The ChEMBL-og

As promised before , there will be a webinar on accessing  ChEMBL REST web services via KNIME and Pipeline Pilot  at 3.30 pm BST on Wednesday, 8th August 2012 . Please  email  me in advance in order to register for this.

ATC Code: R03BB05 Wikipedia: Aclidinium bromide On July 23 th , the FDA approved Aclidinum bromide (Tradename: Tudorza   Pressair TM ; Research Codes: LAS-34273, LAS W-330), a muscarinic acetylcholine M 3 receptor antagonist, for the long-term maintenance treatment of bronchospasm associated with chronic obstructive pulmonary disease (COPD) . Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of chronic bronchitis or emphysema , a pair of commonly co-existing diseases of the lungs in which the airways become narrowed. Bronchial spasms, a sudden constriction of the muscles in the walls of the bronchioles , occur frequently in COPD. Aclidinum bromide is a long-acting antimuscarinic agent that through the inhibition of the muscarinic acetylcholine M 3 receptors present in the airway smooth muscle, leads to bronchodilation, and consequently eases the symptoms of COPD. The muscarinic acetylcholine M 3 receptor (Uniprot: P203...

There's now a BioRuby  API for ChEMBL, written by the excellent Mitsuteru Nakao ( @32nm on twitter). Bio-chembl is a bioruby plugin built on top of the ChEMBL REST web services  -  https://github.com/nakao/bio-chembl Of course, there is also the pychembl project in Python from Marcus Sitzmann of the NCI. -  https://github.com/markussitzmann/pychembl And I've just been reminded of the R ChEMBL package from Rajarshi Guha  -  https://github.com/rajarshi/chemblr   However, the real mark of success will be when we get a ChEMBL f77 library!

ATC Code: L01XX Wikipedia: Carfilzomib On July 20th 2012 the FDA approved Carfilzomib (Kyorolis TM ) for the treatment of patients with multiple myeloma who have received prior therapies including bortezomib and an immunomodulatory therapy, and who have demonstrated disease progression within 60 days of completion of the previous therapy. Multiple myeloma is a cancer of the Plasma Cells and usually in the bone marrow. Five year survival is about 40% in the UK and and the USA . Carfilzomib is a chirally defined modified tetrapeptidyl epoxide substrate analogue with a molecular weight of 719.9. The molecular formula is C40H57N5O7. (SMILES= O=C(N[C@H](C(=O)N[C@H](C(=O)N[C@H(C(=O)N[C@H](C(=O)[C@@]1(OC1)C)CC(C)C)Cc2ccccc2)CC(C)C)CCc3ccccc3)CN4CCOCC4) Cmax and AUC following a single intravenous dose of 27 mg/m2 was 4,232 ng/mL and 379 ng.hr/mL, respectively. The mean steady-state volume of distribution of a 20 mg/m2 dose of carfilzomib was 28 L. Carfilzomib was rapidly an...

When a screen and follow-up have failed to deliver an attractive lead for a 'hard' target, talk amongst the team often turns to running a screen for an allosteric inhibitor; Allosteric regulators are therefore a seductive/tantalising approach to find leads against tough targets such as protein-protein interactions, highly polar binding sites, etc . But, there's a few hard questions to answer, this is just a few. Just how do I run a screen for an allosteric inhibitor? What compounds do I select for allosteric sites? How likely am I to find an allosteric inhibitor?  What sorts of targets can be allosterically modulated? What are the 3-D properties of allosteric sites I've read some of the literature behind the arguments for allosteric inhibitors, and I must say I'm not that convinced as to their general potential benefits at the moment - of course in some cases, they will be perfect, but are the advantages as general as people may think. But I've been...

We are pleased to announce the release of ChEMBL_14. This latest version of the ChEMBL database contains: 1,384,479 compound records 1,213,242 distinct compounds 644,734 assays 10,129,256 bioactivities 9,003 targets 46,133 documents 10 data sources As well as updates to the scientific literature and PubChem data sources, this release also includes data from 2 new sources: DrugMatrix - in vitro pharmacology assays for 870 therapeutic, industrial and environmental chemicals against 132 protein targets.  GSK Published Kinase Inhibitor Set - two data sets screening this compound library have been deposited by Nanosyn and the University of North Carolina. On the interface, we have also added some new compound cross references to Gene Expression Atlas , Drugs of the Future (subset of PubChem) , IUPHAR , NIH Clinical Collection and ZINC . On the target report card pages we have added cross references to CanSAR , Gene Ontology , IntAct , InterPro , IUPHAR , MICAD , R...

As announced also  here , a new malaria data service is available today to researchers around the globe sponsored by the Medicines for Malaria Venture ( MMV ). The service provides access to hundreds of thousands of data points on malaria-related compounds, assays and targets, thus facilitating research for this neglected tropical disease. Inspired by the successful ChEMBL interface, a user may query the database using keywords, synonyms, chemical structures or protein sequences, review and filter the hits using tables or charts and then download the resulting subset. Data provenance is also provided so that the user can filter on the data sources they are interested in, such as scientific literature, the GlaxoSmithKline TCAMS, Novartis GNF and St Jude datasets or the MMV open access Malaria Box . Based on the ChEMBL update cycle, the malaria data database will be regularly updated with depositions by academic and industrial groups who wish to share their malaria screen...