The novel CDK9 inhibitor, XPW1, alone and in combination with BRD4 inhibitor JQ1, for the treatment of clear cell renal cell carcinoma

Design, synthesis, and biological evaluation of N-(2-amino-phenyl)-5-(4-aryl- pyrimidin-2-yl) amino)-1H-indole-2-carboxamide derivatives as novel inhibitors of CDK9 and class I HDACs for cancer treatment

The mechanisms underlying transcriptional dysregulation in tumorigenesis have received considerable attention as promising therapeutic targets to combat human cancer. Cyclin-dependent kinase 9 (CDK9) and class I histone deacetylases (HDACs) are significant therapeutic targets due to their pivotal roles in the dysregulated transcriptional programs characteristic of many cancers. Furthermore, the combinatorial transcriptional therapy with CDK9 and class I HDAC inhibitors has been shown to have a synergistic anticancer effect. In this study, a series of novel N-(2-amino-phenyl)-5-(4-aryl-pyrimidin-2-yl) amino)-1H-indole-2-carboxamide derivatives were designed and synthesized as novel dual-functional inhibitors targeting CDK9 and HDAC signaling pathways for cancer treatment. Among the synthesized compounds, 13ea demonstrated potent anti-proliferative activities (IC50 < 5.0 μM) in various cancer cell lines (HeLa, MDA-MB-231, HepG2). In addition, 13ea was found to significantly inhibit the phosphorylation function of CDK9 and the deacetylation function of class I HDACs. Furthermore, 13ea was found to inhibit the protein activity of CDK9 (IC50 = 0.17 μM), HDAC1 (IC50 = 1.73 μM), and HDAC3 (IC50 = 1.11 μM). The docking studies predicted the binding patterns of 13ea in the active pockets of CDK9 and HDAC1/3. The cellular assays revealed that 13ea induced mitochondria-related apoptosis and G2/M phase arrest in cancer cells, showing superior activities compared to those of AZD-5438 (a CDK9 inhibitor) and Mocetinostat (an inhibitor of class I HDACs). Notably, the in vivo assay demonstrated that 13ea (30 mg/kg) exhibited significant inhibition on MDA-MB-231 xenograft tumor growth, with a tumor shrinkage rate of 76.83 %. In summary, we have identified 13ea as a novel CDK9/HDAC inhibitor with excellent anticancer activity in vitro and in vivo.

Combination therapy and dual-target inhibitors based on cyclin-dependent kinases (CDKs): Emerging strategies for cancer therapy

Cyclin-dependent kinases (CDKs) are pivotal regulators of the cell cycle and transcriptional machinery, making them attractive targets for cancer therapy. While CDK inhibitors have demonstrated promising clinical outcomes, they also face challenges in enhancing efficacy, particularly in overcoming drug resistance. Combination therapies have emerged as a key strategy to augment the effectiveness of CDK inhibitors when used alongside other kinase inhibitors or non-kinase-targeted agents. Dual-target inhibitors that simultaneously inhibit CDKs and other oncogenic drivers are gaining attention, offering novel avenues to optimize cancer therapy. Based on the structural characterization and biological functions of CDKs, this review comprehensively examines the structure-activity relationship (SAR) of existing dual-target CDK inhibitors from a drug design perspective. We also thoroughly investigate the preclinical studies and clinical translational potential of combination therapies and dual-target inhibitors. Tailoring CDK inhibitors to specific cancer subtypes and therapeutic settings will inspire innovative approaches for the next generation of CDK-related therapies, ultimately improving patient survival.

Rational Design of a Potent, Selective, and Metabolically Stable CDK9 Inhibitor to Counteract Osimertinib Resistance through Mcl-1 Suppression and Enhanced BRD4 Co-Targeting

Overcoming osimertinib resistance in NSCLC treatment remains a significant clinical challenge. CDK9 has emerged as a promising target due to its critical role in sustaining oncogenic transcriptional programs, particularly via Mcl-1 regulation. Herein, we report the structure-guided optimization of a previously identified CDK9 inhibitor (Z11), resulting in the discovery of T7, a potent, selective, and metabolically stable candidate (IC50 = 1.2 nM). T7 effectively suppressed cell proliferation, reduced colony formation, and induced apoptosis in Osimertinib-resistant NSCLC cells by downregulating Mcl-1. Furthermore, T7 significantly inhibited the growth of resistant organoids and demonstrated marked antitumor efficacy in a xenograft model. Notably, combining T7 with the BRD4 inhibitor JQ1 further enhanced antitumor activity both in vitro and in vivo, revealing a complementary therapeutic strategy. These findings identify T7 as a promising next-generation CDK9 inhibitor for addressing Osimertinib resistance in NSCLC and underscore the potential of transcriptional cotargeting approaches to improve clinical outcomes.

CDK9 inhibitors for the treatment of solid tumors

Cyclin-dependent kinase 9 (CDK9) regulates mRNA transcription by promoting RNA Pol II elongation. CDK9 is now emerging as a potential therapeutic target for cancer, since its overexpression has been found to correlate with cancer development and worse clinical outcomes. While much work on CDK9 inhibition has focused on hematologic malignancies, the role of this cancer driver in solid tumors is starting to come into focus. Many solid cancers also overexpress CDK9 and depend on its activity to promote downstream oncogenic signaling pathways. In this review, we summarize the latest knowledge of CDK9 biology in solid tumors and the studies of small molecule CDK9 inhibitors. We discuss the results of the latest clinical trials of CDK9 inhibitors in solid tumors, with a focus on key issues to consider for improving the therapeutic impact of this drug class.

The BET inhibitor JQ1 suppresses tumor survival by ABCB5-mediated autophagy in uveal melanoma

Uveal melanoma (UM), the most common adult ocular tumor, is aggressive and resistant to treatment, posing threat to patients' lives. The novel, effective therapies and the exploration of chemosensitizer for UM are imperative. The anticancer efficacy was evaluated with and without JQ1 treatment or ABCB5 gene silencing or overexpression. RNA sequencing identified downstream effectors in JQ1-treated cells. Integrated analysis of The Cancer Genome Atlas data (TCGA) and immunohistochemistry (IHC) revealed the oncogenic role of ABCB5. Functional analyses of JQ1 and defective ABCB5 were conducted using flow cytometry, transmission electron microscopy (TEM), IHC and western blot. The effects of JQ1 were validated in a heterotopic tumor model derived from OCM-1 cells. JQ1 inhibited cell proliferation, migration and invasion, induced cell cycle arrest and promoted apoptosis. JQ1 also suppressed the survival of UM in heterotopic tumor model. RNA sequencing indicated that JQ1 down-regulated the expressions of ABCB5 and autophagy-related genes, which was confirmed in vitro and in vivo by western blot. ABCB5, a marker associated with cancer stem cells and chemo-resistance, exhibited heightened expression in UM tissues, linked to immune infiltration. Notably, disrupting ABCB5 expression impeded UM cell proliferation and interfered with autophagy. Moreover, the overexpression of ABCB5 promoted cell proliferation, migration and invasion, and rescued autophagy related gene expression. Of note, JQ1 enhanced the sensitivity of OCM-1 cells to chemotherapy. Thus JQ1 inhibits UM survival via ABCB5-mediated autophagy and enhances chemo-sensitivity, suggesting potential for BET-based approaches in UM clinical management.

Recent Discovery and Development of Inhibitors that Target CDK9 and Their Therapeutic Indications

CDK9 is a cyclin-dependent kinase that plays pivotal roles in multiple cellular functions including gene transcription, cell cycle regulation, DNA damage repair, and cellular differentiation. Targeting CDK9 is considered an attractive strategy for antitumor therapy, especially for leukemia and lymphoma. Several potent small molecule inhibitors, exemplified by TG02 (4), have progressed to clinical trials. However, many of them face challenges such as low clinical efficacy and multiple adverse reactions and may necessitate the exploration of novel strategies to lead to success in the clinic. In this perspective, we present a comprehensive overview of the structural characteristics, biological functions, and preclinical status of CDK9 inhibitors. Our focus extends to various types of inhibitors, including pan-inhibitors, selective inhibitors, dual-target inhibitors, degraders, PPI inhibitors, and natural products. The discussion encompasses chemical structures, structure-activity relationships (SARs), biological activities, selectivity, and therapeutic potential, providing detailed insight into the diverse landscape of CDK9 inhibitors.