Therapeutic Kinase Inhibitors Research Articles

Microsatellite instability: A 2024 update.

Deficient mismatch repair (dMMR) results in microsatellite instability (MSI), a pronounced mutator phenotype. High-frequency MSI (MSI-H)/dMMR is gaining increasing interest as a biomarker for advanced cancer patients to determine their eligibility for immune checkpoint inhibitors (ICIs). Various methods based on next-generation sequencing (NGS) have been developed to assess the MSI status. Comprehensive genomic profiling (CGP) testing can precisely ascertain the MSI status as well as genomic alterations in a single NGS test. The MSI status can be also ascertained through the liquid biopsy-based CGP assays. MSI-H has thus been identified in various classes of tumors, resulting in a greater adoption of immunotherapy, which is hypothesized to be effective against malignancies that possess a substantial number of mutations and/or neoantigens. NGS-based studies have also characterized MSI-driven carcinogenesis, including significant rates of fusion kinases in colorectal cancers (CRCs) with MSI-H that are targets for therapeutic kinase inhibitors, particularly in MLH1-methylated CRCs with wild-type KRAS/BRAF. NTRK fusion is linked to the colorectal serrated neoplasia pathway. Recent advances in investigations of MSI-H malignancies have resulted in the development of novel diagnostic or therapeutic techniques, such as a synthetic lethal therapy that targets the Werner gene. DNA sensing in cancer cells is required for antitumor immunity induced by dMMR, opening up novel avenues and biomarkers for immunotherapy. Therefore, clinical relevance exists for analyses of MSI and MSI-H-associated genomic alterations in malignancy. In this article, we provide an update on MSI-driven carcinogenesis, with an emphasis on unique landscapes of diagnostic and immunotherapeutic strategies.

A Hybrid Structure-Based Machine Learning Approach for Predicting Kinase Inhibition by Small Molecules.

Kinases have been the focus of drug discovery programs for three decades leading to over 70 therapeutic kinase inhibitors and biophysical affinity measurements for over 130,000 kinase-compound pairs. Nonetheless, the precise target spectrum for many kinases remains only partly understood. In this study, we describe a computational approach to unlocking qualitative and quantitative kinome-wide binding measurements for structure-based machine learning. Our study has three components: (i) a Kinase Inhibitor Complex (KinCo) data set comprising in silico predicted kinase structures paired with experimental binding constants, (ii) a machine learning loss function that integrates qualitative and quantitative data for model training, and (iii) a structure-based machine learning model trained on KinCo. We show that our approach outperforms methods trained on crystal structures alone in predicting binary and quantitative kinase-compound interaction affinities; relative to structure-free methods, our approach also captures known kinase biochemistry and more successfully generalizes to distant kinase sequences and compound scaffolds.

An insight into anti-arthritic property OF C25H34O7 for Rheumatoid arthritis using molecular modelling and molecular dynamics approach

Abstract Rheumatoid Arthritis (RA) is a multifactorial auto-immune disease of unknown etiology. Activation of innate immune systems including B and T lymphocytes is the earliest step in RA pathogenesis. Bruton's Tyrosine Kinase (BTK) plays a crucial role in the activation of B cells and it is being reported as one of the key drug targets for RA. Available therapeutic kinase inhibitors are associated with various side-effects, and none of them satisfies the ultimate goal of treatment options. Concurrently, several herbal compounds have been identified as potential kinase inhibitors in treating RA. In the present study, the BTK inhibition effect of bioactive compounds present in Ocimum sanctum Linn leaf extracts was determined using an in silico approach. Gas Chromatography-Mass Spectrometry was performed for methanol leaf extracts, and the bioactive compounds were screened based on anti-inflammation and anti-arthritic activity. The selected ligands were computationally synthesized and the inhibitory effect of these ligands against BTK mutant was studied through the molecular docking approach. The ligand C25H34O7 was identified as a promising herbal compound which showed a strong binding affinity towards BTK mutant with relatively three hydrogen bonds and the least docking score compared to the other selected ligands. Furthermore, molecular dynamics simulation studies were also performed using Desmond v4.0 for 25ns which revealed that the residues Ser371, Lys391, Asp500, Arg486 and Ile369 of the BTK mutant protein have the stable binding interaction between C25H34O7 throughout the simulation run. Thus, the study showed that C25H34O7 significantly formed five stable interactions which can be further investigated using in vitro and in vivo studies to verify its therapeutic potential in treating RA.

Abstract 4188: Multitargeted tyrosine kinase inhibitor identified as potential therapeutic intervention for liposarcoma using high-throughput profiling

Abstract Liposarcoma is a rare fat cell adult tumor with high risk of recurrence and metastasis, largely underserved by research community and till now limited progress has been made in treatment of this aggressive disease. We used a strategy to identify effective and potential therapeutic kinase inhibitors, irrespective of the activated kinase pathway, using small molecule kinase inhibitor panel. We screened liposarcoma cell lines of different histotypes to a panel of small molecule kinase inhibitors and analyzed using cell proliferation assay. In vitro cell proliferation assay, colony formation, cell cycle analysis, apoptosis assay and western blotting analysis were performed to investigate the effect and mechanism of inhibitor treatment on liposarcoma. Liposarcoma xenograft model system was also employed to investigate anti-tumor in vivo effects of inhibitor treatment. We observed that cell lines demonstrated diverse in vitro drug sensitivity patterns to various kinase inhibitors. Most of the cell lines showed very high sensitivity towards inhibitors targeting proteasome, protein kinase C, Hsp90, PI3K, mTOR and CDKs. Among the receptor tyrosine kinase inhibitors; Ponatinib, Dasatinib, and Sunitinib are the top most sensitive drugs affecting liposarcoma cells lines’ viability irrespective of subtypes and all these are already approved by the U.S. Food and Drug Administration to treat various cancers. We studied multi-targeted tyrosine kinase inhibitor ponatinib as an effective potential drug molecule in liposarcoma. We demonstrated that ponatinib treatment in liposarcoma cell lines reduced the levels of phosphorylated KIT compared to total KIT protein levels in dose dependent manner. Further, western blotting experiments revealed effect of ponatinib treatment on KIT downstream signalling by inhibiting the phosphorylation of AKT, ERK1/2, STAT3, mTOR, P70S6K and RB without affecting their total protein levels. Significant reduction in cell number and colonies with ponatinib treatment implicates anti-neoplastic effects in liposarcoma. Ponatinib treatment causes cell cycle arrest at G0/G1 phase by regulating CDK4 and cyclinD1 proteins levels. It also induces apoptosis of treated cells by downregulating AKT and ERK signaling pathway leading to dephosphorylation of BAD. Similar growth inhibiting effect of ponatinib was demonstrated in in vivo liposarcoma xenograft model. In vitro drug sensitivity profiling of liposarcoma highlighted Ponatinib, an oral FDA approved drug, as potential therapeutic drug candidate for treatment and management of this deadly tumor. Citation Format: Deepika Kanojia, Manoj Garg, Jakki Martinez, Anand M.T., Samuel B Luty, Ngan B Doan, Jonathan W Said, Jeffrey W Tyner, H Phillip Koeffler. Multitargeted tyrosine kinase inhibitor identified as potential therapeutic intervention for liposarcoma using high-throughput profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4188. doi:10.1158/1538-7445.AM2017-4188

Quantification of 11 Therapeutic Kinase Inhibitors in Human Plasma for Therapeutic Drug Monitoring Using Liquid Chromatography Coupled With Tandem Mass Spectrometry.

A liquid chromatography/tandem mass spectrometry assay was developed to facilitate therapeutic drug monitoring (TDM) for 10 anticancer compounds (dasatinib, erlotinib, gefitinib, imatinib, lapatinib, nilotinib, pazopanib, sorafenib, sunitinib, and vemurafenib) and the active metabolite, N-desethyl-sunitinib. The TDM assay is based on reversed-phase chromatography coupled with tandem mass spectrometry in the positive ion mode using multiple reaction monitoring for analyte quantification. Stable isotopically labeled compounds were used as internal standards. The sample pretreatment consisted of protein precipitation with acetonitrile using a small plasma volume of 50 μL. The validation procedures were based on the guidelines on bioanalytical methods issued by the US Food and Drug Administration and were modified to fit the requirements of the clinical TDM environment. The method was validated over a linear range of 5.00-100 ng/mL for dasatinib, sunitinib, and N-desethyl-sunitinib; 50.0-1000 ng/mL for gefitinib and lapatinib; 125-2500 ng/mL for erlotinib, imatinib, and nilotinib; and 500-10,000 ng/mL for pazopanib, sorafenib, and vemurafenib. The results of the validation study demonstrated good intra-assay and interassay accuracy (bias <6.0%) and precision (12.2%) for all analytes. This newly validated method met the criteria for TDM and has successfully been applied to routine TDM service for tyrosine kinase inhibitors.

Kinase Regulation of Human MHC Class I Molecule Expression on Cancer Cells.

The major histocompatibility complex I (MHC-1) presents antigenic peptides to tumor-specific CD8+ T cells. The regulation of MHC-I by kinases is largely unstudied, even though many patients with cancer are receiving therapeutic kinase inhibitors. Regulators of cell-surface HLA amounts were discovered using a pooled human kinome shRNA interference-based approach. Hits scoring highly were subsequently validated by additional RNAi and pharmacologic inhibitors. MAP2K1 (MEK), EGFR, and RET were validated as negative regulators of MHC-I expression and antigen presentation machinery in multiple cancer types, acting through an ERK output-dependent mechanism; the pathways responsible for increased MHC-I upon kinase inhibition were mapped. Activated MAPK signaling in mouse tumors in vivo suppressed components of MHC-I and the antigen presentation machinery. Pharmacologic inhibition of MAPK signaling also led to improved peptide/MHC target recognition and killing by T cells and TCR-mimic antibodies. Druggable kinases may thus serve as immediately applicable targets for modulating immunotherapy for many diseases. Cancer Immunol Res; 4(11); 936-47. ©2016 AACR.

Abstract 4899: The regulation by kinases of the expression of human major histocompatibility class I molecules

Abstract The major histocompatability complex (MHC) is a central receptor in the adaptive immune response and is the underlying target of several effective therapies for cancer. Druggable kinases may provide the opportunity to modulate the immune response toward MHC. However, the regulation of MHC-I by kinases is largely unstudied, even though many patients with cancer are receiving therapeutic kinase inhibitors. The entire human kinome was screened using a pooled shRNA interference-based approach in a human mesothelioma cell line to uncover kinase regulators of MHC-I. Negative and positive regulators of cell surface HLA levels were discovered. A subset of highly scoring positive and negative kinase hits were subsequently validated by additional RNAi, and pharmacologic inhibitors when available. MAP2K1 (MEK), EGFR, and RET were validated as negative regulators of HLA expression in multiple cancer types. We mapped the pathways responsible for increased HLA upon kinase inhibition. Interestingly, inhibition of the MAP Kinase pathway broadly influenced expression of other components of the antigen presentation machinery. Moreover, DDR2 and MINK1 were shown to positively regulate HLA-A*02:01. This had therapeutic relevance, as shown with a therapeutic TCR mimic antibody to a MHC/peptide complex. Druggable kinases may thus serve as immediately applicable targets for modulating immunotherapy for many diseases. Citation Format: Elliott J. Brea, Claire Oh, Eusebio Manchado, Ron Gejman, George Mo, Patrizia Mondello, Ralph Garippa, Neal Rosen, David A. Scheinberg. The regulation by kinases of the expression of human major histocompatibility class I molecules. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4899.

Oncogenes: nothing but a G thing.

Yoda et al. have shown that mutations in G protein-β (Gβ) subunits occur in haematological malignancies and can transform cells. Mutant Gβ can also confer resistance to different therapeutic kinase inhibitors.

Threshold Levels of ABL Tyrosine Kinase Inhibitors Retained in Chronic Myeloid Leukemia Cells Determine Their Commitment to Apoptosis

The imatinib paradigm in chronic myelogenous leukemia (CML) established continuous BCR-ABL inhibition as a design principle for ABL tyrosine kinase inhibitors (TKI). However, clinical responses seen in patients treated with the ABL TKI dasatinib despite its much shorter plasma half-life and the apparent rapid restoration of BCR-ABL signaling activity following once-daily dosing suggested acute, potent inhibition of kinase activity may be sufficient to irrevocably commit CML cells to apoptosis. To determine the specific requirements for ABL TKI-induced CML cell death for a panel of clinically important ABL TKIs (imatinib, nilotinib, dasatinib, ponatinib, and DCC-2036), we interrogated response of CML cell lines and primary CML cells following acute drug exposure using intracellular fluorescence-activated cell sorting and immunoblot analyses of BCR-ABL signaling, apoptosis measurements, liquid chromatography/tandem mass spectrometry of intracellular drug levels, and biochemical TKI dissociation studies. Importantly, significant intracellular TKI stores were detected following drug washout, levels of which tracked with onset of apoptosis and incomplete return of BCR-ABL signaling, particularly pSTAT5, to baseline. Among TKIs tested, ponatinib showed the most robust capacity for apoptotic commitment showing sustained suppression of BCR-ABL signaling even at low intracellular levels following extensive washout, consistent with high-affinity binding and slow dissociation from ABL kinase. Together, our findings suggest commitment of CML cells to apoptosis requires protracted incomplete restoration of BCR-ABL signaling mediated by intracellular retention of TKIs above a quantifiable threshold. These studies refine our understanding of apoptotic commitment in CML cells and highlight parameters important to design of therapeutic kinase inhibitors for CML and other malignancies.

Design and synthesis of tricyclic cores for kinase inhibition

Interest in therapeutic kinase inhibitors continues to grow beyond success in oncology. To date, ATP-mimetic kinase inhibitors have focused primarily on monocyclic and bicyclic heterocyclic cores. We sought to expand on the repertoire of potential cores for kinase inhibition by exploring tricyclic variants of classical bicyclic hinge binding motifs such as pyrrolopyridine and pyrrolopyrazine. Herein we describe the syntheses of eight alternative tricyclic cores as well as in vitro screening results for representative kinases of potential therapeutic interest.

Phosphoprotein phosphatase 2A: a novel druggable target for Alzheimer's disease.

Tau hyperphosphorylation is thought to play an important role in the etiology of Alzheimer's disease by facilitating the formation of neurofibrillary tangles. Reducing phosphorylation through kinase inhibition has therefore emerged as a target for drug development, but despite considerable efforts to develop therapeutic kinase inhibitors, success has been limited. An alternative approach is to develop pharmaceuticals to enhance the activity of the principal phospho-tau phosphatase, phosphoprotein phosphatase 2A (PP2A). In this article we review evidence that this mechanism is pharmacologically achievable and has promise for delivering the next generation of Alzheimer's disease therapeutics. A number of different chemotypes have been reported to lead to enhanced PP2A activity through a range of proposed mechanisms. Some of these compounds appear to act directly as allosteric activators of PP2A, while others act indirectly by inhibiting the binding of PP2A inhibitors or by altering post-translational modifications that act in turn to regulate PP2A activity towards phospho-tau. These results indicate that PP2A may provide a useful target that can be safely, selectively and effectively modulated through pharmaceutical intervention to treat Alzheimer's disease.

Computational Modeling of Kinase Inhibitor Selectivity.

An exhaustive computational exercise on a comprehensive set of 15 therapeutic kinase inhibitors was undertaken to identify as to which compounds hit which kinase off-targets in the human kinome. Although the kinase selectivity propensity of each inhibitor against ∼480 kinase targets is predicted, we compared our predictions to ∼280 kinase targets for which consistent experimental data are available and demonstrate an overall average prediction accuracy and specificity of ∼90%. A comparison of the predictions was extended to an additional ∼60 kinases for sorafenib and sunitinib as new experimental data were reported recently with similar prediction accuracy. The successful predictive capabilities allowed us to propose predictions on the remaining kinome targets in an effort to repurpose known kinase inhibitors to these new kinase targets that could hold therapeutic potential.

Inhibition of insulin/IGF-1 receptor signaling enhances bile acid toxicity in primary hepatocytes

Modulation of ERBB and insulin-like growth factor 1 (IGF-1) receptor function is recognized as a potential mechanism to inhibit tumor growth. We and others have shown that inhibition of ERBB1 can enhance bile acid toxicity. Herein, we extend our analyses to examine the impact of insulin/IGF-1 receptor inhibition on primary hepatocyte survival when exposed to the secondary bile acid deoxycholic acid (DCA) and compare the impact inhibition of this receptor has on bile acid toxicity effects to that of ERBB1/MEK1/2 inhibition. The insulin/IGF-1 receptor inhibitor NVP-ADW742 at concentrations which inhibit both the insulin and IGF-1 receptors had a modest negative impact on hepatocyte viability, and strongly potentiated DCA-induced apoptotic cell death. Identical data were obtained expressing a dominant negative IGF-1 receptor in hepatocytes; a receptor which acts to inhibit both the IGF-1 receptor and the insulin receptor in trans. Inhibition of ERBB1 function using Iressa (gefitinib) or the tyrphostin AG1478 had more modest effects at enhancing DCA lethality than inhibition of the insulin/IGF-1 receptor function. In contrast, over-expression of a dominant negative ERBB1 protein had pleiotropic effects on multiple signaling pathways in an apparently non-specific manner. These findings suggest that novel therapeutic kinase inhibitors, targeted against growth factor receptors, have the potential to promote bile acid toxicity in hepatocyte when bile flow may be impaired.

Activated forms of H-RAS and K-RAS differentially regulate membrane association of PI3K, PDK-1, and AKT and the effect of therapeutic kinase inhibitors on cell survival

The abilities of mutated active RAS proteins to modulate cell survival following exposure to ionizing radiation and small molecule kinase inhibitors were examined. Homologous recombination in HCT116 cells to delete the single allele of K-RAS D13 resulted in a cell line that exhibited an approximately 75% reduction in basal extracellular signal-regulated kinase 1/2, AKT, and c-jun-NH2-kinase 1/2 activity. Transfection of cells lacking K-RAS D13 with H-RAS V12 restored extracellular signal-regulated kinase 1/2 and AKT activity to basal levels but did not restore c-jun-NH2-kinase 1/2 phosphorylation. In cells expressing H-RAS V12, radiation caused prolonged intense activation of AKT. Inhibition of H-RAS V12 function, blockade of phosphatidylinositol 3-kinase (PI3K) function using small interfering RNA/small-molecule inhibitors, or expression of dominant-negative AKT abolished radiation-induced AKT activation, and radiosensitized these cells. Inhibition of PI3K function did not significantly radiosensitize parental HCT116 cells. Inhibitors of the AKT PH domain including perifosine, SH-(5, 23-25) and ml-(14-16) reduced the plating efficiency of H-RAS V12 cells in a dose-dependent fashion. Inhibition of AKT function using perifosine enhanced radiosensitivity in H-RAS V12 cells, whereas the SH and ml series of AKT PH domain inhibitors failed to promote radiation toxicity. In HCT116 H-RAS V12 cells, PI3K, PDK-1, and AKT were membrane associated, whereas in parental cells expressing K-RAS D13, only PDK-1 was membrane bound. In H-RAS V12 cells, membrane associated PDK-1 was phosphorylated at Y373/376, which was abolished by the Src family kinase inhibitor PP2. Inhibition of PDK-1 function using the PH domain inhibitor OSU-03012 or using PP2 reduced the plating efficiency of H-RAS V12 cells and profoundly increased radiosensitivity. OSU-03012 and PP2 did not radiosensitize and had modest inhibitory effects on plating efficiency in parental cells. A small interfering RNA generated against PDK1 also radiosensitized HCT116 cells expressing H-RAS V12. Collectively, our data argue that molecular inhibition of AKT and PDK-1 signaling enhances the radiosensitivity of HCT116 cells expressing H-RAS V12 but not K-RAS D13. Small-molecule inhibitory agents that blocked stimulated and/or basal PDK-1 and AKT function profoundly reduced HCT116 cell survival but had variable effects at enhancing tumor cell radiosensitivity.