Network pharmacology-based research uncovers cold resistance and thermogenesis mechanism of Cinnamomum cassia

Therapeutic Potential of Salvia miltiorrhiza Root Extract in Alleviating Cold-Induced Immunosuppression

The interaction between environmental stressors, such as cold exposure, and immune function significantly impacts human health. Research on effective therapeutic strategies to combat cold-induced immunosuppression is limited, despite its importance. In this study, we aim to investigate whether traditional herbal medicine can counteract cold-induced immunosuppression. We previously demonstrated that cold exposure elevated immunoglobulin G (IgG) levels in mice, similar to the effects of intravenous immunoglobulin (IVIg) treatments. This cold-induced rise in circulating IgG was mediated by the renin-angiotensin-aldosterone system and linked to vascular constriction. In our mouse model, the cold-exposed groups (4 °C) showed significantly elevated plasma IgG levels and reduced bacterial clearance compared with the control groups maintained at room temperature (25 °C), both indicative of immunosuppression. Using this model, with 234 mice divided into groups of 6, we investigated the potential of tanshinone IIA, an active compound in Salvia miltiorrhiza ethanolic root extract (SMERE), in alleviating cold-induced immunosuppression. Tanshinone IIA and SMERE treatments effectively normalized elevated plasma IgG levels and significantly improved bacterial clearance impaired by cold exposure compared with control groups injected with a vehicle control, dimethyl sulfoxide. Notably, bacterial clearance, which was impaired by cold exposure, showed an approximately 50% improvement following treatment, restoring immune function to levels comparable to those observed under normal temperature conditions (25 °C, p < 0.05). These findings highlight the therapeutic potential of traditional herbal medicine in counteracting cold-induced immune dysregulation, offering valuable insights for future strategies aimed at modulating immune function in cold environments. Further research could focus on isolating tanshinone IIA and compounds present in SMERE to evaluate their specific roles in mitigating cold-induced immunosuppression.

Comprehensive Transcriptome and Proteome Analyses Reveal the Drought Responsive Gene Network in Potato Roots

The root system plays a decisive role in the growth and development of plants. The water requirement of a root system depends strongly on the plant species. Potatoes are an important food and vegetable crop grown worldwide, especially under irrigation in arid and semi-arid regions. However, the expected impact of global warming on potato yields calls for an investigation of genes related to root development and drought resistance signaling pathways in potatoes. In this study, we investigated the molecular mechanisms of different drought-tolerant potato root systems in response to drought stress under controlled water conditions, using potato as a model. We analyzed the transcriptome and proteome of the drought-sensitive potato cultivar Atlantic (Atl) and the drought-tolerant cultivar Qingshu 9 (Q9) under normal irrigation (CK) and weekly drought stress (D). The results showed that a total of 14,113 differentially expressed genes (DEGs) and 5596 differentially expressed proteins (DEPs) were identified in the cultivars. A heat map analysis of DEGs and DEPs showed that the same genes and proteins in Atl and Q9 exhibited different expression patterns under drought stress. Weighted gene correlation network analysis (WGCNA) showed that in Atl, Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG)-enriched pathways were related to pyruvate metabolism and glycolysis, as well as cellular signaling and ion transmembrane transporter protein activity. However, GO terms and KEGG-enriched pathways related to phytohormone signaling and the tricarboxylic acid cycle were predominantly enriched in Q9. The present study provides a unique genetic resource to effectively explore the functional genes and uncover the molecular regulatory mechanism of the potato root system in response to drought stress.

Mechanism of action of Coptidis Rhizome in treating periodontitis based on network pharmacology and in vitro validation

OBJECTIVE

Explore the therapeutic mechanism of Coptidis Rhizome (CR) in periodontitis using network pharmacology, and validate it through molecular docking and in vitro experiments.

METHODS

Screened potential active components and target genes of CR from TCMSP and Swiss databases. Identified periodontitis-related target genes using GeneCards. Found common target genes using Venny. Conducted GO and KEGG pathway analysis. Performed molecular docking and in vitro experiments using Berberine, the main active component of CR, on lymphocytes from healthy and periodontitis patients. Assessed effects on inflammatory factors using CCK-8, flow cytometry, and ELISA.

RESULTS

Fourteen active components and 291 targets of CR were identified. 30 intersecting target genes with periodontitis were found. GO and KEGG analysis revealed oxidative stress response and IL-17 signaling pathway as key mechanisms. Molecular docking showed strong binding of Berberine with ALOX5, AKT1, NOS2, and TNF. In vitro experiments have demonstrated the ability of berberine to inhibit the expression of Th17 + and other immune related cells in LPS stimulated lymphocytes, and reduce the secretion of IL-6, IL-8, and IL-17.

CONCLUSION

CR treats periodontitis through a multi-component, multi-target, and multi-pathway approach. Berberine, its key component, acts through the IL-17 signaling pathway to exert anti-inflammatory effects.

Network pharmacology integrated with molecular docking reveals the anticancer mechanism of Jasminum sambac Linn. essential oil against human breast cancer and experimental validation by in vitro and in vivo studies

Jasminum sambac L. (J. sambac) belongs to the family Oleaceae and it is an ornamental subtropical evergreen shrub used in traditional treatments of certain ailments and diseases. This study aimed at devising an integrated strategy attempts to evaluate the bioactive components in the J. sambac essential oil (JEO) against human breast cancer. JEO extracted by distillation process and analyzed by GC-MS was subjected to screening of therapeutic components in their allegiance to the drug-likeness index. The utility and efficacy of its molecular mechanism relating to anticancer potential were probed with network pharmacology analysis. Gene ontology, pathway enrichment, and compound-target-pathway network by Cytoscape helped to harp on hub targets and pathways involved in curative action. Drawing from the network data, molecular docking analysis of selected compounds on breast cancer targets was approached. The anti-proliferative study was carried out in MCF-7 and MDA-MB-231 to evaluate the cytotoxicity of JEO. Finally, in vivo anticancer activity was verified using rat models. The results showed MDA-MB-231 cell growth was highly inhibited than the MCF-7 cell line. Alongside this in vitro trial, in situ effectiveness of JEO was evaluated using female Sprague-Dawley rat animal models. In vivo experiments and histopathological analysis showed convincing results in DMBA tumor-induced rats. The larger aim of this study is to identify the potential ingredients of the JEO in cancer apoptosis by integrating network pharmacology and experimental validation achieved to certain extent confers credence to the concept of hiring J. sambac as floral therapy in dealing with the disastrous disease.

Prospects for the application of traditional Chinese medicine network pharmacology in food science research

There has always been a particular difficulty with in-depth research on the mechanisms of food nutrition and bioactivity. The main function of food is to meet the nutritional needs of the human body, rather than to exert a therapeutic effect. Its relatively modest biological activity makes it difficult to study from the perspective of general pharmacological models. With the popularity of functional foods and the concept of dietary therapy, and the development of information and multi-omics technology in food research, research into these mechanisms is moving towards a more microscopic future. Network pharmacology has accumulated nearly 20 years of research experience in traditional Chinese medicine (TCM), and there has been no shortage of work from this perspective on the medicinal functions of food. Given the similarity between the concept of 'multi-component-multi-target' properties of food and TCM, we think that network pharmacology is applicable to the study of the complex mechanisms of food. Here we review the development of network pharmacology, summarize its application to 'medicine and food homology', and propose a methodology based on food characteristics for the first time, demonstrating its feasibility for food research. © 2023 Society of Chemical Industry.

An inhibitor with GSK3β and DYRK1A dual inhibitory properties reduces Tau hyperphosphorylation and ameliorates disease in models of Alzheimer's disease

Since Alzheimer's disease (AD) is a complex and multifactorial neuropathology, the discovery of multi-targeted inhibitors has gradually demonstrated greater therapeutic potential. Neurofibrillary tangles (NFTs), the main neuropathologic hallmarks of AD, are mainly associated with hyperphosphorylation of the microtubule-associated protein Tau. The overexpression of GSK3β and DYRK1A has been recognized as an important contributor to hyperphosphorylation of Tau, leading to the strategy of using dual-targets inhibitors for the treatment of this disorder. ZDWX-12 and ZDWX-25, as harmine derivatives, were found good inhibition on dual targets in our previous study. Here, we firstly evaluated the inhibition effect of Tau hyperphosphorylation using two compounds by HEK293-Tau P301L cell-based model and okadaic acid (OKA)-induced mouse model. We found that ZDWX-25 was more effective than ZDWX-12. Then, based on comprehensively investigations on ZDWX-25 in vitro and in vivo, 1) the capability of ZDWX-25 to show a reduction in phosphorylation of multiple Tau epitopes in OKA-induced neurodegeneration cell models, and 2) the effect of reduction on NFTs by 3xTg-AD mouse model under administration of ZDWX-25, an orally bioavailable, brain-penetrant dual-targets inhibitor with low toxicity. Our data highlight that ZDWX-25 is a promising drug for treating AD.

Natural Active Ingredients and TRPV1 Modulation: Focus on Key Chemical Moieties Involved in Ligand-Target Interaction

Diseases such as cancer, neurological pathologies and chronic pain represent currently unmet needs. The existing pharmacotherapeutic options available for treating these conditions are limited by lack of efficiency and/or side effects. Transient receptor potential vanilloid 1 ion channel emerged as an attractive therapeutic target for developing new analgesic, anti-cancer and antiepileptic agents. Furthermore, various natural ingredients were shown to have affinity for this receptor. The aim of this narrative review was to summarize the diverse natural scaffolds of TRPV1 modulators based on their agonistic/antagonistic properties and to analyze the structure-activity relationships between the ligands and molecular targets based on the results of the existing molecular docking, mutagenesis and in vitro studies. We present here an exhaustive collection of TRPV1 modulators grouped by relevant chemical features: vanilloids, guaiacols, phenols, alkylbenzenes, monoterpenes, sesquiterpenoids, alkaloids, etc. The information herein is useful for understanding the key structural elements mediating the interaction with TRPV1 and how their structural variation impacts the interaction between the ligand and receptor. We hope this data will contribute to the design of novel effective and safe TRPV1 modulators, to help overcome the lack of effective therapeutic agents against pathologies with high morbidity and mortality.

Transcriptomics integrated with widely targeted metabolomics reveals the cold resistance mechanism in Hevea brasiliensis

The rubber tree is the primary source of natural rubber and is mainly cultivated in Southeast Asian countries. Low temperature is the major abiotic stress affecting the yield of the rubber tree. Therefore, uncovering the cold resistance mechanism in the rubber tree is necessary. The present study used RNA-sequencing technology and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) to analyze the transcriptomic and metabolomic changes in two rubber tree clones with different cold resistance capacities (temperature-sensitive Reyan 8-79 and cold-resistant Yunyan 77-4) at 0 h, 2 h, 6 h, and 20 h of exposure to 4°C. Independent analysis of the transcriptome and metabolitome showed that under prolonged low-temperature treatment, Yunyan 77-4 expressed more genes involved in regulating enzyme activity, changing cell permeability, and synthesizing significant metabolites, such as flavonoids and amino acids, than Reyan 8-79. The KEGG annotation and enrichment analysis identified arginine metabolism and biosynthesis of flavonoids as the major pathway associated with cold resistance. Integrated transcriptome and metabolome analysis showed that the increase in the expression of genes modulated flavonoid biosynthesis, arginine biosynthesis, and anthocyanins biosynthesis, resulting in higher levels of metabolites, such as naringenin chalcone, apigenin, dihydroquercetin, cyanidin 3-glucoside, L-arginosuccinate, N-acetyl-ornithine, ornithine, and N-acetyl-glutamate, in Yunyan 77-4 than in Reyan 8-79 after prolonged low-temperature treatment. Phylogenetic analysis identified the genes, such as CHS (gene356) and F3H (gene33147) of flavonoid biosynthesis and NAGS (gene16028, gene33765), ArgC (gene2487), and ASS (gene6161) of arginine biosynthesis were the key genes involved in the cold resistant of rubber tree. Thus, the present study provides novel insights into how rubber clones resist cold and is a valuable reference for cold-resistance breeding.

Network pharmacology approach and molecular docking to explore the potential mechanism of Wu-Wei-Wen-Tong Chubi capsules in rheumatoid arthritis

Network pharmacology, a holistic approach based on the theory of biological network technology, integrates information from biological systems, drugs, and diseases. Here, this theory was used to predict the targets of Wu-Wei-Wen-Tong Chubi capsule (WWWT) to explore the mechanism in the treatment of rheumatoid arthritis (RA). The ingredients of each herbal medicine in WWWT were collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), and the active ingredients were screened through bioavailability (OB) ≥30% and drug-likeness (DL) ≥ 0.18. SwissTargetPrection and TCMSP were utilized to calculate and predict the targets of active ingredients. RA-related targets were obtained by searching the Genecards and OMIM databases. The common targets of RA and WWWT were used for gene ontology (GO), KEGG pathway enrichment, protein-protein interaction (PPI) analysis, and molecular docking. And then, four key genes were screened for subsequent verification experiments. In total, 90 active compounds and 330 potential targets of WWWT, 1310 targets of RA, and 135 intersection targets were found. Additionally, GO and pathway analysis identified 4610 significant GO terms and 147 significant KEGG pathways. Based on the PPI network, 11 key genes including IL-6, MMP-9, and TNF-α were screened out for molecular docking. Molecular docking showed that these key genes have good binding activities to active compounds of WWWT such as oroxylin a, kaempferol, and luteolin. Simultaneously, Western blot experimental validation demonstrated that the protein expressions of IL-6, MMP-9, TNF-α, and VEGFA significantly decreased after WWWT treatment. The mechanism of WWWT in treating RA involves multiple active compounds acting on multiple targets, and multiple pathways, which provides an important reference for further elucidation the mechanism and clinical applications of WWWT in the treatment of RA.

Impacts of Colored Light-Emitting Diode Illumination on the Reproductive Performance and Bioactive Constituents and the Molecular Mechanism of Hypothalamus Gland in Zi-geese

Goose is a seasonal breeding animal. Its reproduction is regulated by hypothalamus-pituitary-gonad axis and also affected by environmental factors such as light and location. Zi-goose is characterized with long egg-laying period and high egg-laying potential and belongs to the long-day type of seasonal breeding. In this study, the regulation mechanism of different lighting on reproductive performance of Zi-goose by using metabonomics analysis technology. In addition, 1,481 differential metabolites were screened out totally. 583 differential metabolites were identification in hypothalamus of Zi-goose. 196 differential metabolites were identification in pituitary of Zi-goose. 692 differential metabolites were identification in ovary of Zi-goose. Under red light condition for 12 h, expression of 433 differential metabolites were down-regulated and expression of 150 differential metabolites were up regulated in hypothalamus of Zi-goose, expression of 125 differential metabolites were down-regulated and expression of 71 differential metabolites were up-regulated in pituitary of Zi-goose, expression of 355 differential metabolites were down-regulated and expression of 337 differential metabolites were up-regulated in ovary of Zi-goose. 33 differential metabolites were closely associated with 1,264 transcripts and 400 homologous genes of related enzymes in hypothalamus of Zi-goose. 15 differential metabolites were closely associated with 163 transcripts and 47 homologous genes of related enzymes in pituitary of Zi-goose. 55 differential metabolites were closely associated with 1,255 transcripts and 360 homologous genes of related enzymes in ovary of Zi-goose. It was confirmed that four metabolic pathways were closely related to light regulation of reproductive performance of Zi-goose, namely GnRH signaling pathway, prolactin signaling pathway, thyroid hormone synthesis and ovarian steroidogenesis. Typical differential metabolites of arachidonic acid, glucose-6-phosphate, progesterone, glutathione, oxidized glutathione, testosterone, deoxyepiandrosterone and their related protein genes would play an important role in light regulation of reproductive performance of Zi-goose.

Quantitative Trait Locus Analysis and Identification of Candidate Genes Affecting Seed Size and Shape in an Interspecific Backcross Inbred Line Population of Gossypium hirsutum × Gossypium barbadense

Seed size and shape are key agronomic traits affecting seedcotton yield and seed quality in cotton (Gossypium spp.). However, the genetic mechanisms that regulate the seed physical traits in cotton are largely unknown. In this study, an interspecific backcross inbred line (BIL) population of 250 BC1F7 lines, derived from the recurrent parent Upland CRI36 (Gossypium hirsutum) and Hai7124 (Gossypium barbadense), was used to investigate the genetic basis of cotton seed physical traits via quantitative trait locus (QTL) mapping and candidate gene identification. The BILs were tested in five environments, measuring eight seed size and shape-related traits, including 100-kernel weight, kernel length width and their ratio, kernel area, kernel girth, kernel diameter, and kernel roundness. Based on 7,709 single nucleotide polymorphic (SNP) markers, a total of 49 QTLs were detected and each explained 2.91-35.01% of the phenotypic variation, including nine stable QTLs mapped in at least three environments. Based on pathway enrichment, gene annotation, genome sequence, and expression analysis, five genes encoding starch synthase 4, transcription factor PIF7 and MYC4, ubiquitin-conjugating enzyme E27, and THO complex subunit 4A were identified as candidate genes that might be associated with seed size and shape. Our research provides valuable information to improve seed physical traits in cotton breeding.

Kun-Dan Decoction Ameliorates Insulin Resistance by Activating AMPK/mTOR-Mediated Autophagy in High-Fat Diet-Fed Rats

Background: Metabolic syndrome is characterized by central obesity, hyperglycemia and hyperlipidemia. Insulin resistance is the leading risk factor for metabolic syndrome. Kun-Dan decoction (KD), a traditional Chinese medicine, has been applied to treat patients with metabolic syndrome for over ten years. It is increasingly recognized that autophagy deficiency is the key cause of metabolic syndrome. Therefore, we aimed to explore whether KD can activate autophagy to improve metabolic syndrome.

Methods: Network pharmacology was used to explore the underlying mechanism of KD in the treatment of metabolic syndrome. The high-fat diet-fed rats and oleic acid-induced LO2 cells were employed in our study. Oral glucose tolerance test and insulin tolerance test, obesity and histological examination, serum cholesterol, triglyceride, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), homeostasis model assessment of insulin resistance (HOMA-IR) and insulin sensitivity in high-fat diet-fed rats were analyzed. Furthermore, the protein expressions of adenosine 5'-monophosphate (AMP)-activated protein kinase (AMPK), phospho-AMPK, mammalian target of rapamycin (mTOR), phospho-mTOR, p62, autophagy related protein (Atg) 5, Atg7, Atg12, Atg13, Atg16L1 and microtubule-associated protein 1A/1B-light chain 3 (LC3)-Ⅱ/Ⅰ were examined in rats and LO2 cells. Moreover, autophagy activator rapamycin and inhibitor 3-methyladenine, and small interfering RNA against Atg7 were utilized to verify the role of autophagy in the treatment of metabolic syndrome by KD in oleic acid-induced LO2 cells.

Results: Results from network pharmacology indicated that targeted insulin resistance might be the critical mechanism of KD in the treatment of metabolic syndrome. We found that KD significantly suppressed obesity, serum cholesterol, triglyceride and LDL-C levels and increased serum HDL-C level in high-fat diet-fed rats. Furthermore, KD enhanced insulin sensitivity and attenuated HOMA-IR in high-fat diet-fed rats. Western blot showed that KD could enhance autophagy to increase the insulin sensitivity of high-fat diet-fed rats and oleic acid-induced LO2 cells. Furthermore, 3-methyladenine and small interfering RNA against Atg7 could reverse the protective effect of KD on LO2 cells. However, rapamycin could cooperate with KD to enhance autophagic activation to increase insulin sensitivity in LO2 cells.

Conclusion: The induction of autophagy may be the major mechanism for KD to improve insulin resistance and metabolic syndrome.