A network-based pharmacological investigation to identify the mechanistic regulatory pathway of andrographolide against colorectal cancer

An integrated in vitro and in silico approach to assess targeted cytotoxicity against MDA-MB-231 triple-negative breast cancer cells with Psidium guajava peel-derived chitosan nanoparticles

Triple-negative breast cancer (TNBC) is a significant global health issue, with high mortality rates. The chemotherapeutic drugs currently used for TNBC have significant side effects, impacting both normal and cancer cells. In this study, we investigated a potential use of fruit peel extract of Psidium guajava (PGP) encapsulated with chitosan nanoparticles (CSNPs) to combat TNBC. The synthesized PGP-CSNPs were characterized using UV-vis spectroscopy, Fourier transform infra-red (FTIR) spectroscopy, TEM and GC-MS. The maximum loading capacity and encapsulation efficacy of PGP-CSNPs were found to be 72.5 ± 0.49% and 92.9 ± 0.10%, respectively. Furthermore, in vitro cytotoxicity was assessed, and the IC50 value for PGP-CSNPs was 50.13 µg/mL. It was observed that PGP-CSNPs could induce apoptosis in MDA-MB-231 cells in dose-dependent manner. Furthermore, molecular docking was performed for bioactive compounds retrieved from PGP-CSNPs against human tumour suppressor proteins Bcl2, and results showed that the PGP-CSNPs had lower binding energy than cisplatin. This suggests that, the synthesized PGP-CSNPs have the potential to serve as a therapeutic agent for tackling TNBC. However, to validate its efficacy in human therapy, furthermore pre-clinical and clinical procedures should be examined, as this is an ongoing and significant step towards developing an effective and safe anticancer drug.

Transcriptomic signatures of prostate cancer progression: a comprehensive RNA-seq study

Transcriptomics has been entirely transformed by RNA-sequencing (RNA-seq) due to its high sensitivity, accuracy, and precision. This study analyzed RNA-seq data to identify potential biomarkers for prostate cancer (PCa), a serious health issue among aging men. Despite several existing studies, biomarkers that effectively detect PCa or its prognosis have yet to be entirely determined. The differentially expressed genes (DEGs) that are critical and clinically informative were identified in PCa patient samples that had been progression stage categorized into medium risk (MR) and high risk (HR). A total of 174 DEGs were found to be shared between MR and HR samples. Functional enrichment analysis revealed their involvement in crucial biological processes, such as p53 signaling, mitotic nuclear division, and inflammation. To further examine their interactions, a Protein-Protein Interaction (PPI) network was constructed, where key genes, such as KIF20A, TPX2, BUB1, BIRC5, BUB1B, and MKI67, were found in significant modules, hubs, and motifs. Several transcription factors, including STAT5B, MYC, and SOX5 controlled these genes. Heatmap analysis indicates that the expression of the six crucial genes (KIF20A, TPX2, BUB1, BIRC5, BUB1B, and MKI67) increases with progression from benign state to medium-risk and high-risk states. Additionally, a nomogram model was constructed to predict the prognostic value of these biomarkers. Among the studied genes, BIRC5, MKI67, and KIF20A are suggested as potential prognostic biomarkers, while NIFK and PPP1CC are suggested as new therapeutic targets. These findings indicate that these biomarkers show considerable promise in improving early detection and prognosis of PCa.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-025-04297-3.

Uncovering the anti-cancer mechanism of cucurbitacin D against colorectal cancer through network pharmacology and molecular docking

Colorectal cancer is a significant global health challenge due to chemoresistance, necessitating new treatments. Cucurbitacin D, with its anti-cancer properties, shows promise, but its effects on colorectal cancer are not well understood. We investigated the impact of cucurbitacin D on colorectal cancer cell lines using MTT assays and Annexin V/7-AAD staining followed by flow cytometry for apoptosis analysis. Public databases helped identify cucurbitacin D and colorectal cancer-related gene targets for network pharmacology analysis. Protein-protein interaction networks were constructed using STRING and analyzed in Cytoscape. Gene ontology and KEGG pathway enrichment analyses were performed using ClueGo. Molecular docking studies were conducted via Autodock Vina and visualized in Discovery Studio. Western blot assessed protein expression changes in key targets under cucurbitacin D. Cucurbitacin D dose-dependently reduced colorectal cancer cell viability and induced apoptosis. Network pharmacology pinpointed crucial targets like STAT3, AKT1, CCND1, and CASP3. Molecular docking confirmed strong interactions with these targets. Enrichment analysis highlighted involvement in the 'PI3K-AKT,' 'JAK-STAT,' and 'ErbB' signaling pathways. These findings suggest cucurbitacin D as a potential anti-colorectal cancer agent, demonstrating significant effects on cell viability and apoptosis, and engaging critical cancer-related pathways, making it a promising candidate for further colorectal cancer therapeutic research.

Anti-cancer effects of carnosol in DMBA-induced oral experimental carcinogenesis by oncogenic signaling pathways on in vivo and in silico study

The most prevalent malignant tumor in the oral cavity, accounting for more than 90% of all oral malignancies, is oral squamous cell carcinoma (OSCC). Therefore, detection or prevention of malignant transformation remains a viable target for the future. Carnosol is a compound derived from rosemary that contains both antioxidant and anti-carcinogens. This study examined the defensive properties of carnosol in DMBA-induced oral carcinogenesis. We have developed the computational based docking analysis to predict the binding affinity and interaction of carnosol with inflammatory and pro-apoptotic proteins. Carnosol was the most potential bioactive compound shows strong binding affinity to low binding energy to bind above the proteins. Following this, we created a hamster model to study buccal pouch carcinogenesis induced by DMBA and assessed buccal tissues using histopathological, biochemical, and western blotting. Carnosol treatment effectively reduced DMBA-induced pathological changes in buccal tissues: Altered detoxification, increased antioxidant levels, and reduced lipid peroxidation enzymes levels. We then examined the impact of carnosol intervention on the modulation of the levels of inflammatory factors and pro-apoptotic markers in oral carcinogenesis. Binding energy was studied between the carnosol between the inflammatory (NF-κB and COX-2) and apoptotic (Bax, caspase-3, and caspase-9) proteins using molecular docking. Our findings suggest that carnosol enhances antioxidant and detoxification levels, potentially prevents oral carcinogenesis by modifying the inflammatory and pro-apoptotic signaling pathways, and acts as an anti-cancer agent.

Network pharmacology and in silico approach to study the mechanism of quercetin against breast cancer

Breast cancer is a significant health concern among females with an estimated 2.3 million cases reported worldwide in 2022. Traditional treatment methods have now developed resistance and various adverse effects, highlighting an urgent need for attention. Therefore, it is advisable to substitute these conventional therapies with innovative medications. Quercetin is a flavonoid, commonly found in various vegetables and fruits and have been shown to possess anti-cancer properties. Network pharmacology is a comprehensive approach that has significantly assisted in investigating the potential of quercetin as a therapeutic option for breast cancer. The first step includes target fishing for quercetin-targeted genes in breast cancer through various online available databases. All intersecting genes were analysed for the phenotypic- genotypic correlation via online VarElect analysis tool. Using the result from the result the GO enrichment and pathway enrichment analysis was done on 52 common genes; followed by PPI network construction and based on topological parameters top 8 genes were filtered. Based on theVenny2.1 and then GEPIA and HPA analysis the key target were identifies as ABCC1, ABCC4, AKT1, ABCB1, CYP1B1, CYP19A1, ABCB4 and ABCG2. Further, Molecular docking was done to investigate the possible interaction of the identified gene with quercetin. Our finding shows quercetin is the potential natural drug that can treat breast cancer effectively. Quercetin interacts with ABCC1, ABCC4, AKT1, ABCB1, CYP1B1, CYP19A1, ABCB4, and ABCG2 at cellular as well as molecular level. The ADMET analysis suggests the bioavaibility of quercetin is around 0.55. Suggesting that quercetin satisfies drug-likeness rules but may face challenges like low bioavailability, which can be enhanced through structural modifications or formulations (e.g., nanoparticles). The molecular docking result assures the interaction of quercetin with the ABCC1, ABCC4, AKT1, ABCB1, CYP1B1, CYP19A1, ABCB4, and ABCG2 with the binding affinity of - 7.2, - 10.1, - 10.4, - 8.0, - 8.2, - 8.2, - 9.0 and - 8.9 respectively. These results suggest quercetin has a stable interaction with the ABCC4 gene. Considering this interaction the quercetin molecules can rescue the cellular condition by inducing apoptosis, inhibiting proliferation, and suppressing metastasis. Quercetin, a natural compound found in fruits and vegetables, has been found to have significant therapeutic roles in treating breast cancer. It inhibits cell cycle arrest, promotes apoptosis, and reduces blood vessel formation. It also reverses drug resistance and has antioxidant and anti-inflammatory properties. This study concludes that the therapeutic influence of quercetin plays a significant role in treating breast cancer and aids in the advancement of the clinical application of quercetin in future studies.

Graphical Abstract

An integrative analysis of GEO data to identify possible therapeutic biomarkers of prostate cancer and targeting potential protein through Zea mays phytochemicals by virtual screening approaches

Prostate cancer (PC) is a prevalent type of cancer among men. Delaying the treatment of patients with upgraded or upstaged cancer may lead to unmanageable circumstances. The aim of this study is to contribute to the finding of biomarkers that are specific to PC and identify drug candidates derived from plants. The information about cancer is critical for clinicians to make decisions about patient treatment in the era of precision medicine. Advances in genomics technology have opened up new possibilities for identifying genes that are associated with cancer, including PC. This study identifies novel differentially expressed genes for PC. The seven PC microarray datasets were selected from the National Center for Biotechnology Information (NCBI)/Gene Expression Omnibus (GEO). The differentially expressed genes (DEGs) were found based on a fold change of |logFC| ≥ 1 and an adjusted p-value of <0.05. The DEGs were further studied using several bioinformatics tools, including STRING, CytoHubba, SRplot, Coremine Medical database, FunRich and GeneMANIA, cBioPortal. The six new potential biomarkers, GAGE2A, GAGE12G, GAGE2E, GAGE13, GAGE12F and CSAG1 were identified. These biomarkers are associated with biological processes (BPs) such as cell division, and gene expression regulation, so these genes may have a crucial role in PC progression and may serve as potential biomarkers for PC. A total of 497 phytochemicals from corn plants have been screened against the target protein and found LTS0176591 as the best lead molecule with docking score of -6.31 kcal/mol. Further, molecular mechanics-generalized born surface area (MM-GBSA), molecular dynamics simulation, principal component analysis (PCA), free energy landscape (FEL) and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) were carried out to validate the findings.Communicated by Ramaswamy H. Sarma.

Molecular modelling, docking and network analysis of phytochemicals from Haritaki churna: role of protein cross-talks for their action

Phytochemicals are bioactive agents present in medicinal plants with therapeutic values. Phytochemicals isolated from plants target multiple cellular processes. In the current work, we have used fractionation techniques to identify 13 bioactive polyphenols in ayurvedic medicine Haritaki Churna. Employing the advanced spectroscopic and fractionation, structure of bioactive polyphenols was determined. Blasting the phytochemical structure allow us to identify a total of 469 protein targets from Drug bank and Binding DB. Phytochemicals with their protein targets from Drug bank was used to create a phytochemical-protein network comprising of 394 nodes and 1023 edges. It highlights the extensive cross-talk between protein target corresponding to different phytochemicals. Analysis of protein targets from Binding data bank gives a network comprised of 143 nodes and 275 edges. Taking the data together from Drug bank and binding data, seven most prominent drug targets (HSP90AA1, c-Src kinase, EGFR, Akt1, EGFR, AR, and ESR-α) were found to be target of the phytochemicals. Molecular modelling and docking experiment indicate that phytochemicals are fitting nicely into active site of the target proteins. The binding energy of the phytochemicals were better than the inhibitors of these protein targets. The strength and stability of the protein ligand complexes were further confirmed using molecular dynamic simulation studies. Further, the ADMET profiles of phytochemicals extracted from HCAE suggests that they can be potential drug targets. The phytochemical cross-talk was further proven by choosing c-Src as a model. HCAE down regulated c-Src and its downstream protein targets such as Akt1, cyclin D1 and vimentin. Hence, network analysis followed by molecular docking, molecular dynamics simulation and in-vitro studies clearly highlight the role of protein network and subsequent selection of drug candidate based on network pharmacology.Communicated by Ramaswamy H. Sarma.

Caffeic acid, a dietary polyphenol, pre-sensitizes pancreatic ductal adenocarcinoma to chemotherapeutic drug

Resistance to chemotherapeutics is an eminent cause that leads to search for options that help in diminution of pancreatic ductal adenocarcinoma (PDAC) by overcoming resistance issues. Caffeic acid (CFA), a polyphenol occurring in many dietary foods, is known to show antidiabetic and anticancer properties potential. To unveil the effect of CFA on PDAC, we carried out this research in PDAC cells, following which we checked the combination effect of CFA and chemotherapeutics and pre-sensitization effects of CFA. Multitudinous web-based approaches were applied for identifying CFA targets in PDAC and then getting their interconnections. Subsequently, we manifested CFA effects by in-vitro analysis showing IC50 concentrations of 37.37 and 15.06 µM on Panc-1 and Mia-PaCa-2, respectively. The combination index of CFA with different drugs was explored which showed the antagonistic effects of combination treatment leading to further investigation of the pre-sensitizing effects. CFA pre-sensitization reduced IC50 concentration of doxorubicin in both PDAC cell lines which also triggered ROS generation determined by 2',7'-dichlorofluorescin diacetate assay. The differential gene expression analysis after CFA treatment showed discrete genes affected in both cells, i.e. N-Cad and Cas9 in Panc-1 and Pi3K/AkT/mTOR along with p53 in Mia-PaCa-2. Collectively, this study investigated the role of CFA as PDAC therapeutics and explored the mechanism in mitigating resistance of PDAC by sensitizing to chemotherapeutics.

Integrating serum pharmacochemistry and network pharmacology to reveal the mechanism of chickpea in improving insulin resistance

Although chickpea have great potential in the treatment of obesity and diabetes, the bioactive components and therapeutic targets of chickpea to prevent insulin resistance (IR) are still unclear. The purpose of this study was to investigate the chemical and pharmacological characteristics of chickpea on IR through serum pharmacochemistry and network pharmacology. The results revealed that compared with other polar fractions, the ethyl acetate extract of chickpea (CE) had the definitive performance on enhancing the capacities of glucose consumption and glycogen synthesis. In addition, we analyzed the components of CE in vivo and in vitro based on UPLC-Q-Orbitrap HRMS technology. There were 28 kinds of in vitro chemical components, among which the isoflavones included biochanin A, formononetin, ononin, sissotrin, and astragalin, etc. Concerningly, the chief prototype components of CE absorbed into the blood were biochanin A, formononetin, loliolide, and lenticin, etc. Furthermore, a total of 209 common targets between IR and active components of CE were screened out by network pharmacology, among which the key targets involved PI3K p85, NF-κB p65 and estrogen receptor 1, etc. Specifically, KEGG pathway analysis indicated that PI3K-AKT signaling pathway, HIF-1 signaling pathway, and AGE-RAGE signaling pathway may play critical roles in the IR remission by CE. Finally, the in vitro validation experiments disclosed that CE significantly balanced the oxidative stress state of IR-HepG2 cells and inhibited expressions of inflammatory cytokines. In conclusion, the present study will be an important reference for clarifying the pharmacodynamic substance basis and underlying mechanism of chickpea to alleviate IR.

STK25: a viable therapeutic target for cancer treatments?

Serine/threonine protein kinase 25 (STK25) is a critical regulator of ectopic lipid storage, glucose and insulin homeostasis, fibrosis, and meta-inflammation. More and more studies have revealed a strong correlation between STK25 and human diseases. On the one hand, STK25 can affect glucose and fatty acid metabolism in normal cells or tumors. On the other hand, STK25 participates in autophagy, cell polarity, cell apoptosis, and cell migration by activating various signaling pathways. This article reviews the composition and function of STK25, the energy metabolism and potential drugs that may target STK25, and the research progress of STK25 in the occurrence and development of tumors, to provide a reference for the clinical treatment of tumors.

Andrographolide promoted ferroptosis to repress the development of non-small cell lung cancer through activation of the mitochondrial dysfunction

BACKGROUND

Ferroptosis, a form of regulated cell death by lipid peroxidation, was currently considered as a key factor affecting the occurrence and progression in various cancers. Andrographolide (ADE), a major effective ingredient of Andrographis paniculate, has proven to have a substantial anti-tumor effect on multiple cancer types. However, the function and underlying mechanism of ADE in Non-Small Cell Lung Cancer remain unclear.

METHODS

CCK8 assay, colony-formation assay, flow cytometry, scratch test, transwell assay, western blotting, ferroptosis analysis and mitochondria analysis were performed to reveal the role and underlying mechanisms of ADE in NSCLC cell lines (H460 and H1650). In vivo, xenograft model and lung metastatic model were performed to verify the effect of ADE on the growth and metastasis of NSCLC.

RESULTS

In this present study, we demonstrated that treatment with ADE could inhibit cell growth and metastases through eliciting ferroptosis in vitro an in vivo. The IC50 of ADE in H460 and H1650 cells were 33.16 μM and 32.45 μM respectively. In Lewis xenografted animals, i.p. ADE repressed relative tumor growth (p < 0.01) and inhibited metastases (p < 0.01). Notably, the ferroptosis inhibitor Fer-1 abrogated the anti-tumor capacity of ADE. Induction of ferroptosis by ADE was confirmed by elevated levels of reactive oxygen sepsis (ROS), glutathione (GSH), malondialdehyde (MDA), intracellular iron content and lipid ROS reduced glutathione (GSH) accumulation (p < 0.01). Furthermore, ADE inhibited the expression of ferroptosis-related protein GPX4 and SLC7A11. Simultaneously, it also disclosed that ADE enhanced mitochondrial dysfunction, as evidenced by increased mitochondrial ROS release, mitochondrial membrane potential (MMP) depolarization, and decreased mitochondrial ATP. Most interestingly, Mito-TEMPO, a mitochondria-targeted antioxidant, rescued ADE-induced ferroptosis.

CONCLUSION

Our data validated that ADE treatment could restrain proliferation and metastases of NSCLC cells through induction of ferroptosis via potentiating mitochondrial dysfunction.