DNA Microarray-Based Screening and Characterization of Traditional Chinese Medicine. Microarrays (Basel). 2017;6:4. [PMID: 28146102 PMCID: PMC5374364 DOI: 10.3390/microarrays6010004]

Wild Mushrooms: A Hidden Treasure of Novel Bioactive Compounds

Secondary metabolites are hidden gems in mushrooms. Understanding these secondary metabolites' biological and pharmacological effects can be aided by identifying them. The purpose of this work was to profile the mycochemical components of the extracts of Auricularia auricula judae, Microporus xanthopus, Termitomyces umkowaani, Trametes elegans, and Trametes versicolor to comprehend their biological and pharmacological capabilities. Mushroom samples were collected from Kenya's Arabuko-Sokoke and Kakamega National Reserved Forests and identified using morphological and molecular techniques. Chloroform, 70% ethanol, and hot water solvents were used to extract the mycochemical components. Gas chromatography mass spectrometry (GC-MS) was used to analyze the chloroform, 70% ethanol, and hot water extracts of all the species examined. A total of 51 compounds were isolated from all extracts and classified as carboxylic acids, esters, phenols, fatty acids, alcohol, epoxides, aldehydes, fatty aldehydes, isoprenoid lipids, and steroids. Tetracosamethyl-cyclododecasiloxane (18.90%), oleic acid (72.90%), phenol, 2, 6-bis (1, 1-dimethylethyl)-4-methyl-, and methylcarbamate (26.56%) were all found in high concentrations in A. auricular judae, M. xanthopus, T. umkowaani, T. elegans, and T. versicolor, respectively. Fatty acids make up the majority of the compounds isolated from the T. elegans chloroform extract and the T. umkowaani 70% ethanol extract, respectively. Particularly, these fatty acids play crucial roles in the anti-inflammatory, hypocholesterolemic, anticancer, and antibiofilm formation activities. These bioactive elements indicate that the extracts of five wild mushrooms may be reliable sources of secondary metabolites for therapeutic development. Therefore, additional research is required to comprehend the usefulness of these chemicals in many functional areas and to improve the present understanding of macrofungi.

Gongjin-Dan Enhances Neurite Outgrowth of Cortical Neuron by Ameliorating H2O2-Induced Oxidative Damage via Sirtuin1 Signaling Pathway

Gongjin-dan (GJD) is a multiherbal formula produced from 10 medicinal herbs and has been traditonally used as an oriental medicine to treat cardiovascular diseases, alcoholic hepatitis, mild dementia, and anemia. Additionally, increasing evidence suggests that GJD exerts neuroprotective effects by suppressing inflammation and oxidative stress-induced events to prevent neurological diseases. However, the mechanism by which GJD prevents oxidative stress-induced neuronal injury in a mature neuron remains unknown. Here, we examined the preventive effect and mechanism of GJD on primary cortical neurons exposed to hydrogen peroxide (H2O2). In the neuroprotection signaling pathway, Sirtuin1 is involved in neuroprotective action as a therapeutic target for neurological diseases. After pre-treatment with GJD at three concentrations (10, 25, and 50 µg/mL) and stimulation by H2O2 (30 µM) for 24 h, the influence of GJD on Sirtuin1 activation was assessed using immunocytochemistry, real-time PCR, western blotting, and flow cytometry. GJD effectively ameliorated H2O2-induced neuronal death against oxidative damage through Sirtuin1 activation. In addition, GJD-induced Sirtuin1 activation accelerated elongation of new axons and formation of synapses via increased expression of nerve growth factor and brain-derived neurotrophic factor, as well as regeneration-related genes. Thus, GJD shows potential for preventing neurological diseases via Sirtuin1 activation.

Protective effect and mechanisms of action of Mongolian medicine Sulongga-4 on pyloric ligation-induced gastroduodenal ulcer in rats

BACKGROUND

Sulongga-4 (SL-4) is a herbal formula used in traditional Mongolian medical clinics for the treatment of peptic ulcers and gastroenteritis, even though its pharmacological mechanism has not been well characterized.

AIM

To evaluate the protective effect and identify the mechanisms of action of SL-4 on gastroduodenal ulcer induced by pyloric ligation (PL) in rats.

METHODS

PL was performed to induce gastric and duodenal ulcers in rats, which were then treated with oral SL-4 (1.3, 2.6, or 3.9 g/kg per day) for 15 d. PL-induced gastroduodenal ulceration. Therapeutic effects were characterized by pathological and histological evaluations and inflammatory indicators were analyzed by enzyme-linked immunosorbent assay. Microarray analyses were conducted to identify gene expression profiles of gastroduodenal tissue in PL rats with or without SL-4 treatment. The candidate target genes were selected and verified by quantitative reverse transcription polymerase chain reaction (qRT-PCR).

RESULTS

SL-4 decreased histopathological features in the PL-induced ulcerated rats. SL-4 significantly (P < 0.05) decreased expression of tumor necrosis factor-α, interleukin (IL)-1β, IL-6, endotoxin, platelet-activating factor, and increased prostaglandin E2 and epidermal growth factor in ulcer tissue. Microarray analysis was used to identify a panel of candidate target genes for SL-4 acting on PL-induced ulceration. Genes included some complement and coagulation cascade and retinol metabolism pathways that are closely associated with inflammatory responses and gastric mucosal protective mechanisms. qRT-PCR showed that altered expression of the selected genes, such as CYP2b2, UGT2b1, A2m, and MASP1 was consistent with the microarray results.

CONCLUSION

SL-4 exerts protective effects against PL-induced gastroduodenal ulcers via reducing inflammatory cytokines and elevating expression of gastric acid inhibitory factors. Downregulation of CYP2b2 and UGT2b1 genes in retinol metabolism and upregulation of A2m and MASP1 genes in the complement and coagulation cascades pathways are possibly involved in SL-4-mediated protection against gastroduodenal ulcer.

Stepwise rapid tracking strategy to identify active molecules from Ixeris sonchifolia Hance based on "'affinity mass spectrometry-atomic force microscopy imaging'" technology

In this study, a novel stepwise rapid tracking strategy was reported to identify the active molecules from Ixeris sonchifolia Hance (IsH) in the treatment of coronary heart disease (CHD) based on "affinity mass spectrometry (MS)-atomic force microscopy (AFM) imaging" technology. First, vascular endothelial growth factor receptor 2 (VEGFR2) of the vascular endothelial growth factor (VEGF) signal transduction pathway located on the cell membrane was revealed to be the core target protein in CHD treatment through network pharmacology and bioinformatics. In addition, affinity MS screening based on VEGFR2 identified isochlorogenic acid A and luteolin-7-O-glucuronide as having stronger affinity with VEGFR2. Then, the active molecule was elucidated based on the observation that its actions accompanied the molecular morphological changes by AFM imaging and it could act on the binding pocket of VEGFR2 through molecular docking which further demonstrated the analysis and inference of AFM imaging. The methyl thiazolyl tetrazolium (MTT) assay finally confirmed that the active molecules specifically combined with the potential core target protein to protect the viability of cardiomyocytes, which identified the main potential active molecules in IsH for the treatment of CHD and provided a possible mechanism for the protective role of the drug. The technology established in this study could facilitate the rapid tracing of potential active molecules in traditional Chinese medicine (TCM), which would provide further a reference for research on quality, molecular mechanisms and new drugs.

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.

Microarray analysis of genes from animals treated with a traditional formulation ChandraprabhaVati reveals its therapeutic targets

Background

Traditional medicinal preparations have not received global acceptance, and their therapeutic benefits remain disputed due to lack of scientific evidence on their mechanism of action. Microarray analysis has emerged as a powerful technique that can aid in understanding the complex signaling networks activated by these formulations and thereby assess their beneficial as well as adverse effects.

Aim

The present work aims to investigate the differential influence of ChandraprabhaVati, Ayurvedic formulation used in the treatment of diabetes, anemia, urinary, respiratory, skin and liver disorders.

Materials and methods

The RNA from the liver of rats treated with different doses of ChandraprabhaVati for 28 days was isolated and studied for the genome-wide changes in the expression.

Results

The results revealed several molecular targets that could contribute to the therapeutic effects of ChandraprabhaVati. Several genes have been differentially expressed, among those miRNAs miR-434, miR877, and miRlet7e contribute to the anti-diabetic, anti-fibrotic and anti-inflammatory of CPV. The rejuvenative activity of CPV may be due to the MeOX1 and Upf3b genes. Up-regulation of Hbaa2 gene facilitates the anti-anemic effect. Interestingly gender-specific differential expressions of genes were also observed. Rab3d were found to be altered in female when compared to male animals.

Conclusion

Thus the microarray data for the CPV treated animals has revealed molecular targets that may be responsible for the various known therapeutic effects and also identified new beneficial effects of CPV.

Estrogenic Activity of Coffee Constituents

Here, the constituents of coffee with estrogenic activity are summarized by a comprehensive literature search, and their mechanisms of action for their physiological effects are discussed at the molecular and cellular levels. The estrogenic activity of coffee constituents, such as acids, caramelized products, carbohydrates, lignin, minerals, nitrogenous compounds, oil (lipids), and others, such as volatile compounds, was first evaluated by activity assays, such as animal tests, cell assay, ligand-binding assay, protein assay, reporter-gene assay, transcription assay, and yeast two-hybrid assay. Second, the health benefits associated with the estrogenic coffee constituents, such as bone protection, cancer treatment/prevention, cardioprotection, neuroprotection, and the improvement of menopausal syndromes, were summarized, including their potential therapeutic/clinical applications. Inconsistent results regarding mixed estrogenic/anti-estrogenic/non-estrogenic or biphasic activity, and unbeneficial effects associated with the constituents, such as endocrine disruption, increase the complexity of the effects of estrogenic coffee constituents. However, as the increase of the knowledge about estrogenic cell signaling, such as the types of specific signaling pathways, selective modulations of cell signaling, signal crosstalk, and intercellular/intracellular networks, pathway-based assessment will become a more realistic means in the future to more reliably evaluate the beneficial applications of estrogenic coffee constituents.

Fabrication of paper-based enzyme immobilized microarray by 3D-printing technique for screening α-glucosidase inhibitors in mulberry leaves and lotus leaves

Background

The discovery of bioactive compounds in traditional Chinese medicine (TCM) has become an important field in TCM modernization. Ligand fishing is a suitable method for discovery of bioactive compounds in complex mixtures such as TCM with high selectivity. Because of unique advantage of low cost and convenience, paper-based microdevices can be good carriers for enzyme immobilized ligand fishing.

Methods

As an important enzyme for glucose metabolism, α-glucosidase was immobilized on polycaprolactone–chitosan-modified paper to prepare the microdevice with unique microfluid structure generated by 3D printing technology, which can be easily applied to screen active compounds in herbal extracts. The preparation conditions of the paper microarray were optimized. The activity of immobilized α-glucosidase was verified by colorimetric reactions which can be easily monitored by cellphone. The paper microarray with α-glucosidase immobilized was used to screen active compounds in the water extracts of mulberry leaves and lotus leaves.

Results

Several key parameters including Na₂CO₃ solution concentration, Na₂CO₃ solution volume, glutaraldehyde concentration, crosslinking time of glutaraldehyde and time of α-glucosidase immobilization were optimized. The proposed paper-based microarray was successfully applied in screening active compounds in two herbal extracts. Four compounds including chlorogenic acid, quercetin-3-O-glucuronide, isoquercetin, and quercetin were identified as α-glucosidase inhibitors. The compounds with significant non-specific adsorption caused by chitosan, such as isoquercitrin, astragalin, quercetin, were also found to be active compounds.

Conclusions

An enzyme immobilized paper microarray was designed and fabricated in this work. Polycaprolactone and chitosan were used to modify filter paper to prepare paper microarrays. Parameters of paper device preparation were optimized. Our findings suggested that 3D-printing paper-based microarrays can be a simple and low-cost approach for discovery of active compounds of TCM.

Electronic supplementary material

The online version of this article (10.1186/s13020-019-0236-y) contains supplementary material, which is available to authorized users.

Identification of differentially expressed non-coding RNAs and mRNAs involved in Qi stagnation and blood stasis syndrome

Qi stagnation and blood stasis syndrome (QSBSS) is a common Zheng in Traditional Chinese Medicine (TCM), describes the condition of unsmooth flow of Qi and blood, which manifests as distending pain in a fixed body part and emotional disorders, including irritability and depression. However, the underlying molecular mechanisms remain largely elusive. RNAs are the connection between DNA and proteins, which reflect the interaction between the genotypes and the phenotype. Of note, non-coding (nc)RNA is a type of RNA that is not translated into any protein, but has regulatory functions. Despite the growing interest in exploring the biological basis of TCM Zhengs, the specific roles of ncRNAs in QSBSS have remained largely elusive. In the present study, next-generation sequencing was performed to investigate the ncRNA profile in patients with three different types of disease, but who had QSBSS. A total of 104 long non-coding RNAs, 2 circular RNAs and 697 mRNAs were identified to be significantly differentially expressed in QSBSS patients. Further bioinformatics analysis revealed that the most significantly enriched pathways by the differentially expressed RNAs in QSBSS were the sphingolipid signaling pathway, the neurotrophin signaling pathway, 5′AMP-activated protein kinase and endocytosis. In addition, a network pharmacology analysis indicated that several of the differentially expressed RNAs were included in the targets of TCM herbs for treating QSBSS. The present study was the first to identify ncRNAs that are deregulated in QSBSS by next-generation sequencing technology. The results may offer insight into the biological basis of TCM Zheng and the optimization of ancient formulae, as well as the discovery of novel drugs, to pave the way toward advanced TCM theory and improved health care delivery.

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.

Estrogenic Potentials of Traditional Chinese Medicine

Estrogen, a steroid hormone, is associated with several human activities, including environmental, industrial, agricultural, pharmaceutical and medical fields. In this review paper, estrogenic activity associated with traditional Chinese medicines (TCMs) is discussed first by focusing on the assays needed to detect estrogenic activity (animal test, cell assay, ligand-binding assay, protein assay, reporter-gene assay, transcription assay and yeast two-hybrid assay), and then, their sources, the nature of activities (estrogenic or anti-estrogenic, or other types), and pathways/functions, along with the assay used to detect the activity, which is followed by a summary of effective chemicals found in or associated with TCM. Applications of estrogens in TCM are then discussed by a comprehensive search of the literature, which include basic study/pathway analysis, cell functions, diseases/symptoms and medicine/supplements. Discrepancies and conflicting cases about estrogenicity of TCM among assays or between TCM and their effective chemicals, are focused on to enlarge estrogenic potentials of TCM by referring to omic knowledge such as transcriptome, proteome, glycome, chemome, cellome, ligandome, interactome and effectome.