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Find video protocols related to scientific articles indexed in Pubmed.
Transporter assays and assay ontologies: useful tools for drug discovery.
Drug Discov Today Technol
PUBLISHED: 07-17-2014
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Transport proteins represent an eminent class of drug targets and ADMET (absorption, distribution, metabolism, excretion, toxicity) associated genes. There exists a large number of distinct activity assays for transport proteins, depending on not only the measurement needed (e.g. transport activity, strength of ligand–protein interaction), but also due to heterogeneous assay setups used by different research groups. Efforts to systematically organize this (divergent) bioassay data have large potential impact in Public-Private partnership and conventional commercial drug discovery. In this short review, we highlight some of the frequently used high-throughput assays for transport proteins, and we discuss emerging assay ontologies and their application to this field. Focusing on human P-glycoprotein (Multidrug resistance protein 1; gene name: ABCB1, MDR1), we exemplify how annotation of bioassay data per target class could improve and add to existing ontologies, and we propose to include an additional layer of metadata supporting data fusion across different bioassays.
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Exploiting open data: a new era in pharmacoinformatics.
Future Med Chem
PUBLISHED: 03-22-2014
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Within the last decade open data concepts has been gaining increasing interest in the area of drug discovery. With the launch of ChEMBL and PubChem, an enormous amount of bioactivity data was made easily accessible to the public domain. In addition, platforms that semantically integrate those data, such as the Open PHACTS Discovery Platform, permit querying across different domains of open life science data beyond the concept of ligand-target-pharmacology. However, most public databases are compiled from literature sources and are thus heterogeneous in their coverage. In addition, assay descriptions are not uniform and most often lack relevant information in the primary literature and, consequently, in databases. This raises the question how useful large public data sources are for deriving computational models. In this perspective, we highlight selected open-source initiatives and outline the possibilities and also the limitations when exploiting this huge amount of bioactivity data.
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Scientific competency questions as the basis for semantically enriched open pharmacological space development.
Drug Discov. Today
PUBLISHED: 04-17-2013
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Molecular information systems play an important part in modern data-driven drug discovery. They do not only support decision making but also enable new discoveries via association and inference. In this review, we outline the scientific requirements identified by the Innovative Medicines Initiative (IMI) Open PHACTS consortium for the design of an open pharmacological space (OPS) information system. The focus of this work is the integration of compound-target-pathway-disease/phenotype data for public and industrial drug discovery research. Typical scientific competency questions provided by the consortium members will be analyzed based on the underlying data concepts and associations needed to answer the questions. Publicly available data sources used to target these questions as well as the need for and potential of semantic web-based technology will be presented.
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Molecular modelling studies of new potential human DNA polymerase ? inhibitors.
J Enzyme Inhib Med Chem
PUBLISHED: 10-20-2010
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The human polymerase ? (pol ?) is a promising target for the therapy of cancer e.g. of the skin. The authors recently built a homology model of the active site of human DNA pol ?. This 3D model was now used for molecular modelling studies with eight novel analogues of 2-butylanilino-dATP, which is a highly selective nucleoside inhibitor of mammalian pol ?. Our results suggest that a higher hydrophobicity of a carbohydrate side chain (pointing into a spacious hydrophobic cavity) may enhance the strength of the interaction with the target protein. Moreover, acyclic acyclovir-like derivatives outperformed those with a sugar-moiety, indicating that structural flexibility and higher conformational adaptability has a positive effect on the receptor affinity. Cytotoxicity tests confirmed our theoretical findings. Besides, one of our most promising compounds in the molecular modelling studies revealed high selectivity for the SCC-25 cell line derived from squamous cell carcinoma in man.
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Antitumor effects of guanosine-analog phosphonates identified by molecular modelling.
Int J Pharm
PUBLISHED: 03-17-2010
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Aiming to address new drug targets, molecular modelling is gaining increasing importance although the prediction capability of the in silico method is still under debate. For an improved treatment of actinic keratosis and squamous cell carcinoma, inhibitors of human DNA polymerase alpha (pol alpha) are developed by docking nucleoside phosphonate diphosphates into the active site of pol alpha. The most promising prodrugs OxBu and OxHex were then prepared by total synthesis and tested in the squamous cancer cell line SCC25. OxBu and OxHex proved cytotoxic and antiproliferative in the nanomolar concentration range and thus exceeded activity of aphidicolin, the relevant model compound, and 5-fluorouracil, the current standard for the therapy of actinic keratosis. Interestingly, the cytotoxicity in normal human keratinocytes with OxHex was clearly less pronounced and even not detectable with OxBu. Moreover, cytotoxicity of OxBu in particular with the colorectal carcinoma cell line HT29 even surmounted cytotoxicity in SCC25, and other tumor cell lines were influenced, too, by both agents. Taken together, OxBu and OxHex may offer a new approach to cancer therapy, given the agents are sufficiently well tolerated in vivo which is to be suspected beside their chemical structure.
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Human polymerase alpha inhibitors for skin tumors. Part 2. Modeling, synthesis and influence on normal and transformed keratinocytes of new thymidine and purine derivatives.
J Enzyme Inhib Med Chem
PUBLISHED: 03-13-2010
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Recently, the three-dimensional structure of the active site of human DNA polymerase alpha (pol alpha) was proposed based on the application of molecular modeling methods and molecular dynamic simulations. The modeled structure of the enzyme was used for docking selective inhibitors (nucleotide analogs and the non-nucleoside inhibitor aphidicolin) in its active site in order to design new drugs for actinic keratosis and squamous cell carcinoma (SCC). The resulting complexes explained the geometrical and physicochemical interactions of the inhibitors with the amino acid residues involved in binding to the catalytic site, and offered insight into the experimentally derived binding data. The proposed structures were synthesized and tested in vitro for their influence on human keratinocytes and relevant tumor cell lines. Effects were compared to aphidicolin which inhibits pol alpha in a non-competitive manner, as well as to diclofenac and 5-fluorouracil, both approved for therapy of actinic keratosis. Here we describe three new nucleoside analogs inhibiting keratinocyte proliferation by inhibiting DNA synthesis and inducing apoptosis and necrosis. Thus, the combination of modeling studies and in vitro tests should allow the derivation of new drug candidates for the therapy of skin tumors, given that the agents are not relevant substrates of nucleotide transporters expressed by skin cancer cells. Kinases for nucleoside activation were detected, too, corresponding with the observed effects of nucleoside analogs.
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The N terminus of monoamine transporters is a lever required for the action of amphetamines.
J. Biol. Chem.
PUBLISHED: 01-29-2010
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The serotonin transporter (SERT) terminates neurotransmission by removing serotonin from the synaptic cleft. In addition, it is the site of action of antidepressants (which block the transporter) and of amphetamines (which induce substrate efflux). We explored the functional importance of the N terminus in mediating the action of amphetamines by focusing initially on the highly conserved threonine residue at position 81, a candidate site for phosphorylation by protein kinase C. Molecular dynamics simulations of the wild type SERT, compared with its mutations SERT(T81A) and SERT(T81D), suggested structural changes in the inner vestibule indicative of an opening of the inner vestibule. Predictions from this model (e.g. the preferential accumulation of SERT(T81A) in the inward conformation, its reduced turnover number, and a larger distance between its N and C termini) were verified. Most importantly, SERT(T81A) (and the homologous mutations in noradrenaline and dopamine) failed to support amphetamine-induced efflux, and this was not remedied by aspartate at this position. Amphetamine-induced currents through SERT(T81A) were comparable with those through the wild type transporter. Both abundant Na(+) entry and accumulation of SERT(T81A) in the inward facing conformation ought to favor amphetamine-induced efflux. Thus, we surmised that the N terminus must play a direct role in driving the transporter into a state that supports amphetamine-induced efflux. This hypothesis was verified by truncating the first 64 amino acids and by tethering the N terminus to an additional transmembrane helix. Either modification abolished amphetamine-induced efflux. We therefore conclude that the N terminus of monoamine transporters acts as a lever that sustains reverse transport.
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Annotating Human P-Glycoprotein Bioassay Data.
Mol Inform
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Huge amounts of small compound bioactivity data have been entering the public domain as a consequence of open innovation initiatives. It is now the time to carefully analyse existing bioassay data and give it a systematic structure. Our study aims to annotate prominent in vitro assays used for the determination of bioactivities of human P-glycoprotein inhibitors and substrates as they are represented in the ChEMBL and TP-search open source databases. Furthermore, the ability of data, determined in different assays, to be combined with each other is explored. As a result of this study, it is suggested that for inhibitors of human P-glycoprotein it is possible to combine data coming from the same assay type, if the cell lines used are also identical and the fluorescent or radiolabeled substrate have overlapping binding sites. In addition, it demonstrates that there is a need for larger chemical diverse datasets that have been measured in a panel of different assays. This would certainly alleviate the search for other inter-correlations between bioactivity data yielded by different assay setups.
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Taking Open Innovation to the Molecular Level - Strengths and Limitations.
Mol Inform
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The ever-growing availability of large-scale open data and its maturation is having a significant impact on industrial drug-discovery, as well as on academic and non-profit research. As industry is changing to an open innovation business concept, precompetitive initiatives and strong public-private partnerships including academic research cooperation partners are gaining more and more importance. Now, the bioinformatics and cheminformatics communities are seeking for web tools which allow the integration of this large volume of life science datasets available in the public domain. Such a data exploitation tool would ideally be able to answer complex biological questions by formulating only one search query. In this short review/perspective, we outline the use of semantic web approaches for data and knowledge integration. Further, we discuss strengths and current limitations of public available data retrieval tools and integrated platforms.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.