CDK Inhibitor Research Articles

Abstract PO3-18-06: First-in-human phase 1A study of RGT-419B, a next generation CDK4 inhibitor, in patients (pts) with hormone receptor positive (HR+) HER2- advanced/metastatic breast cancer (ABC) who progressed on prior CDK4/6 inhibitors (CDK4/6i)

Abstract Introduction: RGT-419B is a novel next generation CDK inhibitor. It has high potency against CDK4 with additional activity against CDK2 and selectivity against CDK6 to overcome resistance and reduce hematologic toxicity. In addition to anti-cancer activity in preclinical breast cancer models that are resistant to approved CDK4/6 inhibitors, we report the interim data from the first-in-human, multicenter trial of RGT-419B as a single agent in post-menopausal pts with HR+ HER2- ABC. Methods: Eligible pts received ≥2 lines of treatment and progressed on endocrine therapy (ET) and at least 1 line of an FDA approved CDK4/6i. Prior treatments of fulvestrant, other targeted agents and/or chemotherapy were allowed. Dose escalation of RGT-419B as oral (PO) monotherapy was administered in continuous 28-day cycles in 4 cohorts (25, 75,150 mg QD and 150 mg BID). A standard 3+3 design was employed to determine the maximum tolerated dose (MTD)/recommended dose for expansion (RDE). The primary objective was to assess safety and tolerability. The secondary objectives included pharmacokinetic (PK) assessment and exploratory efficacy. Results: At time of abstract submission, 12 eligible post-menopausal pts with HR+/HER2- ABC received RGT-419B. The median age was 64.8y (range 50-80y). All had prior palbociclib + ET (2 pts had abemaciclib or ribociclib after palbociclib); a majority received fulvestrant (67%) and prior chemotherapy (50%). Across the 4 cohorts (12 pts), the most observed treatment-emergent adverse events (TEAEs; all causality) with RGT-419B were nausea, reduced white blood cell counts (neutrophils and/or lymphocytes) and diarrhea. At data cutoff on June 30th 2023, there have been no CTCAE Grade 3 or higher treatment related AE (TRAEs). No ocular toxicity has been observed. No pts have discontinued treatment due to RGT-419B toxicity. Preliminary PK analyses for RGT-419B showed a dose-dependent increase of exposure at steady state with long half-life. Tumor assessments (RECIST v1.1) of pts in the first 3 cohorts treated with RGT-419B monotherapy (25-150 mg QD) showed partial responses in 2 pts (7 pts with measurable disease), 28.6% partial response (PR) (RECIST v. 1.1) and clinical benefit rate (CBR) 44%. Updated safety, PK and efficacy data will be presented. Conclusions: RGT-419B, with potent selective CDK4 activity, CDK2 activity and CDK6 selectivity, demonstrated a favorable safety and PK profile in an ongoing phase I study, with no grade 3 or higher TRAEs observed thus far. RGT-419B administered as once daily monotherapy also demonstrated preliminary evidence of efficacy as well. Dose expansions of RGT-419B as a single agent and in combination with ET in pts with HR+/HER2- ABC following prior CDK4/6i progression are planned. Citation Format: Seth Wander, Dave Valacer, Richard Zuniga, Heather Yeckes-Rodin, Christopher Perkins, Lisa Ge, Lili Yao, Jing Lin, Dawn Begley, Feifei Sun, Andie Zheng, Jing Han, Zhi (Julie) Xie, Aditya Bardia, Kevin Kalinsky. First-in-human phase 1A study of RGT-419B, a next generation CDK4 inhibitor, in patients (pts) with hormone receptor positive (HR+) HER2- advanced/metastatic breast cancer (ABC) who progressed on prior CDK4/6 inhibitors (CDK4/6i) [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO3-18-06.

Abstract PO2-20-04: TACTIVE-U: phase 1b/2 umbrella study of vepdegestrant, a PROteolysis TArgeting Chimera (PROTAC) estrogen receptor (ER) degrader, combined with other anticancer treatments in ER–positive advanced or metastatic breast cancer

Abstract Background: Vepdegestrant (ARV-471), an oral PROTAC ER degrader, was well tolerated and showed evidence of clinical activity in the first-in-human phase 1/2 study in heavily pretreated patients with ER+/human epidermal growth factor receptor 2–negative (HER2-) advanced breast cancer (NCT04072952). The cyclin-dependent kinase (CDK)4/6 inhibitors abemaciclib and ribociclib are approved in combination with an aromatase inhibitor or fulvestrant, or as monotherapy (abemaciclib), for ER+/HER2- advanced or metastatic breast cancer. In preclinical studies, vepdegestrant combined with abemaciclib or ribociclib showed evidence of synergistic interactions in ER+ breast cancer cells and greater tumor growth inhibition in a xenograft breast cancer model compared with fulvestrant in combination with these agents. Inhibitors targeting different CDKs, such as samuraciclib (oral CDK7 inhibitor), are in clinical development for solid tumors. The open-label, phase 1b/2 TACTIVE-U umbrella study will evaluate the safety, efficacy, and pharmacokinetics of vepdegestrant in combination with other anticancer treatments in patients with ER+ advanced or metastatic breast cancer. Vepdegestrant is being evaluated in combination with abemaciclib (sub-study A; NCT05548127), ribociclib (sub-study B; NCT05573555), and samuraciclib (sub-study C). Trial Design: Patients eligible for current sub-studies of TACTIVE-U are aged ≥18 years, have histologically or cytologically confirmed ER+/HER2- advanced or metastatic breast cancer not amenable to surgical resection, and have received prior therapy for advanced or metastatic disease, including any CDK4/6 inhibitor–based regimen in any setting. In each sub-study, patients will receive vepdegestrant orally once daily (QD) continuously in a dose escalation/de-escalation approach. Abemaciclib will be given orally twice daily continuously in sub-study A, ribociclib will be given orally QD for 21 days followed by 7 days off treatment in sub-study B, and samuraciclib will be given orally QD continuously in sub-study C. For all sub-studies, the primary endpoint of the phase 1b portion is dose-limiting toxicities to determine the recommended phase 2 dose of vepdegestrant in combination with the other anticancer treatment. Secondary endpoints of phase 1b are antitumor activity (objective response, clinical benefit rate [CBR], and duration of response [DOR]), progression-free survival (PFS), safety (type, frequency, and severity of adverse events and laboratory abnormalities), and plasma concentrations of study drugs. The phase 2 portion of each sub-study will further evaluate the antitumor activity of the combinations; the primary endpoint is objective response and secondary endpoints include antitumor activity (CBR and DOR), PFS, overall survival, safety, plasma concentration of study drugs, and changes in circulating tumor DNA. Future combination sub-studies will be included in TACTIVE-U. Citation Format: Claudine Isaacs, Katarzyna Jerzak, John Hilton, José Luiz Miranda Guimarães, Rachel Layman, Dongrui Lu, Gary Mo, Anna Maria Calella, Olga Valota, Sibyl Anderson, Cynthia Ma. TACTIVE-U: phase 1b/2 umbrella study of vepdegestrant, a PROteolysis TArgeting Chimera (PROTAC) estrogen receptor (ER) degrader, combined with other anticancer treatments in ER–positive advanced or metastatic breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-20-04.

Abstract PO4-14-01: Synergistic Activity of CDK8/19 Inhibitor RVU120 and MEK Inhibitors in Hormone-Negative Breast Cancer: Implications for Targeted Therapy

Abstract Breast cancer (BC) is a complex disease with distinct subtypes, including triple-negative breast cancer (TNBC), which lacks targeted therapies. CDK8 and CDK19, components of the mediator complex involved in transcriptional regulation, have emerged as potential therapeutic targets in BC. Transcriptomic analysis revealed that elevated CDK8 expression was associated with poor prognosis across all BC subtypes. Furthermore, previous studies demonstrated that sensitivity to CDK8/CDK19 inhibition correlated with high STAT3 phosphorylation and enrichment of TNF/NF-kB and STAT target genes in responder cells. In this study, we evaluated the responsiveness of TNBC cell lines to RVU120, a highly selective and potent CDK8/CDK19 inhibitor currently undergoing clinical trials for acute myeloid leukemia (AML), high-risk myelodysplastic syndrome (HR-MDS), and solid tumors. Notably, the sensitivity of TNBC cell lines to RVU120 varied depending on the culture conditions, with the presence of epidermal growth factor (EGF) identified as a major determinant of response variability. Considering the role of EGFR in activating downstream signaling pathways, including MAPK and STAT, and previous observations of synergy between small molecule CDK8 inhibitors and MEK inhibitors in neuroblastoma, we investigated MEK inhibitors as potential combination partners in hormone-negative BC. Among the 15 tested BC cell lines, a synergy between CDK8/CDK19 inhibitors and MEK inhibitors was observed in 5 cell lines, antagonism in another 5 cell lines, and no synergy in the remaining 5 cell lines, based on the analysis with Combenefit software (Loewe additivity model). Importantly, cell lines where synergy of the combination therapy has been observed, exhibited EGFR amplification and markers of activated RAS pathway. This pattern of response was consistent across different MEK and MEK/RAF inhibitors, including selumetinib, trametinib, and avutometinib. These findings highlight the synergistic potential of combining RVU120 with MEK inhibitors in hormone-negative BC, particularly in TNBC with EGFR amplification and an active RAS pathway. Ongoing studies involving RNAseq analysis and organoid screening aim to further elucidate the underlying mechanisms and confirm the efficacy of this combination therapy. Furthermore, in vivo efficacy experiments are necessary to validate in vitro activity of both compounds. Successful development of this therapeutic concept relies on the validation and implementation of selected partner drugs targeting RAS pathway, as well as the identification of suitable biomarkers such as EGFRamp or RAS-score. Promising findings of this study provide a rationale for exploring the combination of CDK8/CDK19 inhibitor RVU120 and MEK inhibitors as a potential targeted therapy strategy for hormone-negative BC. Citation Format: Urszula Pakulska, Adrianna Moszynska, Justyna Martyka, Jerzy Woznicki, Elzbieta Adamczyk, Marta Obacz, Kinga Keska Izworska, Katarzyna Wiklik, Agata Stachowicz, Hendrik Nogai, Milena Mazan, Tomasz Rzymski. Synergistic Activity of CDK8/19 Inhibitor RVU120 and MEK Inhibitors in Hormone-Negative Breast Cancer: Implications for Targeted Therapy [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-14-01.

Abstract PS12-03: p53 loss enables HR+ breast cancer escape from CDK4/6 inhibitor-induced quiescence via CDK2

Abstract Background: Inhibition of CDK4/6 kinases has led to improved clinical outcomes in hormone receptor positive (HR+) breast cancer. While these are highly effective therapies, only a minority of patients experience long-term disease control. We sought to determine the genomic configurations and underlying mechanisms associated with long-term response. Methods: To identify genomic patterns associated with clinical outcomes, we analyzed a cohort of 447 patients with metastatic HR+ breast cancer treated at MSK with first-line CDK4/6 inhibitors (CDK4/6i) for which tumor-normal sequencing and long-term clinical follow up were available. To identify the pattern of genomic features associated with longer, intermediate, and short response, we implemented an elastic net Cox regression on binary pathogenic variant status of each gene as well as select clinical features (prior endocrine therapy, endocrine therapy partner, de novo metastatic status). Our principal aim was variable interpretability over pure predictive accuracy. Human HR+ breast cancer models including human breast cancer organoids and cell lines were utilized for mechanistic studies. For validation in a clinical setting, we analyzed the association between Ki67 score after neoadjuvant ribociclib plus endocrine therapy and pre-treatment gene mutation from the FELINE trial [NCT02712723] using a Fisher exact test. Results: Our model identified a “longer response” group (n = 124, 27.7%) from patients with a median progression free survival (PFS) of 32.5 months, compared with an “intermediate” (n = 224, 50.1%, median PFS = 13.7 months) and “short response” group (n = 99, 22.1%, median PFS = 5.84 months). TP53 and MDM2 pathogenic variant status were the most important variables to stratify between these groups, obtaining variable selection frequencies of 1.0 and 0.93 and mean hazard ratios of 2.02 and 1.38, respectively. To elucidate the mechanisms whereby the p53 pathway supports long term response, we generated isogenic and patient derived models of TP53 loss or MDM2 overexpression. Using immunoblotting and cell cycle assays, we found that drug-treated p53 KO cells and MDM2 overexpressing cells effectively suppressed RB1 phosphorylation and blocked in G1 after 24-48 hours. However, upon drug withdrawal, these cells could reenter the cell cycle and promote long-term tumor outgrowth. These effects we observed both in vitro and in vivo. Measures of long-term CDK4/6i response such as expression of senescence associated secretory phenotype genes was abrogated by TP53 loss. Mechanistically, we found persistent phosphorylation of the p130 RB1-like protein in the p53 KO cells. Phosphorylation of p130 impaired its interaction with E2F4, thereby blocking DREAM complex assembly and promoting cell cycle reentry. Inhibition of phosphorylation of p130 via p21 overexpression or by selective CDK2 inhibitors could restore irreversible cell cycle arrest in p53 KO cells. The combination of CDK2 and CDK4/6 inhibition led to long-term tumor growth suppression in models with mutant TP53. To validate the human relevance of TP53 mediating CDK4/6i response, we analyzed longitudinal samples from the FELINE trial that evaluated efficacy and feasibility of neoadjuvant ribociclib plus endocrine therapy. Of 45 evaluable patients, 13 (28.9%) harbored a pre-treatment TP53 loss of function variant. Of these 13 cases, 7 (53.8%) did not achieve a low ( < 10%) Ki-67 upon surgical resection as compared to TP53 wildtype tumors (n=32), only one (3.2%) of which did not achieve a low Ki-67 [OR 32.1, 95% CI 3.28 – 1660.3, p = 0.00026]. Conclusion: Loss of p53 was strongly associated with lack of long-term response to CDK4/6i in patients. Complete inhibition of both CDK4/6 and CDK2 appears to be necessary in order to convert quiescent HR+ tumors cells into durably inhibited and effectively dormant cancers. Citation Format: Rei Kudo, Anton Safonov, Edaise M. da Silva, Qing Li, Hong Shao, Marie Will, Harikrishna Nakshatri, Jorge Reis-Filho, Shom Goel, Andrew Koff, Britta Weigelt, Qamar Khan, Pedram Razavi, Sarat Chandarlapaty. p53 loss enables HR+ breast cancer escape from CDK4/6 inhibitor-induced quiescence via CDK2 [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PS12-03.

Molecular Docking and Dynamics Study of Acetogenins Targeting Cyclin-dependent Kinase and In vitro Evaluation of Annona Muricata Fruit Extracts using MDA-MB-231 Breast Cancer Cell Line

Background: Overexpressed CDK1 and CDK2 are targeted as potential sites for cancer treatment. Annona muricata fruit has been reported to have more than 100 acetogenins showing cytotoxic activities against cancer cell lines. Hence the study aims to demonstrate the cytotoxicity of ethyl acetate fruit extract, its role in cell cycle progression, and apoptosis using the MDMBA-231 breast cancer cell line. Docking, dynamics, and ADME studies were also demonstrated to generate lead molecules of AM fruit responsible for cancer treatment. Method: Cell viability was quantified by the MTT assay. Cell cycle arrest and apoptotic cells were determined by flow cytometry and PI annexin V-FITC staining by flow cytometry, respectively. Molecular docking, molecular dynamics, and ADME properties of 11 acetogenins were studied using the schrödinger maestro suite 2018-1. Results: The MTT assay revealed IC50 232.9μg/ml with a high degree of cytotoxicity. The extract effectively caused cell cycle arrest at the G2M and S phases; early and late apoptosis was induced at 160 μg/ml and 320 μg/ml. Docking scores of muricin L, J, and annomuricin A complexed with CDK2 and muricin J, K, and L with CDK1 binding energy ranging is mentioned as a molecular dynamic study envisaged muricin j against CDK2 stable hydrogen and hydrophobic interactions with critical residues like ASP-86, GLN-131, HIS-84, LYS-89, PHE80, PHE82, and PHE83 throughout 200 ns (hinge region). ADMET profiling also confirmed that all 11 ligands passed the rule of 5 and 3. The in vitro and in silico studies revealed that these acetogenins could be CDK1 and CDK2 inhibitors for cancer treatment. Conclusion: The in vitro studies presume that the ethyl acetate fruit extract of AM is an excellent cytotoxic agent. In silico studies demonstrated that muricin j could lead molecules to target kinase proteins responsible for cell proliferation. ADME study enlightened us to take 11 acetogenins for the drug discovery process in managing cancer treatment.

Androgen receptor splice variants drive castration-resistant prostate cancer metastasis by activating distinct transcriptional programs.

One critical mechanism through which prostate cancer (PCa) adapts to treatments targeting androgen receptor (AR) signaling is the emergence of ligand-binding domain-truncated and constitutively active AR splice variants, particularly AR-V7. While AR-V7 has been intensively studied, its ability to activate distinct biological functions compared with the full-length AR (AR-FL), and its role in regulating the metastatic progression of castration-resistant PCa (CRPC), remain unclear. Our study found that, under castrated conditions, AR-V7 strongly induced osteoblastic bone lesions, a response not observed with AR-FL overexpression. Through combined ChIP-seq, ATAC-seq, and RNA-seq analyses, we demonstrated that AR-V7 uniquely accesses the androgen-responsive elements in compact chromatin regions, activating a distinct transcription program. This program was highly enriched for genes involved in epithelial-mesenchymal transition and metastasis. Notably, we discovered that SOX9, a critical metastasis driver gene, was a direct target and downstream effector of AR-V7. Its protein expression was dramatically upregulated in AR-V7-induced bone lesions. Moreover, we found that Ser81 phosphorylation enhanced AR-V7's pro-metastasis function by selectively altering its specific transcription program. Blocking this phosphorylation with CDK9 inhibitors impaired the AR-V7-mediated metastasis program. Overall, our study has provided molecular insights into the role of AR splice variants in driving the metastatic progression of CRPC.

Design, synthesis, and biological evaluation of dinaciclib and CAN508 hybrids as CDK inhibitors.

The scaffolds of two known CDK inhibitors (CAN508 and dinaciclib) were the starting point for synthesizing two series of pyarazolo[1,5-a]pyrimidines to obtain potent inhibitors with proper selectivity. The study presented four promising compounds; 10d, 10e, 16a, and 16c based on cytotoxic studies. Compound 16a revealed superior activity in the preliminary anticancer screening with GI % = 79.02-99.13 against 15 cancer cell lines at 10 μM from NCI full panel 60 cancer cell lines and was then selected for further investigation. Furthermore, the four compounds revealed good safety profile toward the normal cell lines WI-38. These four compounds were subjected to CDK inhibitory activity against four different isoforms. All of them showed potent inhibition against CDK5/P25 and CDK9/CYCLINT. Compound 10d revealed the best activity against CDK5/P25 (IC50 = 0.063 µM) with proper selectivity index against CDK1 and CDK2. Compound 16c exhibited the highest inhibitory activity against CDK9/CYCLINT (IC50 = 0.074 µM) with good selectivity index against other isoforms. Finally, docking simulations were performed for compounds 10e and 16c accompanied by molecular dynamic simulations to understand their behavior in the active site of the two CDKs with respect to both CAN508 and dinaciclib.

CDK9 inhibition activates innate immune response through viral mimicry.

Cancer cells frequently exhibit hyperactivation of transcription, which can lead to increased sensitivity to compounds targeting the transcriptional kinases, in particular CDK9. However, mechanistic details of CDK9 inhibition-induced cancer cell-selective anti-proliferative effects remain largely unknown. Here, we discover that CDK9 inhibition activates the innate immune response through viral mimicry in cancer cells. In MYC over-expressing prostate cancer cells, CDK9 inhibition leads to the gross accumulation of mis-spliced RNA. Double-stranded RNA (dsRNA)-activated kinase can recognize these mis-spliced RNAs, and we show that the activity of this kinase is required for the CDK9 inhibitor-induced anti-proliferative effects. Using time-resolved transcriptional profiling (SLAM-seq), targeted proteomics, and ChIP-seq, we show that, similar to viral infection, CDK9 inhibition significantly suppresses transcription of most genes but allows selective transcription and translation of cytokines related to the innate immune response. In particular, CDK9 inhibition activates NFκB-driven cytokine signaling at the transcriptional and secretome levels. The transcriptional signature induced by CDK9 inhibition identifies prostate cancers with a high level of genome instability. We propose that it is possible to induce similar effects in patients using CDK9 inhibition, which, we show, causes DNA damage invitro. In the future, it is important to establish whether CDK9 inhibitors can potentiate the effects of immunotherapy against late-stage prostate cancer, a currently lethal disease.

Discovering new CDK2 inhibitors by molecular docking and drug-likeness-based virtual screening for potential anticancer uses.

Discovering new CDK2 inhibitors by molecular docking and drug-likeness-based virtual screening for potential anticancer uses.

Focus on current and emerging treatment options for glioma: A comprehensive review.

This comprehensive review delves into the current updates and challenges associated with the management of low-grade gliomas (LGG), the predominant primary tumors in the central nervous system. With a general incidence rate of 5.81 per 100000, gliomas pose a significant global concern, necessitating advancements in treatment techniques to reduce mortality and morbidity. This review places a particular focus on immunotherapies, discussing promising agents such as Zotiraciclib and Lerapolturev. Zotiraciclib, a CDK9 inhibitor, has demonstrated efficacy in glioblastoma treatment in preclinical and clinical studies, showing its potential as a therapeutic breakthrough. Lerapolturev, a viral immunotherapy, induces inflammation in glioblastoma and displays positive outcomes in both adult and pediatric patients. Exploration of immunotherapy extends to Pembrolizumab, Nivolumab, and Entrectinib, revealing the challenges and variabilities in patient responses. Despite promising preclinical data, the monoclonal antibody Depatuxizumab has proven ineffective in glioblastoma treatment, emphasizing the critical need to understand resistance mechanisms. The review also covers the success of radiation therapy in pediatric LGG, with evolving techniques, such as proton therapy, showing potential improvements in patient quality of life. Surgical treatment is discussed in the context of achieving a balance between preserving the patient's quality of life and attaining gross total resection, with the extent of surgical resection significantly influencing the survival outcomes. In addition to advancements in cancer vaccine development, this review highlights the evolving landscape of LGG treatment, emphasizing a shift toward personalized and targeted therapies. Ongoing research is essential for refining strategies and enhancing outcomes in the management of LGG.

Discovery and preclinical evaluations of TQB3616, a novel CDK4-biased inhibitor

Among small-molecule CDK4/6 inhibitors (palbociclib, ribociclib, and abemaciclib) approved for metastatic breast cancers, abemaciclib has a more tolerable adverse effects in clinic. This is attributable to preferential inhibition of CDK4 over CDK6. In our search for a biased CDK4 inhibitor, we discovered a series of pyrimidine-indazole inhibitors. SAR studies led us to TQB3616 as a preferential CDK4 inhibitor. TQB3616 exhibited improvements in both enzymatic and cellular proliferation inhibitory potency when tested side-by-side with the FDA approved palbociclib and abemaciclib. TQB3616 also possessed favorable PK profile in multiple species. These differentiated properties, together with excellent GLP safety profile warranted TQB3616 moving to clinic. TQB3616 entered into clinical development in 2019 and currently in phase III clinical trials (NCT05375461, NCT05365178).

Anti-Tumor Activity and Mechanism of Silibinin Based on Network Pharmacology and Experimental Verification.

Silibinin is a flavonoid compound extracted from the seeds of Silybum marianum (L.) Gaertn. It has the functions of liver protection, blood-lipid reduction and anti-tumor effects. However, the potential molecular mechanism of silibinin against tumors is still unknown. This study aimed to assess the anti-tumor effects of silibinin in adenoid cystic carcinoma (ACC2) cells and Balb/c nude mice, and explore its potential mechanism based on network pharmacology prediction and experimental verification. A total of 347 targets interacting with silibinin were collected, and 75 targets related to the tumor growth process for silibinin were filtrated. Based on the PPI analysis, CASP3, SRC, ESR1, JAK2, PRKACA, HSPA8 and CAT showed stronger interactions with other factors and may be the key targets of silibinin for treating tumors. The predicted target proteins according to network pharmacology were verified using Western blot analysis in ACC2 cells and Balb/c nude mice. In the pharmacological experiment, silibinin was revealed to significantly inhibit viability, proliferation, migration and induce the apoptosis of ACC2 cells in vitro, as well as inhibit the growth and development of tumor tissue in vivo. Western blot analysis showed that silibinin affected the expression of proteins associated with cell proliferation, migration and apoptosis, such as MMP3, JNK, PPARα and JAK. The possible molecular mechanism involved in cancer pathways, PI3K-Akt signaling pathway and viral carcinogenesis pathway via the inhibition of CASP3, MMP3, SRC, MAPK10 and CDK6 and the activation of PPARα and JAK. Overall, our results provided insight into the pharmacological mechanisms of silibinin in the treatment of tumors. These results offer a support for the anti-tumor uses of silibinin.

Prediction model for pheochromocytoma/paraganglioma using nCounter assay.

World Health Organization defined pheochromocytomas/paragangliomas (PPGL) as malignant tumors in 2017 because the existing classification system could not reflect locally aggressive behavior sufficiently. However, predicting the likelihood of metastasis remains a crucial part of the treatment strategy. From one tertiary care hospital and onesecondary hospital, 97 PPGL cases were selected. Medical records of PPGL cases with the presence of formalin-fixed and paraffin-embedded (FFPE) tissue of primary lesion were reviewed. For FFPE tissues, a nCounter assay was conducted to determine differently expressed genes between metastatic and non-metastatic PPGL groups. Performances of prediction models for the likelihood of metastasis were calculated. Of a total of 97 PPGL cases, 39, 20, and 38 were classified as benign, malignant, and validation, respectively. In the nCounter assay, CDK1, TYMS, and TOP2A genes showed significant differences in expression. Tumor size was positively correlated with CDK1 expression level. The Lasso regression model showed supreme performance of sensitivity 91.7% and specificity 95.5% when those significant factors were considered. Machine learning of multi-modal classifiers can be used to create a prediction model for metastasis of PPGL with high sensitivity and specificity using nCounter assay. Moreover, CDK1 inhibitors could be considered for developing drug treatment.

Association between CDK4/6 inhibitors and drug-related osteonecrosis of the jaw: A pharmacoepidemiological study using the FDA Adverse Events Reporting System.

The most common toxicities associated with cyclin-dependent kinase (CDK) 4/6 inhibitor therapy include decreased leukopenia and neutropenia due to the inhibition of CDK6 of leukocyte and neutrophil precursors in bone marrow. These hematological toxicities are more commonly observed with palbociclib administration than with abemaciclib administration, which is approximately 13 times more selective against CDK4 than CDK6. Thus, even though both successfully inhibit CDK4/6, the side effects of palbociclib and abemaciclib differ due to differences in selectivity. Recent reports have suggested an association between palbociclib and medication-related osteonecrosis of the jaw; however, reports on this association are inconsistent. This study investigated the potential association of palbociclib and abemaciclib with MRONJ using the FAERS. Signals of "Osteonecrosis of jaw" were detected only in females using palbociclib (cROR025: 2.08). Other signals detected included stomatitis-related adverse events with abemaciclib and intraoral soft tissue damage and infection with palbociclib. As previous exploratory studies have reported MRONJ signals for bisphosphonates and denosumab, we calculated the aROR for palbociclib-induced osteonecrosis of the jaw using concomitant bisphosphonates and denosumab as covariates. A signal was detected even after adjusting for sex, age, and concomitant medications as covariates (aROR0025: 5.74). A proper understanding of the differences in CDK selectivity is necessary for the appropriate use of CDK4/6 inhibitors. To the best of our knowledge, this is the first report on CDK4/6 inhibitors and drug-related osteonecrosis of the jaw. We believe that these results will offer new insights into adverse events related to the use of CDK4/6 inhibitors, and may aid in the proper use of CDK4/6 inhibitors.

Discovery of structural diversity guided steroidal thiazolidin-4-one derivatives as potential cytotoxic agents targeting CDK1

Structural diversity guided steroidal thiazolidin-4-one conjugates were designed and synthesized based on six steroid skeletons mainly including androst-4-ene-3,17-dione, dehydroepiandrosterone, epiandrosterone, androst-1,4-diene-3,17-dione, dienedione and 9α-hydroxy-androst-4-ene-3,17-dione. Their in vitro inhibition activities against cell proliferation were fully investigated, and some of which exhibited good antiproliferative activities as potential CDK1 inhibitor. The detailed analysis of structure–activity relationships (SARs) based on the inhibition activities, kinase assay, and molecular docking model demonstrated that the structure of different steroidal core ring skeleton as well as the N substituents of the thiazolidin-4-one ring influenced the inhibitory activity on cancer cell lines. Especially, compounds 15c and 16c have certain inhibitory effects on the tyrosine protein kinases CDK1/CyclinA2, ALK, CDK6/CyclinD1, FGFR1 and PIM2. Compounds 16c displayed highest inhibitory effect on the kinases of CDK1/CyclinA2 with inhibition rate 56.38 % at the concentration of 10 μM, which induced cell death in A875 cells at least partly (initially), by apoptosis.

Hit discovery of potential CDK8 inhibitors and analysis of amino acid mutations for cancer therapy through computer-aided drug discovery

Cyclin-dependent kinase 8 (CDK8) has emerged as a promising target for inhibiting cancer cell function, intensifying efforts towards the development of CDK8 inhibitors as potential cancer therapeutics. Mutations in CDK8, a protein kinase, are also implicated as a primary factor associated with tumor formation. In this study, we identified potential inhibitors through virtual screening for CDK8 and single amino acid mutations in CDK8, namely D173A (Aspartate 173 mutate to Alanine), D189N (Aspartate 189 mutate to Asparagine), T196A (Threonine 196 mutate to Alanine) and T196D (Threonine 196 mutate to Aspartate). Four databases (CHEMBEL, ZINC, MCULE, and MolPort) containing 65,209,131 molecules have been searched to identify new inhibitors for CDK8 and its single mutations. In the first step, structure-based pharmacophore modeling in the Pharmit server was used to select the compounds to know the inhibitors. Then molecules with better predicted drug-like molecule properties were selected. The final filter used to select more effective inhibitors among the previously selected molecules was molecular docking. Finally, 13 hits for CDK8, 11 hits for D173A, 11 hits for D189N, 15 hits for T196A, and 12 hits for T196D were considered potential inhibitors. A majority of the virtual screening hits exhibited satisfactorily predict pharmacokinetic characteristics and toxicity properties.

Abstract SY19-03: Mechanisms of sensitivity and resistance to CDK2 inhibitors

Abstract CDK2 is a core cell-cycle kinase that phosphorylates many substrates to drive progression through the cell cycle. We used several CDK2 inhibitors in clinical development to interrogate CDK2 substrate phosphorylation, cell-cycle progression, and drug adaptation in preclinical models. In normal mammary cells and estrogen receptor-positive breast cancer cells, CDK2 inhibition causes a rapid loss of substrate phosphorylation that is rapidly restored by a hard-wired cell-cycle buffering mechanism. In this mechanism, CDK4/6 backstops Rb1 hyper-phosphorylation to maintain Cyclin A2 expression, enabling re-activation of CDK2 in the presence of CDK2 inhibitor. By contrast, CCNE1-amplified ovarian cancers do not exhibit this rapid rebound. Our results augment our understanding of CDK plasticity and CDK dependencies, delineate the genetic backgrounds in which this adaptive rebound upon CDK2 inhibition can occur, and suggest contexts in which CDK2 inhibition will be most effective as a cancer therapy. Citation Format: Sabrina L. Spencer. Mechanisms of sensitivity and resistance to CDK2 inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr SY19-03.

Abstract LB168: A selective, potent, and orally bioavailable CDK7 inhibitor demonstrates superior anti-cancer activity in colorectal cancer models

Abstract Dysregulated cell cycle and gene expression are pivotal factors in cancer development and the regulators of these processes are attractive targets for cancer treatment. The success of CDK4/6 inhibitors such as palbociclib, ribociclib, and abemaciclib underscores the promising role of targeting cell cycle regulators in anti-cancer therapy. On the other hand, a robust correlation has been established between the overexpression of oncogenes and super-enhancer (SE). The genes associated with SE show increased vulnerability to transcription factor disruption compared to genes with typical enhancers. It has been demonstrated in previous studies that inhibiting transcription factors can effectively decrease the expression of SE-associated oncogenes, including c-MYC, thereby highlighting potential anticancer effects for oncogene-addicted cancers. Currently, agents targeting transcription factors are undergoing clinical trials, offering promising therapeutic options for patients with various types of cancers. CDK7 plays a crucial role in orchestrating cell cycle progression and transcription by phosphorylating CDKs, the C-terminal domain of RNA polymerase II, and hormone receptors like estrogen and androgen receptors. The inhibition of CDK7 has been shown to effectively inhibit tumor growth through various mechanisms, including inducing cell cycle arrest and inhibiting transcription, thereby leading to the death of cancer cells. Notably, ongoing clinical studies have demonstrated that small-molecule CDK7 inhibitors effectively control cancer progression as a stand-alone and in combination with other anti-cancer agents. C-16661, a selective, potent, orally bioavailable, and reversible ATP-competitive inhibitor of CDK7, displayed a single-digit nanomolar IC50 value in both biochemical and cellular assays. It exhibited excellent selectivity in a kinase panel assay, and remarkable potency in a human cancer cell line panel assay. C-16661 treatment resulted in strong inhibition of both its direct and indirect downstream targets including pS5-POLII, pT161-CDK1, c-MYC, and MCL1 in HCT116, a human colorectal carcinoma cell line. While C-16661 exhibited good PK profiles in animals, it demonstrated excellent tumor growth inhibition without any tolerability issues in a colorectal cancer CDX mouse efficacy model. Citation Format: Heuijoon Park, Kyoungwan Seo, Jihyun Yu, Jieun Kim, Min Sung Joo, Sungeun Kim, Joonhyung Lee, Jeonghyeon Lee, Eun-Jung Kim, Joonwoo Nam, Wooseok Han. A selective, potent, and orally bioavailable CDK7 inhibitor demonstrates superior anti-cancer activity in colorectal cancer models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB168.

Abstract LB161: Discovery of an oral, potent, and selective CDK9 molecular glue degrader SLX-3065 active in aggressive variant prostate cancers (AVPC)

Abstract Background: The use of new potent targeted therapies in prostate cancers has led to the resistance and development of highly aggressive variant prostate cancers (AVPC), including neuroendocrine prostate cancers (NEPC). N-MYC and C-MYC oncogenes overexpress in all aggressive prostate cancers (PCa). This overexpression is highly prevalent in these lethal subtypes of cancers, detected in 2% of all Prostate Cancers and over 10-17% of mCRPC patients. Transcriptional targets of CDK9 are MYCs, which act as an oncogenic driver, sufficient to transform human-derived prostate cancer cells to take on AVPC and NEPC phenotypic changes. Additionally, N-MYC and C-MYC play key roles in tumor drug resistance, and their downregulation, through CDK9 inhibition or degradation lowers tumor growth. Our efforts have demonstrated that targeting drivers of NEPC and mCRPC with highly selective CDK9 molecular glue degraders SLX-3064 SLX-3065 was designed from reversible SLX-3039 for therapeutic intervention of mCRPC, AVPC, and NEPCs. Materials and Methods: We employed our MolecuLernTM-trained molecular glue library design strategies and in vitro CDK9 kinase binding assays. Other experiments include cellular efficacies of single-agent Molecular Glue degraders and their effect in combination experiments on 22Rv1, LASCPC-01, C4-2, and C4-2B MYC expressed PCa cells. Kinase selectivity, Nano BRET, ADME-Tox, in vitro safety, secondary pharmacological assays, Cell engraftment mouse tumor mode, and PK studies were performed. Results: We designed and synthesized a series of novel small molecule CDK9 Molecular Glue degraders based on our initial CDK9 inhibitor lead SLX-3030 and SLX-3039. The SLX-3064 and SLX-3065 reversibly bind to CDK9 with an IC50 of 9 and 7 nM in kinase binding, in target engagement assays, elicit pharmacological responses in N-MYC, C-MYC, driven prostate cancer cells in vitro in LASCPC-01 (21, 35 nM), 22Rv1 (108, 236 nM), C4-2B (15, 12 nM), C4-2 (2.7, 1.5 nM) and VCap (86, 73 nM) cell lines. SLX-3064 and SLX-3065 exhibited potent activity degrading total, pCDK9, MYCs, Mcl-1, and its downstream RNA Pol II, Ser 2, 5, 7, and pAR Ser-81 in a dose-dependent manner. Additionally, we performed in vitro ADME-Tox, hERG, P450, safety panel screen, and in vivo PK experiments in rodent and beagle dog species. Conclusion: In summary, both SLX-3064 and SLX-3065 molecular glues display complete degradation of CDK9 and its downstream markers, and these degraders possess ideal developable criteria as oral agents. With these characteristics, SLX-3065 was selected as a candidate that had the appropriate developable properties and our plans for conducting additional IND-enabling studies and future clinical trial plans will also be discussed. Citation Format: Chenyu Lin, Zhaoliang Li, Kyle Medley, David J. Bearss, Hariprasad Vankayalapati. Discovery of an oral, potent, and selective CDK9 molecular glue degrader SLX-3065 active in aggressive variant prostate cancers (AVPC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB161.

Abstract LB265: IpY.20: Innovative strategies for post-CDK estrogen receptor (ER)+ metastatic breast cancer (mBC)

Abstract Cyclin-dependent kinases (CDK) 4/6 are key cell cycle regulators that form complexes with cyclin D1 and the master regulator p27Kip1. This ternary complex acts downstream of the ER- and HER2-pathways, which drive cell proliferation. CDK4/6 phosphorylates the Retinoblastoma protein and other substrates, and keeps p27 from inhibiting G1-associated CDK2. Targeted inhibition of CDK4/6 (CDK4/6i) blocks the growth of ER+ and HER2+ BC by dissolving the CDK4/6-cyclin D1 complex and permitting the shuttling of p27 to inhibit CDK2 complex. Approval of CDK 4/6i such as palbociclib, though a game changer for ER+ mBC, resulted in tumor resistance, leaving patients without effective treatments and a 5-yr survival of only 30%. Although CDK2 inhibitors (CDK2i) address compensatory CDK2 activity bypassing CDK4/6i, a key resistance mechanism, they lack selectivity due to CDK homology, resulting in off-target toxicity. To inhibit CDK2/4/6 simultaneously, combinations of CDK4/6i and CDK2i monotherapies were attempted, but the lack of coordination between CDK4/6 and CDK2 inhibition resulted in suboptimal efficacy. Concarlo presents a unique therapeutic rationale for directly targeting the CDK master regulator p27 to simultaneously inhibit CDK2/4/6 in a concerted manner, one that is guided by the role of p27 to turn all of the G1 CDKs ON and OFF during periods of proliferation and quiescence, respectively. This transition is facilitated by BRK (Breast tumor kinase)-mediated phosphorylation of p27. When p27 is Y phosphorylated, it converts CDK4/6 and CDK2 into open, active complexes. An endogenous BRK-spliced variant ALT can competitively bind to p27, block Y phosphorylation and lock CDK2/4/6 in the OFF conformation. Concarlo engineered a shorter variant of ALT (CCL20) and packaged in cationic liposomes for intracellular delivery, creating a novel IpY.20 drug product. As a single agent, IpY.20 inhibits cell proliferation in treatment-naïve and CDK4i-resistant HR+ cells with reduced non-tumor cell activity. In combination, IpY.20 enhances CDK4/6i responses in treatment-naïve HR+ cells, making it a potential front-line mBC therapy. While other CDKi activity is limited to cytostasis, IpY.20 shows dual cytostasis-cytotoxicity, potentially a more durable option. IpY.20 does not cause neutropenia commonly seen with other CDKis, and rescues the CDK4/6i-induced neutropenia in mice, suggesting better clinical tolerability. These findings underscore the significance of coordinated targeting of CDK2/4/6, making IpY.20 a first-in-class product uniquely exploiting p27-mediated CDK2/4/6 regulation. Direct targeting of p27 presents a new treatment paradigm bypassing the challenges of ATP-competitive CDKis, with potential to expand into tumor types with aberrant p27, CDK2/4/6 activity, or RAS/MAPK pathways that increase CDK4/6 activity. Citation Format: Grace Chen, Natalie Dudas, Kate Coleman, Carolina Guido, Natalia Zisman, Krishna Allamneni, Stacy Wister Blain. IpY.20: Innovative strategies for post-CDK estrogen receptor (ER)+ metastatic breast cancer (mBC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB265.