Structure-guided design and development of cyclin-dependent kinase 4/6 inhibitors: A review on therapeutic implications

A patent review of small molecule CDK4/6 inhibitors in the treatment of cancer: 2020-present

INTRODUCTION

Cyclin-dependent protein kinase 4/6 (CDK4/6) is a class of serine/threonine protein kinases that plays a key role in the regulation of the cell cycle. CDK4/6 is highly expressed in cancers such as breast cancer, melanoma, and non-small cell lung cancer (NSCLC). Currently, a variety of CDK4/6 inhibitors have been developed, aiming to develop effective inhibitors to solve CDK4/6 resistance and toxicity.

AREAS COVERED

This article searches patents through Espacenet and reviews the development of widely studied CDK inhibitors and FDA-approved CDK4/6 inhibitors, as well as the latest progress of patented inhibitors with good inhibitory activity against CDK4/6 from 2020 to now.

EXPERT OPINION

CDK4/6 is highly expressed in many tumors and has become an important anti-tumor target. Among the patents from 2020 to the present, many inhibitors have good kinase inhibitory effects on CDK4/6 and also show great development potential in anti-tumor. However, there is still an urgent need to develop novel CDK4/6 inhibitors that address challenges such as drug resistance, toxicity, and selectivity.

Real-world experience with CDK4/6 inhibitors in hormone receptor-positive metastatic and recurrent breast cancer: findings from an Asian population

PURPOSE

Cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) combined with endocrine therapy have demonstrated significant clinical benefits in progression-free and overall survival. This study investigates the outcomes associated with two kinds of CDK4/6i in patients with hormone receptor (HR)-positive metastatic and relapsed breast cancer to inform real-world evidence of treatment strategies.

METHODS

This retrospective study included 340 Taiwanese patients with HR-positive advanced breast cancer from the Taipei Veterans General Hospital, between 2018 and 2023. We analyzed patient characteristics, treatment strategies and outcomes associated with two CDK4/6i. The efficacy of patients who experienced economic burden and interrupted CDK4/6i treatment after 2 years of National Health Insurance (NHI) reimbursement was also investigated.

RESULTS

Patients receiving ribociclib and palbociclib showed no significant differences in age, histology, body mass index(BMI), or pathologic status. The distribution of disease status and endocrine therapy partners was comparable between the two groups. Dose reduction was similar, while patients with palbociclib tended to discontinue CDK4/6i usage, and those with ribociclib tended to switch to the other CDK4/6i or endocrine partners. There was no significant difference in progression-free survival (PFS) between the two CDK4/6i in the first-line setting. Adverse prognostic factors were increasing HER2 IHC score, higher Ki-67 levels, visceral and liver metastasis, prior chemotherapy, and endocrine therapy resistance, while higher BMI, bone-only metastasis, and letrozole treatment were associated with a lower risk of progression. The limited follow-up time in our study was insufficient to assess the outcomes of patients treated with interrupted CDK4/6i for up to two years under the NHI reimbursement policy.

CONCLUSION

Treatment outcomes between the two types of CDK4/6i did not differ significantly, indicating the safety and efficacy of CDK4/6i for the Asian population. Ribociclib and palbociclib showed similar efficacy in PFS in the real-world setting.

A disproportionality analysis of CDK4/6 inhibitors in the FDA Adverse Event Reporting System (FAERS)

OBJECTIVE

The FDA Adverse Event Reporting System (FAERS) was used to mine and evaluate adverse events (AEs) associated with cyclin-dependent kinase (CDK) 4/6 inhibitors, thereby providing a reference for clinical rational drug use.

METHODS

AE data related to CDK4/6 inhibitors from the first quarter of 2015 to the first quarter of 2023 were acquired from FAERS, while the signal mining was processed using the reporting odds ratio (ROR) method and Bayesian confidence propagation neural network (BCPNN) method.

RESULTS

The number of AE reports for CDK4/6 inhibitors was, respectively, 132,494 for palbociclib, 56,151 for ribociclib, and 7,014 for abemaciclib. The corresponding numbers of AE signals were 319, 517, and 59, with the number of involved System Organ Class (SOC) being 23, 23, and 15, mainly involving blood and lymphatic system disorders, respiratory, thoracic and mediastinal disorders, hepatobiliary disorders, skin and subcutaneous tissue disorders, etc.

CONCLUSION

CDK4/6 inhibitors could lead to pulmonary toxicity, myelosuppression, skin reactions, etc. Special attention should be paid to abemaciclib for interstitial lung disease (ILD), erythema multiforme, and thrombosis risk; ribociclib for cardiac toxicity, hepatotoxicity, and musculoskeletal toxicity; palbociclib for neurocognitive impairment and osteonecrosis of the jaw.

PhosAF: An integrated deep learning architecture for predicting protein phosphorylation sites with AlphaFold2 predicted structures

Phosphorylation is indispensable in comprehending biological processes, while biological experimental methods for identifying phosphorylation sites are tedious and arduous. With the rapid growth of biotechnology, deep learning methods have made significant progress in site prediction tasks. Nevertheless, most existing predictors only consider protein sequence information, that limits the capture of protein spatial information. Building upon the latest advancement in protein structure prediction by AlphaFold2, a novel integrated deep learning architecture PhosAF is developed to predict phosphorylation sites in human proteins by integrating CMA-Net and MFC-Net, which considers sequence and structure information predicted by AlphaFold2. Here, CMA-Net module is composed of multiple convolutional neural network layers and multi-head attention is appended to obtaining the local and long-term dependencies of sequence features. Meanwhile, the MFC-Net module composed of deep neural network layers is used to capture the complex representations of evolutionary and structure features. Furthermore, different features are combined to predict the final phosphorylation sites. In addition, we put forward a new strategy to construct reliable negative samples via protein secondary structures. Experimental results on independent test data and case study indicate that our model PhosAF surpasses the current most advanced methods in phosphorylation site prediction.

Recent progress of CDK4/6 inhibitors' current practice in breast cancer

Dysregulated cellular proliferation represents a hallmark feature across all cancers. Aberrant activation of the cyclin-dependent kinase 4 and 6 (CDK4/6) pathway, independent of mitogenic signaling, engenders uncontrolled breast cancer cell proliferation. Consequently, the advent of CDK4/6 inhibition has constituted a pivotal milestone in the realm of targeted breast cancer therapy. The combination of CDK4/6 inhibitors (CDK4/6i) with endocrine therapy (ET) has emerged as the foremost therapeutic modality for patients afflicted with hormone receptor-positive (HR + )/HER2-negative (HER2-) advanced breast cancer. At present, the Food and Drug Administration (FDA) has sanctioned various CDK4/6i for employment as the primary treatment regimen in HR + /HER2- breast cancer. This therapeutic approach has demonstrated a substantial extension of progression-free survival (PFS), often amounting to several months, when administered alongside endocrine therapy. Within this comprehensive review, we systematically evaluate the utilization strategies of CDK4/6i across various subpopulations of breast cancer and explore potential therapeutic avenues following disease progression during application of CDK4/6i therapy.

Design, Synthesis, and Biological Evaluation for First GPX4 and CDK Dual Inhibitors

The coexistence of ferroptosis and other modes of death has great advantages in the treatment of cancers. A series of glutathione peroxidase 4 (GPX4) and cyclin-dependent kinase (CDK) dual inhibitors were designed and synthesized, given the synergistic anticancer effect of ML162 (GPX4 inhibitor) in combination with indirubin-3'-oxime (IO) (CDK inhibitor). Compound B9 exhibited the highest potential cytotoxic activity against all four cell lines and displayed excellent inhibitory activity against GPX4 (IC50 = 542.5 ± 0.9 nM) and selective inhibition of CDK 4/6 (IC50 = 191.2 ± 8.7, 68.1 ± 1.4 nM). Mechanism research showed that B9 could simultaneously induce ferroptosis and arrest cells at the G1 phase in both MDA-MB-231 cells and HCT-116 cells. Compared with ML162 and IO, B9 showed much stronger cancer cell growth inhibition in vivo. These results proved that developing potent GPX4/CDK dual inhibitors is a promising strategy for the malignant cancer therapy.

Cerebral venous sinus thrombosis in a patient treated with ribociclib for metastatic breast cancer. Case reports and literature review

Breast cancer is the most diagnosed cancer among women worldwide. Cyclin dependent kinase 4/6 inhibitors (ribociclib, palbociclib, and abemaciclib) modulate endocrine resistance and are widely used treatment for patients with advanced-stage hormone receptor-positive, human epidermal growth factor receptor 2-negative breast cancer. Reports of both venous and arterial thromboembolic events, as a complication of cyclin dependent kinase 4/6 inhibitors, are increasingly recognized, but none involved cerebral venous sinus. We herein report on a 44-year-old female patient who initially presented with an early-stage breast cancer treated with surgery, chemotherapy, radiation therapy and finished 5 years of tamoxifen uneventfully. Eight years after her initial diagnosis, she relapsed with a solitary brain lesion which was resected and treated with radiation therapy, and was then started on aromatase inhibitors. Few months later, she progressed with biopsy-proven cervical and mediastinal lymph node metastasis. She was then switched to fulvestrant and ribociclib; both were well-tolerated. However, few weeks later she presented with increasing headache and mild dizziness. Imaging studies showed right lateral sinus acute non-occlusive thrombosis with no parenchymal changes. Patient was anticoagulated with low molecular weight heparin and follow-up visits showed stable disease with no bleeding.

Integrated virtual screening and MD simulation study to discover potential inhibitors of Lyn-kinase: targeting cancer therapy

Tyrosine-protein kinase Lyn (LynK) has emerged as one of the most attractive therapeutic targets for cancer and diabetes. In this study, we used a multistep virtual screening process of natural compounds to discover potential inhibitors of LynK from the IMPPAT database. The primary filters were based on Lipinski rules, ADMET properties, and PAINS patterns. Then, binding affinities and interaction analyses were carried out for the high-affinity selectivity of the compounds towards LynK. Eventually, two natural compounds, Glabrene and Lactupicrin, were identified with high affinity and specificity for the LynK-binding pocket. Both compounds exhibited drug-like properties, as predicted by ADMET analysis and physicochemical parameters. The molecular dynamics (MD) simulation study revealed that these compounds bind to the ATP-binding pocket of LynK and interact with functionally significant residues with stability without inducing any significant structural changes to the protein. Ultimately, the identified compounds may be regarded as promising LynK inhibitors and can be used as lead molecules in the drug development against LynK-related diseases.Communicated by Ramaswamy H. Sarma.

Therapeutic targeting of microtubule affinity-regulating kinase 4 in cancer and neurodegenerative diseases

Microtubule affinity-regulating kinase 4 (MARK4) is a member of the Ser/Thr protein kinase family, phosphorylates the microtubule-connected proteins and plays a vital role in causing cancers and neurodegenerative diseases. This kinase modulates multiple signaling pathways, including mammalian target of rapamycin, nuclear factor-κB, and Hippo-signaling, presumably responsible for cancer and Alzheimer's. MARK4 acts as a negative controller of the Hippo-kinase cassette for promoting YAP/TAZ action, and the loss of MARK4 detains the tumorigenic properties of cancer cells. MARK4 is involved in tau hyperphosphorylation that consequently affects neurodegeneration. MARK4 is a promising drug target for cancer, diabetes, and Alzheimer's. Developing the potent and selective inhibitors of MAKR4 are promising in the therapeutic management of associated diseases. Despite its great significance, a few reviews are available to discuss its structure, function and clinical significance. In the current review, we aimed to provide detailed information on the structural features of MARK4 targeted in drug development and its role in various signaling pathways related to cancer and neurodegenerative diseases. We further described the therapeutic potential of MARK4 inhibitors in preventing numerous diseases. Finally, the updated information on MARK4 will be helpful in the further development of effective therapeutic molecules.

Disproportionality Analysis of Abemaciclib in the FDA Adverse Event Reporting System: A Real-World Post-Marketing Pharmacovigilance Assessment

BACKGROUND AND OBJECTIVE

Abemaciclib, a cyclin-dependent kinase 4 and 6 inhibitor, demonstrated efficacy in women with hormone receptor-positive, human epidermal growth factor receptor 2-negative advanced breast cancer. Because of the limitations of clinical trials, which are not representative of large real-world populations, rare events and long-term safety concerns cannot be detected. The current study aimed to evaluate the adverse events of abemaciclib through data mining of the Food and Drug Administration Adverse Event Reporting System (FAERS).

METHODS

Reporting odds ratio and Bayesian confidence propagation neural network of information components were used to quantify the adverse event signals of abemaciclib from the third quarter of 2017 to the first quarter of 2022. Serious and non-serious cases were compared using the Mann-Whitney U test or Chi-squared test, and clinical priority was assigned to signals by scoring (range 0-10 points) five features using a rating scale.

RESULTS

A total of 6125 reports of abemaciclib as the "primary suspected" and 72 significant adverse events of abemaciclib were identified. Common adverse events, such as diarrhea, neutropenia, alanine transaminase, aspartate transaminase, and serum creatinine increases, and other adverse events, including thrombosis, deep vein thrombosis, pulmonary embolism, interstitial lung disease, and pneumonitis were of high concern. Of note, 17 preferred terms were classified as unexpected adverse events that uncovered in the label. In addition, 1, 26, and 45 adverse events were identified as strong, moderate, and weak clinical priorities. The median time to onset for strong, moderate, and weak clinical priority signals was 49, 22, and 28 days, respectively. All of the disproportionality signals had early failure type features, suggesting that adverse events of abemaciclib gradually decreased over time.

CONCLUSIONS

The discovery of disproportionality signals could potentially prompt improved awareness of toxicities for abemaciclib, and the results of time to onset, serious and non-serious reports, and clinical priority analyses provided some supporting evidence for clinicians to manage adverse events.

Therapeutic Targeting of Regulated Signaling Pathways of Non-Small Cell Lung Carcinoma

Non-small cell lung carcinoma (NSCLC) is the most common cancer globally. Phytochemicals and small molecule inhibitors significantly prevent varying types of cancers, including NSCLC. These therapeutic molecules serve as important sources for new drugs that interfere with cellular proliferation, apoptosis, metastasis, and angiogenesis by regulating signaling pathways. These molecules affect several cellular signaling cascades, including p53, NF-κB, STAT3, RAS, MAPK/ERK, Wnt, and AKT/PI3K, and are thus implicated in the therapeutic management of cancers. This review aims to describe the bioactive compounds and small-molecule inhibitors, their anticancer action, and targeting cellular signaling cascades in NSCLC. We highlighted the therapeutic potential of Epigallocatechin gallate (EGCG), Perifosine, ABT-737, Thymoquinine, Quercetin, Venetoclax, Gefitinib, and Genistein. These compounds are implicated in the therapeutic management of NSCLC. This review further offers deeper mechanistic insights into different signaling pathways that could be targeted for NSCLC therapy by phytochemicals and small-molecule inhibitors.

Identification of abemaciclib derivatives targeting cyclin-dependent kinase 4 and 6 using molecular dynamics, binding free energy calculation, synthesis, and pharmacological evaluation

CDK4/6 plays a crucial role in various cancers and is an effective anticancer drug target. However, the gap between clinical requirements and approved CDK4/6 drugs is unresolved. Thus, there is an urgent need to develop selective and oral CDK4/6 inhibitors, particularly for monotherapy. Here, we studied the interaction between abemaciclib and human CDK6 using molecular dynamics simulations, binding free energy calculations, and energy decomposition. V101 and H100 formed stable hydrogen bonds with the amine-pyrimidine group, and K43 interacted with the imidazole ring via an unstable hydrogen bond. Meanwhile, I19, V27, A41, and L152 interacted with abemaciclib through π-alkyl interactions. Based on the binding model, abemaciclib was divided into four regions. With one region modification, 43 compounds were designed and evaluated using molecular docking. From each region, three favorable groups were selected and combined with each other to obtain 81 compounds. Among them, C2231-A, which was obtained by removing the methylene group from C2231, showed better inhibition than C2231. Kinase profiling revealed that C2231-A showed inhibitory activity similar to that of abemaciclib; additionally, C2231-A inhibited the growth of MDA-MB-231 cells to a greater extent than did abemaciclib. Based on molecular dynamics simulation, C2231-A was identified as a promising candidate compound with considerable inhibitory effects on human breast cancer cell lines.

Biochemical features and therapeutic potential of α-Mangostin: Mechanism of action, medicinal values, and health benefits

α-Mangostin (α-MG) is a natural xanthone obtained from the pericarps of mangosteen. It exhibits excellent potential, including anti-cancer, neuroprotective, antimicrobial, antioxidant, and anti-inflammatory properties, and induces apoptosis. α-MG controls cell proliferation by modulating signaling molecules, thus implicated in cancer therapy. It possesses incredible pharmacological features and modulates crucial cellular and molecular factors. Due to its lesser water solubility and pitiable target selectivity, α-MG has limited clinical application. As a known antioxidant, α-MG has gained significant attention from the scientific community, increasing interest in extensive technical and biomedical applications. Nanoparticle-based drug delivery systems were designed to improve the pharmacological features and efficiency of α-MG. This review is focused on recent developments on the therapeutic potential of α-MG in managing cancer and neurological diseases, with a special focus on its mechanism of action. In addition, we highlighted biochemical and pharmacological features, metabolism, functions, anti-inflammatory, antioxidant effects and pre-clinical applications of α-MG.

Intelligent delivery system targeting PD-1/PD-L1 pathway for cancer immunotherapy

The drugs targeting the PD-1/PD-L1 pathway have gained abundant clinical applications for cancer immunotherapy. However, only a part of patients benefit from such immunotherapy. Thus, brilliant novel tactic to increase the response rate of patients is on the agenda. Nanocarriers, particularly the rationally designed intelligent delivery systems with controllable therapeutic agent release ability and improved tumor targeting capacity, are firmly recommended. In light of this, state-of-the-art nanocarriers that are responsive to tumor-specific microenvironments (internal stimuli, including tumor acidic microenvironment, high level of GSH and ROS, specifically upregulated enzymes) or external stimuli (e.g., light, ultrasound, radiation) and release the target immunomodulators at tumor sites feature the advantages of increased anti-tumor potency but decreased off-target toxicity. Given the fantastic past achievements and the rapid developments in this field, the future is promising. In this review, intelligent delivery platforms targeting the PD-1/PD-L1 axis are attentively appraised. Specifically, mechanisms of the action of these stimuli-responsive drug release platforms are summarized to raise some guidelines for prior PD-1/PD-L1-based nanocarrier designs. Finally, the conclusion and outlook in intelligent delivery system targeting PD-1/PD-L1 pathway for cancer immunotherapy are outlined.

A review on regulation of cell cycle by extracellular matrix

The extracellular matrix (ECM) is a network of structural proteins, glycoproteins and proteoglycans that assists independent cells in aggregating and forming highly organized functional structures. ECM serves numerous purposes and is an essential component of tissue structure and functions. Initially, the role of ECM was considered to be confined to passive functions like providing mechanical strength and structural identity to tissues, serving as barriers and platforms for cells. The doors to understanding ECM's proper role in tissue functioning opened with the discovery of cellular receptors, integrins to which ECM components binds and influences cellular activities. Understanding and utilizing ECM's potential to control cellular function has become a topic of much interest in recent decades, providing different outlooks to study processes involved in developmental programs, wound healing and tumour progression. On another front, the regulatory mechanisms operating to prevent errors in the cell cycle have been topics of a titanic amount of studies. This is expected as many diseases, most infamously cancer, are associated with defects in their functioning. This review focuses on how ECM, through different methods, influences the progression of the somatic cell cycle and provides deeper insights into molecular mechanisms of functional communication between adhesion complex, signalling pathways and cell cycle machinery.

Investigating regulated signaling pathways in therapeutic targeting of non-small cell lung carcinoma

Non-small cell lung carcinoma (NSCLC) is the most common malignancy worldwide. The signaling cascades are stimulated via genetic modifications in upstream signaling molecules, which affect apoptotic, proliferative, and differentiation pathways. Dysregulation of these signaling cascades causes cancer-initiating cell proliferation, cancer development, and drug resistance. Numerous efforts in the treatment of NSCLC have been undertaken in the past few decades, enhancing our understanding of the mechanisms of cancer development and moving forward to develop effective therapeutic approaches. Modifications of transcription factors and connected pathways are utilized to develop new treatment options for NSCLC. Developing designed inhibitors targeting specific cellular signaling pathways in tumor progression has been recommended for the therapeutic management of NSCLC. This comprehensive review provided deeper mechanistic insights into the molecular mechanism of action of various signaling molecules and their targeting in the clinical management of NSCLC.