Top PDF Cell-Selective Chemoproteomics for Biological Discovery

Cell-Selective Chemoproteomics for Biological Discovery

Cell-Selective Chemoproteomics for Biological Discovery

Surprisingly, the endogenous B. fragilis MetRS was able to incorporate Aha to a higher degree than other organisms even without depletion of available methionine. A comparison of charging rates of Aha onto tRNA for both mice and Bacteroides may be useful: If Bacteroides incorporate Aha at a significantly higher rate than the host, feeding Aha to mice may result in semi-specific labeling of the Bacteroides’ proteins without the necessity to create a genetically-altered strain. In addition, the expression of a mutant E. coli MetRS did not show labeling with Anl, suggesting an incompatibility with either the Anl ncAA or between the exogenous synthetase and endogenous tRNA. Sequence analysis of the tRNA recognition sites may explain this incompatibility. Overall, these results highlight the value of having more than one choice of enzyme to perform cell- selective BONCAT. Testing different synthetases (aaRS) and ncAAs whenever it is adapted to a new species will be useful for future studies.
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Chemical Genomics: A Systematic Approach in Biological Research and Drug Discovery

Chemical Genomics: A Systematic Approach in Biological Research and Drug Discovery

or liquid chromatography-based protein separation technologies, including the non-porous reversed-phase high-performance liquid chromatography (RP-HPLC) (Chong et al. 2001) and the two dimensional (2D) liquid- phase separation method (Wall et al. 2000). Since these separation methods are based on the biochemical and biophysical properties of the polypeptides, each protein tends to have a unique profile (or migration pattern) that can be used for its identification. In the cases that separation alone cannot provide sufficient information about the protein, its identity can be further revealed by Mass spectrometry (Gygi and Aebersold 2000). When the protein has a change in modification, its unique profile also changes and can be used as the basis for further investigation based on the nature of the modification. For example, phosphorylation of a protein is easily reversed by phosphatase treatment in vitro. Moreover, phosphorylation-, ubiquitin- and acetylation/methylation- specific antibodies can be used to detect the nature of protein modifications. The above approaches apply to any type of modification. Alternatively, modified proteins can be directly captured and examined for their relative abundance under different conditions. Two recent reports described smart chemistry that allows selective modification of phosphopeptides or phosphoproteins within complex mixtures (Zhu et al. 2000; Oda et al. 2001). Modified peptides or polypeptides are then enriched by covalent or high affinity avidin-biotin coupling to immobilized supports, thereby allowing rapid analysis of phosphorylation events in cells. In a similar vein, modifications with ubiquitin, ubiquitin-like peptides, and methyl and acetyl groups can also be used as epitope tags to capture their modified proteins. In addition, antibodies with specificity toward modified peptides can be arrayed on microchips and used to detect changes in modification of individual proteins (Belov et al. 2001; Huang 2001). In any event, total cellular proteins still need to be compared under different conditions to ensure accurate measurement of a change in protein modification. These new protein- profiling technologies can be easily integrated into chemical ligand-directed research.
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The discovery of I-BRD9, a selective cell active chemical probe for bromodomain containing protein 9 inhibition

The discovery of I-BRD9, a selective cell active chemical probe for bromodomain containing protein 9 inhibition

Although BRD9 has been reported as a component of the chromatin remodeling SWI/SNF BAF complex, 41−43 further information regarding its role within disease is somewhat limited. 44 As such, a chemical probe for the BRD9 bromodomain would be invaluable in better understanding the biological role and therapeutic potential of this reader module. The Structural Genomics Consortium have disclosed bromosporine (15), 45 a broad spectrum bromodomain inhibitor, which shows a thermal shift of +3.9 ° C at BRD9, suggesting bromodomain binding. In addition, structurally similar compound 16 was reported as the fi rst nonselective inhibitor of BRD9. 46,47 This compound shows mixed bromodomain pharmacology, with submicromolar activity against BRD9, BRD4, CECR2, and CREBBP. To the best of our knowledge, there are no BRD9 selective chemical probes described in the literature to date. 48 Herein, we report the discovery of I-BRD9, the fi rst selective cellular chemical probe for BRD9. The development of I-BRD9 was driven by iterative medicinal chemistry, utilizing structure based design to deliver nanomolar potency at BRD9, >700-fold selectivity over the BET family and >70-fold against a panel of 34 bromodomains. I-BRD9 meets and exceeds the chemical probe criteria we de fi ned at the outset of this project, inspired by literature from Bunnage and co- workers, 49 who highlighted the importance of high quality chemical probes for target validation: 100 nM or greater potency against the bromodomain of BRD9 as determined by a biochemical assay; 100-fold selectivity over the BET family of bromodomains; 30-fold selectivity over other bromodomain families; cellular activity; and broader selectivity over a range of receptor sites, ion channels, transporters, and enzymes.
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Biological Motif Discovery Algorithm based on Mining Tree Structure

Biological Motif Discovery Algorithm based on Mining Tree Structure

This evolution of biological data as a point of size or nature has caused an appearance of a new concept on the research area, the concept is bioinformatics, so Bioinformatics is conceptualizing biology in term of molecules (in the sense of physical-chemistry) and then applying informatics techniques to understand and organize the information associated with these molecules on large scale [2]. It also can be seen as all the computer techniques and computational statistics for analyzing biological data [1]. There are a few other definitions on the concept of bioinformatics in many different resources in the litterateurs, so in the big picture, bioinformatics is the task that provide necessary search, score, and analyze biological information by algorithms and specific tools from data sets that are accumulated and curated by experts in order to provide a powerful opportunity to improve human health [3].
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Advancing Biological Understanding and Therapeutics Discovery with Small-Molecule Probes

Advancing Biological Understanding and Therapeutics Discovery with Small-Molecule Probes

While methods such as gene-expression profiling and the new image-based profiling assay contain rich information describing biological responses to small molecules, few approaches are available to use these data to understand structure–activity relationships (SAR). To enable more effective multi-parameter optimization of probes and therapeutic leads, the MLP developed a computational method to generate SAR information automatically from high-dimensional small-molecule profiling data (Wawer et al., 2014a). \Gene expression profiling data and cell-painting data were collected for about 20,000 DOS molecules and just over 2000 bioactive compounds. Association-rule mining was then used to define ‘rules’ of varying strengths that connected chemical attributes (e.g., contiguous substructures within compounds, shared synthetic histories) to biological effect patterns in the gene expression and imaging data. In one application of the methodology, identification of a DOS-based molecule that co-clustered with structurally unrelated microtubule destabilizers provided an opportunity for ‘scaffold hopping’ based on the signatures derived from this high-content information.
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Discovery of functionally selective C5aR2 ligands: novel modulators of C5a signalling.

Discovery of functionally selective C5aR2 ligands: novel modulators of C5a signalling.

transfections of HEK cells were performed 24 h after seeding cells at 1 x 10 6 cells per well in a 100-mm dish. X-tremeGENE 9 transfection reagent (Roche, Basel, Switzerland) was used according to the manufacturer’s instructions. Cells were collected 24 h after transfection with 0.05% trypsin-EDTA in PBS (Life Technologies). To generate HMDMs, human monocytes were isolated from buffy coat blood supplied by unknown donors by the Australian Red Cross Blood Service (Kelvin Grove, Australia) using Ficoll-Plaque Plus (GE Healthcare, Rydalmere, NSW, Australia) and density centrifugation. CD14 + cell selection was performed using MACS magnetic beads (Miltenyi Biotec) 42 . Isolated CD14 + monocytes were differentiated in culture for 7 days with 10 ng ml -1 human M-CSF (Miltenyi Biotec) into HMDMs in the presence of IMDM containing L-glutamine supplemented with 10 % FBS, 50 IU ml -1 penicillin and 50 mg ml -1 streptomycin (Life Technologies) 43 .
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Discovery and development of mycoherbicide for biological control of parthenium hysterophorus: opportunities & future needs

Discovery and development of mycoherbicide for biological control of parthenium hysterophorus: opportunities & future needs

Inadequacies discussed earlier may be amenable to correction either by advances in formulation technology for biological or by advanced molecular techniques (Yoder, 1983; Yoder & Turgeon, 1985). Similarly orphaned mycoherbicides can be considered to represent excellent opportunities for a company specializing in a particular group of organisms or a public agency or grower organization interested in providing a service for a specific grower clientele. They may also offers opportunities for biologically active metabolites with weed control potential. Mycoherbicides present suitable opportunities for return on investment from small market because the cost of developing them may be less than that for a chemical herbicide. Production technology ins already available in fermentation industries, thus capital investment for production is low. Registration costs could be significantly less than for synthetic herbicides. Time required for research and development of a potential agent through registration and commercial use may be substantially less than for herbicides, and this would represent a
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iLIR database : a web resource for LIR motif containing proteins in eukaryotes

iLIR database : a web resource for LIR motif containing proteins in eukaryotes

Finally, we sorted proteins that have not been shown to be linked to autophagy or associated pathways, totaling for the human proteome 756 entries sharing their GO terms with the 21 human and yeast proteins that contain experimentally veri- fied LIR motifs in an intrinsically disordered region (refers hereafter as group ‘D’, Table S4). The most represented GO terms are GO:0005634jnucleus (80.16%) for the Cellular Com- ponent class, GO:0005515jprotein binding (40.87%) for the Molecular Function class and GO:0016032jviral process (4.76%) for the Biological Process class (Fig. 5). This observa- tion suggest that these proteins are promising candidates for further investigation.
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The Meisenheimer complex as a paradigm in drug discovery : reversible covalent inhibition through C67 of the ATP binding site of PLK1

The Meisenheimer complex as a paradigm in drug discovery : reversible covalent inhibition through C67 of the ATP binding site of PLK1

baculovirus (from P2 amplification) was added to give a multiplicity of infection of 3; this is equivalent to three virus particles for each insect cell. The flasks were incubated at 27 °C, with shaking at 100 r.p.m., for 48 h. On harvest, cell density and viability were determined, and the cultures were spun down at 2,500 r.p.m. for 5 min and washed with ice-cold (0 °C) phosphate-buffered saline. The wash was re-spun at the same speed and the pellet was snap frozen. Plk1 protein was purified on a metal affinity column. The insect cell pellet was lysed in a buffer (10 mM Tris-HCl, pH 8.0, 150 mM NaCl, 5 mM β-mercaptoethanol, 1 mM PMSF, 1 mM benzamidine, 20 mM imidazole and protease inhibitor cocktail (Sigma)) and the precleared supernatant was loaded onto Ni-NTA-agarose (Qiagen). The affinity column was washed with the lysis buffer and the bound protein was eluted with 250 mM imidazole in the same buffer. After overnight dialysis against 25 mM Tris-HCl, pH 7.5, 100 mM NaCl, 1 mM DTT, 1 mM PMSF, 1 mM benzamidine, protease inhibitor cocktail (Sigma) and 10% glycerol, the purified protein was stored at −70 °C until used.
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Update on Bioactive Molecules of Actinomycetes

Update on Bioactive Molecules of Actinomycetes

Marine and terrestrial regions are explored from many years and their bioactive compounds are being exploited. As the use of therapeutic novel compounds increases, researchers from all over the world started exploring oceans for bioactive compounds. Actinomycetes, filamentous bacteria have been extensively studied for their therapeutic compounds. They are found to occur in aquatic environments; freshwater and marine habitats. Mostly the marine actinomycetes have attracted a great attention as they have unique metabolic and physiological capabilities. Aquatic habitats enable them to survive in extremes of pressure, salinity and temperature, with the potential production of novel secondary metabolites not observed in actinomycetes, isolated from terrestrial habitats. Secondary metabolites produced from these actinomycetes viz. amino glycosides (streptomycin and kanamycin), ansamycins (rifampicin), anthracyclines (doxorubicin), b- lactam (cephalosporines), macrolides (erythromycin and tetracycline) and many others are considered to be bioactive. The biological diversity of actinomycetes is enormous in nature with diverse chemical compounds. These diverse chemical compounds have been responsible for great biological activities such as antimicrobial, antimalarial, antidiabetic, antitumor, antioxidant, insecticidal, antitubercular etc. Hence there is a scope of developing these bioactive metabolites as a potent therapeutic drug or lead compounds. However, the potential of actinomycetes is correctly studied though the exact wealth of these is unexplored.
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ANALYZING THE USES OF DATA MINING IN BIOLOGICAL AND ENVIRONMENTAL PROBLEMS

ANALYZING THE USES OF DATA MINING IN BIOLOGICAL AND ENVIRONMENTAL PROBLEMS

have been more unlike named first is knowledge mining from database and second is knowledge discovery from data set [3]. Many people treat data mining and concepts as a synonym. It’s for another popularly used term and the others view data mining as simply an essential step in the course of data mining. The knowledge discovery process presents in figure1 as an iterative run of the following steps. In this figure we can see that how data mining works [4].

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Novel Strategy for Electroanalytical Detection of Antipsychotic Drugs Chlorpromazine and Thioridazine; Possibilities for Simultaneous Determination

Novel Strategy for Electroanalytical Detection of Antipsychotic Drugs Chlorpromazine and Thioridazine; Possibilities for Simultaneous Determination

The present study is related to the application of unmodified BDDE for determination of prominent phenothiazine derivates, chlorpromazine and thioridazine in human urine samples. The proposed sensor exhibited the advantage of simple preparation, good reproducibility, and electrochemical surface stability. As BDDE is, up to date, one of the best solid electrode materials, this investigation provides valuable information about the possibility of a selective determination of CPZ and TDZ over interfering compounds from biological samples. Moreover, the possibility of simultaneous determination of CPZ and TDZ in and the non-aqueous solution was examined, giving the advantage to determining in DMSO. The developed procedures at BDDE have the potential for use in fast analyzing of biological fluids and pharmaceutical formulations.
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Towards 5G Cellular: Understanding 3D In Building Single Band and Multi band Small Cells with Control/User plane Coupled and Separation Architectures with a Novel Resource Reuse Approach

Towards 5G Cellular: Understanding 3D In Building Single Band and Multi band Small Cells with Control/User plane Coupled and Separation Architectures with a Novel Resource Reuse Approach

The envisaged high capacity demand of next generation, i.e. fifth generation (5G), mobile networks is expected to be driven mainly by three major techniques, namely small cell network densification, spectrum extension, and spectral efficiency technique [1]. The architecture of small cell base stations (SCBSs), i.e. femtocell base stations (FCBSs), for serving control-plane and user-plane (C-/U-plane) data traffic particularly in indoor environments, plays a significant role on how effectively these three major enabling techniques as aforementioned can be applied to achieve the required capacity demand of 5G networks. In existing heterogeneous networks (HetNets), a common feature is tightly coupled control-plane (C-plane) and user-plane (U-plane) irrespective of the degree of density and heterogeneity, which is one of the major reasons for most problems that the network densification is facing, e.g. low energy efficiency, complex interference management, higher signaling overhead and backhaul network requirement, and clumsy mobility management. As the mobile data traffic demand increases, existing networks have been facing problems from providing the necessary capacity that causes to initiate network architectural design innovations.
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1,6-Cyclophellitol Cyclosulfates : A New Class of Irreversible Glycosidase Inhibitor

1,6-Cyclophellitol Cyclosulfates : A New Class of Irreversible Glycosidase Inhibitor

ABSTRACT: The essential biological roles played by glycosidases, coupled to the diverse therapeutic bene fi ts of pharmacologically targeting these enzymes, provide consid- erable motivation for the development of new inhibitor classes. Cyclophellitol epoxides and aziridines are recently established covalent glycosidase inactivators. Inspired by the application of cyclic sulfates as electrophilic equivalents of epoxides in organic synthesis, we sought to test whether cyclophellitol cyclosulfates would similarly act as irreversible glycosidase inhibitors. Here we present the synthesis, conformational analysis, and application of novel 1,6-cyclophellitol cyclo-
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Stem cell biology and drug discovery

Stem cell biology and drug discovery

These studies, and the profusion of those likely to follow in the near future, demonstrate fibroblasts need not be dedifferentiated completely to become other cell types. The potential advantage of this more direct approach, at least from a drug discovery perspective, is that more of the epigenetic modifications of patient­ derived cells might be preserved if it were possible to bypass complete reprogramming. Also, there is some hope that this method may make it easier to produce more mature cells than one that relies on reversion of cells to a more embryonic cell­like state. Both of these differences could help in producing cells that more accurately model components of different diseases, although it is too early to judge how well the method will work. Can the fibroblasts be expanded sufficiently before viral transduction to allow for the generation of a sufficient number of differentiated cells? Can fibroblasts be obtained from older patients and still be trans differentiated?
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Love laughs at Locksmiths: Ubiquitylation of p62 unlocks its autophagy receptor potential.

Love laughs at Locksmiths: Ubiquitylation of p62 unlocks its autophagy receptor potential.

The discovery made a decade ago that the signaling adapter p62/sequestosome-1 (p62) plays a role in selective degradation of ubiquitylated targets paved the way for today’s understanding of how the autophagy pathway handles bulky cargos, such as protein aggregates, damaged mitochondria, and intracellular bacteria 1 . As the prototypic receptor for

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Biological effects of selective COX-2 inhibitor NS398 on human glioblastoma cell lines

Biological effects of selective COX-2 inhibitor NS398 on human glioblastoma cell lines

of cell growth and viability, autophagy, cell migration. Of interest, Kuipers et al. (2007) showed evidence that both the cell growth and radiation-resistance either of COX-2 positive (U87) or negative (D384, U251) GBM cell lines were effectively inhibited by COX-2 inhibitors, includ- ing NS398 at 200  μM. These results led the authors to conclude that the effects of non-steroidal anti-inflamma- tory drugs (NSAIDs) could be independent on enzyme expression and probably caused by interaction with other targets than COX-2 [34]. In 2013, Gurpinar et al. published a detailed description of the major COX inde- pendent mechanisms of NSAIDs and COX-2 inhibitors, including inhibition of cyclic guanosine monophosphate phosphodiesterases (cGMP PDEs), Wingless-related integration site (Wnt) signaling, peroxisome proliferator- activated receptor δ (PPARδ) activity, phosphatidylin- ositol-3-kinase (PI3K)/3-phosphoinositide-dependent kinase-1 (PDK-1)/Protein Kinase B (Akt) pathway [79]. In line with these findings, our results show that U87MG and T98G are similarly sensitive to NS398 treatment, irrespective of the relevant difference in COX-2 expres- sion and activity. So, further experiments with negative GBM COX-2 lines will be necessary to check whether the mechanism behind the observed effects of NS398 could be COX-2 independent. It should be of interest to also evaluate the influence of NS398 on healthy human brain astrocytes. In addition, given the functional implications of COX-1 in cancer the possible involvement of COX-1 should be evaluated in our experimental conditions [80].
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Protein network analysis reveals selectively vulnerable regions and biological processes in FTD

Protein network analysis reveals selectively vulnerable regions and biological processes in FTD

Although defined by a clear clinical syndrome, behavioral variant frontotemporal dementia (bvFTD) is the most path- ologically diverse form of frontotemporal lobar degeneration (FTLD). Despite variable pathology, we and others have shown that a shared, selectively vulnerable brain network, composed of disparate brain regions functionally connected throughout the lifespan, degenerates in bvFTD. 1 The fact that different protein pathologies converge on a relatively consis- tent set of neuroanatomical regions suggests intrinsic mo- lecular properties may predispose this network to disease. Nevertheless, despite extensive advances in our ability to clinically and pathologically diagnose bvFTD, little is known about the protein networks (“nexopathies”) that drive the bi- ological processes (BPs) underlying this selective vulnerability. 2,3 New techniques enable evaluation of experimentally determined protein networks in disease by aggregating single-nucleotide polymorphism (SNP)-level risk metrics across an entire gene. This technique increases statistical power, overcomes locus heterogeneity likely to occur in clinical populations, and allows for better detection of multiple variants contributing to polygenic disease risk. 4 Combining this information with existing protein interaction data has revealed new genetic risk loci and helped unravel the pathophysiology of complex diseases like multiple sclerosis. 5
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Targeted mass spectrometry to quantify brain-derived cerebrospinal fluid biomarkers in Alzheimer’s disease

Targeted mass spectrometry to quantify brain-derived cerebrospinal fluid biomarkers in Alzheimer’s disease

A second goal of this study was to assess whether the targeted AD candidate biomarkers were consistent in their direction of change in AD CSF when measured in a non-depleted sample. To this end, we observed strong concordance between the direction of change between the proteins in the discovery and replication cohorts despite differences in sample preparation and mass spectrometry platforms. Indeed, some of the most dif- ferentially increased proteins in the discovery CSF data- set (SMOC1, MAPT, YWHAG, and  PKM), were highly correlated across the discovery and validation datasets. It should be noted that GSN, C8B, and GC were decreased in AD within the discovery cohort, yet increased in AD in the replication cohort. This difference could be due to the distinct sample preparation procedures between the discovery and validation cohort. For example, the protein depletion procedure used in the discovery cohort can influence levels of specific proteins that interact with the highly abundant proteins depleted in the samples [44]. All of the 25 significantly higher proteins in AD com- pared to controls were also specific to AD when com- pared to patients with non-AD cognitive impairment. This included several synaptic proteins in CSF, which may reflect AD-specific changes linked to dendritic spine
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Discovery of orbital selective Cooper pairing in FeSe

Discovery of orbital selective Cooper pairing in FeSe

One technique for measuring ± pairing symmetry is to detect the enhancement in amplitude of 𝑔𝑞 , 𝐸 at specific BQPI wavevectors when a magnetic field is applied; this was proposed to occ[r]

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