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1.  A-770041 reverses paclitaxel and doxorubicin resistance in osteosarcoma cells 
BMC Cancer  2014;14(1):681.
Background
Reversing multidrug resistance (MDR) has been an important goal for clinical and investigational oncologists. In the last few decades, significant effort has been made to search for inhibitors to reverse MDR by targeting ATP-binding cassette (ABC) transporters (Pgp, MRP) directly, but these efforts have achieved little clinical success. Protein kinases play important roles in many aspects of tumor cell growth and survival. Combinations of kinase inhibitors and chemotherapeutics have been observed to overcome cancer drug resistance in certain circumstances.
Methods
We screened a kinase specific inhibitor compound library in human osteosarcoma MDR cell lines to identify inhibitors that were capable of reversing chemoresistance to doxorubicin and paclitaxel.
Results
We identified 18 small molecules that significantly increase chemotherapy drug-induced cell death in human osteosarcoma MDR cell lines U-2OSMR and KHOSR2. We identified A-770041 as one of the most effective MDR reversing agents when combined with doxorubicin or paclitaxel. A-770041 is a potent Src family kinase (Lck and Src) inhibitor. Western blot analysis revealed A-770041 inhibits both Src and Lck activation and expression. Inhibition of Src expression in U-2OSMR and KHOSR2 cell lines using lentiviral shRNA also resulted in increased doxorubicin and paclitaxel drug sensitivity. A-770041 increases the intracellular drug accumulation as demonstrated by calcein AM assay.
Conclusions
These results indicate that small molecule inhibitor A-770041 may function to reverse ABCB1/Pgp-mediated chemotherapy drug resistance. Combination of Src family kinase inhibitor with regular chemotherapy drug could be clinically effective in MDR osteosarcoma.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2407-14-681) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2407-14-681
PMCID: PMC4177239  PMID: 25236161
Osteosarcoma; MDR; Src kinase; Doxorubicin
2.  Metabolic and Functional Genomic Studies Identify Deoxythymidylate Kinase as a target in LKB1 Mutant Lung Cancer 
Cancer discovery  2013;3(8):870-879.
The LKB1/STK11 tumor suppressor encodes a serine/threonine kinase which coordinates cell growth, polarity, motility, and metabolism. In non-small cell lung cancer, LKB1 is somatically inactivated in 25-30% of cases, often concurrently with activating KRAS mutation. Here, we employed an integrative approach to define novel therapeutic targets in KRAS-driven LKB1 mutant lung cancers. High-throughput RNAi screens in lung cancer cell lines from genetically engineered mouse models driven by activated KRAS with or without coincident Lkb1 deletion led to the identification of Dtymk, encoding deoxythymidylate kinase which catalyzes dTTP biosynthesis, as synthetically lethal with Lkb1 deficiency in mouse and human lung cancer lines. Global metabolite profiling demonstrated that Lkb1-null cells had striking decreases in multiple nucleotide metabolites as compared to the Lkb1-wt cells. Thus, LKB1 mutant lung cancers have deficits in nucleotide metabolism conferring hypersensitivity to DTYMK inhibition, suggesting that DTYMK is a potential therapeutic target in this aggressive subset of tumors.
doi:10.1158/2159-8290.CD-13-0015
PMCID: PMC3753578  PMID: 23715154
LKB1; KRAS; DTYMK; CHEK1; NSCLC; GEMM-derived cell line; genome wide RNAi screen; metabolic profiling
3.  Three-Dimensional Hierarchical Plasmonic Nano-Architecture Enhanced Surface-Enhanced Raman Scattering Immuno-Sensor for Cancer Biomarker Detection in Blood Plasma 
ACS nano  2013;7(6):4967-4976.
A three-dimensional (3D) hierarchical plasmonic nano-architecture has been designed for a sensitive surface-enhanced Raman scattering (SERS) immuno-sensor for protein biomarker detection. The capture antibody molecules are immobilized on a plasmonic gold triangle nano-array pattern. On the other hand, the detection antibody molecules are linked to the gold nano-star@Raman-reporter@silica sandwich nanoparticles. When protein biomarkers are present, the sandwich nanoparticles are captured over the gold triangle nano-array, forming a confined 3D plasmonic field, leading to the enhanced electromagnetic field in intensity and in 3D space. As a result, the Raman reporter molecules are exposed to a high density of “hot spots”, which amplifies the Raman signal remarkably, improving the sensitivity of the SERS immuno-sensor. This SERS immuno-sensor exhibits a wide linear range (0.1 pg/mL to 10 ng/mL), and a low limit of detection (7 fg/mL) toward human immunoglobulin G (IgG) protein in the buffer solution. This biosensor has been successfully used for detection of the vascular endothelial growth factor (VEGF) in the human blood plasma from clinical breast cancer patient samples.
doi:10.1021/nn4018284
PMCID: PMC3732798  PMID: 23659430
Biosensor; Biomarker; Surface-enhanced Raman scattering; Cancer; Surface plasmon; Blood plasma
4.  Discovery and Characterization of Novel Mutant FLT3 Kinase Inhibitors 
Molecular cancer therapeutics  2010;9(9):2468-2477.
For a subpopulation of acute myeloid leukemia (AML) patients, the constitutively activated tyrosine kinase, mutant FLT3, has emerged as a promising target for therapy. The development of drug resistance, however, is a growing concern for mutant FLT3 inhibitors, such as PKC412. Potential therapeutic benefit can arise from the combination of two structurally diverse inhibitors that target- but bind differently to- the same protein or from two inhibitors with completely different mechanisms of action. Thus, there is a need for identification and development of novel FLT3 inhibitors that have the ability to positively combine with PKC412 or standard chemotherapeutic agents used to treat AML as a way to suppress the development of drug resistance and consequently prolong disease remission. Here, we report the effects of the novel type II ATP competitive inhibitors, HG-7-85-01 and HG-7-86-01, which potently and selectively target mutant FLT3 protein kinase activity, and inhibit the proliferation of cells harboring FLT3-ITD or FLT3 kinase domain point mutants via induction of apoptosis and cell cycle inhibition. Anti-leukemic activity of HG-7-85-01 was demonstrated in vivo to be comparable to that observed with PKC412 in a bioluminescence assay utilizing NCr nude mice harboring Ba/F3-FLT3-ITD-luc+ cells. HG-7-85-01 was also observed to override PKC412 resistance. Finally, HG-7-85-01 and HG-7-86-01 synergized with PKC412 and standard chemotherapeutic agents against mutant PKC412-sensitive and some PKC412-resistant, FLT3-positive cells. Thus, we present a structurally novel class of FLT3 inhibitors that warrants consideration for clinical testing against drug-resistant disease in AML patients.
doi:10.1158/1535-7163.MCT-10-0232
PMCID: PMC3967795  PMID: 20807780
5.  Development of ATP-competitive mTOR Inhibitors 
The mTOR mediated signaling transduction pathway has been observed to be deregulated in a wide variety of cancer and metabolic diseases. Despite extensive clinical development efforts, the well-known allosteric mTOR inhibitor rapamycin and structurally related rapalogs have failed to show significant single-agent anti-tumor efficacy in most types of cancer. This limited clinical success maybe due to the inability of the rapalogs to maintain a complete blockade mTOR mediated signaling. Therefore numerous efforts have been initiated to develop ATP-competitive mTOR inhibitors that would block both mTORC1 and mTORC2 complex activity. Here we describe our experimental approaches to develop Torin1 using a medium throughput cell-based screening assay and structure-guided drug design.
doi:10.1007/978-1-61779-430-8_29
PMCID: PMC3964610  PMID: 22125084
mTOR; mTORC1; mTORC2; PI3K; PIKK; Akt; Rapamycin; Torin1
6.  Expression of Hsp90α and cyclin B1 were related to prognosis of esophageal squamous cell carcinoma and keratin pearl formation 
Hsp90α (heat shock protein 90α), one of the important molecular chaperones in cancer cell signal transduction, has been a new candidate target for cancer therapy. Cyclin B1, the client protein of Hsp90α, plays a key role as a mitotic cyclin in the G2-M phase transition during the cell cycle progression. However, the relationship between the level of HSP90α and cyclin B1, the location of Hsp90α and cyclin B1 in prognosis of esophageal squamous cell carcinoma (ESCC) has not been examined. Here, we demonstrate that the diagnostic significance of Hsp90α and cyclin B1 by immunohistochemistry and the association of Hsp90α and cyclin B1 expression in ESCC. In the specimens from 105 ESCC patients (81 stained with Hsp90α antibody by Immunohistochemistry, 65 with cyclin B1 antibody, and among them, 41 paired specimens were stained with Hsp90α and cyclin B1 respectively, and then checked for the correlation of the level and location of Hsp90α and cylcin B1. The positivity rate of Hsp90α and cyclin B1 expression were 96.3% (78 of 81) and 84.6% (55 of 65) respectively. Both of them, the expression levels are associated with the clinical pathological stage (Hsp90α, p=0.027; cyclin B1, p=0.007). No association was found between Hsp90α or cyclin B1 and gender, age, tumor location. As to TMN stage, there is no association with the level of Hsp90α, However, cyclin B1 expression is significantly related to tumor status (p=0.002). Interestingly, Hsp90α expression was negatively correlated to cyclin B1 expression (Gamma=-0.692, p=0.007) in the keratin pearls though there is a positive correlation in the other areas of tumor (Gamma=0.503, p=0.015), which suggest Hsp90α might play diverse roles in the cyclin B1 expression and cyclin B1 related cell cycle regulation in the different area of tumor. These findings demonstrated that the expression of Hsp90α, cyclin B1 protein is associated with tumor malignancy and prognosis for patients with human esophageal squamous cell carcinoma, and Hsp90α might be involved in cyclin B1 expression regulation and cell cycle regulation in keratin peal formation of ESCC.
PMCID: PMC4014234  PMID: 24817950
Hsp90α; cyclin B1; esophageal squamous cell carcinoma; keratin pearl; prognosis; immunohistochemistry
7.  Discovery of 1-(4-(4-propionylpiperazin-1-yl)-3-(trifluoromethyl)phenyl)-9-(quinolin-3-yl)benzo[h][1,6]naphthyridin-2(1H)-one as a highly potent, selective Mammalian Target of Rapamycin (mTOR) inhibitor for the treatment of cancer 
Journal of medicinal chemistry  2010;53(19):7146-7155.
The mTOR protein is a master regulator of cell growth and proliferation, and inhibitors of its kinase activity have the potential to become new class of anti-cancer drugs. Starting from quinoline 1, which was identified in a biochemical mTOR assay, we developed a tricyclic benzonaphthyridinone inhibitor Torin1(26), which inhibited phosphorylation of mTORC1 and mTORC2 substrates in cells at concentrations of 2 nM and 10 nM, respectively. Moreover, Torin1 exhibits 1000-fold selectivity for mTOR over PI3K (EC50 = 1800 nM) and exhibits 100-fold binding selectivity relative to 450 other protein kinases. Torin1 was efficacious at a dose of 20 mg/kg in a U87MG xenograft model, and demonstrated good pharmacodynamic inhibition of downstream effectors of mTOR in tumor and peripheral tissues. These results demonstrate that Torin1 is a useful probe of mTOR-dependent phenomena and that benzonaphthridinones represent a promising scaffold for the further development of mTOR-specific inhibitors with the potential for clinical utility.
doi:10.1021/jm101144f
PMCID: PMC3893826  PMID: 20860370
9.  The Risk of Metabolic Syndrome in Patients with Rheumatoid Arthritis: A Meta-Analysis of Observational Studies 
PLoS ONE  2013;8(10):e78151.
Background
Observational studies suggest an association between the incidence of rheumatoid arthritis (RA) and the prevalence of metabolic syndrome (MetS). However, the relationship between RA and MetS is controversial and research in this area is currently lacking.
Objective
The aim of this study was to assess whether the prevalence of MetS was higher in a group of RA patients compared to subjects without RA.
Design
A PubMed database search was conducted during April 2013 to identify observational studies of RA and risk of MetS. Reference lists of retrieved articles were also reviewed. Two authors independently extracted information on the study design, the characteristics of the study participants, exposure and outcome assessments, and the method used to control for potential confounding factors. A random-effects model was used for the risk estimates.
Results
Our meta-analysis of four cross-sectional controlled studies plus eight case-control studies involving a total of 2283 cases and 4403 controls identified a significant association between RA and risk of MetS, with an overall OR of 1.24 (95% CI, 1.03-1.50).
Conclusion
This meta-analysis provides further evidence supporting patients with RA have a higher prevalence of MetS than subjects without RA. In addition, the geographic region of the population and the criteria used for MetS diagnosis could influence the association. However, these observations would need to be evaluated using prospective, randomized studies.
doi:10.1371/journal.pone.0078151
PMCID: PMC3808281  PMID: 24205134
10.  Development of ‘DFG-out’ inhibitors of gatekeeper mutant kinases 
HG-7-85-01(22) and HG-7-86-01(26) are thiazolo[5,4-b]pyridine containing type II tyrosine kinase inhibitors with potent cellular activity against both wild-type and ‘gatekeeper’ mutant T315I- Bcr-Abl. Here we report on the ‘hybrid design’ concept and subsequent structure activity guided optimization efforts that resulted in the development of these inhibitors.
doi:10.1016/j.bmcl.2012.06.036
PMCID: PMC3415686  PMID: 22819762
T315I Bcr-Abl; Kinase inhibitor; Gatekeeper mutant; Type II inhibitor; Thiazolo[5; 4-b]pyridine
11.  Prevalence of HIV and Syphilis Infection among High School and College Student MSM in China: A Systematic Review and Meta-Analysis 
PLoS ONE  2013;8(7):e69137.
Objectives
The aim of this study is to systematically review the published studies and summarize the estimates of HIV and syphilis prevalences among high school and college student MSM in China in order to provide information for conducting targeted interventions.
Methods
Pubmed, Chinese National Knowledge Infrastructure, Wanfang and Google Scholar databases were searched in January 2013 to identify relevant articles. Data of eligible citations were extracted by two reviewers. All analyses were performed using Comprehensive Meta-Analysis V2.0 and SPSS V17.0.
Results
Twenty-four eligible studies (6 in English and 18 in Chinese), published between 2006 and 2012, with a total of 3083 student MSM participants, were included. The meta-analyses showed that the prevalences of HIV and syphilis among studied student MSM were 4.4% (95% CI: 3.0%, 6.4%) and 5.7% (95% CI: 4.8%, 6.7%), respectively. HIV prevalence increased over the study period (3.0% in 2003–2006; 4.5% in 2007–2008, and 6.8% in 2009–2010, trend test chi-square = 11.3, p = 0.001).
Conclusions
Student MSM have become high-risk populations for HIV infection in China. The high prevalence of syphilis and the increasing HIV prevalence trend indicate the potential for a more severe HIV epidemic. Comprehensive intervention strategies that address condom promotion, syphilis detection and treatment, and health education need to be tailored to this vulnerable population to prevent HIV and syphilis infections.
doi:10.1371/journal.pone.0069137
PMCID: PMC3712943  PMID: 23874891
12.  An Amino-indazole Scaffold with Spectrum Selective Kinase Inhibition of FLT3, PDGFRα and Kit 
Here we describe the synthesis and characterization of a number of 3-amino-1H-indazol-6-yl-benzamides that were designed to target the “DFG-out” conformation of the kinase activation loop. Several compounds such as 4 and 11 exhibit single-digit nanomolar EC50s against FLT3, c-Kit and the gatekeeper T674M mutant of PDGFRα.
doi:10.1016/j.bmcl.2012.05.107
PMCID: PMC3547541  PMID: 22727638
13.  A Complex Network of Factors with Overlapping Affinities Repress Splicing through Intronic Elements 
To better understand splicing regulation, we used a cell-based screen to identify ten diverse motifs that inhibit splicing from intron. Each motif was validated in another human cell type and gene context, and their presence correlated with in vivo splicing changes. All motifs exhibited exonic splicing enhancer or silencer activity, and grouping these motifs based on their distributions yielded clusters with distinct patterns of context-dependent activity. Candidate regulatory factors associated with each motif were identified, recovering 24 known and novel splicing regulators. Specific domains in selected factors were sufficient to confer ISS activity. Many factors bound multiple distinct motifs with similar affinity, and all motifs were recognized by multiple factors, revealing a complex, overlapping network of protein:RNA interactions. This arrangement enables individual cis-element to function differently in distinct cellular contexts depending on the spectrum of regulatory factors present.
doi:10.1038/nsmb.2459
PMCID: PMC3537874  PMID: 23241926
splicing regulation; splicing factors; intronic splicing silencers; RNA binding protein; context dependent activity
14.  Small Molecule Inhibitors of the c-Fes Protein-tyrosine Kinase 
Chemistry & biology  2012;19(4):529-540.
SUMMARY
The c-Fes protein-tyrosine kinase modulates cellular signaling pathways governing differentiation, the innate immune response, and vasculogenesis. Here we report the identification of Type I and II kinase inhibitors with potent activity against c-Fes both in vitro and in cell-based assays. One of the most potent inhibitors is the previously described anaplastic lymphoma kinase inhibitor, TAE684. The crystal structure of TAE684 in complex with the c-Fes SH2-kinase domain showed excellent shape complementarity with the ATP-binding pocket and a key role for the gatekeeper methionine in the inhibitory mechanism. TAE684 and two pyrazolopyrimidines with nanomolar potency against c-Fes in vitro were used to establish a novel role for this kinase in osteoclastogenesis, illustrating the value of these inhibitors as tool compounds to probe the diverse biological functions associated with this unique kinase.
doi:10.1016/j.chembiol.2012.01.020
PMCID: PMC3334838  PMID: 22520759
15.  A Dibutyl Phthalate Sensor Based on a Nanofiber Polyaniline Coated Quartz Crystal Monitor 
Sensors (Basel, Switzerland)  2013;13(3):3765-3775.
Dibutyl phthalate (DBP) is a commonly used plasticizer and additive to adhesives, printing inks and nail polishes. Because it has been found to be a powerful reproductive and developmental toxicant, a sensor to monitor DBP in some working spaces and the environment is required. In this work polyaniline nanofibers were deposited on the electrode of a quartz crystal oscillator to form a Quartz Crystal Microbalance gas sensor. The coated quartz crystal and a non-coated quartz crystal were mounted in a sealed chamber, and their frequency difference was monitored. When DBP vapor was injected into the chamber, gas adsorption decreased the frequency of the coated quartz crystal oscillator and thereby caused an increase in the frequency difference between the two crystals. The change of the frequency difference was recorded as the sensor response. The sensor was extremely sensitive to DBP and could be easily recovered by N2 purging. A low measurement limit of 20 ppb was achieved. The morphologies of the polyaniline films prepared by different approaches have been studied by SEM and BET. How the nanofiber-structure can improve the sensitivity and stability is discussed, while its selectivity and long-term stability were investigated.
doi:10.3390/s130303765
PMCID: PMC3658774  PMID: 23507822
QCM; gas sensor; dibutyl phthalate; nanofiber; polyaniline; PACS 07.07.Df (Gas sensor); 77.65.Fs (Quartz resonator); 82.35.Np (Polymers nanoparticles in); 81.07.-b (Nanoscale materials fabrication and characterization)
16.  Selective Akt Inhibitors Synergize with Tyrosine Kinase Inhibitors and Effectively Override Stroma-Associated Cytoprotection of Mutant FLT3-Positive AML Cells 
PLoS ONE  2013;8(2):e56473.
Objectives
Tyrosine kinase inhibitor (TKI)-treated acute myeloid leukemia (AML) patients commonly show rapid and significant peripheral blood blast cell reduction, however a marginal decrease in bone marrow blasts. This suggests a protective environment and highlights the demand for a better understanding of stromal:leukemia cell communication. As a strategy to improve clinical efficacy, we searched for novel agents capable of potentiating the stroma-diminished effects of TKI treatment of mutant FLT3-expressing cells.
Methods
We designed a combinatorial high throughput drug screen using well-characterized kinase inhibitor-focused libraries to identify novel kinase inhibitors capable of overriding stromal-mediated resistance to TKIs, such as PKC412 and AC220. Standard liquid culture proliferation assays, cell cycle and apoptosis analysis, and immunoblotting were carried out with cell lines or primary AML to validate putative candidates from the screen and characterize the mechanism(s) underlying observed synergy.
Results and Conclusions
Our study led to the observation of synergy between selective Akt inhibitors and FLT3 inhibitors against mutant FLT3-positive AML in either the absence or presence of stroma. Our findings are consistent with evidence that Akt activation is characteristic of mutant FLT3-transformed cells, as well as observed residual Akt activity following FLT3 inhibitor treatment. In conclusion, our study highlights the potential importance of Akt as a signaling factor in leukemia survival, and supports the use of the co-culture chemical screen to identify agents able to potentiate TKI anti-leukemia activity in a cytoprotective microenvironment.
doi:10.1371/journal.pone.0056473
PMCID: PMC3578845  PMID: 23437141
17.  Discovery of potent and selective covalent inhibitors of JNK 
Chemistry & biology  2012;19(1):140-154.
The mitogen activated kinases JNK1/2/3 are key enzymes in signaling modules that transduce and integrate extracellular stimuli into coordinated cellular response. Here we report the discovery of the first irreversible inhibitors of JNK1/2/3. We describe two JNK3 co-crystal structures at 2.60 and 2.97 Å resolutions that show the compounds form covalent bonds with a conserved cysteine residue. JNK-IN-8 is a selective JNK inhibitor that inhibits phosphorylation of c-Jun, a direct substrate of JNK kinase, in cells exposed to sub-micromolar drug in a manner that depends on covalent modification of the conserved cysteine residue. Extensive biochemical, cellular and pathway-based profiling establish the selectivity of JNK-IN-8 for JNK and suggest that the compound will be broadly useful as a pharmacological probe of JNK-dependent signal transduction. Potential lead compounds have also been identified for kinases including IRAK1, PIK3C3, PIP4K2C, and PIP5K3.
doi:10.1016/j.chembiol.2011.11.010
PMCID: PMC3270411  PMID: 22284361
18.  A Putative Gene sbe3-rs for Resistant Starch Mutated from SBE3 for Starch Branching Enzyme in Rice (Oryza sativa L.) 
PLoS ONE  2012;7(8):e43026.
Foods high in resistant starch (RS) are beneficial to prevent various diseases including diabetes, colon cancers, diarrhea and chronic renal or hepatic diseases. Elevated RS in rice is important for public health since rice is a staple food for half of the world population. A japonica mutant ‘Jiangtangdao 1’ (RS = 11.67%) was crossed with an indica cultivar ‘Miyang 23’ (RS = 0.41%). The mutant sbe3-rs that explained 60.4% of RS variation was mapped between RM6611 and RM13366 on chromosome 2 (LOD = 36) using 178 F2 plants genotyped with 106 genome-wide polymorphic SSR markers. Using 656 plants from four F3∶4 families, sbe3-rs was fine mapped to a 573.3 Kb region between InDel 2 and InDel 6 using one STS, five SSRs and seven InDel markers. SBE3 which codes for starch branching enzyme was identified as a candidate gene within the putative region. Nine pairs of primers covering 22 exons were designed to sequence genomic DNA of the wild type for SBE3 and the mutant for sbe3-rs comparatively. Sequence analysis identified a missense mutation site where Leu-599 of the wild was changed to Pro-599 of the mutant in the SBE3 coding region. Because the point mutation resulted in the loss of a restriction enzyme site, sbe3-rs was not digested by a CAPS marker for SpeI site while SBE3 was. Co-segregation of the digestion pattern with RS content among 178 F2 plants further supported sbe3-rs responsible for RS in rice. As a result, the CAPS marker could be used in marker-assisted breeding to develop rice cultivars with elevated RS which is otherwise difficult to accurately assess in crops. Transgenic technology should be employed for a definitive conclusion of the sbe3-rs.
doi:10.1371/journal.pone.0043026
PMCID: PMC3427327  PMID: 22937009
19.  Mapping mechanical properties of organic thin films by force-modulation microscopy in aqueous media 
Summary
The mechanical properties of organic and biomolecular thin films on surfaces play an important role in a broad range of applications. Although force-modulation microscopy (FMM) is used to map the apparent elastic properties of such films with high lateral resolution in air, it has rarely been applied in aqueous media. In this letter we describe the use of FMM to map the apparent elastic properties of self-assembled monolayers and end-tethered protein thin films in aqueous media. Furthermore, we describe a simple analysis of the contact mechanics that enables the selection of FMM imaging parameters and thus yields a reliable interpretation of the FMM image contrast.
doi:10.3762/bjnano.3.53
PMCID: PMC3458590  PMID: 23019540
acoustic atomic force microscopy; biomolecules; elastic modulus mapping; nanomechanical characterization; self-assembled monolayers
20.  In Situ Kinase Profiling Reveals Functionally Relevant Properties of Native Kinases 
Chemistry & biology  2011;18(6):699-710.
Summary
Protein kinases are intensely studied mediators of cellular signaling, yet important questions remain regarding their regulation and in vivo properties. Here we use a probe-based chemoprotemics platform to profile several well studied kinase inhibitors against more than 200 kinases in native cell proteomes and reveal new biological targets for some of these inhibitors. Several striking differences were identified between native and recombinant kinase inhibitory profiles, in particular, for the Raf kinases. The native kinase binding profiles presented here closely mirror the cellular activity of these inhibitors, even when the inhibition profiles differ dramatically from recombinant assay results. Additionally, Raf activation events could be detected upon live cell treatment with inhibitors. These studies highlight the complexities of protein kinase behavior in the cellular context and demonstrate that profiling with only recombinant/purified enzymes can be misleading.
doi:10.1016/j.chembiol.2011.04.011
PMCID: PMC3142620  PMID: 21700206
21.  Discovery of 3,5-Diamino-1,2,4-triazole Ureas as Potent Anaplastic Lymphoma Kinase Inhibitors 
ACS Medicinal Chemistry Letters  2011;2(5):379-384.
A series of novel 3,5-diamino-1,2,4-triazole benzyl ureas was identified as having potent anaplastic lymphoma kinase (ALK) inhibition exemplified by 15a, 20a, and 23a, which exhibited antiproliferative IC50 values of 70, 40, and 20 nM in Tel-ALK transformed Ba/F3 cells, respectively. Moreover, 15a and 23a potently inhibited the growth and survival of NPM-ALK positive anaplastic large cell lymphoma cell (SU-DHL-1) and neuroblastoma cell lines (KELLY, SH-SY5Y) containing the F1174L ALK mutation. These compounds provide novel leads for the development of small-molecule ALK inhibitors for cancer therapy.
doi:10.1021/ml200002a
PMCID: PMC3093683  PMID: 21572589
ALK; 3,5-diamino-1,2,4-triazole urea
22.  Mutations in the DDR2 kinase gene identify a novel therapeutic target in squamous cell lung cancer 
Cancer discovery  2011;1(1):78-89.
While genomically targeted therapies have improved outcomes for patients with lung adenocarcinoma, little is known about the genomic alterations which drive squamous cell lung cancer. Sanger sequencing of the tyrosine kinome identified mutations in the DDR2 kinase gene in 3.8% of squamous cell lung cancers and cell lines. Squamous lung cancer cell lines harboring DDR2 mutations were selectively killed by knock-down of DDR2 by RNAi or by treatment with the multi-targeted kinase inhibitor dasatinib. Tumors established from a DDR2 mutant cell line were sensitive to dasatinib in xenograft models. Expression of mutated DDR2 led to cellular transformation which was blocked by dasatinib. A squamous cell lung cancer patient with a response to dasatinib and erlotinib treatment harbored a DDR2 kinase domain mutation. These data suggest that gain-of-function mutations in DDR2 are important oncogenic events and are amenable to therapy with dasatinib. As dasatinib is already approved for use, these findings could be rapidly translated into clinical trials.
doi:10.1158/2159-8274.CD-11-0005
PMCID: PMC3274752  PMID: 22328973
Squamous cell lung cancer; DDR2; dasatinib; tyrosine kinase inhibitors; lung cancer genomics
23.  Broad Spectrum Alkynyl Inhibitors of T315I Bcr-Abl 
A series of alkyne containing type II inhibitors with potent inhibitory activity of T315I Bcr-Abl has been identified. The most active compound 4 exhibits an EC50 of less than 1 nM against wild-type Bcr-Abl and an EC50 of 10 nM against T315I mutant but is broadly active against a number of other kinases.
doi:10.1016/j.bmcl.2010.05.043
PMCID: PMC2901992  PMID: 20541934
24.  A Structure-guided Approach to Creating Covalent FGFR Inhibitors 
Chemistry & biology  2010;17(3):285-295.
Summary
The fibroblast growth factor receptor tyrosine kinases (FGFR1, 2, 3, and 4) represent promising therapeutic targets in a number of cancers. We have developed the first potent and selective irreversible inhibitor of FGFR1, 2, 3, and 4 which we named FIIN-1 that forms a covalent bond with cysteine 486 located in the P-loop of the FGFR1 ATP-binding site. We demonstrate that the inhibitor potently inhibits Tel-FGFR1 transformed Ba/F3 cells (EC50 = 14 nM) as well as numerous FGFR-dependent cancer cell lines. A biotin-derivatized version of the inhibitor, FIIN-1-biotin, was shown to covalently label FGFR1 at Cys486. FIIN-1 is a useful probe of FGFR-dependent cellular phenomena and may provide a starting point of the development of therapeutically relevant irreversible inhibitors of wild-type and drug-resistant forms of FGFR kinases.
doi:10.1016/j.chembiol.2010.02.007
PMCID: PMC2920453  PMID: 20338520
25.  Targeting wild-type and T315I Bcr-Abl by combining allosteric with ATP-site inhibitors 
Nature  2010;463(7280):501-506.
SUMMARY
In an effort to find new pharmacological modalities to overcome resistance to ATP-site inhibitors of Bcr-Abl, we recently reported the discovery of GNF-2, a selective allosteric Bcr-Abl inhibitor. Here, using solution NMR, X-ray crystallography, mutagenesis and hydrogen exchange mass spectrometry we demonstrate that GNF-2 binds to the myristate binding site of Abl, leading to changes in the structural dynamics of the ATP-binding site. GNF-5, an analog of GNF-2 having improved pharmacokinetic properties, when utilized in combination with the ATP-competitive inhibitors imatinib or nilotinib, suppressed the emergence of resistance mutations in vitro, displayed additive inhibitory activity in biochemical and cellular assays against T315I Bcr-Abl and displayed in vivo efficacy against the recalcitrant T315I Bcr-Abl mutant in a murine bone-marrow transplantation model. These results demonstrate that therapeutically relevant inhibition of Bcr-Abl activity can be achieved using inhibitors that bind to the myristate binding site and that combining allosteric and ATP-competitive inhibitors can overcome resistance to either agent alone.
doi:10.1038/nature08675
PMCID: PMC2901986  PMID: 20072125

Results 1-25 (34)