Omic techniques in systems biology approaches to traditional Chinese medicine research: present and future

Exploiting omic-based approaches to decipher Traditional Chinese Medicine

ETHNOPHARMACOLOGICAL RELEVANCE

Traditional Chinese Medicine (TCM), an ancient health system, faces significant research challenges due to the complexity of its active components and targets, as well as a historical lack of detailed annotation. However, recent advances in omics technologies have begun to unravel these complexities, providing a more informed and nuanced understanding of TCM's therapeutic potential in contemporary healthcare.

AIM OF THE REVIEW

This review summarizes the application of omics technologies in TCM modernization, emphasizing components analysis, quality control, biomarker discovery, target identification, and treatment optimization. In addition, future perspectives on using omics for precision TCM treatment are also discussed.

MATERIALS AND METHODS

We have explored several databases (including PubMed, ClinicalTrials, Google Scholar, and Web of Science) to review related articles, focusing on Traditional Chinese Medicine, Omics Strategy, Precision Medicine, Biomarkers, Quality Control, and Molecular Mechanisms. Paper selection criteria involved English grammar, publication date, high citations, and broad applicability, exclusion criteria included low credibility, non-English publications, and those full-text inaccessible ones.

RESULTS

TCM and the popularity of Chinese herbal medicines (CHMs) are gaining increasing attention worldwide. This is driven, in part, by a large number of technologies, especially omics strategy, which are aiding the modernization of TCM. They contribute to the quality control of CHMs, the identification of cellular targets, discovery of new drugs and, most importantly, the understanding of their mechanisms of action.

CONCLUSION

To fully integrate TCM into modern medicine, further development of robust omics strategies is essential. This vision includes personalized medicine, backed by advanced computational power and secure data infrastructure, to facilitate global acceptance and seamless integration of TCM practices.

Application of multi-omics in the study of traditional Chinese medicine

Traditional Chinese medicine (TCM) is playing an increasingly important role in disease treatment due to the advantages of multi-target, multi-pathway mechanisms, low adverse reactions and cost-effectiveness. However, the complexity of TCM system poses challenges for research. In recent years, there has been a surge in the application of multi-omics integrated research to explore the active components and treatment mechanisms of TCM from various perspectives, which aids in advancing TCM's integration into clinical practice and holds immense importance in promoting modernization. In this review, we discuss the application of proteomics, metabolomics, and mass spectrometry imaging in the study of composition, quality evaluation, target identification, and mechanism of action of TCM based on existing literature. We focus on the workflows and applications of multi-omics based on mass spectrometry in the research of TCM. Additionally, potential research ideas for future exploration in TCM are outlined. Overall, we emphasize the advantages and prospects of multi-omics based on mass spectrometry in the study of the substance basis and mechanism of action of TCM. This synthesis of methodologies holds promise for enhancing our understanding of TCM and driving its further integration into contemporary medical practices.

Radix Saposhnikoviae enhancing Huangqi Chifeng Decoction improves lipid metabolism in AS mice

ETHNOPHARMACOLOGICAL RELEVANCE

Huangqi Chifeng decoction (HQCF) combined with parsnips is a classic Chinese traditional medicine formula that has certain advantages in the clinical treatment of cardiovascular and cerebrovascular diseases. At present, there is an absence of research on the regulatory effect and mechanism of this formula on atherosclerosis (AS). The synergistic effect of Radix Saposhnikoviae (RS) in HQCF is also unclear.

AIM OF THE STUDY

This study was designed to investigate the role of RS, which is designed as a guide drug for HQCF, in improving the lipid metabolism of AS.

MATERIALS AND METHODS

In this study, we studied the effect of HQCF on ApoE-/- mice before and after RS compatibility. Hematoxylin and eosin (HE) staining and oil red staining were used to evaluate atherosclerotic lesions and lipid accumulation in the aorta and liver, respectively. The expression of adenosine monophosphate-activated protein kinase (AMPK) and pAMPK in the aorta was measured by immunofluorescence, and AMPK and sterol regulatory element binding protein-1 (SREBP-1),fatty acid synthase (FAS) and acetyl-CoA carboxylase (ACC) in liver tissue were measured by Western blot analysis. Metabolomics was used to compare the changes in serum and liver metabolites of ApoE-/- mice before and after RS combination.

RESULTS

Compared with the control group, the serum lipid levels of ApoE-/- mice increased, the aortic intima thickened with plaque formation, and liver tissue pathological changes and lipid deposition occurred. Both (HQCFT without RS)HQCS and HQCF can improve the pathological condition of tissue and regulate the blood lipid level. It was noted that HQCF could promote the phosphorylation of AMPK to activate it, inhibit the expression of SREBP-1c and FAS, reduce lipid synthesis, and inhibit ACC to promote the oxidative decomposition of fatty acids. Serum and liver metabolome results showed that HQCS and HQCF treated AS mainly by regulating glycerophospholipid metabolism, sphingolipid metabolism and the arachidonic acid metabolism pathway. Importantly, HQCF showed better efficacy in regulating lipid metabolism than the HQCS group.

CONCLUSION

HQCF decoction reduces atherosclerotic lesions in the aorta and lipid accumulation in the liver, which may regulate lipid transport and metabolic function by activating the AMPK pathway. These effects can be attributed to the guidance and synergism of RS.

Traditional Chinese medicine Zhusha Anshen Wan: protective effects on liver, kidney, and intestine of the individual drugs using 1H NMR metabolomics

Introduction: Zhusha Anshen Wan (ZSASW) is a traditional Chinese medicine compound mainly composed of mineral drugs. In clinical practice, ZSASW did not show the toxicity of administering equal doses of cinnabar alone, suggesting that the four combination herbs in ZSASW can alleviate the damage of cinnabar. The effect of each herb on reducing the toxicity of cinnabar has not been fully explained. Methods: In our study, we utilized a metabonomics approach based on high-resolution 1H nuclear magnetic resonance spectroscopy to investigate the reduction of toxicity by each herb in ZSASW. Liver, kidney and intestinal histopathology examinations and biochemical analysis of the serum were also performed. Results: Partial least squares-discriminant analysis (PLS-DA) was conducted to distinct different metabolic profiles in the urine and serum from the rats. Liver and kidney histopathology examinations, as well as analysis of serum clinical chemistry analysis, were also carried out. The metabolic profiles of the urine and serum of the rats in the CGU (treated with cinnabar and Glycyrrhiza uralensis Fisch) and CCC (treated with cinnabar and Coptis chinensis French) groups were remarkably similar to those of the control group, while those of the CRG (treated with cinnabar and Rehmannia glutinosa Libosch) and CAS (treated with cinnabar and Angelica sinensis) groups were close to those of the cinnabar group. The metabolic profiles of the urine and serum of the rats in the CGU and CCC groups were remarkably similar to those of the control group, while those of the CRG and CAS groups were close to those of the cinnabar group. Changes in endogenous metabolites associated with toxicity were identified. Rehmannia glutinosa, Rhizoma Coptidis and Glycyrrhiza uralensis Fisch could maintain the dynamic balance of the intestinal flora. These results were also verified by liver, kidney and intestinal histopathology examinations and biochemical analysis of the serum. The results suggested that Discussion: The metabolic mechanism of single drug detoxification in compound prescriptions has been elucidated. Coptis chinensis and Glycyrrhiza uralensis serve as the primary detoxification agents within ZSASW for mitigating liver, kidney, and intestinal damage caused by cinnabar. Detoxification can be observed through changes in the levels of various endogenous metabolites and related metabolic pathways.

A Q-marker screening strategy based on ADME studies and systems biology for Chinese herbal medicine, taking Qianghuo Shengshi decoction in treating rheumatoid arthritis as an example

Chinese herbal medicine (CHM) exhibits a broad spectrum of clinical applications and demonstrates favorable therapeutic efficacy. Nonetheless, elucidating the underlying mechanism of action (MOA) of CHM in disease treatment remains a formidable task due to its inherent characteristics of multi-level, multi-linked, and multi-dimensional non-linear synergistic actions. In recent years, the concept of a Quality marker (Q-marker) proposed by Liu et al. has significantly contributed to the monitoring and evaluation of CHM products, thereby fostering the advancement of CHM research. Within this study, a Q-marker screening strategy for CHM formulas has been introduced, particularly emphasising efficacy and biological activities, integrating absorption, distribution, metabolism, and excretion (ADME) studies, systems biology, and experimental verification. As an illustrative case, the Q-marker screening of Qianghuo Shengshi decoction (QHSSD) for treating rheumatoid arthritis (RA) has been conducted. Consequently, from a pool of 159 compounds within QHSSD, five Q-markers exhibiting significant in vitro anti-inflammatory effects have been identified. These Q-markers encompass notopterol, isoliquiritin, imperatorin, cimifugin, and glycyrrhizic acid. Furthermore, by employing an integrated analysis of network pharmacology and metabolomics, several instructive insights into pharmacological mechanisms have been gleaned. This includes the identification of key targets and pathways through which QHSSD exerts its crucial roles in the treatment of RA. Notably, the inhibitory effect of QHSSD on AKT1 and MAPK3 activation has been validated through western blot analysis, underscoring its potential to mitigate RA-related inflammatory responses. In summary, this research demonstrates the proposed strategy's feasibility and provides a practical reference model for the systematic investigation of CHM formulas.

Cell Survival, Death, and Proliferation in Senescent and Cancer Cells: the Role of (Poly)phenols

Cellular senescence has long been considered a permanent state of cell cycle arrest occurring in proliferating cells subject to different stressors, used as a cellular defense mechanism from acquiring potentially harmful genetic faults. However, recent studies highlight that senescent cells might also alter the local tissue environment and concur to chronic inflammation and cancer risk by secreting inflammatory and matrix remodeling factors, acquiring a senescence-associated secretory phenotype (SASP). Indeed, during aging and age-related diseases, senescent cells amass in mammalian tissues, likely contributing to the inevitable loss of tissue function as we age. Cellular senescence has thus become one potential target to tackle age-associated diseases as well as cancer development. One important aspect characterizing senescent cells is their telomere length. Telomeres shorten as a consequence of multiple cellular replications, gradually leading to permanent cell cycle arrest, known as replicative senescence. Interestingly, in the large majority of cancer cells, a senescence escape strategy is used and telomere length is maintained by telomerase, thus favoring cancer initiation and tumor survival. There is growing evidence showing how (poly)phenols can impact telomere maintenance through different molecular mechanisms depending on dose and cell phenotypes. Although normally, (poly)phenols maintain telomere length and support telomerase activity, in cancer cells this activity is negatively modulated, thus accelerating telomere attrition and promoting cancer cell death. Some (poly)phenols have also been shown to exert senolytic activity, thus suggesting both antiaging (directly eliminating senescent cells) and anticancer (indirectly, via SASP inhibition) potentials. In this review, we analyze selective (poly)phenol mechanisms in senescent and cancer cells to discriminate between in vitro and in vivo evidence and human applications considering (poly)phenol bioavailability, the influence of the gut microbiota, and their dose-response effects.

Identifying target organ location of Radix Achyranthis Bidentatae: a bioinformatics approach on active compounds and genes

Background: Herbal medicines traditionally target organs for treatment based on medicinal properties, and this theory is widely used for prescriptions. However, the scientific evidence explaining how herbs act on specific organs by biological methods has been still limited. This study used bioinformatic tools to identify the target organ locations of Radix Achyranthis Bidentatae (RAB), a blood-activating herb that nourishes the liver and kidney, strengthens bones, and directs prescription to the lower body. Methods: RAB's active compounds and targets were collected and predicted using databases such as TCMSP, HIT2.0, and BATMAN-TCM. Next, the RAB's target list was analyzed based on two approaches to obtain target organ locations. DAVID and Gene ORGANizer enrichment-based approaches were used to enrich an entire gene list, and the BioGPS and HPA gene expression-based approaches were used to analyze the expression of core genes. Results: RAB's targets were found to be involved in whole blood, blood components, and lymphatic organs across all four tools. Each tool indicated a particular aspect of RAB's target organ locations: DAVID-enriched genes showed a predominance in blood, liver, and kidneys; Gene ORGANizer showed the effect on low body parts as well as bones and joints; BioGPS and HPA showed high gene expression in bone marrow, lymphoid tissue, and smooth muscle. Conclusion: Our bioinformatics-based target organ location prediction can serve as a modern interpretation tool for the target organ location theory of traditional medicine. Future studies should predict therapeutic target organ locations in complex prescriptions rather than single herbs and conduct experiments to verify predictions.

Systems biology strategy and experimental validation to uncover the pharmacological mechanism of Xihuang Pill in treating non-small cell lung cancer

BACKGROUND

Non-small cell lung cancer (NSCLC) accounts for almost 85% of lung cancer-related deaths worldwide. Xihuang Pill (XHP) is a representative anticancer Chinese patented medicine used to treat NSCLC in China. However, to date, a systematic analysis of XHP's antitumour effects and its impact on the immune microenvironment has not been performed.

PURPOSE

Based on the systems biology strategy and experimental validation, the present study aimed to investigate the pharmacological mechanisms involved in treating NSCLC with XHP.

METHODS

A subcutaneous tumour model was established to evaluate XHP's tumour-inhibitory effect in BALB/c nude mice. RNA sequencing (RNA-seq) and bioinformatics analysis were conducted to identify differentially expressed genes (DEGs) and signalling pathways related to XHP treatment. Network analysis based on network pharmacology and protein-to-protein networks was applied to identify the compounds and genes targeted by XHP. External data from the TCGA-NSCLC cohort were used to verify the clinical significance of XHP-targeted genes in NSCLC. The expression of survival-related candidate genes after XHP treatment was verified via qPCR. The protein expression of calcium voltage-gated channel subunit alpha 1C (CACNA1C) in different NSCLC cell lines was analysed in the Human Protein Atlas database (HPA) and DepMap Portal. Using the Estimation of STromal and Immune cells in MAlignant Tumour tissues using Expression data (ESTIMATE) algorithm and the single-sample gene set enrichment analysis (ssGSEA) algorithm uncovered the role of CACNA1C in the NSCLC tumour microenvironment (TME).

RESULTS

XHP (2 g/kg/d) significantly inhibited the growth of transplanted A549 tumours. RNA-seq identified a total of 529 DEGs (189 upregulated and 340 downregulated). In addition, 542 GO terms, 41 significant KEGG pathways, 9 upregulated hallmarks pathways, and 18 downregulated hallmark pathways were enriched. These GO terms and signalling pathways were closely related to cell proliferation, immunity, energy metabolism, and the inflammatory response of NSCLC. In addition, XHP's network pharmacology analysis identified 301 compounds and 1,432 target genes. A comprehensive strategic analysis identified CACNA1C as a promising gene by which XHP targets and regulates the TME of NSCLC, benefiting patient survival. CACNA1C expression was positively correlated with both the immune score and stromal score but negatively correlated with the tumour purity score. Additionally, CACNA1C expression was significantly correlated with the infiltration levels of 15 types of immune cells and the expression levels of 6 well-known checkpoint genes.

CONCLUSIONS

Our results show that by regulating the pathways associated with cell proliferation and immunity, XHP can suppress cancer cell growth in NSCLC. Additionally, XHP may increase the expression of CACNA1C to suppress immune cell infiltration and regulate the expression of checkpoint-related genes, thereby improving the overall survival of NSCLC patients.

Metabolomics and Network Pharmacology in the Exploration of the Multi-Targeted Therapeutic Approach of Traditional Medicinal Plants

Metabolomic is generally characterized as a comprehensive and the most copious analytical technique for the identification of targeted and untargeted metabolite diversity in a biological system. Recently, it has exponentially been used for phytochemical analysis and variability among plant metabolites, followed by chemometric analysis. Network pharmacology analysis is a computational technique used for the determination of multi-mechanistic and therapeutic evaluation of chemicals via interaction with the genomes involved in targeted or untargeted diseases. In considering the facts, the present review aims to explore the role of metabolomics and network pharmacology in the scientific validation of therapeutic claims as well as to evaluate the multi-targeted therapeutic approach of traditional Indian medicinal plants. The data was collected from different electronic scientific databases such as Google Scholar, Science Direct, ACS publication, PubMed, Springer, etc., using different keywords such as metabolomics, techniques used in metabolomics, chemometric analysis, a bioinformatic tool for drug discovery and development, network pharmacology, methodology and its role in biological evaluation of chemicals, etc. The screened articles were gathered and evaluated by different experts for their exclusion and inclusion in the final draft of the manuscript. The review findings suggest that metabolomics is one of the recent most precious and effective techniques for metabolite identification in the plant matrix. Various chemometric techniques are copiously used for metabolites discrimination analysis hence validating the unique characteristic of herbal medicines and their derived products concerning their authenticity. Network pharmacology remains the only option for the unique and effective analysis of hundreds of chemicals or metabolites via genomic interaction and thus validating the multi-mechanistic and therapeutic approach to explore the pharmacological aspects of herbal medicines for the management of the disease.

Multi-omics approaches for in-depth understanding of therapeutic mechanism for Traditional Chinese Medicine

Traditional Chinese Medicine (TCM) is extensively utilized in clinical practice due to its therapeutic and preventative treatments for various diseases. With the development of high-throughput sequencing and systems biology, TCM research was transformed from traditional experiment-based approaches to a combination of experiment-based and omics-based approaches. Numerous academics have explored the therapeutic mechanism of TCM formula by omics approaches, shifting TCM research from the "one-target, one-drug" to "multi-targets, multi-components" paradigm, which has greatly boosted the digitalization and internationalization of TCM. In this review, we concentrated on multi-omics approaches in principles and applications to gain a better understanding of TCM formulas against various diseases from several aspects. We first summarized frequently used TCM quality assessment methods, and suggested that incorporating both chemical and biological ingredients analytical methods could lead to a more comprehensive assessment of TCM. Secondly, we emphasized the significance of multi-omics approaches in deciphering the therapeutic mechanism of TCM formulas. Thirdly, we focused on TCM network analysis, which plays a vital role in TCM-diseases interaction, and serves for new drug discovery. Finally, as an essential source for storing multi-omics data, we evaluated and compared several TCM databases in terms of completeness and reliability. In summary, multi-omics approaches have infiltrated many aspects of TCM research. With the accumulation of omics data and data-mining resources, deeper understandings of the therapeutic mechanism of TCM have been acquired or will be gained in the future.

Metabolomics reveal the mechanism for anti-renal fibrosis effects of an n-butanol extract from Amygdalus mongolica

To reveal the mechanism of anti-renal fibrosis effects of an n-butanol extract from Amygdalus mongolica, renal fibrosis was induced with unilateral ureteral obstruction (UUO) and then treated with an n-butanol extract (BUT) from Amygdalus mongolica (Rosaceae). Sixty male Sprague-Dawley rats were randomly divided into the sham-operated, renal fibrosis (RF) model, benazepril hydrochloride-treated model (1.5 mg kg^-1) and BUT-treated (1.75, 1.5 and 1.25 g kg^-1) groups and the respective drugs were administered intragastrically for 21 days. Related biochemical indices in rat serum were determined and histopathological morphology observed. Serum metabolomics was assessed with HPLC-Q-TOF-MS. The BUT reduced levels of blood urea nitrogen, serum creatinine and albumin and lowered the content of malondialdehyde and hydroxyproline in tissues. The activity of superoxide dismutase in tissues was increased and an improvement in the severity of RF was observed. Sixteen possible biomarkers were identified by metabolomic analysis and six key metabolic pathways, including the TCA cycle and tyrosine metabolism, were analyzed. After treatment with the extract, 8, 12 and 9 possible biomarkers could be detected in the high-, medium- and low-dose groups, respectively. Key biomarkers of RF, identified using metabolomics, were most affected by the medium dose. A. mongolica BUT extract displays a protective effect on RF in rats and should be investigated as a candidate drug for the treatment of the disease.

Application of metabolomics and network analysis to reveal the ameliorating effect of four typical “hot” property herbs on hypothyroidism rats

Herbs with a “hot” properties are frequently used to treat cold symptoms in TCM. However, the underlying mechanisms of the herbs with “hot” properties on hypothyroidism have not been investigated. This study aimed to explore four typical “hot” and “cold” property herb on hypothyroidism. Firstly, the difference efficacy between the four typical “hot” property herbs and the four typical “cold” property herbs was assessed by physical signs, thyroid function, and the metabolic profile using multivariate statistical analysis. The influence of the four typical “hot” property herbs on hypothyroidism was validated pathologically. The impact mechanism of the four typical “hot” property herbs on hypothyroidism was investigated through a metabolomics method combined with network analysis. Na⁺/K⁺-ATP, ACC1 enzyme, UCP-1, and the PI3K-Akt pathway were used to confirm the metabolite pathways and target-associated metabolites. The results showed that the four typical “hot” property herbs could significantly improve physical signs, thyroid function, and the metabolic profile in hypothyroidism rats, the four typical “cold” property herbs did not show any benefit. Moreover, the four typical “hot” property herbs could improve lipid metabolism, energy metabolism, and thyroid hormone levels by the PI3K-Akt signaling pathway, Ca²⁺- AMPK signaling pathways, purine metabolism, and tryptophan metabolism. Additionally, the levels of UCP-1, Na+/K + -ATP enzyme, and ACC1 were ameliorated by the four typical “hot” property herbs in hypothyroidism rats. Therefore, a metabolomics strategy combined with network analysis was successfully performed and interpreted the mechanism of the four typical “hot” property herbs on hypothyroidism based on the theory of “cold and hot” properties of TCM well.

Holism of Chinese herbal medicine prescriptions for inflammatory bowel disease: A review based on clinical evidence and experimental research

BACKGROUND

Inflammatory bowel disease (IBD) is a chronic nonspecific inflammatory disease that causes a heavy burden and lacks effective treatments. Chinese herbal medicine prescriptions (CHMPs), which are characterized by a synergistic usage of herbs, are widely used in the management of IBD. The molecular mechanisms of action of CHMP are still ambiguous as the canonical "one-compound-one-target" approach has difficulty describing the dynamic bioreactions among CHMP objects. It seems more flexible to define the holism of CHMP for IBD by employing high-throughput analysis. However, studies that discuss the development of CHMP in treating IBD in a holistic view are still lacking.

PURPOSE

This review appraised preclinical and clinical research to fully describe the anti-IBD capacity of CHMPs and discussed CHMPs' holistic characteristics that can contribute to better management of IBD.

METHODS & RESULTS

We screened clinical and preclinical references of CHMP being used as treatments for IBD. We discussed the complexity of IBD and the development of CHMP to present the sophistication of CHMP treatments. To describe the clinical effectiveness of CHMPs against IBD, we performed an umbrella review of CHMP-associated META analyses, in which 1174 records were filtered down to 12 references. Then, we discussed 14 kinds of CHMPs that had a long history of use and analyzed their mechanisms of action. Representative herbs were employed to provide a subordinate explanation for the whole prescription. As holism is the dominant characteristic of CHMPs, we explored applications of CHMPs for IBD with the help of omics, gut microbiome, and network pharmacology, which are potential approaches to a dynamic figure of bioactions of CHMPs.

CONCLUSION

This review is the first to discuss the potential of CHMPs to manage IBD in a holistic context and will provide inspiring explanations for CHMP applications for further product transformation and application to other diseases.

Anti-depressive effects of Jiao-Tai-Wan on CORT-induced depression in mice by inhibiting inflammation and microglia activation

ETHNOPHARMACOLOGICAL RELEVANCE

Jiao-Tai-Wan (JTW) is a very famous traditional Chinese medicine formula for the treatment of psychiatric disorders, especially in anxiety, insomnia and depression. However, its molecular mechanism of treatment remains indistinct.

AIM OF THE STUDY

We aimed to reveal the action mechanism of JTW on anti-depression via inhibiting microglia activation and pro-inflammatory response both in vivo and in vitro.

MATERIAL AND METHODS

The corticosterone (CORT)-induced depression mouse model was used to evaluate the therapeutic efficacy of JTW. Behavioral tests (open field, elevated plus maze, tail suspension and forced swim test) were conducted to evaluate the effect of JTW on depressive-like behaviors. The levels of inflammatory factors and the concentration of neurotransmitters were detected by RT-qPCR or ELISA assays. Then three hippocampal tissue samples per group (Control, CORT, and JTW group) were sent for RNA sequencing (RNA-seq). Transcriptomics data analysis was used to screen the key potential therapeutic targets and signaling pathways of JTW. Based on 8 bioactive species of JTW by our previous study using High-performance liquid chromatography (HPLC) analysis, molecular docking analyses were used to predict the interaction of JTW-derived compounds and depression targets. Finally, the results of transcriptome and molecular docking analyses were combined to verify the targets, key pathways, and efficacy of JTW treatment in vivo and vitro.

RESULTS

JTW ameliorated CORT-induced depressive-like behaviors, neuronal damage and enhanced the levels of monoamine neurotransmitters in the serum of mice. JTW also inhibited CORT-induced inflammatory activation of microglia and decreased the serum levels of interleukin- 6(IL-6) and interleukin- 1β (IL-1β) in vivo. Transcriptomic data analysis showed there were 10 key driver analysis (KDA) genes with the strongest correlation which JTW regulated in depression mice. Molecular docking analysis displayed bioactive compound Magnoflorine had the strongest binding force to the key gene colony-stimulating factor 1 receptor (CSF1R), which is the signaling microglia dependent upon for their survival. Meanwhile, CSF1R staining showed it was consistent with inflammatory activation of microglia. Our vitro experiment also showed JTW and CSF1R inhibitor significantly reduced lipopolysaccharide (LPS)/interferon-gamma (IFNɣ)-induced inflammatory activation response in macrophage cells.

CONCLUSIONS

Our study suggests that JTW might ameliorate CORT-induced neuronal damage in depression mice by inhibiting CSF1R mediated microglia activation and pro-inflammatory response.

The Role of Natural Products as Sources of Therapeutic Agents for Innovative Drug Discovery

Emerging threats to human health require a concerted effort in search of both preventive and treatment strategies, placing natural products at the center of efforts to obtain new therapies and reduce disease spread and associated mortality. The therapeutic value of compounds found in plants has been known for ages, resulting in their utilization in homes and in clinics for the treatment of many ailments ranging from common headache to serious conditions such as wounds. Despite the advancement observed in the world, plant based medicines are still being used to treat many pathological conditions or are used as alternatives to modern medicines. In most cases, these natural products or plant-based medicines are used in an un-purified state as extracts. A lot of research is underway to identify and purify the active compounds responsible for the healing process. Some of the current drugs used in clinics have their origins as natural products or came from plant extracts. In addition, several synthetic analogues are natural product-based or plant-based. With the emergence of novel infectious agents such as the SARS-CoV-2 in addition to already burdensome diseases such as diabetes, cancer, tuberculosis and HIV/AIDS, there is need to come up with new drugs that can cure these conditions. Natural products offer an opportunity to discover new compounds that can be converted into drugs given their chemical structure diversity. Advances in analytical processes make drug discovery a multi-dimensional process involving computational designing and testing and eventual laboratory screening of potential drug candidates. Lead compounds will then be evaluated for safety, pharmacokinetics and efficacy. New technologies including Artificial Intelligence, better organ and tissue models such as organoids allow virtual screening, automation and high-throughput screening to be part of drug discovery. The use of bioinformatics and computation means that drug discovery can be a fast and efficient process and enable the use of natural products structures to obtain novel drugs. The removal of potential bottlenecks resulting in minimal false positive leads in drug development has enabled an efficient system of drug discovery. This review describes the biosynthesis and screening of natural products during drug discovery as well as methods used in studying natural products.

Metabolomic assessment of mechanisms underlying anti-renal fibrosis properties of petroleum ether extract from Amygdalus mongolica

CONTEXT

The petroleum ether extract (PET) of Amygdalus mongolica (Maxim.) Ricker (Rosaceae) has an ameliorative effect on renal fibrosis (RF).

OBJECTIVE

To evaluate the antifibrotic effects of A. mongolica seeds PET on RF by serum metabolomics, biochemical and histopathological analyses.

MATERIALS AND METHODS

Sixty male Sprague-Dawley rats were randomly divided into the sham-operated, RF model, benazepril hydrochloride-treated model (1.5 mg/kg) and PET-treated (1.75, 1.25, 0.75 g/kg) groups, and the respective drugs were administered intragastrically for 21 days. Biochemical indicators including BUN, Scr, HYP, SOD, and MDA were measured. Haematoxylin and eosin and Masson staining were used for histological examination. The serum metabolomic profiles were determined by UPLC-Q-TOF/MS and metabolism network analysis. Acute toxicity test was performed to validate biosafety.

RESULTS

The PET LD₅₀ was >23.9 g/kg in rats. PET significantly alleviated fibrosis by reducing the levels of Scr (from 34.02 to 32.02), HYP (from 403.67 to 303.17) and MDA (from 1.84 to 1.73), and increasing that of SOD (from 256.42 to 271.85). Metabolomic profiling identified 10 potential biomarkers, of which three key markers were significantly associated with RF-related pathways including phenylalanine, tyrosine and tryptophan biosynthesis, amino sugar and nucleotide sugar metabolism and tyrosine metabolism. In addition, three key biomarkers were restored to baseline levels following PET treatment, with the medium dose showing optimal effect.

CONCLUSIONS

These findings revealed the mechanism of A. mongolica PET antifibrotic effects for RF rats on metabolic activity and provided the experimental basis for the clinical application.

A new strategy for discovering effective substances and mechanisms of traditional Chinese medicine based on standardized drug containing plasma and the absorbed ingredients composition, a case study of Xian-Ling-Gu-Bao capsules

ETHNOPHARMACOLOGICAL RELEVANCE

The overall therapeutic effect of traditional Chinese medicine formulae (TCMF) was achieved by the interactions of multiple components with multiple targets. However, current pharmacology research strategies have struggled to identify effective substance groups and encountered challenges in elucidating the underlying mechanisms of TCMF.

AIM

In this study, a comprehensive strategy was proposed and applied to elucidate the interactions of the multiple components that underlie the functions of the famous TCMF: Xian-Ling-Gu-Bao (XLGB) capsule on bone metabolism in vivo and to elucidate the molecular mechanisms underlying the effects of XLGB on bone cells, especially on osteoblasts.

METHODS

The efficacy of XLGB in the protection against bones loss in ovariectomized (OVX) rats was confirmed by Micro-CT analysis. The anti-osteoporosis mechanism involved in the systemic regulatory actions of XLGB was elucidated by transcriptome sequencing analysis on bone marrow mesenchymal stem cells isolated from OVX rats. Moreover, the components absorbed in XLGB-treated plasma were characterized by mass spectrometry analysis, and subsequently, a standardized preparation process of drug-containing plasma was established. The synergistic osteogenic effect of the multiple components in plasma was investigated by a combination and then knockout of components using pre-osteoblast MC3T3-E1 cells. In order to decipher the underlying mechanism of XLGB, the targets of the absorbed components on bone were predicted by target prediction and network pharmacology analysis, then several interactions were validated by biochemical and cell-based assay.

RESULTS

A total of 18 genes, including HDC, CXCL1/2, TNF, IL6 and Il1b, were newly found to be the major target genes regulated by XLGB. Interestingly, we found that a combination of the three absorbed components, i.e. MSP, rather than their single form at the same concentration, stimulated the formation of calcified nodules in MC3T3-E1 cells, suggesting a synergistic effect of these components. Besides, target prediction and experimental validation confirmed the binding affinity of corylin and icaritin for estrogen receptor α and β, the inhibitory activity of isobavachin and isobavachalcone on glycogen synthase kinase-3β, and the inhibitory activity of isobavachalcone on cathepsin K. The cell-based assay further confirmed the result of the biochemical assay. A network that integrated absorbed components of XLGB-targets-perturbation genes-pathways against osteoporosis was established.

CONCLUSION

Our current study provides a new systemic strategy for discovering active ingredient groups of TCM formulae and understanding their underlying mechanisms.

Chemical profile of Swertia mussotii Franch and its potential targets against liver fibrosis revealed by cross-platform metabolomics

ETHNOPHARMACOLOGICAL RELEVANCE

Swertia mussotii Franch (SMF) is a well-known Tibetan medicine for the treatment of liver disease in China. However, the chemical profile and molecular mechanism of SMF against hepatic fibrosis are not yet well explored.

AIM OF THE STUDY

This work aimed to elucidate the chemical profile of SMF and investigate the action mechanisms of SMF against carbon tetrachloride (CCl4)-induced hepatic fibrosis.

MATERIALS AND METHODS

Ultra performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOFMS) and UNIFI platform was firstly employed to reveal the chemical profile of SMF. Cross-platform serum metabolomics based on gas chromatography/liquid chromatography-mass spectrometry were performed to characterize the metabolic fluctuations associated with CCl4-induced hepatic fibrosis in mice and elucidate the underlying mechanisms of SMF. Western blotting was further applied to validate the key metabolic pathways.

RESULTS

A total of 31 compounds were identified or tentatively characterized from SMF. Twenty-seven differential metabolites were identified related with CCl4-induced liver fibrosis, and SMF could significantly reverse the abnormalities of seventeen metabolites. The SMF-reversed metabolites were involved in arachidonic acid metabolism, glycine, serine and threonine metabolism, tyrosine metabolism, arginine and proline metabolism, primary bile acid biosynthesis, glycerophospholipid metabolism and TCA cycle. The results of western blotting analysis showed that SMF could alleviate liver fibrosis by increasing the levels of CYP7A1, CYP27A1 and CYP8B1 and decreasing the level of LPCAT1 to regulate the metabolic disorders of primary bile acid biosynthesis and glycerophospholipid.

CONCLUSION

It could be concluded that primary bile acid biosynthesis and glycerophospholipid metabolism were the two important target pathways for SMF-against liver fibrosis, which provided the theoretical foundation for its clinical use.

Application of Proteomics and Metabonomics to Reveal the Molecular Basis of Atractylodis Macrocephalae Rhizome for Ameliorating Hypothyroidism Instead of Hyperthyroidism

As the treatments of diseases with Chinese herbs are holistic and characterized by multiple components, pathways, and targets, elucidating the efficacy of Chinese herbs in treating diseases, and their molecular basis, requires a comprehensive, network-based approach. In this study, we used a network pharmacology strategy, as well as in vivo proteomics and metabonomics, to reveal the molecular basis by which Atractylodis macrocephalae rhizome (AMR) ameliorates hypothyroidism. Eighteen main compounds from AMR and its fractions (volatile oil fraction, crude polysaccharides fraction, lactones fraction, oligosaccharide fraction, and atractyloside fraction) were identified by HPLC, and their targets were screened using the TCMSP database and Swiss Target Prediction. Disease targets were gathered from the TTD, CTD and TCMSP databases. Hub targets were screened by different plug-ins, such as Bisogene, Merge, and CytoNCA, in Cytoscape 3.7.1 software and analyzed for pathways by the DAVID database. Hypothyroidism and hyperthyroidism pharmacological models were established through systems pharmacology based on proteomic and metabolomic techniques. Finally, AMR and its fractions were able to ameliorate the hypothyroidism model to different degrees, whereas no significant improvements were noted in the hyperthyroidism model. The lactones fraction and the crude polysaccharides fraction were considered the most important components of AMR for ameliorating hypothyroidism. These amelioration effects were achieved through promoting substance and energy metabolism. In sum, the integrative approach used in this study demonstrates how network pharmacology, proteomics, and metabolomics can be used effectively to elucidate the efficacy, molecular basis, and mechanism of action of medicines used in TCM.

Natural Products, the Fourth Industrial Revolution, and the Quintuple Helix

The profound interconnectedness of the sciences and technologies embodied in the Fourth Industrial Revolution is discussed in terms of the global role of natural products, and how that interplays with the development of sustainable and climate-conscious practices of cyberecoethnopharmacolomics within the Quintuple Helix for the promotion of a healthier planet and society.

The Interrelationships between Intestinal Permeability and Phlegm Syndrome and Therapeutic Potential of Some Medicinal Herbs

The gastrointestinal (GI) tract has an intriguing and critical role beyond digestion in both modern and complementary and alternative medicine (CAM), as demonstrated by its link with the immune system. In this review, we attempted to explore the interrelationships between increased GI permeability and phlegm, an important pathological factor in CAM, syndrome, and therapeutic herbs for two disorders. The leaky gut and phlegm syndromes look considerably similar with respect to related symptoms, diseases, and suitable herbal treatment agents, including phytochemicals even though limitations to compare exist. Phlegm may be spread throughout the body along with other pathogens via the disruption of the GI barrier to cause several diseases sharing some parts of symptoms, diseases, and mechanisms with leaky gut syndrome. Both syndromes are related to inflammation and gut microbiota compositions. Well-designed future research should be conducted to verify the interrelationships for evidence based integrative medicine to contribute to the promotion of public health. In addition, systems biology approaches should be adopted to explore the complex synergistic effects of herbal medicine and phytochemicals on conditions associated with phlegm and leaky gut syndromes.

Untargeted metabolomics reveals the synergistic mechanisms of Yuanhu Zhitong oral liquid in the treatment of primary dysmenorrhea

Primary dysmenorrhea is a prevalent gynecological disorder that severely affects the quality of life in women. Yuanhu Zhitong oral liquid (YZOL) is a standardized herbal preparation frequently used in clinical practice and is a promising alternative therapy for primary dysmenorrhea. The findings of previous studies show that YZOL exhibits significant analgesic and spasmolytic effects, however, the involved mechanism remains unclear. Herein, we performed an untargeted plasma metabolomic analysis on a mouse model of oxytocin-induced primary dysmenorrhea to investigate the underlying mechanism of YZOL. We used multivariate and pathway-driven analyses to uncover the treatment targets linked with YZOL therapy and verified the possible mechanisms through biochemical assays. Therefore, we identified 47 plasma biomarkers primarily associated with sphingolipid metabolism, amino acid metabolism, arachidonic acid metabolism, and biosynthesis of steroid hormone as well as primary bile acid. We established that the analgesic effect of YZOL on primary dysmenorrhea relies on multiple constituents that act on multiple targets in multiple pathways. Our correlation analysis showed significant correlations between the biomarkers and biochemical indicators, which is of considerable significance in elucidating the YZOL mechanisms. Moreover, we identified some novel prospective biomarkers linked to primary dysmenorrhea, including bile acids. Collectively, these data provide new insights into the mechanism of YZOL and provide evidence for the analgesic effect of YZOL in the treatment of primary dysmenorrhea.

Metabonomics Study on Serum Characteristic Metabolites of Psoriasis Vulgaris Patients With Blood-Stasis Syndrome

Psoriasis is a chronic, refractory, systemic inflammatory skin disease. Traditional Chinese medicine (TCM) shows unique advantage in the treatment of psoriasis based on syndrome differentiation. An untargeted high-throughput metabonomics method based on liquid chromatography coupled to mass spectrometry was applied to study the serum metabolic characteristics in different TCM syndrome types in patients with psoriasis vulgaris (PV), and to discover potential serum biomarkers for its pathogenesis on the endogenous metabolite differentiation basis. The serum metabolic profiles of 45 healthy controls and 124 patients with PV (50 in the blood-stasis group, 30 in the blood-heat group, and 44 in the blood-dryness group) were acquired. The raw spectrometric data were processed using multivariate statistical analysis, and 14 biomarkers related to TCM syndrome differentiation and psoriasis types were screened and identified. The blood-stasis syndrome group showed abnormal lipid metabolism, which was characterized by a low level of phosphatidylcholine (PC) and a high level of lysophosphatidylcholine (LPC). We propose that platelet-activating factor can be applied as a potential biomarker in clinical diagnosis and differentiation of PV with blood-stasis syndrome. The difference in the serum metabolites among PV types with different TCM syndromes and healthy control group illustrated the objective material basis in TCM syndrome differentiation and classification of psoriasis.

Discovery of Natural Compounds for Cardiac Fibrosis by a Transcriptome-Based Functional Gene Module Reference Approach

Anti-cardiac fibrosis (CF) is one of the key therapeutic strategies for the treatment of various heart diseases. Therefore, development of drugs targeting CF is promising. However, there are very few studies that systemically explore effective drugs for CF. It has been known that many natural compounds display antifibrosis effects. In this work, we aim to build an integrated model for systematic pursuit of anti-CF agents from natural compounds. We first constructed a heart-specific CF marker-gene-centered functional gene module (HCFM) that represents a set of genes specifically involved in CF based on the CF marker genes and known gene coexpression knowledge. Then, we extracted transcriptional data induced by natural compounds from the Gene Expression Omnibus database. The anti-CF effects of compounds were evaluated by the correlation of HCFM in the compound-induced gene expression profiles by gene set enrichment analysis. Finally, the anti-CF effect of a top-predicted natural monomer, schisantherin A, was experimentally validated in the myocardial infarction animal model. This strategy integrating different types of technologies is expected to help create new opportunities for development of drugs targeting CF.

A plasma metabonomics study on the therapeutic effects of the Si-miao-yong-an decoction in hyperlipidemic rats

ETHNOPHARMACOLOGICAL RELEVANCE

The Si-miao-yong-an decoction (SMYAD) is a famous traditional Chinese medicinal formula that has been used for centuries in ancient China for treating thromboangiitis obliterans. Because of its long history of use, it has been used to treat patients in China for thousands of years. In recent years, SMYAD has been widely used for treating cardiovascular and endocrine diseases. It was shown to significantly increase high-density lipoprotein-cholesterol levels and reduce total cholesterol and low-density lipoprotein-cholesterol levels in the serum.

AIM OF THE STUDY

Herein, a serum metabonomics approach based on the HPLC-MS/MS method was adopted to evaluate the therapeutic effect of SMYAD on high-fat diet-induced hyperlipidemia, and investigate the mechanisms for treating hyperlipidemia.

MATERIALS AND METHODS

Firstly, the change in body weight, liver histopathology, and serum biochemistry, including that in the levels of hepatotoxicity-related enzymes, oxidative stress indexes, and inflammatory factors were monitored in rats, to evaluate the therapeutic effect of SMYAD on high-fat diet-induced hyperlipidemia. Then, a serum metabolomics approach was applied, to cluster different groups using principle component analysis (PCA) and partial least squares discriminant analysis (PLS-DA), as well as to screen out sensitive and reliable biomarkers. Finally, the metabolic pathways associated with specific biomarkers were analyzed, to understand the possible mechanism underlying the action of SMYAD.

RESULTS

The results indicated that SMYAD had significant anti-hyperlipidemic, anti-oxidant, and anti-inflammatory effects. Based on the results of serum metabolomics analysis, the hyperlipidemic rats showed completely different results compared to the control rats; metabolite profiles of rats from the SMYAD treatment groups showed a trend comparable to those of the normal control group in a dose-dependent manner. Besides, twelve biomarkers associated with pyruvate metabolism, taurine and hypotaurine metabolism, TCA cycle, bile acid metabolism, and glucose metabolism were identified and confirmed, to clarify the mechanism of action of SMYAD.

CONCLUSION

Using metabonomics technology, it was predicted that the therapeutic effects of SMYAD were associated with its anti-oxidation as well as anti-inflammatory activities and the adjustment of the pyruvate, taurine as well as hypotaurine metabolism pathways in the hyperlipidemic state. This study provided evidence regarding the clinical application of SMYAD and thoroughly explored the mechanism underlying the action of this traditional Chinese medicine.

Simultaneous Determination of Three Alkaloids in Wutou Decoction in Rat Plasma Via the UPLC–MS/MS Method and its Application in Pharmacokinetic Study

Introduction:

Wutou decoction has been wildly applied for the treatment of RA in China for several thousand years.

Methods:

This study aims to develop a highly sensitive and specific ultra performance liquid chromatography coupled with tandem mass spectrometry and electrospray ionization (UPLC-ESI-MS/MS) method to explore the pharmacokinetic properties of three representative bioactive alkaloids after intragastric administration of Wutou decoction in rats. Chromatographic separation was performed on a C18 column under the Multiple Reaction Monitoring (MRM) in the positive electrospray ionization (ESI) mode. The pharmacokinetic parameters were evaluated by software DAS 3. 0.

Results:

The validation of the method was achieved in accordance with the FDA guidelines. The results of pharmacokinetic study showed that the in vivo concentrations of benzoylmesaconine and benzoylhypaconine were significantly higher than benzoylaconine. Our PK results showed that these three compounds were quickly absorbed after the administration of Wutou decoction, and Tmax ranged from 30 min to 45 min.

Conclusion:

The results of pharmacokinetic study showed that the in vivo concentrations of benzoylmesaconine and benzoylhypaconine were significantly higher than benzoylaconine. There were also similar pharmacokinetic behaviors observed among BAC, BHA, and BMA after oral administration of WTD.

Essential Oil Phytocomplex Activity, a Review with a Focus on Multivariate Analysis for a Network Pharmacology-Informed Phytogenomic Approach

Thanks to omic disciplines and a systems biology approach, the study of essential oils and phytocomplexes has been lately rolling on a faster track. While metabolomic fingerprinting can provide an effective strategy to characterize essential oil contents, network pharmacology is revealing itself as an adequate, holistic platform to study the collective effects of herbal products and their multi-component and multi-target mediated mechanisms. Multivariate analysis can be applied to analyze the effects of essential oils, possibly overcoming the reductionist limits of bioactivity-guided fractionation and purification of single components. Thanks to the fast evolution of bioinformatics and database availability, disease-target networks relevant to a growing number of phytocomplexes are being developed. With the same potential actionability of pharmacogenomic data, phytogenomics could be performed based on relevant disease-target networks to inform and personalize phytocomplex therapeutic application.

Omics strategies decipher therapeutic discoveries of traditional Chinese medicine against different diseases at multiple layers molecular-level

Traditional Chinese medicine (TCM) has been broadly used for the personalized treatment of many diseases in China for thousands of years. In the past century, TCM was also introduced to other Asian countries and even the Western world. Increasing evidence has shown that TCM has the capacity to treat numerous complex diseases in the clinic, such as cardiovascular diseases (CVDs), infectious diseases, metabolic diseases, and neurodegenerative diseases. However, the earlier lack of analytical strategies to annotate the chemical complexity has severely impeded the modern study and translational application of TCM. This critical review aims to explore and exploit applications of systems biology-driven omics methods in TCM against a diversity of diseases, toward the specific use of TCM to treat patients with different diseases. Such effort shall enhance the applicability of systems biology-driven omics strategies in deciphering the mechanisms by which TCM treats different diseases and may lead to the discovery of new therapeutic directions. In addition, we proposed the possible strategies to innovate the applicable pattern of omics technologies in TCM niches, such as precision-modification metabolomics and chinmedomics methods, allowing to unveil the complexity of TCM, which must enable TCM to serve better for the population-health. Taken together, this review eventually shall highlight the core value of omics technologies in innovating TCM to combat the diseases in a new horizon.

Bioinformatics-assisted, integrated omics studies on medicinal plants

The immense therapeutic and economic values of medicinal plants have attracted increasing attention from the worldwide researchers. It has been recognized that production of the authentic and high-quality herbal drugs became the prerequisite for maintaining the healthy development of the traditional medicine industry. To this end, intensive research efforts have been devoted to the basic studies, in order to pave a way for standardized authentication of the plant materials, and bioengineering of the metabolic pathways in the medicinal plants. In this paper, the recent advances of omics studies on the medicinal plants were summarized from several aspects, including phenomics and taxonomics, genomics, transcriptomics, proteomics and metabolomics. We proposed a multi-omics data-based workflow for medicinal plant research. It was emphasized that integration of the omics data was important for plant authentication and mechanistic studies on plant metabolism. Additionally, the computational tools for proper storage, efficient processing and high-throughput analyses of the omics data have been introduced into the workflow. According to the workflow, authentication of the medicinal plant materials should not only be performed at the phenomics level but also be implemented by genomic and metabolomic marker-based examination. On the other hand, functional genomics studies, transcriptional regulatory networks and protein-protein interactions will contribute greatly for deciphering the secondary metabolic pathways. Finally, we hope that our work could inspire further efforts on the bioinformatics-assisted, integrated omics studies on the medicinal plants.

The Recent Applications and Developments of Bioinformatics and Omics Technologies in Traditional Chinese Medicine

Background:

Traditional Chinese Medicine (TCM) is widely utilized as complementary health care in China whose acceptance is still hindered by conventional scientific research methodology, although it has been exercised and implemented for nearly 2000 years. Identifying the molecular mechanisms, targets and bioactive components in TCM is a critical step in the modernization of TCM because of the complexity and uniqueness of the TCM system. With recent advances in computational approaches and high throughput technologies, it has become possible to understand the potential TCM mechanisms at the molecular and systematic level, to evaluate the effectiveness and toxicity of TCM treatments. Bioinformatics is gaining considerable attention to unearth the in-depth molecular mechanisms of TCM, which emerges as an interdisciplinary approach owing to the explosive omics data and development of computer science. Systems biology, based on the omics techniques, opens up a new perspective which enables us to investigate the holistic modulation effect on the body.

Objective:

This review aims to sum up the recent efforts of bioinformatics and omics techniques in the research of TCM including Systems biology, Metabolomics, Proteomics, Genomics and Transcriptomics.

Conclusion:

Overall, bioinformatics tools combined with omics techniques have been extensively used to scientifically support the ancient practice of TCM to be scientific and international through the acquisition, storage and analysis of biomedical data.

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.

A billion cups: The diversity, traditional uses, safety issues and potential of Chinese herbal teas

ETHNOPHARMACOLOGICAL RELEVANCE

Herbal teas have long been consumed by Chinese people for preventive and/or therapeutic healthcare. Although herbal teas are widely consumed by many cultural groups in different regions of China, no thorough review has been undertaken to assess the diversity of the country's herbal tea usage. This literature review, complemented by a quantitative survey in an important tea market in Kunming, begins to fill this knowledge gap.

AIMS OF THE STUDY

The study aims to summarize the current knowledge of plant species used as herbal teas by different cultural groups in different regions of China, with a focus on the teas' perceived traditional healthcare functions, related phytochemical/pharmaceutical research, and safety issues.

MATERIALS AND METHODS

The study involved a comprehensive literature review and a market survey. The literature review was based on published ethnobotanical studies of herbal teas in China. We searched the Web of Science™, ELSEVIER, the China National Knowledge Infrastructure (CNKI) and the China Science and Technology Journal Database to locate relevant studies (including journal articles, Masters/PhD dissertations and books) that were published before March 2017. A species list was compiled based on the review and supplemented with information retrieved from the Scifinder database (https://scifinder.cas.org) and the Chinese Pharmacopoeia (2010). A Use Value Index was employed for ranking the most cited species. Based on the 29 most cited species, we discussed the current research status in relation to healthcare benefits and safety concerns of herbal teas in China. To better understand the current status of the herbal tea market in China, we also surveyed 136 tea vendors at the Xiongda Tea Market in Kunming. Information gathered from the survey included the species sold, the sale prices and the form of the herbal tea product.

RESULTS

The literature identified 759 plant species used as herbal tea in China and the market survey identified an additional 23 species. Most of the species used were from the Leguminosae, Compositae and Lamiaceae families. Twenty two provinces and fourteen ethnic minority groups have records on the consumption of herbal teas. Southern China uses up to 82% of the total species, and 211 out of 759 species are used by minority groups. Thirty categories of traditional healthcare functions are linked with herbal teas, with clearing away heat, relieving toxicity and suppressing cough being the most important functions. There is phytochemical/pharmaceutical evidence to support the claimed healthcare benefits of some Chinese herbal teas. Although Chinese herbal teas are generally safe to consume, overdoses of some herbal teas and some unapproved mixtures of species may cause health risks. Based on our market survey, the prices of most herbal teas range between 100 and 200 RMB (US$15-30) per kg.

CONCLUSIONS

A rich array of herbal tea species with various traditional healthcare functions have long been used in China, and as such there is a huge market potential for Chinese herbal teas. More pharmaceutical/phytochemical research is needed to assess a wide range of perceived healthcare benefits of Chinese herbal teas. Our research highlights the need to study herbal teas through an ethnopharmacological perspective and by employing a holistic approach, which requires greater consideration of traditional knowledge in the pharmacological research design. Product safety and sustainability issues should also be considered, so the traditional applications of herbal teas can be transformed to efficient health boosting functional products.

Cinnamon and Cassia Nomenclature Confusion: A Challenge to the Applicability of Clinical Data

Several Cinnamomum species' barks are generally labeled as cinnamon, although only Cinnamomum verum carries the common name of true cinnamon. Cassia, a common name for a related species, is rarely used on labels; instead, various cassia types may also be labeled "cinnamon." Confusion of true cinnamon and cassia spices in foods generally does not present a risk to health, except possibly at the highest intake levels. However, clinical studies with Cinnamomum investigational products have been published that inadequately describe or lack botanical identification information. The results of such studies are confounded by an inability to determine which species was responsible for the observed effects. Due to differences in the quality and composition of various Cinnamomum species, safety and efficacy data are not generalizable or transferable. Pharmacopeial monographs for characterizing the identity, composition, purity, quality, and strength of Cinnamomum investigational products should be applied to remove the ambiguity of cinnamon.

Dose-dependent target diversion of Danhong injection on the Glu-GLT-1/Gly-GlyRα dynamic balance module of cerebral ischemia

Function-oriented modular structure analysis is a great challenge in module-based pharmacological studies. A strategy to uncover target-target interaction (TTI) and dynamic balance regularity (DBR) was established to discover the structural factors influencing modular functions and explore the mechanism of Danhong injection (DHI) in treating cerebral ischemia. The dose-related metabolic features of DHI intervention were investigated using metabolomics and modular pharmacology. The findings indicated that Glu/Gly was a biomarker and Glu-GLT-1/Gly-GlyRα was the core unit regulated by DHI. Gly and Glu displayed opposite patterns and functional roles, representing intra-modular balance. GlyRα was identified as the upstream target and GLT-1 as the downstream target by inhibiting or activating GlyRα, indicating that DHI has two dose-dependent regulatory modes. GlyRα was the major target at low doses, while GLT-1 was activated as the dominant target as doses accumulated. Our study reveals that target-target interaction and dynamic balance regularity are the key factors influencing modular functions, which is a promising breakthrough for module-based pharmacological studies.

Botany, ethnomedicines, phytochemistry and pharmacology of Himalayan paeony (Paeonia emodi Royle.)

ETHNOPHARMACOLOGICAL RELEVANCE

Himalayan paeony (Paeonia emodi Royle.) is an important species used to treat various diseases. This study aimed to compile the detailed traditional medicinal uses, phytochemistry, pharmacology and toxicological investigations on P. emodi. This study also highlights taxonomic validity, quality of experimental designs and shortcomings in previously reported information on Himalayan paeony.

METHODS

The data was extracted from unpublished theses (Pakistan, China, India and Nepal), and different published research articles confined to pharmacology, phytochemistry and antimicrobial activities using different databases through specific keywords. The relevant information regarding medicinal uses, taxonomic/common names, part used, collection and identification source, authentication, voucher specimen number, plant extracts and their characterization, isolation and identification of phytochemicals, methods of study in silico, in vivo or in vitro, model organism used, dose and duration, minimal active concentration, zone of inhibition (antimicrobial study), bioactive compound(s), mechanism of action on single or multiple targets, and toxicological information.

RESULTS

P. emodi is reported for diverse medicinal uses with pharmacological properties like antioxidant, nephroprotective, lipoxygenase inhibitory, cognition and oxidative stress release, cytotoxic, anti-inflammatory, antiepileptic, anticonvulsant, haemaglutination, alpha-chymotrypsin inhibitory, hepatoprotective, hepatic chromes and pharmacokinetics of carbamazepine expression, β-glucuronidase inhibitory, spasmolytic and spasmogenic, and airway relaxant. Data confined to its taxonomic validity, shows 10% studies with correct taxonomic name while 90% studies with incorrect taxonomic, pharmacopeial and common names. The literature reviewed, shows lack of collection source (11 reports), without proper source of identification (15 reports), 33 studies without voucher specimen number, 26 reports lack information on authentic herbarium submission and most of the studies (90%) without validation of taxonomic names using recognized databases. In reported methods, 67% studies without characterization of extracts, 25% lack proper dose, 40% without duration and 31% reports lack information on proper controls. Similarly, only 18% studies reports active compound(s) responsible for pharmacological activities, 14% studies show minimal active concentration, only 2.5% studies report mechanism of action on target while none of the reports mentioned in silico approach.

CONCLUSION

P. emodi is endemic to Himalayan region (Pakistan, China, India and Nepal) with diverse traditional therapeutic uses. Majority of reviewed studies showed confusion in its taxonomic validity, incomplete methodologies and ambiguous findings. Keeping in view the immense uses of P. emodi in various traditional medicinal systems, holistic pharmacological approaches in combination with reverse pharmacology, system biology, and "omics" technologies are recommended to improve the quality of research which leads to natural drug discovery development at global perspectives.

Natural Products for Drug Discovery in the 21st Century: Innovations for Novel Drug Discovery

The therapeutic properties of plants have been recognised since time immemorial. Many pathological conditions have been treated using plant-derived medicines. These medicines are used as concoctions or concentrated plant extracts without isolation of active compounds. Modern medicine however, requires the isolation and purification of one or two active compounds. There are however a lot of global health challenges with diseases such as cancer, degenerative diseases, HIV/AIDS and diabetes, of which modern medicine is struggling to provide cures. Many times the isolation of "active compound" has made the compound ineffective. Drug discovery is a multidimensional problem requiring several parameters of both natural and synthetic compounds such as safety, pharmacokinetics and efficacy to be evaluated during drug candidate selection. The advent of latest technologies that enhance drug design hypotheses such as Artificial Intelligence, the use of 'organ-on chip' and microfluidics technologies, means that automation has become part of drug discovery. This has resulted in increased speed in drug discovery and evaluation of the safety, pharmacokinetics and efficacy of candidate compounds whilst allowing novel ways of drug design and synthesis based on natural compounds. Recent advances in analytical and computational techniques have opened new avenues to process complex natural products and to use their structures to derive new and innovative drugs. Indeed, we are in the era of computational molecular design, as applied to natural products. Predictive computational softwares have contributed to the discovery of molecular targets of natural products and their derivatives. In future the use of quantum computing, computational softwares and databases in modelling molecular interactions and predicting features and parameters needed for drug development, such as pharmacokinetic and pharmacodynamics, will result in few false positive leads in drug development. This review discusses plant-based natural product drug discovery and how innovative technologies play a role in next-generation drug discovery.

Integrated metabonomic-proteomic studies on blood enrichment effects of Angelica sinensis on a blood deficiency mice model

CONTEXT

Angelica sinensis (Oliv.) Diels (Umbelliferae) (AS) is a well-known Traditional Chinese Medicine (TCM) that enriches and regulates the blood.

OBJECTIVE

An integrated metabonomic and proteomic method was developed and applied to study the blood enrichment effects and mechanisms of AS on blood deficiency (BD) mouse model.

MATERIALS AND METHODS

Forty mice were randomly divided into the control, BD, High-dose of AS (ASH), Middle-dose of AS (ASM), and Low-dose of AS (ASL) groups. BD model mice were established by injecting N-acetylphenylhydrazine (APH) and cyclophosphamide (CTX) (ip). The aqueous extract of AS was administered at three dose of 20, 10, or 5 g/kg b. wt. orally for 7 consecutive days before/after APH and CTX administration. Gas chromatography-mass spectrometry (GC-MS) combined with pattern recognition method and 2D gel electrophoresis (2-DE) proteomics were performed in this study to discover the underlying hematopoietic regulation mechanisms of AS on BD mouse model.

RESULTS

Unlike in the control group, the HSP90 and arginase levels increased significantly (p < 0.05) in the BD group, but the levels of carbonic anhydrase, GAPDH, catalase, fibrinogen, GSTP, carboxylesterase and hem binding protein in the BD group decreased significantly (p < 0.05). Unlike the levels in the BD group, the levels of these biomarkers were regulated to a normal state near the control group in the ASM group. Unlike in the control group, l-alanine, arachidonic acid, l-valine, octadecanoic acid, glycine, hexadecanoic acid, l-threonine, butanoic acid, malic acid, l-proline and propanoic acid levels increased significantly (p < 0.05) in the BD group, the levels of d-fructose in the BD group decreased significantly (p < 0.05). The relative concentrations of 12 endogenous metabolites were also significantly affected by the ASL, ASM, and ASH treatments. Notably, most of the altered BD-related metabolites were restored to normal state after ASM administration.

CONCLUSION

AS can promote hematopoietic activities, inhibit production of reactive oxygen species, regulate energy metabolism, increase antiapoptosis, and potentially contribute to the blood enrichment effects of AS against APH- and CTX-induced BD mice.

Differences in Chemical Component and Anticancer Activity of Green and Ripe Forsythiae Fructus

Forsythiae Fructus, Lianqiao in Chinese, is one of the most fundamental herbs in Traditional Chinese Medicine. Both green Forsythia (GF) and ripe Forsythia (RF) are referred to Forsythiae Fructus in medicinal applications. In most cases, they are used without distinction. In this study, a metabolomics approach was performed to compare componential differences of two Forsythiae Fructus aqueous extracts subtypes. Principal component analysis (PCA) score plots from the UPLC-MS data showed clear separation between the two subtypes, indicating there are significant differences in the chemical components between GF and RF. Meanwhile, the anticancer activity of them was also compared. GF exhibited much stronger antitumor activity than RF against B16-F10 murine melanoma both in vitro and in vivo. 15 chemical compounds were identified as specific markers for distinguishing GF and RF. Among these marker compounds, forsythoside I, forsythoside A, forsythoside E and pinoresinol were demonstrated to be key important active compounds that account for the different anticancer efficacies of GF and RF. Our data suggest that GF and RF should be distinctively used in clinical applications, particularly in the anticancer formulas, in which GF should be preferentially prescribed.

Human Adenocarcinoma Cell Line Sensitivity to Essential Oil Phytocomplexes from Pistacia Species: a Multivariate Approach

Principal component analysis (PCA) multivariate analysis was applied to study the cytotoxic activity of essential oils from various species of the Pistacia genus on human tumor cell lines. In particular, the cytotoxic activity of essential oils obtained from P. lentiscus, P. lentiscus var. chia (mastic gum), P. terebinthus, P. vera, and P. integerrima, was screened on three human adenocarcinoma cell lines: MCF-7 (breast), 2008 (ovarian), and LoVo (colon). The results indicate that all the Pistacia phytocomplexes, with the exception of mastic gum oil, induce cytotoxic effects on one or more of the three cell lines. PCA highlighted the presence of different cooperating clusters of bioactive molecules. Cluster variability among species, and even within the same species, could explain some of the differences seen among samples suggesting the presence of both common and species-specific mechanisms. Single molecules from one of the most significant clusters were tested, but only bornyl-acetate presented cytotoxic activity, although at much higher concentrations (IC₅₀ = 138.5 µg/mL) than those present in the essential oils, indicating that understanding of the full biological effect requires a holistic vision of the phytocomplexes with all its constituents.