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1.  Discovery of Type II Inhibitors of TGFβ-Activated Kinase 1 (TAK1) and Mitogen-Activated Protein Kinase Kinase Kinase Kinase 2 (MAP4K2) 
Journal of Medicinal Chemistry  2014;58(1):183-196.
We developed a pharmacophore model for type II inhibitors that was used to guide the construction of a library of kinase inhibitors. Kinome-wide selectivity profiling of the library resulted in the identification of a series of 4-substituted 1H-pyrrolo[2,3-b]pyridines that exhibited potent inhibitory activity against two mitogen-activated protein kinases (MAPKs), TAK1 (MAP3K7) and MAP4K2, as well as pharmacologically well interrogated kinases such as p38α (MAPK14) and ABL. Further investigation of the structure–activity relationship (SAR) resulted in the identification of potent dual TAK1 and MAP4K2 inhibitors such as 1 (NG25) and 2 as well as MAP4K2 selective inhibitors such as 16 and 17. Some of these inhibitors possess good pharmacokinetic properties that will enable their use in pharmacological studies in vivo. A 2.4 Å cocrystal structure of TAK1 in complex with 1 confirms that the activation loop of TAK1 assumes the DFG-out conformation characteristic of type II inhibitors.
doi:10.1021/jm500480k
PMCID: PMC4292808  PMID: 25075558
2.  Fluorescent Visualization of Src Using Dasatinib-BODIPY 
Many biological experiments are not compatible with the use of immunofluorescence or genetically-encoded fluorescent tags or FRET-based reporters. Conjugation of existing kinase inhibitors to cell-permeable fluorophores can provide a generalized approach to develop fluorescent probes of intracellular kinases. Here, we report the development of a small molecule probe of Src through conjugation of BODIPY to two well-established, dual Src-Abl kinase inhibitors, dasatinib and saracatinib. We show that this approach is not successful for saracatinib, but that largely dasatinib-BODIPY retains the biological activity of its parent compound and can be used to monitor the presence of Src kinase in individual cells by flow cytometry and to track the localization of Src by fixed and live-cell fluorescence microscopy. This strategy may enable generation of additional kinase-specific probes useful in systems not amenable to genetic manipulation or used together with fluorescent proteins to enable a multiplexed assay read-out.
doi:10.1002/cbic.201402010
PMCID: PMC4130483  PMID: 24828915
fluorescent probes; proteins; signal transduction; cell recognition; kinase inhibitor
3.  Identification of Mitral Annulus Hinge Point Based on Local Context Feature and Additive SVM Classifier 
The position of the hinge point of mitral annulus (MA) is important for segmentation, modeling and multimodalities registration of cardiac structures. The main difficulties in identifying the hinge point of MA are the inherent noisy, low resolution of echocardiography, and so on. This work aims to automatically detect the hinge point of MA by combining local context feature with additive support vector machines (SVM) classifier. The innovations are as follows: (1) designing a local context feature for MA in cardiac ultrasound image; (2) applying the additive kernel SVM classifier to identify the candidates of the hinge point of MA; (3) designing a weighted density field of candidates which represents the blocks of candidates; and (4) estimating an adaptive threshold on the weighted density field to get the position of the hinge point of MA and exclude the error from SVM classifier. The proposed algorithm is tested on echocardiographic four-chamber image sequence of 10 pediatric patients. Compared with the manual selected hinge points of MA which are selected by professional doctors, the mean error is in 0.96 ± 1.04 mm. Additive SVM classifier can fast and accurately identify the MA hinge point.
doi:10.1155/2015/419826
PMCID: PMC4450883  PMID: 26089964
4.  USA’s expanded overseas tuberculosis screening program: a retrospective study in China 
BMC Public Health  2015;15:231.
Background
To address increasing tuberculosis (TB) incidence in foreign-born populations, immigrant TB screening programs have been implemented in the USA. These programs are modified periodically, the effectiveness of which have been disputed. The aim of this retrospective study was to assess the value of the 2009 Technical Instructions for Tuberculosis Screening and Treatment Using Cultures and Directly Observed Therapy (CDOT TB TI) in a cohort of the USA permanent-resident applicants from China.
Methods
Standardized forms were used to collect demographic, clinical, and laboratory data of Chinese individuals screened at the Guangdong International Travel Healthcare Center for permanent residence in the USA between October 08, 2009 and December 31, 2012. Applicants’ data were further retrospectively evaluated by three experienced panel physicians and radiologists according to the 1991 Technical Instructions for Tuberculosis Screening and Treatment (TI). TB cases and characteristics identified by the 1991 and expanded 2009 programs were compared.
Results
The CDOT TB TI identified more than twice as many TB cases that required treatment completion before clearance for travel than the 1991 TI (270 vs. 131). In addition, the expanded screening program identified more cases of negative sputum smear but positive culture (181 vs. 44), and more cases of radiography suggestive of inactive (22 vs. 3) and active (248 vs. 128) TB. Specifically, the 1991 TI screening program failed to identify 25/38 (65.79%) cases carrying drug-resistant isolates, and 13/131 (9.92%) would have been inappropriately treated. Moreover, 220/270 (81.48%) of the cases were asymptomatic, which were identified by screening and subsequently treated. Improved chest radiograph and sputum negative conversion occurred in all treated cases.
Conclusion
CDOT TB TI, a screening program that includes sputum culture and drug susceptibility tests, identifies a greater number of TB cases, likely contributing to the overall decrease in TB prevalence in host (USA) and origin (China) countries.
doi:10.1186/s12889-015-1558-z
PMCID: PMC4364631  PMID: 25886508
Benefit; Immigrant; Overseas; Screening; Tuberculosis; USA; China
5.  Systematic Identification of Culture Conditions for Induction and Maintenance of Naive Human Pluripotency 
Cell Stem Cell  2014;15(4):471-487.
Summary
Embryonic stem cells (ESCs) of mice and humans have distinct molecular and biological characteristics, raising the question of whether an earlier, “naive” state of pluripotency may exist in humans. Here we took a systematic approach to identify small molecules that support self-renewal of naive human ESCs based on maintenance of endogenous OCT4 distal enhancer activity, a molecular signature of ground state pluripotency. Iterative chemical screening identified a combination of five kinase inhibitors that induces and maintains OCT4 distal enhancer activity when applied directly to conventional human ESCs. These inhibitors generate human pluripotent cells in which transcription factors associated with the ground state of pluripotency are highly upregulated and bivalent chromatin domains are depleted. Comparison with previously reported naive human ESCs indicates that our conditions capture a distinct pluripotent state in humans that closely resembles that of mouse ESCs. This study presents a framework for defining the culture requirements of naive human pluripotent cells.
Graphical Abstract
Highlights
•TALEN-mediated engineering of a reporter system for naive human pluripotency•Chemical screen for maintenance of naive reporter activity in absence of transgenes•Optimized chemical conditions capture a distinct state of human pluripotency•Gene expression of naive human cells is highly similar to that of naive mouse cells
Through sequential chemical screening, Theunissen et al. identify a combination of kinase inhibitors that induces and maintains defining features of naive pluripotency in human embryonic stem cells.
doi:10.1016/j.stem.2014.07.002
PMCID: PMC4184977  PMID: 25090446
6.  A-770041 reverses paclitaxel and doxorubicin resistance in osteosarcoma cells 
BMC Cancer  2014;14:681.
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
7.  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
8.  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
9.  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
10.  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
11.  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
12.  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
14.  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
15.  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
16.  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
17.  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
18.  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
19.  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
20.  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)
21.  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
22.  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
23.  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
24.  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
25.  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

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