Retraction: Tumors with TSC mutations are sensitive to CDK7 inhibition through NRF2 and glutathione depletion.

Discovery and research progress of CDK8 inhibitors.

The overall response rate of patients with advanced metastatic melanoma treated with anticancer agents remains poor, and their prognosis is extremely unfavorable. Combination therapy has become a prevalent treatment strategy, but resistance to the key drug dacarbazine (DTIC) contributes significantly to poor outcomes. We focused on programmed cell death 4 (Pdcd4), a tumor suppressor gene, as a potential target for overcoming drug resistance. Recent studies indicate that Pdcd4 expression impacts cell cycle regulation, with its specific function varying with cancer type. To date, detailed mechanisms remain unclear. We established DTIC-resistant mouse melanoma cells and evaluated whether resistance was acquired by measuring the proliferation of those cells. To evaluate the resistance mechanism, we investigated cell cycle regulatory factors using western blotting and flow cytometry. We also examined the relationship between Pdcd4 expression and cell cycle regulation. DTIC-resistant cells showed significantly decreased Pdcd4 protein levels, while expression of Cyclin D1 (a G1 phase regulator) and Cyclin E (involved in S-phase progression) was significantly increased. Expression of p21, a CDK inhibitor, also increased. Flow cytometric analysis revealed that DTIC treatment reduces the S-phase population in non-resistant cells, but not in resistant cells, and Cyclin D1 expression remains elevated in resistant cells even after extended culture in the absence of DTIC. Pdcd4 expression is downregulated in highly malignant DTIC-resistant melanoma cells and the resulting disruption in cell cycle control may contribute to drug resistance. Reactivating Pdcd4 to modulate cell cycle progression may offer a promising approach for overcoming chemotherapy resistance in patients with tumors.

Hecogenin derivative as an anti-breast cancer agent: Mechanistic insights from multi-computational analysis.

Pulsed electromagnetic fields (PEMF) can be used to improve the efficacy of chemotherapeutic agents, such as doxorubicin (DOX). DOX induces mitotic slippage, leading to cell death in various cancers including breast cancer. Herein, we investigated whether PEMF exposure enhances DOX-induced mitotic slippage and subsequent cell death in breast cancer cells. DOX-treated MDA-MB-231 breast cancer cells were stimulated with a 60 min PEMF session three times daily. Cell viability was assessed using the trypan blue exclusion assay. Cell cycle distribution and polyploidy were assessed using flow cytometry, and the morphological features of mitotic slippage were observed microscopically. Western blotting and confocal microscopy were used to evaluate the key molecules involved in G2/M transition, mitotic transition, and caspase-mediated cell death. DOX treatment for three days induced mitotic slippage including cell enlargement, polyploidy, and multinucleation, which was further enhanced by PEMF exposure. DOX treatment also induced CDK1 activation, histone H3 dephosphorylation, and survivin and PLK1 downregulation, which were further increased by PEMF exposure. In addition, CDK1 inhibition reduced mitotic slippage phenotypes and suppressed caspase-2-dependent cell death, resulting in partial restoration of cell viability in the DOX+PEMF group. PEMF promotes DOX-induced mitotic slippage and subsequent caspase-2-dependent cell death in MDA-MB-231 cells by modulating cell cycle checkpoint regulators such as CDK1, survivin, and PLK1. These findings suggest that PEMF may serve as a novel adjuvant to potentiate the anticancer efficacy of DOX by increasing DOX-induced mitotic slippage.

PROTACs are commonly developed by linking E3 ligase-recruiting ligands to established inhibitors of a protein target, often resulting in degraders that retain enzymatic inhibition. Type II inhibition of cyclin-dependent kinases (CDKs) has been challenging, as reported compounds generally exhibit weak biochemical potency and limited cellular activity. Consistent with these limitations, most reported CDK degraders have been derived from type I ATP-competitive inhibitors. Here, we explored whether targeted protein degradation could enable functional CDK targeting from a type II kinase scaffold. Using the multikinase inhibitor regorafenib as a starting scaffold, we generated a focused library of CRL4CRBN-recruiting bifunctional molecules and profiled their degradation activity using quantitative mass spectrometry-based proteomics. This analysis unexpectedly revealed CDK5 and CDK6, kinases not inhibited by the parent scaffold, as degradation targets. Optimization of this series led to JHK-02-108-2, a selective CDK6 degrader that does not display a hook effect and promotes potent CDK6 degradation despite weak CDK6 binding and negligible CDK6 inhibition. In cellular models of acute myeloid leukemia (AML) and glioblastoma, JHK-02-108-2 induced sustained G1 arrest and reduced phosphorylation of the retinoblastoma protein. Interestingly, subtle modifications in PROTAC architecture redirected degradation selectivity, yielding JHK-02-102-1 as a selective type II CDK5 degrader derived from the same scaffold. Together, these findings establish the first type II inhibitor-derived selective CDK6 degrader and demonstrate that targeted protein degradation can enable functional CDK targeting from type II kinase scaffolds.

Primary amebic meningoencephalitis (PAM) caused by Naegleria fowleri is a highly fatal central nervous system infection for which effective treatment options remain limited. This study explored CDK-related pathways in N. fowleri using a focused CDK inhibitor library and structure-based analysis of a selected CDK-like protein. A library of 126 CDK inhibitors was screened against N. fowleri trophozoites using a luminescence-based ATP viability assay, and active compounds were further evaluated in dose-response assays. Human CDK1-9 sequences were used for BLASTp searches against the N. fowleri proteome, followed by comparative sequence analysis with Trypanosoma brucei cdc2-related kinases (CRKs). Nf_CDK-like protein1 (FDP41_013684) was selected for homology modeling, molecular docking, and 100-ns molecular dynamics simulations. Screening identified 23 active CDK inhibitors with IC50 values ≤ 10μM against N. fowleri, including five prioritized compounds with submicromolar activity: AZD5438, GSK-3 inhibitor IX, milciclib, roniciclib, and SU9516 (IC50, 0.30-0.88μM). Sequence analysis identified five CDK-like proteins in the N. fowleri proteome, among which Nf_CDK-like protein1 showed the highest similarity to T. brucei CRK3 and shared approximately 58-61% sequence identity with human CDK1/2. Conserved kinase features, including the glycine-rich loop, αC-helix, hinge region, DFG motif, and activation loop, were retained in Nf_CDK-like protein1. Docking analysis placed all five prioritized compounds within the predicted ATP-binding cleft, with shared interactions around Lys60, Tyr42, Asp113, and the hinge-proximal residues Ile110 and Asp111. Molecular dynamics simulations showed generally stable protein backbones and ligand poses over 100ns. This study identified multiple CDK inhibitor scaffolds with potent in vitro activity against N. fowleri and supports Nf_CDK-like protein1 as a plausible CDK-like kinase target candidate through integrated phenotypic and structure-based analyses, with direct biochemical validation needed in future studies. These findings suggest that CDK-like pathways may represent a relevant molecular axis in N. fowleri and provide a basis for future structure-guided optimization of anti-amoebic candidates.

Targeting HR-positive breast cancer via the inhibition of CDK4 and CDK6 has become the standard of care. However, progression inevitably occurs, and emerging data suggest the implication of CDK2 in this resistance mechanism. As part of our efforts to target this resistance, we embarked on a medicinal chemistry campaign to selectively inhibit CDK2 over the broadly essential CDK1. In order to obtain selectivity against CDK1, we utilized a molecular dynamics approach focused on interaction with a conserved lysine in the active site. Additionally, we uncovered a unique mechanism of clearance driven by both metabolism and efflux in rats and demonstrated that we could counter efflux-driven clearance with high permeability. Our efforts resulted in compound 19, which was potent against CDK2, exhibited good selectivity vs CDK4 and CDK1, and had pharmacokinetic properties that enabled evaluation in a CDK2 xenograft model of cancer, where it achieved nearly 80% tumor growth inhibition.

Recent advances in activity-based proteome profiling (ABPP) have enabled the global mapping of cysteine ligandability, uncovering novel biological insights and opportunities for identifying disease vulnerabilities. While both live-cell-based and native-lysate-based ABPP have been applied, how cysteine ligandability differs between these systems and what factors influence these measurements remain unclear. Building on our previous development of a high-throughput TMT-ABPP workflow for native lysates, here we adapt the protocol for live cells and systematically compare cysteine ligandability across both platforms. Our analysis reveals three major contributors to the discrepancies: in-cellular cysteine accessibility, protein abundance changes, and protein relocalization. Notably, we highlight that the CDK7 inhibitor THZ1 induces substantial protein relocalization and promotes chromatin binding. Together, these results provide a practical framework for ABPP experimental design and data interpretation, supporting the more accurate application of ABPP in functional proteomics and drug discovery.

Inhibitors of ATR, a central kinase controlling DNA replication origin firing and cellular checkpoints, are undergoing clinical trials, yet mechanisms underpinning sensitivity to ATR inhibitors (ATRi) and patient stratification biomarkers are lacking. Here, we perform in parallel, proteomics, transcriptomics and functional analyses and demonstrate that sensitive cancer cell lines have higher expression of DNA replication initiation factors, and exhibit higher origin firing, increased pan-nuclear γH2AX signals and cell death upon ATRi treatment. ATRi sensitivity is causally associated with origin firing rates, since we could modulate ATRi sensitivity by either up- or down-regulating origin firing capacity using CDC7 inhibition, CDK2 inhibition or CDC45 overexpression in both breast and colorectal cancer cells. High expression of replication initiation factors predicts ATRi sensitivity across cell lines from multiple cancer types and acute myeloid leukemia patient samples. This study reveals a contribution of lethal origin firing capacity to ATR sensitivity, providing key steps towards developing a multimodal clinically applicable biomarker.

Despite considerable pathological diversity, pediatric sarcomas lack molecularly targeted treatments, demanding deeper pathobiological insights and innovative therapeutic strategies. Here, we demonstrate that overexpressed MDM2 functions as an important pathogenic driver in these malignancies, rewiring oncogenic programs through both p53-independent chromatin occupancy to regulate active transcription and conventional proteasome-mediated p53 degradation leading to pathway suppression. To leverage this dependency for targeted eradication of pediatric sarcomas with MDM2 overexpression, we develop MDM2-recruiting proteolysis-targeting chimeras that selectively degrade the CDK9/Cyclin T complex (P-TEFb). Among the lead compounds, dCDK9-010 demonstrates superior activity compared to its parental CDK9 inhibitor or MDM2 antagonist either alone or in combination, by coordinatedly disrupting the MDM2-p53 axis and super-enhancer-driven transcription. Remarkably, the transcriptional effects of P-TEFb degradation by dCDK9-010 are phenocopied by MDM2-mediated BET degradation, resulting in potent anti-sarcoma efficacy alongside a favorable therapeutic index and minimal toxicity in nonmalignant cells. Moreover, these MDM2-recruiting transcriptional/epigenetic machinery degraders (termed MDM2-TEMADs) consistently impair the homologous recombination repair pathway and confer synthetic lethality with PARP inhibitors. Together, this work elucidates MDM2's central role in pediatric sarcoma pathogenesis and presents dCDK9-010 as a first-in-class, MDM2-recruiting P-TEFb degrader and an exemplary MDM2-TEMAD that enables precise targeting of MDM2-dependent oncogenic transcriptional addiction.

The cyclin-dependent kinase 6 (CDK6) is a central regulator of cell cycle progression and an important contributor to the development of acute leukemia, particularly in poor prognosis subtypes. Preclinical studies have demonstrated activity of CDK6-targeting drugs in acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL), but clinical trials with CDK4/6 inhibitors as monotherapy were disappointing. In contrast, clinical efficacy was observed for the combination of the dual CDK4/6 inhibitor, palbociclib, with chemotherapy in pediatric acute leukemia and lymphoma patients. We sought to evaluate the potential of CDK6 inhibition to sensitize AML cells to both standard-of-care and novel targeted therapies. We found the CDK2- targeting drug, tegtociclib, to be particularly effective in potentiating the inhibitory effects of CDK4/6 inhibitors against acute leukemia cells. While similar strategies have been considered for solid tumors where CDK4/6 targeted agents may work as monotherapy, we have discovered a unique and novel approach to introduce this class of drugs to acute leukemias. Our results also demonstrate that synergy between these agents, as has been previously shown in breast cancer, is also observed in acute leukemia and correlates with suppression of the Rb/E2F axis and inhibition of cell cycle progression. The universality between the underlying mechanisms of synergy for CDK2 inhibitors combined with CDK4/6 inhibitors in breast cancer and AML warrants further evaluation in other malignancies characterized by dependencies on these CDK subtypes.

CDK4-selective inhibitors are emerging as promising anticancer agents. Relative to dual CDK4/6 inhibitors, CDK4-selective inhibitors have the potential to retain efficacy while improving tolerability. However, the therapeutic value and mechanistic consequences of selectively targeting CDK4 in prostate cancer remain largely undefined. Here, we investigated the anti-tumour activity and mode of action of the CDK4 inhibitors AU2-94 and atirmociclib across diverse prostate cancer models. Antiproliferative activity was assessed in a panel of AR-driven and AR-independent prostate cancer cell lines spanning hormone-sensitive and castration-resistant states. Efficacy was further evaluated in organoids derived from patient-derived xenografts and in xenograft mouse models. Biochemical and molecular analyses were performed to evaluate CDK4 selectivity, RB pathway engagement, transcriptional reprogramming, and downstream effects on cell-cycle regulation, and resistance-associated programmes. AU2-94 was also tested in combination with standard-of-care therapies (enzalutamide and docetaxel) and the PI3K inhibitor alpelisib. AU2-94 exhibited greater selectivity for CDK4 compared with atirmociclib. AU2-94 suppressed proliferation across prostate cancer models irrespective of AR status and retained activity in aggressive and therapy-resistant settings. In RB-proficient in vitro models, AU2-94 reduced RB phosphorylation, attenuated E2F1-dependent transcriptional outputs, activated AR signalling, and decreased expression of proliferation-associated factors such as FOXM1. In vivo, AU2-94 inhibited the growth of both AR-driven (LNCaP) and AR-independent (PC3) xenografts and suppressed RB pathway signalling. Moreover, AU2-94 demonstrated additive or synergistic effects when combined with enzalutamide, docetaxel, or alpelisib that were associated with reinforced cell-cycle blockade and suppression of resistance-associated signalling. These findings establish selective CDK4 inhibition as a therapeutically active and mechanistically rational strategy in prostate cancer and support AU2-94 as a candidate for further preclinical and clinical development, including in combination regimens for advanced and therapy-resistant disease.

β-Carboline alkaloids are natural products built around an indole-pyridine tricyclic core. Their relatively simple structure and ease of modification have drawn lasting interest from medicinal chemists. This review organizes their pharmacological activities according to structural types: simple β-carbolines, those with substitutions at the C-1, N-2/N-9 or C-3 positions, cyclized derivatives, and bis-β-carboline dimers. For each type, we discuss reported mechanisms, such as inhibition of CDK4, HDAC, and topoisomerases. The available data point to promising applications in cancer, inflammatory disorders, and infectious diseases. Overall, the structural diversity of β-carbolines makes them a valuable source of lead compounds for drug discovery.

Dysregulation of the c-Myc oncogene is a pivotal event in leukemia pathogenesis and therapy resistance. This review synthesizes current evidence, illustrating that c-Myc drives leukemogenesis by enhancing proliferation, inhibiting apoptosis, and upregulating immune checkpoints like PD-L1. Its overexpression is linked to poor treatment outcomes across various leukemia subtypes. Directly targeting c-Myc remains challenging; however, indirect epigenetic modifiers (BET inhibitors), transcriptional disruption (CDK9 inhibitors), and combination therapies emerge as promising strategies to suppress its oncogenic activity and overcome resistance, paving the way for improved clinical management.

Design, synthesis and biological evaluation of novel CDK8/BRD4 dual inhibitors.

Multiple myeloma (MM) is a common hematological malignancy, while the prognostic value of tumor-infiltrating immune cells in MM remains elusive. This study aimed to construct an immune-related prognostic model and identify potential therapeutic targets for MM. RNA-seq and clinical data of 751 newly diagnosed MM patients were analyzed. LASSO regression was applied to establish an immune pathway-based prognostic model for patient risk stratification. WGCNA was used to screen hub genes, and in vitro and in vivo experiments validated gene functions and therapeutic effects. Five immune cell pathways were significantly correlated with MM prognosis. MCM2 was identified as the key hub gene associated with risk scores. MCM2 knockdown induced G2-phase cell cycle arrest and suppressed MM proliferation both in vitro and in vivo. Moreover, MCM2 inhibition enhanced the antitumor efficacy of PD1/PDL1 inhibitor BMS1, and CDK inhibitor PHA767491 sensitized MM to immunotherapy. The immune-based model reliably predicts MM prognosis. MCM2 serves as a vital prognostic biomarker. Targeting MCM2 combined with PD1/PDL1 and CDK inhibitors represents a promising therapeutic strategy for MM.

Epithelial cell expansion drives cyst progression in genetic models of autosomal recessive polycystic kidney disease

Luminal breast cancer is rising rapidly among East Asian women, particularly younger patients, with variable clinical outcome, yet current risk-stratification models inadequately predict early recurrence of under-studied young-onset cases. We hypothesize that the interplay between endogenous mutagenic processes and overlooked environmental carcinogen exposure drives molecular diversity, revealing novel etiologic and therapeutic insights. We performed integrative proteogenomic profiling of 164 prospective, treatment-naïve early-stage Taiwanese breast cancer patients using whole-exome sequencing, transcriptomics, proteomics, and phosphoproteomics. Functional validation in luminal models confirmed therapeutic vulnerabilities and biomarkers, with an independent cohort (n = 270) used to stratify high-risk recurrence patients. Our integrative proteogenomic analysis revealed distinct molecular etiologies and actionable vulnerabilities. For the first time, mutation signature analysis revealed both environmental carcinogen exposure (DBAC) and endogenous APOBEC mutagenesis as key contributors to poor disease-free survival, particularly in younger patients. A high-mutation-burden, immune-evasive subgroup revealed immunoepigenetic vulnerabilities. DBAC-driven tumors exhibited overexpression of ROS-detoxifying enzymes, DNA-damage checkpoint activation, and suppressed DNA repair pathways, supporting an environmental-genomic cooperative mechanism. APOBEC-associated tumors exhibited upregulation of APOBEC3B/3F/3G, steroid hormone biosynthesis enzymes, and downstream oncogenic signaling, forming an immunotherapy-responsive subtype. Proteomic classification further resolved luminal heterogeneity beyond PAM50, identifying two clinically relevant groups: (1) a young DBAC-proteome subset with suppressed DNA-repair machinery and favorable chemotherapy response; and (2) a recurrence-prone subtype characterized by co-activating ER, PI3K-AKT-mTOR, and CDK4/6/9 signaling. Functional validation demonstrated that selective CDK9 inhibition targeting the p-POLR2A-Ser2 axis significantly outperformed CDK4/6 blockade. Furthermore, a companion panel (HDAC2, ALDH1L2, ARF4, SCAMP3) stratified high-risk recurrence patients in an independent cohort, supporting biomarker-guided therapy for aggressive luminal breast cancer. This study uncovers environmental mutagenesis as a previously overlooked but critical driver of luminal breast cancer heterogeneity in East Asian patients. We establish a proteogenomics-transformative scheme to guide risk stratification and subtype-specific vulnerabilities, offering a precision oncology strategy for early-stage East Asian breast cancer management.

A sustainable and effective one-pot synthesis of new 4,5-dihydro-[1,2,4]triazolo[1,5-a]pyrimidine-6-carbonitrile derivatives was accomplished using Mn₃O₄ nanoparticles as a recyclable nanocatalyst under moderate and environmentally benign conditions. The approach provided outstanding yields and adheres to sustainable chemical principles. Analysis revealed CDK4 as a possible therapeutic target linked to breast cancer growth, therefore elucidating its biological potential. In silico molecular docking validated the robust binding affinities of the synthesized derivatives to the CDK4 active site, especially compound 4, which demonstrated the greatest interaction energy and stable orientation inside the binding pocket. In vitro cytotoxic studies on MCF-7 and MDA-MB-231 breast cancer cell lines demonstrated that compound 4 had the highest antiproliferative activity (IC₅₀ = 5.80 and 6.44 µM, respectively), equivalent to doxorubicin and sorafenib. Compound 3 had significant effects, whereas compounds 9 and 10 showed modest efficacy. Notably, compound 4 exhibited little toxicity to WI-38 normal fibroblasts (IC₅₀ = 51.61 µM), suggesting selectivity for cancer cells. Flow cytometric analyses demonstrated that compound 4 produced G₀/G₁ cell-cycle arrest (82.77%) and initiated apoptosis (35.19%) with little necrosis, therefore validating its CDK4-dependent mechanism. These results together identify compound 4 as a powerful, selective, and environmentally friendly synthetic CDK4 inhibitor, serving as a viable candidate for the future development of tailored anti-breast cancer therapies.