Exploration of hanshi zufei prescription for treatment of COVID-19 based on network pharmacology

Epimedium brevicornum Maxim alleviates diabetes osteoporosis by regulating AGE-RAGE signaling pathway

OBJECTIVES

Epimedium brevicornum Maxim (EP) has a history of utilization in Chinese traditional medicine for the treatment of bone diseases. However, the precise mechanism by which EP extract (EPE) operates in Diabetes osteoporosis (DOP) remains ambiguous. The study was aimed to explore the effects and underlying mechanisms of EPE on DOP, with particular emphasis on the AGE-RAGE pathway.

METHODS

The DOP model was induced through a combination of a high-sugar and high-fat diet along with streptozotocin injection. Following treatment with EPE, blood glucose levels, body weight, and serum biomarkers were measured. The trabecular microstructure of the femur was analyzed using micro-CT tomography and H&E staining. Bioinformatics techniques, including network pharmacology and molecular docking, were utilized to identify key targets of EP for DOP. The predicted targets and pathways were further validated through RT-PCR, TSA analysis ELISA, and western blotting (WB), respectively.

RESULTS

The findings from animal experiments indicate that EPE has a positive impact on weight and blood glucose levels, particularly in reversing the decrease and disordered arrangement of bone trabeculae. Bioinformatics analysis reveals the involvement of the AGE-RAGE pathways in the treatment of DOP with EPE. Subsequent animal validation experiments demonstrate that EPE can regulate key proteins AGE-RAGE pathway, resulting in reducing the inflammatory factors and apoptosis, including advanced Glycation End-products (RGEs), receptor for Advanced Glycation End-products (RAGE), Interleukin-6 (IL-6), Interleukin-1β (IL-1β), Nuclear Factor Kappa B (NF-κB), BCL2-Associated X protein (Bax), B-cell lymphoma 2(Bcl2), and etc. CONCLUSION: This study provides clear evidence that EPE mitigates DOP through enhancement of the AGE-RAGE pathways, offering innovative insights and approaches for clinical utilization.

Carrier-free immobilized enzyme for ligand fishing of carbonic anhydrase inhibitors in Salvia miltiorrhiza

The traditional method for natural products discovering could be time-consuming and labor-intensive, thus ligand fishing has attracted a lot of attention as a fast-screening method. Nevertheless, ligand fishing often relied on immobilized enzyme with solid carriers, which can be expensive and complicated to prepare. In this study, a carrier-free enzyme immobilization technology, cross-linked enzyme aggregates (CLEAs), was introduced by preparing carbonic anhydrase cross-linked enzyme aggregates (CA-CLEAs), aiming to develop a method for ligand fishing that is simpler, faster and more cost-effective. CA-CLEAs were synthesized with optimal conditions, and were proven to have the ability to capture CA inhibitors and recycle. The crude extract of Salvia miltiorrhiza (SM) was determined to have inhibitory activity against CA, and two major components of SM, i.e., phenolic acids and diterpenoids, were prepared and incubated with CA-CLEAs, respectively. Seven potential inhibitors were fished out and identified using liquid chromatography-mass spectrometry (LC-MS), and all of them were verified to have inhibitory activity, with two novel inhibitors, salvianolic acid C and tanshinone IIA, being discovered. Molecular docking simulations revealed the different inhibitory mechanisms of phenolic acids and diterpenoids. Furthermore, combination effect analysis was carried out, and the synergistic effects were discovered between two components, as well as between their representative compounds, i.e., salvianolic acid B and tanshinone IIA. In this study, a ligand fishing method based on carrier-free immobilized enzyme was established and applied to discover CA inhibitors. A variety of inhibitors with different inhibitory mechanisms were identified successfully, which could accelerate the development of CA inhibitors, demonstrating the efficiency and potential of the method in new bioactive compounds discovery.

Saiga antelope horn suppresses febrile seizures in rats by regulating neurotransmitters and the arachidonic acid pathway

BACKGROUND

Saiga antelope horn (SAH) is a traditional Chinese medicine for treating febrile seizure (FS) with precise efficacy, but its mechanism of action and functional substances are still unclear. Given the need for further research on SAH, our group conducted studies to elucidate its mechanisms and active substances.

METHODS

An FS rat pup model was constructed through intraperitoneal injection of LPS and hyperthermia induction. Behavioural indicators of seizures, hippocampal histopathological alterations, serum levels of inflammatory cytokines and hippocampal levels of neurotransmitters were observed and measured to investigate the effects of SAH on FS model rats. Hippocampal metabolomics and network pharmacology analyses were conducted to reveal the differential metabolites, key peptides and pathways involved in the suppression of FS by SAH.

RESULTS

SAH suppressed FS, decreased the inflammatory response and regulated the Glu-GABA balance. Metabolomic analysis revealed 13 biomarkers of FS, of which SAH improved the levels of 8 differential metabolites. Combined with network pharmacology, a "biomarker-core target-key peptide" network was constructed. The peptides of SAH, such as YGQL and LTGGF, could exert therapeutic effects via the arachidonic acid pathway. Molecular docking and ELISA results indicated that functional peptides of SAH could bind to PTGS2 target, inhibiting the generation of AA and its metabolites in hippocampal samples.

CONCLUSION

In summary, the functional peptides contained in SAH are the main material basis for the treatment of FS, potentially acting through neurotransmitter regulation and the arachidonic acid pathway.

Combination of in silico prediction and convolutional neural network framework for targeted screening of metabolites from LC-HRMS fingerprints: A case study of "Pericarpium Citri Reticulatae - FructusAurantii"

In this study, a novel approach is introduced, merging in silico prediction with a Convolutional Neural Network (CNN) framework for the targeted screening of in vivo metabolites in Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS) fingerprints. Initially, three predictive tools, supplemented by literature, identify potential metabolites for target prototypes derived from Traditional Chinese Medicines (TCMs) or functional foods. Subsequently, a CNN is developed to minimize false positives from CWT-based peak detection. The Extracted Ion Chromatogram (EIC) peaks are then annotated using MS-FINDER across three levels of confidence. This methodology focuses on analyzing the metabolic fingerprints of rats administered with "Pericarpium Citri Reticulatae - Fructus Aurantii" (PCR-FA). Consequently, 384 peaks in positive mode and 282 in negative mode were identified as true peaks of probable metabolites. By contrasting these with "blank serum" data, EIC peaks of adequate intensity were chosen for MS/MS fragment analysis. Ultimately, 14 prototypes (including flavonoids and lactones) and 40 metabolites were precisely linked to their corresponding EIC peaks, thereby providing deeper insight into the pharmacological mechanism. This innovative strategy markedly enhances the chemical coverage in the targeted screening of LC-HRMS metabolic fingerprints.

A strategy for deciphering the bioactive metabolites of Farfarae Flos by the inter-individual variability of the antitussive effect

Farfarae Flos is a commonly used traditional herb for the treatment of respiratory disorders. In this study, ultra-high-performance liquid chromatography coupled with time-of-flight mass spectrometry combined with the mass defect filter method was used for the qualitative analysis of Farfarae Flos metabolites in the lung tissues. Then a method for the simultaneous determination of 14 Farfarae Flos metabolites was developed and validated in terms of specificity, linearity, precision and accuracy, matrix effect and recovery. The method was applied to compare the lung tissue of Farfarae Flos treated mice, and 10 caffeoylquinic acid metabolites were higher in the mice with better antitussive effect. Further network pharmacology analysis and molecular docking results showed that these metabolites played an important role in the antitussive effect of Farfarae Flos. This study presented a novel strategy for deciphering the active compounds of herbal medicine by inter-individual variability of bioactivities.

An efficient approach addressing the chemical complexity of Jiawei Fangji Huangqi decoction by integrating ultra-high-performance liquid chromatography/ion mobility-quadrupole time-of-flight mass spectrometry and intelligent data processing workflows

A challenge in the quality control of traditional Chinese medicine is the systematic multicomponent characterization of the compound formulae. Jiawei Fangji Huangqi, a modified form of Fangji Huangqi, is a prescription comprising seven herbal medicines. To address the chemical complexity of the Jiawei Fangji Huangqi decoction, we integrated ion mobility-quadrupole time-of-flight high-definition MSE coupled to ultra-high-performance liquid chromatography and intelligent data processing workflows available in the UNIFI software package. Good chromatographic separation was achieved on CORTECS UPLC T3 column within 52 min, and high-accuracy MS2 data were acquired using high-definition MSE in the negative and positive modes. A chemical library of 1250 compounds was created and incorporated into the UNIFI software to enable automatic peak annotation of the high-definition MSE data. We identified or tentatively characterize 430 compounds in the Jiawei Fangji Huangqi decoction. The potential superiority of high-definition MSE over conventional MS data acquisition approaches was revealed in its spectral quality (MS2 ), differentiation of isomers, separation of coeluting compounds, and target mass coverage. The multiple components of the Jiawei Fangji Huangqi decoction were elucidated, offering insight into its improved pharmacological action compared with that of the Fangji Huangqi formula.

Integrated LC-MS and network pharmacology methods to screen quantitative indicators in the Hippocampus histrix Kaup and method transfer

Hippocampus histrix Kaup is a popular marine medicine with high medicinal and healthcare values. In this study, liquid chromatography-mass spectrometry (LC-MS) analysis combined with network pharmacological method was used to screen for suitable quantitative indicators for the quality control of H. histrix Kaup. Firstly, an LC-MS analytical method for the simultaneous determination of 12 nucleosides in extracts of H. histrix Kaup was established. And then, a network pharmacological method incorporated target prediction, protein-protein interaction network, components-targets network, and targets-pathways network was performed to screen for quantitative indicators. Finally, the developed LC-MS method was transferred to liquid chromatographs to improve the generalizability of the method. All 12 nucleotides were authenticated in extracts of H. histrix Kaup by comparing with the standards. The optimal chromatographic separation conditions are as follows: the chromatographic separation was achieved on an Acquire BEH-C18 column (2.1 mm * 100 mm, 1.7 µm) and gradient elution was performed using methanol solution and buffer (0.30% formic acid and 10 mmol/L ammonium acetate) as mobile phase at a flow rate of 0.15 mL/min and an acquisition wavelength of 260 nm. Network pharmacology results showed that adenosine, and uridine show excellent pharmacological activity. Integration the content, correlation, chromatographic separation, and pharmacological activity of each compound in H. histrix Kaup, uridine and adenosine were tentatively determined as quantitative indicators for quality control in H. histrix Kaup. The established LC-MS method was successfully transferred to liquid chromatographs, and the method is stable and reliable for the quality control of H. histrix Kaup. This developed integrated strategy was successfully used to screen quantitative indicators in the H. histrix Kaup.

De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae)

BACKGROUND

Amomum tsaoko is a medicinal and food dual-use crop that belongs to the Zingiberaceae family. However, the lack of transcriptomic and genomic information has limited the understanding of the genetic basis of this species. Here, we performed transcriptome sequencing of samples from different A. tsaoko tissues, and identified and characterized the expressed sequence tag-simple sequence repeat (EST-SSR) markers.

RESULTS

A total of 58,278,226 high-quality clean reads were obtained and de novo assembled to generate 146,911 unigenes with an N50 length of 2002 bp. A total of 128,174 unigenes were successfully annotated by searching seven protein databases, and 496 unigenes were identified as annotated as putative terpenoid biosynthesis-related genes. Furthermore, a total of 55,590 EST-SSR loci were detected, and 42,333 primer pairs were successfully designed. We randomly selected 80 primer pairs to validate their polymorphism in A. tsaoko; 18 of these primer pairs produced distinct, clear, and reproducible polymorphisms. A total of 98 bands and 96 polymorphic bands were amplified by 18 pairs of EST-SSR primers for the 72 A. tsaoko accessions. The Shannon's information index (I) ranged from 0.477 (AM208) to 1.701 (AM242) with an average of 1.183, and the polymorphism information content (PIC) ranged from 0.223 (AM208) to 0.779 (AM247) with an average of 0.580, indicating that these markers had a high level of polymorphism. Analysis of molecular variance (AMOVA) indicated relatively low genetic differentiation among the six A. tsaoko populations. Cross-species amplification showed that 14 of the 18 EST-SSR primer pairs have transferability between 11 Zingiberaceae species.

CONCLUSIONS

Our study is the first to provide transcriptome data of this important medicinal and edible crop, and these newly developed EST-SSR markers are a very efficient tool for germplasm evaluation, genetic diversity, and molecular marker-assisted selection in A. tsaoko.

Curcumin and its nano-formulations: Defining triple-negative breast cancer targets through network pharmacology, molecular docking, and experimental verification

Background: Curcumin (CUR) displays the capability of suppressing the proliferation and metastasis of various cancer cells. However, the effects and underline mechanisms of CUR to treat triple-negative breast cancer (TNBC) have not been systematically elucidated with an appropriate method.

Methods: In the present research, a combination method of network pharmacology, molecular docking, and in vitro bio-experiment was used to investigate the pharmacological actions and underline mechanisms of CUR against TNBC. First, common targets of CUR and TNBC were screened via Venny 2.1.0 after potential CUR-related targets and targets of TNBC were got from several public databases. Then, the Gene Ontology (GO) function and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment were performed on the Metascape website, and the network of compound-targets-pathways was constructed via Cytoscape software. Moreover, the network of protein-protein interaction was constructed by the STRING database to screen potential targets. Moreover, molecular docking was applied to affirm the interaction of CUR with the screened top 10 potential targets. Finally, in vitro experiments were used to further verify the effects and mechanisms of CUR and its nano-formulation (CUR-NPs) against TNBC.

Results: Forty potential targets of CUR against TNBC were obtained. STAT3, AKT1, TNF, PTGS2, MMP9, EGFR, PPARG, NFE2L2, EP300, and GSK3B were identified as the top 10 targets of CUR against TNBC. In vitro experiment verified that CUR and CUR-NPs could not only restrain the invasion, migration, and proliferation of MDA-MB-231 cells but also induce their apoptosis. In addition, molecular docking demonstrated that CUR could bind spontaneously with the screened top 10 targeted proteins, and a real-time PCR experiment demonstrated that both CUR and CUR-NPs could downregulate the genetic expression levels of the 10 targets. Moreover, according to the CUR-targets-pathways network, PI3K-Akt, EGFR tyrosine kinase inhibitor resistance, JAK-STAT, Foxo, and HIF-1 signaling pathways were identified as the important pathways of CUR effects on TNBC. Among them, the inhibiting effects of CUR and CUR-NPs on the JAK-STAT signaling pathway were further verified by the western blot analysis.

Conclusion: Taken together, the present research demonstrates that CUR and CUR-NPs have pharmacological effects against TNBC via a multi-target and multi-pathway manner.