Drugs targeted against protein kinases

Novel mechanism of napabucasin, a naturally derived furanonaphthoquinone: apoptosis and autophagy induction in lung cancer cells through direct targeting on Akt/mTOR proteins

Background

Akt and mTOR are aberrantly activated in cancers and targeting these proteins are interesting for cancer drug discovery. Napabucasin (NB), a phytochemical compound, has been reported as potential anti-cancer agent, however, Akt and mTOR targeting mechanisms remain unclear. 

Method

Apoptosis induction was investigated by Hoechst 33342/PI double staining and annexin V/PI staining with flowcytometry. Autophagy was evaluated by monodansylcadaverine staining and Western blot analysis. Binding affinity of NB and essential signaling proteins (PI3K, Akt, and mTOR) was investigated using molecular docking and confirmed by Western blot analysis.

Result

A structure modification from changing methyl moiety of acetyl group of NB to hydroxyl moiety of carboxyl group of NB derivative (napabucasin-acid or NB-acid) greatly affected the compound activities. NB showed more potent anti-cancer activity. NB reduced cell viability with an approximately 20 times lower IC₅₀ and inhibited the colony formation capacity much more than NB-acid treated cells. NB induced cell apoptosis, which was accompanied by decrease Bcl‑2 and Mcl-1 and clevage of PARP, while NB-acid show lesser effect on Mcl-1. NB was found to strongly induce autophagy indicated by acidic vesicle staining and the LC3B conversion. Interestingly, computational molecular docking analysis further demonstrated that NB directly bound to Akt and mTOR (complex 1 and 2) proteins at their critical sites indicating that NB targets the upstream regulators of apoptosis and autophagy. The docking results were confirmed by decrease of p-Akt/Akt, p-mTOR/mTOR, and c-Myc a downstream target of Akt protein levels.

Conclusion

Results show for the first time that NB exerts an anti-cancer activity through the direct interaction to Akt and mTOR proteins. The methyl moiety of acetyl group of NB is required for its potent anti-cancer activities. These data encourage further development of NB compounds for Akt and mTOR driven cancers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12906-022-03727-6.

Novel PI3K/Akt/mTOR pathway inhibitors plus radiotherapy: Strategy for non-small cell lung cancer with mutant RAS gene

Non-small cell lung cancer (NSCLC) with RAS -mutant gene has been the most difficult obstacle to overcome. Over 25% of muted lung adenocarcinomas have RAS mutation. The prognosis of NSCLC patients with RAS-mutant genes is always poor because there is no effective drug to suppress RAS-mutant genes. NSCLC patients with RAS-mutant usually develop resistance to radiotherapy and chemotherapy, which in some cases leads to a 5-10% survival rate for non-small cell lung cancer (NSCLC). As little clinical symptom of NSCLC was presented at its early stages, thus it always brings in disappointing treatment outcome. Currently, NSCLC presents the highest morbidity and mortality all over the world. The combination of PI3K/AKT/mTOR pathway inhibitors with radiotherapy is a novel strategy to improve radiosensitivity and therapeutic outcome of NSCLC with a RAS-mutant gene. There have been many preclinical studies and clinical trials on the effect of PI3K/AKT/mTOR pathway inhibitors combined with radiotherapy in NSCLC with a RAS-mutant gene have been reported in the past years. This review provides current knowledge of the combination of PI3K/Akt/mTOR pathway inhibitors with radiotherapy, which prove to be a significant improvement for the treatment of NSCLC patients with RAS mutations and will benefit NSCLC patients with RAS mutations.

Challenges and future of biomarker tests in the era of precision oncology: Can we rely on immunohistochemistry (IHC) or fluorescence in situ hybridization (FISH) to select the optimal patients for matched therapy?

Molecular techniques have improved our understanding of the pathogenesis of cancer development. These techniques have also fueled the rational development of targeted drugs for patient populations stratified by their genetic characteristics. These novel methods have changed the classic paradigm of diagnostic pathology; among them are IHC, FISH, polymerase chain reaction (PCR) and microarray technology. IHC and FISH detection methods for human epidermal growth factor receptor-2 (HER2), epidermal growth factor receptor (EGFR) and programmed death ligand-1 (PD-L1) were recently approved by the Food and Drug Administration (FDA) as routine clinical practice for cancer patients. Here, we discuss general challenges related to the predictive power of these molecular biomarkers for targeted therapy in cancer medicine. We will also discuss the prospects of utilizing new biomarkers for fibroblast growth factor receptor (FGFR) and hepatocyte growth factor receptor (cMET/MET) targeted therapies for developing new and robust predictive biomarkers in oncology.

Repurposing Kinase Inhibitors as Antiviral Agents to Control Influenza A Virus Replication

Influenza A virus (IAV) infection causes seasonal epidemics of contagious respiratory illness that causes substantial morbidity and some mortality. Regular vaccination is the principal strategy for controlling influenza virus, although vaccine efficacy is variable. IAV antiviral drugs are available; however, substantial drug resistance has developed to two of the four currently FDA-approved antiviral drugs. Thus, new therapeutic approaches are being sought to reduce the burden of influenza-related disease. A high-throughput screen using a human kinase inhibitor library was performed targeting an emerging IAV strain (H7N9) in A549 cells. The inhibitor library contained 273 structurally diverse, active cell permeable kinase inhibitors with known bioactivity and safety profiles, many of which are at advanced stages of clinical development. The current study shows that treatment of human A549 cells with kinase inhibitors dinaciclib, flavopiridol, or PIK-75 exhibits potent antiviral activity against H7N9 IAV as well as other IAV strains. Thus, targeting host kinases can provide a broad-spectrum therapeutic approach against IAV. These findings provide a path forward for repurposing existing kinase inhibitors safely as potential antivirals, particularly those that can be tested in vivo and ultimately for clinical use.

The Biological Role of PI3K Pathway in Lung Cancer

Lung cancer is the primary cause of cancer-related mortality worldwide and although improvements in treatment have been achieved over the last few years, long-term survival rates for lung cancer patients remain poor. Therefore, there is an imperative need for molecularly targeted agents that will achieve long-term disease control. Numerous downstream molecular pathways, such as EGF/RAS/RAF/MEK/ERK and PI3K/AKT/mTOR are identified as having a key role in the pathogenesis of various forms of human cancer, including lung cancer. PI3K/AKT/mTOR signal pathway is an important intracellular signal transduction pathway with a significant role in cell proliferation, growth, survival, vesicle trafficking, glucose transport, and cytoskeletal organization. Aberrations in many primary and secondary messenger molecules of this pathway, including mutations and amplifications, are accounted for tumor cell proliferation, inhibition of apoptosis, angiogenesis, metastasis and resistance to chemotherapy-radiotherapy. In this review article, we investigate thoroughly the biological role of PI3K pathway in lung cancer and its contribution in the development of future therapeutic strategies.

Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts

Background

Alternative splicing (AS) is a central mechanism in the generation of genomic complexity and is a major contributor to transcriptome and proteome diversity. Alterations of the splicing process can lead to deregulation of crucial cellular processes and have been associated with a large spectrum of human diseases. Cancer-associated transcripts are potential molecular markers and may contribute to the development of more accurate diagnostic and prognostic methods and also serve as therapeutic targets. Alternative splicing-enriched cDNA libraries have been used to explore the variability generated by alternative splicing. In this study, by combining the use of trapping heteroduplexes and RNA amplification, we developed a powerful approach that enables transcriptome-wide exploration of the AS repertoire for identifying AS variants associated with breast tumor cells modulated by ERBB2 (HER-2/neu) oncogene expression.

Results

The human breast cell line (C5.2) and a pool of 5 ERBB2 over-expressing breast tumor samples were used independently for the construction of two AS-enriched libraries. In total, 2,048 partial cDNA sequences were obtained, revealing 214 alternative splicing sequence-enriched tags (ASSETs). A subset with 79 multiple exon ASSETs was compared to public databases and reported 138 different AS events. A high success rate of RT-PCR validation (94.5%) was obtained, and 2 novel AS events were identified. The influence of ERBB2-mediated expression on AS regulation was evaluated by capillary electrophoresis and probe-ligation approaches in two mammary cell lines (Hb4a and C5.2) expressing different levels of ERBB2. The relative expression balance between AS variants from 3 genes was differentially modulated by ERBB2 in this model system.

Conclusions

In this study, we presented a method for exploring AS from any RNA source in a transcriptome-wide format, which can be directly easily adapted to next generation sequencers. We identified AS transcripts that were differently modulated by ERBB2-mediated expression and that can be tested as molecular markers for breast cancer. Such a methodology will be useful for completely deciphering the cancer cell transcriptome diversity resulting from AS and for finding more precise molecular markers.

From the bench to the bed side: PI3K pathway inhibitors in clinical development

A number of intracellular kinase components of the PI3K/Akt/mTOR pathway have been targeted over the past few years, leading to a new generation of anticancer agents that effectively and specifically disrupt this pathway in tumor cells. Here, progress in the identification and clinical evaluation of compounds designed to modulate the enzymatic activity of PI3K, Akt, mTOR, and Hsp90 is reviewed.

Synthesis and characterization of 5'-p-fluorosulfonylbenzoyl-2' (or 3')-(biotinyl)adenosine as an activity-based probe for protein kinases

Most of the kinase inhibitors that are approved for therapeutic uses or that are undergoing clinical trials are directed toward the adenosine triphosphate (ATP) binding site of protein kinases. 5'-Fluorosulfonylbenzoyl 5'-adenosine (FSBA) is an activitybased probe (ABP) that covalently modifies a conserved lysine present in the nucleotide binding site of most kinases. Here the authors describe synthesis of FSBA derivatives, 2'-biotinyl-FSBA and 3'-biotinyl-FSBA as kinase ABPs, and delineate a Western blot method to screen and validate ATP competitive protein kinase inhibitors using biotinyl-FSBA as a nonselective activity-based probe for protein kinases.

1,3-Disubstituted-imidazo[1,5-a]pyrazines as insulin-like growth-factor-I receptor (IGF-IR) inhibitors

A series of novel 8-amino-1,3-disubstituted-imidazo[1,5-a]pyrazines was designed and synthesized as IGF-IR inhibitors.

Cyclic nucleotide Response Element Binding protein (CREB) activation promotes survival signal in human K562 erythroleukemia cells exposed to ionising radiation/etoposide combined treatment

Anticancer therapy addresses the destruction of tumour cells which try to counteract the effect of drugs and/or ionising radiation. Thus the knowledge of the threshold over which the cells do not resist such agents could help in the setting up of therapy protocols. Since a key role was assigned to Cyclic nucleotide Response Element Binding protein (CREB) multigenic family (which is composed of several nuclear transcription factors involved in c-AMP signalling in cell differentiation, proliferation, apoptosis, survival and adaptive response and in hematopoiesis and acute leukemias), attention was paid to the activation of Erk cascade and of the downstream kinases and transcription factors such as p90RSK and CREB. K562 erythroleukemia cell survival to 1.5 Gy ionising radiation with or without etoposide treatment seemed to involve Erk phosphorylation which, regulating p90 RSK, should activate CREB. In parallel, p38 MAP kinase activity down-modulation, along with low caspase-3 activity, and no modification of Bax and Bcl2 levels, supported such evidence. Thus, endogenous CREB activation, triggering a potent survival signal in K562 cells exposed to 1.5 Gy with or without etoposide, led us to suggest that using specific inhibitors against CREB, such as modified phosphorothionate oligodeoxynucleotides (ODN) corresponding to CREB-1 sequence, anticancer therapy efficacy could be improved.

A liquid chromatography/mass spectrometry-based method for the selection of ATP competitive kinase inhibitors

The currently approved kinase inhibitors for therapeutic uses and a number of kinase inhibitors that are undergoing clinical trials are directed toward the adenosine triphosphate (ATP) binding site of protein kinases. The 5'-fluorosulfonylbenzoyl 5'-adenosine (FSBA) is an ATP-affinity reagent that covalently modifies a conserved lysine present in the nucleotide-binding site of most kinases. The authors have developed a liquid chromatography/mass spectrometry-based method to monitor binding of ATP competitive protein kinase inhibitors using FSBA as a nonselective activity-based probe for protein kinases. Their method provides a general, rapid, and reproducible means to screen and validate selective ATP competitive inhibitors of protein kinases.

Development of a fluorescence polarization bead-based coupled assay to target different activity/conformation states of a protein kinase

Most of the protein kinase inhibitors being developed are directed toward the adenosine triphosphate (ATP) binding site that is highly conserved in many kinases. A major issue with these inhibitors is the specificity for a given kinase. Structure determination of several kinases has shown that protein kinases adopt distinct conformations in their inactive state, in contrast to their strikingly similar conformations in their active states. Hence, alternative assay formats that can identify compounds targeting the inactive form of a protein kinase are desirable. The authors describe the development and optimization of an Immobilized Metal Assay for Phosphochemicals (IMAP)-based couple d assay using PDK1 and inactive Akt-2 enzymes. PDK1 phosphorylates Akt-2 at Thr 309 in the catalytic domain, leading to enzymatic activation. Activation of Akt by PDK1 is measured by quantitating the phosphorylation of Akt-specific substrate peptide using the IMAP assay format. This IMAP-coupled assay has been formatted in a 384-well microplate format with a Z' of 0.73 suitable for high-throughput screening. This assay was evaluated by screening the biologically active sample set LOPAC trade mark and validated with the protein kinase C inhibitor staurosporine. The IC(50) value generated was comparable to the value obtained by the radioactive (33)P-gamma-ATP flashplate transfer assay. This coupled assay has the potential to identify compounds that target the inactive form of Akt and prevent its activation by PDK1, in addition to finding inhibitors of PDK1 and activated Akt enzymes.

Omega-carboxypyridyl substituted ureas as Raf kinase inhibitors

Bis-aryl ureas have been disclosed previously as a potent class of Raf kinase inhibitors. Modifications in the amide portion led to an improvement in aqueous solubility, an important characteristic for an oral drug. Based on this finding, we hypothesize that this portion of the molecule is directed towards the solvent in Raf-1.

Discovery of a new class of synthetic protein kinase inhibitors that suppress selective aspects of glial activation and protect against beta-amyloid induced injury: a foundation for future medicinal chemistry efforts focused on targeting Alzheimer's disease progression

A prevailing hypothesis in Alzheimer's disease (AD) research is that chronically activated glia may contribute to neuronal dysfunction, through generation of a detrimental state of neuroinflammation. This raises the possibility in drug discovery research of targeting the cycle of untoward glial activation and neuronal dysfunction that characterizes neuroinflammation. Success over the past century with effective anti-inflammatory drug development, in which the molecular targets are intracellular enzymes involved in signal transduction events and cellular homeostasis, demands that a similar approach be tried with neuroinflammation. Suggestive clinical correlations between inflammation markers and AD contribute to the urgency in addressing the hypothesis that targeting selective glial activation processes might be a therapeutic approach complementary to existing drugs and discovery efforts. An academic collaboratorium initiated a rapid inhibitor discovery effort 2 yr ago, focused on development of novel compounds with new mechanisms of action in AD-relevant cellular processes, in order to obtain the small-molecule compounds required to address the neuroinflammation hypothesis and provide a proof of concept for future medicinal chemistry efforts. We summarize here our progress toward this goal in which novel pyridazine-based inhibitors of gene-regulating protein kinases have been discovered. Feasibility studies indicate their potential utility in current medicinal chemistry efforts focused on improvement in molecular properties and the longer term targeting of AD-related pathogenic processes.

Unraveling the complexities of the Raf/MAP kinase pathway for pharmacological intervention

The Ras-MAP kinase pathway has attracted much attention from academic and pharmaceutical laboratories because of its central role in regulating tumor cell growth and survival, differentiation and angiogenesis. Although the central players in this pathway -Ras, Raf, and MEK - have been well studied, how best to exploit them for therapeutic gain has eluded oncology researchers in the past. Several small-molecule inhibitors that target specific steps of the MAP kinase cascade have recently entered the clinical arena. While we await answers on their ultimate therapeutic use, the availability of translational assays for monitoring target suppression will no doubt play a significant role in optimizing our chances of success.

Death-associated protein kinase as a potential therapeutic target

Death associated protein kinase (DAPK) is a calmodulin (CaM)-regulated serine/threonine protein kinase implicated in diverse apoptosis pathways, including those involved in neuronal cell death and tumour suppression. The requirement of DAPK catalytic activity for its proposed cell functions and the validation of protein kinases as therapeutic targets demand that DAPK be examined as a potential therapeutic target in human disease. The relevant placement of DAPK activity in apoptosis pathways is at an early stage of investigation, making its study as a therapeutic target tenuous. However, the current body of knowledge raises the possibility of DAPK as a therapeutic target for diseases characterised by rapid neurodegeneration, such as stroke or traumatic brain injury. The unmet need in these diseases is for an acute treatment schedule that might reduce neuronal loss. Bioavailable inhibitors of DAPK catalytic activity that target the central nervous system have a potential to fill this need. The development of such DAPK inhibitors is now feasible based on the recent emergence of enabling technology and knowledge. These include a quantitative and selective enzyme assay, a high resolution structure of the active catalytic domain and discovery of cell-permeable, low molecular weight inhibitors of CaM kinases that cross the blood-brain barrier. DAPK as a potential therapeutic target for cancer is less attractive due to the incomplete state of knowledge about DAPK and inherent limitations in drug development for the discovery of specific activators of genes downregulated by promoter hypermethylation. This article provides a brief summary of relevant research and the rationale that is at the foundation of this opinion.

Therapeutic modulation of inflammatory gene transcription by kinase inhibitors

Altered gene expression contributes to the aetiology of inflammatory disease by modulation of the concentration of disease-related proteins. The expression of inflammatory genes is controlled through the concerted actions of specific transcription factors. Signal transduction networks positively or negatively regulate the activity of these transcription factors. Key components of these networks are protein kinases, which phosphorylate substrates on tyrosine, threonine or serine residues. During the disease process, pro-inflammatory signalling at the cell surface leads to a cascade of kinase activation, which ultimately culminates in modulation of the activity of transcription factors. Thus, pharmacological inhibition of protein kinases is a potential therapeutic strategy to treat inflammation. There are approximately 500 protein kinases in the human genome. Targeted small molecule inhibitors of these kinases should allow for tissue- and disease-specific therapies of unprecedented selectivity. Heralding this new era in molecular medicine is imatinib (Gleevec, Norvartis) a recently marketed tyrosine kinase inhibitor. This review focuses on kinase inhibitors that are currently in development for inflammatory diseases and the transcription factors that are involved.

Pharmacological interventions for stroke: failures and future

Given the few options currently available for patients following ischaemic stroke, the recent disappointing failures of several large-scale Phase III clinical trials has made the search for novel therapeutic approaches even more critical. Experimental evidence has suggested that the majority of stroke patients have a slow evolution of brain injury which can occur over several hours. Progressive microcirculatory failure following the initial onset of ischaemia may contribute to the expansion of brain injury. Included among the pathophysiological changes that are speculated to occur as a secondary response to the initial ischaemia are free radical production, excitotoxicity (for example, glutamate) disruption of ionic homeostasis (for example, sodium and calcium influx), enzymatic changes, stimulation of the inflammatory process, endothelin release, activation of platelets and leukocytes, delayed coagulation and endothelial dysfunction. All of these pathophysiological reactions could contribute to an increase in local vascular resistance and therefore cause progressive hypoperfusion of the brain following the onset of stroke. The scope of this review will focus on recent clinical failures in addition to agents currently in clinical development, comparing vascular targets to the common neuroprotective strategies.