Data mining of classical formulas in Shang Han Za Bing Lun and mechanisms of actions of Coptis Chinensis and its combinations for the management of Atopic Dermatitis
Creators: name: SUN, Yue
Publisher: name: RMIT University
Year: 2024
Subjects: classificationCode: 420803
subject: Traditional Chinese medicine and treatments

description: Atopic dermatitis (AD) is a long-lasting and relapsing skin inflammation disease characterised by itchiness, dry skin, and eczematous lesions which has reached prevalence rates of AD was up to approximately 20% in Australia. Although this is not a life-threatening condition, it has significantly impacted on sufferers’ quality of life and caused a severe financial burden to individuals with this condition due to long-term unsatisfactory management. Currently, the most effective treatment is steroids and immunosuppressant medication which have side effects and need application restrictions. Thus, an increasing number of individuals are seeking alternative management from complementary medicine including Chinese herbal medicine.<br><br>

Chinese herbal medicine has been applied for the management of dermatological diseases including AD for a long time. There are many herbs and formulas recorded in Shang Han Za Bing Lun (Treatise on Cold Damage and Miscellaneous Diseases), the most fundamental text of herbal formulas throughout the Chinese medicine history, for the management of signs and symptoms related to dermatological diseases. In addition, those herbs and formulas have still been popularly used in modern times. However, their mechanisms of actions have not been examined comprehensively.<br><br>

There were five aims in the present research project: (1) to review and select from classic literature the Chinese herbs most frequently used for the management of AD; (2) to review the phytochemistry, pharmacological effects, pharmacokinetics, and toxicology of selected herbs from modern literature; (3) to identify chemical compounds of the selected herbs as well as the key target protein identifications and ontology pathway enrichment for AD; (4) to perform molecular docking for identified chemical compounds and AD target proteins; also screen and predict the properties of identified chemical compounds for their pharmacokinetic properties (drug-likeness, water-solubility, medicinal chemistry, and toxicity); and (5) to create molecular docking simulations and uncover the networks among the identified herbs, chemical compounds, and AD key target proteins. <br><br>

Review of classic literature (Study I)

A previous Ph.D. project has reviewed the classic literature and listed the most commonly used Chinese herbs for AD management. With consideration of the important contribution of Shang Han Za Bing Lun to the clinical dermatology, the two texts compiled from Shang Han Za Bing Lun, Shang Han Lun (Treatise on Cold Damage Diseases) and Jin Gui Yao Lue (Essential Prescriptions of the Golden Cabinet), were manually searched. From this additional search, 19 dermatological symptom-related clauses and 19 herbal formulas used for their management were identified. Among them, Coptidies Rhizoma (Huang lian) was the only herb prescribed for the management of the AD-like symptom in both of these texts. Thus, Huang lian with another four herbs Glycyrrhizae Radix et Rhizoma (Gan cao), Phellodendri Chinensis Cortex (Huang bai), Rumex Japonicus Houtt (Yang ti), and Cnidium monnieri (L.) Cusson. (She chuang zi) from the previous Ph.D. project were selected for further investigation. Comprehensive review of phytochemistry, pharmacology, pharmacokinetics, and toxicology of identified herbs for atopic dermatitis (Study II).<br><br>

A total of eleven bibliographic electronic databases were searched to identify clinical and experimental studies and review their pharmacological effects and chemical constitutions. The Chinese herb She chuang zi showcased comprehensive beneficial effects on allergies, bacterial infections, and fungal infections. The Chinese herb Huang bai and its compounds could exert mitigating effects on inflammation and microbial infections. The Chinese herb and compounds of Yang ti could yield multiple pharmaceutical effects on sepsis, bacterial infections, and dermatological disease. For identified chemical compounds, the chemical structures were prepared for the following molecular docking study. As a result, a total of 1223 chemical compounds were identified, including 129 for 140 for Huang bai, Huang lian, 480 for Gan cao, 429 for She chuang zi, 45 for Yang ti. (Publications 1, 2, and 3 in Appendices). <br><br>

Identification of key target proteins and ontology pathway analysis (Study III) An online database, Open targets platform, was searched to identify target genes related to AD management. The selected AD target genes were further analysed to investigate protein-protein interactions using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING). The Cytoscape software and its plug-in CytoHubba was applied to identify the key target proteins. The Cytoscape plugin functions were used for the pathway enrichment to identify the AD-related major pathways with the participation of these key target proteins. A total of nine target genes (BCL2L11, EGFR, KIT, KITLG, KRAS, PDGFRB, RARA, RELB, VDR) involved in AD progression as an individual target, and 13 key target genes (CREBBP, FOXP3, IL2, IL4R, IL13, IL21, IL21R, JAK1, JAK2, MYC, RARα, STAT3, NFκBIA) participated in two pathways (JAK-STAT signalling pathway, Notch signalling pathway) and one biological process (Th17 cell differentiation). These identified target genes were prepared for molecular docking.<br><br>

Molecular docking and pharmacokinetic properties prediction and screening (Study IV)

Molecular docking included 1,223 identified chemical compounds and 22 AD key target genes to obtain their binding affinity values using Pyrx software. A cut-off value for further study was a binding affinity was ≤ -10 Kcal/mol. The identified chemical compounds with eligible binding affinity values were selected for the next study. The identified chemical compounds with eligible binding affinity values were predicted and screened for their pharmacokinetic properties via online database “PreADME” and “SwissADME”. The selected chemical compounds were water-soluble, suitable for the Lipinski’s rule, the non-carcinogenic effect on both mouse and rat, and low risk for hERG inhibition. The results identified the following chemical compounds for further analysis: (+) Pinoresinol glucoside and 8,13-Dioxocoptisine hydroxide from Huang lian; Isoglycyrol from Gan cao; Chilenine and Litcubine from Huang bai; 1-hydroxymethyl-3,6-dimethoxyl-2,8-dihydroxylanthraquinone from Yang ti; Cnidiadin, Cnidimol C, and Methylpicraquassioside B from She chuang zi. <br><br>

Molecular docking included 1,223 identified chemical compounds and 22 AD key genes to obtain their binding affinity values using PyRx software. A cut-off value for further study was a binding affinity was ≤ –10 kcal/mol. The identified chemical compounds with eligible binding affinity values were selected for the next study. The identified chemical compounds with eligible binding affinity values were predicted and screened for their pharmacokinetic properties via online database “PreADME” and “SwissADME”. The selected chemical compounds were water-soluble, suitable for the Lipinski’s rule, the non-carcinogenic effect on both mouse and rat, and low risk for hERG inhibition. The results identified the following chemical compounds for further analysis: (+) Pinoresinol glucoside and 8,13-Dioxocoptisine hydroxide from Huang lian; Isoglycyrol from Gan cao; Chilenine and Litcubine from Huang bai; 1-hydroxymethyl-3,6-dimethoxyl-2,8-dihydroxylanthraquinone from Yang ti; Cnidiadin, Cnidimol C, and Methylpicraquassioside B from She chuang zi.<br><br>

Molecular docking simulations (Study V)
The identified key target genes and chemical compounds with eligible binding affinity values and eligible pharmacokinetic properties were simulated in molecular docking using Biovia Discovery Studio software. The presentation of their binding sites used 2-Dimensional diagrams within the Cytoscape software for the network analysis among the identified herbs, chemical compounds, and AD target genes. Eight chemical compounds from five selected herbs were identified via molecular docking studies to potentially interact with EGFR, JAK1, JAK2, NR3C1, and Vitamin D receptor. In particular, Huang lian has most interactions with AD-associated targets among all the five herbs as its two compounds could strongly bind with EGFR, JAK1, JAK2, and NR3C1. 8,13-Dioxocoptisine hydroxide from Huang lian has the highest interactive properties among all chemical compounds identified from the five selected herbs.<br><br>

Conclusions

The five selected herbs have been used for AD symptomatic management since ancient times. Modern clinical research supports the classical literature as these five herbs have indicated anti-inflammatory, anti-allergic and antimicrobial effects. Molecular docking has demonstrated the chemical compounds from these herbs may interact with five target proteins related to AD. It is recommended that these findings be validated in further in vivo and in vitro studies.