Discovery of novel indole derivatives that inhibit NEDDylation and MAPK pathways against gastric cancer MGC803 cells

Predicting the anticancer activity of indole derivatives: A novel GP-tree-based QSAR model optimized by ALO with insights from molecular docking and decision-making methods

Indole derivatives have demonstrated significant potential as anticancer agents; however, the complexity of their structure-activity relationships and the high dimensionality of molecular descriptors present challenges in the drug discovery process. This study addresses these challenges by introducing a modified GP-Tree feature selection algorithm specifically designed for regression tasks and high-dimensional feature spaces. The algorithm effectively identifies relevant descriptors for predicting LogIC50 values, the target variable. Furthermore, the GP-Tree method adeptly balances the selection of both positively and negatively contributing descriptors, enhancing the performance of DT, k-NN, and RF models. Additionally, the SMOGN technique was employed to address class imbalances, expanding the dataset to 1381 instances and enhancing the accuracy of IC50 predictions. Various machine learning models were optimized using probabilistic and nature-inspired algorithms, with the Ant Lion Optimizer (ALO) demonstrating the highest efficacy. The AdaBoost-ALO (ADB-ALO) model outperformed all other models, such as MLR, SVR, ANN, k-NN, DT, XGBoost, and RF, achieving an R2 of 0.9852 across the entire dataset, an RMSE of 0.1470, and a high CCC of 0.9925. SHAP analysis revealed critical descriptors, such as TopoPSA and electronic properties, which are essential for potent anticancer activity. Furthermore, molecular docking, in conjunction with the Weighted Sum Method (WSM), identified promising candidates, particularly N-amide derivatives of indole-benzimidazole-isoxazoles, which exhibit dual inhibition against topoisomerase I and topoisomerase II enzymes. Consequently, this research integrates computational predictions with experimental insights to accelerate the discovery of novel anticancer therapies through the accurate prediction and interpretation of the anti-prostate cancer activity of indole derivatives.

Ultrasonic-assisted extraction of flavonoids from Amomum villosum Lour. Using natural deep eutectic solvent: Process optimization, comparison, identification, and bioactivity

Amomum villosum Lour. (A. villosum) is widely utilized in culinary and medicinal contexts due to its rich diversity of bioactive compounds. In this study, an ultrasonic-assisted extraction (UAE) method using a natural deep eutectic solvent (NaDES) was employed to extract flavonoids from A. villosum. The NaDES composed of betaine and glycerol (Bet-Gly) exhibited effective performance as an extraction solvent, as evidenced by its high efficiency. Optimal extraction conditions (water content: 30 %, solid-liquid ratio: 1:20 g/mL, temperature: 70 °C, ultrasonic power: 85 % P, time: 30 mins) were established via single-factor experiments. The maximum total flavonoid content (TFC) of 82.22 ± 0.39 mg rutin equivalent per gram dry weight (mg Rut/g DW) was achieved under optimized conditions. Comparative studies revealed that the UAE-NaDES method afforded higher TFC and DPPH radical scavenging activity values, broader flavonoid diversity, and demonstrated a better capacity to stabilize them compared to conventional solutions. Furthermore, NaDES exhibited favorable biocompatibility properties, and the resulting extract displayed remarkable anti-inflammatory and anti-cancer effects. These findings demonstrate that NaDES is an efficient solvent for flavonoids extraction from A. villosum, with potential applications in food and pharmaceutical industries, thereby minimizing solvent removal steps.

Gastric Cancer and Intestinal Metaplasia: Differential Metabolic Landscapes and New Pathways to Diagnosis

Gastric cancer (GC) is the fifth most common cause of cancer-related death worldwide. Early detection is crucial for improving survival rates and treatment outcomes. However, accurate GC-specific biomarkers remain unknown. This study aimed to identify the metabolic differences between intestinal metaplasia (IM) and GC to determine the pathways involved in GC. A metabolic analysis of IM and tissue samples from 37 patients with GC was conducted using ultra-performance liquid chromatography with tandem mass spectrometry. Overall, 665 and 278 significant features were identified in the aqueous and 278 organic phases, respectively, using false discovery rate analysis, which controls the expected proportion of false positives among the significant results. sPLS-DA revealed a clear separation between IM and GC samples. Steroid hormone biosynthesis, tryptophan metabolism, purine metabolism, and arginine and proline metabolism were the most significantly altered pathways. The intensity of 11 metabolites, including N1, N2-diacetylspermine, creatine riboside, and N-formylkynurenine, showed significant elevation in more advanced GC. Based on pathway enrichment analysis and cancer stage-specific alterations, we identified six potential candidates as diagnostic biomarkers: aldosterone, N-formylkynurenine, guanosine triphosphate, arginine, S-adenosylmethioninamine, and creatine riboside. These metabolic differences between IM and GC provide valuable insights into gastric carcinogenesis. Further validation is needed to develop noninvasive diagnostic tools and targeted therapies to improve the outcomes of patients with GC.

Semisynthesis and biological evaluation of novel honokiol thioethers against colon cancer cells HCT116 via inhibiting the transcription and expression of YAP protein

Honokiol, derived from Magnolia officinalis (a traditional Chinese medicine), has been reported to have anticancer activity. Here, a series of novel honokiol thioethers bearing a 1,3,4-oxadiazole moiety were prepared and evaluated for their anticancer activities against three types of digestive system tumor cells. Biological evaluation showed that honokiol derivative 3k exhibited the best antiproliferative activity against HCT116 cells with an IC50 value of 6.1 μmol/L, superior to the reference drug 5-fluorouracil (IC50: 9.63 ± 0.27 µmol/L). The structure-activity relationships (SARs) indicated that the introduction of -(4-NO2)Ph, 3-pyridyl, -(2-F)Ph, -(4-F)Ph, -(3-F)Ph, -(4-Cl)Ph, and -(3-Cl)Ph groups was favorable for enhancing the anticancer activity of the title honokiol thioethers. Further study revealed that honokiol thioether 3k can well inhibit the proliferation of colon cancer cells HCT116, arresting the cells in G1 phase and inducing cell death. Moreover, a preliminary mechanism study indicated that 3k directly inhibits the transcription and expression of YAP protein without activating the Hippo signaling pathway. Thus, honokiol thioether 3k could be deeply developed for the development of honokiol-based anticancer candidates.

Protein neddylation and its role in health and diseases

NEDD8 (Neural precursor cell expressed developmentally downregulated protein 8) is an ubiquitin-like protein that is covalently attached to a lysine residue of a protein substrate through a process known as neddylation, catalyzed by the enzyme cascade, namely NEDD8 activating enzyme (E1), NEDD8 conjugating enzyme (E2), and NEDD8 ligase (E3). The substrates of neddylation are categorized into cullins and non-cullin proteins. Neddylation of cullins activates CRLs (cullin RING ligases), the largest family of E3 ligases, whereas neddylation of non-cullin substrates alters their stability and activity, as well as subcellular localization. Significantly, the neddylation pathway and/or many neddylation substrates are abnormally activated or over-expressed in various human diseases, such as metabolic disorders, liver dysfunction, neurodegenerative disorders, and cancers, among others. Thus, targeting neddylation becomes an attractive strategy for the treatment of these diseases. In this review, we first provide a general introduction on the neddylation cascade, its biochemical process and regulation, and the crystal structures of neddylation enzymes in complex with cullin substrates; then discuss how neddylation governs various key biological processes via the modification of cullins and non-cullin substrates. We further review the literature data on dysregulated neddylation in several human diseases, particularly cancer, followed by an outline of current efforts in the discovery of small molecule inhibitors of neddylation as a promising therapeutic approach. Finally, few perspectives were proposed for extensive future investigations.

Discovery of the 2,4-disubstituted quinazoline derivative as a novel neddylation inhibitor for tumor therapy

Overactivation of neddylation has been found in a number of common human tumor-related diseases. In recent years, targeting the neddylation pathway has become an appealing anti-cancer strategy, and it is critical to find neddylation inhibitors with novel structures and higher efficacy. Here, we present the discovery of novel inhibitors of the NEDD8-activating enzyme (NAE) and their antitumor activity in vitro. All synthesized 1,4-disubstituted piperidine compounds were evaluated for antiproliferative activity against MGC-803, MCF-7, A549, and KYSE-30 cells. Among five representative compounds, III-26 bearing a quinazoline motif was identified as the lead one due to the fact that it significantly hindered the neddylation of Cullin1. Cellular mechanisms elucidated that III-26 inhibited the proliferation, migration, and invasion of UBC12-overexpressed MGC-803 cell lines, as well as induced apoptosis and arrested the cell cycle at G2/M phase. Importantly, III-26 reduced NAE activity, thus selectively preventing neddylation of Cullin3 and Cullin1 over other Cullin members. At a dose of 4 μM, III-26 virtually entirely blocked UBC12-NEDD8 conjugation in MGC-803 cells. Our molecular modeling and kinetic investigation suggested that this compound may function as a non-covalent inhibitor of NAE.

Role of non-canonical post-translational modifications in gastrointestinal tumors

Post-translational modifications (PTMs) of proteins contribute to the occurrence and development of tumors. Previous studies have suggested that canonical PTMs such as ubiquitination, glycosylation, and phosphorylation are closely implicated in different aspects of gastrointestinal tumors. Recently, emerging evidence showed that non-canonical PTMs play an essential role in the carcinogenesis, metastasis and treatment of gastrointestinal tumors. Therefore, we summarized recent advances in sumoylation, neddylation, isoprenylation, succinylation and other non-canonical PTMs in gastrointestinal tumors, which comprehensively describe the mechanisms and functions of non-classical PTMs in gastrointestinal tumors. It is anticipated that targeting specific PTMs could benefit the treatment as well as improve the prognosis of gastrointestinal tumors.

Recent advances in nitrogen-containing heterocyclic compounds as receptor tyrosine kinase inhibitors for the treatment of cancer: Biological activity and structural activity relationship

Erratic cell proliferation is the initial symptom of cancer, which can eventually metastasize to other organs. Before cancer becomes metastatic, its spread is triggered by pro-angiogenic factors including vascular endothelial growth factor receptor (VEGFR), epidermal growth factor receptor (EGFR), Platelet-derived growth factor receptor (PDGFR), fibroblast growth factor receptor (FGFR) and Platelet Factor (PF4), all of which are part of receptor tyrosine kinase (RTK) family. Receptor tyrosine kinases (RTKs) are cell-surface proteins and aresignaling enzymes that transfer ATP-phosphate to tyrosine residue substrates. Important biological processes like proliferation, differentiation, motility, and cell-cycle regulation are all possessedby these proteins. Unusual RTK expression is typically associated with cell growth abnormalities, which is linked to tumor acquisition, angiogenesis, and cancer progression. In addition to the already available medications, numerous other heterocyclic are being studied for their potential action against a variety of cancers. In the fight against cancer, in particular, these heterocycles have been used for their dynamic core scaffold and their inherent adaptability. In this review article, we have compiled last five years research work including nitrogen containing heterocycles that have targeted RTK. Herein, the SAR and activity of various compounds containing diverse heterocyclic (pyrimidine, indole, pyridine, pyrazole, benzimidazole, and pyrrole) scaffolds are discussed, and they may prove useful in the future for designing new leads against RTKs. Our focus in this manuscript is to comprehensively review the latest research on the biological activity and structural activity relationship of nitrogen compounds as RTK inhibitors. We believe that this may be an important contribution to the field, as it can help guide future research efforts and facilitate the development of more effective cancer therapies.

Targeting NEDD8-activating enzyme for cancer therapy: developments, clinical trials, challenges and future research directions

NEDDylation, a post-translational modification through three-step enzymatic cascades, plays crucial roles in the regulation of diverse biological processes. NEDD8-activating enzyme (NAE) as the only activation enzyme in the NEDDylation modification has become an attractive target to develop anticancer drugs. To date, numerous inhibitors or agonists targeting NAE have been developed. Among them, covalent NAE inhibitors such as MLN4924 and TAS4464 currently entered into clinical trials for cancer therapy, particularly for hematological tumors. This review explains the relationships between NEDDylation and cancers, structural characteristics of NAE and multistep mechanisms of NEDD8 activation by NAE. In addition, the potential approaches to discover NAE inhibitors and detailed pharmacological mechanisms of NAE inhibitors in the clinical stage are explored in depth. Importantly, we reasonably investigate the challenges of NAE inhibitors for cancer therapy and possible development directions of NAE-targeting drugs in the future.

Discovery of dual tubulin-NEDDylation inhibitors with antiproliferative activity

Although various dual-target tubulin inhibitors have been designed and synthesised, no dual tubulin-NEDDylation inhibitors as antiproliferative agents were reported so far. In this work, a series of trimethoxyphenyl analogues as potential dual tubulin-NEDDylation inhibitors were synthesised and evaluated for their antiproliferative activity. Among them, compound C11 exhibited the most potent inhibitory activity with IC₅₀ values of 1.17, 2.48, and 1.47 μM against HepG2, PC3, and MCF7 cells, respectively. In addition, it displayed the potent inhibitory activity against tubulin with an IC₅₀ value of 2.40 μM and obviously inhibited tubulin polymerisation in HepG2 cells. Furthermore, C11 inhibited NEDDylation by a ATP-dependent manner. Molecular docking studies revealed that the methoxy group and dithiocarbamate group of C11 could form hydrogen bonds with residues of tubulin and E1 NEDD8-activating enzyme (NAE). These results suggested that compound C11 was a dual tubulin-NEDDylation inhibitor with antiproliferative activity.

Design, synthesis and anti-tumor activity studies of novel pyrido[3, 4-d]pyrimidine derivatives

In order to find high-efficiency and low-toxic anti-tumor drugs, 29 pyrido[3,4-d]pyrimidine compounds were designed, synthesized and evaluated by MTT assay in vitro. The results presented that most of the compounds had good antitumor activities, among which compound 30 had the best anti-tumor activity on MGC803 cells (IC50 = 0.59 μM). Mechanistic studies exhibited that compound 30 inhibited migration of MGC803 and induced apoptosis. It was proved that compound 30 up-regulated expression of Bid and PARP, down-regulated expression of CycD1 by western blot experiments. This study indicated that compound 30 might be served as a lead agent for the treatment of human gastric cancers.

Discovery of 1,2,4-triazine dithiocarbamate derivatives as NEDDylation agonists to inhibit gastric cancers

NEDDylation process regulates multiple physiological functions and signaling pathways, which are still in an equilibrium that favors the survival and proliferation of tumor cells. Unlike inhibitors, NEDDylation agonists are rarely studied. In this work, novel 1,2,4-triazine-dithiocarbamate derivatives were synthesized and evaluated for antiproliferative activity against MGC-803, PC-3 and EC-109 cells. Among them, compound K3 displayed the most potent activity MGC-803, PC-3 and EC-109 cells with IC₅₀ values of 2.35, 5.71 and 10.1 μM, respectively, which were more potent than 5-FU. Further cellular mechanisms suggested that compound K3 inhibited the cell viability, induced proliferation inhibition, arrested cell cycle at G2/M phase and induced cell apoptosis in MGC-803 and HGC-27 cells. Importantly, compound K3 could interact with NAE1 to promote the NEDDylation of MGC-803 and HGC-27 cells. The promotion of NEDDylation resulted in the degradation of c-IAP and YAP/TAZ, which leads to the induction of cell apoptosis and inhibition of proliferation in MGC-803 and HGC-27 cells. Therefore, as a NEDDylation agonist, compound K3 could effectively inhibit gastric cancer cells. Here, we reported NEDDylation promotion induced by compound K3, which could inhibit the cancer cell lines MGC-803 and HGC-27 and induce the cancer cell apoptosis via prompting the degradation of c-IAP and YAP/TAZ.

Identification of uterine leiomyosarcoma-associated hub genes and immune cell infiltration pattern using weighted co-expression network analysis and CIBERSORT algorithm

BACKGROUND

While large-scale genomic analyses symbolize a precious attempt to decipher the molecular foundation of uterine leiomyosarcoma (ULMS), bioinformatics results associated with the occurrence of ULMS based totally on WGCNA and CIBERSORT have not yet been reported. This study aimed to screen the hub genes and the immune cell infiltration pattern in ULMS by bioinformatics methods.

METHODS

Firstly, the GSE67463 dataset, including 25 ULMS tissues and 29 normal myometrium (NL) tissues, was downloaded from the public database. The differentially expressed genes (DEGs) were screened by the 'limma' package and hub modules were identified by weighted gene co-expression network analysis (WGCNA). Subsequently, gene function annotations were performed to investigate the biological role of the genes from the intersection of two groups (hub module and DEGs). The above genes were calculated in the protein-protein interaction (PPI) network to select the hub genes further. The hub genes were validated using external data (GSE764 and GSE68295). In addition, the differential immune cell infiltration between UL and ULMS tissues was investigated using the CIBERSORT algorithm. Finally, we used western blot to preliminarily detect the hub genes in cell lines.

RESULTS

WGCNA analysis revealed a green-yellow module possessed the highest correlation with ULMS, including 1063 genes. A total of 172 DEGs were selected by thresholds set in the 'limma' package. The above two groups of genes were intersected to obtain 72 genes for functional annotation analysis. Interestingly, it indicated that 72 genes were mainly involved in immune processes and the Neddylation pathway. We found a higher infiltration of five types of cells (memory B cells, M0-type macrophages, mast cells activated, M1-type macrophages, and T cells follicular helper) in ULMS tissues than NL tissues, while the infiltration of two types of cells (NK cells activated and mast cells resting) was lower than in NL tissues. In addition, a total of five genes (KDR, CCL21, SELP, DPT, and DCN) were identified as the hub genes. Internal and external validation demonstrated that the five genes were over-expressed in NL tissues compared with USML tissues. Finally, the correlation analysis results indicate that NK cells activated and mast cells activated positively correlated with the hub genes. However, M1-type macrophages had a negative correlation with the hub genes. Moreover, only the DCN may be associated with the Neddylation pathway.

CONCLUSION

A series of evidence confirm that the five hub genes and the infiltration of seven types of immune cells are related to USML occurrence. These hub genes may affect the occurrence of USML through immune-related and Neddylation pathways, providing molecular evidence for the treatment of USML in the future.