Kinase Binding Assay Research Articles

Abstract 4538: A novel assay platform for the detection of kinase-inhibitor binding in intact mammalian cells.

Abstract Kinase binding assays have become an integral part of inhibitor characterization. These tools have been applied in KINOME-wide screening systems as well as the detailed characterization of inhibitor residence time for lead optimization and MOA studies. However in cells, assays are limited to monitoring kinase activity and downstream substrate phosphorylation events. Although these types of cellular assays are critical to move programs forward, their ability to characterize inhibitor function is limited, requires targeted antibody reagents, and knowledge of specific substrates which are often not available. To circumvent these issues and apply the power of binding assays to a cellular format we have devised a method for monitoring compound binding to kinase targets in intact mammalian cells termed InCELL Hunter. The assay is shown to retain the benefits of cellular assays such as assessing compound permeability, toxicity, and target engagement; while exhibiting the generic applicability of a kinase binding assay. The InCELL hunter assay correctly describes type I, type II, and Type III inhibitors with the expected rank order cellular potencies. The assay is activity and substrate independent making it amenable to previously intractable targets and provides novel cellular information that complements both biochemical and existing cellular formats. Citation Format: Abhi Saharia, William Raab, Daniel Bassoni, Jeremy Hunt, Daniel K. Treiber, Tom Wehrmann. A novel assay platform for the detection of kinase-inhibitor binding in intact mammalian cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4538. doi:10.1158/1538-7445.AM2013-4538

Fluorophore Labeled Kinase Detects Ligands That Bind within the MAPK Insert of p38α Kinase

The vast majority of small molecules known to modulate kinase activity, target the highly conserved ATP-pocket. Consequently, such ligands are often less specific and in case of inhibitors, this leads to the inhibition of multiple kinases. Thus, selective modulation of kinase function remains a major hurdle. One of the next great challenges in kinase research is the identification of ligands which bind to less conserved sites and target the non-catalytic functions of protein kinases. However, approaches that allow for the unambiguous identification of molecules that bind to these less conserved sites are few in number. We have previously reported the use of fluorescent labels in kinases (FLiK) to develop direct kinase binding assays that exclusively detect ligands which stabilize inactive (DFG-out) kinase conformations. Here, we present the successful application of the FLiK approach to develop a high-throughput binding assay capable of directly monitoring ligand binding to a remote site within the MAPK insert of p38α mitogen-activated protein kinase (MAPK). Guided by the crystal structure of an initially identified hit molecule in complex with p38α, we developed a tight binding ligand which may serve as an ideal starting point for further investigations of the biological function of the MAPK insert in regulating the p38α signaling pathway.

Detection of Allosteric Kinase Inhibitors by Displacement of Active Site Probes

Non–adenosine triphosphate (ATP) competitive, allosteric inhibitors provide a promising avenue to develop highly selective small-molecule kinase inhibitors. Although this class of compounds is growing, detection of such inhibitors can be challenging as standard kinase activity assays preferentially detect compounds that bind to active kinases in an ATP competitive manner. We have previously described a time-resolved fluorescence resonance energy transfer (TR-FRET)–based kinase binding assay using the competitive displacement of ATP competitive active site fluorescent probes (“tracers”). Although this format has gained acceptance, published data with this and related formats are almost entirely without examples of non-ATP competitive compounds. Thus, this study addresses whether this format is useful for non-ATP competitive inhibitors. To this end, 15 commercially available non-ATP competitive inhibitors were tested for their ability to displace ATP competitive probes. Despite the diversity of both compound structures and their respective targets, 14 of the 15 compounds displaced the tracers with IC50 values comparable to literature values. We conclude that such binding assays are well suited for the study of non-ATP competitive inhibitors. In addition, we demonstrate that allosteric inhibitors of BCR-Abl and MEK bind preferentially to the nonphosphorylated (i.e., inactive) form of the kinase, indicating that binding assays may be a preferred format in some cases.

Comparison of LanthaScreen Eu Kinase Binding Assay and Surface Plasmon Resonance Method in Elucidating the Binding Kinetics of Focal Adhesion Kinase Inhibitors

An understanding of the dynamics of drug-target interactions is important in the drug discovery process. Information related to the binding kinetics of a drug toward its target or off-target aids in determining the efficacy or toxicity of a drug. Biophysical techniques such as surface plasmon resonance (SPR) have been available for over 20 years, but have been predominantly utilized to characterize protein-protein interactions. With improvements in instrument sensitivity and data analysis software, interactions between proteins (such as kinases) and small molecules have been successfully evaluated. More recently, the LanthaScreen Eu kinase binding assay for characterizing kinase inhibitors has been described. This assay monitors displacement of an Alexa Fluor 647-labeled tracer from the ATP-binding site of an epitope-tagged kinase by a test compound. Such behavior results in a decrease in time-resolved fluorescence energy transfer signal. In this report, a side-by-side comparison of the LanthaScreen Eu kinase binding assay and the SPR method was performed using inhibitors of focal adhesion kinase. The two methods yielded comparable results and identified compounds with time-dependent inhibition and relatively slow dissociation.

In vitro and in silico studies on substrate recognition and acceptance of human PKMYT1, a Cdk1 inhibitory kinase

The human Myt1 kinase (PKMYT1) is an important regulator of the G2/M transition in the cell cycle. Presently, limited knowledge about its substrate recognition is available. Here, various potential substrates were investigated by different antibody based techniques including fluorescence polarization immunoassays and immunoblotting. Regarding both Thr and Tyr kinase activity, only protein substrates were found to be phosphorylated by Myt1, whereas any tested peptide was not recognized. In silico molecular dynamics studies were used to compare the stability of the Myt1 peptide complex with Wee1 peptide complex and support the biochemical findings. Furthermore, a Myt1 kinase binding assay suggests Myt1 being insensitive to staurosporine.

Abstract A240: Preclinical molecular stratification of human tumors sensitive or resistant to S 49076, a novel MET/FGFR/AXL kinase inhibitor.

Abstract Protein kinase inhibitors constitute a class of anticancer agents with demonstrated clinical efficacy. However, the clinical benefit of these agents is often limited to a subset of patients with specific genomic lesions in their tumor cells rendering them sensitive to inhibition of one or more target kinases. It is therefore becoming increasingly important to identify biomarkers of patient stratification to enable personalized care. For those inhibitors targeting just one kinase this stratification strategy is relatively straightforward, although the number of patients who will benefit from these highly selective inhibitors alone is in general severely limited. In the majority of cases, the simultaneous targeting of more than one kinase, possibly by the same drug, will be required for therapeutic efficacy. However, for multi-target kinase drugs, patient stratification is considerably more complex and is becoming a major challenge during clinical development. S 49076 is a novel, potent, ATP-competitive tyrosine kinase inhibitor with activity demonstrated in cell and animal assays against the receptor tyrosine kinases MET, FGFR1/2/3 and AXL, all of which are associated with progression of a wide range of human malignancies. In kinase binding assays, S 49076 also binds to clinically-relevant MET mutated isoforms and 32 other kinases, many of which have also been implicated in cancer pathology. In the present study, the antitumor activity of S 49076 was assessed in a panel of 53 patient-derived tumors of diverse origin growing in three-dimensional in vitro culture. Sixteen (30%) of these tumors were sensitive to S 49076 at 1 μM or less. With the aim to define molecular signatures of sensitivity or resistance, all 53 tumors were characterized for expression, activation and mutation of all of the known target kinases using protein, mRNA and DNA analysis techniques. On an individual basis, no clear relationship between expression level or activity of each target kinase and sensitivity or resistance to S 49076 could be established. However, analysis of microarray data using z-score transformation enabled a clear link to emerge between the sum of the z-scores of all potential target kinases (z-score) and tumor response to S 49076. Moreover, when the presence of RAS or PIK3CA activating mutations was taken into account, the predictive power of the analysis (in particular the positive predictive value for sensitivity) was even more striking. Overall, 91% (29/32) of tumors with a z-score less than 0 were resistant to S 49076, whilst 85% (11/13) of tumors with a z-score greater than 0 and with no known mutations in RAS or PIK3CA were sensitive. Six out of the 8 tumors with a z-score greater than 0 but with mutations in RAS or PIK3CA were resistant. In vivo evaluation of the response to S 49076 of several of the sensitive tumors is in progress in xenograft studies. Together, these data demonstrate the potential power of molecular profiling and, in particular, transcriptomic analyzes in the stratification of patient tumors for treatment with a multi-kinase inhibitor. It is hoped that similar analysis of patient tumors during clinical trials of S 49076 will ultimately contribute to the progress towards a more personalized approach to cancer patient care. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr A240.

Abstract A238: S 49076, a novel, potent, MET/FGFR/AXL kinase inhibitor with wide antitumor activity.

Abstract Receptor tyrosine kinases (RTKs) are key regulators of a multitude of cell processes, including survival, proliferation, migration, invasion and angiogenesis. Aberrant activity of certain of these receptor tyrosine kinases has been associated with tumor progression in a wide variety of human malignancies, making them promising drug targets for cancer therapy. Although, in some instances, specific inhibition of just one of these RTKs suffices for inhibition of tumor progression, in the majority of cases, targeting more than one RTK could be required for therapeutic efficacy. These RTKs include MET, the receptor for hepatocyte growth factor (HGF), the fibroblast growth factor receptor, FGFR, and AXL. Dysregulation of MET activity, due to its overexpression or mutation, or overexpression of its ligand, has been consistently associated with aggressive phenotype, resistance to certain anti-cancer therapies and poor outcome. The FGFRs have a well-documented role in tumor angiogenesis, and, more recently, have been implicated directly in tumor cell survival, proliferation and metastasis in a wide range of tumor types. AXL is one of a family of three tyrosine kinase receptors (TAM family) involved in the pathogenesis of several human cancers and has also recently incited interest as a cancer therapeutic target. S 49076 is a novel, potent, ATP-competitive tyrosine kinase inhibitor of MET, FGFR1/2/3 and AXL. S 49076 blocks autophosphorylation of these RTKs and their downstream signaling in cells with IC50 values of between 1 and 200 nM depending on the target and cell line. Furthermore, in kinase binding assays, S 49076 also binds to clinically-relevant MET mutated isoforms and a number of other kinases implicated in cancer pathology at concentrations of less than 100 nM. S 49076 is not, however, a potent inhibitor of VEGFR2. Although VEGFR2 is implicated in tumor angiogenesis, it also plays a major physiological role in the maintenance of vascular tone, and its inhibition by other RTK inhibitors has limited dosing of these molecules in the clinic. The unique inhibition profile of S 49076 may allow inhibition of oncogenic RTKs potentially without toxic effects encountered by VEGFR2 inhibitors. In vitro, S 49076 inhibits the proliferation of MET- and FGFR2-dependent gastric cancer cells, blocks MET-driven migration of lung carcinoma cells and inhibits colony formation of AXL-overexpressing hepatocarcinoma cells. In vivo, oral administration of S 49076 inhibits > 80% MET autophosphorylation in subcutaneous GTL-16 human gastric carcinoma tumors at 3 mg/kg. In both this GTL-16 model and in the MET-dependent U87-MG human glioblastoma model, S 49076 inhibits > 80% tumor growth at 6 mg/kg/day. S 49076 also inhibits FGFR2 autophosphorylation, downstream signaling and tumor growth in FGFR2-dependent SNU-16 gastric tumors, and tumor growth in LS-174T colon carcinoma. Based on these preclinical studies showing a favorable and novel pharmacological profile and the potential of S 49076 as innovative anticancer agent, a phase I study is planned soon to evaluate an oral formulation of S 49076 in patients with advanced solid tumors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr A238.

Chemical kinomics: a powerful strategy for target deconvolution

Kinomics is an emerging and promising approach for deciphering kinomes. Chemical kinomics is a discipline of chemical genomics that is also referred to as "chemogenomics", which is derived from chemistry and biology. Chemical kinomics has become a powerful approach to decipher complicated phosphorylation-based cellular signaling networks with the aid of small molecules that modulate kinase functions. Moreover, chemical kinomics has played a pivotal role in the field of kinase drug discovery as it enables identification of new molecular targets of small molecule kinase modulators and/or exploitation of novel functions of known kinases and has also provided novel chemical entities as hit/lead compounds. In this short review, contemporary chemical kinomics technologies such as activity-based protein profiling, T7 kinasetagged phages, kinobeads, three-hybrid systems, fluorescenttagged kinase binding assays, and chemical genomic profiling are discussed along with a novel allosteric Bcr-Abl kinase inhibitor (GNF-2/GNF-5) as a successful application of chemical kinomics approaches.

2-Arylthiazolidine-4-carboxylic acid amides (ATCAA) target dual pathways in cancer cells: 5'-AMP-activated protein kinase (AMPK)/mTOR and PI3K/Akt/mTOR pathways

Phosphatidylinositol-3-kinase (PI3K)/Akt and 5'-AMP-activated protein kinase (AMPK) are attractive targets for anti-cancer drug development. Inhibition of Akt or activation of AMPK is cytotoxic to human cancer cells in vitro and in vivo. We previously demonstrated that 2-arylthiazolidine-4-carboxylic acid amides (ATCAA) are effective cytotoxic agents in prostate and melanoma cancer cell lines, with IC(50) values in the low/sub micromolar range. Using in vitro and in vivo studies, we further characterized the anti-cancer efficacy and mechanism of action of ATCAA-10, a potent lead. ATCAA-10 exhibited equal potency on both MES/SA and P-glycoprotein over-expressing multidrug resistant MES/SA/Dx5 cells, suggesting that ATCAA-10 may overcome multiple drug resistance. Cell-free kinase binding assays excluded the direct binding of ATCAA-10 to several kinases, including IGF-1R, EGFR, FGFR and PDGFR. However, in A549 and HeLa cells, ATCAA-10 effectively dephosphorylated Akt, with concomitant phosphorylation of AMPK. Determination of intracellular ATP and AMP concentrations revealed that ATCAA-10 activated AMPK by altering the intracellular AMP/ATP ratio. ATCAA-10 exhibited favorable pharmacokinetic properties in both mice and rats, including low clearance, low hepatic extraction rate, moderate volume of distribution and long half-life. In addition, ATCAA-10 inhibited A549 tumor xenograft growth with 46% tumor growth inhibition (TGI) at 20 mg/kg dose. Taken together; these results suggest that ATCAA-10 modulates the activity of two signaling pathways, PI3K/AKT/mTOR and AMPK/mTOR, resulting in the inhibition of cancer cell growth.

Development of an online p38α mitogen-activated protein kinase binding assay and integration of LC–HR-MS

A high-resolution screening method was developed for the p38α mitogen-activated protein kinase to detect and identify small-molecule binders. Its central role in inflammatory diseases makes this enzyme a very important drug target. The setup integrates separation by high-performance liquid chromatography with two parallel detection techniques. High-resolution mass spectrometry gives structural information to identify small molecules while an online enzyme binding detection method provides data on p38α binding. The separation step allows the individual assessment of compounds in a mixture and links affinity and structure information via the retention time. Enzyme binding detection was achieved with a competitive binding assay based on fluorescence enhancement which has a simple principle, is inexpensive, and is easy to interpret. The concentrations of p38α and the fluorescence tracer SK&F86002 were optimized as well as incubation temperature, formic acid content of the LC eluents, and the material of the incubation tubing. The latter notably improved the screening of highly lipophilic compounds. For optimization and validation purposes, the known kinase inhibitors BIRB796, TAK715, and MAPKI1 were used among others. The result is a high-quality assay with Z′ factors around 0.8, which is suitable for semi-quantitative affinity measurements and applicable to various binding modes. Furthermore, the integrated approach gives affinity data on individual compounds instead of averaged ones for mixtures. FigureP38 α online screening platform Electronic supplementary materialThe online version of this article (doi:10.1007/s00216-010-4087-8) contains supplementary material, which is available to authorized users.

Abstract 3622: Preclinical characterization of EMD1214063, a potent and highly selective inhibitor of the c-Met kinase in Phase I clinical trials

Abstract c-Met, the receptor for hepatocyte growth factor (HGF), is a well characterized receptor tyrosine kinase, which is crucial for cell functions, such as survival, proliferation, motility and migration. Activating point mutations of c-Met have been identified in human malignancies, including renal carcinoma and lung cancer and constitutive activation of the HGF/c-Met pathway leads to tumor development and progression in cancer animal models. In the light of these findings, c-Met has become a key target for oncology therapeutics. In order to develop c-Met specific inhibitors, we have conducted a biochemical HTS run with the recombinant kinase domain of c-Met. This approach has enabled us to identify a new class of c-Met inhibitors. Our report will focus on pharmacological and pre-clinical data, characterising EMD1214063, a promising therapeutic candidate currently under clinical testing. Inhibition of the c-Met kinase by EMD1214063 was potent and highly selective. In in vitro kinase reactions and binding assays, EMD1214063 at a dose of 1μM, inhibited only 5 additional kinases in a panel of more than 250 different potential off-targets more than 50%. In vitro, EMD1214063 interfered with survival, anchorage-independent growth and HGF-induced migration of tumor cells, by blocking HGF-dependent as well as constitutive phosphorylation of c-Met. In vivo, oral administration of EMD1214063 resulted in a strong inhibition - ranging from delayed growth to complete regression - of HGF-dependent and -independent c-Met driven tumor xenografts. Such anti-tumor activity was observed at a broad dose range, suggesting that EMD1214063 has a wide therapeutic index. The inhibitor was well tolerated, as indicated by the lack of significant weight loss in treated mice. The mechanism of action of EMD1214063 was investigated in vivo in a series of PK/PD studies. Administration of a single dose of EMD1214063 induced a complete and long-lasting inhibition of c-Met phosphorylation in the tumor xenografts. Furthermore, it strongly reduced the plasma levels of tumor-derived IL-8. c-Met phosphorylation and plasma IL-8 levels decreased as a function of the drug concentration in the tumor and plasma. Taken together, the high c-Met selectivity, potency and in vivo efficacy of EMD1214063 render this compound a very promising candidate for the treatment of patients bearing c-Met-driven tumors. 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 3622.

Abstract 5499: Kinase inhibitor selectivity profiling utilizing a versatile TR-FRET kinase binding assay platform

Abstract There is great potential for the utilization of selective kinase inhibitors in the treatment of many clinical indications, especially in oncology and autoimmune conditions. Kinase inhibitor selectivity profiling has become an important tool during lead development to understand a compound's selectivity, potential off-target effects and possible new indications for the compound. We have utilized the LanthaScreen® Eu Kinase Binding Assay platform to develop a simple, robust means for profiling compounds across the kinome utilizing pre-plated reagents and controls. The assay is based on competitive displacement of a tracer (a fluorophore conjugated to a kinase inhibitor scaffold) from specific kinases of interest. Binding of the tracer to a kinase is detected by addition of a europium-labeled anti-tag antibody. Binding of the tracer and antibody to a kinase results in a high degree of FRET, whereas displacement of the tracer with a kinase inhibitor results in a loss of FRET. This platform is useful to explore activation-state binding selectivity, time-dependent binding, and binding to kinases for which substrates have not been identified. The assay detects both ATP-competitive as well as non-competitive, allosteric kinase inhibitors. We will present data demonstrating the utility of these reagents for kinase profiling efforts with a variety of kinase inhibitors. 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 5499.

Displacement Assay for the Detection of Stabilizers of Inactive Kinase Conformations

Targeting protein kinases with small molecules outside the highly conserved ATP pocket to stabilize inactive kinase conformations is becoming a more desirable approach in kinase inhibitor research, since these molecules have advanced pharmacological properties compared to compounds exclusively targeting the ATP pocket. Traditional screening approaches for kinase inhibitors are often based on enzyme activity, but they may miss inhibitors that stabilize inactive kinase conformations by enriching the active state of the kinase. Here we present the development of a kinase binding assay employing a pyrazolourea type III inhibitor and enzyme fragment complementation (EFC) technology that is suitable to screen stabilizers of enzymatically inactive kinases. To validate this assay system, we report the binding characteristics of a series of kinase inhibitors to inactive p38alpha and JNK2. Additionally, we present protein X-ray crystallography studies to examine the binding modes of potent quinoline-based DFG-out binders in p38alpha.

Development and Applications of a Broad-Coverage, TR-FRET-Based Kinase Binding Assay Platform

The expansion of kinase assay technologies over the past decade has mirrored the growing interest in kinases as drug targets. As a result, there is no shortage of convenient, fluorescence-based methods available to assay targets that span the kinome. The authors recently reported on the development of a non-activity-based assay to characterize kinase inhibitors that depended on displacement of an Alexa Fluor 647 conjugate of staurosporine (a "tracer") from a particular kinase. Kinase inhibitors were characterized by a change in fluorescence lifetime of the tracer when it was bound to a kinase relative to when it was displaced by an inhibitor. Here, the authors report on improvements to this strategy by reconfiguring the assay in a time-resolved fluorescence resonance energy transfer (TR-FRET) format that simplifies instrumentation requirements and allows for the use of a substantially lower concentration of kinase than was required in the fluorescence-lifetime-based format. The authors use this new assay to demonstrate several aspects of the binding assay format that are advantageous relative to traditional activity-based assays. The TR-FRET binding format facilitates the assay of compounds against low-activity kinases, allows for the characterization of type II kinase inhibitors either using nonactivated kinases or by monitoring compound potency over time, and ensures that the signal being detected is specific to the kinase of interest and not a contaminating kinase.

Development of a Fluorescent-Tagged Kinase Assay System for the Detection and Characterization of Allosteric Kinase Inhibitors

Kinase disregulation disrupts the intricate network of intracellular signaling pathways and contributes to the onset of diseases such as cancer. Although several kinase inhibitors are on the market, inhibitor selectivity and drug resistance mutations persist as fundamental challenges in the development of effective long-term treatments. Chemical entities binding to less conserved allosteric sites would be expected to offer new opportunities for scaffold development. Because no high-throughput method was previously available, we developed a fluorescence-based kinase binding assay for identifying and characterizing ligands which stabilize the inactive kinase conformation. Here, we present a description of the development and validation of this assay using the serine/threonine kinase p38alpha. By covalently attaching fluorophores to the activation loop of the kinase, we were able to detect conformational changes and measure the K(d), k(on), and k(off) associated with the binding and dissociation of ligands to the allosteric pocket. We report the SAR of a synthesized focused library of pyrazolourea derivatives, a scaffold known to bind with high affinity to the allosteric pocket of p38alpha. Additionally, we used protein X-ray crystallography together with our assay to examine the binding and dissociation kinetics to characterize potent quinazoline- and quinoline-based type II inhibitors, which also utilize this binding pocket in p38alpha. Last, we identified the b-Raf inhibitor sorafenib as a potent low nanomolar inhibitor of p38alpha and used protein X-ray crystallography to confirm a unique binding mode to the inactive kinase conformation.

Fluorescent-tagged Kinases: A New Assay System For Detecting And Screening For Allosteric Kinase Inhibitors

Targeting the ATP binding pocket has been the most common strategy for inhibiting kinases. Recently, a less-conserved allosteric site was identified in some kinases (i.e. Abl, EGFR and p38α), opening up patent space for novel drug scaffolds which are more kinase specific. Kinases are typically in the active conformation (DFG-in) with the activation loop open and extended, allowing ATP and substrates to bind. Alternatively, the adjacent allosteric site is available only in the inactive conformation (DFG-out) in which the activation loop undergoes a large conformational change. It was our aim to develop a new fluorescence-based kinase binding assay which could sense this conformational switch and screen for new allosteric kinase inhibitors.We used crystal structures of p38α (active and inactive) to identify positions in the activation loop which undergo significant movement and could be mutated into Cys for the subsequent attachment of environmentally-sensitive fluorophores. Other solvent-exposed Cys were mutated into Ser to minimize non-specific labeling. Using acrylodan-labeled p38α, we developed the first sensitive (Z-factor = 0.85) HTS method for screening inhibitor libraries for allosteric kinase inhibitors. Endpoint fluorescence measurements can be used to directly determine the Kd of inhibitor binding. Real-time fluorescence measurements provide information about the kinetics of association and dissociation.Adaptation of this approach to other kinases has allowed us to identify weakly binding scaffolds which bind to the allosteric site. Using structure-based drug design, we were able to further develop these smaller compounds into more potent kinase inhibitors (Kd = low nM). These new tight binding compounds have also become powerful tools for identifying which kinases can and cannot be inhibited allosterically, a critical question which remains to be answered in the kinase field.

Clinical Pharmacokinetics and FLT3 Phosphorylation of AC220, a Highly Potent and Selective Inhibitor of FLT3

Several different FLT3 inhibitors have now been tested as monotherapy for AML patients and have met with only limited success. To date, none of these inhibitors have resulted in complete, sustained inhibition of phosphorylated FLT3 in vivo, as measured by immunoblotting techniques. AC220 is a novel FLT3 kinase inhibitor with greater potency and kinase selectivity than others previously characterized. To establish a dose of AC220 that will lead to complete, sustained inhibition of phosphorylated FLT3, a Phase I open-label, sequential dose escalation study investigating safety, tolerability, pharmacokinetics, and pharmacodynamics in patients with relapsed or refractory acute myeloid leukemia is being conducted. AC220 is administered once daily as an oral solution for 14 days followed by a 14-day rest period, (one cycle) with a starting dose of 12 mg. Patients showing clinical benefit may continue to receive further cycles of therapy. The study is a standard 3+3 dose escalation design with 50% dose increments. Currently 52 patients have been enrolled and AC220 has been well tolerated and escalated to 450 mg daily (10th dose cohort) on this intermittent dosing regimen and PK has been evaluated up to 300 mg. AC220 is orally bio-available and has a long effective half-life, estimated to be 2.5 days, exhibiting minimal peak and trough variation of plasma levels. AC220 plasma exposure in AML patients is sustained between dose intervals and continues to increase in a dose-proportional manner from 12 mg to 300 mg daily, with steady-state plasma concentrations achieving greater than 1,500 nM at 300 mg. In addition, a pharmacologically active metabolite, AC886, has been identified in patient urine and plasma samples, which has similar potency and kinase selectivity to AC220 as determined by in vitro kinase binding and cell assays. The IC50s for AC220 and AC886 in FLT3-ITD-expressing cell lines and in primary FLT3-ITD AML patient blast samples are in the low nanomolar range (1.7 and 0.3 nM, respectively) and are in good agreement with cytotoxicity (Annexin V and MTT) assays. Both drugs display a high degree of selectivity for FLT3 in an IL-3 rescue assay. AC220 and AC886 also potently inhibit wild type FLT3 (3.6 and 4.2 nM, respectively). In standard immunoblot curves using AC220 and AC886 spiked into plasma, FLT3-ITD phosphorylation was completely inhibited at 50 and 200 nM, respectively. As predicted from the standard curve data, plasma from AC220-treated AML patients completely suppresses FLT3 phosphorylation on Day 1 and at steady-state in an ex vivo plasma inhibitory activity (PIA) assay, even at the lowest dose of 12 mg daily. AC220, with its metabolite AC886, is a potent, selective inhibitor of both mutant and wild type FLT3. It is orally bio-available with sustained plasma exposure, and the pharmacological impact of AC220 is further enhanced by the presence of AC886. In vivo, therefore, AC220 is expected to completely inhibit FLT3-ITD at >100 nM (achieved at the lowest AC220 dose of 12 mg) and FLT3-WT at 500 nM (achieved by the 60 mg dose). AC220 is the most potent and selective FLT3 inhibitor tested using the PIA assay thus far, and, unlike other FLT3 inhibitors that have been assessed in this assay, is the first to completely suppress FLT3 phosphorylation ex vivo at doses that are easily achievable and sustainable in the clinic. Therefore, AC220 should be able to effect substantial and prolonged target inhibition in patients. This makes it an ideal compound with which to test the hypothesis that complete, sustained inhibition of FLT3 activity will lead to clinical benefit in FLT3 mutant AML patients.

Activation of the Small GTPase Rac2 via the B Cell Receptor Regulates B Cell Adhesion and Immunological-Synapse Formation

The integrin leukocyte function-associated antigen-1 (LFA-1) is important in the promotion of B cell adhesion, thereby facilitating immunological synapse (IS) formation and B cell activation. Despite this significance, the associated signaling mechanisms regulating LFA-1 activation remain elusive. Here, we show that both isoforms of the small GTPase Rac expressed by primary B cells, Rac1 and Rac2, were activated rapidly downstream of Src-family kinases, guanine-nucleotide exchange factors Vav1 and Vav2, and phosphoinositide-3 kinase (PI3K) after BCR engagement. We identify Rac2, but not Rac1, as critical for B cell adhesion to intercellular adhesion molecule-1 (ICAM-1) and IS formation. Furthermore, B cells expressing constitutively active Rac2 are highly adhesive. We observe that Rac2-deficient B cells exhibit lower amounts of Rap1-GTP and severe actin polymerization defects, identifying a potential mechanism underlying their behavior. We postulate that this critical role for Rac2 in mediating B cell adhesion and IS formation might apply in all lymphocytes.

A Fluorescence Lifetime–Based Binding Assay to Characterize Kinase Inhibitors

The authors present a fluorescence lifetime-based kinase binding assay that identifies and characterizes compounds that bind to the adenosine triphosphate (ATP)-binding pocket of a range of tyrosine and serine/threonine kinases. The assay is based on displacement of an Alexa Fluor 647 conjugate of staurosporine from the ATP-binding site of a kinase, which is detected by a change in the fluorescence lifetime of the probe between the free (displaced) and kinase-bound states. The authors screened 257 kinases for specific binding and displacement of the Alexa Fluor 647-staurosporine probe and found that approximately half of the kinases tested could potentially be assayed with this method. They present inhibitor binding data against 4 selected serine/threonine kinases and 4 selected tyrosine kinases, using 6 commonly used kinase inhibitors. Two of these kinases were chosen for further studies, in which inhibitor binding data were compared to inhibition of kinase activity using 2 separate activity assay formats. Rank-order potencies of compounds were similar, but not identical, between the binding and activity assays. It was postulated that these differences could be caused by the fact that the assays are measuring distinct phenomena, namely, activity versus binding, and in a purified recombinant kinase preparation, there can exist a mixture of active and nonactivated kinases. To explore this possibility, the authors compared binding affinity for the probe using 2 kinases in their respective nonactivated and activated (phosphorylated) forms and found a kinase-dependent difference between the 2 forms. This assay format therefore represents a simple method for the identification and characterization of small-molecule kinase inhibitors that may be useful in screening a wide range of kinases and may be useful in identifying small molecules that bind to kinases in their active or nonactivated states.

Enzyme Fragment Complementation Binding Assay for p38α Mitogen-Activated Protein Kinase to Study the Binding Kinetics of Enzyme Inhibitors

The majority of protein kinase assays used in drug discovery research are enzyme activity assays. These assays are based on the measurement of phosphorylated protein or peptide substrate, which is the end product of the enzyme reaction. Since most kinase inhibitors are ATP competitive, prediction of the activity of compounds in cellular systems based on potency values in enzyme activity assays is complex, as this should take into account the affinity of the enzyme for ATP and the cellular ATP concentration. The fact that some of the most successful kinase inhibitors, such as STI 571 (imatinib mesylate, Gleevec, Novartis Pharmaceuticals, East Hanover, NJ), act through binding to the inactive isoform of the kinase provides another limitation of enzyme activity assays. Binding assays allow separate measurement of compound affinity to active and inactive kinase and do not require ATP or substrate in the reaction. Recently, a non-radioactive kinase binding assay for p38 mitogen-activated protein kinase has become available from DiscoveRx (Fremont, CA). The assay method, called HitHunter, utilizes enzyme fragment complementation of Escherichia coli beta-galactosidase to generate an assay signal by chemiluminescence. We have reconfigured the commercial assay kit to study the binding kinetics of two known reference inhibitors of the alpha-isoform of p38, the pyridinyl imidazole SB 203580 and the diaryl urea BIRB 796. Our data confirm the slow association kinetics of BIRB 796 as compared to SB 203580, which corresponded with the requirement of a relatively long preincubation time to obtain maximal effect in a cellular assay. Although neither of the two compounds showed preference for either active or inactive p38alpha, our data demonstrate that the HitHunter kinase binding assay can be used to select compounds that specifically target inactive kinase.