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Article

The Active Compounds and Therapeutic Mechanisms of Pentaherbs Formula for Oral and Topical Treatment of Atopic Dermatitis Based on Network Pharmacology

by
Man Chu
1,
Miranda Sin-Man Tsang
2,3,
Ru He
1,
Christopher Wai-Kei Lam
4,
Zhi Bo Quan
1,* and
Chun Kwok Wong
2,3,5,*
1
Faulty of Medical Technology, Shaanxi University of Chinese Medicine, Xianyang 712046, China
2
Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, Hong Kong 999077, China
3
State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants and Institute of Chinese Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong 999077, China
4
State Key Laboratory of Quality Research in Chinese Medicines and Faculty of Medicine, Macau University of Science and Technology, Macau 999078, China
5
Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong 999077, China
*
Authors to whom correspondence should be addressed.
Plants 2020, 9(9), 1166; https://doi.org/10.3390/plants9091166
Submission received: 23 July 2020 / Revised: 3 September 2020 / Accepted: 7 September 2020 / Published: 9 September 2020
(This article belongs to the Special Issue In Vitro Anti-inflammatory Effects of Traditionally Used Herbal Remedies)
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Abstract

:
To examine the molecular targets and therapeutic mechanism of a clinically proven Chinese medicinal pentaherbs formula (PHF) in atopic dermatitis (AD), we analyzed the active compounds and core targets, performed network and molecular docking analysis, and investigated interacting pathways. Information on compounds in PHF was obtained from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, and target prediction was performed using the Drugbank database. AD-related genes were gathered using the GeneCards and Online Mendelian Inheritance in Man (OMIM) databases. Network analysis was performed by Cytoscape software and protein-protein interaction was analyzed by the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). The Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resources were applied for the enrichment analysis of the potential biological process and pathways associated with the intersection targets between PHF and AD. Autodock software was used to perform protein compound docking analysis. We identified 43 active compounds in PHF associated with 117 targets, and 57 active compounds associated with 107 targets that form the main pathways linked to oral and topical treatment of AD, respectively. Among them, quercetin, luteolin, and kaempferol are key chemicals targeting the core genes involved in the oral use of PHF against AD, while apigenin, ursolic acid, and rosmarinic acid could be used in topical treatment of PHF against AD. The compound–target–disease network constructed in the current study reveals close interactions between multiple components and multiple targets. Enrichment analysis further supports the biological processes and signaling pathways identified, indicating the involvement of IL-17 and tumor necrosis factor signaling pathways in the action of PHF on AD. Our data demonstrated the main compounds and potential pharmacological mechanisms of oral and topical application of PHF in AD.

1. Introduction

Atopic dermatitis (AD) is a common allergic skin disease affecting all ages of people in the world, especially children [1,2]. The prevalence of AD has been increasing globally. The onset of AD occurs before the age of five in about 70% of AD patients [3,4]. In Hong Kong, more than 19% of adolescent schoolchildren are suffering from AD [5]. While AD is not directly life-threatening, the chronic disease causes a significant burden on daily lives, affecting quality of life for the individual, their families, and the communities they live in, both socially and financially. It is characterized by redness, cracking, dryness, itchiness, thickening, and inflammation of the skin, accompanying the apoptosis of keratinocytes that compromises the quality of life of patients [6]. The pathogenesis of AD involves the abnormal T helper (Th)2 lymphocytes-related cytokine interleukin (IL)-4, IL-5, and IL-13 and serum immunoglobin-(Ig)E levels in response to environmental allergens, which is putatively associated with the disturbance of the epidermal barrier [7]. The dysfunction of the epidermal barrier leads to the penetration of allergens that drives dendritic cells to initiate Th2 polarization and eosinophilic inflammation [8,9].
There is no definitive cure for AD, and the present clinical treatment of AD mainly includes topical anti-inflammatory agent corticosteroids and calcineurin inhibitors. As a potent drug for inflammatory diseases, corticosteroids have been shown to be effective for both acute and chronic AD, though treatment with systemic corticosteroids is not recommended [10]. However, prolonged use of topical corticosteroids can lead to undesirable side effects, including irreversible skin thinning as well as systemic suppression of adrenal function and growth induced by absorption [3]. Topical calcineurin inhibitors, including tacrolimus and pimecrolimus, have been shown to alleviate AD symptoms by suppressing the gene transcription of critical AD-related cytokines such as IL-2, IL-4, and IL-5. However, an alert issued by the Food and Drug Administration demonstrated a potential risk between calcineurin inhibitors and cancer [11,12,13]. Traditional Chinese Medicine (TCM) has become a more widely accepted treatment for immunomodulation of chronic diseases with fewer side effects. According to the concept of TCM, AD can be classified as “cubito-popliteal eczema”, “itching eruptions due to wind-heat in blood” and “prurigo”, namely “Si Wan Feng” in Chinese. Unlike Western medicine, Chinese medicine emphasizes the importance of internal treatment in the control of disease, and is often prescribed as a decoction. However, the mechanisms of multicomponent and multitarget TCM treatment from an integrative and holistic point of view should be explored and revealed.
Pentaherbs formula (PHF), an improved herbal formula with five Chinese medicines, was developed with reference to their specific properties by the Institute of Chinese Medicine, The Chinese University of Hong Kong (commercial name: Shi Min Qing capsule). PHF is composed of five herbs, namely Cortex Moutan (CM), Cortex Phellodendri (CP), Flos Lonicerae (FL), Herba Menthae (HM), and Rhizoma Atractylodis (RA), which are the root bark of Paeonia suffruticosa Andr. (Ranunculaceae), the bark of Phellodendron chinensis Schneid. (Rutaceae), the flower of Lonicera japonica Thunb. (Capri-foliaceae), the aerial part of Mentha haplocalyx Briq. (Labiatae) and the rhizome of Atractylodes lancea (Thunb.) DC. (Compositae), respectively. In the concept of TCM, these five herbs can clear the heat, resolve toxicity, dispel wind-heat from the exterior, dry dampness, drain fire, and cool the blood, and were thus applied for the treatment of AD. Previous clinical trials performed by our group showed that moderate-to-severe AD children had significant improvement in the quality of life after a 12-week treatment with PHF [14]. Their concurrent use of topical corticosteroids was also reduced [14]. PHF capsules were also shown to be well tolerated by children and adverse effects were not noticeable clinically [15]. The findings suggested that PHF is a potential alternative adjunct therapy for treating AD. The anti-inflammatory actions of PHF were further elucidated in vitro. With an increased ratio of Danpi in the formula, inflammatory cytokines IL-6 and IL-1 released from human mast cells HMC-1 was greatly inhibited [16]. Our previous studies showed that PHF, Danpi, and one of its compounds—gallic acid—can suppress AD-related pro-inflammatory cytokines/chemokines from human basophils, and interfere with the maturation of monocyte-derived dendritic cells, which are crucial cells for initiating allergic sensitization [17,18]. Oral and topical treatment of PHF can also reduce inflammation on the challenged ears of our oxazolone-mediated dermatitis mice [19]. We also demonstrated the anti-inflammatory activities of three ingredients in PHF in eosinophils/dermal fibroblasts coculture upon IL-31 and IL-33 stimulation [19]. Together, PHF treatment may be a novel modality for managing AD. However, its pharmacological mechanism has not been elucidated completely as PHF is a multicomponent and multitargeted agent that demonstrates therapeutic efficacy within the body system.
Network pharmacology interprets the disease pathogenesis from the perspective of systems biology and the balance of biological networks, and hence provides guidance for the discovery of new drugs based on high-throughput data technologies with computational data analysis [20,21]. Therefore, it has been utilized to identify molecular mechanisms involved in the therapeutic actions of herbal medicine and its multitargeted compounds in biological networks [22]. Based on our previous studies, we now aim at applying a comprehensive network pharmacology approach to predict active compounds and molecular targets of PHF for both oral and topical treatment against AD. Moreover, the putative targets of PHF against AD and the associated potential pathways of how PHF exerts its therapeutic effects on AD will be explored in the present study.

1.1. Active Compounds and Compound Targets in PHF

From the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database, a total of 644 compounds were retrieved, namely, 164 in HM, 49 in RA, 55 in CM, 140 in CP, and 236 in FL. For active compound screening, drug-likeness (DL) ≥ 0.18 was adopted as DL is a qualitative notion used for estimating the drugability of a substance in drug design [23]. The compounds with higher oral bioavailability (OB) (OB ≥ 30%) and lower OB (OB < 30%) were screened for oral and topical use of PHF. The compounds and their putative targets of each herb in PHF are shown in Figure 1.
As a matter of fact, a total of 90 compounds including 10 (6.1%) compounds in HM, 9 (18.4%) compounds in RA, 11 (20%) compounds in CM, 37 (26.4%) compounds in CP, and 23 (9.7%) compounds in FL satisfied the criteria of OB ≥ 30% and DL ≥ 0.18. Therefore, 83 candidate compounds were then obtained after the removal of duplications (Supplementary Table S1). These compounds in PHF were associated with 1278 target proteins (165 in HM, 62 in RA, 435 in CM, 214 in CP, and 402 in FL) and 240 predicted targets were selected after eliminating the redundancy.
A total of 159 compounds including 23 (14.0%) compounds in HM, 11 (22.4%) compounds in RA, 33 (60.0%) compounds in CM, 25 (17.9%) compounds in CP, and 67 (28.4%) compounds in FL satisfied the criteria of OB < 30% and DL ≥ 0.18. Hence, 150 candidate compounds were obtained after the removal of duplications (Supplementary Table S2). These compounds in PHF were associated with 867 target proteins (244 in HM, 22 in RA, 264 in CM, 15 in CP, and 322 in FL) and 204 predicted targets were selected after eliminating the redundancy.

1.2. AD-Related Targets

After searching with the keyword “atopic dermatitis”, 1255 targets were acquired based on GeneCards database, and 12 targets were obtained based on Online Mendelian Inheritance in Man (OMIM) database. Finally, a total of 1256 known therapeutic targets for AD treatment were identified in this study after eliminating the redundancy (Supplementary Table S3).

1.3. Network Analysis

The compound–target network of the screened compounds and putative targets against AD was constructed. As shown in Figure 2A, there are 117 intersection targets between compound (OB ≥ 30% and DL ≥ 0.18) and AD-related targets. The intersection targets are derived from 43 of 83 active compounds in PHF. Most compounds affected multiple targets, and the key compounds acting on more than 34 targets are quercetin (MOL000098), which is from CM, FL, and CP, luteolin (MOL000006) which is from HM and FL, and kaempferol (MOL000422) which is from CM and FL (Table 1). As shown in Figure 2B, there are 107 intersection targets between compounds (OB < 30% and DL ≥ 0.18) and AD-related targets. The intersection targets are derived from 57 of 150 active compounds in PHF. Similarly, most active compounds are predicted to affect multiple targets. The key compounds acting on more than 24 targets are apigenin (MOL000008), which is from HM and FL, ursolic acid (MOL000511), which is from HM and FL, and rosmarinic acid (MOL011865), which is from HM (Table 2).

1.4. Protein–Protein Interaction and Network Analysis

The protein–protein interaction (PPI) analysis of the intersection targets was visualized by Cytoscape software and is shown in Figure 3. As shown in Figure 3A, the hub genes of compounds with OB ≥ 30% and DL ≥ 0.18 against AD are activator protein 1 (AP-1, also known as JUN, degree = 28), RAC-alpha serine/threonine-protein kinase (AKT1, degree = 26), mitogen-activated protein kinase 1 (MAPK1, degree = 26), MAPK3 (degree = 26), transcription factor p65 (RELA, degree = 25), IL-6 (degree = 22), MAPK8 (degree = 21), heat shock protein 90 alpha family class A member 1 (HSP90AA1, degree = 19), epidermal growth factor receptor (EGFR, degree = 18), MAPK14 (degree = 18), and estrogen receptor (ESR1, degree = 18). These hub genes were acted on by 34 compounds and the main compounds are quercetin, luteolin, and kaempferol (Figure 3B). As shown in Figure 3C, the hub genes of compounds with OB < 30% and DL ≥ 0.18 against AD are signal transducer and activator of transcription 3 (STAT3, degree = 39), AKT1 (degree = 30), JUN (degree = 27), MAPK1 (degree = 24), IL-6 (degree = 19), RELA (degree = 19), IL-2 (degree = 18), MAPK14 (degree = 17), vascular endothelial growth factor A (VEGFA, degree = 17), IL-4 (degree = 17), and MAPK8 (degree = 17). These hub genes were acted on by eight compounds, and the main compounds are apigenin, ursolic acid, and rosmarinic acid (Figure 3D).

1.5. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Enrichment Analysis

According to the GO enrichment analysis, the top 20 significant biological processes of intersection targets between compound (OB ≥ 30% and DL ≥ 0.18) and AD-related targets, and compound (OB < 30% and DL ≥ 0.18) targets and AD-related targets are shown in Figure 4 (adjusted p < 0.05). Importantly, the two different groups of intersection targets formed several similar biological processes involved in AD, including negative regulation of apoptotic process (GO: 0043066), inflammatory response (GO: 0006954), response to hypoxia (GO: 0071456), and positive regulation of nitric oxide biosynthetic process (GO: 0045428). The pathway analysis was performed to discover the underlying molecular mechanisms of PHF in AD treatment. The top 20 significant pathways of intersection targets between compound (OB ≥ 30% and DL ≥ 0.18), compound (OB < 30% and DL ≥ 0.18), and AD-related targets are shown in Figure 5 (adjusted p < 0.05). We also found the same signaling pathways in the different groups including TNF, IL-17, and hypoxia-inducible factor (HIF)-1 signaling pathway. The complete biological processes and signaling pathways formed by the intersection targets are listed in Supplementary Tables S4–S7.

1.6. Molecular Docking Analysis

The docking structural models were collected from the lowest-energy docking solution of 20 docked conformations and are shown in Figure 6. The energy score represents the degree of docking coincidence of molecules. The lower the energy is, the better the binding of ligands to receptor proteins is [24]. Molecular docking results showed that PHF had good affinity for the binding of active ingredients to key AD target protein molecules. At the same time, these findings also indirectly verified that active ingredients had a regulatory effect on AD targets, such as RELA, IL-6, JUN, AKT1, and VEGFA. Moreover, the molecular docking results were consistent with the network pharmacology screening results, and the reliability of network pharmacology was verified by molecular docking in the present study.

2. Discussion

Based on the postulation of synergism, it has been a common clinical practice to combine multiple compatible herbs into a complex herbal formulation to improve therapeutic effects in China for thousands of years. In the theory of TCM syndrome (ZHENG in Chinese), “wind,” “dampness,” and “heat” are regarded as the major pathogenic factors for inflammatory skin diseases. The five herbal medicines in PHF are proposed to work as follows: clearing of the exterior wind-heat by FL and HM, clearing the heat from the blood by CM, and clearing of the interior heat by RA and CP. Each of the above herbal medicines have been extensively used in patients suffering from allergy, including asthma and AD, in China. Pharmacological studies documented that these herbs have antiallergic, anti-inflammatory, and sedative action for pruritus conditions, and they have been previously used in the study of childhood AD [17,19,25]. Different from the conventional “one drug–one target–one illness” research approach, the concept of network pharmacology aligns with the TCM theory and is therefore applicable for the investigation of multi-herbs and multitargets in complex TCM formulas in a holistic view [21].
In the present study, the active compounds and molecular mechanism of oral and topical application of PHF against AD were investigated based on OB and DL. The compounds with lower OB were considered to possibly participate in topical treatment, as we indeed found both oral and topical treatments of PHF are effective in treating AD [17,19]. In total, 43 compounds with OB ≥ 30% and 57 compounds with OB < 30% in PHF were selected after DL screening (Table 1 and Table 2). It was found that most of the compounds are multitargeted, hence the core targets against AD were screened (Figure 3). The key compounds acting on the core targets are quercetin, luteolin, and kaempferol among the compounds with higher OB; apigenin, ursolic acid, and rosmarinic acid among the compounds with lower OB. Quercetin, derived from three herbs CM, FL, and CP in PHF, is a potent pleiotropic polyphenol with antioxidant, anti-inflammatory, and antiallergic activities. It was shown that quercetin could inhibit mast cells from releasing histamine, and studies suggested it as a promising natural treatment for AD [26,27,28]. Importantly, preliminary human studies showed that no adverse effects were observed upon an oral intake of quercetin in doses up to one gram per day over three months, although higher doses up to 51.3 mg/kg body weight were associated with renal toxicity [29]. Luteolin, derived from HM and FL, exhibits anti-inflammatory activities by the activation of antioxidative enzymes, suppression of the NF-κB pathway and inhibition of proinflammatory substances, and antiallergic activities by inhibiting AP-1 activation in basophils [30,31]. It has also been reported that luteolin significantly inhibited the scratching behavior in skin-allergic mice [32]. The suppression role of kaempferol from CM and FL in immunoglobulin E (IgE)-mediated allergic responses has been proven, and kaempferol also exhibits anti-inflammatory activity in immune response [28,33]. The above three chemicals from four herbs in PHF mainly exerted the potential therapeutic action through both oral and topical treatments of AD because of their high OB. For apigenin, ursolic acid, and rosmarinic acid from FL and HM with lower OB, the potential therapeutic action through topical use was considered. Studies have reported potential therapeutic mechanisms of apigenin in cell cycle arrest, apoptosis, as well as anti-inflammatory and antioxidant actions. Dietary and topical use of apigenin attenuates the development of cutaneous inflammation in murine models [34,35]. Apigenin is safe because it does not cause any toxic effects, even at high doses [36]. Ursolic acid also exerts prominent antimicrobial, anticancer, anti-inflammatory, antioxidant, antidepressant, and anti-aging effects although their roles in AD are currently not clear [37,38,39]. The above results indicated that these six key compounds in PHF regulated most of the AD-related targets and all of them possess immunomodulatory properties. They may play crucial roles synergistically in the treatment of AD. Moreover, the screening of key compounds and herbal source can provide a novel strategy for optimizing the herbal ratio for different route of PHF administration.
For oral and topical treatment of AD by different compounds in PHF, similar biological processes and signaling pathways were found in the present study (Figure 4 and Figure 5). According to the result of enrichment analysis, several biological processes, including the negative regulation of apoptotic process, inflammatory response, response to hypoxia, and the positive regulation of nitric oxide biosynthetic process, were revealed for the treatment of AD with PHF (Figure 4). Cell renewal requires apoptosis; however, excessive cytokines and chemokines induced by skin infection often leads to extensive apoptosis of keratinocytes and thus causes eczema and spongiosis in AD patients [40]. PHF is involved in the negative regulation of apoptotic process in AD, which may benefit for keratinocyte renewal. In the present study, cellular response to hypoxia was also found to be involved in the PHF treatment for AD because the terminal differentiation of keratinocytes and the formation of the epidermal barrier can be impaired by low O2 tension [41]. Nitric oxide (NO), a promising topical antimicrobial agent with broad spectrum and less resistance potential in skin and soft tissue infection, can diffuse freely through the plasma membrane of a cell [42]. Positive regulation of NO biosynthetic process by PHF herbs was found in the present study. Moreover, positive regulation of blood vessel endothelial cell migration, angiogenesis, and wound healing were found to play crucial roles in the treatment of AD. AD is the most ubiquitous inflammatory skin disorder, and the involvement of multiple signaling pathways could contribute to the pathogenesis of AD simultaneously. The KEGG pathway analysis revealed that PHF acts on several signaling pathways, including TNF signaling, IL-17 signaling, and HIF-1 signaling in the treatment of AD (Figure 5). As TNF-TNFR2 interaction contributes to the exacerbation of AD, targeting TNF-TNFR2 in AD is a promising therapy [43]. HIF hydroxylases and HIF pathway have been reported in AD, and pharmacologic inhibition of HIF hydroxylases has been suggested to be a novel therapeutic approach in treating allergic contact dermatitis [44]. Although AD is a Th2-dominated disease with overexpression of IL-4, IL-5, and IL-13, the dysregulation of IL-17/Th17 in AD was reported in several studies [45,46]. Besides, advanced glycation end products-receptor for advanced glycation end products (AGE-RAGE) signaling pathways involved in diabetic complications were also found by enrichment analysis as skin injury has been reported in diabetes mellitus; however, the role of AGE-RAGE signaling pathways in AD needs further experimental validations [47]. The PPI analysis revealed several critical genes against AD including AKT1, RELA, JUN, IL-6 and so on. It has been reported that the decreased expression and activity of AKT1 in the skin will lead to the change of protease expression, the decrease in filaggrin expression, and finally the destruction of the skin barrier [48]. Nucleic acid drug that targeting RELA (p65 NF-κB) gene has been studied in clinical trials in inflammatory diseases including AD [49] (www.anges.co.jp, AnGes, Japan). It also has been reported that activation of JUN (AP-1) may cause increased expression of IL-31 in AD skin [50]. Studies reported that IL-6 and IL-6 receptor signaling was also one of the risk factors in AD and blocking of IL-6R could alleviate AD [51,52]. Further investigation should be performed to verify the mechanism of these core targets and the signaling pathway exerted by PHF herbs.

3. Methods

3.1. Information of PHF Active Compounds, Compound Targets and AD-Related Targets

The chemical ingredients of the five herbs contained in PHF were obtained by the TCMSP database (TCMSP, Version: 2.3, http://lsp.nwu.edu.cn/tcmsp.php) with the absorption, distribution, metabolism, and excretion (ADME) system predicting the OB and DL [53]. The PHF compound and compound target interactions were determined by the DrugBank database (https://www.drugbank.ca/) [54]. AD-related targets were gathered from the GeneCards database (https://www.genecards.org/, version 4.12) [55] and the OMIM database (http://www.omim.org/, updated on 21 March 2020) [56].

3.2. Network Construction

The networks of compounds, compound targets and AD-related targets were merged using Cytoscape software (version 3.7.2, Boston, MA, USA) [57] to visualize the association between the active chemicals and AD-related targets.

3.3. Protein–Protein Interaction Analysis

The data of PPI came from the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) (http://stringdb.org/, ver. 10) with the species limited to “Homo sapiens” and a confidence score > 0.9 [58]. STRING is a functional protein association database for forecasting protein–protein interactions. It defines PPI as confidence ranges (low confidence: scores > 0.15; medium: >0.4; high: >0.7; highest: >0.9). The PPI results were visualized using Cytoscape software to obtain the core targets. The core targets and compounds, and herbal sources, were also visualized using Cytoscape software.

3.4. Gene Ontology and KEGG Enrichment Analysis

The GO of the biological process (BP) was analyzed to further validate the relation between the potential targets and AD. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was adopted to predict the potential signaling pathway of PHF in AD. The GO and KEGG enrichment analysis was performed by the Database for Annotation, Visualization and Integrated Discovery (DAIVD) Bioinformatics Resources 6.7 (https://david-d.ncifcrf.gov/), which provide functional interpretations of large lists of genes derived from genomic studies [59]. The statistical significance was calculated using the classical hypergeometric test. After using the Benjamini–Hochberg method to control the false discovery rate (FDR) for multiple hypothesis tests, the adjusted p value < 0.05 was used as the significant cutoff in our study.

3.5. Docking Steps and Results Evaluation

Autodock software (AutoDock 4.2, San Carlos, CA, USA) was used to perform protein compound docking analysis [24]. Briefly, two-dimensional (2D) structures of the compounds were obtained from NCBI PubChem structure files, and 3D structures were built using ChemBio 3D Ultra software (CambridgeSoft, version 14.0) after energy minimization with MM2. The crystal structures of the proteins were obtained from the Protein Data Bank (https://www.rcsb.org/) [60]. The ligands within the crystal structure complex were extracted by PyMOL software (San Carlos, CA, USA). AutoDock software was used to add polar hydrogen to the entire receptor, and the grid box was set to contain the entire receptor region. For all the docking studies, 20 docked conformations were generated for each pair of ligand and receptor, and the energy calculations were performed employing the genetic algorithms. A binding energy of less than zero indicates that a ligand can spontaneously bind to the receptor. It is generally accepted that when the conformation of ligand and receptor binding is stable, the lower the energy score is, the more likely the binding is to occur [24].

4. Conclusions

The existing treatment of AD still cannot satisfy the needs in clinics, and the side effects caused by the prolonged use of Western medicine cannot be neglected. As an important health resource in China, TCM with multitarget and multicomponent properties can exert therapeutic effects on incurable diseases in a systematic and holistic manner. Our study has successfully revealed the potential biological processes and signaling pathways of PHF against AD and uncovered the rationality of herbal combinations. These results can shed light on the therapeutic mechanism of herbal medicine for the oral and topical treatment of AD and facilitate TCM drug discovery. We believe the rational use of Chinese herbal medicine can provide convenient, high-quality, and inexpensive basic health services for community residents.

Supplementary Materials

The following are available online at https://www.mdpi.com/2223-7747/9/9/1166/s1, Table S1: Detailed information of active compounds (OB ≥ 30% and DL ≥ 0.18) in PHF; Table S2: Detailed information of active compounds (OB < 30% and DL ≥ 0.18) in PHF; Table S3: Detailed information of human disease targets of atopic dermatitis; Table S4: The gene ontology enrichment analysis for intersection targets between compound (OB ≥ 30% and DL ≥ 0.18) and AD related targets; Table S5: The gene ontology enrichment analysis for intersection targets between compound (OB < 30% and DL ≥ 0.18) and AD related targets; Table S6: The enriched KEGG pathways for intersection targets between compound (OB ≥ 30% and DL ≥ 0.18) and AD related targets; Table S7: The enriched KEGG pathways for intersection targets between compound (OB < 30% and DL ≥ 0.18) and AD related targets.

Author Contributions

Z.B.Q., C.K.W. and M.C. conceived and designed the work; M.C., M.S.-M.T., and R.H. collected the data and performed the analysis; M.C. wrote the original draft; C.K.W., Z.B.Q. and C.W.-K.L. reviewed and revised the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the Project of Educational Commission of Shaanxi Province of China (Ref. 20JK0608), the Project of Shaanxi University of Chinese Medicine (Ref: 2020GP14), the State Key Laboratory of Research on Bioactivities and Clinical Applications of Medicinal Plants (The Chinese University of Hong Kong/CUHK) and Innovation and Technology Fund Tier 2 (Ref: ITS/457/18FX) from Innovation and Technology Commission, Hong Kong, and Li Dak Sum Yip Yio Chin R & D Centre for Chinese Medicine, CUHK, Hong Kong.

Conflicts of Interest

The authors declare no conflict of interest.

Abbreviations

ADAtopic dermatitis
ThT helper
TCMTraditional Chinese Medicine
PHFpentaherbs formula
CMCortex Moutan
CPCortex Phellodendri
FLFlos Lonicerae
HM Herba Menthae
RARhizoma Atractylodis
TCMSPTraditional Chinese Medicine Systems Pharmacology Database
ADMEThe absorption, distribution, metabolism and excretion
OB oral bioavailability
DLdrug-likeness
OMIMOnline Mendelian Inheritance in Man
PPIprotein–protein interaction
GOgene ontology
BPbiological process
KEGGKyoto Encyclopedia of Genes and Genomes
FDRfalse discovery rate
AP-1activator protein 1
AKT1RAC-alpha serine/threonine-protein kinase
MAPK1mitogen-activated protein kinase 1
MAPK3mitogen-activated protein kinase 3
RELAtranscription factor p65
IL-6interleukin-6
MAPK8mitogen-activated protein kinase 8
HSP90AA1heat shock protein 90 alpha family class A member 1
EGFRepidermal growth factor receptor
MAPK14mitogen-activated protein kinase 14
ESR1estrogen receptor
STAT3signal transducer and activator of transcription 3
VEGFAvascular endothelial growth factor A
HIFhypoxia-inducible factor
IgEimmunoglobulin E
CUHKThe Chinese University of Hong Kong
DAVIDDatabase for Annotation, Visualization and Integrated Discovery
STRINGSearch Tool for the Retrieval of Interacting Genes/Proteins
AGE-RAGEadvanced glycation end products-receptor for advanced glycation end products

References

  1. Barbarot, S.; Auziere, S.; Gadkari, A.; Girolomoni, G.; Puig, L.; Simpson, E.L.; Margolis, D.J.; Bruin-Weller, M.; Eckert, L. Epidemiology of atopic dermatitis in adults: Results from an international survey. Allergy 2018, 73, 1284–1293. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  2. Sophie, N. Atopic Dermatitis: Global Epidemiology and Risk Factors. Ann. Nutr. Metab. 2015, 66, 8–16. [Google Scholar]
  3. Williams, H.C. Clinical practice. Atopic dermatitis. N. Engl. J. Med. 2005, 352, 2314–2324. [Google Scholar] [CrossRef] [PubMed]
  4. Williams, H.C. Is the prevalence of atopic dermatitis increasing? Clin. Exp. Dermatol. 2010, 17, 385–391. [Google Scholar] [CrossRef] [PubMed]
  5. Wong, G.W.; Hui, D.S.; Chan, H.; Fok, T.; Zhong, N.; Chen, Y.; Lai, C.K. Prevalence of respiratory and atopic disorders in Chinese schoolchildren. Chin. J. Tuberc. Respir. Dis. 2010, 31, 1225–1231. [Google Scholar] [CrossRef] [PubMed]
  6. Boguniewicz, M.; Leung, D.Y.M. Atopic dermatitis: A disease of altered skin barrier and immune dysregulation. Immunol. Rev. 2011, 242, 233–246. [Google Scholar] [CrossRef] [PubMed]
  7. Elias, P.M.; Hatano, Y.; Williams, M.L. Basis for the barrier abnormality in atopic dermatitis: Outside-inside-outside pathogenic mechanisms. J. Allergy Clin. Immunol. 2008, 121, 1337–1343. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  8. Liu, F.T.; Goodarzi, H.; Chen, H.Y. IgE, Mast Cells, and Eosinophils in Atopic Dermatitis. Clin. Rev. Allergy Immunol. 2011, 41, 298–310. [Google Scholar] [CrossRef]
  9. Jiao, D.; Wong, C.K.; Qiu, H.N.; Dong, J.; Cai, Z.; Chu, M.; Hon, K.L.; Tsang, M.S.M.; Lam, C.W.K. NOD2 and TLR2 ligands trigger the activation of basophils and eosinophils by interacting with dermal fibroblasts in atopic dermatitis-like skin inflammation. Cell. Mol. Immunol. 2016, 13, 535–550. [Google Scholar] [CrossRef]
  10. Alexander, T.; Maxim, E.; Cardwell, L.A.; Chawla, A.; Feldman, S.R. Prescriptions for atopic dermatitis: Oral corticosteroids remain commonplace. J. Dermatol. Treat. 2017, 29, 238–240. [Google Scholar] [CrossRef]
  11. Nghiem, P.; Pearson, G.; Langley, R.G. Tacrolimus and pimecrolimus: From clever prokaryotes to inhibiting calcineurin and treating atopic dermatitis. J. Am. Acad. Dermatol. 2002, 46, 228–241. [Google Scholar] [CrossRef] [Green Version]
  12. Ashcroft, D.M.; Dimmock, P.; Garside, R.; Stein, K.; Williams, H.C. Efficacy and tolerability of topical pimecrolimus and tacrolimus in the treatment of atopic dermatitis: Meta-analysis of randomised controlled trials. Br. Med. J. 2005, 330, 516–525. [Google Scholar] [CrossRef] [Green Version]
  13. Ormerod, A.D. Topical tacrolimus and pimecrolimus and the risk of cancer: How much cause for concern? Br. J. Dermatol. 2005, 153, 701–705. [Google Scholar] [CrossRef] [PubMed]
  14. Hon, K.L.E.; Leung, T.F.; Ng, P.C.; Lam, M.C.A.; Kam, W.Y.C.; Wong, K.Y.; Lee, K.C.K.; Sung, Y.T.; Cheng, K.F.; Fok, T.F.; et al. Efficacy and tolerability of a Chinese herbal medicine concoction for treatment of atopic dermatitis: A randomized, double-blind, placebo-controlled study. Br. J. Dermatol. 2007, 157, 357–363. [Google Scholar] [CrossRef] [PubMed]
  15. Hon, K.L.E.; Leung, T.F.; Wong, Y.; Lam, W.K.C.; Guan, D.Q.B.; Ma, K.C.; Sung, Y.T.R.; Fok, T.F.; Leung, P.C. A Pentaherbs Capsule as a Treatment Option for Atopic Dermatitis in Children: An Open-Labeled Case Series. Am. J. Chin. Med. 2004, 32, 941–950. [Google Scholar] [CrossRef]
  16. Chan, B.C.L.; Hon, K.L.E.; Leung, P.C.; Sam, S.W.; Fung, K.P.; Lee, M.Y.H.; Lau, H.Y.A. Traditional Chinese medicine for atopic eczema: PentaHerbs formula suppresses inflammatory mediators release from mast cells. J. Ethnopharmacol. 2008, 120, 85–91. [Google Scholar] [CrossRef]
  17. Liu, K.Y.P.; Hu, S.Q.; Chan, B.C.L.; Wat, E.C.L.; Lau, C.B.S.; Hon, K.L.; Fung, K.P.; Leung, P.C.; Hui, P.C.L.; Lam, C.W.K. Anti-Inflammatory and Anti-Allergic Activities of Pentaherb Formula, Moutan Cortex (Danpi) and Gallic Acid. Molecules 2013, 18, 2483–2500. [Google Scholar] [CrossRef] [PubMed]
  18. Chan, B.C.; Li, L.F.; Hu, S.Q.; Wat, E.; Wong, E.C.; Zhang, V.X.; Lau, C.B.; Wong, C.K.; Hon, K.L.; Hui, P.C.; et al. Gallic Acid Is the Major Active Component of Cortex Moutan in Inhibiting Immune Maturation of Human Monocyte-Derived Dendritic Cells. Molecules 2015, 20, 16388–16403. [Google Scholar] [CrossRef] [PubMed]
  19. Tsang, M.S.M.; Jiao, D.; Chan, B.C.L.; Hon, K.L.; Leung, P.C.; Lau, C.B.S.; Wong, E.C.W.; Cheng, L.; Chan, C.K.M.; Lam, C.W.K.; et al. Anti-Inflammatory Activities of Pentaherbs Formula, Berberine, Gallic Acid and Chlorogenic Acid in Atopic Dermatitis-Like Skin Inflammation. Molecules 2016, 21, 519–540. [Google Scholar] [CrossRef] [Green Version]
  20. Hopkins, A.L. Network pharmacology: The next paradigm in drug discovery. Nat. Chem. Biol. 2008, 4, 682–690. [Google Scholar] [CrossRef]
  21. Li, S.; Zhang, B. Traditional Chinese medicine network pharmacology: Theory, methodology and application. Chin. J. Nat. Med. 2013, 11, 110–120. [Google Scholar] [CrossRef] [PubMed]
  22. Li, H.; Zhao, L.; Zhang, B.; Jiang, Y.; Wang, X.; Guo, Y.; Liu, H.; Li, S.; Tong, X. A network pharmacology approach to determine active compounds and action mechanisms of Ge-Gen-Qin-Lian decoction for treatment of type 2 diabetes. Evid.-Based Compl. Alt. Med. 2014, 2014, 495840. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  23. Shen, M.; Tian, S.; Li, Y.; Li, Q.; Xu, X.; Wang, J.; Hou, T. Drug-likeness analysis of traditional Chinese medicines: 1. property distributions of drug-like compounds, non-drug-like compounds and natural compounds from traditional Chinese medicines. J. Cheminform. 2012, 4, 31–36. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  24. Trott, O.; Olson, A.J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. J. Comput. Chem. 2010, 31, 455–461. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  25. Huang, T. A Handbook of the Composition and Pharmacology of Common Chinese Drugs; China Medical Science and Technology: Beijing, China, 1994. [Google Scholar]
  26. Mehrbani, M.; Choopani, R.; Fekri, A.; Mehrabani, M.; Mosaddegh, M.; Mehrabani, M. The efficacy of whey associated with dodder seed extract on moderate-to-severe atopic dermatitis in adults: A randomized, double-blind, placebo-controlled clinical trial. J. Ethnopharmacol. 2015, 172, 325–332. [Google Scholar] [CrossRef]
  27. Weng, Z.; Zhang, B.; Asadi, S.; Sismanopoulos, N.; Butcher, A.; Fu, X.; Katsarou-Katsari, A.; Antoniou, C.; Theoharides, T.C. Quercetin is more effective than cromolyn in blocking human mast cell cytokine release and inhibits contact dermatitis and photosensitivity in humans. PLoS ONE 2012, 7, e33805. [Google Scholar] [CrossRef]
  28. Lee, E.J.; Ji, G.E.; Sung, M.K. Quercetin and kaempferol suppress immunoglobulin E-mediated allergic inflammation in RBL-2H3 and Caco-2 cells. Inflamm. Res. 2010, 59, 847–854. [Google Scholar] [CrossRef]
  29. Harwood, M.; Danielewska-Nikiel, B.; Borzelleca, J.F.; Flamm, G.W.; Williams, G.M.; Lines, T.C. 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. 2007, 45, 2179–2205. [Google Scholar] [CrossRef]
  30. Hirano, T.; Higa, S.; Arimitsu, J.; Naka, T.; Ogata, A.; Shima, Y.; Fujimoto, M.; Yamadori, T.; Ohkawara, T.; Kuwabara, Y. Luteolin, a flavonoid, inhibits AP-1 activation by basophils. Biochem. Biophys. Res. Commun. 2006, 340, 1–7. [Google Scholar] [CrossRef]
  31. Seelinger, G.; Merfort, I.; Schempp, C. Anti-Oxidant, Anti-Inflammatory and Anti-Allergic Activities of Luteolin. Planta Med. 2008, 74, 1667–1677. [Google Scholar] [CrossRef]
  32. Liu, B.L.; Wu, W.W.; Tang, N. Topical application of luteolin inhibits scratching behavior associated with allergic cutaneous reaction in mice. Planta Med. 2005, 71, 424–428. [Google Scholar]
  33. Cortes, J.R.; Perez, G.M.; Rivas, M.D.; Zamorano, J. Kaempferol inhibits IL-4-induced STAT6 activation by specifically targeting JAK3. J. Immunol. 2007, 179, 3881–3887. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  34. Man, M.Q.; Hupe, M.; Sun, R.; Man, G.; Mauro, T.M.; Elias, P.M. Topical Apigenin Alleviates Cutaneous Inflammation in Murine Models. Evid.-Based Complement. Alternat. Med. 2012, 2012, 912028. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  35. Yano, S.; Umeda, D.; Yamashita, S.; Yamada, K.; Tachibana, H. Dietary apigenin attenuates the development of atopic dermatitis-like skin lesions in NC/Nga mice. J. Nutr. Biochem. 2009, 20, 876–881. [Google Scholar] [CrossRef]
  36. Ross, J.A.; Kasum, C.M. Dietary flavonoids: Bioavailability, metabolic effects, and safety. Annu. Rev. Nutr. 2002, 22, 19–34. [Google Scholar] [CrossRef]
  37. Ikeda, Y.; Murakami, A.; Ohigashi, H. Ursolic acid: An anti- and pro-inflammatory triterpenoid. Mol. Nutr. Food Res. 2010, 52, 26–42. [Google Scholar] [CrossRef]
  38. Shanmugam, M.K.; Dai, X.; Kumar, A.P.; Tan, B.K.; Sethi, G.; Bishayee, A. Ursolic acid in cancer prevention and treatment: Molecular targets, pharmacokinetics and clinical studies. Biochem. Pharmacol. 2013, 85, 1579–1587. [Google Scholar] [CrossRef] [Green Version]
  39. Osakabe, N.; Yasuda, A.; Natsume, M.; Yoshikawa, T. Rosmarinic acid inhibits epidermal inflammatory responses: Anticarcinogenic effect of Perilla frutescens extract in the murine two-stage skin model. Carcinogenesis 2004, 25, 549–557. [Google Scholar] [CrossRef] [PubMed]
  40. Trautmann, A.; Akdis, M.; Schmid-Grendelmeier, P.; Disch, R.; Bröcker, E.B.; Blaser, K.; Akdis, C.A. Targeting keratinocyte apoptosis in the treatment of atopic dermatitis and allergic contact dermatitis. J. Allergy Clin. Immunol. 2001, 108, 839–846. [Google Scholar] [CrossRef] [PubMed]
  41. Wong, W.J.; Richardson, T.; Seykora, J.T.; Cotsarelis, G.; Simon, M.C. Hypoxia-inducible factors regulate filaggrin expression and epidermal barrier function. J. Investig. Dermatol. 2015, 135, 454–461. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  42. Adler, B.L.; Friedman, A.J. Nitric oxide therapy for dermatologic disease. Future Sci. OA 2015, 1, 1–5. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  43. Jacobi, A.; Antoni, C.; Manger, B.; Schuler, G.; Hertl, M. Infliximab in the treatment of moderate to severe atopic dermatitis. J. Am. Acad. Dermatol. 2005, 52, 522–526. [Google Scholar] [CrossRef] [PubMed]
  44. Manresa, M.C.; Smith, L.; Casals-Diaz, L.; Fagundes, R.R.; Brown, E.; Radhakrishnan, P.; Murphy, S.J.; Crifo, B.; Strowitzki, M.J.; Halligan, D.N. Pharmacologic inhibition of hypoxia-inducible factor (HIF)-hydroxylases ameliorates allergic contact dermatitis. Allergy 2019, 74, 753–766. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  45. Nograles, K.E.; Zaba, L.C.; Shemer, A.; Fuentes-Duculan, J.; Cardinale, I.; Kikuchi, T.; Ramon, M.; Bergman, R.; Krueger, J.G.; Guttman-Yassky, E. IL-22–producing “T22” T cells account for upregulated IL-22 in atopic dermatitis despite reduced IL-17–producing TH17 T cells. J. Allergy Clin. Immunol. 2009, 123, 1244–1252. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  46. Ma, L.; Xue, H.B.; Guan, X.H.; Qi, R.Q.; An, R.Z.; Shu, C.M.; Zhang, Y.J.; Wei, Y.H.; Zhang, J.H. Possible role of Th17 cells and IL-17 in the pathogenesis of atopic dermatitis in northern China. J. Dermatol. Sci. 2012, 68, 66–68. [Google Scholar] [CrossRef]
  47. Quondamatteo, F. Skin and diabetes mellitus: What do we know? Cell Tissue Res. 2014, 355, 1–21. [Google Scholar] [CrossRef]
  48. Naeem, A.S.; Tommasi, C.; Cole, C. A mechanistic target of rapamycin complex 1/2 (mTORC1)/V-Akt murine thymoma viral oncogene homolog 1 (AKT1)/cathepsin H axis controls filaggrin expression and processing in skin, a novel mechanism for skin barrier disruption in patients with atopic dermatitis. J. Allergy Clin. Immunol. 2017, 139, 1228–1241. [Google Scholar]
  49. Tamai, K.; Kaneda, Y.; Morishita, R. Development of NF-kappa B decoy ointment and clinical trial for atopic dermatitis. Dermatitis 2008, 19, 293–294. [Google Scholar]
  50. Melnik, B.C. The potential role of impaired Notch signalling in atopic dermatitis. Acta Derm.-Venereol. 2015, 95, 5–13. [Google Scholar] [CrossRef] [Green Version]
  51. Navarini, A.A.; French, L.E.; Hofbauer, G.F.L. Interrupting IL-6–receptor signaling improves atopic dermatitis but associates with bacterial superinfection. J. Allergy Clin. Immunol. 2011, 128, 1128–1130. [Google Scholar] [CrossRef]
  52. Esparza-Gordillo, J.; Schaarschmidt, H.; Liang, L. A functional IL-6 receptor (IL6R) variant is a risk factor for persistent atopic dermatitis. J. Allergy Clin. Immunol. 2013, 132, 371–377. [Google Scholar] [CrossRef] [PubMed]
  53. Ru, J.; Li, P.; Wang, J.; Zhou, W.; Li, B.; Huang, C.; Li, P.; Guo, Z.; Tao, W.; Yang, Y. TCMSP: A database of systems pharmacology for drug discovery from herbal medicines. J. Cheminform. 2014, 6, 13–18. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  54. Wishart, D.S.; Craig, K.; Guo, A.C.; Cheng, D.; Savita, S.; Dan, T.; Bijaya, G.; Murtaza, H. DrugBank: A knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 2007, 36, D901–D906. [Google Scholar] [CrossRef] [PubMed]
  55. Stelzer, G.; Rosen, N.; Plaschkes, I.; Zimmerman, S.; Twik, M.; Fishilevich, S.; Stein, T.I.; Nudel, R.; Lieder, I.; Mazor, Y. The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses. Curr. Protoc. Bioinform. 2016, 54, 30–38. [Google Scholar] [CrossRef] [PubMed]
  56. Hamosh, A.; Scott, A.F.; Amberger, J.S.; Bocchini, C.A.; McKusick, A.V. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res. 2005, 33, 514–517. [Google Scholar] [CrossRef] [PubMed]
  57. Lopes, C.T.; Franz, M.; Kazi, F.; Donaldson, S.L.; Bader, G.D. Cytoscape Web: An interactive web-based network browser. Bioinformatics 2010, 26, 2347–2348. [Google Scholar] [CrossRef] [Green Version]
  58. von Mering, C.; Huynen, M.; Jaeggi, D.; Schmidt, S.; Bork, P.; Snel, B. STRING: A database of predicted functional associations between proteins. Nucleic Acids Res. 2003, 31, 258–261. [Google Scholar] [CrossRef]
  59. Da, W.H.; Sherman, B.T.; Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2008, 4, 44–57. [Google Scholar]
  60. Berman, H.M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.; Weissig, H.; Shindyalov, I.N.; Bourne, P.E. The Protein Data Bank. Nucleic Acids Res. 2000, 28, 235–242. [Google Scholar] [CrossRef] [Green Version]
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Figure 1. The counting of (A) compounds and (B) putative targets in the Pentaherb Formula. OB: oral bioavailability; DL: drug-likeness; CM: Cortex Moutan; CP: Cortex Phellodendri; FL: Flos Lonicerae; HM: Herba Menthae; RA: Rhizoma Atractylodis.
Figure 1. The counting of (A) compounds and (B) putative targets in the Pentaherb Formula. OB: oral bioavailability; DL: drug-likeness; CM: Cortex Moutan; CP: Cortex Phellodendri; FL: Flos Lonicerae; HM: Herba Menthae; RA: Rhizoma Atractylodis.
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Figure 2. Compound–intersection targets network analysis. (A) Network of 43 compounds (OB ≥ 30% and DL ≥ 0.18) and intersection targets between compound and AD-related targets. (B) Network of 57 compounds (OB < 30% and DL ≥ 0.18) and intersection targets between compound and AD-related targets. The green rectangles represent PHF targets against AD; the Kelly green, yellow, orange, blue, and violet rectangles represent compounds from HM, CP, FL, RA, and CM, respectively. The red rectangles represent compounds from more than two herbs in PHF. PHF: Pentaherbs Formula; AD: atopic dermatitis; OB: oral bioavailability; DL: drug-likeness; CM: Cortex Moutan; CP: Cortex Phellodendri; FL: Flos Lonicerae; HM: Herba Menthae; RA: Rhizoma Atractylodis.
Figure 2. Compound–intersection targets network analysis. (A) Network of 43 compounds (OB ≥ 30% and DL ≥ 0.18) and intersection targets between compound and AD-related targets. (B) Network of 57 compounds (OB < 30% and DL ≥ 0.18) and intersection targets between compound and AD-related targets. The green rectangles represent PHF targets against AD; the Kelly green, yellow, orange, blue, and violet rectangles represent compounds from HM, CP, FL, RA, and CM, respectively. The red rectangles represent compounds from more than two herbs in PHF. PHF: Pentaherbs Formula; AD: atopic dermatitis; OB: oral bioavailability; DL: drug-likeness; CM: Cortex Moutan; CP: Cortex Phellodendri; FL: Flos Lonicerae; HM: Herba Menthae; RA: Rhizoma Atractylodis.
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Figure 3. Protein–protein interaction (PPI) and network analysis. (A) PPI analysis of intersection targets between compound (OB ≥ 30% and DL ≥ 0.18) and AD-related targets, and (B) network analysis of screened core genes and related compounds. (C) PPI analysis of intersection targets between compound (OB < 30% and DL ≥ 0.18) and AD-related targets, and (D) network analysis of screened core genes and related compounds. The light gray circles represent intersection targets. The circles get larger with increasing degree. The Kelly green, yellow, orange, blue, and violet rectangles represent compounds from HM, CP, FL, RA, and CM, respectively. The red rectangles represent compounds from more than two herbs in PHF. The green rectangles represent core targets against AD. PHF: Pentaherbs Formula; AD: atopic dermatitis; OB: oral bioavailability; DL: drug-likeness; CM: Cortex Moutan; CP: Cortex Phellodendri; FL: Flos Lonicerae; HM: Herba Menthae; RA: Rhizoma Atractylodis.
Figure 3. Protein–protein interaction (PPI) and network analysis. (A) PPI analysis of intersection targets between compound (OB ≥ 30% and DL ≥ 0.18) and AD-related targets, and (B) network analysis of screened core genes and related compounds. (C) PPI analysis of intersection targets between compound (OB < 30% and DL ≥ 0.18) and AD-related targets, and (D) network analysis of screened core genes and related compounds. The light gray circles represent intersection targets. The circles get larger with increasing degree. The Kelly green, yellow, orange, blue, and violet rectangles represent compounds from HM, CP, FL, RA, and CM, respectively. The red rectangles represent compounds from more than two herbs in PHF. The green rectangles represent core targets against AD. PHF: Pentaherbs Formula; AD: atopic dermatitis; OB: oral bioavailability; DL: drug-likeness; CM: Cortex Moutan; CP: Cortex Phellodendri; FL: Flos Lonicerae; HM: Herba Menthae; RA: Rhizoma Atractylodis.
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Figure 4. The top 20 significant gene ontology enrichment analysis for intersection targets between (A) compound (OB ≥ 30% and DL ≥ 0.18) and AD-related targets, and (B) compound (OB < 30% and DL ≥ 0.18) and AD-related targets. The circles represent the gene count of each biological process. AD: atopic dermatitis. OB: oral bioavailability; DL: drug-likeness.
Figure 4. The top 20 significant gene ontology enrichment analysis for intersection targets between (A) compound (OB ≥ 30% and DL ≥ 0.18) and AD-related targets, and (B) compound (OB < 30% and DL ≥ 0.18) and AD-related targets. The circles represent the gene count of each biological process. AD: atopic dermatitis. OB: oral bioavailability; DL: drug-likeness.
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Figure 5. The top 20 significant enriched KEGG pathways for intersection targets between (A) compound (OB ≥ 30% and DL ≥ 0.18) and AD-related targets, and (B) compound (OB < 30% and DL ≥ 0.18) and AD-related targets. AD: atopic dermatitis. OB: oral bioavailability; DL: drug-likeness.
Figure 5. The top 20 significant enriched KEGG pathways for intersection targets between (A) compound (OB ≥ 30% and DL ≥ 0.18) and AD-related targets, and (B) compound (OB < 30% and DL ≥ 0.18) and AD-related targets. AD: atopic dermatitis. OB: oral bioavailability; DL: drug-likeness.
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Figure 6. Molecular docking of compounds with core targets. (A1–A3) Docking process of quercetin with AKT1, IL-6, and RELA, respectively. (B1–B3) Docking process of luteolin with AKT1, REAL, and JUN, respectively. (C1–C3) Docking process of apigenin with JUN, RELA, and VEGFA, respectively. (D1–D3) Docking process of ursolic acid with AKT1, RELA, and VEGFA, respectively.
Figure 6. Molecular docking of compounds with core targets. (A1–A3) Docking process of quercetin with AKT1, IL-6, and RELA, respectively. (B1–B3) Docking process of luteolin with AKT1, REAL, and JUN, respectively. (C1–C3) Docking process of apigenin with JUN, RELA, and VEGFA, respectively. (D1–D3) Docking process of ursolic acid with AKT1, RELA, and VEGFA, respectively.
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Table
Table 1. The screening of active compounds in PHF for oral treatment of AD.
Table 1. The screening of active compounds in PHF for oral treatment of AD.
MOL IDMOL NameOB (%)DLHerb SourceTargets (No.)
1MOL000098quercetin46.430.28CM, FL, CP84
2MOL000006luteolin36.160.25HM, FL37
3MOL000422kaempferol41.880.24CM, FL34
4MOL000173wogonin30.680.23RA28
5MOL004328naringenin59.290.21HM19
6MOL001689acacetin34.970.24HM17
7MOL002773beta-carotene37.180.58FL16
8MOL000358beta-sitosterol36.910.75CP, FL14
9MOL000471aloe-emodin83.380.24HM12
10MOL0030955-hydroxy-7-methoxy-2-(3,4,5-trimethoxyphenyl)chromone51.960.41FL12
11MOL002662rutaecarpine40.30.6CP11
12MOL000449Stigmasterol43.830.76CP, FL10
13MOL002670Cavidine35.640.81CP10
14MOL000790Isocorypalmine35.770.59CP10
15MOL003044Chryseriol35.850.27FL10
16MOL001455(S)-Canadine53.830.77CP9
17MOL0001883β-acetoxyatractylone40.570.22RA8
18MOL001454berberine36.860.78CP8
19MOL002651Dehydrotanshinone II A43.760.4CP8
20MOL000785palmatine64.60.65CP8
21MOL000787Fumarine59.260.83CP8
22MOL005573Genkwanin37.130.24HM7
23MOL000492(+)-catechin54.830.24CM7
24MOL006422thalifendine44.410.73CP7
25MOL002644Phellopterin40.190.28CP6
26MOL002894berberrubine35.740.73CP6
27MOL002881Diosmetin31.140.27HM5
28MOL005190eriodictyol71.790.24HM5
29MOL001458coptisine30.670.86CP5
30MOL003111Centauroside_qt55.790.5FL5
31MOL002668Worenine45.830.87CP4
32MOL001131phellamurin_qt56.60.39CP4
33MOL0073745-[[5-(4-methoxyphenyl)-2-furyl]methylene]barbituric acid43.440.3CM3
34MOL002666Chelerythrine34.180.78CP3
35MOL002914Eriodyctiol (flavanone)41.350.24FL3
36MOL003006(-)-(3R,8S,9R,9aS,10aS)-9-ethenyl-8-(beta-D-glucopyranosyloxy)-2,3,9,9a,10,10a-hexahydro-5-oxo-5H,8H-pyrano[4,3-d]oxazolo[3,2-a]pyridine-3-carboxylic acid_qt87.470.23FL3
37MOL003117Ioniceracetalides B_qt61.190.19FL3
38MOL002641Phellavin_qt35.860.44CP2
39MOL002663Skimmianin40.140.2CP2
40MOL001494Mandenol420.19FL2
41MOL003014secologanic dibutylacetal_qt53.650.29FL2
42MOL003128dinethylsecologanoside48.460.48FL2
43MOL001495Ethyl linolenate46.10.2FL1
PHF: Pentaherbs Formula; AD: atopic dermatitis. OB: oral bioavailability; DL: drug-likeness; CM: Cortex Moutan; CP: Cortex Phellodendri; FL: Flos Lonicerae; HM: Herba Menthae; RA: Rhizoma Atractylodis.
Table
Table 2. The screening of active compounds in PHF for topical treatment of AD.
Table 2. The screening of active compounds in PHF for topical treatment of AD.
MOL IDMOL NameOB (%)DLHerb SourceTargets (No.)
1MOL000008apigenin23.060.21HM, FL40
2MOL000511ursolic acid16.770.75HM, FL38
3MOL011865rosmarinic acid1.380.35HM24
4MOL000415rutin3.200.68FL18
5MOL000472emodin24.40.24HM16
6MOL000782Menisporphine24.330.52CP12
7MOL000786STOCK1N-1440722.280.64CP11
8MOL002891magnoflorine0.480.55CP11
9MOL0030962-(3,4-dimethoxyphenyl)-5-hydroxy-7-methoxy-chromone29.240.34FL11
10MOL003097Flavone der.27.120.27FL11
11MOL000794menisperine26.170.59CP10
12MOL002083tricin27.860.34FL10
13MOL000764magnoflorine26.690.55CP9
14MOL001457columbamine26.940.59CP9
15MOL002642phellodendrine2.610.58CP8
16MOL002655Amurensin_qt26.370.44CP8
17MOL0030982-(2,4-dimethoxyphenyl)-3-hydroxy-7-methoxy-chromone12.940.33FL8
18MOL000357Sitogluside20.630.62CP, HM, FL7
19MOL000789jatrorrizine19.650.59CP7
20MOL0025663-O-Methylquercetin10.10.3FL7
21MOL002635(±)-lyoniresinol4.870.54CP7
22MOL002901phellodendrine2.50.58CP7
23MOL000347Syrigin14.640.32CP6
24MOL013434Auraptene25.620.24CP6
25MOL000561Astragalin14.030.74FL5
26MOL0001903,5-dimethoxy-4-glucosyloxyphenylallylalcohol290.32RA4
27MOL000263oleanolic acid29.020.76CM, HM, FL4
28MOL000476Physcion22.290.27HM4
29MOL004368Hyperin6.940.77CP, FL4
30MOL005093Diosmin12.700.66HM4
31MOL0006501H,3H-Pyrano(3,4-c)pyran-1-one, 5-ethenyl-6-(beta-D-glucopyranosyloxy)-4,4a,5,6-tetrahydro-, (4aS-(4aalpha,5beta,6alpha))-4.960.38FL3
32MOL000655Loganic acid4.920.4FL3
33MOL000741(2S,3S)-3,5,7-trihydroxy-2-(4-hydroxyphenyl)chroman-4-one24.150.24CP3
34MOL001729Crysophanol18.640.21HM3
35MOL001965Dauricine (8CI)23.650.37CP3
36MOL003011Secologanate17.560.33FL3
37MOL003018SCG23.590.36FL3
38MOL003109Caeruloside C_qt5.40.37FL3
39MOL000009luteolin-7-o-glucoside7.290.78HM, FL2
40MOL001680Loganin5.90.44FL2
41MOL002215Oleanic acid8.410.77CM2
42MOL003022Secoxyloganin3.790.39FL2
43MOL0030738-epiloganin11.680.44FL2
44MOL0030997-epi-Loganin4.780.44FL2
45MOL007367paeonoside18.520.24CM2
46MOL000007Cosmetin9.680.74FL1
47MOL003020secologanoside 7-methylester3.880.45FL1
48MOL0030654-caffeoylquinic acid10.480.33FL1
49MOL003066Neochlorogenic acid10.650.33FL1
50MOL003071secologanoside26.920.37FL1
51MOL003113Dehydroxymorroniside20.690.46FL1
52MOL003867Paeonolide6.30.64CM1
53MOL003959limonin21.30.57CP1
54MOL0063844-[(1R,3aS,4R,6aS)-4-(4-hydroxy-3,5-dimethoxyphenyl)-1,3,3a,4,6,6a-hexahydrofuro[4,3-c]furan-1-yl]-2,6-dimethoxyphenol3.290.72CP1
55MOL007377mudanoside A13.390.29CM1
56MOL009072Prunin9.330.74HM1
57MOL013068Oroxindin7.070.77RA1
PHF: Pentaherbs Formula; AD: atopic dermatitis. OB: Oral bioavailability; DL: drug-likeness; CM: Cortex Moutan; CP: Cortex Phellodendri; FL: Flos Lonicerae; HM: Herba Menthae; RA: Rhizoma Atractylodis.

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MDPI and ACS Style

Chu, M.; Tsang, M.S.-M.; He, R.; Lam, C.W.-K.; Quan, Z.B.; Wong, C.K. The Active Compounds and Therapeutic Mechanisms of Pentaherbs Formula for Oral and Topical Treatment of Atopic Dermatitis Based on Network Pharmacology. Plants 2020, 9, 1166. https://doi.org/10.3390/plants9091166

AMA Style

Chu M, Tsang MS-M, He R, Lam CW-K, Quan ZB, Wong CK. The Active Compounds and Therapeutic Mechanisms of Pentaherbs Formula for Oral and Topical Treatment of Atopic Dermatitis Based on Network Pharmacology. Plants. 2020; 9(9):1166. https://doi.org/10.3390/plants9091166

Chicago/Turabian Style

Chu, Man, Miranda Sin-Man Tsang, Ru He, Christopher Wai-Kei Lam, Zhi Bo Quan, and Chun Kwok Wong. 2020. "The Active Compounds and Therapeutic Mechanisms of Pentaherbs Formula for Oral and Topical Treatment of Atopic Dermatitis Based on Network Pharmacology" Plants 9, no. 9: 1166. https://doi.org/10.3390/plants9091166

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