Small Compound Inhibitors Research Articles

Replenishing the cyclic-di-AMP pool: regulation of diadenylate cyclase activity in bacteria.

Bacteria can sense environmental cues and alter their physiology accordingly through the use of signal transduction pathways involving second messenger nucleotides. One broadly conserved second messenger is cyclic-di-AMP (c-di-AMP) which regulates a range of processes including cell wall homeostasis, potassium uptake, DNA repair, fatty acid synthesis, biofilm formation and central metabolism in bacteria. The intracellular pool of c-di-AMP is maintained by the activities of diadenylate cyclase (DAC) and phosphodiesterase (PDE) enzymes, as well as possibly via c-di-AMP export. Whilst extracellular stimuli regulating c-di-AMP levels in bacteria are poorly understood, recent work has identified effector proteins which directly interact and alter the activity of DACs. These include the membrane bound CdaR and the phosphoglucosamine mutase GlmM which both bind directly to the membrane bound CdaA DAC and the recombination protein RadA which binds directly to the DNA binding DisA DAC. The genes encoding these multiprotein complexes are co-localised in many bacteria providing further support for their functional connection. The roles of GlmM in peptidoglycan synthesis and RadA in Holliday junction intermediate processing suggest that c-di-AMP synthesis by DACs will be responsive to these cellular activities. In addition to these modulatory interactions, permanent dysregulation of DAC activity due to suppressor mutations can occur during selection to overcome growth defects, rapid cell lysis and osmosensitivity. DACs have also been investigated as targets for the development of new antibiotics and several small compound inhibitors have recently been identified. This review aims to provide an overview of how c-di-AMP synthesis by DACs can be regulated.

Oncogenic roles of TOPK and MELK, and effective growth suppression by small molecular inhibitors in kidney cancer cells.

T–lymphokine-activated killer cell–originated protein kinase (TOPK) and maternal embryonic leucine zipper kinase (MELK) have been reported to play critical roles in cancer cell proliferation and maintenance of stemness. In this study, we investigated possible roles of TOPK and MELK in kidney cancer cells and found their growth promotive effect as well as some feedback mechanism between these two molecules. Interestingly, the blockade of either of these two kinases effectively caused downregulation of forkhead box protein M1 (FOXM1) activity which is known as an oncogenic transcriptional factor in various types of cancer cells. Small molecular compound inhibitors against TOPK (OTS514) and MELK (OTS167) effectively suppressed the kidney cancer cell growth, and the combination of these two compounds additively worked and showed the very strong growth suppressive effect on kidney cancer cells. Collectively, our results suggest that both TOPK and MELK are promising molecular targets for kidney cancer treatment and that dual blockade of OTS514 and OTS167 may bring additive anti-tumor effects with low risk of side effects.

Abstract POSTER-BIOL-1313: Loss of INPP4B causes a DNA repair defect and upregulation of EGFR expression and can be targeted with PARP inhibitor treatment

Abstract Treatment options for ovarian cancer patients remain limited and overall survival is less than 50 percent despite recent clinical advances. This study aimed to identify treatment options for ovarian tumors deficient in the lipid phosphatase inositol polyphosphate 4-phosphatase type II (INPP4B). INPP4B has been described as a tumor suppressor in the PI3K/Akt pathway with loss of expression found most pronounced in breast, ovarian cancer and melanoma. Using microarray technology we identified a DNA repair defect in INPP4B-deficient cells, which we further characterized by comet assays and quantification of γH2AX, RAD51 and 53BP1 foci formation. INPP4B loss resulted in significantly increased sensitivity towards PARP inhibition, comparable to loss of BRCA1 in two- and three-dimensional in vitro models, as well as in in vivo xenograft models. Mechanistically, we discovered that INPP4B forms a protein complex with the key players of DNA repair, ATR and BRCA1, and INPP4B loss affects BRCA1, ATM and ATR protein stability resulting in the observed DNA repair defect. To identify further synthetic-lethal gene interactions in INPP4B-deficient ovarian cancer cells we employed the GlaxoSmithKline small compound library in a high-throughput screen. We successfully validated 9 out of initial 19 hit compounds which target Akt, VEGFR (Vascular Endothelial Growth Factor Receptor), p38α, LCK (Lymphocyte-specific protein Kinase) and TGFRβ1 (Transforming Growth Factor Receptor beta 1). Interestingly, we found that INPP4B loss resulted in increased efficacy of small compound inhibitors directed against EGFR (Epidermal Growth Factor Receptor), contrary to expectation from the literature given the documented activation of Akt in these cells. Cancer cells with high phosphorylation levels of Akt through PTEN loss or PI3-kinase mutation have been shown to be resistant to EGFR inhibitors. Using cell proliferation, clonogenic and xenograft assays we demonstrated that loss of INPP4B in the human ovarian cancer cell line OVCA433 and Hey resulted in significant sensitivity towards EGFR inhibition using Gefitinib, Erlotinib and Lapatinib compared to PTEN knockdown pools. Inhibition of ErbB2 using Herceptin did not result in synthetic lethality in Ovca433 INPP4B knockdown pools. As anticipated, Ovca429 INPP4B knockdown cell pools showed resistance to Gefitinib treatment due to an inherent PIK3CA mutation in Ovca429 ovarian cancer cells. Given that INPP4B loss has been found in 40% of ovarian cancer patients, this study provides the rationale for establishing INPP4B as a biomarker of PARP and EGFR inhibitor response, and consequently offering novel therapeutic options for a significant patient subgroup. Citation Format: Christina Anja Gewinner. Loss of INPP4B causes a DNA repair defect and upregulation of EGFR expression and can be targeted with PARP inhibitor treatment [abstract]. In: Proceedings of the 10th Biennial Ovarian Cancer Research Symposium; Sep 8-9, 2014; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(16 Suppl):Abstract nr POSTER-BIOL-1313.

Influenza virus non-structural protein NS1: interferon antagonism and beyond.

Most viruses express one or several proteins that counter the antiviral defences of the host cell. This is the task of non-structural protein NS1 in influenza viruses. Absent in the viral particle, but highly expressed in the infected cell, NS1 dramatically inhibits cellular gene expression and prevents the activation of key players in the IFN system. In addition, NS1 selectively enhances the translation of viral mRNAs and may regulate the synthesis of viral RNAs. Our knowledge of the virus and of NS1 has increased dramatically during the last 15 years. The atomic structure of NS1 has been determined, many cellular partners have been identified and its multiple activities have been studied in depth. This review presents our current knowledge, and attempts to establish relationships between the RNA sequence, the structure of the protein, its ligands, its activities and the pathogenicity of the virus. A better understanding of NS1 could help in elaborating novel antiviral strategies, based on either live vaccines with altered NS1 or on small-compound inhibitors of NS1.

Pharmacological inhibition of MALT1 protease activity protects mice in a mouse model of multiple sclerosis.

BackgroundThe paracaspase mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1) is crucial for lymphocyte activation through signaling to the transcription factor NF-κB. Besides functioning as a scaffold signaling protein, MALT1 also acts as a cysteine protease that specifically cleaves a number of substrates and contributes to specific T cell receptor-induced gene expression. Recently, small molecule inhibitors of MALT1 proteolytic activity were identified and shown to have promising anticancer properties in subtypes of B cell lymphoma. However, information on the therapeutic potential of small compound inhibitors that target MALT1 protease activity in autoimmunity is still lacking.MethodsThe present study aimed to elucidate whether MALT1 protease inhibitors are also useful in the treatment of lymphocyte-mediated autoimmune pathologies such as multiple sclerosis (MS). For this, we studied the therapeutic potential of a recently identified inhibitor of MALT1 protease activity, the phenothiazine derivative mepazine, in the context of experimental autoimmune encephalomyelitis (EAE), the main animal model for MS.ResultsWe demonstrate that administration of mepazine prophylactically or after disease onset, can attenuate EAE. Importantly, while complete absence of MALT1 affects the differentiation of regulatory T (Treg) cells in vivo, the MALT1 protease inhibitor mepazine did not affect Treg development.ConclusionsAltogether, these data indicate that small molecule inhibitors of MALT1 not only hold great promise for the treatment of B cell lymphomas but also for autoimmune disorders such as MS.

Computational methods for analysis and inference of kinase/inhibitor relationships.

The central role of kinases in virtually all signal transduction networks is the driving motivation for the development of compounds modulating their activity. ATP-mimetic inhibitors are essential tools for elucidating signaling pathways and are emerging as promising therapeutic agents. However, off-target ligand binding and complex and sometimes unexpected kinase/inhibitor relationships can occur for seemingly unrelated kinases, stressing that computational approaches are needed for learning the interaction determinants and for the inference of the effect of small compounds on a given kinase. Recently published high-throughput profiling studies assessed the effects of thousands of small compound inhibitors, covering a substantial portion of the kinome. This wealth of data paved the road for computational resources and methods that can offer a major contribution in understanding the reasons of the inhibition, helping in the rational design of more specific molecules, in the in silico prediction of inhibition for those neglected kinases for which no systematic analysis has been carried yet, in the selection of novel inhibitors with desired selectivity, and offering novel avenues of personalized therapies.

Mapping orphan proteases by proteomics: Meprin metalloproteases deciphered as potential therapeutic targets

The protease web is a synonym for highly regulated molecular networks comprising enzymes, substrates, inhibitors, and other regulatory proteins. Latest high-throughput methods provided huge data sets, revealing an amazing complexity of proteolytic systems important for health and disease. Based on our previous studies, we discuss major problems and questions that have to be solved to gain precise insight into the regulation of the protease web and its impact on pathophysiological conditions. The goal is a combination of different proteomic approaches that help to investigate specific protease function at a glance. Exemplarily, the characterization of the metalloproteases meprin α and meprin β by proteomic identification of cleavage sites and terminal amine isotopic labeling of substrates demonstrates the power of MS-based techniques. Meprins are rather orphan proteases and could not be assigned to precise biological functions until recently. Proteomics helped to identify meprin α and meprin β being important for collagen assembly and deposition in skin, which makes them potential therapeutic targets in fibrotic conditions. Additionally, identification of the cleavage site specificity provides the basis for the development of activity-based probes and small compound inhibitors, important for the regulation of meprin activity and subsequent treatment of associated diseases.

Abstract 815: The role of spleen tyrosine kinase (SYK) in paclitaxel resistant ovarian cancer

Abstract The development of resistance to paclitaxel represents a general challenge in clinical oncology, particularly in ovarian serous carcinomas (OSCs), the most common and lethal form of ovarian cancer. Initial treatment with a taxane and platinum combination regimen is standard and while the majority of women will achieve a major response to this treatment, the mortality of ovarian cancer is directly related to the tumor's development of chemoresistance. Using a proteomic approach to comprehensively compare the protein expression profiles of primary and recurrent OSC clinical samples, our laboratory previously identified several novel candidate proteins associated with the development of recurrent OSC. In this study, we focus on evaluating one of these proteins, spleen tyrosine kinase (SYK), a non-receptor tyrosine kinase, and its role in the maintenance of paclitaxel resistance in OSC. We have determined that increased expression of SYK in OSC tumor cells obtained from ascites and/or pleural effusion fluid is associated with a poorer response to chemotherapy. Using a cell culture system, we found that two OSC cell lines show an increased expression of SYK after development of in vitro resistance to paclitaxel treatment. More importantly, we demonstrate that SYK small compound inhibitors significantly resensitize the tumor cells to paclitaxel. Our results suggest that SYK plays a role in maintaining paclitaxel resistance in OSC. Recently an oral SYK inhibitor was found to be safe and effective in treating rheumatoid arthritis and non-Hodgkin lymphoma; our results suggest a potential translational use for this inhibitor as a chemosensitizing agent in patients with OSC. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 815. doi:1538-7445.AM2012-815

Targeting the cytoskeleton inhibits proliferation of hepatoma cells by suppressing mitogenic signalling

Hepatocellular carcinoma (HCC) develops almost exclusively on a background of chronic liver inflammation and cirrhosis. We have shown before, that hepatoma cells are able to sense and respond to the increased stiffness of the cirrhotic liver leading to increased cellular tension, stress fibre formation and proliferation. The FAK-Rho/ROCK-MLC2/Myosin pathway has been identified in other tissues to be a central regulator of cellular responses to increased environmental stiffness.The aim of the study was to evaluate the relevance of the stiffness-sensing pathway in the regulation of the cytoskeleton and to test, whether targeting this pathway might influence proliferation and survival of hepatoma cells. Therefore small compound inhibitors for FAK, ROCK and Myosin were evaluated in the human hepatoma cell lines HepG2 and Huh7 cultured on standard plastic (stiff) cell culture plates.Inhibitors for ROCK and Myosin reduced cellular spreading in the hepatoma cells, leading to a rounded phenotype with reduced stress fibres. In contrast upon FAK inhibition the cells were still spread out and displayed stress fibres albeit less organized in comparison to non-inhibited cells. Inhibitor treated cells displayed a reduced proliferative index and a reduced cell number after 5 days of treatment compared to untreated control cells. Accordingly, there was a dose-dependent inhibition of mitogenic signalling through Erk and Stat3 by all inhibitors. Cell survival was decreased in inhibitor treated cells after incubation with the chemotherapeutic drug cisplatin in a synergistical manner. The increased induction of apoptosis by cisplatin in inhibitor treated cells was verified by showing enhanced PARP cleavage compared to non-inhibited cells.In conclusion, interfering with the mechano-sensing machinery in the tumour cells might prove to be a new therapeutic target in HCCs arising in a stiff cirrhotic liver.

Small compound inhibitors of basal glucose transport inhibit cell proliferation and induce apoptosis in cancer cells via glucose-deprivation-like mechanisms

Cancer cells depend heavily on glucose as both energy and biosynthesis sources and are found to upregulate glucose transport and switch their main energy supply pathway from oxidative phosphorylation to glycolysis. These molecular and metabolic changes also provide targets for cancer treatment. Here we report that novel small molecules inhibited basal glucose transport and cell proliferation, and induced apoptosis in lung and breast cancer cells without affecting much their normal cell counterparts. Cancer cells survived the compound treatment lost their capability to proliferate. Mechanistic study indicates that the cancer cell inhibition by the test compounds has a component of apoptosis and the induced apoptosis was p53-independent and caspase 3-dependent, similar to those resulted from glucose deprivation. Compound treatment also led to cell cycle arrest in G1/S phase. The inhibition of cancer cell growth was partially relieved when additional glucose was supplied to cells, suggesting that the inhibition was due to, at least in part, the inhibition of basal glucose transport. When used in combination, the test compounds demonstrated synergistic effects with anticancer drugs cisplatin or paclitaxel in inhibition of cancer cell growth. All these results suggest that these glucose transport inhibitors mimic glucose deprivation and work through inhibiting basal glucose transport. These inhibitors have the potential to complement and replace traditional glucose deprivation, which cannot be used in animals, as new tools to study the effects of glucose transport and metabolism on cancer and normal cells.

Notch: Implications of endogenous inhibitors for therapy

Soluble components of Notch signalling can be applied to manipulate a central pathway essential for the development of metazoans and often deregulated in illnesses such as stroke, cancer or cardiovascular diseases. Commonly, the Notch cascade is inhibited by small compound inhibitors, which either block the proteolysis of Notch receptors by gamma-secretases or interfere with the transcriptional activity of the Notch intracellular domain. Specific antibodies can also be used to inhibit ligand-induced activation of Notch receptors. Alternatively, naturally occurring endogenous inhibitors of Notch signalling might offer a specific way to block receptor activation. Examples are the soluble variants of the canonical Notch ligand Jagged1 and the non-canonical Notch ligand Dlk1, both deprived of their transmembrane regions upon ectodomain shedding, or the bona fide secreted molecule EGFL7. We present frequently used methods to decrease Notch signalling, and we discuss how soluble Notch inhibitors may be used to treat diseases.

Transcriptional Repression of SKP2 Is Impaired in MYCN-Amplified Neuroblastoma

The cell cycle regulator, SKP2, is overexpressed in various cancers and plays a key role in p27 degradation, which is involved in tumor cell dedifferentiation. Little is known about the mechanisms leading to impaired SKP2 transcriptional control in tumor cells. We used neuroblastoma as a model to study SKP2 regulation because SKP2 transcript levels gradually increase with aggressiveness of neuroblastoma subtypes. The highest SKP2 levels are found in neuroblastomas with amplified MYCN. Accordingly, we found 5.5-fold (range, 2-9.5) higher SKP2 core promoter activity in MYCN-amplified cells. Higher SKP2 core promoter activity in MYCN-amplified cells is mediated through a defined region at the transcriptional start site. This region includes a specific E2F-binding site that makes SKP2 activation largely independent of mitogenic signals integrated through the SP1/ELK-1 site. We show by chromatin immunoprecipitation that SKP2 activation through the transcriptional start site in MYCN-amplified cells is associated with the low abundance of pRB-E2F1 complexes bound to the SKP2 promoter. Transcriptional control of SKP2 through this regulatory mechanism can be reestablished in MYCN-amplified cells by restoring pRB activity using selective small compound inhibitors of CDK4. In contrast, doxorubicin or nutlin-3 treatment-both leading to p53-p21 activation-or CDK2 inhibition had no effect on SKP2 regulation in MYCN-amplified cells. Together, this implies that deregulated MYCN protein levels in MYCN-amplified neuroblastoma cells activate SKP2 through CDK4 induction, abrogating repressive pRB-E2F1 complexes bound to the SKP2 promoter.

Abstract 568: Transcriptional repression of SKP2 is impaired in MYCN-amplified neuroblastoma

Abstract The cell cycle regulator, SKP2, is overexpressed in various cancers, and plays a key role in p27 degradation, which is involved in tumor cell dedifferentiation. Little is known about the mechanisms leading to impaired SKP2 transcriptional control in tumor cells. We used neuroblastoma as a model to study SKP2 regulation because SKP2 transcript levels gradually increase with aggressiveness of neuroblastoma subtypes. Highest SKP2 levels are found in neuroblastomas with amplified MYCN. Accordingly, we found 5.5-fold (range 2-9.5) higher SKP2 core promoter activity in MYCN-amplified cells. Higher SKP2 core promoter activity in MYCN-amplified cells is mediated through a defined region at the transcriptional start site (TSSR). This region includes a specific E2F-binding site that makes SKP2 activation largely independent of mitogenic signals integrated through the SP1/ELK-1 site. We demonstrate by chromatin immunoprecipitation that SKP2 activation through the TSSR in MYCN-amplified cells is associated with low abundance of pRB-E2F1 complexes bound to the SKP2 promoter. Transcriptional control of SKP2 via this regulatory mechanism can be re-established in MYCN-amplified cells by restoring pRB activity using selective small compound inhibitors of CDK4. In contrast, doxorubicin or nutlin-3 treatment - both leading to p53-p21 activation - or CDK2 inhibition had no effect on SKP2 regulation in MYCN-amplified cells. Together, this implies that deregulated MYCN protein levels in MYCN-amplified neuroblastoma cells activate SKP2 through CDK4 induction, abrogating repressive pRB-E2F1 complexes bound to the SKP2 promoter. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 568.

Identification and characterization of small compound inhibitors of human FATP2

Fatty acid transport proteins (FATPs) are bifunctional proteins, which transport long chain fatty acids into cells and activate very long chain fatty acids by esterification with coenzyme A. In an effort to understand the linkage between cellular fatty acid transport and the pathology associated with excessive accumulation of exogenous fatty acids, we targeted FATP-mediated fatty acid transport in a high throughput screen of more than 100,000 small diverse chemical compounds in yeast expressing human FATP2 (hsFATP2). Compounds were selected for their ability to depress the transport of the fluorescent long chain fatty acid analogue, C 1-BODIPY-C 12. Among 234 hits identified in the primary screen, 5 compounds, each representative of a structural class, were further characterized in the human Caco-2 and HepG2 cell lines, each of which normally expresses FATP2, and in 3T3-L1 adipocytes, which do not. These compounds were effective in inhibiting uptake with IC 50s in the low micromolar range in both Caco-2 and HepG2 cells. Inhibition of transport was highly specific for fatty acids and there were no effects of these compounds on cell viability, trans-epithelial electrical resistance, glucose transport, or long chain acyl-CoA synthetase activity. The compounds were less effective when tested in 3T3-L1 adipocytes suggesting selectivity of inhibition. These results suggest fatty acid transport can be inhibited in a FATP-specific manner without causing cellular toxicity.

Blocking T cell co-stimulation using a CD80 blocking small molecule reduces delayed type hypersensitivity responses in rhesus monkeys

Blockade of co-stimulation signals between T cells and antigen-presenting cells could be an important approach for treatment of autoimmune diseases and transplant rejection. Recently a series of small compound inhibitors which bind human CD80 (B7-1) and inhibit T cell co-stimulation has been described. To investigate their potency for clinical use, one of these compounds, RhuDex, was evaluated for reactivity with rhesus monkey CD80. The in vitro biological effect on rhesus monkey lymphocytes, the potency for suppression of an inflammatory recall response and the protein-induced delayed type hypersensitivity (DTH) response in the skin were studied. In a rhesus monkey T cell co-stimulation assay RhuDex inhibited proinflammatory cytokine release and cellular proliferation with micromolar potency. Systemic administration of RhuDex to rhesus monkeys inhibited the DTH response significantly, indicating that this compound may inhibit autoimmune mediated inflammatory processes where the target, CD80, is up-regulated.

Strategies to Overcome Resistance to Targeted Protein Kinase Inhibitors in??the Treatment of Cancer

Inhibition of oncogenic protein kinases by small compound inhibitors has proven to be a valuable strategy for the directed and target-specific treatment of an ever-increasing number of cancer types. These include the treatment of chronic myeloid leukemia with the Bcr-Abl inhibitor imatinib and non-small-cell lung cancer with the epidermal growth factor inhibitors erlotinib and gefitinib. Unfortunately, initially successful therapy is often hampered by relatively rapid onset of resistance to the drug and subsequent relapse, particularly in patients with advanced disease. In the majority of cases this is caused by expansion of clones containing mutated forms of the targeted kinases, which confer insensitivity to the drug of the cancer cell. In addition, multiple factors including pharmacokinetic issues such as suboptimal drug delivery further contribute to resistance formation. Loss of target dependence due to the activation of parallel signaling pathways has also been reported as cause for acquired drug insensitivity. Here, we discuss currently applied as well as potential future strategies that can be applied to overcome and avoid resistance to drug therapy.

High-Affinity Small Molecule Inhibitors of T Cell Costimulation: Compounds for Immunotherapy

Costimulatory molecules are important regulators of T cell activation and thus favored targets for therapeutic manipulation of immune responses. One of the key costimulatory receptors is CD80, which binds the T cell ligands, CD28, and CTLA-4. We describe a set of small compounds that bind with high specificity and low nanomolar affinity to CD80. The compounds have relatively slow off-rates and block both CD28 and CTLA-4 binding, implying that they occlude the shared ligand binding site. The compounds inhibit proinflammatory cytokine release in T cell assays with submicromolar potency, and as such, they represent promising leads for the development of novel therapeutics for immune-mediated inflammatory disease. Our results also suggest that other predominantly beta proteins, such as those that dominate the cell surface, may also be accessible as potentially therapeutic targets.