Página 1 dos resultados de 5996 itens digitais encontrados em 0.019 segundos

‣ Chemical Biology is.....

Ostler, Elizabeth L
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Publicado em 19/02/2007 Português
Relevância na Pesquisa
46.98165%
Chemical Biology is a relatively new field, and as such is not yet simply or succinctly defined. It includes such a wide range of fundamental problems that this commentary could only include just a few snapshots of potential areas of interest. Overarching themes and selected recent successes and ideas in chemical biology are described to illustrate broadly the scope of the field, but should not be taken as exhaustive. The Chemical Biology Section of Chemistry Central Journal is pleased to receive manuscripts describing research into all and any aspects of the subject.

‣ Chemical Biology Investigation of Cell Death Pathways Activated by Endoplasmic Reticulum Stress Reveals Cytoprotective Modulators of ASK1*S⃞

Kim, InKi; Shu, Chih-Wen; Xu, Wenjie; Shiau, Chung-Wai; Grant, Daniel; Vasile, Stefan; Cosford, Nicholas D. P.; Reed, John C.
Fonte: American Society for Biochemistry and Molecular Biology Publicador: American Society for Biochemistry and Molecular Biology
Tipo: Artigo de Revista Científica
Publicado em 16/01/2009 Português
Relevância na Pesquisa
56.725024%
The accumulation of unfolded proteins in the endoplasmic reticulum (ER) is caused by many disease-relevant conditions, inducing conserved signaling events collectively known as the unfolded protein response. When ER stress is excessive or prolonged, cell death (usually occurring by apoptosis) is triggered. We undertook a chemical biology approach for investigating mechanisms of ER stress-induced cell death. Using a cell-based high throughput screening assay to identify compounds that rescued a neuronal cell line from thapsigargin-induced cell death, we identified benzodiazepinones that selectively inhibit cell death caused by inducers of ER stress (thapsigargin and tunicamycin) but not by inducers of extrinsic (tumor necrosis factor) or intrinsic (mitochondrial) cell death pathways. The compounds displayed activity in several cell lines and primary cultured neurons. Mechanism of action studies revealed that these compounds inhibit ER stress-induced activation of p38 MAPK and kinases responsible for c-Jun phosphorylation. Active benzodiazepinones suppressed cell death at the level of apoptotic signal kinase-1 (ASK1) within the IRE1 pathway but without directly inhibiting the kinase activity of ASK1 or >400 other kinases tested. Rather...

‣ Bright Ideas for Chemical Biology

Lavis, Luke D.; Raines, Ronald T.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 20/03/2008 Português
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46.9589%
Small-molecule fluorescent probes embody an essential facet of chemical biology. Although numerous compounds are known, the ensemble of fluorescent probes is based on a modest collection of modular “core” dyes. The elaboration of these dyes with diverse chemical moieties is enabling the precise interrogation of biochemical and biological systems. The importance of fluorescence-based technologies in chemical biology elicits a necessity to understand the major classes of small-molecule fluorophores. Here, we examine the chemical and photophysical properties of oft-used fluorophores, and highlight classic and contemporary examples in which utility has been built upon these scaffolds.

‣ ChemProt: a disease chemical biology database

Taboureau, Olivier; Nielsen, Sonny Kim; Audouze, Karine; Weinhold, Nils; Edsgärd, Daniel; Roque, Francisco S.; Kouskoumvekaki, Irene; Bora, Alina; Curpan, Ramona; Jensen, Thomas Skøt; Brunak, Søren; Oprea, Tudor I.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
47.112188%
Systems pharmacology is an emergent area that studies drug action across multiple scales of complexity, from molecular and cellular to tissue and organism levels. There is a critical need to develop network-based approaches to integrate the growing body of chemical biology knowledge with network biology. Here, we report ChemProt, a disease chemical biology database, which is based on a compilation of multiple chemical–protein annotation resources, as well as disease-associated protein–protein interactions (PPIs). We assembled more than 700 000 unique chemicals with biological annotation for 30 578 proteins. We gathered over 2-million chemical–protein interactions, which were integrated in a quality scored human PPI network of 428 429 interactions. The PPI network layer allows for studying disease and tissue specificity through each protein complex. ChemProt can assist in the in silico evaluation of environmental chemicals, natural products and approved drugs, as well as the selection of new compounds based on their activity profile against most known biological targets, including those related to adverse drug events. Results from the disease chemical biology database associate citalopram, an antidepressant, with osteogenesis imperfect and leukemia and bisphenol A...

‣ The Chemical Biology of Protein Phosphorylation

Tarrant, Mary Katherine; Cole, Philip A.
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em //2009 Português
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46.99355%
The explosion of scientific interest in protein kinase-mediated signaling networks has led to the infusion of new chemical methods and their applications related to the analysis of phosphorylation pathways. We highlight some of these chemical biology approaches across three areas. First, we discuss the development of chemical tools to modulate the activity of protein kinases to explore kinase mechanisms and their contributions to phosphorylation events and cellular processes. Second, we describe chemical techniques developed in the past few years to dissect the structural and functional effects of phosphate modifications at specific sites in proteins. Third, we cover newly developed molecular imaging approaches to elucidate the spatiotemporal aspects of phosphorylation cascades in live cells. Exciting advances in our understanding of protein phosphorylation have been obtained with these chemical biology approaches, but continuing opportunities for technological innovation remain.

‣ Computational Systems Chemical Biology

Oprea, Tudor I.; May, Elebeoba E.; Leitão, Andrei; Tropsha, Alexander
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em //2011 Português
Relevância na Pesquisa
46.993345%
There is a critical need for improving the level of chemistry awareness in systems biology. The data and information related to modulation of genes and proteins by small molecules continue to accumulate at the same time as simulation tools in systems biology and whole body physiologically-based pharmacokinetics (PBPK) continue to evolve. We called this emerging area at the interface between chemical biology and systems biology systems chemical biology, SCB (Oprea et al., 2007).

‣ Chemical Biology Approaches for the study of Apicomplexan Parasites

Child, Matthew Andrew
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Português
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46.91093%
Chemical biology and the techniques the field encompasses provide scientists with the means to address biological questions in ever evolving and technically sophisticated ways. They facilitate the dissection of molecular mechanisms of cell phenomena on timescales not achievable by other means. Libraries of small molecules, bioorthogonal chemistries and technical advances in mass-spectrometry techniques enable the modern chemical biologist to tackle even the most difficult of biological questions. It is because of their broad applicability that these approaches are well suited to systems less tractable to more classical genetic methods. As such, the parasite community has embraced them with great success. Some of these successes and the continuing evolution of chemical biology applied to apicomplexans will be discussed.

‣ Chromatin as an expansive canvas for chemical biology

Fierz, Beat; Muir, Tom W
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 17/04/2012 Português
Relevância na Pesquisa
47.07754%
Chromatin is extensively chemically modified and thereby acts as a dynamic signaling platform controlling gene function. Chromatin regulation is integral to cell differentiation, lineage commitment and organism development, whereas chromatin dysregulation can lead to age-related and neurodegenerative disorders as well as cancer. Investigating chromatin biology presents a unique challenge, as the issue spans many disciplines, including cell and systems biology, biochemistry and molecular biophysics. In recent years, the application of chemical biology methods for investigating chromatin processes has gained considerable traction. Indeed, chemical biologists now have at their disposal powerful chemical tools that allow chromatin biology to be scrutinized at the level of the cell all the way down to the single chromatin fiber. Here we present recent examples of how this rapidly expanding palette of chemical tools is being used to paint a detailed picture of chromatin function in organism development and disease.

‣ Identification of Drug Targets Related to the Induction of Ventricular Tachyarrhythmia Through a Systems Chemical Biology Approach

Ivanov, Sergey M.; Lagunin, Alexey A.; Pogodin, Pavel V.; Filimonov, Dmitry A.; Poroikov, Vladimir V.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica Formato: text/html
Português
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66.840107%
Ventricular tachyarrhythmia (VT) is one of the most serious adverse drug reactions leading to death. The in vitro assessment of the interaction of lead compounds with HERG potassium channels, which is one of the primary known causes of VT induction, is an obligatory test during drug development. However, experimental and clinical data support the hypothesis that the inhibition of ion channels is not the only mechanism of VT induction. Therefore, the identification of other drug targets contributing to the induction of VT is crucial. We developed a systems chemical biology approach for searching for such targets. This approach involves the following steps: (1) creation of special sets of VT-causing and non-VT-causing drugs, (2) statistical analysis of in silico predicted drug-target interaction profiles of studied drugs with 1738 human protein targets for the identification of potential VT-related targets, (3) gene ontology and pathway enrichment analysis of the revealed targets for the identification of biological processes underlying drug-induced VT etiology, (4) creation of a cardiomyocyte regulatory network (CRN) based on general and heart-specific signaling and regulatory pathways, and (5) simulation of changes in the behavior of the CRN caused by the inhibition of each node for the identification of potential VT-related targets. As a result...

‣ Structural Biology with Carbon Nanotube AFM Probes

Hafner, Jason H.; Woolley, Adam T.; Cheung, Chin Li; Lieber, Charles
Fonte: Current Biology Ltd. Publicador: Current Biology Ltd.
Português
Relevância na Pesquisa
56.91083%
Carbon nanotubes represent ideal probes for high-resolution structural and chemical imaging of biomolecules with atomic force microscopy. Recent advances in fabrication of carbon nanotube probes with sub-nanometer radii promise to yield unique insights into the structure, dynamics and function of biological macromolecules and complexes.; Chemistry and Chemical Biology

‣ Separation of Electromagnetic and Chemical Contributions to Surface-Enhanced Raman Spectra on Nanoengineered Plasmonic Substrates

Saikin, Semion K.; Chu, Yizhuo; Rappoport, Dmitrij; Crozier, Kenneth B.; Aspuru-Guzik, Alán
Fonte: American Chemical Society Publicador: American Chemical Society
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
56.685405%
Raman signals from molecules adsorbed on a noble metal surface are enhanced by many orders of magnitude due to the plasmon resonances of the substrate. Additionally, the enhanced spectra are modified compared to the spectra of neat molecules; many vibrational frequencies are shifted, and relative intensities undergo significant changes upon attachment to the metal. With the goal of devising an effective scheme for separating the electromagnetic and chemical effects, we explore the origin of the Raman spectra modification of benzenethiol adsorbed on nanostructured gold surfaces. The spectral modifications are attributed to the frequency dependence of the electromagnetic enhancement and to the effect of chemical binding. The latter contribution can be reproduced computationally using molecule−metal cluster models. We present evidence that the effect of chemical binding is mostly due to changes in the electronic structure of the molecule rather than to the fixed orientation of molecules relative to the substrate.; Chemistry and Chemical Biology; Engineering and Applied Sciences

‣ Chemistry and the Worm: Caenorhabditis elegans as a Platform for Integrating Chemical and Biological Research

Hulme, S. Elizabeth; Whitesides, George McClelland
Fonte: Wiley-Blackwell Publicador: Wiley-Blackwell
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
57.02956%
This Review discusses the potential usefulness of the worm Caenorhabditis elegans as a model organism for chemists interested in studying living systems. C. elegans, a 1 mm long roundworm, is a popular model organism in almost all areas of modern biology. The worm has several features that make it attractive for biology: it is small (<1000 cells), transparent, and genetically tractable. Despite its simplicity, the worm exhibits complex phenotypes associated with multicellularity: the worm has differentiated cells and organs, it ages and has a well-defined lifespan, and it is capable of learning and remembering. This Review argues that the balance between simplicity and complexity in the worm will make it a useful tool in determining the relationship between molecular-scale phenomena and organism-level phenomena, such as aging, behavior, cognition, and disease. Following an introduction to worm biology, the Review provides examples of current research with C. elegans that is chemically relevant. It also describes tools—biological, chemical, and physical—that are available to researchers studying the worm.; Chemistry and Chemical Biology

‣ Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data

Ding, Ying; Wild, David J; Zhu, Qian; Wang, Huijun; Jiao, Dazhi; Dong, Xiao; Chen, Bin
Fonte: BMC Bioinformatics Publicador: BMC Bioinformatics
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
47.02963%
Background: Recently there has been an explosion of new data sources about genes, proteins, genetic variations, chemical compounds, diseases and drugs. Integration of these data sources and the identification of patterns that go across them is of critical interest. Initiatives such as Bio2RDF and LODD have tackled the problem of linking biological data and drug data respectively using RDF. Thus far, the inclusion of chemogenomic and systems chemical biology information that crosses the domains of chemistry and biology has been very limited. Results: We have created a single repository called Chem2Bio2RDF by aggregating data from multiple chemogenomics repositories that is cross-linked into Bio2RDF and LODD. We have also created a linked-path generation tool to facilitate SPARQL query generation, and have created extended SPARQL functions to address specific chemical/biological search needs. We demonstrate the utility of Chem2Bio2RDF in investigating polypharmacology, identification of potential multiple pathway inhibitors, and the association of pathways with adverse drug reactions. Conclusions: We have created a new semantic systems chemical biology resource, and have demonstrated its potential usefulness in specific examples of polypharmacology...

‣ Chem2Bio2RDF: a semantic framework for linking and data mining chemogenomic and systems chemical biology data

Ding, Ying; Zhu, Qian; Wang, Huijun; Jiao, Dazhi; Dong, Xiao; Chen, Bin; Wild, David J.
Fonte: BioMed Central Publicador: BioMed Central
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
47.02963%
Background: Recently there has been an explosion of new data sources about genes, proteins, genetic variations, chemical compounds, diseases and drugs. Integration of these data sources and the identification of patterns that go across them is of critical interest. Initiatives such as Bio2RDF and LODD have tackled the problem of linking biological data and drug data respectively using RDF. Thus far, the inclusion of chemogenomic and systems chemical biology information that crosses the domains of chemistry and biology has been very limited Results: We have created a single repository called Chem2Bio2RDF by aggregating data from multiple chemogenomics repositories that is cross-linked into Bio2RDF and LODD. We have also created a linked-path generation tool to facilitate SPARQL query generation, and have created extended SPARQL functions to address specific chemical/biological search needs. We demonstrate the utility of Chem2Bio2RDF in investigating polypharmacology, identification of potential multiple pathway inhibitors, and the association of pathways with adverse drug reactions. Conclusions: We have created a new semantic systems chemical biology resource, and have demonstrated its potential usefulness in specific examples of polypharmacology...

‣ Improving integrative searching of systems chemical biology data using semantic annotation

Wild, David J.; Ding, Ying; Chen, Bin
Fonte: Chemistry Central Ltd. Publicador: Chemistry Central Ltd.
Tipo: Artigo de Revista Científica
Português
Relevância na Pesquisa
47.07754%
Background: Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. Results: We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i) simplifies the process of building SPARQL queries, (ii) enables useful new kinds of queries on the data and (iii) makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. Availability: Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http:// chem2bio2owl.wikispaces.com.

‣ Free Radicals in Chemical Biology: from Chemical Behavior to Biomarker Development

Chatgilialoglu, Chryssostomos; Ferreri, Carla; Masi, Annalisa; Melchiorre, Michele; Sansone, Anna; Terzidis, Michael A.; Torreggiani, Armida
Fonte: MyJove Corporation Publicador: MyJove Corporation
Tipo: Artigo de Revista Científica
Publicado em 15/04/2013 Português
Relevância na Pesquisa
46.9589%
The involvement of free radicals in life sciences has constantly increased with time and has been connected to several physiological and pathological processes. This subject embraces diverse scientific areas, spanning from physical, biological and bioorganic chemistry to biology and medicine, with applications to the amelioration of quality of life, health and aging. Multidisciplinary skills are required for the full investigation of the many facets of radical processes in the biological environment and chemical knowledge plays a crucial role in unveiling basic processes and mechanisms. We developed a chemical biology approach able to connect free radical chemical reactivity with biological processes, providing information on the mechanistic pathways and products. The core of this approach is the design of biomimetic models to study biomolecule behavior (lipids, nucleic acids and proteins) in aqueous systems, obtaining insights of the reaction pathways as well as building up molecular libraries of the free radical reaction products. This context can be successfully used for biomarker discovery and examples are provided with two classes of compounds: mono-trans isomers of cholesteryl esters, which are synthesized and used as references for detection in human plasma...

‣ Chem2Bio2RDF: A Linked Open Data Portal for Chemical Biology

Chen, Bin; Wild, David J; Zhu, Qian; Ding, Ying; Dong, Xiao; Sankaranarayanan, Madhuvanthi; Wang, Huijun; Sun, Yuyin
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 21/12/2010 Português
Relevância na Pesquisa
56.795747%
The Chem2Bio2RDF portal is a Linked Open Data (LOD) portal for systems chemical biology aiming for facilitating drug discovery. It converts around 25 different datasets on genes, compounds, drugs, pathways, side effects, diseases, and MEDLINE/PubMed documents into RDF triples and links them to other LOD bubbles, such as Bio2RDF, LODD and DBPedia. The portal is based on D2R server and provides a SPARQL endpoint, but adds on few unique features like RDF faceted browser, user-friendly SPARQL query generator, MEDLINE/PubMed cross validation service, and Cytoscape visualization plugin. Three use cases demonstrate the functionality and usability of this portal.; Comment: 8 pages, 10 figures

‣ Synthetic Biology in Leishmaniasis: Design,simulation and validation of constructed Genetic circuit

Limbachiya, Dixita
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Publicado em 01/04/2013 Português
Relevância na Pesquisa
47.01951%
Building circuits and studying their behavior in cells is a major goal of systems and synthetic biology. Synthetic biology enables the precise control of cellular states for systems studies, the discovery of novel parts, control strategies, and interactions for the design of robust synthetic systems. To the best of our knowledge,there are no literature reports for the synthetic circuit construction for protozoan parasites. This paper describes the construction of genetic circuit for the targeted enzyme inositol phosphorylceramide synthase belonging to the protozoan parasite Leishmania. To explore the dynamic nature of the circuit designed, simulation was done followed by circuit validation by qualitative and quantitative approaches. The genetic circuit designed for inositol phosphorylceramide synthase shows responsiveness, oscillatory and bistable behavior, together with intrinsic robustness.; Comment: This is Master of Science thesis from Sardar Patel university. Part of the thesis has been published as the following paper: "Mandlik, Vineetha, Dixita Limbachiya, Sonali Shinde, Milsee Mol, and Shailza Singh. "Synthetic circuit of inositol phosphorylceramide synthase in Leishmania: a chemical biology approach." Journal of Chemical Biology (2012): 1-12" in the Journal of Chemical Biology

‣ ACBD: Database for Ascidian Chemical Genomics

Yuichiro Hira; Jun Terai; Masaya Imoto; Etsu Tashiro; Kohji Hotta
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
Relevância na Pesquisa
47.110977%
Chemical biology approach enables us to understand the complex biological systems, using small molecules such as a specific activator or inhibitor of protein, a hormone-like inducer, or a neurotransmitter. When such approach is performed genome-widely, that research is especially called "chemical genomics". We are planning to make a new start of chemical genomics using one of chordate model animal, ascidian. As a first step, we constructed a database called ACBD (Ascidians Chemical Biology Database). First, we reviewed and annotated past articles which describe the uses of small chemicals in the field of ascidians biology. In ACBD, chemical information and effects on ascidian are manually extracted from more than 900 articles in PubMed database from 1964 to 2010. ACBD is free and open to the public on the web. ACBD has two main parts. One part consists of information about already-used chemicals to ascidians. This part is based on the record of already-published articles. In this part, we realized that more than 351 kinds of chemicals were applied for ascidian and that more than 399 kinds of chemicals were isolated from 120 kinds of tunicates! The other part consists of “not-yet-used chemicals” information. Although the total number of Ciona protein model (KH model...

‣ ACBD: Database for Ascidian Chemical Genomics

Yuichiro Hira; Jun Terai; Mitsuru Nakamura; Etsu Tashiro; Masaya Imoto; Kotaro Oka; Kohji Hotta
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
Relevância na Pesquisa
47.110977%
Chemical biology approach enables us to understand the complex biological systems,using small molecules such as a specific activator or inhibitor of protein, a hormone-likeinducer, or a neurotransmitter etc. When such approach is performed genome-widely, that research is especially called "chemical genomics". We are planning to make a new start of chemical genomics using one of chordate model animal, ascidian. As a first step, we constructed a database called ACBD (Ascidians Chemical Biology Database). First, we reviewed and annotated past articles which describe the uses of small chemicals in the field of ascidians biology. In ACBD, chemical information and effects on ascidian are manually extracted from more than 900 articles in PubMed database since 1964. ACBD is free and open to the public on the web. ACBD consists of two main parts. One part consists of information about already-used chemicals to ascidians. This part is based on the record of already-published articles. In this part, we realized that more than 351 kinds of chemicals were applied for ascidian and that more than 399 kinds of chemicals were isolated from 120 kinds of tunicates. The other part consists of "not-yet-used chemicals" information. Although the total number of Ciona protein model (KH model...