Identification of Potential Biomarkers of Depression and Network Pharmacology Approach to Investigate the Mechanism of Key Genes and Therapeutic Traditional Chinese Medicine in the Treatment of Depression

Association of dietary flavonoid intake with the prevalence and all-cause mortality of depressive symptoms: Findings from analysis of NHANES

BACKGROUND

This study aimed to explore the relationship between flavonoids intake and the prevalence and all-cause mortality of depressive symptoms in American adults.

METHODS

Analyzing 2007-2008, 2009-2010, and 2017-2018 NHANES data, we examined the association between dietary flavonoid and depressive symptoms, including specific subclasses assessment and mortality outcomes tracking until December 31, 2019. Our methodology included weighted multivariate logistic regression, weighted cox proportional hazards regression and restricted cubic spline (RCS) models, supported by stratified and sensitivity analyses.

RESULTS

Among the 12,340 participants in total, 1129 exhibited depressive symptoms. The multiple logistic regression analysis showed a significant reduction in total flavonoid and subclass intake in individuals with current depressive symptoms. Adjusted odds ratios (ORs) for the highest quartiles were 0.69 for anthocyanidins and 0.63 for flavones. Interaction effects emerged in non-hypertensive, higher-income, and normal-weight groups for flavones intake. The RCS model indicated an L-shaped association between depressive symptoms and total flavonoid intake, with inflection points at 346 mg/day. During a median follow-up of 119 months, 148 deaths occurred among patients with depressive symptoms. Hazard ratios (HRs) for all-cause mortality showed a significant positive correlation between total flavonoid intake and survival in model 1 (HR = 0.56), with an optimal intake range of 45.2-948.3 mg/day according to the RCS model.

LIMITATIONS

The study relied on U.S. population survey data, potentially limiting generalizability. Unmeasured confounding factors may exist, and genetic factors were not considered.

CONCLUSIONS

Adequate intake of flavonoids, especially anthocyanidins and flavones, is associated with reduced odds of depressive symptoms. Additionally, optimal intake ranges of flavonoid intake for mental health benefits were observed for all-cause mortality in population with depressive symptoms.

Network analysis-guided drug repurposing strategies targeting LPAR receptor in the interplay of COVID, Alzheimer's, and diabetes

The COVID-19 pandemic caused by the SARS-CoV-2 virus has greatly affected global health. Emerging evidence suggests a complex interplay between Alzheimer's disease (AD), diabetes (DM), and COVID-19. Given COVID-19's involvement in the increased risk of other diseases, there is an urgent need to identify novel targets and drugs to combat these interconnected health challenges. Lysophosphatidic acid receptors (LPARs), belonging to the G protein-coupled receptor family, have been implicated in various pathological conditions, including inflammation. In this regard, the study aimed to investigate the involvement of LPARs (specifically LPAR1, 3, 6) in the tri-directional relationship between AD, DM, and COVID-19 through network analysis, as well as explore the therapeutic potential of selected anti-AD, anti-DM drugs as LPAR, SPIKE antagonists. We used the Coremine Medical database to identify genes related to DM, AD, and COVID-19. Furthermore, STRING analysis was used to identify the interacting partners of LPAR1, LPAR3, and LPAR6. Additionally, a literature search revealed 78 drugs on the market or in clinical studies that were used for treating either AD or DM. We carried out docking analysis of these drugs against the LPAR1, LPAR3, and LPAR6. Furthermore, we modeled the LPAR1, LPAR3, and LPAR6 in a complex with the COVID-19 spike protein and performed a docking study of selected drugs with the LPAR-Spike complex. The analysis revealed 177 common genes implicated in AD, DM, and COVID-19. Protein-protein docking analysis demonstrated that LPAR (1,3 & 6) efficiently binds with the viral SPIKE protein, suggesting them as targets for viral infection. Furthermore, docking analysis of the anti-AD and anti-DM drugs against LPARs, SPIKE protein, and the LPARs-SPIKE complex revealed promising candidates, including lupron, neflamapimod, and nilotinib, stating the importance of drug repurposing in the drug discovery process. These drugs exhibited the ability to bind and inhibit the LPAR receptor activity and the SPIKE protein and interfere with LPAR-SPIKE protein interaction. Through a combined network and targeted-based therapeutic intervention approach, this study has identified several drugs that could be repurposed for treating COVID-19 due to their expected interference with LPAR(1, 3, and 6) and spike protein complexes. In addition, it can also be hypothesized that the co-administration of these identified drugs during COVID-19 infection may not only help mitigate the impact of the virus but also potentially contribute to the prevention or management of post-COVID complications related to AD and DM.

Molecular docking, ADMET profiling of gallic acid and its derivatives (N-alkyl gallamide) as apoptosis agent of breast cancer MCF-7 Cells

Background

In 2020, breast cancer has become the most common cancer in the world and in Indonesia. Searching for anticancer drugs using computational methods is considered more effective and selective than other methods. Gallic acid and its derivatives (esters and amides) are compounds that have biological activities such as anticancer effects. The purpose of this study was to analyse the molecular modelling and ADMET (Adsorption, Distribution, Metabolism, Excretion and Toxicity) profile of gallic acid derivative compounds (N-alkyl gallamides) as anticancer agents.

Methods

Target proteins were selected by analysis of protein-protein and drug-protein interactions. Molecular modelling was done by molecular docking and molecular dynamic simulation. Predictive analysis of the ADMET profile of gallic acid and its derivatives (N-alkyl gallamide) was conducted using Marvin Sketch, Swissadme, protox II, and pkCSM pharmacokinetics. The selected target proteins were JUN, AKT1, CASP3, and CASP7.

Results

Compounds N-octyl gallamide, N-ters-butyl gallamide, and N-isoamil gallamide were the three best gallic acid derivatives based on molecular modelling analysis of target proteins associated with breast cancer. The ADMET profile of the N-alkyl gallamide compound is predictable and shows a good profile as a candidate for anticancer drugs.

Conclusion

N-octyl gallamide, N-ters-butyl gallamide, and N-isoamil gallamide have potential as anti-breast cancer agents.

Identification of the shared molecular mechanisms between major depressive disorder and COVID-19 from postmortem brain transcriptome analysis

OBJECTIVES

This study aims to investigate the molecular mechanisms underlying the interaction of major depressive disorder (MDD) and COVID-19, and on this basis, diagnostic biomarkers and potential therapeutic drugs are further explored.

METHODS

Differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) were employed to identify common key genes involved in the pathogenesis of COVID-19 and MDD. Correlations with clinical features were explored. Detailed mechanisms were further investigated through protein interaction networks, GSEA, and immune cell infiltration analysis. Finally, Enrichr's Drug Signature Database and Coremine Medical were used to predict the potential drugs associated with key genes.

RESULTS

The study identified 18 genes involved in both COVID-19 and MDD. Four key genes (MBP, CYP4B1, ERMN, and SLC26A7) were selected based on clinical relevance. A multi-gene prediction model showed good diagnostic efficiency for the two diseases: AUC of 0.852 for COVID-19 and 0.915 for MDD. GO and GSEA analyses identified specific biological functions and pathways associated with key genes in COVID-19 (axon guidance, metabolism, stress response) and MDD (neuron ensheathment, biosynthesis, glutamatergic neuron differentiation). The key genes also affected immune infiltration. Potential therapeutic drugs, including small molecules and traditional Chinese medicines, targeting these genes were identified.

CONCLUSION

This study provides insights into the complex biological mechanisms underlying COVID-19 and MDD, develops an effective diagnostic model, and predicts potential therapeutic drugs, which may contribute to the prevention and treatment of these two prevalent diseases.

Network pharmacology and bioinformatics to identify the molecular mechanisms of Gleditsiae Spina against colorectal cancer

Objective

In this study, network pharmacology, bioinformatics and molecular docking were used to explore the active phytochemicals, hub genes, and potential molecular mechanisms of Gleditsiae Spina in treating of colorectal cancer..

Methods

The targets of Gleditsiae Spina, and targets related to CRC were derived from databases. We identified the hub genes for Gleditsiae Spina anti-colorectal cancer following the protein-protein-interaction (PPI) network. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment were used to analyze the hub genes from a macro perspective. Finally, we verified the hub genes by molecular docking, GEPIA, HPA, and starBase database.

Results

We identified nine active phytochemicals and 36 intersection targets. The GO enrichment analysis results showed that Gleditsiae Spina may be involved in gene targets affecting multiple biological processes, including response to radiation, response to ionizing radiation, cyclin-dependent protein kinase holoenzyme complex, serine/threonine protein kinase complex, cyclin-dependent protein serine/threonine kinase regulator activity and protein kinase regulator activity. KEGG enrichment analysis results indicated that the P53 signaling pathway, IL-17 signaling pathway, Toll-like receptor signaling pathway, PI3K-Akt signaling pathway, and JAK-STAT signaling pathway were mainly related to the effect of Gleditsiae Spina on colorectal cancer. Molecular docking analysis suggested that the active phytochemicals of Gleditsiae Spina could combine well with hub genes (PTGS1, PIK3CG, CCND1, CXCL8 and ADRB2).

Conclusion

This study provides clues for further study of anti-CRC phytochemicals as well as their mechanisms of provides a basis for their development model.

The modulatory effects of alkaloid extracts of Cannabis sativa, Datura stramonium, Nicotiana tabacum and male Carica papaya on neurotransmitter, neurotrophic and neuroinflammatory systems linked to anxiety and depression

This study investigated the modulatory effects of alkaloid extracts of Cannabis sativa (CSAE), Datura stramonium (DSAE), Nicotiana tabacum (NTAE) and male Carica papaya (CMAE) on neurotransmitter, neurotrophic and neuro-inflammatory systems linked to anxiety and depression. Male Wistar rats were orally administered the alkaloid extracts in doses of 5, 50, 500, and 2000 mg/kg for 90 days. On day 91, neurobehavioural studies were evaluated, rats were sacrificed, brain hippocampus removed and tissue homogenate prepared. Biochemical, cytokine and neurotransmitter metabolisms were estimated in the hippocampus. Expressions of genes linked to anxiety and depression were evaluated by RT-qPCR. Results showed CSAE, NTAE and CMAE act as anxiolytic and antidepressant agents by depleting TNF-α, IL-1β and reactive oxygen species concentrations, and monoamine oxidase, angiotensin 1-converting enzyme and acetylcholinesterase activities while elevating IL-10 and dopamine concentrations and glutamate dehydrogenase activity at doses of 5, 50 and 500. Same doses of CSAE, NTAE and CMAE also depleted the gene expressions of GSK3β, JNK, NF-ĸB, and Nesfatin-1 while increasing expressions of CREB, BDNF, serotonin and Nrf2. However, administration of DSAE and 2000 mg/kg CSAE, NTAE and CMAE had adverse modulatory effects on the neurochemical concentrations and activities as well as the gene expressions of the evaluated neurotransmitter, neurotrophic and inflammatory systems. In conclusion, the study established the sub-chronic instrumentalization potential of CSAE, CMAE, and NTAE for anxiolytic and anti-depressive moods, though their use may be associated with dependence and addiction, which may result in more detrimental effects than any therapeutic potential they may proffer.

Identification of Markers for Diagnosis and Treatment of Diabetic Kidney Disease Based on the Ferroptosis and Immune

BACKGROUND

In advanced diabetic kidney disease (DKD), iron metabolism and immune dysregulation are abnormal, but the correlation is not clear. Therefore, we aim to explore the potential mechanism of ferroptosis-related genes in DKD and their relationship with immune inflammatory response and to identify new diagnostic biomarkers to help treat and diagnose DKD.

METHODS

Download data from gene expression omnibus (GEO) database and FerrDb database, and construct random forest tree (RF) and support vector machine (SVM) model to screen hub ferroptosis genes (DE-FRGs). We used consistent unsupervised consensus clustering to cluster DKD samples, and enrichment analysis was performed by Gene Set Variation Analysis (GSVA), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) and then assessed immune cell infiltration abundance using the single-sample gene set enrichment analysis (ssGSEA) and CIBERSORT algorithms. Ferroptosis scoring system was established based on the Boruta algorithm, and then, core compounds were screened, and binding sites were predicted by Coremine Medical database.

RESULTS

We finally established a 7-gene signature (DUSP1, PRDX6, PEBP1, ZFP36, GABARAPL1, TSC22D3, and RGS4) that exhibited good stability across different datasets. Consistent clustering analysis divided the DKD samples into two ferroptosis modification patterns. Meanwhile, autophagy and peroxisome pathways and immune-related pathways can participate in the regulation of ferroptosis modification patterns. The abundance of immune cell infiltration differs significantly across patterns. Further, molecular docking results showed that the core compound could bind to the protein encoded by the core gene.

CONCLUSIONS

Our findings suggest that ferroptosis modification plays a crucial role in the diversity and complexity of the DKD immune microenvironment, and the ferroptosis score system can be used to effectively verify the relationship between ferroptosis and immune cell infiltration in DKD patients. Kaempferol and quercetin may be potential drugs to improve the immune and inflammatory mechanisms of DKD by affecting ferroptosis.