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.

Identifying the essential nodes in network pharmacology based on multilayer network combined with random walk algorithm

Compared with the general complex network, the multilayer network is more suitable for the description of reality. It can be used as a tool of network pharmacology to analyze the mechanism of drug action from an overall perspective. Combined with random walk algorithm, it measures the importance of nodes from the entire network rather than a single layer. Here a four-layer network was constructed based on the data about the action process of prescriptions, consisting of ingredients, target proteins, metabolic pathways and diseases. The random walk algorithm was used to calculate the betweenness centrality of the protein layer nodes to get the rank of their importance. According to above method, we screened out the top 10% proteins that play a key role in treatment. Prescriptions Xiaochaihu Decoction was taken as example to prove our method. The selected proteins were measured with the ones that have been validated to be associated with the treated diseases. The results showed that its accuracy was no less than the topology-based method of single-layer network. The applicability of our method was proved by another prescription Yupingfeng Decoction. Our study demonstrated that multilayer network combined with random walk algorithm was an effective method for pre-screening vital target proteins related to prescriptions.

Whole Transcriptome Analysis of Obese Adipose Tissue Suggests u001kfc.1 as a Potential Regulator to Glucose Homeostasis

Long non-coding RNA (LncRNAs) are newly highlighted key factors controlling brown adipogenesis and development, but their regulatory effect to white adipocyte is still merely understood. Deciphering their underlying mechanism could be a novel way to discovering potential targets of obesity. Therefore, we conducted a whole transcriptome analysis in white adipose tissue from obese patients for the first time. Six obese patients and five control subjects were selected for microarray assay. Differentially expressed coding genes (DEGs), targets of lncRNAs, and alternatively spliced genes in obesity group were systematically compared in a functional framework based on a global gene regulatory network. It was demonstrated that all the three kinds of transcripts were enriched in pathways related to glucose metabolism while only DEGs showed closer proximity to neuro-endocrine-immune system. Thus, a lncRNA-regulated core network was constructed by a stepwise strategy using DEGs as seed nodes. From the core network, we identified a decreased lncRNA, uc001kfc.1, as potential cis-regulator for phosphatase and tensin homolog (PTEN) to enhance insulin sensitivity of white adipocytes in obese patients. We further validated the down-regulation of uc001kfc.1 and PTEN in an independent testing sample set enrolling 22 subjects via qRT-PCR. Although whether the decreased uc001kfc.1 correlated with low risk of diabetes deserved to be examined in an expanded cohort with long-term follow-up visit, the present study highlighted the potential of lncRNA regulating glucose homeostasis in human adipose tissue from a global perspective. With further improvement, such network-based analyzing protocol proposed in this study could be applied to interpreting function of more lncRNAs from other whole transcriptome data.

Knowledge-Based Neuroendocrine Immunomodulation (NIM) Molecular Network Construction and Its Application

Growing evidence shows that the neuroendocrine immunomodulation (NIM) network plays an important role in maintaining and modulating body function and the homeostasis of the internal environment. The disequilibrium of NIM in the body is closely associated with many diseases. In the present study, we first collected a core dataset of NIM signaling molecules based on our knowledge and obtained 611 NIM signaling molecules. Then, we built a NIM molecular network based on the MetaCore database and analyzed the signaling transduction characteristics of the core network. We found that the endocrine system played a pivotal role in the bridge between the nervous and immune systems and the signaling transduction between the three systems was not homogeneous. Finally, employing the forest algorithm, we identified the molecular hub playing an important role in the pathogenesis of rheumatoid arthritis (RA) and Alzheimer’s disease (AD), based on the NIM molecular network constructed by us. The results showed that GSK3B, SMARCA4, PSMD7, HNF4A, PGR, RXRA, and ESRRA might be the key molecules for RA, while RARA, STAT3, STAT1, and PSMD14 might be the key molecules for AD. The molecular hub may be a potentially druggable target for these two complex diseases based on the literature. This study suggests that the NIM molecular network in this paper combined with the forest algorithm might provide a useful tool for predicting drug targets and understanding the pathogenesis of diseases. Therefore, the NIM molecular network and the corresponding online tool will not only enhance research on complex diseases and system biology, but also promote the communication of valuable clinical experience between modern medicine and Traditional Chinese Medicine (TCM).

Systematic analysis of new drug indications by drug-gene-disease coherent subnetworks

Drug targets and disease genes may work as driver factors at the transcriptional level, which propagate signals through gene regulatory network and cause the downstream genes' differential expression. How to analyze transcriptional response data to identify meaningful gene modules shared by both drugs and diseases is still a critical issue for drug-disease associations and molecular mechanism. In this article, we propose the drug-gene-disease coherent subnetwork concept to group the biological function related drugs, diseases, and genes. It was defined as the subnetwork with drug, gene, and disease as nodes and their interactions coherently crossing three data layers as edges. Integrating differential expression profiles of 418 drugs and 84 diseases, we develop a computational framework and identify 13 coherent subnetworks such as inflammatory bowel disease and melanoma relevant subnetwork. The results demonstrate that our coherent subnetwork approach is able to identify novel drug indications and highlight their molecular basis.

Traditional Chinese medicine network pharmacology: theory, methodology and application

Traditional Chinese medicine (TCM) has a long history of viewing an individual or patient as a system with different statuses, and has accumulated numerous herbal formulae. The holistic philosophy of TCM shares much with the key ideas of emerging network pharmacology and network biology, and meets the requirements of overcoming complex diseases, such as cancer, in a systematic manner. To discover TCM from a systems perspective and at the molecular level, a novel TCM network pharmacology approach was established by updating the research paradigm from the current "one target, one drug" mode to a new "network target, multi-components" mode. Subsequently, a set of TCM network pharmacology methods were created to prioritize disease-associated genes, to predict the target profiles and pharmacological actions of herbal compounds, to reveal drug-gene-disease co-module associations, to screen synergistic multi-compounds from herbal formulae in a high-throughput manner, and to interpret the combinatorial rules and network regulation effects of herbal formulae. The effectiveness of the network-based methods was demonstrated for the discovery of bioactive compounds and for the elucidation of the mechanisms of action of herbal formulae, such as Qing-Luo-Yin and the Liu-Wei-Di-Huang pill. The studies suggest that the TCM network pharmacology approach provides a new research paradigm for translating TCM from an experience-based medicine to an evidence-based medicine system, which will accelerate TCM drug discovery, and also improve current drug discovery strategies.

Fuzi-Lizhong pill compensates hypothyroid-hypothermia via ghrelin release

ETHNOPHARMACOLOGICAL RELEVANCE

Fuzi-Lizhong pill (FLZ) is a traditional Chinese medicine for treating patients with Spleen Yang deficient syndrome. Ghrelin, a peptide with 28 amino acid residues, plays multiple roles in thermogenesis. This study aims to explore FLZ regulating ghrelin to compensate hypothermia in rats with hypothyroid and indigestion.

MATERIALS AND METHODS

In litter-matched rats, hypothermia was developed with both thyroidectomy at d1 and interscapular brown adipose (IBA) removal at d42, indigestion was induced with both high fat diet and fasting-feeding cycle from d56; the littermates with hypothermia and indigestion were administrated with FLZ from d70. Adaptive thermogenesis, thyroid hormones, metabolites, ghrelin dynamics were measured at d98.

RESULTS

The results showed that plasma ghrelin levels were inversely correlated with the gastric ghrelin levels and adaptive thermogenesis in rats undergone both thyroidectomy and IBA removal. Fatty diet and FLZ enhanced the increase of plasma ghrelin of hypothyroid rats. These were supported by the changes of plasma thyroid related hormones, plasma metabolites, gastric ghrelin mRNA and protein, and the effects of fatty diet or FLZ.

CONCLUSIONS

Our results suggest that more ghrelin release compensate chronic hypothermia in rats with both hypothyroidism and indigestion. It could explain the mechanisms of FLZ in relieving chronic hypothermia.

Potential metabolic mechanism of girls' central precocious puberty: a network analysis on urine metabonomics data

BACKGROUND

Central precocious puberty (CPP) is a common pediatric endocrine disease caused by early activation of hypothalamic-putuitary-gonadal (HPG) axis, yet the exact mechanism was poorly understood. Although there were some proofs that an altered metabolic profile was involved in CPP, interpreting the biological implications at a systematic level is still in pressing need. To gain a systematic understanding of the biological implications, this paper analyzed the CPP differential urine metabolites from a network point of view.

RESULTS

In this study, differential urine metabolites between CPP girls and age-matched normal ones were identified by LC-MS. Their basic topological parameters were calculated in the background network. The network decomposition suggested that CPP differential urine metabolites were most relevant to amino acid metabolism. Further proximity analysis of CPP differential urine metabolites and neuro-endocrine metabolites showed a close relationship between CPP metabolism and neuro-endocrine system. Then the core metabolic network of CPP was successfully constructed among all these differential urine metabolites. As can be demonstrated in the core network, abnormal aromatic amino acid metabolism might influence the activity of HPG and hypothalamic pituitary adrenal (HPA) axis. Several adjustments to the early activation of puberty in CPP girls could also be revealed by urine metabonomics.

CONCLUSIONS

The present article demonstrated the ability of urine metabonomics to provide several potential metabolic clues for CPP's mechanism. It was revealed that abnormal metabolism of amino acid, especially aromatic amino acid, might have a close correlation with CPP's pathogenesis by activating HPG axis and suppressing HPA axis. Such a method of network-based analysis could also be applied to other metabonomics analysis to provide an overall perspective at a systematic level.

Underlying mechanism of aconitum lizhong acting on experimental hypothermia with indigestion in rats: role of ghrelin

This study is aimed to investigate the Aconitum Lizhong pill (ALZ) pharmacological actions on hypothermia with indigestion, especially the ghrelin roles. The littermate-matched rats were randomly divided into four groups. Control did sham operation or standard diet, Model carried out interscapular brown adipose (IBA) removal with standard diet, Fat-diet did IBA removal with fat-diet, and ALZ did IBA removal and fat-diet with 4.536 g/kg/d ALZ. The potency of adaptive thermogenesis, ghrelin levels in plasma or gastric mucosa, thyroid hormones and metabolite in sera, expression of ghrelin mRNA, and protein in gastric mucous membrane were determined. ALZ relieved the hypothermia processes with indigestion, via inhibiting ghrelin expression and increasing ghrelin secretion; the dynamics from the therapy is supported with the energy changes as less body weight loss, less plasma lipid decrease, more plasma T₃ or T₄ increase with TSH decrease, and more compensation of thermogenic AUC decrease. Ghrelin played key roles in the actions of ALZ on the hypothermia with indigestion. The pharmacological mechanisms of ALZ involved the homeostasis of ghrelin expression and secretion.

Effects on neuroendocrinoimmune network of Lizhong Pill in the reserpine induced rats with spleen deficiency in traditional Chinese medicine

AIM OF THE STUDY

Lizhong Pill, composed of radix Ginseng (Panax ginseng C.A. Meyer), rhizoma Zingiberis (Zingiber officinale Roscoe), rhizoma Atractylodis Macrocephalae (Atractylodes macrocephala Koidz.) and radix Glycytthizae (Glycyrrhiza uralensis Fisch.), is a classical herbal product for curing spleen deficiency in traditional Chinese medicine (TCM), and reserpine treated rats show similar signs to TCM spleen deficiency pattern. This paper is aimed to explore the regulatory effect on neuroendocrinoimmune network by Lizhong Pill in reserpine induced TCM spleen deficiency rats.

MATERIALS AND METHODS

100 healthy adult male SD rats, with a mean weight of 200 g, were randomly divided into five groups in average: control group, reserpine treated group, atropine treated group, treatment groups with Lizhong Pill at high dose and low dose (equal to the dosage of crude drugs for 4 g/kg/d and 8 g/kg/d). Rats in reserpine treated group were induced by intraperitoneal injection of reserpine at 0.5 mg/kgd for 4 weeks. The levels of IL-1, IL-6 and gastrin were measured with radioimmunoassay, TNF-α and IFN-γ in serum were measured with ELISA, the level of vasoactive intestinal peptide (VIP) and substance P (SP) in small intestine were determined with radioimmunoassay, and the TNF-α and TGF-β positive cells in small intestine were detected by immunohistological staining. Data were analyzed with SAS 9.1 software package.

RESULTS

The rats in reserpine treated group, body weight, concentrations of IFN-γ, IL-1 and TNF-α in serum, expression of TGF-β in small intestine, VIP in small intestine decreased (P<0.05), and the level of IL-6 in serum, expression of TNF-α, SP in small intestine and gastrin were increased (P<0.05). Administration of Lizhong Pill at high dose could increase the body weights at day 21, and the weights of rats in Lizhong Pill groups were much higher compared to reserpine treated group. At high dose of Lizhong Pill could increase the level of TNF-α in serum. Lizhong Pill at high dose and low dose could reverse the changes of IL-1, IL-6 and IFN-γ, gastrin, expression of TGF-β and TNF-α, VIP and SP in small intestine.

CONCLUSIONS

The rats treated with reserpine, with similar signs to TCM spleen deficiency, show neuroendocrinoimmune disorders, and the restoration of the neuroendocrinoimmune disorders might be the part of mechanism of Lizhong Pill for reinforcing TCM spleen deficiency.

Bridging the gap between traditional Chinese medicine and systems biology: the connection of Cold Syndrome and NEI network

Systems biology is a general trend of contemporary scientific development. When coupling the classical traditional Chinese medicine (TCM) Cold Syndrome and methodology of systems biology, we conformed to the genome, transcriptome, proteome, and metabolome that are supposed to run through the overall macro behavior, and explored the macro and micro framework of systems biology of TCM Syndrome. We introduced a new way to probe into the implicit stratification of Cold Syndrome, after surveying 4575 cases of Cold Syndrome patients and examining gene expression information of a typical Cold Syndrome pedigree by microarray. We underlined the genetic background of the Cold Syndrome family based on the molecular foundation to understand Syndrome, one of our earlier discoveries in which genes and chemical compounds in neuro-endocrine-immune (NEI) system are scored as Cold or Hot (or both) property. Results indicate that Cold Syndrome related genes play an essential role in energy metabolism, which are tightly correlated with the genes of neurotransmitters, hormones and cytokines in the NEI interaction network. Therefore, NEI interaction not only opens out mechanism of classical TCM theory on Syndrome but also enriches current research on complex diseases as well as systems biology.