Pyrido[2,3-b][1,5]benzoxazepin-5(6H)-one derivatives as CDK8 inhibitors

An Effective Reaction-Based Virtual Screening Method to Discover New CDK8 Ligands

Cyclin Dependent Kinase 8 (CDK8) is a valuable drug target for cancer suppression. Through an effective reaction-based virtual screening method consisting of pharmacophore modeling, Scifinder database searches, and energy evaluations, a number of new type II CDK8 ligands were discovered with comparable or better binding free energies than the ones reported in literature. In this method, a pharmacophore model, derived from seven crystal structures of CDK8 and type II ligands, was able to catch the key interactions for ligands binding at the ATP binding site of CDK8. This model then was used to screen the results from Scifinder database searches that apply chemical reaction rules in the search cycles, and the output compounds were evaluated and ranked first by a fast energy estimation method and then by the VM2 free energy calculation method. Among the top discovered ligands, three have lower Kd values against CDK8 than a potent reference ligand, and compound F (3-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-1-(8-hydroxynaphthalen-1-yl)urea) is the most potent one with an Kd value of 7.5 nM. Compound F has a relatively small molecular structure, receives both strong van der Waals energy and optimized overall electrostatic energy when binding with CDK8, and deserves to be a promising lead compound for further development. This effective virtual screening method and the novel compounds found in this work have implications for CDK8 drug discovery.

Identification of a Potent CDK8 Inhibitor Using Structure-Based Virtual Screening

Pulmonary fibrosis is excessive scarring of the lung tissues. Transforming growth factor-beta (TGF-β) has been implicated in pulmonary fibrosis due to its ability to induce the epithelial-to-mesenchymal transition (EMT) and promote epithelial cell migration. Cyclin-dependent kinase 8 (CDK8) can mediate the TGF-β signaling pathways and could function as an alternative therapeutic target for treating pulmonary fibrosis. Here, we performed a structure-based virtual screening campaign to identify CDK8 inhibitors from a library of 1.6 million compounds. The screening process ended with the identification of a novel CDK8 inhibitor, P162-0948 (IC50: 50.4 nM). An interaction analysis highlighted important CDK8-ligand interactions that support its binding and inhibitory activity. Testing against a panel of 60 different kinases demonstrated P162-0948 selectivity toward CDK8. Crucially, the inhibitor was found to be structurally novel when compared to known CDK8 inhibitors. Testing in A549 human alveolar epithelial cell lines showed that the P162-0948 can reduce cell migration and protein expression of EMT-related proteins. When P162-0948 was treated in cells at 5 μM, phosphorylation of Smad in the nucleus was reduced, which suggests disruption of the TGF-β/Smad signaling pathway. The identification of P162-0948 shows that it is not only potent, but its structural novelty can inform future design studies for potential therapeutics targeting pulmonary fibrosis.

Targeting cyclin-dependent kinases: From pocket specificity to drug selectivity

The development of selective modulators of cyclin-dependent kinases (CDKs), a kinase family with numerous members and functional variations, is a significant preclinical challenge. Recent advancements in crystallography have revealed subtle differences in the highly conserved CDK pockets. Exploiting these differences has proven to be an effective strategy for achieving excellent drug selectivity. While previous reports briefly discussed the structural features that lead to selectivity in individual CDK members, attaining inhibitor selectivity requires consideration of not only the specific structures of the target CDK but also the features of off-target members. In this review, we summarize the structure-activity relationships (SARs) that influence selectivity in CDK drug development and analyze the pocket features that lead to selectivity using molecular-protein binding models. In addition, in recent years, novel CDK modulators have been developed, providing more avenues for achieving selectivity. These cases were also included. We hope that these efforts will assist in the development of novel CDK drugs.

A Synthetic Overview of Benzoxazines and Benzoxazepines as Anticancer Agents

Benzoxazines and benzoxazepines are nitrogen and oxygen-containing six and seven-membered benzo-fused heterocyclic scaffolds, respectively. Benzoxazepines and benzoxazines are well-known pharmacophores in pharmaceutical chemistry, which are of significant interest and have been extensively studied because of their promising activity against various diseases including their wide range of anticancer activity. Several reports are known for synthesizing benzoxazine and benzoxazepine-based compounds in the literature. Herein this review provides a critical analysis of synthetic strategies towards benzoxazines and benzoxazepines along with various ranges of anticancer activities based on these molecules that have been reported from 2010 onwards. This review also focuses on the structure-activity relationship of the benzoxazine and benzoxazepine scaffolds containing bioactive compounds and describes how the structural modification affects their anticancer activity.

Lessons Learned from Past Cyclin-Dependent Kinase Drug Discovery Efforts

Inhibition of cyclin-dependent kinases (CDKs) has become an effective therapeutic strategy for treating various diseases, especially cancer. Over almost three decades, although great efforts have been made to discover CDK inhibitors, many of which have entered clinical trials, only four CDK inhibitors have been approved. In the process of CDK inhibitor development, many difficulties and misunderstandings have hampered their discovery and clinical applications, which mainly include inadequate understanding of the biological functions of CDKs, less attention paid to pan- and multi-CDK inhibitors, nonideal isoform selectivity of developed selective CDK inhibitors, overlooking the metabolic stability of early discovered CDK inhibitors, no effective resistance solutions, and a lack of available combination therapy and effective biomarkers for CDK therapies. After reviewing the mechanisms of CDKs and the research progress of CDK inhibitors, this perspective summarizes and discusses these difficulties or lessons, hoping to facilitate the successful discovery of more useful CDK inhibitors.

Transcriptional cyclin-dependent kinases: Potential drug targets in cancer therapy

In the wake of the development of the concept of cell cycle and its limiting points, cyclin-dependent kinases (CDKs) are considered to play a central role in regulating cell cycle progression. Recent studies have strongly demonstrated that CDKs also has multiple functions, especially in response to extracellular and intracellular signals by interfering with transcriptional events. Consequently, how to inhibit their function has been a hot research topic. It is worth noting that the key role of CDKs in regulating transcription has been explored in recent years, but its related pharmacological targets are less developed, and most inhibitors have not entered the clinical stage. Accordingly, this perspective focus on the biological functions of transcription related CDKs and their complexes, some key upstream and downstream signals, and inhibitors for cancer treatment in recent years. In addition, some corresponding combined treatment strategies will provide a more novel perspective for future cancer remedy.

Potent and orally bioavailable CDK8 inhibitors: Design, synthesis, structure-activity relationship analysis and biological evaluation

CDK8 regulates transcription either by phosphorylation of transcription factors or, as part of a four-subunit kinase module, through a reversible association of the kinase module with the Mediator complex, a highly conserved transcriptional coactivator. Deregulation of CDK8 has been found in various types of human cancer, while the role of CDK8 in supressing anti-cancer response of natural killer cells is being understood. Currently, CDK8-targeting cancer drugs are highly sought-after. Herein we detail the discovery of a series of novel pyridine-derived CDK8 inhibitors. Medicinal chemistry optimisation gave rise to 38 (AU1-100), a potent CDK8 inhibitor with oral bioavailability. The compound inhibited the proliferation of MV4-11 acute myeloid leukaemia cells with the kinase activity of cellular CDK8 dampened. No systemic toxicology was observed in the mice treated with 38. These results warrant further pre-clinical studies of 38 as an anti-cancer agent.

Angel or Devil ? - CDK8 as the new drug target

Cyclin-dependent kinase 8 (CDK8) plays an momentous role in transcription regulation by forming kinase module or transcription factor phosphorylation. A large number of evidences have identified CDK8 as an important factor in cancer occurrence and development. In addition, CDK8 also participates in the regulation of cancer cell stress response to radiotherapy and chemotherapy, assists tumor cell invasion, metastasis, and drug resistance. Therefore, CDK8 is regarded as a promising target for cancer therapy. Most studies in recent years supported the role of CDK8 as a carcinogen, however, under certain conditions, CDK8 exists as a tumor suppressor. The functional diversity of CDK8 and its exceptional role in different types of cancer have aroused great interest from scientists but even more controversy during the discovery of CDK8 inhibitors. In addition, CDK8 appears to be an effective target for inflammation diseases and immune system disorders. Therefore, we summarized the research results of CDK8, involving physiological/pathogenic mechanisms and the development status of compounds targeting CDK8, provide a reference for the feasibility evaluation of CDK8 as a therapeutic target, and guidance for researchers who are involved in this field for the first time.