Current Medicinal Chemistry - Online First

Hepatocellular carcinoma (HCC) is a life-threatening cancer with rising incidence and mortality rates. Identifying new prognostic biomarkers is crucial for improving HCC management.

This study investigates the role of Double PHD Fingers 1 (DPF1) in hepatocellular carcinoma (HCC), exploring its potential as a prognostic indicator and therapeutic target.

We analyzed DPF1 expression in 374 hepatocellular carcinoma (HCC) tissues and 50 normal tissues from the TCGA-HCC database, as well as in 240 HCC tissues and 202 normal tissues from the ICGC-HCC repository. We examined the correlation between DPF1 expression and clinical parameters, immune cell infiltration, drug response profiles, cancer stem cell (CSC) characteristics, and its diagnostic/prognostic potential using various bioinformatics tools and statistical analyses. Validation was performed using the ICGC and HPA databases, and qRT-PCR was used to confirm DPF1 expression in HCC cell lines.

DPF1 exhibited abnormal expression in HCC and several other malignancies. Elevated DPF1 levels were significantly associated with higher Alpha-fetoprotein (AFP) levels (p = 0.043) and poorer clinical outcomes, including diminished overall survival (OS) (p = 0.002), progression-free survival (PFS) (p = 0.018), and disease-specific survival (DSS) (p = 0.001). DPF1 expression was also linked to immune cell infiltration, immune checkpoint gene expression, drug sensitivity, and CSC characteristics. Notably, DPF1 was significantly overexpressed in HCC tissues and cell lines at both transcriptional and translational levels.

Our study reveals that DPF1 is a novel prognostic biomarker in HCC, with potential implications for immunotherapy and drug resistance. Elevated DPF1 expression is associated with adverse clinical outcomes and may serve as a target for future therapeutic interventions in HCC.

High glucose-induced angiogenesis is the main component in Proliferative Diabetic Retinopathy (PDR) development. In PDR, ischemia and hypoxia have been identified as key stimuli that promote pathological neoangiogenesis by increasing Vascular Endothelial Growth Factor A (VEGFA). Furthermore, it has been demonstrated that TRIM65 knockdown in tumor cells reduces VEGFA expression. Building on these findings, the present study aimed to study the role of TRIM protein members in proliferative diabetic retinopathy.

In comparison to the control group, TRIM65 expression was significantly increased in human retinal endothelial cells (HREC) after high glucose treatment. Moreover, FITC/PI staining, cell wound scratch assay, transwell assay, tube formation assay, and immunofluorescence staining of VEGFA and HIF-3α were carried out, which indicated that TRIM65 knockdown inhibited high glucose-induced HREC cell apoptosis and angiogenesis and decreased the expression of VEGFA and HIF-3α, both of which are potential targets of miR-29a-3p. MIR-29a-3p inhibitor significantly reduced the effects of TRIM65 knockdown on VEGFA and HIF-3α expression levels in cells. TRIM65 induced ubiquitination and degradation of TNRC6A, resulting in suppressed miR-29a-3p expression.

Furthermore, in vivo studies revealed that intravitreal injection of miR-29a-3p inhibited neoangiogenesis in mice with Oxygen-Induced Retinopathy (OIR). The retinal tissues of OIR mice showed higher TRIM65 mRNA expression and lower miR-29a-3p expression than those of control mice. Furthermore, the analysis showed a negative correlation between the expression of miR-29a-3p and TRIM65 in the retinal tissues of OIR mice.

In conclusion, this study demonstrated that the knockdown of TRIM65 inhibits neoangiogenesis in proliferative diabetic retinopathy by regulating miR-29a-3p.

Stanniocalcin 1 (STC1) has been implicated in cancer pathogenesis, yet its pan-cancer implications and mechanistic roles in tumor progression and immune modulation remain incompletely characterized. The clinical relevance of STC1 in predicting prognosis and its interaction with tumor immune microenvironment components requires systematic investigation.

This study aims to establish the pan-cancer prognostic significance of STC1 and elucidate its associations with immunological characteristics, including immune checkpoint proteins, tumor mutational burden (TMB), microsatellite instability (MSI), and immune cell infiltration. This study focuses specifically on validating its role in the pathogenesis of gastric adenocarcinoma (STAD).

Multi-omics analysis was performed using TCGA pan-cancer datasets and bioinformatics tools (UALCAN, cBioPortal, HPA, GTA). Experimental validation included multiplex fluorescence staining of STAD tissue microarrays (n=30) and Western blot analysis of STAD cell lines. Key parameters analyzed encompassed clinical outcomes, cancer stemness indices, neoantigen load, and epithelial-mesenchymal transition (EMT) signatures.

Pan-cancer analysis revealed significant STC1 overexpression in 18/33 cancer types (54.5%), particularly in prostate adenocarcinoma (94% deep deletions). STC1 expression correlated with poor prognosis (HR=1.32, p<0.01), elevated TMB (r=0.43), and MSI (r=0.38) across multiple malignancies. Single-cell RNA sequencing demonstrated a strong association with EMC (NES=2.18, FDR<0.001). In STAD, this study confirmed 3.7-fold protein overexpression (p=0.008) and identified positive correlations with CD8+ T cell infiltration (r=0.62, p=0.002) and CD4+ T cell infiltration (r=0.58, p=0.004).

This multi-modal study establishes STC1 as a novel pan-oncogenic factor with dual roles in tumor progression (via EMT and stemness regulation) and immune microenvironment remodeling. The strong association with immune checkpoints (PD-L1, CTLA4) and T cell infiltration patterns positions STC1 as a promising immunotherapeutic target, particularly in STAD and MSI-high cancers. These findings provide mechanistic insights for developing STC1-directed therapeutic strategies.

Hepatocellular carcinoma (HCC) has a poor prognosis due to late diagnosis and rapid progression, highlighting the need for a deeper understanding of its pathogenesis. Lysine crotonylation (Kcr), a unique post-translational modification, plays a crucial role in epigenetic regulation. However, the role of crotonylation-related genes (CRGs) in HCC remains poorly understood, necessitating an investigation of their prognostic and therapeutic relevance.

Transcriptomic and clinical data were obtained from TCGA and GEO databases. A CRG-based risk score was developed using Cox and LASSO regression analyses. To enhance survival prediction, a nomogram incorporating the risk score was constructed. Immune cell infiltration and drug sensitivity were assessed using CIBERSORT and 'OncoPredict.' Single-cell sequencing was employed to examine CRG expression within the HCC tumor microenvironment.

An 8-gene risk score model (HDAC2, ACADS, HDAC1, ENO1, PPARG, ACADL, ACSL6, and AGPAT5) was established, effectively stratifying patients into high- and low-risk groups in the training set. Cox regression and Kaplan-Meier analyses validated its prognostic value in the test set. The nomogram demonstrated enhanced prognostic accuracy for survival prediction. Differences in immune cell infiltration and immune checkpoint expression between risk groups highlighted the association between CRGs and the tumor immune microenvironment. Single-cell sequencing revealed that CRGs were highly expressed in key immune cells within the HCC microenvironment. Additionally, drug sensitivity analysis suggested that specific targeted therapies may be more effective in HCC patients.

Crotonylation-related gene signature demonstrates strong prognostic value in hepatocellular carcinoma (HCC), effectively stratifying patients into high- and low-risk groups and recapitulating known oncogenic roles of HDAC1/2, ENO1, PPARG, AGPAT5 and the protective functions of ACADS, ACADL, and ACSL6. It was found that crotonylation not only influences tumor cell metabolism and epigenetic regulation but also shapes the immune microenvironment, highlighted by distinct checkpoint expression, differential immune cell infiltration, and drug sensitivity profiles, which position our model as a promising tool for personalized therapeutic decision-making. However, clinical translation will require standardized, reproducible assays for crotonylation measurement and rigorous validation across diverse HCC etiologies (e.g., viral vs. non-viral), along with mechanistic and longitudinal studies to dissect causality versus correlation, assess off- target effects of crotonylation modulators, and confirm functional impacts on immune modulation before routine diagnostic or therapeutic use.

This study identifies a prognostic CRG signature for HCC and provides novel insights into personalized treatment strategies.

Over 85% of biologically active compounds are heterocycles or contain heterocyclic groups, underscoring their vital importance in contemporary drug development. Among them, nitrogen-containing derivatives, such as pyridines and pyrimidines, are considered privileged structures in approved drugs or are extensively studied due to their promising therapeutic effects.

In the current work, we would like to verify the hypothesis that incorporating heterocyclic pharmacophores into derivatives of pyrimidine-2(1H)-thione (PMT), 2-pyridone (P), pyridine-2(1H)-thione (PT), dihydropyrimidine-2(1H)-thione (DHPMT), dihydropyridin-2(1H)-one (DHP), and dihydropyridine-2(1H)-thione (DHPT) rings enhances antitumor activity.

A range of novel pyridine- and pyrimidine-based compounds were synthesized and assessed for their anticancer properties against the melanoma A375 cell line. The two most potent compounds (16b and 29) were then chosen for further evaluation of their effects on non-cancerous human dermal fibroblasts, cancer cell apoptosis, cell cycle phase distribution, and tubulin polymerization. Furthermore, in silico analyses were performed to assess the pharmacokinetics, toxicity, drug-likeness, and molecular target of the selected compounds.

Among the 33 compounds tested, pyridine analogs 16b and 29 demonstrated the strongest antiproliferative activity (with IC50 values of 1.85 ± 0.44 µM and 4.85 ± 1.67 µM, respectively) and selectivity (SI=65.08 and SI> 100, respectively) against cancer cells. Additional studies revealed that compound 16b, which features a thiophene ring at the C-5 position and a 3,4,5-trimethoxyphenyl (TMP) group, showed the most promising cell cycle arrest and tubulin polymerization inhibition (IC50=37.26 ± 10.86 µM), resulting in cancer cell apoptosis. In silico ADMET analysis confirmed the drug- likeness of the synthesized compounds.

This research reinforced the significance of heterocyclic rings as valuable pharmacophores. Additionally, it highlighted the antiproliferative and antimitotic potential of modified pyridine derivatives.

Boron-containing compounds (BCC) are attracting attention in drug design. Certain chemical features invite the exploration of efficacious interactions on known and potential drug targets for human use.

The objective of this study is to analyze the reported crystal structure studies to determine trends resulting from the inclusion of boron atoms in potential drugs.

Published data in the Protein Data Bank (PDB) with at least one BCC were analyzed; both ligands and targets were analyzed to describe the inferred or reported biological activity and the potential application as a drug in the treatment of human diseases.

Data from the PDB indicated targets for certain infectious diseases and cancers; however, potential treatments may extend to many other human pathologies as a consequence of the careful analysis of BCCs with proteins. All classes of enzymes and receptors have been crystallized with BCCs as ligands with most complexes demonstrating interactions in the regions known as relevant to protein function.

The number of crystallized BCC-proteins complexes is increasing, and the variability of proteins expands the possibilities of medical applications. Currently, most systems are related to cancer growth and treatment, but deeper analysis may expand BCC utility and efficacy to many other chronic and degenerative diseases.

This study investigated the causes of Mitochondrial Dysfunction (MD) in Diabetic Kidney Disease (DKD) progression, and identified genes associated with DKD, especially those with significant genetic causal effects, to provide a theoretical basis for DKD treatment.

Using a large database and single-cell RNA sequencing (scRNA-seq) data, 333 MDRDEGs were discovered. MDRDEGs were linked to AGE-RAGE signaling, RNA processing, protein transport, and energy metabolism using functional enrichment analysis. Seven MDRDEGs with significant genetic causal effects in DKD were discovered using SMR and MR analyses: ACTN1, ALG11, CCNB1, HIVEP2, MANBA, TUBA1A, and WFS1. Co-localization and scRNA-seq analyses examined these genes' DKD connections. Due to the high significance of its prediction model and DKD expression, ACTN1 was studied in depth. PheWAS and molecular dynamics analysis assessed ACTN1's safety and efficacy as a therapeutic target, and its connection with other symptoms. ACTN1 protein expression in DKD tissues was confirmed by immunofluorescence.

Functional enrichment analysis revealed that MDRDEGs were mostly related to AGE-RAGE signaling, RNA processing, protein transport, and energy metabolism. Seven MDRDEGs caused DKD genetically in SMR and MR investigations. Genetic variations in ACTN1, ALG11, MANBA, and TUBA1A were linked to DKD by co-localization studies. scRNA-seq showed a dramatic increase in ACTN1 expression in DKD. Molecular dynamics analysis demonstrated that Dihydroergocristine can safely bind to ACTN1, while the PheWAS investigation found no significant relationships. DKD tissues exhibited higher ACTN1 protein levels via immunofluorescence.

This study identified MDRDEGs linked to inflammation, cytoskeletal stabilization, and glucose metabolism pathways critical in Diabetic Kidney Disease (DKD) pathogenesis, highlighting their clinical potential as therapeutic targets. Notably, ACTN1 emerged as a causally linked gene overexpressed in DKD, with the prediction of dihydroergocristine as a targeting compound, offering novel avenues for clinical intervention.

This study suggests that ACTN1 may be a therapeutic target for DKD and sheds light on its molecular pathogenesis, clinical prevention, and treatment.

Ovarian cancer, a significant contributor to global female mortality and the third most prevalent gynecological cancer in India, poses challenges for conventional treatments like chemotherapy and radiotherapy.

This study explores the effect of omega-3 polyunsaturated fatty acids (n-3 PUFAs) on the efficacy of chemotherapy, particularly doxorubicin (DOXO), in ovarian teratocarcinoma (PA-1) cells. Rigorous cell viability assays demonstrated that n-3 PUFAs in combination significantly enhanced DOXO-induced cytotoxicity, reducing cell survival and migration potential. N-3 PUFAs and DOXO synergistically reduced colony formation in the group receiving the combination treatment as seen in the clonogenic assays, as further validated by hanging drop and apoptosis assays results.

Network pharmacological investigations pinpointed the gene topoisomerase II A (TOP2A) as a pivotal target, while molecular docking simulations revealed structural similarities between n-3 PUFAs (DHA or EPA) and DOXO, implying probable common mechanisms such as DNA intercalation and topoisomerase II inhibition. Molecular dynamics simulations delineated distinct interaction profiles for Docosahexaenoic acid (DHA) and Eicosapentaenoic acid (EPA) with TOP2A, offering mechanistic insights. Combining computational and experimental methodologies reveals the synergistic benefits of n-3 PUFAs and DOXO in treating ovarian cancer, leading to improved therapeutic outcomes.

These results provide a comprehensive view of the potential of combining n-3 PUFAs with DOXO for more potent ovarian cancer treatments.