Discovery and Synthesis of a Pyrimidine-Based Aurora Kinase Inhibitor to Reduce Levels of MYC Oncoproteins

Targeting HASPIN in gemcitabine-resistant pancreatic cancer cells by lead optimization of thioadenosine analogue

Despite multiple kinase inhibitors having been developed for cancer therapy, mitotic kinases remain difficult to target with small molecules due to severe adverse effects on proliferating normal cells. Recently, HASPIN, a mitotic kinase responsible for histone H3 phosphorylation, has emerged as a promising cancer-specific target. In this study, we synthesized a novel thioadenosine analogue, LJ5157, based on the structure of the previously developed HASPIN inhibitor LJ4827. In silico transcriptome analysis of pancreatic cancer patient data from The Cancer Genome Atlas identified HASPIN as not only a cancer-specific target but also a potential key player in overcoming gemcitabine resistance. To evaluate the therapeutic potential of LJ5157, we tested its efficacy in pancreatic cancer cells, particularly gemcitabine-resistant Panc-1 (GR) cells. The inhibitor exhibited potent anti-cancer activity, effectively suppressing the growth of GR cells, which showed more dysregulated cell cycle progression and greater proportion of polyploid cells compared to wild-type Panc-1 cells. Furthermore, it demonstrated superior efficacy in reducing the mitotic population of polyploid GR cells, which correlated with significant tumor growth inhibition in a GR-cell-derived xenograft model. Further optimization of LJ4827 led to development of LJ5242, an analogue with enhanced selectivity for HASPIN and improved cell cycle inhibitory potency. These findings highlight HASPIN inhibition as a promising strategy for targeting chemoresistant pancreatic cancer and further identify thioadenosine as a valuable pharmacophore for developing clinically viable HASPIN inhibitors.

Unravelling the potency of the 4-oxo-2-thioxo-1,2,3,4-tetrahydropyrimidine-5-carbonitrile scaffold with S-arylamide hybrids as PIM-1 kinase inhibitors: synthesis, biological activity and in silico studies

PIM-1 is a type of serine/threonine kinase that plays a crucial role in controlling several vital processes, including proliferation and apoptosis. New synthetic S-amide tetrahydropyrimidinone derivatives were designed and synthesized as PIM-1 inhibitors with potential anticancer activity. Several biochemical assays were performed for anticancer assessment, including PIM-1 inhibitory assays, MTT, apoptosis and cell cycle, gene expression analysis, c-MYC analysis, and ATPase inhibitory assays. Compounds (8c, 8d, 8g, 8h, 8k, and 8l) exhibited strong in vitro broad antiproliferative activity against MCF-7, DU-145, and PC-3, with a relatively higher SI index suggesting minimal cytotoxicity to normal cells. Furthermore, these compounds induced mixed late apoptosis and necrosis with cell cycle arrest at the G2/M phase. Moreover, compounds 8b, 8f, 8g, 8k, and 8l showed potent inhibitory action against PIM-1 kinase, with corresponding IC50 values of 660, 909, 373, 518, and 501 nM. In silico prediction studies of physiochemical properties, molecular dynamics, and induced fit docking studies were performed for these compounds to explain their potent biological activity. In conclusion, new pyrimidinone compounds (8c, 8d, 8g, 8h, 8k, and 8l) exhibit potential PIM-1 inhibitory activity and can be used as promising scaffolds for further optimization of new leads with selective PIM-inhibitors and anticancer activity.

Recent advancements in mechanistic research, therapeutic potential, and structure-activity relationships of aurora kinase inhibitors in cancer therapies

Aurora kinases (AURKs)-a family of serine/threonine protein kinases consisting of AURK-A, AURK-B, and AURK-C, are critical regulators of chromosomal segregation, centrosome maturation, and cytokinesis during the cell cycle. Each kinase is activated via phosphorylation at unique threonine residues: Thr288 (AURK-A), Thr232 (AURK-B), and Thr195 (AURK-C). Activation of AURK-A and AURK-B through phosphorylation triggers a series of downstream signaling pathways, including RalA, NF-κB, p53, PLK1, BRCA1/BRCA2, H2AX, and Kif2C, as well as multiple transmembrane kinase receptors. Dysregulation of these pathways has been implicated in cancer development and progression, positioning AURKs as pivotal targets for anticancer drug research. Inhibition of AURKs has demonstrated significant efficacy in tumor growth suppression and induction of cancer cell death, thereby focusing recent research on the development of potent AURK inhibitors. This review provides an in-depth exploration of AURK inhibitors, discussing their biological activities, structure-activity relationships, selectivity profiles, and mechanisms of action. Notably, compounds 6, 27, and 16 exhibit potent AURK-A inhibition with IC50 values of 1.7 nM, 11.83 nM, and 15 nM, respectively. Similarly, compounds 28, 16, and 7 demonstrate strong AURK-B inhibitory activity, with IC50 values of 10.5 nM, 12 nM, and 14.09 nM, respectively. This comprehensive overview aims to support medicinal chemists in developing more potent, selective, and safe AURK inhibitors as potential anticancer therapeutics.

An update on small molecule compounds targeting synthetic lethality for cancer therapy

Targeting cancer-specific vulnerabilities through synthetic lethality (SL) is an emerging paradigm in precision oncology. A SL strategy based on PARP inhibitors has demonstrated clinical efficacy. Advances in DNA damage response (DDR) uncover novel SL gene pairs. Beyond BRCA-PARP, emerging SL targets like ATR, ATM, DNA-PK, CHK1, WEE1, CDK12, RAD51, and RAD52 show clinical promise. Selective and bioavailable small molecule inhibitors have been developed to induce SL, but optimization for potency, specificity, and drug-like properties remains challenging. This article illuminated recent progress in the field of medicinal chemistry centered on the rational design of agents capable of eliciting SL specifically in neoplastic cells. It is envisioned that innovative strategies harnessing SL for small molecule design may unlock novel prospects for targeted cancer therapeutics going forward.

Prediction of Multi-Pharmacokinetics Property in Multi-Species: Bayesian Neural Network Stacking Model with Uncertainty

Pharmacokinetic (PK) properties of a drug are vital attributes influencing its therapeutic effectiveness, playing an important role in the drug development process. Focusing on the difficult task of predicting PK parameters, we compiled an extensive data set comprising parameters across multiple species. Building upon this groundwork, we introduced the PKStack ensemble model to predict PK parameters across diverse species. PKStack integrates a variety of base models and includes uncertainty in its predictions. We also manually collected PK data from animals as an external test set. We predicted a total of 45 tasks for nine PK parameters in five species, and in general, the prediction accuracy was better for intravenous injections, including parameters such as human Vd (R2 = 0.72, RMSE = 0.31), human CL (R2 = 0.52, RMSE = 0.32), and others. In addition to predictive accuracy, we also considered the interpretability of the results and the definition of the model's application domain. Based on the findings, our model has great potential for practical applications in drug discovery.

Small cell lung cancer: emerging subtypes, signaling pathways, and therapeutic vulnerabilities

Small cell lung cancer (SCLC) is a recalcitrant cancer characterized by early metastasis, rapid tumor growth and poor prognosis. In recent decades, the epidemiology, initiation and mutation characteristics of SCLC, as well as abnormal signaling pathways contributing to its progression, have been widely studied. Despite extensive investigation, fewer drugs have been approved for SCLC. Recent advancements in multi-omics studies have revealed diverse classifications of SCLC that are featured by distinct characteristics and therapeutic vulnerabilities. With the accumulation of SCLC samples, different subtypes of SCLC and specific treatments for these subtypes were further explored. The identification of different molecular subtypes has opened up novel avenues for the treatment of SCLC; however, the inconsistent and uncertain classification of SCLC has hindered the translation from basic research to clinical applications. Therefore, a comprehensives review is essential to conclude these emerging subtypes and related drugs targeting specific therapeutic vulnerabilities within abnormal signaling pathways. In this current review, we summarized the epidemiology, risk factors, mutation characteristics of and classification, related molecular pathways and treatments for SCLC. We hope that this review will facilitate the translation of molecular subtyping of SCLC from theory to clinical application.

Discovery of a Long Half-Life AURKA Inhibitor to Treat MYC-Amplified Solid Tumors as a Monotherapy and in Combination with Everolimus

Aurora kinase inhibitors, such as alisertib, can destabilize MYC-family oncoproteins and have demonstrated compelling antitumor efficacy. In this study, we report 6K465, a novel pyrimidine-based Aurora A inhibitor, that reduces levels of c-MYC and N-MYC oncoproteins more potently than alisertib. In an analysis of the antiproliferative effect of 6K465, the sensitivities of small cell lung cancer (SCLC) and breast cancer cell lines to 6K465 were strongly associated with the protein levels of c-MYC and/or N-MYC. We also report DBPR728, an acyl-based prodrug of 6K465 bearing fewer hydrogen-bond donors, that exhibited 10-fold improved oral bioavailability. DBPR728 induced durable tumor regression of c-MYC- and/or N-MYC-overexpressing xenografts including SCLC, triple-negative breast cancer, hepatocellular carcinoma, and medulloblastoma using a 5-on-2-off or once-a-week dosing regimen on a 21-day cycle. A single oral dose of DBPR728 at 300 mg/kg induced c-MYC reduction and cell apoptosis in the tumor xenografts for more than 7 days. The inhibitory effect of DBPR728 at a reduced dosing frequency was attributed to its uniquely high tumor/plasma ratio (3.6-fold within 7 days) and the long tumor half-life of active moiety 6K465. Furthermore, DBPR728 was found to synergize with the mTOR inhibitor everolimus to suppress c-MYC- or N-MYC-driven SCLC. Collectively, these results suggest DBPR728 has the potential to treat cancers overexpressing c-MYC and/or N-MYC.

Discovery of N-benzylbenzamide-based allosteric inhibitors of Aurora kinase A

Aurora kinases (AurkA/B/C) regulate the assembly of bipolar mitotic spindles and the fidelity of chromosome segregation during mitosis, and are attractive therapeutic targets for cancers. Numerous ATP-competitive AurkA inhibitors have been developed as potential anti-cancer agents. Recently, a few allosteric inhibitors have been reported that bind to the allosteric Y-pocket within AurkA kinase domain and disrupt the interaction between AurkA and its activator TPX2. Herein we report a novel allosteric AurkA inhibitor (6h) of N-benzylbenzamide backbone. Compound 6h suppressed the both catalytic activity and non-catalytic functions of AurkA. The inhibitory activity of 6h against AurkA (IC50 = 6.50 μM) was comparable to that of the most potent allosteric AurkA inhibitor AurkinA. Docking analysis against the Y-pocket revealed important pharmacophores and interactions that were coherent with structure-activity relationship. In addition, 6h suppressed DNA replication in G1-S phase, which is a feature of allosteric inhibition of AurA. Our current study may provide a useful insight in designing potent allosteric AurkA inhibitors.

HDAC6-MYCN-CXCL3 axis mediates allergic inflammation and is necessary for allergic inflammation-promoted cellular interactions

Histone deacetylase 6 (HDAC6) has been shown to play an important role in allergic inflammation. This study hypothesized that novel downstream targets of HDAC6 would mediate allergic inflammation. Experiments employing HDAC6 knock out C57BL/6 mice showed that HDAC6 mediated passive cutaneous anaphylaxis (PCA) and passive systemic anaphylaxis (PSA). Antigen stimulation increased expression of N-myc (MYCN) and CXCL3 in an HDAC6-dependent manner in the bone marrow-derived mast cells. MYCN and CXCL3 were necessary for both PCA and PSA. The role of early growth response 3 (EGR3) in the regulation of HDAC6 expression has been reported. ChIP assays showed EGR3 as a direct regulator of MYCN. miR-34a-5p was predicted to be a negative regulator of MYCN. Luciferase activity assays showed miR-34a-5p as a direct regulator of MYCN. miR-34a-5p mimic negatively regulated PCA and PSA. MYCN decreased miR-34a-5p expression in antigen-stimulated rat basophilic leukemia cells (RBL2H3). MYCN was shown to bind to the promoter sequence of CXCL3. In an IgE-independent manner, recombinant CXCL3 protein increased expression of HDAC6, MYCN, and β-hexosaminidase activity in RBL2H3 cells. Mouse recombinant CXCL3 protein enhanced the angiogenic potential of the culture medium of RBL2H3. CXCL3 was necessary for the enhanced angiogenic potential of the culture medium of antigen-stimulated RBL2H3. The culture medium of RBL2H3 was able to induce M2 macrophage polarization in a CXCL3-dependent manner. Recombinant CXCL3 protein also increased the expression of markers of M2 macrophage. Thus, the identification of the novel role of HDAC6-MYCN-CXCL3 axis can help better understand the pathogenesis of anaphylaxis.

Molecular classification of small cell lung cancer subtypes: Characteristics, prognostic factors, and clinical translation

ABSTRACT

Small cell lung cancer (SCLC) is a highly malignant tumor with a very poor prognosis; therefore, more effective treatments are urgently needed for patients afflicted with the disease. In recent years, emerging molecular classifications based on key transcription factors of SCLC have provided more information on the tumor pathophysiology, metastasis, immune microenvironment, and acquired therapeutic resistance and reflected the intertumoral heterogeneity of the various SCLC phenotypes. Additionally, advances in genomics and single-cell sequencing analysis have further revealed the high intratumoral heterogeneity and plasticity of the disease. Herein, we review and summarize these recent lines of evidence and discuss the possible pathogenesis of SCLC.

Synthetic Strategies of Pyrimidine-Based Scaffolds as Aurora Kinase and Polo-like Kinase Inhibitors

The past few decades have witnessed significant progress in anticancer drug discovery. Small molecules containing heterocyclic moieties have attracted considerable interest for designing new antitumor agents. Of these, the pyrimidine ring system is found in multitude of drug structures, and being the building unit of DNA and RNA makes it an attractive scaffold for the design and development of anticancer drugs. Currently, 22 pyrimidine-containing entities are approved for clinical use as anticancer drugs by the FDA. An exhaustive literature search indicates several publications and more than 59 patents from the year 2009 onwards on pyrimidine derivatives exhibiting potent antiproliferative activity. These pyrimidine derivatives exert their activity via diverse mechanisms, one of them being inhibition of protein kinases. Aurora kinase (AURK) and polo-like kinase (PLK) are protein kinases involved in the regulation of the cell cycle. Within the numerous pyrimidine-based small molecules developed as anticancer agents, this review focuses on the pyrimidine fused heterocyclic compounds modulating the AURK and PLK proteins in different phases of clinical trials as anticancer agents. This article aims to provide a comprehensive overview of synthetic strategies for the preparation of pyrimidine derivatives and their associated biological activity on AURK/PLK. It will also present an overview of the synthesis of the heterocyclic-2-aminopyrimidine, 4-aminopyrimidine and 2,4-diaminopyrimidine scaffolds, and one of the pharmacophores in AURK/PLK inhibitors is described systematically.