017)(https://string-db.org/) with the species defined as human as well as the confidence score > 0.4. Cytoscape software 3.8.2 (https://cytoscape.org/) was used to visualize the PPI network for common targets. In the component-key target network, nodes represent components and targets, and edges represent the interactions between nodes. The targets without interaction were removed from the network. Afterward, the topological parameters of each node in the net were analyzed by using Network Analyzer tool Cytohubba pluginin(Chin et al., 2014) in Cytoscape. Cytohubba is a plug-in of Cytoscape, was employed to study essential nodes in the network with 11 methods (MCC exhibits a satisfied comparative performance) The topological parameters including degree, betweenness centrality, and closeness centrality were used to evaluate the significance of the nodes in networks. The nodes with “Degree” values 2-fold greater than all the network nodes’ median value, “Closeness centrality” and “Betweenness centrality” values above all the network nodes’ median value were identified as the key targets(J. B. Wang et al., 2018).

GO Function and KEGG pathway enrichment analysis

For Biological Processes (BP), Cellular Components (CC), Molecular Functions (MF), and KEGG Pathways, the R software analysis package's clusterProiler, Digest, and Goplot programs, as well as Cytoscape's CluePledia plug-in and Cluego plug-in, were utilized. The threshold P < 0.05 was set. The enrichment score (ES) represents the degree to which the set S is overexpressed at the top or bottom of the sorted list L. The higher the enrichment score, the more relevant the pathway is for disease progression. The more genes contained in a pathway, the larger the bubble represented by that pathway. The top 10 GO results with the lowest P.adjust values were displayed in the form of bar chart and cnet plot. The top 15 pathways were mapped to the oral ulcer disease related pathways in the CTD database to get common pathways.

Molecular docking of core targets to HB components

The molecular docking performance was operated by site-features directed docking for the study of the interactions between receptor and ligand(Pinzi & Rastelli, 2019). The protein structure of hub genes was obtained from the PDB database (http://www.rcsb.org), The molecular structure of key components ligand files in mol2 formats were obtained from PubChem (https://pubchem.ncbi.nlm.nih. gov/). CB-Dock (http://cao.labshare.cn/cb-dock/) was used for molecular docking. The CB-Dock server, developed by Dr. Liu's research team, is a user-friendly blind docking network server. Autodock Vina is used for docking, and it employs a unique curvature-based cavity detection technique(Y. Liu et al., 2020). This method had a success rate of more than 70%, outperforming even the most advanced blind docking tools. The atom positional root-mean-square deviation (RMSD) was developed as a metric for structural comparison by crystallographers. it has become a standard tool for comparing pairs of structures, characterizing ensemble(Pitera, 2014). RMSD ≤ 2 was considered the threshold for conformation of the ligand after docking to match the conformation of the original ligand.

Acknowledgments

The research was carried out without funding

Author contributions

Tll. wrote the main manuscript ，Tll. and Lst. analyze data and interpretation. Oww. and. Hl analyze Bioinformatics statistical. All authors reviewed the manuscript.

Availability of Data and Materials

The datasets analysed during the current study are available in the GEO database repository. GEO Accession viewer (nih.gov)

Funding

None.

Declarations

Ethical Approval

The data were obtained from public databases, so the ethics committee approval was unnecessary.

Consent for publication

The authors declare that they consent for publication.

Competing interests

The authors declare no conflicts of interest.

Author details

lulu Tang: [email protected], shuting Lu: [email protected], weiwei Ou: [email protected], ling Huang: [email protected]

Department: ¹The First College of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou, China. ²Department of anesthesiology, First Affiliated Hospital of Guangzhou University of Chinese Medicine, Ghangzhou, China.

Aggour, R. L., Mahmoud, S. H., & Abdelwhab, A. (2021). Evaluation of the effect of probiotic lozenges in the treatment of recurrent aphthous stomatitis: a randomized, controlled clinical trial. Clin Oral Investig, 25(4), 2151-2158. doi:10.1007/s00784-020-03527-7
Akintoye, S. O., & Greenberg, M. S. (2014). Recurrent aphthous stomatitis. Dent Clin North Am, 58(2), 281-297. doi:10.1016/j.cden.2013.12.002
Alam, M. A., Al-Jenoobi, F. I., Al-Mohizea, A. M., & Ali, R. (2015). Understanding and managing oral bioavailability: physiological concepts and patents. Recent Pat Anticancer Drug Discov, 10(1), 87-96. doi:10.2174/1574892809666140917103834
Amorim Dos Santos, J., Normando, A. G. C., de Toledo, I. P., Melo, G., De Luca Canto, G., Santos-Silva, A. R., & Guerra, E. N. S. (2020). Laser therapy for recurrent aphthous stomatitis: an overview. Clin Oral Investig, 24(1), 37-45. doi:10.1007/s00784-019-03144-z
Apel, K., & Hirt, H. (2004). Reactive oxygen species: metabolism, oxidative stress, and signal transduction. Annu Rev Plant Biol, 55, 373-399. doi:10.1146/annurev.arplant.55.031903.141701
Arafa, M. G., Ghalwash, D., El-Kersh, D. M., & Elmazar, M. M. (2018). Propolis-based niosomes as oromuco-adhesive films: A randomized clinical trial of a therapeutic drug delivery platform for the treatment of oral recurrent aphthous ulcers. Sci Rep, 8(1), 18056. doi:10.1038/s41598-018-37157-7
Baccaglini, L., Lopez, C. M., Shuster, J. J., Bhattacharyya, I., Mans, J. J., Handfield, M., . . . Baker, H. V. (2010). Differential gene expression patterns in patients with recurrent aphthous stomatitis. Oral Dis, 16(6), 525-526. Retrieved from <Go to ISI>://WOS:000281287500054.
Balasuriya, N., Davey, N. E., Johnson, J. L., Liu, H., Biggar, K. K., Cantley, L. C., . . . O'Donoghue, P. (2020). Phosphorylation-dependent substrate selectivity of protein kinase B (AKT1). J Biol Chem, 295(24), 8120-8134. doi:10.1074/jbc.RA119.012425
Bazrafshani, M. R., Hajeer, A. H., Ollier, W. E., & Thornhill, M. H. (2002). IL-1B and IL-6 gene polymorphisms encode significant risk for the development of recurrent aphthous stomatitis (RAS). Genes Immun, 3(5), 302-305. doi:10.1038/sj.gene.6363882
Bogdan, C. (2015). Nitric oxide synthase in innate and adaptive immunity: an update. Trends Immunol, 36(3), 161-178. doi:10.1016/j.it.2015.01.003
Chen CH, H. H., Tong L. (2009). "Clinical study on the treatment of Aphthous ulcer by Huangbai San". China Modern Doctor, 47(05), 61+66.
Cheng, B., Zeng, X., Liu, S., Zou, J., & Wang, Y. (2020). The efficacy of probiotics in management of recurrent aphthous stomatitis: a systematic review and meta-analysis. Sci Rep, 10(1), 21181. doi:10.1038/s41598-020-78281-7
Cheng, Y., Liu, L., Mo, S., Gao, J., Zhang, H., Zhang, H., . . . Geng, Z. (2021). The Immunomodulatory Effects of Phellodendri Cortex Polysaccharides on Cyclophosphamide-Induced Immunosuppression in Mice. Evid Based Complement Alternat Med, 2021, 3027708. doi:10.1155/2021/3027708
Chiang, C. P., Yu-Fong Chang, J., Wang, Y. P., Wu, Y. H., Wu, Y. C., & Sun, A. (2019). Recurrent aphthous stomatitis - Etiology, serum autoantibodies, anemia, hematinic deficiencies, and management. J Formos Med Assoc, 118(9), 1279-1289. doi:10.1016/j.jfma.2018.10.023
Chin, C. H., Chen, S. H., Wu, H. H., Ho, C. W., Ko, M. T., & Lin, C. Y. (2014). cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC Syst Biol, 8 Suppl 4(Suppl 4), S11. doi:10.1186/1752-0509-8-s4-s11
Cho, M. H., Shim, S. M., Lee, S. R., Mar, W., & Kim, G. H. (2005). Effect of Evodiae fructus extracts on gene expressions related with alcohol metabolism and antioxidation in ethanol-loaded mice. Food Chem Toxicol, 43(9), 1365-1371. doi:10.1016/j.fct.2005.03.010
Dalessandri, D., Zotti, F., Laffranchi, L., Migliorati, M., Isola, G., Bonetti, S., & Visconti, L. (2019). Treatment of recurrent aphthous stomatitis (RAS; aphthae; canker sores) with a barrier forming mouth rinse or topical gel formulation containing hyaluronic acid: a retrospective clinical study. BMC Oral Health, 19(1), 153. doi:10.1186/s12903-019-0850-1
García-de-la-Mària, C., Gasch, O., García-Gonzalez, J., Soy, D., Shaw, E., Ambrosioni, J., . . . Miró, J. M. (2018). The Combination of Daptomycin and Fosfomycin Has Synergistic, Potent, and Rapid Bactericidal Activity against Methicillin-Resistant Staphylococcus aureus in a Rabbit Model of Experimental Endocarditis. Antimicrob Agents Chemother, 62(6). doi:10.1128/aac.02633-17
Ge, B., Guo, C., Liang, Y., Liu, M., & Wu, K. (2019). Network analysis, and human and animal studies disclose the anticystitis glandularis effects of vitamin C. Biofactors, 45(6), 912-919. doi:10.1002/biof.1558
Girardelli, M., Valencic, E., Moressa, V., Margagliotta, R., Tesser, A., Pastore, S., . . . Tommasini, A. (2021). Genetic and immunologic findings in children with recurrent aphthous stomatitis with systemic inflammation. Pediatr Rheumatol Online J, 19(1), 70. doi:10.1186/s12969-021-00552-y
Gorsky, M., Epstein, J., Rabenstein, S., Elishoov, H., & Yarom, N. (2007). Topical minocycline and tetracycline rinses in treatment of recurrent aphthous stomatitis: a randomized cross-over study. Dermatol Online J, 13(2), 1.
Guimarães, A. L., Correia-Silva Jde, F., Sá, A. R., Victória, J. M., Diniz, M. G., Costa Fde, O., & Gomez, R. S. (2007). Investigation of functional gene polymorphisms IL-1beta, IL-6, IL-10 and TNF-alpha in individuals with recurrent aphthous stomatitis. Arch Oral Biol, 52(3), 268-272. doi:10.1016/j.archoralbio.2006.08.008
Gurel, A., Altinyazar, H. C., Unalacak, M., Armutcu, F., & Koca, R. (2007). Purine catabolic enzymes and nitric oxide in patients with recurrent aphthous ulceration. Oral Dis, 13(6), 570-574. doi:10.1111/j.1601-0825.2006.01338.x
Habibzadeh, S., Sheikh Rahimi, M., Edalatkhah, H., Piri, H., & Maleki, N. (2021). Effectiveness of booster dose of tetanus and diphtheria toxoids (Td) vaccine in management of recurrent aphthous stomatitis: a prospective, randomized, triple-blind and placebo-controlled clinical trial. J Dermatolog Treat, 32(3), 361-366. doi:10.1080/09546634.2019.1654597
Hamdy, A. A., & Ibrahem, M. A. (2010). Management of aphthous ulceration with topical quercetin: a randomized clinical trial. J Contemp Dent Pract, 11(4), E009-016.
Hamedi, S., Sadeghpour, O., Shamsardekani, M. R., Amin, G., Hajighasemali, D., & Feyzabadi, Z. (2016). The Most Common Herbs to Cure the Most Common Oral Disease: Stomatitis Recurrent Aphthous Ulcer (RAU). Iran Red Crescent Med J, 18(2), e21694. doi:10.5812/ircmj.21694
Han, M., Hu, L., & Chen, Y. (2019). Rutaecarpine may improve neuronal injury, inhibits apoptosis, inflammation and oxidative stress by regulating the expression of ERK1/2 and Nrf2/HO-1 pathway in rats with cerebral ischemia-reperfusion injury. Drug Des Devel Ther, 13, 2923-2931. doi:10.2147/dddt.S216156
Harwood, M., Danielewska-Nikiel, B., Borzelleca, J. F., Flamm, G. W., Williams, G. M., & Lines, T. C. (2007). A critical review of the data related to the safety of quercetin and lack of evidence of in vivo toxicity, including lack of genotoxic/carcinogenic properties. Food Chem Toxicol, 45(11), 2179-2205. doi:10.1016/j.fct.2007.05.015
Hibino, T., Yuzurihara, M., Kase, Y., & Takeda, A. (2009). synephrine, a component of Evodiae Fructus, constricts isolated rat aorta via adrenergic and serotonergic receptors. J Pharmacol Sci, 111(1), 73-81. doi:10.1254/jphs.09077fp
Higaki, S., Hasegawa, Y., Morohashi, M., & Takayoshi, Y. (1995). The correlation of Kampo formulations and their ingredients on anti-bacterial activities against Propionibacterium acnes. J Dermatol, 22(1), 4-9. doi:10.1111/j.1346-8138.1995.tb03332.x
Huang, J., Tang, H., Cao, S., He, Y., Feng, Y., Wang, K., & Zheng, Q. (2017). Molecular Targets and Associated Potential Pathways of Danlu Capsules in Hyperplasia of Mammary Glands Based on Systems Pharmacology. Evid Based Complement Alternat Med, 2017, 1930598. doi:10.1155/2017/1930598
Jin, S. W., Hwang, Y. P., Choi, C. Y., Kim, H. G., Kim, S. J., Kim, Y., . . . Jeong, H. G. (2017). Protective effect of rutaecarpine against t-BHP-induced hepatotoxicity by upregulating antioxidant enzymes via the CaMKII-Akt and Nrf2/ARE pathways. Food Chem Toxicol, 100, 138-148. doi:10.1016/j.fct.2016.12.031
Karasneh, J. A., Bani-Hani, M. E., Alkhateeb, A. M., Hassan, A. F., & Thornhill, M. H. (2014). Association of MMP but not TIMP-1 gene polymorphisms with recurrent aphthous stomatitis. Oral Dis, 20(7), 693-699. doi:10.1111/odi.12190
Khomtchouk, B. B., Van Booven, D. J., & Wahlestedt, C. (2014). HeatmapGenerator: high performance RNAseq and microarray visualization software suite to examine differential gene expression levels using an R and C++ hybrid computational pipeline. Source Code Biol Med, 9(1), 30. doi:10.1186/s13029-014-0030-2
Ko, H. C., Wang, Y. H., Liou, K. T., Chen, C. M., Chen, C. H., Wang, W. Y., . . . Shen, Y. C. (2007). Anti-inflammatory effects and mechanisms of the ethanol extract of Evodia rutaecarpa and its bioactive components on neutrophils and microglial cells. Eur J Pharmacol, 555(2-3), 211-217. doi:10.1016/j.ejphar.2006.10.002
L, S. H. H. (2021). "30 cases of oral ulcers complicated by tracheal intubation treated with honey-roasted phellodendron and yellow phellodendron combined with rehabilitation new liquid". 28(02), 295-296.
Lalla, R. V., Choquette, L. E., Feinn, R. S., Zawistowski, H., Latortue, M. C., Kelly, E. T., & Baccaglini, L. (2012). Multivitamin therapy for recurrent aphthous stomatitis: a randomized, double-masked, placebo-controlled trial. J Am Dent Assoc, 143(4), 370-376. doi:10.14219/jada.archive.2012.0179
Lee, S. H., Kwak, S. C., Kim, D. K., Park, S. W., Kim, H. S., Kim, Y. S., . . . Chang, G. T. (2016). Effects of Huang Bai (Phellodendri Cortex) and Three Other Herbs on GnRH and GH Levels in GT1-7 and GH3 Cells. Evid Based Complement Alternat Med, 2016, 9389028. doi:10.1155/2016/9389028
Li, J., Fu, A., & Zhang, L. (2019). An Overview of Scoring Functions Used for Protein-Ligand Interactions in Molecular Docking. Interdiscip Sci, 11(2), 320-328. doi:10.1007/s12539-019-00327-w
Li, R., Ma, X., Song, Y., Zhang, Y., Xiong, W., Li, L., & Zhou, L. (2019). Anti-colorectal cancer targets of resveratrol and biological molecular mechanism: Analyses of network pharmacology, human and experimental data. J Cell Biochem. doi:10.1002/jcb.28404
Li, Y., Zhang, G., Chen, M., Tong, M., Zhao, M., Tang, F., . . . Wen, H. (2019). Rutaecarpine inhibited imiquimod-induced psoriasis-like dermatitis via inhibiting the NF-κB and TLR7 pathways in mice. Biomed Pharmacother, 109, 1876-1883. doi:10.1016/j.biopha.2018.10.062
Liochev, S. I. (2013). Reactive oxygen species and the free radical theory of aging. Free Radic Biol Med, 60, 1-4. doi:10.1016/j.freeradbiomed.2013.02.011
Liu, H., Wang, J., Zhou, W., Wang, Y., & Yang, L. (2013). Systems approaches and polypharmacology for drug discovery from herbal medicines: an example using licorice. J Ethnopharmacol, 146(3), 773-793. doi:10.1016/j.jep.2013.02.004
Liu, Y., Grimm, M., Dai, W. T., Hou, M. C., Xiao, Z. X., & Cao, Y. (2020). CB-Dock: a web server for cavity detection-guided protein-ligand blind docking. Acta Pharmacol Sin, 41(1), 138-144. doi:10.1038/s41401-019-0228-6
Liu, Y. N., Pan, S. L., Liao, C. H., Huang, D. Y., Guh, J. H., Peng, C. Y., . . . Teng, C. M. (2009). Evodiamine represses hypoxia-induced inflammatory proteins expression and hypoxia-inducible factor 1alpha accumulation in RAW264.7. Shock, 32(3), 263-269. doi:10.1097/SHK.0b013e31819940cb
Mao, Y. F., Li, Y. Q., Zong, L., You, X. M., Lin, F. Q., & Jiang, L. (2010). Methanol extract of Phellodendri cortex alleviates lipopolysaccharide-induced acute airway inflammation in mice. Immunopharmacol Immunotoxicol, 32(1), 110-115. doi:10.3109/08923970903193325
Miller, M. F., Garfunkel, A. A., Ram, C. A., & Ship, II. (1980). The inheritance of recurrent aphthous stomatitis. Observations on susceptibility. Oral Surg Oral Med Oral Pathol, 49(5), 409-412. doi:10.1016/0030-4220(80)90284-4
Nguyen, N. V., Lee, K. R., Lee, Y. J., Choi, S., Kang, J. S., Mar, W., & Kim, K. H. (2013). Chiral high-performance liquid chromatographic separation of evodiamine enantiomers and rutaecarpine, isolated from Evodiae fructus. J Pharm Biomed Anal, 81-82, 151-159. doi:10.1016/j.jpba.2013.04.018
Niedbala, W., Besnard, A. G., Nascimento, D. C., Donate, P. B., Sonego, F., Yip, E., . . . Liew, F. Y. (2014). Nitric oxide enhances Th9 cell differentiation and airway inflammation. Nat Commun, 5, 4575. doi:10.1038/ncomms5575
Oliveira, B. V., Barros Silva, P. G., Nojosa Jde, S., Brizeno, L. A., Ferreira, J. M., Sousa, F. B., . . . Alves, A. P. (2016). TNF-alpha expression, evaluation of collagen, and TUNEL of Matricaria recutita L. extract and triamcinolone on oral ulcer in diabetic rats. J Appl Oral Sci, 24(3), 278-290. doi:10.1590/1678-775720150481
Pandya, M., Kalappanavar, A. N., Annigeri, R. G., & Rao, D. S. (2017). Relative Efficacy of Quercetin Compared with Benzydamine Hydrochloride in Minor Aphthae: A Prospective, Parallel, Double Blind, Active Control, Preliminary Study. Int J Dent, 2017, 7034390. doi:10.1155/2017/7034390
Park, Y. K., Chung, Y. S., Kim, Y. S., Kwon, O. Y., & Joh, T. H. (2007). Inhibition of gene expression and production of iNOS and TNF-alpha in LPS-stimulated microglia by methanol extract of Phellodendri cortex. Int Immunopharmacol, 7(7), 955-962. doi:10.1016/j.intimp.2006.03.018
Pinzi, L., & Rastelli, G. (2019). Molecular Docking: Shifting Paradigms in Drug Discovery. Int J Mol Sci, 20(18). doi:10.3390/ijms20184331
Pitera, J. W. (2014). Expected distributions of root-mean-square positional deviations in proteins. J Phys Chem B, 118(24), 6526-6530. doi:10.1021/jp412776d
Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., & Smyth, G. K. (2015). limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res, 43(7), e47. doi:10.1093/nar/gkv007
Sánchez-Bernal, J., Conejero, C., & Conejero, R. (2020). Recurrent Aphthous Stomatitis. Actas Dermosifiliogr (Engl Ed), 111(6), 471-480. doi:10.1016/j.ad.2019.09.004
Schmidt, R. (1994). The Pharmacology of Chinese Herbs, Kee Chang Huang, CRC Press, Boca Raton, Florida. 1993. 10.
Scully, C., & Porter, S. (2008). Oral mucosal disease: recurrent aphthous stomatitis. Br J Oral Maxillofac Surg, 46(3), 198-206. doi:10.1016/j.bjoms.2007.07.201
Shao, Y., Ding, B., Ji, J., Lei, S., Dong, Y., Fan, Y., . . . Xu, L. (2021). The Anti-Inflammatory Effect of Zhibaidihuang Decoction on Recurrent Oral Ulcer with Sirt1 as the Key Regulatory Target. Evid Based Complement Alternat Med, 2021, 8886699. doi:10.1155/2021/8886699
Ship, II. (1972). Epidemiologic aspects of recurrent aphthous ulcerations. Oral Surg Oral Med Oral Pathol, 33(3), 400-406. doi:10.1016/0030-4220(72)90469-0
Skulason, S., Holbrook, W. P., & Kristmundsdottir, T. (2009). Clinical assessment of the effect of a matrix metalloproteinase inhibitor on aphthous ulcers. Acta Odontol Scand, 67(1), 25-29. doi:10.1080/00016350802526559
Ślebioda, Z., Szponar, E., & Kowalska, A. J. A. i. e. t. e. (2014). Etiopathogenesis of recurrent aphthous stomatitis and the role of immunologic aspects: literature review. 62(3), 205-215.
Slomiany, B. L., & Slomiany, A. (2002). Activation of peroxisome proliferator-activated receptor gamma suppresses inducible cyclooxygenase and nitric oxide synthase during oral mucosal ulcer healing. J Physiol Pharmacol, 53(2), 159-169.
Sun, H., Wang, H., Zhang, A., Yan, G., Han, Y., Li, Y., . . . Wang, X. (2016). Chemical Discrimination of Cortex Phellodendri amurensis and Cortex Phellodendri chinensis by Multivariate Analysis Approach. Pharmacogn Mag, 12(45), 41-49. doi:10.4103/0973-1296.176023
Szklarczyk, D., Morris, J. H., Cook, H., Kuhn, M., Wyder, S., Simonovic, M., . . . von Mering, C. (2017). The STRING database in 2017: quality-controlled protein-protein association networks, made broadly accessible. Nucleic Acids Res, 45(D1), D362-d368. doi:10.1093/nar/gkw937
Tao, Y. G., Huang, X. F., Wang, J. Y., Kang, M. R., Wang, L. J., & Xian, S. X. (2020). Exploring Molecular Mechanism of Huangqi in Treating Heart Failure Using Network Pharmacology. Evid Based Complement Alternat Med, 2020, 6473745. doi:10.1155/2020/6473745
Walters, W. P., & Murcko, M. A. (2002). Prediction of 'drug-likeness'. Adv Drug Deliv Rev, 54(3), 255-271. doi:10.1016/s0169-409x(02)00003-0
Wang, H., Yan, G., Zhang, A., Li, Y., Wang, Y., Sun, H., . . . Wang, X. (2013). Rapid discovery and global characterization of chemical constituents and rats metabolites of Phellodendri amurensis cortex by ultra-performance liquid chromatography-electrospray ionization/quadrupole-time-of-flight mass spectrometry coupled with pattern recognition approach. Analyst, 138(11), 3303-3312. doi:10.1039/c3an36902a
Wang, J. B., Cui, H. R., Wang, R. L., Zhang, C. E., Niu, M., Bai, Z. F., . . . Xiao, X. H. (2018). A systems pharmacology-oriented discovery of a new therapeutic use of the TCM formula Liuweiwuling for liver failure. Sci Rep, 8(1), 5645. doi:10.1038/s41598-018-21515-6
Xian, X., Sun, B., Ye, X., Zhang, G., Hou, P., & Gao, H. (2014). Identification and analysis of alkaloids in cortex Phellodendron amurense by high-performance liquid chromatography with electrospray ionization mass spectrometry coupled with photodiode array detection. J Sep Sci, 37(13), 1533-1545. doi:10.1002/jssc.201400012
Xian, Y. F., Lin, Z. X., Ip, S. P., Su, Z. R., Chen, J. N., & Lai, X. P. (2013). Comparison the neuropreotective effect of Cortex Phellodendri chinensis and Cortex Phellodendri amurensis against beta-amyloid-induced neurotoxicity in PC12 cells. Phytomedicine, 20(2), 187-193. doi:10.1016/j.phymed.2012.09.028
Xian, Y. F., Mao, Q. Q., Ip, S. P., Lin, Z. X., & Che, C. T. (2011). Comparison on the anti-inflammatory effect of Cortex Phellodendri Chinensis and Cortex Phellodendri Amurensis in 12-O-tetradecanoyl-phorbol-13-acetate-induced ear edema in mice. J Ethnopharmacol, 137(3), 1425-1430. doi:10.1016/j.jep.2011.08.014
Xu, X., Zhang, W., Huang, C., Li, Y., Yu, H., Wang, Y., . . . Ling, Y. (2012). A novel chemometric method for the prediction of human oral bioavailability. Int J Mol Sci, 13(6), 6964-6982. doi:10.3390/ijms13066964
Yang JM, M. Y., Zhou ML,Bin C, Jinag QQ, Zhang WG,Liu MC. (2013). “The effect of Phellodendron Bark on oral ulcers in rats and its effect on the level of TNF-α”. Chinese Journal of Traditional Medical Science and Technology, 20(06), 614-615.
Yang, L., Liu, W., Hu, Z., Yang, M., Li, J., Fan, X., & Pan, H. (2019). A Systems Pharmacology Approach for Identifying the Multiple Mechanisms of Action of the Wei Pi Xiao Decoction for the Treatment of Gastric Precancerous Lesions. Evid Based Complement Alternat Med, 2019, 1562707. doi:10.1155/2019/1562707
Yang, W., Zhang, W., & Wang, X. (2017). Post-translational control of ABA signalling: the roles of protein phosphorylation and ubiquitination. Plant Biotechnol J, 15(1), 4-14. doi:10.1111/pbi.12652
Zhou, H., Li, F., Niu, J. Y., Zhong, W. Y., Tang, M. Y., Lin, D., . . . Tu, Y. S. (2019). Ferroptosis was involved in the oleic acid-induced acute lung injury in mice. Sheng Li Xue Bao, 71(5), 689-697.
Zhou, Y., Zhou, H., Hua, L., Hou, C., Jia, Q., Chen, J., . . . Jia, E. (2021). Verification of ferroptosis and pyroptosis and identification of PTGS2 as the hub gene in human coronary artery atherosclerosis. Free Radic Biol Med, 171, 55-68. doi:10.1016/j.freeradbiomed.2021.05.009

No competing interests reported.

PDF

Version 1

posted 27 Apr, 2022

You are reading this latest preprint version

Network pharmacology and bioinformatics analyses identify the intersection genes and mechanism of Huangbai for Recurrent Aphthous Stomatitis

Status:

Version 1

Abstract

Figures

Introduction

Results

Discussion

Conclusion

Materials And Methods

Declarations

References

Competing Interests

Supplementary Files

Status:

Version 1