Herb-target interaction network analysis helps to disclose molecular mechanism of traditional Chinese medicine

Network pharmacology to uncover potential anti-inflammatory and immunomodulatory constituents in Curcuma longa rhizome as complementary treatment in COVID-19

The immune status of patients plays an essential role in COVID-19. Herbal medicine with immunomodulatory and anti-inflammatory effect could have potential as a complementary therapeutic along with modern medicine. This study aims to investigate the anti-inflammatory and immunomodulatory constituents of Curcuma longa (C. longa) and its possible mechanisms in COVID-19. We systematically sorted the biochemical of C. longa rhizome from literature and repository. Next, we investigated targets related to COVID-19 in the selected active phytochemical constituents and analyzed the possible mechanisms against COVID-19 and performed molecular docking with four essential target proteins in COVID-19 for further verification. Ten active phytochemical constituents of C. longa were predicted to interact with four protein targets. The epidermal growth factor was the most interacted protein targeted by Calebin A, curcumin, cyclocurcumin, demethoxycurcumin, turmeronol a, turmeronol b, caffeic acid, and quercetin. Interferon-gamma was performed as the most critical protein targeted by 4-hydroxycinnamic acid. Curcumin was also predicted to interact with toll-like receptor 4 and Ar-turmerone with angiotensin II receptor type 2. We also reported four signaling pathways associated with target proteins-active phytochemical constituents against COVID-19: cytokine-cytokine receptor interaction, toll-like receptor signaling pathway, Jak-STAT signaling pathway, and PI3K-Akt signaling pathway. In conclusion, multi compounds in C. longa might act synergistically against COVID-19 by affecting the inflammatory and immune responses, and other pathological processes through multiple targets and pathways.

Network pharmacology-based analysis of signaling pathways of an anti-osteoporotic triterpenoid from Acyranthes bidentata Blume root

In Korea folk remedies, Acyranthes bidentata Blume is a functional food plant to treat bone diseases; especially, its roots have been used to alleviate osteoporosis (OP), but its key chemical compound(s) and mechanism of action against osteoporosis have not reported yet. This study suggests that Acyranthes bidentata Blume root (ABBR) has promising compound(s) against OP. We utilized network pharmacology to evaluate the therapeutic value. The chemical compounds from Acyranthes bidentata Blume root (ABBR) were identified by gas chromatography-mass spectrum (GC-MS); their physicochemical properties have been evaluated by SwissADME. Next, the target(s) related to a triterpenoid or OP-related targets were investigated by public databases. The signaling pathways from final targets were visualized, constructed, and analyzed by RPackage. Finally, we performed a molecular docking (MD) to explore key target(s) and compound(s) by employing AutoDockVina tools; the residues of amino acids interacted with ligands were identified by LigPlot + v.22. A total of 24 chemicals were accepted by the Lipinski's rules. We found a sole triterpenoid from ABBR via GC-MS, suggesting that might be a potent ligand to alleviate OP. Thereby, the 42 targets were associated with the triterpenoid; the 19 targets among them were connected to OP-targets (1426). The final 19 targets were related directly to 8 signaling pathways on STRING database. On Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and a key signaling pathway (PPAR signaling pathway), four key targets (PPARA, PPARD, FABP3, and FABP4) and a key compound (Methyl 3β-hydroxyolean-18-en-28-oate) were selected via MD. Collectively, the triterpenoid from ABBR might have potent anti-osteoporotic efficacy by activating PPARA, PPARD, FABP3, and FABP4 on PPAR signaling pathway.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03362-5.

Network Analysis of Herbs Recommended for the Treatment of COVID-19

PURPOSE

In this study, we aimed to identify the pattern and combination of herbs used in the formulae recommended for treating different stages of COVID-19 using a network analysis approach.

METHODS

The herbal formulae recommended by official guidelines for the treatment of COVID-19 are included in the present analysis. To describe the tendency of herbs to form a "herb pair", we computed the mutual information (MI) value and distance-based mutual information model (DMIM) score. We also performed modularity, degree, betweenness, and closeness centrality analysis. Network analyses were performed and visualized for each disease stage.

RESULTS

A total of 142 herbal formulae comprising 416 herbs were analyzed. All possible herbal pairs were examined, and the top frequently used herbal pairs were identified for each disease stage. The herb Glycyrrhizae radix et rhizoma is only identified in one herb pair, even though this herb is identified as one of the herbs with high frequency of use for every disease stage. This suggests that the DMIM score could be used to identify the optimal combination rule of herbal formulae by achieving a balance among the herbs' frequency and relative distance in herbal formulae.

CONCLUSION

Our results presented the prescription patterns and herbal combinations of the herbal formulae recommended for the treatment of COVID-19. This study may provide new insights and ideas for clinical research in the future.

β-Caryophyllene Ameliorates MSU-Induced Gouty Arthritis and Inflammation Through Inhibiting NLRP3 and NF-κB Signal Pathway: In Silico and In Vivo

Gouty arthritis serves as an acute reaction initiated by the deposition of monosodium urate (MSU) crystals around the joints. In this study, the anti-inflammatory effects of phytochemical β-caryophyllene on MSU crystal-induced acute gouty arthritis in vivo and in silico were explored. Through bioinformatics methods and molecular docking, it screened the specific influence pathway of β-caryophyllene on gout. Certain methods including enzyme-linked immunosorbent assay, western blotting, and immunohistochemical staining were adopted to quantify. β-caryophyllene significantly reduced inflammation and function of ankle joints in MSU Crystals-induced gouty arthritis rats, while decreasing serum cytokine levels. Furthermore, it inhibited the expressions of NLRP3, Caspase-1, ASC, TLR4, MyD88, p65, and IL-1β in the synovial tissue so as to reduce inflammation and protect ankle joints’ function. A new research approach in which β-caryophyllene treatment to acute attacks of gout is provided through the research results.

Chinmedomics, a new strategy for evaluating the therapeutic efficacy of herbal medicines

Herbal medicines have accumulated valuable clinical experience in thousands of years of applications in traditional Chinese medicine (TCM) or ethnomedicine. The unique multi-target efficacy on complex diseases made herbal medicines gained a global popularity in recent years. However, the characteristic of multi-component acting on multi-target poses a dilemma for the evaluation of therapeutic efficacy of herbal medicines. Advances in metabolomics enable efficient identification of the various changes in biological systems exposed to different treatments or conditions. The use of serum pharmacochemistry of TCM has significant implications for tackling the major issue in herbal medicines development-pharmacodynamic material basis. Chinmedomics integrates metabolomics and serum pharmacochemistry of TCM to investigate the pharmacodynamic material basis and effective mechanisms of herbal medicines on the basis of TCM syndromes and holds the promise of explaining therapeutic efficacy of herbal medicines in scientific language. In this review, the historical development of chinmedomics from concept formation to successful applications was discussed. We also took the systematic research of Yin Chen Hao Tang (YCHT) as an example to show the research strategy of chinmedomics.

Network pharmacology based virtual screening of active constituents of Prunella vulgaris L. and the molecular mechanism against breast cancer

Prunella vulgaris L, a perennial herb widely used in Asia in the treatment of various diseases including cancer. In vitro studies have demonstrated the therapeutic effect of Prunella vulgaris L. against breast cancer through multiple pathways. However, the nature of the biological mechanisms remains unclear. In this study, a Network pharmacology based approach was used to explore active constituents and potential molecular mechanisms of Prunella vulgaris L. for the treatment of breast cancer. The methods adopted included active constituents prescreening, target prediction, GO and KEGG pathway enrichment analysis. Molecular docking experiments were used to further validate network pharmacology results. The predicted results showed that there were 19 active ingredients in Prunella vulgaris L. and 31 potential gene targets including AKT1, EGFR, MYC, and VEGFA. Further, analysis of the potential biological mechanisms of Prunella vulgaris L. against breast cancer was performed by investigating the relationship between the active constituents, target genes and pathways. Network analysis showed that Prunella vulgaris L. exerted a promising preventive effect on breast cancer by acting on tumor-associated signaling pathways. This provides a basis to understand the mechanism of the anti-breast cancer activity of Prunella vulgaris L.

Harringtonine Inhibits Zika Virus Infection through Multiple Mechanisms

Mosquito-borne Zika virus (ZIKV) is a Flavivirus that came under intense study from 2014 to 2016 for its well-known ability to cause congenital microcephaly in fetuses and neurological Guillain-Barré disease in adults. Substantial research on screening antiviral agents against ZIKV and preventing ZIKV infection are globally underway, but Food and Drug Administration (FDA)-approved treatments are not available yet. Compounds from Chinese medicinal herbs may offer an opportunity for potential therapies for anti-ZIKV infection. In this study, we evaluated the antiviral efficacy of harringtonine against ZIKV. Harringtonine possessed anti-ZIKV properties against the binding, entry, replication, and release stage through the virus life cycle. In addition, harringtonine have strong virucidal effects in ZIKV and exhibited prophylaxis antiviral ability prior ZIKV infection. The antiviral activity also observed in the treatment against Japanese encephalitis reporter virus (RP9-GFP strain). Overall, this study demonstrated that harringtonine would be a favorable potential candidate for the development of anti-ZIKV infection therapies.

Discovery of Targeted Covalent Natural Products against PLK1 by Herb-Based Screening

Natural products (NPs) are a rich source of drug discovery, and some of them act by covalently binding to the targets. Recently, targeted covalent natural product (TCNP) design has gained considerable attention since this approach offers significant benefits in improving biological efficacy and decreasing the off-target side effects. However, most of the known TCNPs were discovered by chance. Rational approaches for a systematic screen of TCNPs are much needed. Here, we developed a combined computational and experimental approach to carry out herb-based screening to identify TCNPs against proper cysteine residues in the target proteins. The herb-based TCNP screening approach (HB-TCNP) starts from a druggable pocket and cysteine residue prediction, followed by virtual screening of a covalent NP database and herb-based mapping to identify candidate herbs for experimental validation. Herbs with time-dependent activity are selected, and their NPs are experimentally tested to further screen covalent NPs. We have successfully applied HB-TCNP to screen anti-PLK1 herbs and NPs with high efficacy. Cys67 and Cys133 in the ATP binding pocket of PLK1 were used in the search. Five herbs were tested and exhibited PLK1 inhibition activity to some extent, among which Scutellaria baicalensis showed the most potent activity with time dependency. Further experimental studies showed that the main active compounds in Scutellaria baicalensis, baicalein and baicalin, covalently bind PLK1 through Cys133. Our study provided an efficient way to rationally design TCNPs and to make better use of herb medicines. The Cys133 residue in PLK1 serves as a novel covalent site for further drug discovery against PLK1.

Moslea Herba flavonoids alleviated influenza A virus-induced pulmonary endothelial barrier disruption via suppressing NOX4/NF-κB/MLCK pathway

ETHNOPHARMACOLOGICAL RELEVANCE

Moslae Herba, a common traditional Chinese herb with special flavor, has potential for treating respiratory and gastrointestinal diseases.

AIM OF THIS STUDY

Lung endothelial barrier dysfunction (LEBD) accelerates the pathogenesis of influenza A virus (IAV)-induced secondary acute lung injury. New strategies against LEBD provide benefits in prevention and treatment of IAV. Previous studies showed that flavonoids (MHF), main bioactivity fraction derived from M. Herba, exerted anti-inflammatory and antiviral activities, but the underlying protection of MHF against IAV-induced acute lung injury remained obscure. The present study was to investigate the protection of MHF against IAV-induced LEBD in vivo and in vitro.

MATERIALS AND METHODS

Mice were intranasally challenged with IAV and orally administered with MHF for 5 days. The pulmonary hyperpermeability of infected mice was evaluated by Evans Blue staining and in vivo imaging. Serum levels of inflammatory cytokines and mediators were detected by ELISA assay. The transepithelial electrical resistance (TER) of human pulmonary microvascular endothelial cells (HPMVECs) was measured by using TER meter. The expressions of key proteins in NOX4-mediated NF-κB/MLCK pathways were determined by western blotting.

RESULTS

MHF treatment reduced lung index, W/D ratios, and serum levels of inflammatory factors (IL-6, TNF-α, IL-1β, PLA₂, LBT₄ and ICAM-1) in IAV-infected mice. Evans blue staining and in vivo imaging results revealed that MHF alleviated IAV-induced barrier dysfunction and pulmonary hyperpermeability. Moreover, luteolin and kaempferol, the main activity compounds in MHF, significantly inhibited TNF-α-induced HPMVEC apoptosis, and downregulated NF-κB/MLCK pathway by targeting NOX4.

CONCLUSION

MHF attenuated IAV-induced barrier dysfunction by suppressing NOX4/NF-κB/MLCK pathway and may serve as a potential agent for the prevention of LEBD and IAV.

Associating 197 Chinese herbal medicine with drug targets and diseases using the similarity ensemble approach

Chinese herbal medicine (CHM) addresses complex diseases through polypharmacological interactions. However, systematic studies of herbal medicine pharmacology remain challenging due to the complexity of CHM ingredients and their interactions with various targets. In this study, we aim to address this challenge with computational approaches. We investigated the herb-target-disease associations of 197 commonly prescribed CHMs using the similarity ensemble approach and DisGeNET database. We demonstrated that this method can be applied to associate herbs with their putative targets. In the case study of three well-known herbs, Radix Glycyrrhizae, Flos Lonicerae, and Rhizoma Coptidis, approximately 70% of the predicted targets were supported by scientific literature. By linking 406 targets to 2439 annotated diseases, we further analyzed the pharmacological functions of 197 herbs. Finally, we proposed a strategy of target-oriented herbal formula design and illustrated the target profiles for four common chronic diseases, namely, Alzheimer's disease, depressive disorder, hypertensive disease, and non-insulin-dependent diabetes mellitus. This computational approach holds great potential in the target identification of herbs, understanding the molecular mechanisms of CHM, and designing novel herbal formulas.

Predicting Meridian in Chinese traditional medicine using machine learning approaches

Plant-derived nature products, known as herb formulas, have been commonly used in Traditional Chinese Medicine (TCM) for disease prevention and treatment. The herbs have been traditionally classified into different categories according to the TCM Organ systems known as Meridians. Despite the increasing knowledge on the active components of the herbs, the rationale of Meridian classification remains poorly understood. In this study, we took a machine learning approach to explore the classification of Meridian. We determined the molecule features for 646 herbs and their active components including structure-based fingerprints and ADME properties (absorption, distribution, metabolism and excretion), and found that the Meridian can be predicted by machine learning approaches with a top accuracy of 0.83. We also identified the top compound features that were important for the Meridian prediction. To the best of our knowledge, this is the first time that molecular properties of the herb compounds are associated with the TCM Meridians. Taken together, the machine learning approach may provide novel insights for the understanding of molecular evidence of Meridians in TCM.

Network pharmacology study of traditional Chinese medicines for stroke treatment and effective constituents screening

ETHNOPHARMACOLOGICAL RELEVANCE

Stroke is one of the most frequent causes of death and disability. So far there are no effective preventives or treatments. The therapeutic system of traditional Chinese medicines (TCMs) has been in use for several thousand years and still affords a valuable resource for today's clinicians in preserving health.

MATERIALS AND METHODS

We had collected the Chinese medicinal formulae and then commonly used single herbs or drug combinations were analyzed through data mining. The ingredients from the top 30 frequently used herbs which have good druggability and blood-brain barrier permeability were collected as a natural product library. Targets of the related ingredients were predicted using various databases and analyzed by GO and KEGG pathway mapping. The potential stroke targets were validated in the market or from clinical trials, and used to establish molecular docking, HipHop and SBP models to screen new compounds for multi-target activity. Lastly, in vitro experiments with models for oxygen and glucose deprivation and reperfusion (OGDR) were conducted to test the activities of compounds identified by screening.

RESULTS

A total of 1679 Chinese medicinal formulas were selected and their prescription rules were analyzed. 4277 compounds were from the top 30 herbs and 3560 molecules were filtered to build the natural product library. The ingredient-target network, target-disease network and target-target interaction network were established to explain the characteristics and mechanisms of the TCMs. Thirty-one molecules were selected to have multi-target activity on targets of stroke via virtual screening. Five of these had already been reported to have therapeutic effects on stroke. Three of the eight compounds which have been examined showed protective effects on OGDR model.

CONCLUSIONS

This paper details a novel strategy for exploring the characteristics and mechanisms of herbal medicines from a systematic standpoint in an attempt to identify those affecting specific target pathways related to stroke. Using this methodology on our natural products library, we found a number of lead candidates with multi-target activity.

Hepatoprotective Effect of Jianpi Huoxue Formula on Nonalcoholic Fatty Liver Disease Induced by Methionine-Choline-Deficient Diet in Rat

In parallel with the prevalence metabolic syndrome, nonalcoholic fatty liver disease (NAFLD) has become the most common chronic liver disease in most countries. It features a constellation of simple steatosis, nonalcoholic steatohepatitis (NASH), fibrosis, cirrhosis, and even hepatocellular carcinoma. There are no approved drugs for effective management of NAFLD and NASH. Jianpi Huoxue formula (JPHX) mainly consists of Atractylodes macrocephal (Baizhu), Salvia miltiorrhiza (Danshen), Rasux Paeonia Alba (Baishao), Rhizoma Alismatis (Zexie), and Fructus Schisandrae Chinensis (Wuweizi), which may have beneficial effects on NAFLD. The aim of the study was to identify the effect of JPHX on NAFLD. A NAFLD model was induced by methionine-choline-deficient food (MCD) in Wistar rats and orally administered with simultaneous JPHX, once a day for 8 weeks. Hepatocellular injury, lipid profile, inflammation, fibrosis, and apoptosis were evaluated. The results showed that JPHX significantly decreased the abnormal serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels compared with the MCD model (P<0.05). Furthermore, JPHX protected MCD diet-fed rats from accumulation of hepatic triglycerides (TG) and total cholesterol (TC). Histological examination demonstrated that JPHX noticeably normalized the NAFLD activity score (NAS). Moreover, JPHX ameliorated liver inflammation by decreasing TNF-α levels and reduced collagen and matrix metalloproteinases in MCD diet-fed rats. In addition, JPHX prevented rats from MCD-induced cellular apoptosis, as suggested by TUNEL staining, and suppressed the activation of caspase 3 and 7 proteins. JPHX also inhibited the phosphorylation of JNK. In conclusion, JPHX exhibited a hepatoprotective effect against NAFLD in an MCD experimental model.

Efficient ligand discovery from natural herbs by integrating virtual screening, affinity mass spectrometry and targeted metabolomics

Although natural herbs have been a rich source of compounds for drug discovery, identification of bioactive components from natural herbs suffers from low efficiency and prohibitive cost of the conventional bioassay-based screening platforms. Here we develop a new strategy that integrates virtual screening, affinity mass spectrometry (MS) and targeted metabolomics for efficient discovery of herb-derived ligands towards a specific protein target site. Herb-based virtual screening conveniently selects herbs of potential bioactivity whereas affinity MS combined with targeted metabolomics readily screens candidate compounds in a high-throughput manner. This new integrated approach was benchmarked on screening chemical ligands that target the hydrophobic pocket of the nucleoprotein (NP) of Ebola viruses for which no small molecule ligands have been reported. Seven compounds identified by this approach from the crude extracts of three natural herbs were all validated to bind to the NP target in pure ligand binding assays. Among them, three compounds isolated from Piper nigrum (HJ-1, HJ-4 and HJ-6) strongly promoted the formation of large NP oligomers and reduced the protein thermal stability. In addition, cooperative binding between these chemical ligands and an endogenous peptide ligand was observed, and molecular docking was employed to propose a possible mechanism. Taken together, we established a platform integrating in silico and experimental screening approaches for efficient discovery of herb-derived bioactive ligands especially towards non-enzyme protein targets.

Pairwise combinations of chemical compounds that delay yeast chronological aging through different signaling pathways display synergistic effects on the extent of aging delay

We have recently discovered six plant extracts that delay yeast chronological aging. Most of them affect different nodes, edges and modules of an evolutionarily conserved network of longevity regulation that integrates certain signaling pathways and protein kinases; this network is also under control of such aging-delaying chemical compounds as spermidine and resveratrol. We have previously shown that, if a strain carrying an aging-delaying single-gene mutation affecting a certain node, edge or module of the network is exposed to some of the six plant extracts, the mutation and the plant extract enhance aging-delaying efficiencies of each other so that their combination has a synergistic effect on the extent of aging delay. We therefore hypothesized that a pairwise combination of two aging-delaying plant extracts or a combination of one of these plant extracts and spermidine or resveratrol may have a synergistic effect on the extent of aging delay only if each component of this combination targets a different element of the network. To test our hypothesis, we assessed longevity-extending efficiencies of all possible pairwise combinations of the six plant extracts or of one of them and spermidine or resveratrol in chronologically aging yeast. In support of our hypothesis, we show that only pairwise combinations of naturally-occurring chemical compounds that slow aging through different nodes, edges and modules of the network delay aging in a synergistic manner.

Anti-virus reagents targeting the capsid protein assembly

The capsid protein is a promising target for the development of therapeutic anti-virus agents.

Understanding molecular mechanisms of Rhodiola rosea for the treatment of acute mountain sickness through computational approaches (a STROBE-compliant article)

Rhodiola rosea has been used in the treatment of acute mountain sickness (AMS) for a long time, but the mechanism of its action is not still completely clear. In this paper, the therapeutic mechanism of R rosea for AMS was investigated by analysis of the relationship between R rosea compositions and hypoxia-inducible factor 1 (HIF-1) degradation pathway.System biology and network biology, computational approaches were used to explore the molecular mechanisms of traditional Chinese medicine (TCM).Our results showed that chemical compositions of R rosea could inhibit the targets of HIF-1 degradation pathway in multi-composition/multi-target ways.We conclude that the 18 components with more than 2 targets and 5 targets (arrest-defective-1 [ARD1], forkhead transcription factor [FOXO4], osteosarcoma-9 [OS-9], prolyl hydroxylase 2 [PHD2], human double minute 2 [Hdm2]) deserve to be noticed, and PHD2, receptor for activated C-kinase1 (RACK1) and spermidine/spermine-N1-acetyltransferase-1 (SSAT1) may be the targets of active ingredients of rhodionin, rhodiosin, and rhodiolatuntoside, respectively.

Systems Pharmacology-Based Approach of Connecting Disease Genes in Genome-Wide Association Studies with Traditional Chinese Medicine

Traditional Chinese medicine (TCM) originated in ancient China has been practiced over thousands of years for treating various symptoms and diseases. However, the molecular mechanisms of TCM in treating these diseases remain unknown. In this study, we employ a systems pharmacology-based approach for connecting GWAS diseases with TCM for potential drug repurposing and repositioning. We studied 102 TCM components and their target genes by analyzing microarray gene expression experiments. We constructed disease-gene networks from 2558 GWAS studies. We applied a systems pharmacology approach to prioritize disease-target genes. Using this bioinformatics approach, we analyzed 14,713 GWAS disease-TCM-target gene pairs and identified 115 disease-gene pairs with q value < 0.2. We validated several of these GWAS disease-TCM-target gene pairs with literature evidence, demonstrating that this computational approach could reveal novel indications for TCM. We also develop TCM-Disease web application to facilitate the traditional Chinese medicine drug repurposing efforts. Systems pharmacology is a promising approach for connecting GWAS diseases with TCM for potential drug repurposing and repositioning. The computational approaches described in this study could be easily expandable to other disease-gene network analysis.

A novel dual-luciferase assay for anti-HIV drug screening based on the CCR5/CXCR4 promoters

Acquired immunodeficiency syndrome (AIDS) is a serious worldwide disease caused by infection with the human immunodeficiency virus (HIV). C-C chemokine receptor 5 (CCR5) and C-X-C chemokine receptor 4 (CXCR4) are important coreceptors mediating HIV-1 cell entry. Many new anti-HIV drugs are currently in preclinical and clinical trials; however, drug development has proceeded slowly partly because of the lack of a high-throughput system to screen these drugs. Here, we describe the development of a novel dual-luciferase assay using a CCR5/CXCR4 promoter-driven firefly and Renilla luciferase vector (pGL4.10-RLUC-CCR5/CXCR4). Drugs were screened for the ability to regulate CCR5 and CXCR4 promoter activities. The CCR5 and CXCR4 promoters were inserted separately into the recombinant vector and transfected into the acute T lymphocyte leukemia cell line H9. Treatment of stable transfected cells with four traditional Chinese medicine compounds resulted in the dose-dependent inhibition of the CXCR4 and CCR5 promoter activities. The dual-luciferase reporter assay provides a rapid and direct method to screen anti-AIDS/HIV drugs.

Dissecting the Underlying Pharmaceutical Mechanism of Chinese Traditional Medicine Yun-Pi-Yi-Shen-Tong-Du-Tang Acting on Ankylosing Spondylitis through Systems Biology Approaches

Traditional Chinese Medicine (TCM) has been served as complementary medicine for Ankylosing Spondylitis (AS) treatment for a long time. Yun-Pi-Yi-Shen-Tong-Du-Tang (Y-Y-T) is a novel empirical formula designed by Prof. Chengping Wen. In this study, a retrospective investigation supported efficacy of Y-Y-T and then we deciphered the underlying molecular mechanism of the efficacy. Herbal ingredients and targeting proteins were collected from TCMID. PPI networks were constructed to further infer the relationship among Y-Y-T, drugs used for treating AS, differentially expressed genes of AS patients and AS disease proteins. Finally, it was suggested that TLR signaling pathway and T cell receptor signaling pathway may involve in the biological processes of AS progression and contribute to the curative effect and proteins such as JAK2, STAT3, HSP90AA1, TNF and PTEN were the key targets. Our systemic investigation to infer therapeutic mechanism of Y-Y-T for AS treatment provides a new insight in understanding TCM pharmacology.

Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective

With the rapid development of cheminformatics, computational biology, and systems biology, great progress has been made recently in the computational research of Chinese herbal medicine with in-depth understanding towards pharmacognosy. This paper summarized these studies in the aspects of computational methods, traditional Chinese medicine (TCM) compound databases, and TCM network pharmacology. Furthermore, we chose arachidonic acid metabolic network as a case study to demonstrate the regulatory function of herbal medicine in the treatment of inflammation at network level. Finally, a computational workflow for the network-based TCM study, derived from our previous successful applications, was proposed.