Bio Saga Blog - A Chronicle of Life Sciences & Informatics

While this is very encouraging what's going to be it's impact on the industry on proprietary database vendors? More & more of open database consortia and open curation models are on the offing, with high level of participation from both the academia and the Industry. The European Molecular Biology Laboratory's European Bioinformatics Institute has launched a "vast online database" of genomic-based drug and small molecule information available in an open access format for researchers seeking new therapeutics, according to EMBL-EBI. The ChEMBLdb holds translational information on more than 520,000 small molecules, including data on target binding, the affect these compounds have on cells and organisms, and information about the molecules' absorption, distribution, metabolism, excretion, and toxicity. "The data lie at the heart of translating information from the human genome into successful new drugs in the clinic," EMBL-EBI said this week. EMB...

Drugs that encourage the growth of new neurons in the brain are now headed for clinical trials. The drugs, which have already shown success in alleviating symptoms of depression and boosting memory in animal models, are being developed by BrainCells, a San Diego-based start-up that screens drugs for their brain-growing power. The company hopes the compounds will provide an alternative to existing antidepressants and says they may also prove effective in treating cognitive disorders, such as Alzheimer's . Do you want to know more? Be a part of the XTractor community. XTractor is the first of its kind - Literature alert service , that provides manually curated and annotated sentences for the Keywords of user preference. XTractor maps the extracted entities (genes, processes, drugs, diseases etc) to multiple ontologies and enables customized report generation. With XTractor the sentences are categorized into biological significant relationships and it also provides the user with ...

Scientists report a remarkable improvement in Alzheimer's transgenic mice following treatment with a new drug. The study provides the first demonstration that an ionophore, a compound that transports metal ions across cell membranes, can elicit rapid and pronounced improvement in neuropathology and cognitive function in mouse models of Alzheimer's Disease (AD). Recent research has implicated dysregulation of metal ions in the brain, particularly copper and zinc, in the pathogenesis of AD and the damaging accumulation of amyloid beta (Aβ) protein that is characteristic of this devastating disease. The ionophore clioquinol (CQ), an 8-hydroxyquinoline, has been shown to increase intracellular copper and zinc levels and decrease Aβ levels in cultured cells and in the brains of transgenic (Tg) AD mice. However, further studies in mice and humans demonstrated that brain entry of CQ was quite limited. This research is published by Cell Press in the July 10th issue of the journal Neuro...

A new computer-based method of analyzing cellular activity has correctly predicted the anti-tumour activity of several molecules. Research published today in BioMed Central's open access journal Molecular Cancer describes 'CoMet' – a tool that studies the integrated machinery of the cell and predicts those components that will have an effect on cancer. Jeffrey Skolnick, in collaboration with John McDonald, led a team from the Georgia Institute of Technology who have developed this new strategy. As Skolnick explains, "This opens up the possibility of novel therapeutics for cancer and develops our understanding of why such metabolites work. CoMet provides a deeper understanding of the molecular mechanisms of cancer". Identification of metabolites with anticancer properties by Computational Metabolomics The small molecules that are naturally produced in cells are called metabolites. Enzymes, the biological catalysts that produce and consume these metabolites are cr...

The last time i blogged on stem cells it was rather about a challenge in Fresh hurdle for stem cell hunt , but this time its more on a positive note and fairly quite an interesting and welcome news... a SERENDIPITY! Inspired by a chance discovery during another experiment, researchers at UT Southwestern Medical Center have created a small molecule that stimulates nerve stem cells to begin maturing into nerve cells in culture. "This provides a critical starting point for neuro-regenerative medicine and brain cancer chemotherapy," said Dr. Jenny Hsieh, assistant professor of molecular biology and senior author of the paper, Small-molecule activation of neuronal cell fate, Jay W Schneider, Zhengliang Gao, Shijie Li, Midhat Farooqi, Tie-Shan Tang, Ilya Bezprozvanny, Doug E Frantz, Jenny Hsieh SUMMARY: We probed an epigenetic regulatory path from small molecule to neuronal gene activation. Isoxazole small molecules triggered robust neuronal differentiation in adult neural ...

Many of you involved in structure based drug discovery will know very well about the numerous problems and errors in the data found in the Protein Data Bank (PDB) especially concerning the ligand structures. There have been a lot of publications about such errors, e.g. in Jones et al. J Mol. Biol. (1997) 267 :727, and I heard various conference presentations about this topic too, e.g. by Gerard Kleywegt (University of Uppsala), titled “Protein crystallography: not as simple as ABC then?” at Bryn Mawr, Philadelphia (15-19 October 2007) eChemInfo meeting . The errors are often blamed on the low resolution of the structures involving large protein structures (often thousands of atoms). One would assume that the small molecule crystal structures of the Cambridge Structural Database ( CSD ) do not have such errors, since they have much higher resolution and dealing with small molecules. Let me correct that wrong assumption! Do you want to know more?

By activating a cancer suppressor gene, a small molecule called nutlin-3a can block cancer cell division, according to researchers at the National Cancer Institute (NCI), part of the National Institutes of Health. This activation of the p53 gene leads to cellular senescence. An opportunity for new genetic mutations occurs each time a cell divides, so limiting the number of cell divisions in a cancer cell inhibits tumor progression. Activation of p53 can suppress tumor growth through more than one mechanism. It can interfere with the cell cycle, prompting a cell with unrepaired DNA damage to commit suicide through a complex signaling pathway called apoptosis. Alternatively, p53 may trigger cellular senescence in response to DNA damage or cellular stress. The expression of p53 is regulated by Mdm2, a protein that is overexpressed in several human cancers. Nutlins are small-molecule ...