Label-free quantitative proteomics positions the effects and mechanisms of Herba Lysimachiae on synovial diseases based on biolabel-led research pattern

Combination of omics, bioinformatics, molecular docking, and experimental validation to elucidate the hepatoprotective effects, mechanisms, and active compounds of Shandougen

Omics, bioinformatics, molecular docking, and experimental validation were used to elucidate the hepatoprotective effects, mechanisms, and active compounds of Shandougen (SDG) based on the biolabel-led research pattern. Integrated omics were used to explore the biolabels of SDG intervention in liver tissue. Subsequently, bioinformatics and molecular docking were applied to topologically analyze its therapeutic effects, mechanisms, and active compounds based on biolabels. Finally, an animal model was used to verify the biolabel analysis results. Omics, bioinformatics, and molecular docking revealed that SDG may exert therapeutic effects on liver diseases in the multicompound and multitarget synergistic modes, especially liver cirrhosis. In the validation experiment, SDG and its active compounds (betulinic acid and gallic acid) significantly improved the liver histopathological damage in the CCl4-induced liver cirrhosis model. Meanwhile, they also produced significant inhibitory effects on the focal adhesion pathway (integrin alpha-1, myosin regulatory light chain 2, laminin subunit gamma-1, etc.) and alleviated the associated pathological processes: focal adhesion (focal adhesion kinase 1)-extracellular matrix (collagen alpha-1(IV) chain, collagen alpha-1(VI) chain, and collagen alpha-2(VI) chain) dysfunction, carcinogenesis (alpha-fetoprotein, NH3, and acetylcholinesterase), inflammation (tumor necrosis factor alpha, interleukin-1 [IL-1], IL-6, and IL-10), and oxidative stress (reactive oxygen species, malonaldehyde, and superoxide dismutase). This study provides new evidence and insights for the hepatoprotective effects, mechanisms, and active compounds of SDG.

Sophora tonkinensis and active compounds inhibit mitochondrial impairments, inflammation, and LDLR deficiency in myocardial ischemia mice through regulating the vesicle-mediated transport pathway

Ancient Chinese medicine literature and modern pharmacological studies show that Sophora tonkinensis Gagnep. (ST) has a protective effect on the heart. A biolabel research based on omics and bioinformatics and experimental validation were used to explore the application value of ST in the treatment of heart diseases. Therapeutic potential, mechanism of action, and material basis of ST in treating heart diseases were analyzed by proteomics, metabolomics, bioinformatics, and molecular docking. Cardioprotective effects and mechanisms of ST and active compounds were verified by echocardiography, HE and Masson staining, biochemical analysis, and ELISA in the isoproterenol hydrochloride-induced myocardial ischemia (MI) mice model. The biolabel research suggested that the therapeutic potential of ST for MI may be particularly significant among the heart diseases it may treat. In the isoprenaline hydrochloride-induced MI mice model, ST and its five active compounds (caffeic acid, gallic acid, betulinic acid, esculetin, and cinnamic acid) showed significant protective effects against echocardiographic changes and histopathological damages of the ischemic myocardial tissue. Meanwhile, they showed a tendency to correct mitochondrial structure and function damage and the abnormal expression of 12 biolables (DCTN1, DCTN3, and SCARB2, etc.) in the vesicle-mediated transport pathway, inflammatory cytokines (IL-1β, IL-6, and IL-10, etc.), and low density lipoprotein receptor (LDLR). The biolabel research identifies a new application value of ST in the treatment of heart diseases. ST and its active compounds inhibit mitochondrial impairments, inflammation, and LDLR deficiency through regulating the vesicle-mediated transport pathway, thus achieving the purpose of treating MI.

Biolabel-led research pattern reveals serum profile in rats after treatment with Herba Lysimachiae: Combined analysis of metabonomics and proteomics

In traditional Chinese medicine, Herba Lysimachiae (HL) is mainly used to treat rheumatic arthralgia. Current pharmacological studies also showed that HL has therapeutic potential for synovial diseases. HL is an oral drug, whose compounds need to enter the blood circulation before reaching the injured tissue, thus potentially causing activity or toxicity to the blood system. In this study, the biolabel-led research pattern was used to analyze the serum profile after HL intervention, based on which the safety and efficacy of HL were explored. Metabonomics and proteomics were combined to analyze the biolabels responsible for the interventions of HL on serum. Bioinformatics databases were used to screen for the material basis that may interfere with biolabels. Omics analysis showed that differentially expressed 19 proteins and 5 metabolites were identified and considered as the potential biolabels, which were involved in 8 biochemical processes (platelet activation and aggregation, blood glucose release, immune and inflammatory regulation, oxidative stress, endoplasmic reticulum stress, tumor progression, blood pressure regulation, and uric acid synthesis). Thirty-one compounds may be the material basis to interfere with eleven biolabels. The present research reveals that the potential activities and toxicities of HL can be explored based on the biolabel-led research pattern.

Biolabel-led research pattern positions the effects and mechanisms of Sophorae Tonkinensis radix et rhizome on lung diseases: A novel strategy for computer-aided herbal medicine research based on omics and bioinformatics

Previous studies have shown that Sophorae Tonkinensis radix et rhizome (ST) can be used to treat some lung diseases. However, the therapeutic potentials, therapeutic advantages, mechanism of action, and material basis of ST treatment of lung diseases remain unclear. Thus, the aim of this study was to carry out an integrated analysis based on the biolabel-led research pattern. Proteomics and metabonomics were applied to explore the biolabels responsible for the effect of ST on lung tissue. Based on the biolabels, a bioinformatics database was used to topologically analyze the therapeutic potentials, therapeutic advantages, mechanism of action, and material basis of ST in treating lung diseases. Four human lung-cancer cell models were used to validate the results of the biolabel analysis. In total, 45 proteins and 3 metabolites were significantly enriched in 13 pathways and were considered as biolabels. Bioinformatics revealed that the therapeutic potentials of ST involved a variety of lung diseases, especially lung neoplasms. Under the mediation of 40 biolabels, 29 compounds may be the material basis of ST in treating lung diseases. In a verification experiment, ST had a significant inhibitory effect on the H226 cell line (lung squamous cell carcinoma), which ranks first in morbidity and mortality among lung cancers in China. Additionally, five biolabels (CPS1, CKM, CPT1B, COX5B, and COX4I1) were involved in the anti-lung cancer mechanism of ST and 3 compounds (gallic acid, betulinic acid, and caffeic acid). These findings indicate that the biolabel-led research pattern was helpful in achieving the objectives of this study.

The active ingredients analysis of Herba Lysimachiae treating osteoarthritis based on the LC-MS/MS technology and public bioinformatics platforms

Herba Lysimachiae inhibits synovial damage in osteoarthritis via regulating two bio labels (integrin alpha 2b/beta 3). However, the relevant active ingredients are still unknown. Here, the active ingredients of herbal medicines were analyzed based on the liquid chromatography-tandem mass spectrometry technology and public bioinformatics platforms. The liquid chromatography-tandem mass spectrometry technology was used for compound analysis, and public databases (PubChem BioAssay and STRING) were applied to establish the links between herbal compounds and both bio labels, and identify which herbal compounds may regulate these bio labels. Subsequently, the osteoarthritis model was used to confirm the results. Totally, ninety compounds in Herba Lysimachiae were identified based on the liquid chromatography-tandem mass spectrometry technology. Bioinformatics analysis showed that five compounds (myricetin, fisetin, esculetin, 7-hydroxycoumarin-4-acetic acid, and caffeic acid) may synergistically regulate bio labels through 11 targets, which may be the active ingredients of Herba Lysimachiae for osteoarthritis treatment. In the verification experiments, five compounds markedly suppressed the overexpression of bio labels in the synovium of the osteoarthritis model. In conclusion, the present study effectively and rapidly analyzed the active ingredients of Herba Lysimachiae for osteoarthritis treatment.

A biolabel research based on metabonomics reveals the therapeutic potentials of Herba Lysimachiae in synovial diseases: The dual effects on synovial platelet aggregation by prostaglandin E1/E2

Previous research has demonstrated that Herba Lysimachiae (HL) exerts the dual effects on platelet aggregation in the synovium, which may contribute to its protection against synovial lesions under different situations. However, the mechanism is unclear. In the present experiment, a biolabel research based on metabonomics was used to mine the information about the intervention of HL on synovium at the metabolite level, which may help to analyze the regulation of HL on synovial platelet aggregation and its possible treatment in synovial diseases. Synovial metabolic profiling was analyzed using a Shimadzu Nexera UHPLC LC-30A system and an AB SCIEX Triple TOF 4600 mass spectrometer. Enzyme-linked immunosorbent assay (ELISA) was used to verify the biolabels analysis results in the healthy and osteoarthritis rats. Totally, thirteen common metabolites were differentially expressed after treating with HL, and implicated in 2 key pathways (arachidonic acid metabolism and glycerophospholipid metabolism). ELISA showed that HL regulated the expression of prostaglandins E1 and E2 in synovial tissues of the healthy and osteoarthritis rats. This study reveals that HL may regulate synovial platelet aggregation through prostaglandin E1/E2. Additionally, HL is suitable for treating synovial diseases, especially osteoarthritis, which may be associated with platelet aggregation, apoptosis, inflammation, angiogenesis, and carcinogenesis processes.

Integrated omics and bioinformatics analyses for the toxic mechanism and material basis of Sophorae Tonkinensis radix et rhizome-induced hepatotoxicity

In traditional Chinese medicine theory, Sophorae Tonkinensis radix et rhizome (ST) has the effects of treating tonsillitis, sore throats, and heat-evil-induced diseases. However, the utilization of ST is relatively restricted owing to its toxicity. The previous studies have made some progress on the mechanism and material basis of ST-induced hepatotoxicity, but there is still no significant breakthrough. In this study, integrated omics and bioinformatics analyses were used to investigate the mechanism and material basis of ST-induced hepatotoxicity. Integrated omics were used to analyze the differentially expressed proteins and metabolites, based on which the significantly dysregulated pathways were analyzed by using MetaboAnalyst. Bioinformatics was applied to screen the toxic targets and material basis. Integrated omics revealed that 254 proteins and 42 metabolites were differentially expressed after the treatment with ST, out of which 7 proteins were significantly enriched in 3 pathways. Bioinformatics showed that 20 compounds may interfere with the expression of 7 toxic targets of ST. Multiple toxic targets of ST-induced hepatotoxicity were found in the study, whose dysregulation may trigger hepatocyte necrosis/apoptosis, liver metastasis, and liver cirrhosis. Multiple compounds may be the toxic material basis in response to these effects.

Recent advance in treatment of osteoarthritis by bioactive components from herbal medicine

Osteoarthritis (OA) is a common chronic articular degenerative disease, and characterized by articular cartilage degradation, synovial inflammation/immunity, and subchondral bone lesion, etc. The disease affects 2-6% of the population around the world, and its prevalence rises with age and exceeds 40% in people over 70. Recently, increasing interest has been devoted to the treatment or prevention of OA by herbal medicines. In this paper, the herbal compounds with anti-OA activities were reviewed, and the cheminformatics tools were used to predict their drug-likeness properties and pharmacokinetic parameters. A total of 43 herbal compounds were analyzed, which mainly target the damaged joints (e.g. cartilage, subchondral bone, and synovium, etc.) and circulatory system to improve the pathogenesis of OA. Through cheminformatics analysis, over half of these compounds have good drug-likeness properties, and the pharmacokinetic behavior of these components still needs to be further optimized, which is conducive to the enhancement in their drug-likeness properties. Most of the compounds can be an alternative and valuable source for anti-OA drug discovery, which may be worthy of further investigation and development.