Approaches in studying the pharmacology of Chinese Medicine formulas: bottom-up, top-down-and meeting in the middle

Walnut Protein Peptides Ameliorate DSS-Induced Ulcerative Colitis Damage in Mice: An in Silico Analysis and in Vivo Investigation

Walnut (Juglans regia L.) is a food with food-medicine homology, whose derived protein peptides have been shown to have anti-inflammatory activity in vitro. However, the effects and mechanisms of walnut protein peptides on ulcerative colitis (UC) in vivo have not been systematically and thoroughly investigated. In this study, we applied virtual screening and network pharmacology screening of bioactive peptides to obtain three novel WPPs (SHTLP, HYNLN, and LGTYP) that may alleviate UC through TLR4-MAPK signaling. In vivo studies have shown that WPPs improve intestinal mucosal barrier dysfunction and reduce inflammation by inhibiting activation of the TLR4-MAPK pathway. In addition, WPPs restore intestinal microbial homeostasis by reducing harmful bacteria (Helicobacter and Bacteroides) and increasing the relative abundance of beneficial bacteria (Candidatus_Saccharimonas). Our study showed that the WPPs obtained by virtual screening were effective in ameliorating colitis, which has important implications for future screening of bioactive peptides from medicinal food homologues as drugs or dietary supplements.

Network pharmacology, a promising approach to reveal the pharmacology mechanism of Chinese medicine formula

ETHNOPHARMACOLOGICAL RELEVANCE

Network pharmacology is a new discipline based on systems biology theory, biological system network analysis, and multi-target drug molecule design specific signal node selection. The mechanism of action of TCM formula has the characteristics of multiple targets and levels. The mechanism is similar to the integrity, systematization and comprehensiveness of network pharmacology, so network pharmacology is suitable for the study of the pharmacological mechanism of Chinese medicine compounds.

AIM OF THE STUDY

The paper summarizes the present application status and existing problems of network pharmacology in the field of Chinese medicine formula, and formulates the research ideas, up-to-date key technology and application method and strategy of network pharmacology. Its purpose is to provide guidance and reference for using network pharmacology to reveal the modern scientific connotation of Chinese medicine.

MATERIALS AND METHODS

Literatures in this review were searched in PubMed, China National Knowledge Infrastructure (CNKI), Web of Science, ScienceDirect and Google Scholar using the keywords "traditional Chinese medicine", "Chinese herb medicine" and "network pharmacology". The literature cited in this review dates from 2002 to 2022.

RESULTS

Using network pharmacology methods to predict the basis and mechanism of pharmacodynamic substances of traditional Chinese medicines has become a trend.

CONCLUSION

Network pharmacology is a promising approach to reveal the pharmacology mechanism of Chinese medicine formula.

Discovery of anti-flu substances and mechanism of Shuang-Huang-Lian water extract based on serum pharmaco-chemistry and network pharmacology

ETHNOPHARMACOLOGICAL RELEVANCE

Shuang-Huang-Lian preparation has captured wide attention since its clinical applications for the successful treatment of upper respiratory tract infection. However, its functional basis under actual therapeutic dose in vivo was still unrevealed.

AIM OF THE STUDY

This study aimed to reveal the anti-flu substances and mechanism of Shuang-Huang-Lian water extract (SHL) on H1N1 infected mouse model by a strategy based on serum pharmaco-chemistry under actual therapeutic dose and network pharmacology.

MATERIALS AND METHODS

H1N1 infected mouse model was employed for evaluation of the anti-flu effects of SHL. A simultaneous quantification method was developed by UPLC-TQ-XS MS coupled switch-ions mode and applied to characterize the pharmacokinetics of the multiple components of SHL under actual therapeutic dose. The potential active ingredients were screened out based on their pharmacokinetic parameters. And then, a compound mixture of these active candidates was re-evaluated for the anti-flu activity on H1N1 infected mouse model. Furthermore, the anti-flu mechanism of SHL was also predicted by network pharmacology coupled with the experimental result.

RESULTS

SHL significantly increased the survival rate and prolonged survival days on H1N1 infected mice at a dosage of 20 g crude drug/kg/day by reversing the increased lung index, down-regulating the inflammatory cytokines (TNF-α, IL-1β, IL-6) and inhibiting the release of IFN-β in bronchoalveolar lavage fluids (BALF). Concomitantly, the pharmacokinetic parameters of fourteen quantified and twenty-one semi-quantified constituents of SHL were characterized. And then, five compounds (baicalin, sweroside, chlorogenic acid, forsythoside A and phillyrin), which displayed satisfactory pharmacokinetic features, were considered as potential active ingredients. Thus, a mixture of these five ingredients was administered to H1N1-infected mice at a dose of 4.24 mg/kg/day. As a result, the therapeutical effects of the mixture were similar to SHL in terms of survival rate, lung index and the release of cytokines (TNF-α, IL-1β and IL-6) in BALF. Moreover, network pharmacology analysis indicated that the TNF-signal pathways might play a role in the anti-flu mechanism of SHL.

CONCLUSIONS

A mixture of five compounds (baicalin, sweroside, chlorogenic acid, forsythoside A and phillyrin) were the anti-flu substances of SHL. The strategy based on serum pharmaco-chemistry under actual therapeutic dose provided a new sight on exploring in vivo effective substances of TCM.

Xiaoyaosan decoction alleviated rat liver fibrosis via the TGFβ/Smad and Akt/FoxO3 signaling pathways based on network pharmacology analysis

ETHNOPHARMACOLOGICAL RELEVANCE

Liver fibrosis is an outcome of many chronic liver diseases and often results in cirrhosis, liver failure, and even hepatocarcinoma. Xiaoyaosan decoction (XYS) as a classical Traditional Chinese Medicine (TCM) formula is used to liver fibrosis in clinical practice while its mechanism is unclear.

AIM OF THE STUDY

The aim of this study was to investigate the anti-fibrosis effect of XYS and to explore the molecular mechanisms by combining network pharmacology and transcriptomic technologies.

MATERIALS AND METHODS

The carbon tetrachloride (CCl4)-induced liver fibrosis rat were treated with three doses of XYS. The liver fibrosis and function were evaluated by histopathological examination and serum biochemical detection. The fibrosis related protein a-SMA and collagen I were assessed by Western blot. Different expressed genes (DEGs) between XYS-treated group and model group were analyzed. The herb-component-target network was constructed combined the network pharmacology. The predict targets and pathways were validated by in vitro and in vivo experiments.

RESULTS

With XYS treatment, the liver function was significantly improved, and fibrotic changes were alleviated. The a-SMA and collagen I expression levels in the liver were also decreased in XYS-treated rats compared with CCl4 model rats. 108 active components and 42 targets from 8 herbs constituted herb-compound-target network by transcriptomics and network pharmacology analysis. The KEGG pathway and GO enrichment analyses showed that the FoxO, TGFβ, AMPK, MAPK, PPAR, and hepatitis B and C pathways were involved in the anti-fibrosis effects of XYS. In the liver tissues, p-FoxO3a and p-Akt expression levels were significantly increased in the CCl4 model group but decreased in the XYS-treated group. The TGFβ1/Smad pathway and Akt/FoxO3 pathway were verified in LX2 cells by inhibiting phosphorylation of Smad3 and Akt activity, respectively.

CONCLUSIONS

Our findings suggested that XYS markedly alleviated CCl4-induced liver fibrosis in histopathological and serum liver function analyses, and this effect may occur via the TGFβ1/Smad and Akt/FoxO signaling pathways.

Prediction of the mechanisms of action of Shenkang in chronic kidney disease: A network pharmacology study and experimental validation

ETHNOPHARMACOLOGICAL RELEVANCE

Traditional Chinese medicine provides a unique curative treatment of complex chronic diseases, including chronic kidney disease (CKD), which is not effectively treated with the current therapies. The pharmacological mechanisms of Shenkang (SK), a herbal medicine containing rhubarb (Rheum palmatum L. or R. tanguticum Maxim. ex Balf.), red sage (Salvia miltiorrhiza Bunge), safflower (Carthamus tinctorius L.), and astragalus (Astragalus mongholicus Bunge), widely used to treat CKD in China, are still unclear.

AIM OF THE STUDY

In this study, the comprehensive approach used for elucidating the pharmacological mechanisms of SK included the identification of the effective constituents, target prediction and network analysis, by investigating the interacting pathways between these molecules in the context of CKD. These results were validated by performing an in vivo study and by comparison with literature reviews.

MATERIALS AND METHODS

This approach involved the following main steps: first, we constructed a molecular database for SK and screened for active molecules by conducting drug-likeness and drug half-life evaluations; second, we used a weighted ensemble similarity drug-targeting model to accurately identify the direct drug targets of the bioactive constituents; third, we constructed compound-target, target-pathway, and target-disease networks using the Cytoscape 3.2 software and determined the distribution of the targets in tissues and organs according to the BioGPS database. Finally, the resulting drug-target mechanisms were compared with those proposed by previous research on SK and validated in a mouse model of CKD.

RESULTS

By using Network analysis, 88 potential bioactive compounds in the four component herbs of SK and 85 CKD-related targets were identified, including pathways that involve the nuclear factor-κB, mitogen-activated protein kinase, transient receptor potential, and vascular endothelial growth factor, which were categorized as inflammation, proliferation, migration, and permeability modules. The results also included different tissues (kidneys, liver, lungs, and heart) and different disease types (urogenital, metabolic, endocrine, cardiovascular, and immune diseases as well as pathological processes) closely related to CKD. These findings agreed with those reported in the literature. However, our findings with the network pharmacology prediction did not account for all the effects reported for SK found in the literature, such as regulation of the hemodynamics, inhibition of oxidative stress and apoptosis, and the involvement of the transforming growth factor-β/SMAD3, sirtuin/forkhead box protein O (SIRT/FOXO) and B-cell lymphoma-2-associated X protein pathways. The in vivo validation experiment revealed that SK ameliorated CKD through antifibrosis and anti-inflammatory effects, by downregulating the levels of vascular cell adhesion protein 1, vitamin D receptor, cyclooxygenase-2, and matrix metalloproteinase 9 proteins in the unilateral ureteral obstruction mouse model. This was consistent with the predicted target and pathway networks.

CONCLUSIONS

SK exerted a curative effect on CKD and CKD-related diseases by targeting different organs, regulating inflammation and proliferation processes, and inhibiting abnormal extracellular matrix accumulation. Thus, pharmacological network analysis with in vivo validation explained the potential effects and mechanisms of SK in the treatment of CKD. However, these findings need to be further confirmed with clinical studies.

Screening of potential biomarkers for Yin-deficiency-heat syndrome based on UHPLC-MS method and the mechanism of Zhibai Dihuang granule therapeutic effect

BACKGROUND

Yin-deficiency-heat (YDH) syndrome is a subhealth state of the individual, mainly manifested as oral ulcers, dry mouth, constipation, and other symptoms. Zhibai Dihuang granule (ZDG), as a classic traditional Chinese medicine, is effective in treating YDH syndrome. We screened the potential biomarkers for diagnosing YDH syndrome, and explored the mechanisms of the therapeutic effect of ZDG.

METHODS

Plasma samples from the Pinghe (PH, healthy control) group, the Shanghuo (SH, YDH syndrome) group, and the ZDG treated group (therapeutic group) were analyzed by using metabolomics profiling. The data were analyzed by multivariate statistical and bioinformatics analyses.

RESULTS

We screened four differential metabolites such as, decanoylcarnitine, dodecanoylcarnitine, phosphatidylcholine (PC), and Aspartate (Asp) Arginine (Arg) Proline (Pro) in the SH group and the PH group. The results showed that the combination of above four metabolites could serve as a potential biomarker for the early diagnosis of YDH syndrome. The metabolites decanoylcarnitine and glucose were found to be differentially expressed in the YDH syndrome group and tended to be normalized after ZDG treatment.

CONCLUSION

The increased levels of four differential metabolites (decanoylcarnitine, dodecanoylcarnitine, PC, and Asp Arg Pro) revealed that individuals with YDH syndrome may have increased energy metabolism in the body, which could lead to disorders of fatty acids β-oxidation and immune function. The levels of two differential metabolites including decanoylcarnitine and glucose returned to normal after ZDG treatment, indicating that ZDG could treat YDH syndrome by regulating glucose metabolism and fatty acids β-oxidation. Our study provides a new method for the diagnosis of YDH syndrome, and may provide theoretical basis for novel therapeutic strategies of YDH syndrome.

The complete chloroplast genome of Pholidota imbricata (Orchidaceae)

Pholidota imbricata belongs to tribe Coelogninae in Orchidaceae distributed in Sichuan, Xizang, and Yunnan. Here, we report the first complete chloroplast (cp) genome and the cp genome features of P. imbricata. The complete cp genome sequence of P. imbricata is 159,292 bp in length and presented a typical quadripartite structure including one large single-copy region (LSC, 87,515 bp), one small single-copy region (SSC, 20,999 bp), and two inverted repeat regions (IRs, 25,389 bp each). The cp genome encoded 141 genes, of which 108 were unique genes (80 protein-coding genes, 24 tRNAs, and 4 rRNAs). The phylogenetic relationships show that P. imbricata is sister to the species of the genus Pleione in tribe Coelogninae.

Understanding the Mechanistic Contribution of Herbal Extracts in Compound Kushen Injection With Transcriptome Analysis

Herbal compatibility is the knowledge of which herbs to combine in traditional Chinese medicine (TCM) formulations. The lack of understanding of herbal compatibility is one of the key problems for the application and popularization of TCM in western society. Because of the chemical complexity of herbal medicines, it is simpler to begin to conduct compatibility research based on herbs rather than component plant secondary metabolites. We have used transcriptome analysis to explore the effects and interactions of two plant extracts (Kushen and Baituling) combined in Compound Kushen Injection (CKI). Based on shared chemical compounds and in vitro cytotoxicity comparisons, we found that both the major compounds in CKI, and the cytotoxicity effects of CKI were mainly derived from the extract of Kushen (Sophorae flavescentis). We generated and analyzed transcriptome data from MDA-MB-231 cells treated with single-herb extracts or CKI and results showed that Kushen contributed to the perturbation of the majority of cytotoxicity/cancer related pathways in CKI such as cell cycle and DNA replication. We also found that Baituling (Heterosmilax yunnanensis Gagnep) could not only enhance the cytotoxic effects of Kushen in CKI, but also activate immune-related pathways. Our analyses predicted that IL-1β gene expression was upregulated by Baituling in CKI and we confirmed that IL-1β protein expression was increased using an ELISA assay. Altogether, these findings help to explain the rationale for combining Kushen and Baituling in CKI, and show that transcriptome analysis using single herb extracts is an effective method for understanding herbal compatibility in TCM.

Differential proteomics for studying action mechanisms of traditional Chinese medicines

Differential proteomics, which has been widely used in studying of traditional Chinese medicines (TCMs) during the past 10 years, is a powerful tool to visualize differentially expressed proteins and analyzes their functions. In this paper, the applications of differential proteomics in exploring the action mechanisms of TCMs on various diseases including cancers, cardiovascular diseases, diabetes, liver diseases, kidney disorders and obesity, etc. were reviewed. Furthermore, differential proteomics in studying of TCMs identification, toxicity, processing and compatibility mechanisms were also included. This review will provide information for the further applications of differential proteomics in TCMs studies.

Anti-Angiogenic Alternative and Complementary Medicines for the Treatment of Endometriosis: A Review of Potential Molecular Mechanisms

Endometriosis is caused by the growth or infiltration of endometrial tissues outside of the endometrium and myometrium. Symptoms include pain and infertility. Surgery and hormonal therapy are widely used in Western medicine for the treatment of endometriosis; however, the side effects associated with this practice include disease recurrence and menopause, which can severely influence quality of life. Angiogenesis is the main biological mechanism underlying the development of endometriosis. Numerous natural products and Chinese medicines with potent anti-angiogenic effects have been investigated, and the molecular basis underlying their therapeutic effects in endometriosis has been explored. This review aims to describe natural products and compounds that suppress angiogenesis associated with endometriosis and to assess their diverse molecular mechanisms of action. Furthermore, this review provides a source of information relating to alternative and complementary therapeutic products that mediate anti-angiogenesis. An extensive review of the literature and electronic databases, such as the China National Knowledge Infrastructure, PubMed, and Embase, was conducted using the keywords 'endometriosis,' 'traditional Chinese medicine,' 'Chinese herbal medicine,' 'natural compounds,' and 'anti-angiogenic' therapy. Anti-angiogenic therapy is an emerging strategy for the treatment of endometriosis. Natural anti-angiogenic products and Chinese medicines provide several beneficial clinical effects, including pain relief. In this review, we summarize clinical trials and experimental studies of endometriosis using natural products and Chinese medicines. In particular, we focus on anti-angiogenic products and alternative and complementary medicines for the treatment of endometriosis and additionally examine their therapeutic efficacy and mechanisms of action. Anti-angiogenic natural products and/or compounds provide a new approach for the treatment of endometriosis. Future work will require randomized trials with larger numbers of subjects, as well as long-term follow-up to confirm the findings described here.